Science.gov

Sample records for quantitative detection approach

  1. MAPS: A Quantitative Radiomics Approach for Prostate Cancer Detection.

    PubMed

    Cameron, Andrew; Khalvati, Farzad; Haider, Masoom A; Wong, Alexander

    2016-06-01

    This paper presents a quantitative radiomics feature model for performing prostate cancer detection using multiparametric MRI (mpMRI). It incorporates a novel tumor candidate identification algorithm to efficiently and thoroughly identify the regions of concern and constructs a comprehensive radiomics feature model to detect tumorous regions. In contrast to conventional automated classification schemes, this radiomics-based feature model aims to ground its decisions in a way that can be interpreted and understood by the diagnostician. This is done by grouping features into high-level feature categories which are already used by radiologists to diagnose prostate cancer: Morphology, Asymmetry, Physiology, and Size (MAPS), using biomarkers inspired by the PI-RADS guidelines for performing structured reporting on prostate MRI. Clinical mpMRI data were collected from 13 men with histology-confirmed prostate cancer and labeled by an experienced radiologist. These annotated data were used to train classifiers using the proposed radiomics-driven feature model in order to evaluate the classification performance. The preliminary experimental results indicated that the proposed model outperformed each of its constituent feature groups as well as a comparable conventional mpMRI feature model. A further validation of the proposed algorithm will be conducted using a larger dataset as future work.

  2. Comparison of qualitative and quantitative approach to prostate MR spectroscopy in peripheral zone cancer detection.

    PubMed

    Klijn, Stijn; De Visschere, Pieter J; De Meerleer, Gert O; Villeirs, Geert M

    2012-03-01

    To compare the diagnostic performance of a qualitative (pattern recognition) and a quantitative (numerical assessment) approach to magnetic resonance spectroscopy (MRS) in the diagnosis of peripheral zone prostate cancer. 185 patients (131 with histopathologically proven cancer, 54 normal/benign after at least 12 months follow-up) were prospectively evaluated with qualitative MRS using a 4-point scale between 3/2004 and 1/2008, and retrospectively reassessed using a prototype quantitative postprocessing software in April 2008. Based on pathology and follow-up data, diagnostic performance parameters were calculated. The qualitative and quantitative approaches were concordant in 78.9% (146/185) of cases. The difference between the areas under the ROC curve (0.791 versus 0.772, respectively) was not statistically significant. The sensitivity, specificity and accuracy were 55.7%, 94.4% and 67.0% for the qualitative approach, and 55.0%, 83.3% and 63.2% for the quantitative approach. The sensitivity for high grade tumours (Gleason 4+3 or higher) was 85.2% (23/27) for both approaches. All cancers missed on either one approach separately (31/31) and 91% of cancers missed on both approaches together (23/27) were of lower grade (Gleason 3+4 or lower). Qualitative and quantitative approaches to MRS yield similar diagnostic results. Discordances in tumour detection only occurred in lower grade cancers. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  3. [Quantitative Approach to Melamine Detection in Egg White with Surface-Enhanced Raman Spectroscopy].

    PubMed

    Wang, Qiao-hua; Liu, Ya-li; Ma, Mei-hu; Wang, Hong

    2015-04-01

    Due to the harmfulness of melamine to human, the quantitative detection of melamine in egg is very necessary. In the present study, the surface enhanced Raman spectra technology combined with chemometric analysis method was used to conduct melamine quantitative detection in egg white. Firstly, the melamine egg sample could be got by the method of artificial feeding hens usingdifferent feeding formulation. Then the surface enhanced Raman spectra of egg white was determined using portable Raman spectroscopy (Opto Trace RamTracer-200) and Raman enhancement reagents, and the melamine content within the white eggs was measured with gas chromatography mass spectrometry technology. The software of Raman Analyzer was used for baseline correction of Raman spectra. The correlation coefficient method was used to choose 320 spectral variables from the surface enhanced Raman spectroscopy as input variables to establish partial least squares quantitative calibration model . And the peaks-decomposition method was used to establish peaks-decomposition quantitative calibration model. Both models selected 90 and 44 samples respectively as calibration sets and validation sets during model establishment, and both models achieved good prediction effect. The determination coefficient between predicted values of partial least squares quantitative calibration model and measured values of gas chromatography mass spectrometry was 0.856, and root mean square error of prediction was 1.547. The determination coefficient was 0.947 and RMSEP was 0.893 for the peaks-decomposition quantitative calibration model. This study demonstrated that the method can effectively quantitatively detect melamine in eggs. Testing a sample only takes 15 minutes, which can provide a new way for the melamine egg detection.

  4. Comparison of Maximum Likelihood Estimation Approach and Regression Approach in Detecting Quantitative Trait Lco Using RAPD Markers

    Treesearch

    Changren Weng; Thomas L. Kubisiak; C. Dana Nelson; James P. Geaghan; Michael Stine

    1999-01-01

    Single marker regression and single marker maximum likelihood estimation were tied to detect quantitative trait loci (QTLs) controlling the early height growth of longleaf pine and slash pine using a ((longleaf pine x slash pine) x slash pine) BC, population consisting of 83 progeny. Maximum likelihood estimation was found to be more power than regression and could...

  5. Highly sensitive detection of glucose: A quantitative approach employing nanorods assembled plasmonic substrate.

    PubMed

    Chen, Qiulan; Fu, Yu; Zhang, Weihong; Ye, Suibo; Zhang, Hao; Xie, Fangyan; Gong, Li; Wei, Zhanxiao; Jin, Haoyu; Chen, Jian

    2017-04-01

    Sensitive glucose detection enables indirect blood glucose sensing through easily accessible biofluids such as saliva and sweat. In this work, silver coated gold nanorods (Au@Ag NRs) were synthesized and used to prepare plasmonic substrate for surface-enhanced Raman spectroscopy (SERS) to leverage highly sensitive detection of glucose for quantitative analysis. By synthetically manipulating of gold NRs and the outer silver shell, the size and aspect ratio of Au@Ag NRs were optimized, and the plasmon resonance wavelength was tuned to approximately the excitation wavelength. 4-Mercaptophenyl-boronic acid (4-MPBA) and 4-Cyanophenylboronic acid (4-CPBA) were used as primary and secondary receptors respectively to specifically capture glucose molecules. The distinct Raman peak at 2226cm(-1) of the cyano group in 4-CPBA was used as a signal reporter for glucose sensing. It is located in a biological silent region (1800-2800cm(-1)), thus offering specific sensing of glucose, without the interference of other endogenous molecules. Our results showed that the SERS substrate was long-term stable. Glucose in urine solution with additive glucose was quantitatively and specifically determined, with the detection limit down to 10(-8)M. Further experiments using urine from mild diabetes shows positive results, demonstrating the feasibility of clinical use.

  6. Novel approach to quantitative detection of specific rRNA in a microbial community, using catalytic DNA.

    PubMed

    Suenaga, Hikaru; Liu, Rui; Shiramasa, Yuko; Kanagawa, Takahiro

    2005-08-01

    We developed a novel method for the quantitative detection of the 16S rRNA of a specific bacterial species in the microbial community by using deoxyribozyme (DNAzyme), which possesses the catalytic function to cleave RNA in a sequence-specific manner. A mixture of heterogeneous 16S rRNA containing the target 16S rRNA was incubated with a species-specific DNAzyme. The cleaved target 16S rRNA was separated from the intact 16S rRNA by electrophoresis, and then their amounts were compared for the quantitative detection of target 16S rRNA. This method was used to determine the abundance of the 16S rRNA of a filamentous bacterium, Sphaerotilus natans, in activated sludge, which is a microbial mixture used in wastewater treatment systems. The result indicated that this DNAzyme-based approach would be applicable to actual microbial communities.

  7. A Quantitative Relationship between Signal Detection in Attention and Approach/Avoidance Behavior

    PubMed Central

    Viswanathan, Vijay; Sheppard, John P.; Kim, Byoung W.; Plantz, Christopher L.; Ying, Hao; Lee, Myung J.; Raman, Kalyan; Mulhern, Frank J.; Block, Martin P.; Calder, Bobby; Lee, Sang; Mortensen, Dale T.; Blood, Anne J.; Breiter, Hans C.

    2017-01-01

    This study examines how the domains of reward and attention, which are often studied as independent processes, in fact interact at a systems level. We operationalize divided attention with a continuous performance task and variables from signal detection theory (SDT), and reward/aversion with a keypress task measuring approach/avoidance in the framework of relative preference theory (RPT). Independent experiments with the same subjects showed a significant association between one SDT and two RPT variables, visualized as a three-dimensional structure. Holding one of these three variables constant, further showed a significant relationship between a loss aversion-like metric from the approach/avoidance task, and the response bias observed during the divided attention task. These results indicate that a more liberal response bias under signal detection (i.e., a higher tolerance for noise, resulting in a greater proportion of false alarms) is associated with higher “loss aversion.” Furthermore, our functional model suggests a mechanism for processing constraints with divided attention and reward/aversion. Together, our results argue for a systematic relationship between divided attention and reward/aversion processing in humans. PMID:28270776

  8. A Quantitative Relationship between Signal Detection in Attention and Approach/Avoidance Behavior.

    PubMed

    Viswanathan, Vijay; Sheppard, John P; Kim, Byoung W; Plantz, Christopher L; Ying, Hao; Lee, Myung J; Raman, Kalyan; Mulhern, Frank J; Block, Martin P; Calder, Bobby; Lee, Sang; Mortensen, Dale T; Blood, Anne J; Breiter, Hans C

    2017-01-01

    This study examines how the domains of reward and attention, which are often studied as independent processes, in fact interact at a systems level. We operationalize divided attention with a continuous performance task and variables from signal detection theory (SDT), and reward/aversion with a keypress task measuring approach/avoidance in the framework of relative preference theory (RPT). Independent experiments with the same subjects showed a significant association between one SDT and two RPT variables, visualized as a three-dimensional structure. Holding one of these three variables constant, further showed a significant relationship between a loss aversion-like metric from the approach/avoidance task, and the response bias observed during the divided attention task. These results indicate that a more liberal response bias under signal detection (i.e., a higher tolerance for noise, resulting in a greater proportion of false alarms) is associated with higher "loss aversion." Furthermore, our functional model suggests a mechanism for processing constraints with divided attention and reward/aversion. Together, our results argue for a systematic relationship between divided attention and reward/aversion processing in humans.

  9. Quantitative assessment of hyperspectral imaging in detection of plasmonic nanoparticles: a modified contrast-detail analysis approach

    NASA Astrophysics Data System (ADS)

    Wang, Jianting; Chen, Yu; Pfefer, T. Joshua

    2016-03-01

    Hyperspectral reflectance imaging (HRI) is an emerging imaging modality being applied for clinical indications such as tissue oximetry, and cancer detection based on endogenous biological constituents including plasmonic nanoparticles. However, there is currently a lack of standardized test methods for objective, quantitative evaluation of HRI system performance. Contrast-detail analysis (CDA) is a phantom-based test method commonly used to evaluate medical imaging devices (e.g., mammography systems) in terms of their lower detection limit. We investigated a modified CDA (mCDA) method to quantify the detectability of gold nanoparticles by HRI systems. Silicone-based turbid phantoms containing micro-fluidic channels were developed for the mCDA tests. Polydimethylsiloxane (PDMS) phantom materials were doped with chromophores and scatterers to achieve biologically relevant optical properties (OPs). Molds were used to produce cylindrical channels of diameters 0.3 to 1.65 mm and depths of 0.2 mm inside the phantoms. Channels were filled with a mixture of hemoglobin and concentrations of gold nanorods (GNR) and measured with our HRI system. The contrast of GNRs was solved with a spectral unmixing algorithm from the reflectance spectra. The lowest detectable concentration was determined as a function of inclusion size and depth and plotted as modified contrast detail curve (mCDC). mCDCs were used to compare the detectabilities of the HRI system with different data processing algorithms. It is demonstrated that our mCDA test method involving turbid microchannel phantoms can help to elucidate the combined performance of imaging devices and plasmonic nanoparticle contrast agents. This approach may be useful for performing clinical trial standardization and device re-calibration, thus ensuring quality control and clinical performance.

  10. New approach for quantitative coronary analysis (QCA) tool using multiresolution edge detection technique

    NASA Astrophysics Data System (ADS)

    Al-Fahoum, Amjed S.; Zanoun, Jalal

    2003-05-01

    Variations of vessel's sizes, inter and intra-observer variability, nontrivial noise distribution, and the fuzzy representation of vessel's parameters are issues of concern for enhancing precision and accuracy of the available QCA techniques. In this paper, we present new multiresolution edge detection algorithm for determining vessel boundaries, and enhancing their centerline features. A bank of Canny filters of different resolutions is created. These filters are convolved with vascular images in order to obtain an edge image. Each filter will give maximum response to the segment of vessel having the same spatial resolution as the filter. The resulting responses across filters of different resolutions are combined to create an edge map for edge optimization. Boundaries of vessels are represented by edge-lines and are optimized on filter outputs with dynamic programming. The determined edge-lines are used to create vessel centerline. The centerline is then used to compute percent-diameter stenosis and coronary lesions. The system has been validated using synthetic images, flexible tube phantoms, and real angiograms. It has also been tested on coronary lesions with independent operators for inter-operator and intra-operator variability and reproducibility. The system has been found to be especially robust in complex images involving vessel branching and incomplete contrast filling.

  11. Quantitative multiplex detection of pathogen biomarkers

    DOEpatents

    Mukundan, Harshini; Xie, Hongzhi; Swanson, Basil I.; Martinez, Jennifer; Grace, Wynne K.

    2016-02-09

    The present invention addresses the simultaneous detection and quantitative measurement of multiple biomolecules, e.g., pathogen biomarkers through either a sandwich assay approach or a lipid insertion approach. The invention can further employ a multichannel, structure with multi-sensor elements per channel.

  12. Quantitative multiplex detection of pathogen biomarkers

    DOEpatents

    Mukundan, Harshini; Xie, Hongzhi; Swanson, Basil I; Martinez, Jennifer; Grace, Wynne K

    2014-10-14

    The present invention addresses the simultaneous detection and quantitative measurement of multiple biomolecules, e.g., pathogen biomarkers through either a sandwich assay approach or a lipid insertion approach. The invention can further employ a multichannel, structure with multi-sensor elements per channel.

  13. Rapid and direct quantitative detection of viable bifidobacteria in probiotic yogurt by combination of ethidium monoazide and real-time PCR using a molecular beacon approach.

    PubMed

    Meng, X C; Pang, R; Wang, C; Wang, L Q

    2010-11-01

    The potential of ethidium monoazide (EMA) real-time PCR method based on molecular beacon probe for rapid detection of viable bifidobacteria present in probiotic yogurt was evaluated in this work. A real-time PCR with molecular beacon assay was developed to determine genus Bifidobacterium quantitatively in order to increase the sensitivity and specificity of assay. EMA was used to treat probiotic yogurt prior to DNA extraction and real-time PCR detection to allow detection of only viable bacteria. The primer set of Bif-F/Bif-R which is genus-specific for Bifid. was designed. The specificity of the probes ensures that no signal is generated by non-target amplicons. Linear regression analysis demonstrated a good correlation (R² = 0·9948) between the EMA real-time PCR results and the plate counting, and real-time quantitative PCR results correlated adequately with enumeration of bifidobacteria by culture for commercial probiotic yogurt. This culture-independent approach is promising for the direct and rapid detection of viable bifidobacteria in commercial probiotic yogurt, and the detection can be carried out within 4 h. The detection limit for this method is about 10⁴ cell/ml. In conclusion, the direct quantitative EMA real-time PCR assay based on molecular beacon described in this research is a rapid and quantitative method.

  14. The Role of Pathology Correlation Approach in Prostate Cancer Index Lesion Detection and Quantitative Analysis with Multiparametric MRI

    PubMed Central

    Fedorov, Andriy; Penzkofer, Tobias; Hirsch, Michelle S.; Flood, Trevor A.; Vangel, Mark G.; Masry, Paul; Tempany, Clare M.; Mulkern, Robert V.; Fennessy, Fiona M.

    2015-01-01

    Rationale and Objectives Development of imaging biomarkers often relies on their correlation with histopathology. Our aim was to compare two approaches for correlating pathology to multiparametric magnetic resonance (MR) imaging (mpMRI) for localization and quantitative assessment of prostate cancer (PCa) index tumor using whole mount (WM) pathology (WMP) as the reference. Materials and Methods Patients (N = 30) underwent mpMRI that included diffusion-weighted imaging and dynamic contrast-enhanced (DCE) MRI at 3 T before radical prostatectomy (RP). RP specimens were processed using WM technique (WMP) and findings summarized in a standard surgical pathology report (SPR). Histology index tumor volumes (HTVs) were compared to MR tumor volumes (MRTVs) using two approaches for index lesion identification on mpMRI using annotated WMP slides as the reference (WMP) and using routine SPR as the reference. Consistency of index tumor localization, tumor volume, and mean values of the derived quantitative parameters (mean apparent diffusion coefficient [ADC], Ktrans, and ve) were compared. Results Index lesions from 16 of 30 patients met the selection criteria. There was WMP/SRP agreement in index tumor in 13 of 16 patients. ADC-based MRTVs were larger (P < .05) than DCE-based MRTVs. ADC MRTVs were smaller than HTV (P < .005). There was a strong correlation between HTV and MRTV (Pearson r > 0.8; P < .05). No significant differences were observed in the mean values of Ktrans and ADC between the WMP and SPR. Conclusions WMP correlation is superior to SPR for accurate localization of all index lesions. The use of WMP is however not required to distinguish significant differences of mean values of quantitative MRI parameters within tumor volume. PMID:25683501

  15. A microfluidic immunoassay platform for the detection of free prostate specific antigen: a systematic and quantitative approach.

    PubMed

    Madaboosi, Narayanan; Soares, Ruben R G; Chu, Virginia; Conde, João Pedro

    2015-07-07

    As a leading cause of cancer-related deaths in men globally, prostate cancer (PCa) demands immense attention for theranostic purposes. There is an increasing need for the development of rapid, sensitive, economical, miniaturized and multiplexable assays. Towards this goal, we present a systematic approach for the optimisation of a microfluidic sandwich immunoassay, which can be applied as a generic biosensor platform for PCa detection. Prostate specific antigen (PSA) was used as the model biomarker, and its free form was captured using commercially available antibodies and detected using chemiluminescence, both in spiked buffer and matrix solutions. Along with the optimisation of surface chemistry and microfluidic parameters, we report a bio-affinity amplification strategy based on biotin-streptavidin chemistry to bring the limits of detection for free-PSA from 21.4 ng mL(-1) down to 2.7 ng mL(-1), within the clinically relevant range. An estimate of the surface coverage and simulations of the interactions taking place in the microfluidic biosensor during the assay are also presented. This novel platform using a simple passive adsorption-based bio-affinity strategy, when coupled with multiplexing and integrated detection, can serve as a promising point-of-care diagnostic tool for PCa.

  16. Precipitation evidences on X-Band Synthetic Aperture Radar imagery: an approach for quantitative detection and estimation

    NASA Astrophysics Data System (ADS)

    Mori, Saverio; Marzano, Frank S.; Montopoli, Mario; Pulvirenti, Luca; Pierdicca, Nazzareno

    2017-04-01

    Spaceborne synthetic aperture radars (SARs) operating at L-band and above are nowadays a well-established tool for Earth remote sensing; among the numerous civil applications we can indicate flood areas detection and monitoring, earthquakes analysis, digital elevation model production, land use monitoring and classification. Appealing characteristics of this kind of instruments is the high spatial resolution ensured in almost all-weather conditions and with a reasonable duty cycle and coverage. This result has achieved by the by the most recent generation of SAR missions, which moreover allow polarimetric observation of the target. Nevertheless, atmospheric clouds, in particular the precipitating ones, can significantly affect the signal backscattered from the ground surface (e.g. Ferrazzoli and Schiavon, 1997), on both amplitude and phase, with effects increasing with the operating frequency. In this respect, proofs are given by several recent works (e.g. Marzano et al., 2010, Baldini et al., 2014) using X-Band SAR data by COSMO-SkyMed (CSK) and TerraSAR-X (TSX) missions. On the other hand, this sensitivity open interesting perspectives towards the SAR observation, and eventually quantification, of precipitations. In this respect, a proposal approach for X-SARs precipitation maps production and cloud masking arise from our work. Cloud masking allows detection of precipitation compromised areas. Respect precipitation maps, satellite X-SARs offer the unique possibility to ingest within flood forecasting model precipitation data at the catchment scale. This aspect is particularly innovative, even if work has been done the late years, and some aspects need to still address. Our developed processing framework allows, within the cloud masking stage, distinguishing flooded areas, precipitating clouds together with permanent water bodies, all appearing dark in the SAR image. The procedure is mainly based on image segmentation techniques and fuzzy logic (e.g. Pulvirenti et

  17. A novel approach for quantitation of nonderivatized sialic acid in protein therapeutics using hydrophilic interaction chromatographic separation and nano quantity analyte detection.

    PubMed

    Chemmalil, Letha; Suravajjala, Sreekanth; See, Kate; Jordan, Eric; Furtado, Marsha; Sun, Chong; Hosselet, Stephen

    2015-01-01

    This paper describes a novel approach for the quantitation of nonderivatized sialic acid in glycoproteins, separated by hydrophilic interaction chromatography, and detection by Nano Quantity Analyte Detector (NQAD). The detection technique of NQAD is based on measuring change in the size of dry aerosol and converting the particle count rate into chromatographic output signal. NQAD detector is suitable for the detection of sialic acid, which lacks sufficiently active chromophore or fluorophore. The water condensation particle counting technology allows the analyte to be enlarged using water vapor to provide highest sensitivity. Derivatization-free analysis of glycoproteins using HPLC/NQAD method with PolyGLYCOPLEX™ amide column is well correlated with HPLC method with precolumn derivatization using 1, 2-diamino-4, 5-methylenedioxybenzene (DMB) as well as the Dionex-based high-pH anion-exchange chromatography (or ion chromatography) with pulsed amperometric detection (HPAEC-PAD). With the elimination of derivatization step, HPLC/NQAD method is more efficient than HPLC/DMB method. HPLC/NQAD method is more reproducible than HPAEC-PAD method as HPAEC-PAD method suffers high variability because of electrode fouling during analysis. Overall, HPLC/NQAD method offers broad linear dynamic range as well as excellent precision, accuracy, repeatability, reliability, and ease of use, with acceptable comparability to the commonly used HPAEC-PAD and HPLC/DMB methods.

  18. Quantitative approaches to detect donor and passage differences in adipogenic potential and clonogenicity in human bone marrow-derived mesenchymal stem cells.

    PubMed

    Lo Surdo, Jessica; Bauer, Steven R

    2012-11-01

    Bone marrow-derived multipotent stromal cells (MSCs), also known as mesenchymal stem cells, have great promise due to their capacity for tri-lineage differentiation and immunosuppressive properties, which allows for their allogeneic use and ultimately may allow for treatment of many diseases. MSCs will require extensive expansion and passaging to obtain cells in sufficient numbers necessary for cell therapies. MSCs from many donors could potentially be used. Because of this, there is a need to understand the role of passaging and donor differences on differentiation capacity using quantitative approaches. Here, we evaluated MSCs from two donors (noted as PCBM1632 and PCBM1641 by the manufacturer) at tissue culture passages 3, 5, and 7. We used a colony forming unit (CFU) assay and limiting dilution to quantify clonogenicity and precursor frequency during adipogenesis, and quantitative real-time-polymerase chain reaction for adipogenic markers to evaluate changes on a gene expression level. Further, we observed changes in cell size, and we sorted small and large populations to evaluate size-related adipogenic potential. While the adipogenic precursor frequency of ∼1 in 76 cells remained similar through passages for cells from PCBM1641, we found a large decrease in the adipogenic potential of MSCs from PCBM1632, with 1 in 2035 cells being capable of differentiating into an adipocyte at passage 7. MSCs from both donors showed an increase in cell diameter with increasing passage, which correlates with a decrease in clonogenicity by CFU analysis. We also measured adipose lineage gene expression following induction of adipocyte differentiation. Expression of these genes decreased with passage number for MSCs from PCBM1632 and correlated with the decrease in adipogenic potential by passage 7. In contrast, MSCs from PCBM1641 showed increased expression of these genes with increasing passage. We have shown that several quantitative assays can detect differences in MSC

  19. Comparison of different approaches for evaluation of the detection and quantitation limits of a purity method: a case study using a capillary isoelectrofocusing method for a monoclonal antibody.

    PubMed

    Apostol, Izydor; Miller, Karen J; Ratto, Joseph; Kelner, Drew N

    2009-02-01

    Several different techniques suggested by the International Conference on Harmonization (ICH) Q2R1 guideline were used to assess the signal and concentration at the limit of detection (LOD) and limit of quantitation (LOQ) for a purity method. These approaches were exemplified with a capillary isoelectrofocusing (cIEF) method, which has been developed to quantify the distribution of the charge isoforms of a monoclonal antibody. The charge isoforms are the result of incomplete posttranslational processing of C-terminal lysine residues of the heavy chain by carboxypeptidase. Results showed no significant discrepancy between LOD/LOQ obtained by the different techniques. Validation experiments corroborated the calculated LOQ. The results indicate that any single technique can provide meaningful values for the LOD and LOQ. Finally, important points to consider when applying these techniques to purity methods are discussed.

  20. 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach.

    PubMed

    Kildare, Beverly J; Leutenegger, Christian M; McSwain, Belinda S; Bambic, Dustin G; Rajal, Veronica B; Wuertz, Stefan

    2007-08-01

    We report the design and validation of new TaqMan((R)) assays for microbial source tracking based on the amplification of fecal 16S rRNA marker sequences from uncultured cells of the order Bacteroidales. The assays were developed for the detection and enumeration of non-point source input of fecal pollution to watersheds. The quantitative "universal"Bacteroidales assay BacUni-UCD detected all tested stool samples from human volunteers (18 out of 18), cat (7 out of 7), dog (8 out of 8), seagull (10/10), cow (8/8), horse (8/8), and wastewater effluent (14/14). The human assay BacHum-UCD discriminated fully between human and cow stool samples but did not detect all stool samples from human volunteers (12/18). In addition, there was 12.5% detection of dog stool (1/8), but no cross-reactivity with cat, horse, or seagull fecal samples. In contrast, all wastewater samples were positive for the BacHum-UCD marker, supporting its designation as 100% sensitive for mixed-human source identification. The cow-specific assay BacCow-UCD fully discriminated between cow and human stool samples. There was 38% detection of horse stool (3/8), but no cross-specificity with any of the other animal stool samples tested. The dog assay BacCan-UCD discriminated fully between dog and cow stool or seagull guano samples and detected 62.5% stool samples from dogs (5/8). There was some cross-reactivity with 22.2% detection of human stool (4/18), 14.3% detection of cat stool (1/7), and 28.6% detection of wastewater samples (4/14). After validation using stool samples, single-blind tests were used to further demonstrate the efficacy of the developed markers; all assays were sensitive, reproducible, and accurate in the quantification of mixed fecal sources present in aqueous samples. Finally, the new assays were compared with previously published sequences, which showed the new methodologies to be more specific and sensitive. Using Bayes' Theorem, we calculated the conditional probability that the

  1. Aptasensors for quantitative detection of kanamycin.

    PubMed

    Robati, Rezvan Yazdian; Arab, Atefeh; Ramezani, Mohammad; Langroodi, Fatemeh Alebooye; Abnous, Khalil; Taghdisi, Seyed Mohammad

    2016-08-15

    Up till now, various techniques have been developed to detect kanamycin in biological samples. However, due to some problems involved in these methods including time-consuming, expensive equipment and high consumption of reagents, new strategies for detection and quantitative determination of kanamycin are needed. Aptamer-based biosensors with unique recognition capability have attracted more attention of scientists because of its rapid response, high sensitivity and simple fabrication. Hence, we summarized optical and electrochemical kanamycin aptasensors and focuses on recent advances and modern techniques in aptasensor-based kanamycin detection techniques in order to provide readers with an inclusive understanding of its improvement and progress.

  2. A Complementary Isothermal Amplification Method to the U.S. EPA Quantitative Polymerase Chain Reaction Approach for the Detection of Enterococci in Environmental Waters

    PubMed Central

    2017-01-01

    We report a novel molecular assay, based on helicase-dependent amplification (HDA), for the detection of enterococci as markers for fecal pollution in water. This isothermal assay targets the same Enterococcus 23S rRNA gene region as the existing quantitative polymerase chain reaction (qPCR) assays of U.S. Environmental Protection Agency Methods 1611 and 1609 but can be entirely performed on a simple heating block. The developed Enterococcus HDA assay successfully discriminated 15 enterococcal from 15 non-enterococcal reference strains and reliably detected 48 environmental isolates of enterococci. The limit of detection was 25 target copies per reaction, only 3 times higher than that of qPCR. The applicability of the assay was tested on 30 environmental water sample DNA extracts, simulating a gradient of fecal pollution. Despite the isothermal nature of the reaction, the HDA results were consistent with those of the qPCR reference. Given this performance, we conclude that the developed Enterococcus HDA assay has great potential as a qualitative molecular screening method for resource-limited settings when combined with compatible up- and downstream processes. This amplification strategy can pave the way for developing a new generation of rapid, low-cost, and field-deployable molecular diagnostic tools for water quality monitoring. PMID:28541661

  3. Reproducibility and quantitation of amplicon sequencing-based detection

    PubMed Central

    Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

    2011-01-01

    To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

  4. A novel quantitation approach for maximizing detectable targets for offensive/volatile odorants with diverse functional groups by thermal desorption-gas chromatography-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2016-07-01

    A multitude of analytical systems are needed to analyze diverse odorants with various functionalities. In this study, an experimental method was developed to assess the maximum covering range of odorants using a single experimental setup consisting of a thermal desorber-gas chromatography-mass spectrometry system. To this end, a total of 20 offensive odorants (aldehyde, ketone, ester, alcohol, aromatic, sulfide, amine, and carboxyl) were selected and tested by a single system. The analytical results of standards and environmental samples were evaluated in a number of respects. In the analysis of the standards, all targets were quantified via Carbopack (C + B + X) tube sampling while operating the thermal desorber at ‑25 °C. The method detection limits of 18 targets (exception of 2 out of the 20 targets: acetaldehyde and methanethiol) were excellent (mean 0.04 ± 0.03 ppb) in terms of their odor threshold values (74.7 ± 140 ~ 624 ± 1,729 ppb). The analysis of organic fertilizer plant samples at a pig farm (slurry treatment facility, compost facility, and ambient air) confirmed the presence of 18 odorants from 0.03 ppb (dimethyldisulfide, ambient sample) to 522 ppb (methyl ethyl ketone, slurry treatment facility). As such, our method allowed simultaneous quantitation of most key odorants with sufficient reliability and sensitivity.

  5. A novel quantitation approach for maximizing detectable targets for offensive/volatile odorants with diverse functional groups by thermal desorption-gas chromatography-mass spectrometry

    PubMed Central

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2016-01-01

    A multitude of analytical systems are needed to analyze diverse odorants with various functionalities. In this study, an experimental method was developed to assess the maximum covering range of odorants using a single experimental setup consisting of a thermal desorber-gas chromatography-mass spectrometry system. To this end, a total of 20 offensive odorants (aldehyde, ketone, ester, alcohol, aromatic, sulfide, amine, and carboxyl) were selected and tested by a single system. The analytical results of standards and environmental samples were evaluated in a number of respects. In the analysis of the standards, all targets were quantified via Carbopack (C + B + X) tube sampling while operating the thermal desorber at −25 °C. The method detection limits of 18 targets (exception of 2 out of the 20 targets: acetaldehyde and methanethiol) were excellent (mean 0.04 ± 0.03 ppb) in terms of their odor threshold values (74.7 ± 140 ~ 624 ± 1,729 ppb). The analysis of organic fertilizer plant samples at a pig farm (slurry treatment facility, compost facility, and ambient air) confirmed the presence of 18 odorants from 0.03 ppb (dimethyldisulfide, ambient sample) to 522 ppb (methyl ethyl ketone, slurry treatment facility). As such, our method allowed simultaneous quantitation of most key odorants with sufficient reliability and sensitivity. PMID:27404037

  6. A novel quantitation approach for maximizing detectable targets for offensive/volatile odorants with diverse functional groups by thermal desorption-gas chromatography-mass spectrometry.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2016-07-11

    A multitude of analytical systems are needed to analyze diverse odorants with various functionalities. In this study, an experimental method was developed to assess the maximum covering range of odorants using a single experimental setup consisting of a thermal desorber-gas chromatography-mass spectrometry system. To this end, a total of 20 offensive odorants (aldehyde, ketone, ester, alcohol, aromatic, sulfide, amine, and carboxyl) were selected and tested by a single system. The analytical results of standards and environmental samples were evaluated in a number of respects. In the analysis of the standards, all targets were quantified via Carbopack (C + B + X) tube sampling while operating the thermal desorber at -25 °C. The method detection limits of 18 targets (exception of 2 out of the 20 targets: acetaldehyde and methanethiol) were excellent (mean 0.04 ± 0.03 ppb) in terms of their odor threshold values (74.7 ± 140 ~ 624 ± 1,729 ppb). The analysis of organic fertilizer plant samples at a pig farm (slurry treatment facility, compost facility, and ambient air) confirmed the presence of 18 odorants from 0.03 ppb (dimethyldisulfide, ambient sample) to 522 ppb (methyl ethyl ketone, slurry treatment facility). As such, our method allowed simultaneous quantitation of most key odorants with sufficient reliability and sensitivity.

  7. Photoelectric AFP quantitative detection of immunochromatographic assay strip

    NASA Astrophysics Data System (ADS)

    Du, Min; Jiang, Hai-yan

    2006-09-01

    An immunochromatographic assay (ICA) system for quantitative determination of analyte in sample is described in this paper. The designed system not only quantitatively detect target analytes in sample but also enhance detection precision in immunochromatographic assay technique.

  8. Influence analysis in quantitative trait loci detection

    PubMed Central

    Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

    2014-01-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods—the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. PMID:24740424

  9. Influence analysis in quantitative trait loci detection.

    PubMed

    Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

    2014-07-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. © 2014 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Two quantitative approaches for estimating content validity.

    PubMed

    Wynd, Christine A; Schmidt, Bruce; Schaefer, Michelle Atkins

    2003-08-01

    Instrument content validity is often established through qualitative expert reviews, yet quantitative analysis of reviewer agreements is also advocated in the literature. Two quantitative approaches to content validity estimations were compared and contrasted using a newly developed instrument called the Osteoporosis Risk Assessment Tool (ORAT). Data obtained from a panel of eight expert judges were analyzed. A Content Validity Index (CVI) initially determined that only one item lacked interrater proportion agreement about its relevance to the instrument as a whole (CVI = 0.57). Concern that higher proportion agreement ratings might be due to random chance stimulated further analysis using a multirater kappa coefficient of agreement. An additional seven items had low kappas, ranging from 0.29 to 0.48 and indicating poor agreement among the experts. The findings supported the elimination or revision of eight items. Pros and cons to using both proportion agreement and kappa coefficient analysis are examined.

  11. Analysis of Two Quantitative Ultrasound Approaches.

    PubMed

    Muleki-Seya, Pauline; Han, Aiguo; Andre, Michael P; Erdman, John W; O'Brien, William D

    2017-09-01

    There are two well-known ultrasonic approaches to extract sets of quantitative parameters: Lizzi-Feleppa (LF) parameters: slope, intercept, and midband; and quantitative ultrasound (QUS)-derived parameters: effective scatterer diameter (ESD) and effective acoustic concentration (EAC). In this study, the relation between the LF and QUS-derived parameters is studied theoretically and experimentally on ex vivo mouse livers. As expected from the theory, LF slope is correlated to ESD ([Formula: see text]), and from experimental data, LF midband is correlated to EAC ([Formula: see text]). However, LF intercept is not correlated to ESD ([Formula: see text]) nor EAC ([Formula: see text]). The unexpected correlation observed between LF slope and EAC ([Formula: see text]) results likely from the high correlation between ESD and EAC due to the inversion process. For a liver fat percentage estimation, an important potential medical application, the parameters presenting the better correlation are EAC ([Formula: see text]) and LF midband ([Formula: see text]).

  12. Standardization approaches in absolute quantitative proteomics with mass spectrometry.

    PubMed

    Calderón-Celis, Francisco; Encinar, Jorge Ruiz; Sanz-Medel, Alfredo

    2017-07-31

    Mass spectrometry-based approaches have enabled important breakthroughs in quantitative proteomics in the last decades. This development is reflected in the better quantitative assessment of protein levels as well as to understand post-translational modifications and protein complexes and networks. Nowadays, the focus of quantitative proteomics shifted from the relative determination of proteins (ie, differential expression between two or more cellular states) to absolute quantity determination, required for a more-thorough characterization of biological models and comprehension of the proteome dynamism, as well as for the search and validation of novel protein biomarkers. However, the physico-chemical environment of the analyte species affects strongly the ionization efficiency in most mass spectrometry (MS) types, which thereby require the use of specially designed standardization approaches to provide absolute quantifications. Most common of such approaches nowadays include (i) the use of stable isotope-labeled peptide standards, isotopologues to the target proteotypic peptides expected after tryptic digestion of the target protein; (ii) use of stable isotope-labeled protein standards to compensate for sample preparation, sample loss, and proteolysis steps; (iii) isobaric reagents, which after fragmentation in the MS/MS analysis provide a final detectable mass shift, can be used to tag both analyte and standard samples; (iv) label-free approaches in which the absolute quantitative data are not obtained through the use of any kind of labeling, but from computational normalization of the raw data and adequate standards; (v) elemental mass spectrometry-based workflows able to provide directly absolute quantification of peptides/proteins that contain an ICP-detectable element. A critical insight from the Analytical Chemistry perspective of the different standardization approaches and their combinations used so far for absolute quantitative MS-based (molecular and

  13. Quantitative approaches in climate change ecology

    PubMed Central

    Brown, Christopher J; Schoeman, David S; Sydeman, William J; Brander, Keith; Buckley, Lauren B; Burrows, Michael; Duarte, Carlos M; Moore, Pippa J; Pandolfi, John M; Poloczanska, Elvira; Venables, William; Richardson, Anthony J

    2011-01-01

    Contemporary impacts of anthropogenic climate change on ecosystems are increasingly being recognized. Documenting the extent of these impacts requires quantitative tools for analyses of ecological observations to distinguish climate impacts in noisy data and to understand interactions between climate variability and other drivers of change. To assist the development of reliable statistical approaches, we review the marine climate change literature and provide suggestions for quantitative approaches in climate change ecology. We compiled 267 peer-reviewed articles that examined relationships between climate change and marine ecological variables. Of the articles with time series data (n = 186), 75% used statistics to test for a dependency of ecological variables on climate variables. We identified several common weaknesses in statistical approaches, including marginalizing other important non-climate drivers of change, ignoring temporal and spatial autocorrelation, averaging across spatial patterns and not reporting key metrics. We provide a list of issues that need to be addressed to make inferences more defensible, including the consideration of (i) data limitations and the comparability of data sets; (ii) alternative mechanisms for change; (iii) appropriate response variables; (iv) a suitable model for the process under study; (v) temporal autocorrelation; (vi) spatial autocorrelation and patterns; and (vii) the reporting of rates of change. While the focus of our review was marine studies, these suggestions are equally applicable to terrestrial studies. Consideration of these suggestions will help advance global knowledge of climate impacts and understanding of the processes driving ecological change.

  14. Toward a quantitative approach to migrants integration

    NASA Astrophysics Data System (ADS)

    Barra, A.; Contucci, P.

    2010-03-01

    Migration phenomena and all the related issues, like integration of different social groups, are intrinsically complex problems since they strongly depend on several competitive mechanisms as economic factors, cultural differences and many others. By identifying a few essential assumptions, and using the statistical mechanics of complex systems, we propose a novel quantitative approach that provides a minimal theory for those phenomena. We show that the competitive interactions in decision making between a population of N host citizens and P immigrants, a bi-partite spin-glass, give rise to a social consciousness inside the host community in the sense of the associative memory of neural networks. The theory leads to a natural quantitative definition of migrant's "integration" inside the community. From the technical point of view this minimal picture assumes, as control parameters, only general notions like the strength of the random interactions, the ratio between the sizes of the two parties and the cultural influence. Few steps forward, toward more refined models, which include a digression on the kind of the felt experiences and some structure on the random interaction topology (as dilution to avoid the plain mean-field approach) and correlations of experiences felt between the two parties (biasing the distribution of the coupling) are discussed at the end, where we show the robustness of our approach.

  15. A novel approach to the quantitative detection of anabolic steroids in bovine muscle tissue by means of a hybrid quadrupole time-of-flight-mass spectrometry instrument.

    PubMed

    Bussche, Julie Vanden; Decloedt, Anneleen; Van Meulebroek, Lieven; De Clercq, Nathalie; Lock, Stephen; Stahl-Zeng, Jianru; Vanhaecke, Lynn

    2014-09-19

    In recent years, the analysis of veterinary drugs and growth-promoting agents has shifted from target-oriented procedures, mainly based on liquid chromatography coupled to triple-quadrupole mass spectrometry (LC-QqQ-MS), towards accurate mass full scan MS (such as Time-of-Flight (ToF) and Fourier Transform (FT)-MS). In this study, the performance of a hybrid analysis instrument (i.e. UHPLC-QuadrupoleTime-of-Flight-MS (QqToF-MS)), able to exploit both full scan HR and MS/MS capabilities within a single analytical platform, was evaluated for confirmatory analysis of anabolic steroids (gestagens, estrogens including stilbenes and androgens) in meat. The validation data was compared to previously obtained results (CD 2002/657/EC) for QqQ-MS and single stage Orbitrap-MS. Additionally, a fractional factorial design was used to shorten and optimize the sample extraction. Validation according to CD 2002/657/EC demonstrated that steroid analysis using QqToF has a higher competing value towards QqQ-MS in terms of selectivity/specificity, compared to single stage Orbitrap-MS. While providing excellent linearity, based on lack-of-fit calculations (F-test, α=0.05 for all steroids except 17β-ethinylestradiol: α=0.01), the sensitivity of QqToF-MS proved for 61.8% and 85.3% of the compounds more sensitive compared to QqQ-MS and Orbitrap-MS, respectively. Indeed, the CCα values, obtained upon ToF-MS/MS detection, ranged from 0.02 to 1.74μgkg(-1) for the 34 anabolic steroids, while for QqQ-MS and Orbitrap-MS values ranged from 0.04 to 0.88μgkg(-1) and from 0.07 to 2.50μgkg(-1), respectively. Using QqToF-MS and QqQ-MS, adequate precision was obtained as relative standard deviations for repeatability and within-laboratory reproducibility, were below 20%. In case of Orbitrap-MS, some compounds (i.e. some estrogens) displayed poor precision, which was possibly caused by some lack of sensitivity at lower concentrations and the absence of MRM-like experiments. Overall, it can be

  16. Allometric Trajectories and "Stress": A Quantitative Approach.

    PubMed

    Anfodillo, Tommaso; Petit, Giai; Sterck, Frank; Lechthaler, Silvia; Olson, Mark E

    2016-01-01

    The term "stress" is an important but vague term in plant biology. We show situations in which thinking in terms of "stress" is profitably replaced by quantifying distance from functionally optimal scaling relationships between plant parts. These relationships include, for example, the often-cited one between leaf area and sapwood area, which presumably reflects mutual dependence between sources and sink tissues and which scales positively within individuals and across species. These relationships seem to be so basic to plant functioning that they are favored by selection across nearly all plant lineages. Within a species or population, individuals that are far from the common scaling patterns are thus expected to perform negatively. For instance, "too little" leaf area (e.g., due to herbivory or disease) per unit of active stem mass would be expected to incur to low carbon income per respiratory cost and thus lead to lower growth. We present a framework that allows quantitative study of phenomena traditionally assigned to "stress," without need for recourse to this term. Our approach contrasts with traditional approaches for studying "stress," e.g., revealing that small "stressed" plants likely are in fact well suited to local conditions. We thus offer a quantitative perspective to the study of phenomena often referred to under such terms as "stress," plasticity, adaptation, and acclimation.

  17. A quantitative approach to scar analysis.

    PubMed

    Khorasani, Hooman; Zheng, Zhong; Nguyen, Calvin; Zara, Janette; Zhang, Xinli; Wang, Joyce; Ting, Kang; Soo, Chia

    2011-02-01

    Analysis of collagen architecture is essential to wound healing research. However, to date no consistent methodologies exist for quantitatively assessing dermal collagen architecture in scars. In this study, we developed a standardized approach for quantitative analysis of scar collagen morphology by confocal microscopy using fractal dimension and lacunarity analysis. Full-thickness wounds were created on adult mice, closed by primary intention, and harvested at 14 days after wounding for morphometrics and standard Fourier transform-based scar analysis as well as fractal dimension and lacunarity analysis. In addition, transmission electron microscopy was used to evaluate collagen ultrastructure. We demonstrated that fractal dimension and lacunarity analysis were superior to Fourier transform analysis in discriminating scar versus unwounded tissue in a wild-type mouse model. To fully test the robustness of this scar analysis approach, a fibromodulin-null mouse model that heals with increased scar was also used. Fractal dimension and lacunarity analysis effectively discriminated unwounded fibromodulin-null versus wild-type skin as well as healing fibromodulin-null versus wild-type wounds, whereas Fourier transform analysis failed to do so. Furthermore, fractal dimension and lacunarity data also correlated well with transmission electron microscopy collagen ultrastructure analysis, adding to their validity. These results demonstrate that fractal dimension and lacunarity are more sensitive than Fourier transform analysis for quantification of scar morphology.

  18. A Quantitative Approach to Scar Analysis

    PubMed Central

    Khorasani, Hooman; Zheng, Zhong; Nguyen, Calvin; Zara, Janette; Zhang, Xinli; Wang, Joyce; Ting, Kang; Soo, Chia

    2011-01-01

    Analysis of collagen architecture is essential to wound healing research. However, to date no consistent methodologies exist for quantitatively assessing dermal collagen architecture in scars. In this study, we developed a standardized approach for quantitative analysis of scar collagen morphology by confocal microscopy using fractal dimension and lacunarity analysis. Full-thickness wounds were created on adult mice, closed by primary intention, and harvested at 14 days after wounding for morphometrics and standard Fourier transform-based scar analysis as well as fractal dimension and lacunarity analysis. In addition, transmission electron microscopy was used to evaluate collagen ultrastructure. We demonstrated that fractal dimension and lacunarity analysis were superior to Fourier transform analysis in discriminating scar versus unwounded tissue in a wild-type mouse model. To fully test the robustness of this scar analysis approach, a fibromodulin-null mouse model that heals with increased scar was also used. Fractal dimension and lacunarity analysis effectively discriminated unwounded fibromodulin-null versus wild-type skin as well as healing fibromodulin-null versus wild-type wounds, whereas Fourier transform analysis failed to do so. Furthermore, fractal dimension and lacunarity data also correlated well with transmission electron microscopy collagen ultrastructure analysis, adding to their validity. These results demonstrate that fractal dimension and lacunarity are more sensitive than Fourier transform analysis for quantification of scar morphology. PMID:21281794

  19. Quantitative linkage: a statistical procedure for its detection and estimation.

    PubMed

    Hill, A P

    1975-05-01

    A new approach for detecting and estimating quantitative linkage which uses sibship data is presented. Using a nested analysis of variance design (with marker genotype nested within sibship), it is shown that under the null hypothesis of no linkage, the expected between marker genotype within sibship mean square (EMSbeta) is equal to the expected within marker genotype within sibship mean square (EMSe), while under the alternative hypothesis of linkage, the first is greater than the second. Thus the regular F-ratio, MSbeta/MSe, can be used to test for quantitative linkage. This is true for both backcross and intercross matings and whether or not there is dominance at the marker locus. A second test involving the comparison of the within marker genotype within sibship variances is available for intercross matings. A maximum likelihood procedure for the estimation for the recombination frequency is also presented.

  20. Multiple Regression Analysis of Sib-Pair Data on Reading to Detect Quantitative Trait Loci.

    ERIC Educational Resources Information Center

    Fulker, D. W.; And Others

    1991-01-01

    Applies an extension of an earlier multiple regression model for twin analysis to the problem of detecting linkage in a quantitative trait. Detects a number of possible linkages, indicating that the approach is effective. Discusses detecting genotype-environment interaction and the issue of power. (RS)

  1. Anomaly Detection Using Behavioral Approaches

    NASA Astrophysics Data System (ADS)

    Benferhat, Salem; Tabia, Karim

    Behavioral approaches, which represent normal/abnormal activities, have been widely used during last years in intrusion detection and computer security. Nevertheless, most works showed that they are ineffective for detecting novel attacks involving new behaviors. In this paper, we first study this recurring problem due on one hand to inadequate handling of anomalous and unusual audit events and on other hand to insufficient decision rules which do not meet behavioral approach objectives. We then propose to enhance the standard decision rules in order to fit behavioral approach requirements and better detect novel attacks. Experimental studies carried out on real and simulated http traffic show that these enhanced decision rules improve detecting most novel attacks without triggering higher false alarm rates.

  2. Nested-quantitative PCR approach with improved sensitivity for the detection of low titer levels of Candidatus Liberibacter asiaticus in the Asian citrus psyllid, Diaphorina citri Kuwayama.

    PubMed

    Coy, M R; Hoffmann, M; Kingdom Gibbard, H N; Kuhns, E H; Pelz-Stelinski, K S; Stelinski, L L

    2014-07-01

    Candidatus Liberibacter asiaticus (CLas) is a phloem-limited bacterium transmitted by the Asian citrus psyllid, Diaphorina citri, and the presumptive causal agent of citrus greening disease. The current method of detection for CLas within plant and insect samples is by a presence/absence qPCR assay using the CLas 16S rDNA gene target. Although qPCR is highly sensitive, low bacterial titers or suboptimal qPCR conditions can result in false-negatives. Using a nested qPCR assay, we determined the false-negative rate of the 16S presence/absence qPCR assay was greater than 50%. Studies to determine the performance parameters of the qPCR assays for CLas 16S and Wingless (Wg), the D. citri endogenous gene, using plasmid and psyllid DNA, revealed suboptimal and variable performance of the 16S assay in psyllid samples. Average efficiencies and sensitivity limits of the plasmid assays were 99.0% and 2.7 copies of template for Wg, respectively, and 98.5% and 2.2-22.1 copies for 16S, respectively. Variability in efficiency was significantly greater in psyllid samples for both gene targets compared to the corresponding plasmid assays, and efficiencies as low as 76% were obtained for 16S. A secondary structure analysis revealed the formation of two stem-loop structures that block the forward and probe binding sites in the 16S template, which could hinder amplification. In summary, our results suggest that suboptimal qPCR efficiency is not uncommon for the 16S presence/absence qPCR assay, which combined with lowCLas titers in some samples, could contribute significantly to the under-reporting of CLas infection in psyllid and plant samples.

  3. Towards automated early cancer detection: Non-invasive, fluorescence-based approaches for quantitative assessment of cells and tissue to identify pre-cancers

    NASA Astrophysics Data System (ADS)

    Levitt, Jonathan Michael

    Cancer is the second leading cause of death globally, second only to heart disease. As in many diseases, patient survival is directly related to how early lesions are detected. Using conventional screening methods, the early changes associated with cancer, which occur on the microscopic scale, can easily go overlooked. Due to the inherent drawbacks of conventional techniques we present non-invasive, optically based methods to acquire high resolution images from live samples and assess cellular function associated with the onset of disease. Specifically, we acquired fluorescence images from NADH and FAD to quantify morphology and metabolic activity. We first conducted studies to monitor monolayers of keratinocytes in response to apoptosis which has been shown to be disrupted during cancer progression. We found that as keratinocytes undergo apoptosis there are populations of mitochondria that exhibit a higher metabolic activity that become progressively confined to a gradually smaller perinuclear region. To further assess the changes associated with early cancer growth we developed automated methods to rapidly quantify fluorescence images and extract morphological and metabolic information from life tissue. In this study, we simultaneously quantified mitochondrial organization, metabolic activity, nuclear size distribution, and the localization of the structural protein keratin, to differentiate between normal and pre-cancerous engineered tissues. We found the degree mitochondrial organization, as determined from the fractal derived Hurst parameter, was well correlated to level of cellular differentiation. We also found that the metabolic activity in the pre-cancerous cells was greater and more consistent throughout tissue depths in comparison to normal tissue. Keratin localization, also quantified from the fluorescence images, we found it to be confined to the uppermost layers of normal tissue while it was more evenly distributed in the precancerous tissues. To

  4. A Quantitative Approach to Assessing System Evolvability

    NASA Technical Reports Server (NTRS)

    Christian, John A., III

    2004-01-01

    When selecting a system from multiple candidates, the customer seeks the one that best meets his or her needs. Recently the desire for evolvable systems has become more important and engineers are striving to develop systems that accommodate this need. In response to this search for evolvability, we present a historical perspective on evolvability, propose a refined definition of evolvability, and develop a quantitative method for measuring this property. We address this quantitative methodology from both a theoretical and practical perspective. This quantitative model is then applied to the problem of evolving a lunar mission to a Mars mission as a case study.

  5. Quantitative evaluation of phase processing approaches in susceptibility weighted imaging

    NASA Astrophysics Data System (ADS)

    Li, Ningzhi; Wang, Wen-Tung; Sati, Pascal; Pham, Dzung L.; Butman, John A.

    2012-03-01

    Susceptibility weighted imaging (SWI) takes advantage of the local variation in susceptibility between different tissues to enable highly detailed visualization of the cerebral venous system and sensitive detection of intracranial hemorrhages. Thus, it has been increasingly used in magnetic resonance imaging studies of traumatic brain injury as well as other intracranial pathologies. In SWI, magnitude information is combined with phase information to enhance the susceptibility induced image contrast. Because of global susceptibility variations across the image, the rate of phase accumulation varies widely across the image resulting in phase wrapping artifacts that interfere with the local assessment of phase variation. Homodyne filtering is a common approach to eliminate this global phase variation. However, filter size requires careful selection in order to preserve image contrast and avoid errors resulting from residual phase wraps. An alternative approach is to apply phase unwrapping prior to high pass filtering. A suitable phase unwrapping algorithm guarantees no residual phase wraps but additional computational steps are required. In this work, we quantitatively evaluate these two phase processing approaches on both simulated and real data using different filters and cutoff frequencies. Our analysis leads to an improved understanding of the relationship between phase wraps, susceptibility effects, and acquisition parameters. Although homodyne filtering approaches are faster and more straightforward, phase unwrapping approaches perform more accurately in a wider variety of acquisition scenarios.

  6. Sensitivity of Quantitative Signal Detection in Regards to Pharmacological Neuroenhancement

    PubMed Central

    Gahr, Maximilian; Connemann, Bernhard J.; Schönfeldt-Lecuona, Carlos; Zeiss, René

    2017-01-01

    Pharmacological neuroenhancement (PNE) is a form of abuse and has not yet been addressed by methods of pharmacovigilance. In the present study, we tested if quantitative signal detection may be sensitive in regards to PNE. We evaluated the risk of drug abuse and dependence (DAAD) related to substances that are known to be used for PNE and divided this group into agents with (methylphenidate) and without a known abuse potential outside the field of PNE (atomoxetine, modafinil, acetylcholine esterase inhibitors, and memantine). Reporting odds ratios (RORs) were calculated using a case/non-case approach based on global and country-specific drug safety data from the Uppsala Monitoring Centre (UMC). Both control substances (diazepam and lorazepam) and methylphenidate were statistically associated with DAAD in all datasets (except methylphenidate in Italy). Modafinil was associated with DAAD in the total dataset (ROR, 2.7 (95% confidence interval (CI), 2.2–3.3)), Germany (ROR, 4.6 (95% CI, 1.8–11.5)), and the USA (ROR, 2.0 (95% CI, 1.6–2.5)). Atomoxetine was associated with DAAD in the total dataset (ROR, 1.3 (95% CI, 1.2–1.5)) and in the UK (ROR, 3.3 (95% CI, 1.8–6.1)). Apart from memantine, which was associated with DAAD in Germany (ROR, 1.8 (95% CI, 1.0–3.2)), no other antidementia drug was associated with DAAD. Quantitative signal detection is suitable to detect agents with a risk for DAAD. Its sensitivity regarding PNE is limited, although atomoxetine and modafinil, which do not have a known abuse potential outside PNE, and no antidementia drugs, whose use in PNE is presumably low, were associated with DAAD in our analysis. PMID:28067776

  7. An overview of quantitative approaches in Gestalt perception.

    PubMed

    Jäkel, Frank; Singh, Manish; Wichmann, Felix A; Herzog, Michael H

    2016-09-01

    Gestalt psychology is often criticized as lacking quantitative measurements and precise mathematical models. While this is true of the early Gestalt school, today there are many quantitative approaches in Gestalt perception and the special issue of Vision Research "Quantitative Approaches in Gestalt Perception" showcases the current state-of-the-art. In this article we give an overview of these current approaches. For example, ideal observer models are one of the standard quantitative tools in vision research and there is a clear trend to try and apply this tool to Gestalt perception and thereby integrate Gestalt perception into mainstream vision research. More generally, Bayesian models, long popular in other areas of vision research, are increasingly being employed to model perceptual grouping as well. Thus, although experimental and theoretical approaches to Gestalt perception remain quite diverse, we are hopeful that these quantitative trends will pave the way for a unified theory.

  8. Lesion detection and quantitation of positron emission mammography

    SciTech Connect

    Qi, Jinyi; Huesman, Ronald H.

    2001-12-01

    A Positron Emission Mammography (PEM) scanner dedicated to breast imaging is being developed at our laboratory. We have developed a list mode likelihood reconstruction algorithm for this scanner. Here we theoretically study the lesion detection and quantitation. The lesion detectability is studied theoretically using computer observers. We found that for the zero-order quadratic prior, the region of interest observer can achieve the performance of the prewhitening observer with a properly selected smoothing parameter. We also study the lesion quantitation using the test statistic of the region of interest observer. The theoretical expressions for the bias, variance, and ensemble mean squared error of the quantitation are derived. Computer simulations show that the theoretical predictions are in good agreement with the Monte Carlo results for both lesion detection and quantitation.

  9. Detection and validation of quantitative trait loci for soybean isoflavones

    USDA-ARS?s Scientific Manuscript database

    Interest in soybean [Glycine max (L.) Merrill] isoflavones has increased in recent years due to numerous potential health benefits. Consequently, quantitative trait loci (QTL) detection for marker assisted breeding is being examined for potential genetic gains. This study sought to detect QTL for ...

  10. A quantitative approach to painting styles

    NASA Astrophysics Data System (ADS)

    Vieira, Vilson; Fabbri, Renato; Sbrissa, David; da Fontoura Costa, Luciano; Travieso, Gonzalo

    2015-01-01

    This research extends a method previously applied to music and philosophy (Vilson Vieira et al., 2012), representing the evolution of art as a time-series where relations like dialectics are measured quantitatively. For that, a corpus of paintings of 12 well-known artists from baroque and modern art is analyzed. A set of 99 features is extracted and the features which most contributed to the classification of painters are selected. The projection space obtained provides the basis to the analysis of measurements. These quantitative measures underlie revealing observations about the evolution of painting styles, specially when compared with other humanity fields already analyzed: while music evolved along a master-apprentice tradition (high dialectics) and philosophy by opposition, painting presents another pattern: constant increasing skewness, low opposition between members of the same movement and opposition peaks in the transition between movements. Differences between baroque and modern movements are also observed in the projected "painting space": while baroque paintings are presented as an overlapped cluster, the modern paintings present minor overlapping and are disposed more widely in the projection than the baroque counterparts. This finding suggests that baroque painters shared aesthetics while modern painters tend to "break rules" and develop their own style.

  11. New approaches in GMO detection.

    PubMed

    Querci, Maddalena; Van den Bulcke, Marc; Zel, Jana; Van den Eede, Guy; Broll, Hermann

    2010-03-01

    The steady rate of development and diffusion of genetically modified plants and their increasing diversification of characteristics, genes and genetic control elements poses a challenge in analysis of genetically modified organisms (GMOs). It is expected that in the near future the picture will be even more complex. Traditional approaches, mostly based on the sequential detection of one target at a time, or on a limited multiplexing, allowing only a few targets to be analysed at once, no longer meet the testing requirements. Along with new analytical technologies, new approaches for the detection of GMOs authorized for commercial purposes in various countries have been developed that rely on (1) a smart and accurate strategy for target selection, (2) the use of high-throughput systems or platforms for the detection of multiple targets and (3) algorithms that allow the conversion of analytical results into an indication of the presence of individual GMOs potentially present in an unknown sample. This paper reviews the latest progress made in GMO analysis, taking examples from the most recently developed strategies and tools, and addresses some of the critical aspects related to these approaches.

  12. New optical approaches to the quantitative characterization of crystal growth, segregation and defect formation

    NASA Technical Reports Server (NTRS)

    Carlson, D. J.; Wargo, M. J.; Cao, X. Z.; Witt, A. F.

    1991-01-01

    Elemental and compound semiconductors were characterized using new optical approach based on NIR microscopy in conjunction with computational image analysis and contrast enhancement. The approach made it possible to perform a quantitative microsegregation analysis of GaAs and InP. NIR dark file illumination in transmission mode makes it possible to detect submicron precipitates in semiinsulating GaAs.

  13. Fast quantitative single-molecule detection at ultralow concentrations.

    PubMed

    Haas, Philippe; Then, Patrick; Wild, Andreas; Grange, Wilfried; Zorman, Sylvain; Hegner, Martin; Calame, Michel; Aebi, Ueli; Flammer, Josef; Hecht, Bert

    2010-07-15

    The applicability of single-molecule fluorescence assays in liquids is limited by diffusion to concentrations in the low picomolar range. Here, we demonstrate quantitative single-molecule detection at attomolar concentrations within 1 min by excitation and detection of fluorescence through a single-mode optical fiber in presence of turbulent flow. The combination of high detectability and short measurement times promises applications in ultrasensitive assays, sensors, and point-of-care medical diagnostics.

  14. Developing a Research Program Using Qualitative and Quantitative Approaches.

    ERIC Educational Resources Information Center

    Beck, Cheryl Tatano

    1997-01-01

    A research program on postpartum depression is used to illustrate the use of both qualitative and quantitative approaches. The direction of a research program is thus not limited by the type of methods in which a researcher has expertise. (SK)

  15. Developing a Research Program Using Qualitative and Quantitative Approaches.

    ERIC Educational Resources Information Center

    Beck, Cheryl Tatano

    1997-01-01

    A research program on postpartum depression is used to illustrate the use of both qualitative and quantitative approaches. The direction of a research program is thus not limited by the type of methods in which a researcher has expertise. (SK)

  16. Pain relief by touch: A quantitative approach

    PubMed Central

    Mancini, Flavia; Nash, Thomas; Iannetti, Gian Domenico; Haggard, Patrick

    2014-01-01

    Pain relief by touch has been studied for decades in pain neuroscience. Human perceptual studies revealed analgesic effects of segmental tactile stimulation, as compared to extrasegmental touch. However, the spatial organisation of touch–pain interactions within a single human dermatome has not been investigated yet. In 2 experiments we tested whether, how, and where within a dermatome touch modulates the perception of laser-evoked pain. We measured pain perception using intensity ratings, qualitative descriptors, and signal detection measures of sensitivity and response bias. Touch concurrent with laser pulses produced a significant analgesia, and reduced the sensitivity in detecting the energy of laser stimulation, implying a functional loss of information within the ascending Aδ pathway. Touch also produced a bias to judge laser stimuli as less painful. This bias decreased linearly when the distance between the laser and tactile stimuli increased. Thus, our study provides evidence for a spatial organisation of intrasegmental touch–pain interactions. PMID:24361816

  17. [Pharmacoproteomic approach by quantitative targeted proteomics].

    PubMed

    Ohtsuki, Sumio

    2012-01-01

    Omics analyses provided many candidates for drug targets and biomarkers. However, these analyses have not contributed to drug development efficiently because of top-down omics analyses. To solve this problem, we have recently developed quantitative targeted proteomics with multiplexed-multiple reaction monitoring (multiplexed-MRM) method, which enables us to perform bottom-up proteomics. In this method, the target proteins for quantification are selected prior to analysis based on the knowledge related to interesting phenomena. Target peptides for quantification are selected only from sequence information, so time-consuming procedures such as antibody preparation and protein purification are unnecessary. In this review, we introduce the technical features of multiplexed-MRM method as novel protein quantification method, and summarize its advantages with reference to recently reported results, including species differences, in vitro-to-in vivo reconstruction and personalized chemotherapy. This novel simultaneous protein quantification method overcomes problems of antibody-based quantification and would open new drug research based of protein as "Pharmacoproteomics".

  18. A quantitative approach to spring hydrograph decomposition

    NASA Astrophysics Data System (ADS)

    Kovács, Attila; Perrochet, Pierre

    2008-04-01

    SummaryA combined analytical-numerical study for the characterization of spring hydrographs is presented. Two-dimensional analytical solutions for diffusive flux from rectangular blocks of arbitrary shape facilitate a quantitative characterization of exponential hydrograph components. Together with analytical solutions for block discharge, a systematic analysis of numerically simulated spring hydrographs of synthetic karst systems provides an insight into karst hydrodynamics. Different hydrograph components do not represent different classes of rock permeability. Hydrographs of individual homogeneous blocks can be decomposed into several exponential components. Discharge hydrographs of symmetric rectangular blocks can be reconstructed by the sum of only three exponential components. Increasing block asymmetry results in an increasing number of exponential components contributing significantly to total discharge. Spring hydrographs represent a sum of individual block discharges originating from diffuse infiltration and conduit discharge originating from concentrated recharge. Beyond the inflection of the recession limb, a spring hydrograph can be decomposed in a similar manner to that of individual homogeneous blocks. The presented hydrograph analytical method facilitates the estimation of hydraulic and geometric parameters of karst hydrogeological systems.

  19. Quantitative detection of fluid distribution using time-lapse seismic

    NASA Astrophysics Data System (ADS)

    Tsuneyama, Futoshi

    The quantitative evaluation of time-lapse seismic data remains a challenge due to poor match between the model predictions and the actual seismic data. Velocity anisotropy is one important reason for the mismatch. I compile experimental velocity-anisotropy data from cores to explore the empirical relationships between anisotropy parameters and general well-log information. Then, I develop a method to estimate Thomsen's anisotropy parameters ε and gamma using a regression of the data in the crossplot domain between velocity and porosity. I present an application result of the method to demonstrate the significance of the correction. Next, using the corrected velocity, I present a method of impedance decomposition into Vp, Vs, and rho using three elastic impedances derived from the seismic inversion of angle stacks. In general, the maximum stack angle of seismic data is limited to be less than 30°, which is not wide enough to obtain the stable calculation result. I discuss the effect of noise on the analysis as the most important reason that decomposition is difficult. I show an innovative method incorporating rock-physics bounds as constraints for the analysis. I apply it to an actual dataset from an offshore oil field; I demonstrate the result of analysis for sand-body detection. Based on the estimated Vp, V s, rho and shale volume from the elastic impedances, I develop a workflow to determine the saturation of formation-water, oil and gas from seismic data. First, I consider the pressure effect and the saturation scale of fluids for time-lapse seismic analysis. Second, I demonstrate a deterministic approach to computing the fluid saturation to evaluate time-lapse seismic data. In this approach, I derive the physical properties of the water-saturated sandstone reservoir. Then, by comparing the in-situ-fluid-saturated properties with the 100% formation-water-saturated reservoir properties, I determine the bulk modulus and the density of the fluid phase in the

  20. Quantitative detection of settled coal dust over green canopy

    NASA Astrophysics Data System (ADS)

    Brook, Anna; Sahar, Nir

    2017-04-01

    /sq m. The stage 2 is completed by calculating: 1. Unmixing between the green canopy and the settle dust extraction only coal dust fraction, 2. Converting spectral feature of coal dust to concentration via PLSR spectral model. The spectral model was trained and validated PLSR model developed at laboratory using spectra across MIR (FTIR reflectance spectra) and NIR regions and XRD analysis. The obtained RMSE was satisfying for both spectral regions. Thus, it was concluded that field spectroscopy can be used for this purpose, and it can provide fully quantitative measures of settle coal dust. Nowadays this approach (both spectrometer and algorithm) has been accepted as a practical operational tool for environmental monitoring near power station Orot Rabin in Hadera and will be used by the Sharon-Carmel Districts Municipal Association for Environmental Protection, Israel as a regulatory tool. In summary, this work shows that coal dust can be assessed using in situ spectroscopy, making it a potentially powerful tool for environmental studies. References Chudnovsky, A., & Ben-Dor, E. (2009). Reflectance spectroscopy as a tool for settled dust monitoring in office environment. International Journal of Environment and Waste Management, 4(1), 32-49. Brook, A. (2014). Quantitative Detection of Settled dust over Green Canopy using Sparse Unmixing of Airborne Hyperspectral Data. IEEE-Whispers 6th Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing, 2014, Switzerland, 4-8. Brook, A. and Ben-Dor, E. (2016). Quantitative detection of settled dust over Green Canopy using sparse unmixing of airborne hyperspectral data. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 9(2), pp.884-897. Brook, A. (2016). Quantitative Detection and Long-Term Monitoring of Settle Dust Using Semisupervised Learning for Spectral Data. Water, Air, & Soil Pollution, 227(3), pp.1-9. Bioucas-Dias, J.M., Plaza, A., Dobigeon, N., Parente, M., Du, Q

  1. Current Approaches Toward Quantitative Mapping of the Interactome

    PubMed Central

    Buntru, Alexander; Trepte, Philipp; Klockmeier, Konrad; Schnoegl, Sigrid; Wanker, Erich E.

    2016-01-01

    Protein–protein interactions (PPIs) play a key role in many, if not all, cellular processes. Disease is often caused by perturbation of PPIs, as recently indicated by studies of missense mutations. To understand the associations of proteins and to unravel the global picture of PPIs in the cell, different experimental detection techniques for PPIs have been established. Genetic and biochemical methods such as the yeast two-hybrid system or affinity purification-based approaches are well suited to high-throughput, proteome-wide screening and are mainly used to obtain qualitative results. However, they have been criticized for not reflecting the cellular situation or the dynamic nature of PPIs. In this review, we provide an overview of various genetic methods that go beyond qualitative detection and allow quantitative measuring of PPIs in mammalian cells, such as dual luminescence-based co-immunoprecipitation, Förster resonance energy transfer or luminescence-based mammalian interactome mapping with bait control. We discuss the strengths and weaknesses of different techniques and their potential applications in biomedical research. PMID:27200083

  2. Microfluidic approaches to malaria detection.

    PubMed

    Gascoyne, Peter; Satayavivad, Jutamaad; Ruchirawat, Mathuros

    2004-02-01

    Microfluidic systems are under development to address a variety of medical problems. Key advantages of micrototal analysis systems based on microfluidic technology are the promise of small size and the integration of sample handling and measurement functions within a single, automated device having low mass-production costs. Here, we review the spectrum of methods currently used to detect malaria, consider their advantages and disadvantages, and discuss their adaptability towards integration into small, automated micro total analysis systems. Molecular amplification methods emerge as leading candidates for chip-based systems because they offer extremely high sensitivity, the ability to recognize malaria species and strain, and they will be adaptable to the detection of new genotypic signatures that will emerge from current genomic-based research of the disease. Current approaches to the development of chip-based molecular amplification are considered with special emphasis on flow-through PCR, and we present for the first time the method of malaria specimen preparation by dielectrophoretic field-flow-fractionation. Although many challenges must be addressed to realize a micrototal analysis system for malaria diagnosis, it is concluded that the potential benefits of the approach are well worth pursuing.

  3. Facile and quantitative electrochemical detection of yeast cell apoptosis

    NASA Astrophysics Data System (ADS)

    Yue, Qiulin; Xiong, Shiquan; Cai, Dongqing; Wu, Zhengyan; Zhang, Xin

    2014-03-01

    An electrochemical method based on square wave anodic stripping voltammetry (SWASV) was developed to detect the apoptosis of yeast cells conveniently and quantitatively through the high affinity between Cu2+ and phosphatidylserine (PS) translocated from the inner to the outer plasma membrane of the apoptotic cells. The combination of negatively charged PS and Cu2+ could decrease the electrochemical response of Cu2+ on the electrode. The results showed that the apoptotic rates of cells could be detected quantitatively through the variations of peak currents of Cu2+ by SWASV, and agreed well with those obtained through traditional flow cytometry detection. This work thus may provide a novel, simple, immediate and accurate detection method for cell apoptosis.

  4. Graphics processing unit-accelerated quantitative trait Loci detection.

    PubMed

    Chapuis, Guillaume; Filangi, Olivier; Elsen, Jean-Michel; Lavenier, Dominique; Le Roy, Pascale

    2013-09-01

    Mapping quantitative trait loci (QTL) using genetic marker information is a time-consuming analysis that has interested the mapping community in recent decades. The increasing amount of genetic marker data allows one to consider ever more precise QTL analyses while increasing the demand for computation. Part of the difficulty of detecting QTLs resides in finding appropriate critical values or threshold values, above which a QTL effect is considered significant. Different approaches exist to determine these thresholds, using either empirical methods or algebraic approximations. In this article, we present a new implementation of existing software, QTLMap, which takes advantage of the data parallel nature of the problem by offsetting heavy computations to a graphics processing unit (GPU). Developments on the GPU were implemented using Cuda technology. This new implementation performs up to 75 times faster than the previous multicore implementation, while maintaining the same results and level of precision (Double Precision) and computing both QTL values and thresholds. This speedup allows one to perform more complex analyses, such as linkage disequilibrium linkage analyses (LDLA) and multiQTL analyses, in a reasonable time frame.

  5. A microarray scanner for the real-time quantitative detection

    NASA Astrophysics Data System (ADS)

    Liu, Quanjun; Zhuang, Ying; Wu, Lingwei; Wu, Zhongwei; Hu, Song; Lu, Zuhong

    2007-05-01

    The real-time and quantitative detection assay is important for the gene detection. With the TaqMan probes for the detection based polymerase chain reaction (PCR), four targets could be checked in a single process in solution assay. A new method is developed to immobilize the TaqMan probes on a microarray, which could be used to the multi-target gene fragment quantitative detection with PCR. A new type microarray scanner is designed for the assay. A thermocycler system was built into the scanner platform. A new type of the vessel sealed with the gene amplification solution which could perform the thermo-cycling and scanning. To decrease the background intensity a confocal system was used as the fluorescent intensity detection in the scanner. To calculate the gene quantity, a standard liner graph was draw with the fluorescent intensity versus the cycles. From the standard liner, the quantity of the original gene fragment could be calculated in time with the cycles. This scanner offers the great advantage of real-time quantitative detection of DNA targets in a microarray.

  6. Quantitation and detection of vanadium in biologic and pollution materials

    NASA Technical Reports Server (NTRS)

    Gordon, W. A.

    1974-01-01

    A review is presented of special considerations and methodology for determining vanadium in biological and air pollution materials. In addition to descriptions of specific analysis procedures, general sections are included on quantitation of analysis procedures, sample preparation, blanks, and methods of detection of vanadium. Most of the information presented is applicable to the determination of other trace elements in addition to vanadium.

  7. Competitor internal standards for quantitative detection of mycoplasma DNA.

    PubMed

    Sidhu, M K; Rashidbaigi, A; Testa, D; Liao, M J

    1995-05-01

    Homologous internal controls were used as competitor DNA in the polymerase chain reaction for the quantitative detection of mycoplasma DNA. PCR primer sets were designed on the basis of the most conserved nucleotide sequences of the 16S rRNA gene of mycoplasma species. Amplification of this gene was examined in five different mycoplasma species: Mycoplasma orale, M. hyorhinus, M. synoviae, M. gallisepticum and M. pneumoniae. To evaluate the primers, a number of different cell lines were assayed for the detection of mycoplasma infections. All positive cell lines showed a distinct product on agarose gels while uninfected cells showed no DNA amplification. Neither bacterial nor eukaryotic DNA produced any cross-reaction with the primers used, thus confirming their specificity. Internal control DNA to be used for quantitation was constructed by modifying the sizes of the wild-type amplified products and cloning them in plasmid vectors. These controls used the same primer binding sites as the wild-type and the amplified products were differentiated by a size difference. The detection limits for all the mycoplasma species by competitive quantitative PCR were estimated to range from 4 to 60 genome copies per assay as determined by ethidium bromide-stained agarose gels. These internal standards also serve as positive controls in PCR-based detection of mycoplasma DNA, and therefore accidental contamination of test samples with wild-type positive controls can be eliminated. The quantitative PCR method developed will be useful in monitoring the progression and significance of mycoplasma in the disease process.

  8. A qualitative/quantitative approach for the detection of 37 tryptamine-derived designer drugs, 5 β-carbolines, ibogaine, and yohimbine in human urine and plasma using standard urine screening and multi-analyte approaches.

    PubMed

    Meyer, Markus R; Caspar, Achim; Brandt, Simon D; Maurer, Hans H

    2014-01-01

    The first synthetic tryptamines have entered the designer drug market in the late 1990s and were distributed as psychedelic recreational drugs. In the meantime, several analogs have been brought onto the market indicating a growing interest in this drug class. So far, only scarce analytical data were available on the detectability of tryptamines in human biosamples. Therefore, the aim of the presented study was the development and full validation of a method for their detection in human urine and plasma and their quantification in human plasma. The liquid chromatography-linear ion trap mass spectrometry method presented covered 37 tryptamines as well as five β-carbolines, ibogaine, and yohimbine. Compounds were analyzed after protein precipitation of urine or fast liquid-liquid extraction of plasma using an LXQ linear ion trap coupled to an Accela ultra ultra high-performance liquid chromatography system. Data mining was performed via information-dependent acquisition or targeted product ion scan mode with positive electrospray ionization. The assay was selective for all tested substances with limits of detection in urine between 10 and 100 ng/mL and in plasma between 1 and 100 ng/mL. A validated quantification in plasma according to international recommendation could be demonstrated for 33 out of 44 analytes.

  9. Sexual Harassment Prevention Initiatives: Quantitative and Qualitative Approaches

    DTIC Science & Technology

    2010-10-28

    is met. Gelo, Braakman, and Benetka (2008) describe qualitative and quantitative paradigms as such: Quantitative paradigms see reality as single...and tangible, where the knower and the known are considered as relatively separate and independent. Qualitative paradigms , however, view reality as a...experimental research or the positivist approach) will typically be utilized to explore and answer questions about relationships with measured variables that

  10. Accounting for imperfect detection in ecology: a quantitative review.

    PubMed

    Kellner, Kenneth F; Swihart, Robert K

    2014-01-01

    Detection in studies of species abundance and distribution is often imperfect. Assuming perfect detection introduces bias into estimation that can weaken inference upon which understanding and policy are based. Despite availability of numerous methods designed to address this assumption, many refereed papers in ecology fail to account for non-detection error. We conducted a quantitative literature review of 537 ecological articles to measure the degree to which studies of different taxa, at various scales, and over time have accounted for imperfect detection. Overall, just 23% of articles accounted for imperfect detection. The probability that an article incorporated imperfect detection increased with time and varied among taxa studied; studies of vertebrates were more likely to incorporate imperfect detection. Among articles that reported detection probability, 70% contained per-survey estimates of detection that were less than 0.5. For articles in which constancy of detection was tested, 86% reported significant variation. We hope that our findings prompt more ecologists to consider carefully the detection process when designing studies and analyzing results, especially for sub-disciplines where incorporation of imperfect detection in study design and analysis so far has been lacking.

  11. Problems in Achieving a Quantitative Approach to Technologic Proliferation Resistance

    SciTech Connect

    Wiborg, James C.; Omberg, Ronald P.; Zentner, Michael D.

    2001-07-06

    In spite of setbacks, substantial success has been achieved by the various nonproliferation efforts over the past 50 years. Because the pace of technology evolution remains high and the cost of entry to nuclear weapons technology is decreasing, improved approaches are critical if similar success is to be achieved over the next 20 years. Recent analyses have been published that provide a semi-quantitative assessment of proliferation risk, which can serve as the foundation for a meaningful quantitative approach to assessing proliferation risk. These methods represent an important step, but represent only one step in the work that must be achieved in the next few years. This paper presents perspectives on evaluating the merits of institutional arrangements and the role of design versus institutional features in proliferation prevention. It concludes by proposing methodology and quantitative approaches to be considered for evaluating proliferation-resistant measures in innovative reactor and fuel cycle technologies.

  12. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods

    PubMed Central

    Gauci, Victoria J.; Wright, Elise P.

    2010-01-01

    Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist. PMID:21686332

  13. The evolution of hominoid cranial diversity: A quantitative genetic approach.

    PubMed

    Schroeder, Lauren; von Cramon-Taubadel, Noreen

    2017-09-12

    Hominoid cranial evolution is characterized by substantial phenotypic diversity, yet the cause of this variability has rarely been explored. Quantitative genetic techniques for investigating evolutionary processes underlying morphological divergence are dependent on the availability of good ancestral models, a problem in hominoids where the fossil record is fragmentary and poorly understood. Here, we use a maximum likelihood approach based on a Brownian motion model of evolutionary change to estimate nested hypothetical ancestral forms from 15 extant hominoid taxa. These ancestors were then used to calculate rates of evolution along each branch of a phylogenetic tree using Lande's generalized genetic distance. Our results show that hominoid cranial evolution is characterized by strong stabilizing selection. Only two instances of directional selection were detected; the divergence of Homo from its last common ancestor with Pan, and the divergence of the lesser apes from their last common ancestor with the great apes. In these two cases, selection gradients reconstructed to identify the specific traits undergoing selection indicated that selection on basicranial flexion, cranial vault expansion and facial retraction characterizes the divergence of Homo, whereas the divergence of the lesser apes was defined by selection on neurocranial size reduction. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  14. Detection and Quantitation of T-2 Mycotoxin Using a Simplified Protein Synthesis Inhibition Assay.

    DTIC Science & Technology

    1983-07-18

    chemical agents. It is presently being used in studies of mycotoxin mecha- ism of action and approaches toward in vivo neutralization of the toxic effects... neutralization of the toxic effects of mycotoxins . 3 Introduction Numerous approaches have been used in the past for the detection and quantitation of...study would be the srsarch for a means of in vivo neutralization of mycotoxin effects using antibodies .. ’ chemical agents by first testing for

  15. An approach for quantitative image quality analysis for CT

    NASA Astrophysics Data System (ADS)

    Rahimi, Amir; Cochran, Joe; Mooney, Doug; Regensburger, Joe

    2016-03-01

    An objective and standardized approach to assess image quality of Compute Tomography (CT) systems is required in a wide variety of imaging processes to identify CT systems appropriate for a given application. We present an overview of the framework we have developed to help standardize and to objectively assess CT image quality for different models of CT scanners used for security applications. Within this framework, we have developed methods to quantitatively measure metrics that should correlate with feature identification, detection accuracy and precision, and image registration capabilities of CT machines and to identify strengths and weaknesses in different CT imaging technologies in transportation security. To that end we have designed, developed and constructed phantoms that allow for systematic and repeatable measurements of roughly 88 image quality metrics, representing modulation transfer function, noise equivalent quanta, noise power spectra, slice sensitivity profiles, streak artifacts, CT number uniformity, CT number consistency, object length accuracy, CT number path length consistency, and object registration. Furthermore, we have developed a sophisticated MATLAB based image analysis tool kit to analyze CT generated images of phantoms and report these metrics in a format that is standardized across the considered models of CT scanners, allowing for comparative image quality analysis within a CT model or between different CT models. In addition, we have developed a modified sparse principal component analysis (SPCA) method to generate a modified set of PCA components as compared to the standard principal component analysis (PCA) with sparse loadings in conjunction with Hotelling T2 statistical analysis method to compare, qualify, and detect faults in the tested systems.

  16. Biotechnology Approaches to Life Detection

    NASA Technical Reports Server (NTRS)

    Steele, Andrew; McKay, David; Schweitzer, Mary

    2001-01-01

    The direct detection of organic biomarkers for living or fossil microbes on Mars by an in situ instrument is a worthy goal for future lander missions. Several new and innovative biotechnology approaches are being explored. Firstly we have proposed an instrument based on immunological reactions to specific antibodies to cause activation of fluorescent stains. Antibodies are raised or acquired to a variety of general and specific substances that might be in Mars soil. These antibodies are then combined with various fluorescent stains and applied to micron sized numbered spots on a small (2-3 cm) test plate where they become firmly attached after freeze drying. Using technology that has been developed for gene mining in DNA technology up to 10,000 tests per square inch can now be applied to a test plate. On Mars or the planet/moon of interest, a sample of soil from a trench or drill core is extracted with water and/or an organic solvent and ultrasonication and then applied to the test plate. Any substance, which has an antibody on the test plate, will react with its antibody and activate its fluorescent stain. At the moment a small UV light source will illuminate the test plate, which is observed with a small CCD camera, although other detection systems will be applied. The numbered spots that fluoresce indicate the presence of the tested-for substance, and the intensity indicates relative amounts. Furthermore with up to a thousand test plates available false positives and several variations of antibody can also be screened for. The entire instrument can be quite small and light, on the order of 10 cm in each dimension. A possible choice for light source may be small UV lasers at several wavelengths. Some of the wells or spots can contain simply standard fluorescent stains used to detect live cells, dead cells, DNA, etc. The stains in these spots may be directly activated, with no antibodies being necessary. The proposed system will look for three classes of

  17. Biotechnology Approaches to Life Detection

    NASA Technical Reports Server (NTRS)

    Steele, Andrew; McKay, David; Schweitzer, Mary

    2001-01-01

    The direct detection of organic biomarkers for living or fossil microbes on Mars by an in situ instrument is a worthy goal for future lander missions. Several new and innovative biotechnology approaches are being explored. Firstly we have proposed an instrument based on immunological reactions to specific antibodies to cause activation of fluorescent stains. Antibodies are raised or acquired to a variety of general and specific substances that might be in Mars soil. These antibodies are then combined with various fluorescent stains and applied to micron sized numbered spots on a small (2-3 cm) test plate where they become firmly attached after freeze drying. Using technology that has been developed for gene mining in DNA technology up to 10,000 tests per square inch can now be applied to a test plate. On Mars or the planet/moon of interest, a sample of soil from a trench or drill core is extracted with water and/or an organic solvent and ultrasonication and then applied to the test plate. Any substance, which has an antibody on the test plate, will react with its antibody and activate its fluorescent stain. At the moment a small UV light source will illuminate the test plate, which is observed with a small CCD camera, although other detection systems will be applied. The numbered spots that fluoresce indicate the presence of the tested-for substance, and the intensity indicates relative amounts. Furthermore with up to a thousand test plates available false positives and several variations of antibody can also be screened for. The entire instrument can be quite small and light, on the order of 10 cm in each dimension. A possible choice for light source may be small UV lasers at several wavelengths. Some of the wells or spots can contain simply standard fluorescent stains used to detect live cells, dead cells, DNA, etc. The stains in these spots may be directly activated, with no antibodies being necessary. The proposed system will look for three classes of

  18. Rapid and quantitative detection of hepatitis B virus.

    PubMed

    Liu, Yue-Ping; Yao, Chun-Yan

    2015-11-14

    Despite availability of a universal vaccine, hepatitis B virus (HBV) infection has a huge impact on public health worldwide. Accurate and timely diagnosis of HBV infection is needed. Rapid developments have been made in the diagnostic and monitoring methods for HBV infection, including serological and molecular assays. In clinical practice, qualitative hepatitis B surface antigen (HBsAg) testing has long served as a diagnostic marker for individuals infected with HBV. More recently, HBsAg level has been used to predict treatment outcome when determined early during treatment or at baseline. However, identification of HBV DNA positive cases that do not have detectable HBsAg has encouraged the application of molecular tests. Hence, combination of quantitative detection of HBV DNA and HBsAg can be used to discriminate patients during the course of HBV infection and to monitor therapy. This article reviews the most commonly used quantitative methods for HBsAg and HBV DNA.

  19. Infusing Quantitative Approaches throughout the Biological Sciences Curriculum

    ERIC Educational Resources Information Center

    Thompson, Katerina V.; Cooke, Todd J.; Fagan, William F.; Gulick, Denny; Levy, Doron; Nelson, Kären C.; Redish, Edward F.; Smith, Robert F.; Presson, Joelle

    2013-01-01

    A major curriculum redesign effort at the University of Maryland is infusing all levels of our undergraduate biological sciences curriculum with increased emphasis on interdisciplinary connections and quantitative approaches. The curriculum development efforts have largely been guided by recommendations in the National Research Council's "Bio…

  20. Infusing Quantitative Approaches throughout the Biological Sciences Curriculum

    ERIC Educational Resources Information Center

    Thompson, Katerina V.; Cooke, Todd J.; Fagan, William F.; Gulick, Denny; Levy, Doron; Nelson, Kären C.; Redish, Edward F.; Smith, Robert F.; Presson, Joelle

    2013-01-01

    A major curriculum redesign effort at the University of Maryland is infusing all levels of our undergraduate biological sciences curriculum with increased emphasis on interdisciplinary connections and quantitative approaches. The curriculum development efforts have largely been guided by recommendations in the National Research Council's "Bio…

  1. Approaches to Combining Quantitative and Qualitative Social Support Research.

    ERIC Educational Resources Information Center

    Ingersoll, Berit

    Social scientists tend to adopt either a qualitative or a quantitative perspective in research on social support. As single methods, each perspective has unique distinctions, limitations, and trade-offs. These approaches are based on differing epistemological assumptions. Qualitative research attempts to understand human behavior from the…

  2. Quantitative analysis of lunar crater's landscape: automatic detection, classification and geological applications

    NASA Astrophysics Data System (ADS)

    Li, Ke; Chen, Jianping; He, Shujun; Zhang, Mingchao

    2013-04-01

    Lunar craters are the most important geological tectonic features on the moon; they are among the most studied subjects when it comes to the analysis of the surface of the moon since they provide us with the relative age of the surface unit and more information about lunar geology. Quantitative analysis of landscape on lunar crater is an important approach in lunar geological unit dating which plays a key role in understanding and reconstruction of lunar geological evolution. In this paper, a new approach of automatic crater detection and classification is proposed based on the quantitative analysis of crater's landscape with different spatial resolution digital terrain models. The approach proposed in this paper includes the following key points: 1) A new crater detection method which selects profile similarity parameters as the distinguishing marks is presented. The new method overcomes the high error defect of former DTM based crater detection algorithm; 2) Craters are sorted by the morphological characteristics of profiles. The new quantitative classification method overcomes the subjectivity of the previously descriptive classification method. In order to verify the usefulness of the proposed method the pre-selected landing area of China's Chang'e-III lunar satellite-Sinus Iridum is chosen as the experimental zone. DTM with different resolutions from the Chang'e-I Laser Altimeter, the Chang'e-I Stereoscopic Camera and the Lunar Orbiter Laser Altimeter (LOLA) are used for crater detection and classification. Dating results of each geological unit are gotten using crater size-frequency distribution method (CSFD). By comparing the former dating and manual classification data, we found that the results obtained by our method and the former results have the strong consistency. With the combination of automatic crater detection and classification, this paper basically provided a quantitative approach which can analyze the lunar crater's landscape and get geological

  3. A microfabrication-based approach to quantitative isothermal titration calorimetry.

    PubMed

    Wang, Bin; Jia, Yuan; Lin, Qiao

    2016-04-15

    Isothermal titration calorimetry (ITC) directly measures heat evolved in a chemical reaction to determine equilibrium binding properties of biomolecular systems. Conventional ITC instruments are expensive, use complicated design and construction, and require long analysis times. Microfabricated calorimetric devices are promising, although they have yet to allow accurate, quantitative ITC measurements of biochemical reactions. This paper presents a microfabrication-based approach to integrated, quantitative ITC characterization of biomolecular interactions. The approach integrates microfabricated differential calorimetric sensors with microfluidic titration. Biomolecules and reagents are introduced at each of a series of molar ratios, mixed, and allowed to react. The reaction thermal power is differentially measured, and used to determine the thermodynamic profile of the biomolecular interactions. Implemented in a microdevice featuring thermally isolated, well-defined reaction volumes with minimized fluid evaporation as well as highly sensitive thermoelectric sensing, the approach enables accurate and quantitative ITC measurements of protein-ligand interactions under different isothermal conditions. Using the approach, we demonstrate ITC characterization of the binding of 18-Crown-6 with barium chloride, and the binding of ribonuclease A with cytidine 2'-monophosphate within reaction volumes of approximately 0.7 µL and at concentrations down to 2mM. For each binding system, the ITC measurements were completed with considerably reduced analysis times and material consumption, and yielded a complete thermodynamic profile of the molecular interaction in agreement with published data. This demonstrates the potential usefulness of our approach for biomolecular characterization in biomedical applications.

  4. Rapid detection and quantitation of ganciclovir resistance in cytomegalovirus quasispecies.

    PubMed

    Ruiz-Carrascoso, Guillermo; Romero-Gómez, María Pilar; Plaza, Diego; Mingorance, Jesús

    2013-07-01

    Human cytomegalovirus (HCMV) may cause severe or fatal disease among immunocompromised patients. The first line prophylaxis and systemic HCMV disease therapy is ganciclovir (GCV). The presence of GCV-resistant virus has been linked to fatal HCMV disease. The implementation of rapid and sensitive techniques for the early detection and monitoring of GCV-resistance may be helpful to support antiviral therapy management. A pyrosequencing assay for the detection and quantitation of the most frequent mutations conferring moderate- and high-grade GCV resistance was implemented. The pyrosequencing achieved an analytical sensitivity for adequate interpretation of ≥10(3)  copies/ml. The assay was validated with 18 whole blood samples taken over a 6-month period from an umbilical cord blood recipient infected persistently with HCMV and allowed the detection and monitoring of the M460I and A594V GCV-resistant mutations. The percentage of resistant quasispecies ranged from 7.9% to 55.2% for the M460I mutation and from 19.8% to 43% for the A594V mutation. Clearance of the M460I mutation occurred in parallel with a decrease in the HCMV viremia, while the A594V mutation persisted. The pyrosequencing method for detection of GCV is sensitive enough to be used directly on clinical samples for the early identification of resistance mutations and allows the quantitation of resistant and wild type virus quasispecies within hours. The quantitation of minor resistant variants is an important issue to understand their relationship with viral load modification, and potentially anticipate treatment adjustment.

  5. Quantitative bioanalysis: an integrated approach for drug discovery and development

    NASA Astrophysics Data System (ADS)

    Ong, Voon S.; Cook, Kevin L.; Kosara, Christine M.; Brubaker, William F.

    2004-11-01

    An integrated approach to quantitative bioanalysis, incorporating turbulent flow chromatography (TFC) with mass spectrometric detection, was developed to support in-house drug discovery and development efforts. Activities such as metabolic stability screening and pharmacokinetic characterization support are carried out on a single unified platform. Two different TFC column-switching configurations, parallel and serial, are presented. The first, a parallel TFC column configuration, is capable of high-throughput analysis but carryover can reach as high as 0.24%. The characteristics of the instrument operating in the parallel configuration are provided for analysis of samples generated during in vitro metabolic stability assessments, a key screen during the lead optimization phase of drug discovery. Operating in this configuration, the system has the capability of performing on-line solid phase extraction and analysis of approximately 400 samples containing phosphate-buffered saline in approximately 14 h. The second, a serial TFC column configuration, was used to perform direct plasma injection analysis. The advantage of the serial configuration is the relatively low carryover (<0.040%) observed due to increased number of valve washes; however these extra washes lead to increased injection cycle times. A method developed using the serial TFC column configuration for the determination of dihydropyridines in plasma samples is given as an example. Analytical performance criteria examined during method development and validation included linearity, accuracy, precision, and recovery. The robustness of the technique was demonstrated by applying the method in the analysis of over 2500 plasma samples generated during preclinical drug development studies. Further, combined analysis of plasma and brain tissue was performed using acetonitrile precipitation as sample pretreatment for both matrices.

  6. Blastomyces dermatitidis Antigen Detection by Quantitative Enzyme Immunoassay

    PubMed Central

    Hage, Chadi A.; Bariola, J. Ryan; Bensadoun, Eric; Rodgers, Mark; Bradsher, Robert W.; Wheat, L. Joseph

    2012-01-01

    The second-generation MVista Blastomyces antigen enzyme immunoassay was not quantitative; therefore, specimens obtained previously were tested in the same assay as new specimens to assess the change in antigen levels. Furthermore, the sensitivity in serum had not been fully evaluated. The purpose of this study was to evaluate a quantitative Blastomyces antigen assay and detection of antigen in serum. Calibrators containing known concentrations of Blastomyces galactomannan were used to quantify antigen in urine and serum from patients with proven blastomycosis and from controls. Paired current and previously obtained urine specimens were tested to determine if quantification eliminated the need for concurrent testing to assess change in antigen. Pretreatment of serum with EDTA at 104°C was evaluated to determine if dissociation of immune complexes improved detection of antigenemia. Antigenuria was detected in 89.9% of patients with culture- or histopathology-proven blastomycosis. Specificity was 99.0% in patients with nonfungal infections and healthy subjects, but cross-reactions occurred in 95.6% of patients with histoplasmosis. Change in antigen level categorized as increase, no change, or decrease based on antigen units determined in the same assay agreed closely with the category of change in ng/ml determined from different assays. Pretreatment increased the sensitivity of detection of antigenemia from 35.7% to 57.1%. Quantification eliminated the need for concurrent testing of current and previously obtained specimens for assessment of changes in antigen concentration. Pretreatment increased the sensitivity for detection of antigenemia. Differentiation of histoplasmosis and blastomycosis is not possible by antigen detection. PMID:22116687

  7. Quantitative Proteomic Approaches for Analysis of Protein S-Nitrosylation.

    PubMed

    Qu, Zhe; Greenlief, C Michael; Gu, Zezong

    2016-01-04

    S-Nitrosylation is a redox-based post-translational modification of a protein in response to nitric oxide (NO) signaling, and it participates in a variety of processes in diverse biological systems. The significance of this type of protein modification in health and diseases is increasingly recognized. In the central nervous system, aberrant S-nitrosylation, due to excessive NO production, is known to cause protein misfolding, mitochondrial dysfunction, transcriptional dysregulation, and neuronal death. This leads to an altered physiological state and consequently contributes to pathogenesis of neurodegenerative disorders. To date, much effort has been made to understand the mechanisms underlying protein S-nitrosylation, and several approaches have been developed to unveil S-nitrosylated proteins from different organisms. Interest in determining the dynamic changes of protein S-nitrosylation under different physiological and pathophysiological conditions has underscored the need for the development of quantitative proteomic approaches. Currently, both gel-based and gel-free mass spectrometry-based quantitative methods are widely used, and they each have advantages and disadvantages but may also be used together to produce complementary data. This review evaluates current available quantitative proteomic techniques for the analysis of protein S-nitrosylation and highlights recent advances, with emphasis on applications in neurodegenerative diseases. An important goal is to provide a comprehensive guide of feasible quantitative proteomic methodologies for examining protein S-nitrosylation in research to yield insights into disease mechanisms, diagnostic biomarkers, and drug discovery.

  8. Quantitative detection of settled dust over green canopy

    NASA Astrophysics Data System (ADS)

    Brook, Anna

    2016-04-01

    NMF (SS-NMF), 6) Alternating Least-Square (ALS), and 2) Lin's Projected Gradient (LPG). The performance is evaluated on real hyperspectral imagery data via detailed experimental assessment. The study showed that in certain compression tasks content-adapted sparse representation is provided by state-of-the-art solutions. The NMF algorithm estimates endmembers that are used to remove spurious information. If computationally feasible, it should include interaction terms to make the model more flexible. The optimal NMF algorithms, such as ALS and LPG, are assumed to be the simplest methods that achieve the minimum error on the test set. In summary, this work shows that sediment dust can be assessed using airborne HSI data, making it a potentially powerful tool for environmental studies. References Keshava, N., Mustard, J. (2002). Spectral unmixing. IEEE Signal Process. Mag., 19(1), 44-57. Chudnovsky, A., & Ben-Dor, E. (2009). Reflectance spectroscopy as a tool for settled dust monitoring in office environment. International Journal of Environment and Waste Management, 4(1), 32-49. Brook, A. (2014). Quantitative Detection of Settled dust over Green Canopy using Sparse Unmixing of Airborne Hyperspectral Data. IEEE-Whispers 6th Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing, 2014, Switzerland, 4-8. Keshava, N., Mustard, J. (2002). Spectral unmixing. IEEE Signal Process. Mag., 19(1), 44-57. Bioucas-Dias et al. (2012). Hyperspectral unmixing overview: Geometrical, statistical, and sparse regression-based approaches, IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 5(2), 354 -379.

  9. Quantitative optical imaging for the detection of early cancer

    NASA Astrophysics Data System (ADS)

    Wu, Tao

    The objectives of this thesis are to provide insight of fundamental mechanisms of acetowhitening effect, upon which the colposcopic diagnosis of human cervical cancer is based and to develop novel quantitative optical imaging technologies supplementing colposcopy to improve its performance in detecting early cancer. Firstly, the temporal characteristics of acetowhitening process are studied on monolayer cell cultures. It is found that the dynamic acetowhitening processes in normal and cancerous cells are significantly different. Secondly, the changes in light scattering induced by acetic acid in intact cells and isolated cellular fractions are investigated by using confocal microscopy and light scattering spectroscopy. The results provide evidence that the small-sized components in the cytoplasm are the major contributors to the acetowhitening effect. Thirdly, a unified Mie and fractal model is proposed to interpret light scattering by biological cells. It is found that light scattering in forward directions is dominated by Mie scattering by bare cells and nuclei, whereas light scattering at large angles is determined by fractal scattering by subcellular structures. Fourthly, an optical imaging system based on active stereo vision and motion tracking is built to measure the 3-D surface topology of cervix and track the motion of patient. The information of motion tracking is used to register the time-sequenced images of cervix recorded during colposcopic examination. The imaging system is evaluated by tracking the movements of cervix models. The results demonstrate that the imaging technique holds the promise to enable the quantitative mapping of the acetowhitening kinetics over cervical surface for more accurate diagnosis of cervical cancer. At last, a calibrated autofluorescence imaging system is instrumented for detecting neoplasia in vivo. It is found that the calibrated autofluorescence signals from neoplasia are generally lower than signals from normal

  10. Quantitative Genetic Interaction Mapping Using the E-MAP Approach

    PubMed Central

    Collins, Sean R.; Roguev, Assen; Krogan, Nevan J.

    2010-01-01

    Genetic interactions represent the degree to which the presence of one mutation modulates the phenotype of a second mutation. In recent years, approaches for measuring genetic interactions systematically and quantitatively have proven to be effective tools for unbiased characterization of gene function and have provided valuable data for analyses of evolution. Here, we present protocols for systematic measurement of genetic interactions with respect to organismal growth rate for two yeast species. PMID:20946812

  11. Universal and specific quantitative detection of botulinum neurotoxin genes

    PubMed Central

    2010-01-01

    Background Clostridium botulinum, an obligate anaerobic spore-forming bacterium, produces seven antigenic variants of botulinum toxin that are distinguished serologically and termed "serotypes". Botulinum toxin blocks the release of acetylcholine at neuromuscular junctions resulting in flaccid paralysis. The potential lethality of the disease warrants a fast and accurate means of diagnosing suspected instances of food contamination or human intoxication. Currently, the Food and Drug Administration (FDA)-accepted assay to detect and type botulinum neurotoxins (BoNTs) is the mouse protection bioassay. While specific and sensitive, this assay requires the use of laboratory animals, may take up to four days to achieve a diagnosis, and is unsuitable for high-throughput analysis. We report here a two-step PCR assay that identifies all toxin types, that achieves the specificity of the mouse bioassay while surpassing it in equivalent sensitivity, that has capability for high-throughput analysis, and that provides quantitative results within hours. The first step of our assay consists of a conventional PCR that detects the presence of C. botulinum regardless of the neurotoxin type. The second step uses quantitative PCR (qPCR) technology to determine the specific serotype of the neurotoxin. Results We assayed purified C. botulinum DNA and crude toxin preparations, as well as food and stool from healthy individuals spiked with purified BoNT DNA, and one stool sample from a case of infant botulism for the presence of the NTNH gene, which is part of the BoNT gene cluster, and for the presence of serotype-specific BoNT genes. The PCR surpassed the mouse bioassay both in specificity and sensitivity, detecting positive signals in BoNT preparations containing well below the 1 LD50 required for detection via the mouse bioassay. These results were type-specific and we were reliably able to quantify as few as 10 genomic copies. Conclusions While other studies have reported

  12. Well vulnerability: a quantitative approach for source water protection.

    PubMed

    Frind, E O; Molson, J W; Rudolph, D L

    2006-01-01

    The concept of vulnerability of drinking water sources is reviewed, and a quantitative approach for assessing well vulnerability for complex three-dimensional ground water systems is developed. The approach focuses on the relative expected impact of potential contaminant sources at unknown locations within a well capture zone, providing relative measures of intrinsic well vulnerability, including the expected times of arrival of a contaminant, the dispersion-related reduction in concentration, the time taken to breach a certain quality objective, and the corresponding exposure times. Thus, the result of the analysis includes the usual advective travel time information used in conventional wellhead protection analysis, plus a set of selected quantitative measures expressing the expected impact. The technique is based on adjoint theory and combines forward- and backward-in-time transport modeling using a standard numerical flow and transport code. The methodology is demonstrated using the case study of a complex glacial multiaquifer system in Ontario. The new approach will be useful in helping water managers develop more physically based and quantitative wellhead protection strategies.

  13. Immunoliposome-PCR: a generic ultrasensitive quantitative antigen detection system

    PubMed Central

    2012-01-01

    Background The accurate quantification of antigens at low concentrations over a wide dynamic range is needed for identifying biomarkers associated with disease and detecting protein interactions in high-throughput microarrays used in proteomics. Here we report the development of an ultrasensitive quantitative assay format called immunoliposome polymerase chain reaction (ILPCR) that fulfills these requirements. This method uses a liposome, with reporter DNA encapsulated inside and biotin-labeled polyethylene glycol (PEG) phospholipid conjugates incorporated into the outer surface of the liposome, as a detection reagent. The antigenic target is immobilized in the well of a microplate by a capture antibody and the liposome detection reagent is then coupled to a biotin-labeled second antibody through a NeutrAvidin bridge. The liposome is ruptured to release the reporter DNA, which serves as a surrogate to quantify the protein target using real-time PCR. Results A liposome detection reagent was prepared, which consisted of a population of liposomes ~120 nm in diameter with each liposome possessing ~800 accessible biotin receptors and ~220 encapsulated reporters. This liposome detection reagent was used in an assay to quantify the concentration of carcinoembryonic antigen (CEA) in human serum. This ILPCR assay exhibited a linear dose–response curve from 10-10 M to 10-16 M CEA. Within this range the assay coefficient of variance was <6 % for repeatability and <2 % for reproducibility. The assay detection limit was 13 fg/mL, which is 1,500-times more sensitive than current clinical assays for CEA. An ILPCR assay to quantify HIV-1 p24 core protein in buffer was also developed. Conclusions The ILPCR assay has several advantages over other immuno-PCR methods. The reporter DNA and biotin-labeled PEG phospholipids spontaneously incorporate into the liposomes as they form, simplifying preparation of the detection reagent. Encapsulation of the reporter inside the

  14. Comparison of Droplet Digital PCR and Quantitative PCR Assays for Quantitative Detection of Xanthomonas citri Subsp. citri

    PubMed Central

    Yin, Youping; Wang, Zhongkang

    2016-01-01

    Droplet digital polymerase chain reaction (ddPCR) is a novel molecular biology technique providing absolute quantification of target nucleic acids without the need for an external calibrator. Despite its emerging applications in medical diagnosis, there are few reports of its use for the detection of plant pathogens. This work was designed to assess the diagnosis potential of the ddPCR for absolute quantitative detection of Xanthomonas citri subsp. citri, a quarantine plant pathogenic bacterium that causes citrus bacterial canker in susceptible Citrus species. We transferred an established quantitative PCR (qPCR) assay for citrus bacterial canker diagnosis directly to the ddPCR format and compared the performance of the two methods. The qPCR assay has a broader dynamic range compared to the ddPCR assay and the ddPCR assay has a significantly higher degree of sensitivity compared to the qPCR assay. The influence of PCR inhibitors can be reduced considerably in the ddPCR assay because the collection of end-point fluorescent signals and the counting of binomial events (positive or negative droplets) are associated with a Poisson algorithm. The ddPCR assay also shows lower coefficient of variation compared to the qPCR assay especially in low target concentration. The linear association of the measurements by ddPCR and qPCR assays is strong (Pearson correlation = 0.8633; P<0.001). Receiver operating characteristic analysis indicates the ddPCR methodology is a more robust approach for diagnosis of citrus bacterial canker. In summary, the results demonstrated that the ddPCR assay has the potential for the quantitative detection of X. citri subsp. citri with high precision and accuracy as compared with the results from qPCR assay. Further studies are required to evaluate and validate the value of ddPCR technology in the diagnosis of plant disease and quarantine applications. PMID:27427975

  15. IWGT report on quantitative approaches to genotoxicity risk ...

    EPA Pesticide Factsheets

    This is the second of two reports from the International Workshops on Genotoxicity Testing (IWGT) Working Group on Quantitative Approaches to Genetic Toxicology Risk Assessment (the QWG). The first report summarized the discussions and recommendations of the QWG related to the need for quantitative dose–response analysis of genetic toxicology data, the existence and appropriate evaluation of threshold responses, and methods to analyze exposure-response relationships and derive points of departure (PoDs) from which acceptable exposure levels could be determined. This report summarizes the QWG discussions and recommendations regarding appropriate approaches to evaluate exposure-related risks of genotoxic damage, including extrapolation below identified PoDs and across test systems and species. Recommendations include the selection of appropriate genetic endpoints and target tissues, uncertainty factors and extrapolation methods to be considered, the importance and use of information on mode of action, toxicokinetics, metabolism, and exposure biomarkers when using quantitative exposure-response data to determine acceptable exposure levels in human populations or to assess the risk associated with known or anticipated exposures. The empirical relationship between genetic damage (mutation and chromosomal aberration) and cancer in animal models was also examined. It was concluded that there is a general correlation between cancer induction and mutagenic and/or clast

  16. A quantitative approach to evolution of music and philosophy

    NASA Astrophysics Data System (ADS)

    Vieira, Vilson; Fabbri, Renato; Travieso, Gonzalo; Oliveira, Osvaldo N., Jr.; da Fontoura Costa, Luciano

    2012-08-01

    The development of new statistical and computational methods is increasingly making it possible to bridge the gap between hard sciences and humanities. In this study, we propose an approach based on a quantitative evaluation of attributes of objects in fields of humanities, from which concepts such as dialectics and opposition are formally defined mathematically. As case studies, we analyzed the temporal evolution of classical music and philosophy by obtaining data for 8 features characterizing the corresponding fields for 7 well-known composers and philosophers, which were treated with multivariate statistics and pattern recognition methods. A bootstrap method was applied to avoid statistical bias caused by the small sample data set, with which hundreds of artificial composers and philosophers were generated, influenced by the 7 names originally chosen. Upon defining indices for opposition, skewness and counter-dialectics, we confirmed the intuitive analysis of historians in that classical music evolved according to a master-apprentice tradition, while in philosophy changes were driven by opposition. Though these case studies were meant only to show the possibility of treating phenomena in humanities quantitatively, including a quantitative measure of concepts such as dialectics and opposition, the results are encouraging for further application of the approach presented here to many other areas, since it is entirely generic.

  17. IWGT report on quantitative approaches to genotoxicity risk ...

    EPA Pesticide Factsheets

    This is the second of two reports from the International Workshops on Genotoxicity Testing (IWGT) Working Group on Quantitative Approaches to Genetic Toxicology Risk Assessment (the QWG). The first report summarized the discussions and recommendations of the QWG related to the need for quantitative dose–response analysis of genetic toxicology data, the existence and appropriate evaluation of threshold responses, and methods to analyze exposure-response relationships and derive points of departure (PoDs) from which acceptable exposure levels could be determined. This report summarizes the QWG discussions and recommendations regarding appropriate approaches to evaluate exposure-related risks of genotoxic damage, including extrapolation below identified PoDs and across test systems and species. Recommendations include the selection of appropriate genetic endpoints and target tissues, uncertainty factors and extrapolation methods to be considered, the importance and use of information on mode of action, toxicokinetics, metabolism, and exposure biomarkers when using quantitative exposure-response data to determine acceptable exposure levels in human populations or to assess the risk associated with known or anticipated exposures. The empirical relationship between genetic damage (mutation and chromosomal aberration) and cancer in animal models was also examined. It was concluded that there is a general correlation between cancer induction and mutagenic and/or clast

  18. Competitive PCR-High Resolution Melting Analysis (C-PCR-HRMA) for large genomic rearrangements (LGRs) detection: A new approach to assess quantitative status of BRCA1 gene in a reference laboratory.

    PubMed

    Minucci, Angelo; De Paolis, Elisa; Concolino, Paola; De Bonis, Maria; Rizza, Roberta; Canu, Giulia; Scaglione, Giovanni Luca; Mignone, Flavio; Scambia, Giovanni; Zuppi, Cecilia; Capoluongo, Ettore

    2017-07-01

    Evaluation of copy number variation (CNV) in BRCA1/2 genes, due to large genomic rearrangements (LGRs), is a mandatory analysis in hereditary breast and ovarian cancers families, if no pathogenic variants are found by sequencing. LGRs cannot be detected by conventional methods and several alternative methods have been developed. Since these approaches are expensive and time consuming, identification of alternative screening methods for LGRs detection is needed in order to reduce and optimize the diagnostic procedure. The aim of this study was to investigate a Competitive PCR-High Resolution Melting Analysis (C-PCR-HRMA) as molecular tool to detect recurrent BRCA1 LGRs. C-PCR-HRMA was performed on exons 3, 14, 18, 19, 20 and 21 of the BRCA1 gene; exons 4, 6 and 7 of the ALB gene were used as reference fragments. This study showed that it is possible to identify recurrent BRCA1 LGRs, by melting peak height ratio between target (BRCA1) and reference (ALB) fragments. Furthermore, we underline that a peculiar amplicon-melting profile is associated to a specific BRCA1 LGR. All C-PCR-HRMA results were confirmed by Multiplex ligation-dependent probe amplification. C-PCR-HRMA has proved to be an innovative, efficient and fast method for BRCA1 LGRs detection. Given the sensitivity, specificity and ease of use, c-PCR-HRMA can be considered an attractive and powerful alternative to other methods for BRCA1 CNVs screening, improving molecular strategies for BRCA testing in the context of Massive Parallel Sequencing. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Functional infrared imaging in medicine: a quantitative diagnostic approach.

    PubMed

    Merla, A; Romani, G L

    2006-01-01

    The role and the potentialities of high-resolution infrared thermography, combined to bio-heat modelling, have been largely described in the last years in a wide variety of biomedical applications. Quantitative assessment over time of the cutaneous temperature and/or of other biomedical parameters related to the temperature (e.g., cutaneous blood flow, thermal inertia, sympathetic skin response) allows for a better and more complete understanding and description of functional processes involved and/or altered in presence of ailment and interfering with the regular cutaneous thermoregulation. Such an approach to thermal medical imaging requires both new methodologies and tools, like diagnostic paradigms, appropriate software for data analysis and, even, a completely new way to look at data processing. In this paper, some of the studies recently made in our laboratory are presented and described, with the general intent of introducing the reader to these innovative methods to obtain quantitative diagnostic tools based on thermal imaging.

  20. Downhill simplex approach for vehicle headlights detection

    NASA Astrophysics Data System (ADS)

    Kang, Ho-Joong; Kim, Ho-Kun; Oh, Il-Whan; Choi, Kyoung-Ho

    2014-03-01

    Nighttime vehicle detection is an essential problem to be solved in the development of highway surveillance systems that provide information about the vehicle speed, traffic volume, and traffic jams, and so on. In this paper, a novel downhill simplex approach for vehicle headlights detection is presented. In the proposed approach, a rough position of vehicle headlights is detected first. Then, a downhill simplex optimization approach is adopted to find the accurate location of vehicle headlights. For the optimization process, a novel cost function is designed and various headlights are evaluated for possible headlight positions on the detected vehicles, locating an optimal headlight position. Simulation results are provided to show the robustness of the proposed approach for headlights detection.

  1. Salient object detection approach in UAV video

    NASA Astrophysics Data System (ADS)

    Zhang, Yueqiang; Su, Ang; Zhu, Xianwei; Zhang, Xiaohu; Shang, Yang

    2013-10-01

    The automatic detection of visually salient information from abundant video imagery is crucial, as it plays an important role in surveillance and reconnaissance tasks for Unmanned Aerial Vehicle (UAV). A real-time approach for the detection of salient objects on road, e.g. stationary and moving vehicle or people, is proposed, which is based on region segmentation and saliency detection within related domains. Generally, the traditional method specifically depends upon additional scene information and auxiliary thermal or IR sensing for secondary confirmation. However, this proposed approach can detect the interesting objects directly from video imagery captured by optical camera fixed on the small level UAV platform. To validate this proposed salient object detection approach, the 25 Hz video data from our low speed small UAV are tested. The results have demonstrated the proposed approach performs excellently in isolated rural environments.

  2. Lateral supraorbital approach vs pterional approach: an anatomic qualitative and quantitative evaluation.

    PubMed

    Salma, Asem; Alkandari, Abdulrahman; Sammet, Steffen; Ammirati, Mario

    2011-06-01

    Several minimally invasive modifications of the standard pterional approach have been proposed recently. The lateral supraorbital approach is one of these modifications. To provide a qualitative and quantitative anatomic comparison of the surgical exposure and the operability afforded by the standard pterional approach and the lateral supraorbital approach. Eight pterional approaches and 8 lateral supraorbital approaches were used in 8 fresh human cadaver heads. One qualitative and 2 quantitative tools were used to assess the surgical exposure. Qualitatively, the lateral supraorbital approach has the advantages of reduced trauma to the temporalis muscle and exposure that is comparable to that provided by the standard pterional approach to the sellar and suprasellar regions. This approach offers limited exposure of the interpeduncular fossa compared with the pterional one. Quantitatively, the pterional approach provides a greater surgical volume than the lateral supraorbital approach (32.90 mL vs 23.60 mL with P < .05). Also, the pterional approach provides a greater associated surgical operability than the lateral supraorbital approach (exposure score of 66 and 53, respectively). However, the lateral supraorbital approach offers an equivalent access to the anterior communicating artery complex, optic nerve, optic chiasm, and sellar area (the exposure scores were 19 for both approaches). From an anatomic point of view, both approaches provide similar exposure to the sellar, suprasellar, and anterior communicating artery areas. The pterional approach provides better exposure of the retrosellar area. The ability to operate in the retrosellar area, as judged by our model, was higher with the pterional than with the lateral supraorbital approach.

  3. Auditory detection and localization of approaching vehicles.

    PubMed

    Barton, Benjamin K; Ulrich, Thomas A; Lew, Roger

    2012-11-01

    Pedestrians must use a variety of cues when making safe decisions, many of which require processing of auditory information. We examined detection and localization of approaching vehicles using auditory cues. 50 adults ages 18-49 were presented with actual sounds of vehicles approaching at 5, 12, 25, and 35 mph. Three indices were of interest: the distance at which vehicles were detected, participants' decision regarding the direction from which vehicles were approaching, and their determination of the vehicles' arrival at their location. Participants more easily detected vehicles moving at higher speeds and vehicles approaching from the right. Determination of the direction of approach reached 90% accuracy or better when vehicles were traveling at, or greater than, 12 mph, and were more approaching from the right. Determination of vehicle arrival deteriorated significantly as speeds increased. Implications of the use of auditory cues in pedestrian settings, and future directions, are discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Distance-based microfluidic quantitative detection methods for point-of-care testing.

    PubMed

    Tian, Tian; Li, Jiuxing; Song, Yanling; Zhou, Leiji; Zhu, Zhi; Yang, Chaoyong James

    2016-04-07

    Equipment-free devices with quantitative readout are of great significance to point-of-care testing (POCT), which provides real-time readout to users and is especially important in low-resource settings. Among various equipment-free approaches, distance-based visual quantitative detection methods rely on reading the visual signal length for corresponding target concentrations, thus eliminating the need for sophisticated instruments. The distance-based methods are low-cost, user-friendly and can be integrated into portable analytical devices. Moreover, such methods enable quantitative detection of various targets by the naked eye. In this review, we first introduce the concept and history of distance-based visual quantitative detection methods. Then, we summarize the main methods for translation of molecular signals to distance-based readout and discuss different microfluidic platforms (glass, PDMS, paper and thread) in terms of applications in biomedical diagnostics, food safety monitoring, and environmental analysis. Finally, the potential and future perspectives are discussed.

  5. Detection of alternative lengthening of telomeres by telomere quantitative PCR

    PubMed Central

    Lau, Loretta M. S.; Dagg, Rebecca A.; Henson, Jeremy D.; Au, Amy Y. M.; Royds, Janice A.; Reddel, Roger R.

    2013-01-01

    Alternative lengthening of telomeres (ALT) is one of the two known telomere length maintenance mechanisms that are essential for the unlimited proliferation potential of cancer cells. Existing methods for detecting ALT in tumors require substantial amounts of tumor material and are labor intensive, making it difficult to study prevalence and prognostic significance of ALT in large tumor cohorts. Here, we present a novel strategy utilizing telomere quantitative PCR to diagnose ALT. The protocol is more rapid than conventional methods and scrutinizes two distinct characteristics of ALT cells concurrently: long telomeres and the presence of C-circles (partially double-stranded circles of telomeric C-strand DNA). Requiring only 30 ng of genomic DNA, this protocol will facilitate large-scale studies of ALT in tumors and can be readily adopted by clinical laboratories. PMID:22923525

  6. On the detection of early osteoarthritis by quantitative microscopic imaging

    NASA Astrophysics Data System (ADS)

    Mittelstaedt, Daniel John

    Articular cartilage is a thin layer of connective tissue that protects the ends of bones in diarthroidal joints. Cartilage distributes mechanical forces during daily movement throughout its unique depth-dependent structure. The extracellular matrix (ECM) of cartilage primarily contains water, collagen, and glycosaminoglycan (GAG). The collagen fibers are intertwined with negatively charged GAG and surround the cells (i.e. chondrocytes) in cartilage. Degradation to the ECM reduces the load bearing properties of cartilage which can be initiated by injury (e.g. anterior cruciate ligament (ACL) rupture) or disease (e.g. osteoarthritis (OA)). Magnetic resonance imaging (MRI) and x-ray computed tomography (CT) are noninvasive imaging techniques that are increasingly being used in the clinical detection of cartilage degradation. The aim of the first project in this dissertation was to quantify and compare the depth-dependent GAG concentration from healthy and biochemically degraded humeral ex vivo articular cartilage using quantitative contrast enhanced micro-computed tomography (qCECT) at high resolution. The second project in this dissertation was aimed to measure the topographical and depth-dependent GAG concentration using qCECT and delayed gadolinium enhanced magnetic resonance imaging of cartilage (dGEMRIC) from the medial tibia cartilage three weeks after unilateral ACL transection which is an animal model of OA (i.e. modified Pond-Nuki model). These GAG measurements were correlated with a biochemical method, inductively couple plasma optical emission spectrometry, to compare the degradation on the medial tibia between the OA and contralateral cartilage. The third project in this dissertation used the same cartilage specimens as in project two to investigate the change in T2 due to OA and the effect on T2 from a contrast agent. Furthermore, the change in T2 relaxation was investigated from static unconfined compression with correlations by biomechanical

  7. A FRET approach to phosgene detection.

    PubMed

    Zhang, Hexiang; Rudkevich, Dmitry M

    2007-03-28

    A FRET approach towards potential detection of phosgene is presented, which is based on a selective chemical reaction between phosgene (or triphosgene as a simulant) and donor and acceptor fluorophores.

  8. A Nonparametric Approach for Mapping Quantitative Trait Loci

    PubMed Central

    Kruglyak, L.; Lander, E. S.

    1995-01-01

    Genetic mapping of quantitative trait loci (QTLs) is performed typically by using a parametric approach, based on the assumption that the phenotype follows a normal distribution. Many traits of interest, however, are not normally distributed. In this paper, we present a nonparametric approach to QTL mapping applicable to any phenotypic distribution. The method is based on a statistic Z(w), which generalizes the nonparametric Wilcoxon rank-sum test to the situation of whole-genome search by interval mapping. We determine the appropriate significance level for the statistic Z(w), by showing that its asymptotic null distribution follows an Ornstein-Uhlenbeck process. These results provide a robust, distribution-free method for mapping QTLs. PMID:7768449

  9. Allometric Trajectories and “Stress”: A Quantitative Approach

    PubMed Central

    Anfodillo, Tommaso; Petit, Giai; Sterck, Frank; Lechthaler, Silvia; Olson, Mark E.

    2016-01-01

    The term “stress” is an important but vague term in plant biology. We show situations in which thinking in terms of “stress” is profitably replaced by quantifying distance from functionally optimal scaling relationships between plant parts. These relationships include, for example, the often-cited one between leaf area and sapwood area, which presumably reflects mutual dependence between sources and sink tissues and which scales positively within individuals and across species. These relationships seem to be so basic to plant functioning that they are favored by selection across nearly all plant lineages. Within a species or population, individuals that are far from the common scaling patterns are thus expected to perform negatively. For instance, “too little” leaf area (e.g., due to herbivory or disease) per unit of active stem mass would be expected to incur to low carbon income per respiratory cost and thus lead to lower growth. We present a framework that allows quantitative study of phenomena traditionally assigned to “stress,” without need for recourse to this term. Our approach contrasts with traditional approaches for studying “stress,” e.g., revealing that small “stressed” plants likely are in fact well suited to local conditions. We thus offer a quantitative perspective to the study of phenomena often referred to under such terms as “stress,” plasticity, adaptation, and acclimation. PMID:27881990

  10. Sonar detection range index estimation approach in uncertain environments

    NASA Astrophysics Data System (ADS)

    Li, Fan; Guo, Sheng-ming; Chen, Yao-ming

    2010-09-01

    The traditional detection range index prediction of sonar systems assumes a deterministic environment and causes overestimation of the detection range index. The realistic ocean environment consists of a quantitative measure of environmental uncertainty such as sound speed profile, sea depth and so on. An estimation approach that incorporates the effects of environmental uncertainty into the sonar detection range index is proposed in this paper. The sonar detection range index prediction has been implemented by using Monte Carlo simulation. In simulation, the sound speed gradient, sea depth and bottom geo-acoustic parameters as important uncertainty environmental parameters are generalized to stochastic variables and satisfy the normal distribution. The sonar detection range index with unknown source depth is also considered.

  11. [Parametric biomedical imaging--what defines the quality of quantitative radiological approaches?].

    PubMed

    Glüer, C-C; Barkmann, R; Hahn, H K; Majumdar, S; Eckstein, F; Nickelsen, T N; Bolte, H; Dicken, V; Heller, M

    2006-12-01

    Quantitative parametric imaging approaches provide new perspectives for radiological imaging. These include quantitative 2D, 3D, and 4D visualization options along with the parametric depiction of biological tissue properties and tissue function. This allows the interpretation of radiological data from a biochemical, biomechanical, or physiological perspective. Quantification permits the detection of small changes that are not yet visually apparent, thus allowing application in early disease diagnosis and monitoring therapy with enhanced sensitivity. This review outlines the potential of quantitative parametric imaging methods and demonstrates this on the basis of a few exemplary applications. One field of particular interest, the use of these methods for investigational new drug application studies, is presented. Assessment criteria for judging the quality of quantitative imaging approaches are discussed in the context of the potential and the limitations of these methods. While quantitative parametric imaging methods do not replace but rather supplement established visual interpretation methods in radiology, they do open up new perspectives for diagnosis and prognosis and in particular for monitoring disease progression and therapy.

  12. A gold nanoparticle-based semi-quantitative and quantitative ultrasensitive paper sensor for the detection of twenty mycotoxins.

    PubMed

    Kong, Dezhao; Liu, Liqiang; Song, Shanshan; Suryoprabowo, Steven; Li, Aike; Kuang, Hua; Wang, Libing; Xu, Chuanlai

    2016-03-07

    A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg(-1), and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg(-1), respectively. The quantitative results were obtained using a hand-held strip scan reader, with the calculated limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.04-0.17, 0.06-49, 0.15-0.22, 0.056-0.49 and 0.53-1.05 μg kg(-1), respectively. The analytical results of spiked samples were in accordance with the accurate content in the simultaneous detection analysis. This newly developed ICA strip assay is suitable for the on-site detection and rapid initial screening of mycotoxins in cereal samples, facilitating both semi-quantitative and quantitative determination.

  13. Multiplexed paper test strip for quantitative bacterial detection.

    PubMed

    Hossain, S M Zakir; Ozimok, Cory; Sicard, Clémence; Aguirre, Sergio D; Ali, M Monsur; Li, Yingfu; Brennan, John D

    2012-06-01

    Rapid, sensitive, on-site detection of bacteria without a need for sophisticated equipment or skilled personnel is extremely important in clinical settings and rapid response scenarios, as well as in resource-limited settings. Here, we report a novel approach for selective and ultra-sensitive multiplexed detection of Escherichia coli (non-pathogenic or pathogenic) using a lab-on-paper test strip (bioactive paper) based on intracellular enzyme (β-galactosidase (B-GAL) or β-glucuronidase (GUS)) activity. The test strip is composed of a paper support (0.5 × 8 cm), onto which either 5-bromo-4-chloro-3-indolyl-β-D: -glucuronide sodium salt (XG), chlorophenol red β-galactopyranoside (CPRG) or both and FeCl(3) were entrapped using sol-gel-derived silica inks in different zones via an ink-jet printing technique. The sample was lysed and assayed via lateral flow through the FeCl(3) zone to the substrate area to initiate rapid enzyme hydrolysis of the substrate, causing a change from colorless-to-blue (XG hydrolyzed by GUS, indication of nonpathogenic E. coli) and/or yellow to red-magenta (CPRG hydrolyzed by B-GAL, indication of total coliforms). Using immunomagnetic nanoparticles for selective preconcentration, the limit of detection was ~5 colony-forming units (cfu) per milliliter for E. coli O157:H7 and ~20 cfu/mL for E. coli BL21, within 30 min without cell culturing. Thus, these paper test strips could be suitable for detection of viable total coliforms and pathogens in bathing water samples. Moreover, inclusion of a culturing step allows detection of less than 1 cfu in 100 mL within 8 h, making the paper tests strips relevant for detection of multiple pathogens and total coliform bacteria in beverage and food samples.

  14. Quantitative Thallium-201 exercise scintigraphy for detection of coronary artery disease

    SciTech Connect

    Berger, B.C.; Watson, D.D.; Taylor, G.J.; Craddock, G.B.; Martin, R.P.; Teates, C.D.; Beller, G.A.

    1981-07-01

    In 140 patients with chest pain quantitation of regional myocardial Tl-201 activity was performed by serial scintigraphic images after treadmill exercise. Criteria for an abnormal thallium scintigram included: (a) greater than or equal to 25% persistent reduction in Tl-201 uptake in anterolateral, anteroseptal, posterolateral, and inferoapical segments, or greater than or equal to 35% reduction in the inferior segment; (b) an initial defect with delayed redistribution; and (c) abnormal Tl-201 washout. Of 110 patients with significant coronary artery disease (CAD), 100 had abnormal Tl-201 scintigrams, while 27 of 30 patients with angiographically normal coronary arteries had normal scintigrams; 91% sensitivity, 90% specificity, and 97% predictive accuracy. Sensitivity and specificity were not significantly different when the 95 patients with diagnostic (greater than or equal to 85% maximum heart rate) and 45 with inconclusive (less than or equal to 85% maximum HR) Ex tests were compared. Comparison of qualitative and quantitative image analyses in a subset of these patients showed that both specificity and multivessel disease prediction were greater when the quantitative approach was used (90 against 73% and 78 against 39%, respectively). Sensitivity for CAD detection was reduced by 10% with visual interpretation alone. Thus, quantitative exercise Tl-201 scintigraphy appears highly sensitive and specific for CAD detection in patients with chest pain.

  15. A systems approach to the quantitative condition monitoring of pipelines

    SciTech Connect

    Shannon, R.W.; Argent, C.J.

    1988-01-01

    In Service deterioration is a problem on all pipelines. British Gas operates procedures for in-service inspection and surveillance, corrosion control and condition monitoring from which remedial maintenance action is initiated. These procedures include helicopter patrols, foot patrols, landowner liaison, cathodic protection monitoring, hydrostatic testing, on-line inspection by intelligent pig and above ground survey. All fault data is logged and the reasons for particular faults investigated. The experience gained through this process has permitted a quantitative re-assessment of pipeline behaviour - real rather than perceived behaviour - and has enabled the contribution of each monitoring technique to be established. Using this information, soundly based monitoring and preventative maintenance strategies have been derived for British Gas high-pressure pipelines. By integrating the different procedures into a co-ordinated policy, the basis for a technically acceptable, cost effective approach to pipeline preventative maintenance has been achieved.

  16. Quantitative systems pharmacology: a promising approach for translational pharmacology.

    PubMed

    Gadkar, K; Kirouac, D; Parrott, N; Ramanujan, S

    Biopharmaceutical companies have increasingly been exploring Quantitative Systems Pharmacology (QSP) as a potential avenue to address current challenges in drug development. In this paper, we discuss the application of QSP modeling approaches to address challenges in the translational of preclinical findings to the clinic, a high risk area of drug development. Three cases have been highlighted with QSP models utilized to inform different questions in translational pharmacology. In the first, a mechanism based asthma model is used to evaluate efficacy and inform biomarker strategy for a novel bispecific antibody. In the second case study, a mitogen-activated protein kinase (MAPK) pathway signaling model is used to make translational predictions on clinical response and evaluate novel combination therapies. In the third case study, a physiologically based pharmacokinetic (PBPK) model it used to guide administration of oseltamivir in pediatric patients.

  17. From screening to quantitative sensitivity analysis. A unified approach

    NASA Astrophysics Data System (ADS)

    Campolongo, Francesca; Saltelli, Andrea; Cariboni, Jessica

    2011-04-01

    The present work is a sequel to a recent one published on this journal where the superiority of 'radial design' to compute the 'total sensitivity index' was ascertained. Both concepts belong to sensitivity analysis of model output. A radial design is the one whereby starting from a random point in the hyperspace of the input factors one step in turn is taken for each factor. The procedure is iterated a number of times with a different starting random point as to collect a sample of elementary shifts for each factor. The total sensitivity index is a powerful sensitivity measure which can be estimated based on such a sample. Given the similarity between the total sensitivity index and a screening test known as method of the elementary effects (or method of Morris), we test the radial design on this method. Both methods are best practices: the total sensitivity index in the class of the quantitative measures and the elementary effects in that of the screening methods. We find that the radial design is indeed superior even for the computation of the elementary effects method. This opens the door to a sensitivity analysis strategy whereby the analyst can start with a small number of points (screening-wise) and then - depending on the results - possibly increase the numeral of points up to compute a fully quantitative measure. Also of interest to practitioners is that a radial design is nothing else than an iterated 'One factor At a Time' (OAT) approach. OAT is a radial design of size one. While OAT is not a good practice, modelers in all domains keep using it for sensitivity analysis for reasons discussed elsewhere (Saltelli and Annoni, 2010) [23]. With the present approach modelers are offered a straightforward and economic upgrade of their OAT which maintain OAT's appeal of having just one factor moved at each step.

  18. Detection of group a streptococcal pharyngitis by quantitative PCR.

    PubMed

    Dunne, Eileen M; Marshall, Julia L; Baker, Ciara A; Manning, Jayne; Gonis, Gena; Danchin, Margaret H; Smeesters, Pierre R; Satzke, Catherine; Steer, Andrew C

    2013-07-11

    Group A streptococcus (GAS) is the most common bacterial cause of sore throat. School-age children bear the highest burden of GAS pharyngitis. Accurate diagnosis is difficult: the majority of sore throats are viral in origin, culture-based identification of GAS requires 24-48 hours, and up to 15% of children are asymptomatic throat carriers of GAS. The aim of this study was to develop a quantitative polymerase chain reaction (qPCR) assay for detecting GAS pharyngitis and assess its suitability for clinical diagnosis. Pharyngeal swabs were collected from children aged 3-18 years (n = 91) and adults (n = 36) located in the Melbourne area who presented with sore throat. Six candidate PCR assays were screened using a panel of reference isolates, and two of these assays, targeting speB and spy1258, were developed into qPCR assays. The qPCR assays were compared to standard culture-based methods for their ability to detect GAS pharyngitis. GAS isolates from culture positive swabs underwent emm-typing. Clinical data were used to calculate McIsaac scores as an indicator of disease severity. Twenty-four of the 127 samples (18.9%) were culture-positive for GAS, and all were in children (26%). The speB qPCR had 100% sensitivity and 100% specificity compared with gold-standard culture, whereas the spy1258 qPCR had 87% sensitivity and 100% specificity. Nine different emm types were found, of which emm 89, 3, and 28 were most common. Bacterial load as measured by qPCR correlated with culture load. There were no associations between symptom severity as indicated by McIsaac scores and GAS bacterial load. The speB qPCR displayed high sensitivity and specificity and may be a useful tool for GAS pharyngitis diagnosis and research.

  19. Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis

    SciTech Connect

    Goldman, D.; Merril, C.R.

    1983-09-01

    A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of /sup 14/C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P . 19/186 . .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses.

  20. Alternative approach to community detection in networks

    NASA Astrophysics Data System (ADS)

    Medus, A. D.; Dorso, C. O.

    2009-06-01

    The problem of community detection is relevant in many disciplines of science and modularity optimization is the widely accepted method for this purpose. It has recently been shown that this approach presents a resolution limit by which it is not possible to detect communities with sizes smaller than a threshold, which depends on the network size. Moreover, it might happen that the communities resulting from such an approach do not satisfy the usual qualitative definition of commune; i.e., nodes in a commune are more connected among themselves than to nodes outside the commune. In this paper we present a different method for community detection in complex networks. We define merit factors based on the weak and strong community definitions formulated by Radicchi [Proc. Natl. Acad. Sci. U.S.A. 101, 2658 (2004)] and we show that these local definitions avoid the resolution limit problem found in the modularity optimization approach.

  1. Quantitative Laughter Detection, Measurement, and Classification-A Critical Survey.

    PubMed

    Cosentino, Sarah; Sessa, Salvatore; Takanishi, Atsuo

    2016-01-01

    The study of human nonverbal social behaviors has taken a more quantitative and computational approach in recent years due to the development of smart interfaces and virtual agents or robots able to interact socially. One of the most interesting nonverbal social behaviors, producing a characteristic vocal signal, is laughing. Laughter is produced in several different situations: in response to external physical, cognitive, or emotional stimuli; to negotiate social interactions; and also, pathologically, as a consequence of neural damage. For this reason, laughter has attracted researchers from many disciplines. A consequence of this multidisciplinarity is the absence of a holistic vision of this complex behavior: the methods of analysis and classification of laughter, as well as the terminology used, are heterogeneous; the findings sometimes contradictory and poorly documented. This survey aims at collecting and presenting objective measurement methods and results from a variety of different studies in different fields, to contribute to build a unified model and taxonomy of laughter. This could be successfully used for advances in several fields, from artificial intelligence and human-robot interaction to medicine and psychiatry.

  2. Quantitative Label-Free Cell Proliferation Tracking with a Versatile Electrochemical Impedance Detection Platform

    NASA Astrophysics Data System (ADS)

    Caviglia, C.; Carminati, M.; Heiskanen, A.; Vergani, M.; Ferrari, G.; Sampietro, M.; Andresen, T. L.; Emnéus, J.

    2012-12-01

    Since the use of impedance measurements for label-free monitoring of cells has become widespread but still the choice of sensing configuration is not unique though crucial for a quantitative interpretation of data, we demonstrate the application of a novel custom multipotentiostat platform to study optimal detection strategies. Electrochemical Impedance Spectroscopy (EIS) has been used to monitor and compare adhesion of different cell lines. HeLa cells and 3T3 fibroblasts have been cultured for 12 hours on interdigitated electrode arrays integrated into a tailor-made cell culture platform. Both vertical and coplanar interdigitated sensing configuration approaches have been used and compared on the same cell populations.

  3. Radioactive Contraband Detection: A Bayesian Approach

    SciTech Connect

    Candy, J; Breitfeller, E; Guidry, B; Manatt, D; Sale, K; Chambers, D; Axelrod, M; Meyer, A

    2009-03-16

    Radionuclide emissions from nuclear contraband challenge both detection and measurement technologies to capture and record each event. The development of a sequential Bayesian processor incorporating both the physics of gamma-ray emissions and the measurement of photon energies offers a physics-based approach to attack this challenging problem. It is shown that a 'physics-based' structure can be used to develop an effective detection technique, but also motivates the implementation of this approach using or particle filters to enhance and extract the required information.

  4. High-throughput and quantitative approaches for measuring circadian rhythms in cyanobacteria using bioluminescence.

    PubMed

    Shultzaberger, Ryan K; Paddock, Mark L; Katsuki, Takeo; Greenspan, Ralph J; Golden, Susan S

    2015-01-01

    The temporal measurement of a bioluminescent reporter has proven to be one of the most powerful tools for characterizing circadian rhythms in the cyanobacterium Synechococcus elongatus. Primarily, two approaches have been used to automate this process: (1) detection of cell culture bioluminescence in 96-well plates by a photomultiplier tube-based plate-cycling luminometer (TopCount Microplate Scintillation and Luminescence Counter, Perkin Elmer) and (2) detection of individual colony bioluminescence by iteratively rotating a Petri dish under a cooled CCD camera using a computer-controlled turntable. Each approach has distinct advantages. The TopCount provides a more quantitative measurement of bioluminescence, enabling the direct comparison of clock output levels among strains. The computer-controlled turntable approach has a shorter set-up time and greater throughput, making it a more powerful phenotypic screening tool. While the latter approach is extremely useful, only a few labs have been able to build such an apparatus because of technical hurdles involved in coordinating and controlling both the camera and the turntable, and in processing the resulting images. This protocol provides instructions on how to construct, use, and process data from a computer-controlled turntable to measure the temporal changes in bioluminescence of individual cyanobacterial colonies. Furthermore, we describe how to prepare samples for use with the TopCount to minimize experimental noise and generate meaningful quantitative measurements of clock output levels for advanced analysis.

  5. High throughput and quantitative approaches for measuring circadian rhythms in cyanobacteria using bioluminescence

    PubMed Central

    Shultzaberger, Ryan K.; Paddock, Mark L.; Katsuki, Takeo; Greenspan, Ralph J.; Golden, Susan S.

    2016-01-01

    The temporal measurement of a bioluminescent reporter has proven to be one of the most powerful tools for characterizing circadian rhythms in the cyanobacterium Synechococcus elongatus. Primarily, two approaches have been used to automate this process: (1) detection of cell culture bioluminescence in 96-well plates by a photomultiplier tube-based plate-cycling luminometer (TopCount Microplate Scintillation and Luminescence Counter, Perkin Elmer) and (2) detection of individual colony bioluminescence by iteratively rotating a Petri dish under a cooled CCD camera using a computer-controlled turntable. Each approach has distinct advantages. The TopCount provides a more quantitative measurement of bioluminescence, enabling the direct comparison of clock output levels among strains. The computer-controlled turntable approach has a shorter set-up time and greater throughput, making it a more powerful phenotypic screening tool. While the latter approach is extremely useful, only a few labs have been able to build such an apparatus because of technical hurdles involved in coordinating and controlling both the camera and the turntable, and in processing the resulting images. This protocol provides instructions on how to construct, use, and process data from a computer-controlled turntable to measure the temporal changes in bioluminescence of individual cyanobacterial colonies. Furthermore, we describe how to prepare samples for use with the TopCount to minimize experimental noise, and generate meaningful quantitative measurements of clock output levels for advanced analysis. PMID:25662451

  6. Quantitative PCR for detection of Nosema bombycis in single silkworm eggs and newly hatched larvae.

    PubMed

    Fu, Zhangwuke; He, Xiangkang; Cai, Shunfeng; Liu, Han; He, Xinyi; Li, Mingqian; Lu, Xingmeng

    2016-01-01

    Pebrine disease is the only mandatory quarantine item in sericultural production due to its destructive consequences. So far, the mother moth microscopic examination method established by Pasteur (1870) remains the only detection method for screening for the causative agent Nosema bombycis (N. bombycis). Because pebrine is a horizontal and vertical transmission disease, it is better to inspect silkworm eggs and newly hatched larvae to investigate the infection rate, vertical transmission rate and spore load of the progenies. There is a rising demand for a more direct, effective and accurate detection approach in the sericultural industry. Here, we developed a molecular detection approach based on real-time quantitative PCR (qPCR) for pebrine inspection in single silkworm eggs and newly hatched larvae. Targeting the small-subunit rRNA gene of N. bombycis, this assay showed high sensitivity and reproducibility. Ten spores in a whole sample or 0.1 spore DNA (1 spore DNA represents the DNA content of one N. bombycis spore) in a reaction system was estimated as the detection limit of the isolation and real-time qPCR procedure. Silkworm egg tissues impact the detection sensitivity but are not significant in single silkworm egg detection. Of 400 samples produced by infected moths, 167 and 195 were scored positive by light microscopy and real-time qPCR analysis, respectively. With higher accuracy and the potential capability of high-throughput screening, this method is anticipated to be adaptable for pebrine inspection and surveillance in the sericultural industry. In addition, this method can be applied to ecology studies of N. bombycis-silkworm interactions due to its quantitative function. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. A quantitative risk analysis approach to port hydrocarbon logistics.

    PubMed

    Ronza, A; Carol, S; Espejo, V; Vílchez, J A; Arnaldos, J

    2006-01-16

    A method is presented that allows quantitative risk analysis to be performed on marine hydrocarbon terminals sited in ports. A significant gap was identified in the technical literature on QRA for the handling of hazardous materials in harbours published prior to this work. The analysis is extended to tanker navigation through port waters and loading and unloading facilities. The steps of the method are discussed, beginning with data collecting. As to accident scenario identification, an approach is proposed that takes into account minor and massive spills due to loading arm failures and tank rupture. Frequency estimation is thoroughly reviewed and a shortcut approach is proposed for frequency calculation. This allows for the two-fold possibility of a tanker colliding/grounding at/near the berth or while navigating to/from the berth. A number of probability data defining the possibility of a cargo spill after an external impact on a tanker are discussed. As to consequence and vulnerability estimates, a scheme is proposed for the use of ratios between the numbers of fatal victims, injured and evacuated people. Finally, an example application is given, based on a pilot study conducted in the Port of Barcelona, where the method was tested.

  8. A gold nanoparticle-based semi-quantitative and quantitative ultrasensitive paper sensor for the detection of twenty mycotoxins

    NASA Astrophysics Data System (ADS)

    Kong, Dezhao; Liu, Liqiang; Song, Shanshan; Suryoprabowo, Steven; Li, Aike; Kuang, Hua; Wang, Libing; Xu, Chuanlai

    2016-02-01

    A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan reader, with the calculated limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.04-0.17, 0.06-49, 0.15-0.22, 0.056-0.49 and 0.53-1.05 μg kg-1, respectively. The analytical results of spiked samples were in accordance with the accurate content in the simultaneous detection analysis. This newly developed ICA strip assay is suitable for the on-site detection and rapid initial screening of mycotoxins in cereal samples, facilitating both semi-quantitative and quantitative determination.A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan

  9. Anomalous human behavior detection: an adaptive approach

    NASA Astrophysics Data System (ADS)

    van Leeuwen, Coen; Halma, Arvid; Schutte, Klamer

    2013-05-01

    Detection of anomalies (outliers or abnormal instances) is an important element in a range of applications such as fault, fraud, suspicious behavior detection and knowledge discovery. In this article we propose a new method for anomaly detection and performed tested its ability to detect anomalous behavior in videos from DARPA's Mind's Eye program, containing a variety of human activities. In this semi-unsupervised task a set of normal instances is provided for training, after which unknown abnormal behavior has to be detected in a test set. The features extracted from the video data have high dimensionality, are sparse and inhomogeneously distributed in the feature space making it a challenging task. Given these characteristics a distance-based method is preferred, but choosing a threshold to classify instances as (ab)normal is non-trivial. Our novel aproach, the Adaptive Outlier Distance (AOD) is able to detect outliers in these conditions based on local distance ratios. The underlying assumption is that the local maximum distance between labeled examples is a good indicator of the variation in that neighborhood, and therefore a local threshold will result in more robust outlier detection. We compare our method to existing state-of-art methods such as the Local Outlier Factor (LOF) and the Local Distance-based Outlier Factor (LDOF). The results of the experiments show that our novel approach improves the quality of the anomaly detection.

  10. Quantitative Analysis of Mutant Subclones in Chronic Myeloid Leukemia: Comparison of Different Methodological Approaches.

    PubMed

    Preuner, Sandra; Barna, Agnes; Frommlet, Florian; Czurda, Stefan; Konstantin, Byrgazov; Alikian, Mary; Machova Polakova, Katerina; Sacha, Tomasz; Richter, Johan; Lion, Thomas; Gabriel, Christian

    2016-04-29

    Identification and quantitative monitoring of mutant BCR-ABL1 subclones displaying resistance to tyrosine kinase inhibitors (TKIs) have become important tasks in patients with Ph-positive leukemias. Different technologies have been established for patient screening. Various next-generation sequencing (NGS) platforms facilitating sensitive detection and quantitative monitoring of mutations in the ABL1-kinase domain (KD) have been introduced recently, and are expected to become the preferred technology in the future. However, broad clinical implementation of NGS methods has been hampered by the limited accessibility at different centers and the current costs of analysis which may not be regarded as readily affordable for routine diagnostic monitoring. It is therefore of interest to determine whether NGS platforms can be adequately substituted by other methodological approaches. We have tested three different techniques including pyrosequencing, LD (ligation-dependent)-PCR and NGS in a series of peripheral blood specimens from chronic myeloid leukemia (CML) patients carrying single or multiple mutations in the BCR-ABL1 KD. The proliferation kinetics of mutant subclones in serial specimens obtained during the course of TKI-treatment revealed similar profiles via all technical approaches, but individual specimens showed statistically significant differences between NGS and the other methods tested. The observations indicate that different approaches to detection and quantification of mutant subclones may be applicable for the monitoring of clonal kinetics, but careful calibration of each method is required for accurate size assessment of mutant subclones at individual time points.

  11. Quantitative Analysis of Mutant Subclones in Chronic Myeloid Leukemia: Comparison of Different Methodological Approaches

    PubMed Central

    Preuner, Sandra; Barna, Agnes; Frommlet, Florian; Czurda, Stefan; Konstantin, Byrgazov; Alikian, Mary; Machova Polakova, Katerina; Sacha, Tomasz; Richter, Johan; Lion, Thomas; Gabriel, Christian

    2016-01-01

    Identification and quantitative monitoring of mutant BCR-ABL1 subclones displaying resistance to tyrosine kinase inhibitors (TKIs) have become important tasks in patients with Ph-positive leukemias. Different technologies have been established for patient screening. Various next-generation sequencing (NGS) platforms facilitating sensitive detection and quantitative monitoring of mutations in the ABL1-kinase domain (KD) have been introduced recently, and are expected to become the preferred technology in the future. However, broad clinical implementation of NGS methods has been hampered by the limited accessibility at different centers and the current costs of analysis which may not be regarded as readily affordable for routine diagnostic monitoring. It is therefore of interest to determine whether NGS platforms can be adequately substituted by other methodological approaches. We have tested three different techniques including pyrosequencing, LD (ligation-dependent)-PCR and NGS in a series of peripheral blood specimens from chronic myeloid leukemia (CML) patients carrying single or multiple mutations in the BCR-ABL1 KD. The proliferation kinetics of mutant subclones in serial specimens obtained during the course of TKI-treatment revealed similar profiles via all technical approaches, but individual specimens showed statistically significant differences between NGS and the other methods tested. The observations indicate that different approaches to detection and quantification of mutant subclones may be applicable for the monitoring of clonal kinetics, but careful calibration of each method is required for accurate size assessment of mutant subclones at individual time points. PMID:27136541

  12. Structure Prior Effects in Bayesian Approaches of Quantitative Susceptibility Mapping

    PubMed Central

    Chen, Weiwei; Wang, Chunmei; Liu, Tian; Wang, Yi; Pan, Chu; Mu, Ketao; Zhu, Ce; Zhang, Xiang; Cheng, Jian

    2016-01-01

    Quantitative susceptibility mapping (QSM) has shown its potential for anatomical and functional MRI, as it can quantify, for in vivo tissues, magnetic biomarkers and contrast agents which have differential susceptibilities to the surroundings substances. For reconstructing the QSM with a single orientation, various methods have been proposed to identify a unique solution for the susceptibility map. Bayesian QSM approach is the major type which uses various regularization terms, such as a piece-wise constant, a smooth, a sparse, or a morphological prior. Six QSM algorithms with or without structure prior are systematically discussed to address the structure prior effects. The methods are evaluated using simulations, phantom experiments with the given susceptibility, and human brain data. The accuracy and image quality of QSM were increased when using structure prior in the simulation and phantom compared to same regularization term without it, respectively. The image quality of QSM method using the structure prior is better comparing, respectively, to the method without it by either sharpening the image or reducing streaking artifacts in vivo. The structure priors improve the performance of the various QSMs using regularized minimization including L1, L2, and TV norm. PMID:28097129

  13. Comparative and Quantitative Global Proteomics Approaches: An Overview

    PubMed Central

    Deracinois, Barbara; Flahaut, Christophe; Duban-Deweer, Sophie; Karamanos, Yannis

    2013-01-01

    Proteomics became a key tool for the study of biological systems. The comparison between two different physiological states allows unravelling the cellular and molecular mechanisms involved in a biological process. Proteomics can confirm the presence of proteins suggested by their mRNA content and provides a direct measure of the quantity present in a cell. Global and targeted proteomics strategies can be applied. Targeted proteomics strategies limit the number of features that will be monitored and then optimise the methods to obtain the highest sensitivity and throughput for a huge amount of samples. The advantage of global proteomics strategies is that no hypothesis is required, other than a measurable difference in one or more protein species between the samples. Global proteomics methods attempt to separate quantify and identify all the proteins from a given sample. This review highlights only the different techniques of separation and quantification of proteins and peptides, in view of a comparative and quantitative global proteomics analysis. The in-gel and off-gel quantification of proteins will be discussed as well as the corresponding mass spectrometry technology. The overview is focused on the widespread techniques while keeping in mind that each approach is modular and often recovers the other. PMID:28250403

  14. A Voxel-Map Quantitative Analysis Approach for Atherosclerotic Noncalcified Plaques of the Coronary Artery Tree

    PubMed Central

    Li, Ying; Chen, Wei; Chen, Yonglin; Chu, Chun; Fang, Bingji; Tan, Liwen

    2013-01-01

    Noncalcified plaques (NCPs) are associated with the presence of lipid-core plaques that are prone to rupture. Thus, it is important to detect and monitor the development of NCPs. Contrast-enhanced coronary Computed Tomography Angiography (CTA) is a potential imaging technique to identify atherosclerotic plaques in the whole coronary tree, but it fails to provide information about vessel walls. In order to overcome the limitations of coronary CTA and provide more meaningful quantitative information for percutaneous coronary intervention (PCI), we proposed a Voxel-Map based on mathematical morphology to quantitatively analyze the noncalcified plaques on a three-dimensional coronary artery wall model (3D-CAWM). This approach is a combination of Voxel-Map analysis techniques, plaque locating, and anatomical location related labeling, which show more detailed and comprehensive coronary tree wall visualization. PMID:24348749

  15. [Identification and quantitative determination of baclofen in human blood by HPLC with mass spectrometry detection].

    PubMed

    Dukova, O A; Kotlovsky, M Yu; Pokrovsky, A A; Suvorova, E V; Shivrina, T G; Krasnov, E A; Efremov, A A

    2016-03-01

    A method of identification and quantitative determination of baclofen in blood by HPLC with mass spectrometry detection has been developed. It is characterized by high sensitivity, specificity, linearity, accuracy, reproducibility, and a low detection for quantitative determination. The method has been used for diagnostics of acute baclofen poisoning in patients.

  16. Automatic detection and quantitative analysis of cells in the mouse primary motor cortex

    NASA Astrophysics Data System (ADS)

    Meng, Yunlong; He, Yong; Wu, Jingpeng; Chen, Shangbin; Li, Anan; Gong, Hui

    2014-09-01

    Neuronal cells play very important role on metabolism regulation and mechanism control, so cell number is a fundamental determinant of brain function. Combined suitable cell-labeling approaches with recently proposed three-dimensional optical imaging techniques, whole mouse brain coronal sections can be acquired with 1-μm voxel resolution. We have developed a completely automatic pipeline to perform cell centroids detection, and provided three-dimensional quantitative information of cells in the primary motor cortex of C57BL/6 mouse. It involves four principal steps: i) preprocessing; ii) image binarization; iii) cell centroids extraction and contour segmentation; iv) laminar density estimation. Investigations on the presented method reveal promising detection accuracy in terms of recall and precision, with average recall rate 92.1% and average precision rate 86.2%. We also analyze laminar density distribution of cells from pial surface to corpus callosum from the output vectorizations of detected cell centroids in mouse primary motor cortex, and find significant cellular density distribution variations in different layers. This automatic cell centroids detection approach will be beneficial for fast cell-counting and accurate density estimation, as time-consuming and error-prone manual identification is avoided.

  17. Quantitative asymmetric-detection time-stretch optical microscopy (Q-ATOM) for ultrafast quantitative phase imaging flow cytometry (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Lau, Andy K. S.; Tang, Anson H. L.; Chung, Bob M. F.; Tsang, Kwok Yeung; Chan, Antony C. S.; Wei, Xiaoming; Wong, Kenneth K.; Lam, Edmund Y.; Cheah, Kathryn S. E.; Shum, Anderson H. C.; Tsia, Kevin K.

    2016-03-01

    Based on the interferometric or holographic approaches, recent QPM techniques provide quantitative-phase information, e.g cell volume, dry mass and optical scattering properties for label-free cellular physical phenotyping. These approaches generally rely on iterative phase-retrieval algorithms to obtain quantitative-phase information, which are computationally intensive. Moreover, current QPM techniques can only offer limited image acquisition rate by using CMOS/CCD image sensors, these two limitations hinder QPM for high-throughput quantitative image-based single-cell analysis in real-time. To this end, we demonstrate an interferometry-free quantitative phase microscopy developed on a new generation of time-stretch microscopy, asymmetric-detection time-stretch optical microscopy (ATOM), which is coined quantitative ATOM (Q-ATOM) - featuring an unprecedented cell measurement throughput together with the assorted intrinsic optical phenotypes (e.g. angular light scattering profile) and the derived physical properties of the cells (e.g. cell size, dry mass density etc.). Based on a similar concept to Schlieren imaging, Q-ATOM retrieves quantitative-phase information through multiple off-axis light-beam detection at a line-scan rate of <10 MHz - a speed unachievable by any existing QPM techniques. Phase retrieval in Q-ATOM relies on a non-iterative method, significantly reducing the computational complexity of the technique. It is a particularly important feature which facilitates real-time continuous label-free single-cell analysis in Q-ATOM. With the use of a non-interferometric configuration, we demonstrate ultrafast Q-ATOM of mouse chondrocytes and hypertrophic chondrocytes in ultrafast microfluidic flow with sub-cellular resolution at an imaging throughput equivalent to ~100,000 cells/sec without image blur. This technique shows a great potential for ultrahigh throughput label-free image-based single-cell biophysical phentotyping.

  18. Detection of quantitative trait loci in outbred populations with incomplete marker data.

    PubMed Central

    Bink, M C; Van Arendonk, J A

    1999-01-01

    Augmentation of marker genotypes for ungenotyped individuals is implemented in a Bayesian approach via the use of Markov chain Monte Carlo techniques. Marker data on relatives and phenotypes are combined to compute conditional posterior probabilities for marker genotypes of ungenotyped individuals. The presented procedure allows the analysis of complex pedigrees with ungenotyped individuals to detect segregating quantitative trait loci (QTL). Allelic effects at the QTL were assumed to follow a normal distribution with a covariance matrix based on known QTL position and identity by descent probabilities derived from flanking markers. The Bayesian approach estimates variance due to the single QTL, together with polygenic and residual variance. The method was empirically tested through analyzing simulated data from a complex granddaughter design. Ungenotyped dams were related to one or more sons or grandsires in the design. Heterozygosity of the marker loci and size of QTL were varied. Simulation results indicated a significant increase in power when ungenotyped dams were included in the analysis. PMID:9872977

  19. Quantitative Approaches to Group Research: Suggestions for Best Practices

    ERIC Educational Resources Information Center

    McCarthy, Christopher J.; Whittaker, Tiffany A.; Boyle, Lauren H.; Eyal, Maytal

    2017-01-01

    Rigorous scholarship is essential to the continued growth of group work, yet the unique nature of this counseling specialty poses challenges for quantitative researchers. The purpose of this proposal is to overview unique challenges to quantitative research with groups in the counseling field, including difficulty in obtaining large sample sizes…

  20. Quantitative Approaches to Group Research: Suggestions for Best Practices

    ERIC Educational Resources Information Center

    McCarthy, Christopher J.; Whittaker, Tiffany A.; Boyle, Lauren H.; Eyal, Maytal

    2017-01-01

    Rigorous scholarship is essential to the continued growth of group work, yet the unique nature of this counseling specialty poses challenges for quantitative researchers. The purpose of this proposal is to overview unique challenges to quantitative research with groups in the counseling field, including difficulty in obtaining large sample sizes…

  1. Fluorescent microscopy approaches of quantitative soil microbial analysis

    NASA Astrophysics Data System (ADS)

    Ivanov, Konstantin; Polyanskaya, Lubov

    2015-04-01

    Classical fluorescent microscopy method was used during the last decades in various microbiological studies of terrestrial ecosystems. The method provides representative results and simple application which is allow to use it both as routine part of amplitudinous research and in small-scaled laboratories. Furthermore, depending on research targets a lot of modifications of fluorescent microscopy method were established. Combination and comparison of several approaches is an opportunity of quantitative estimation of microbial community in soil. The first analytical part of the study was dedicated to soil bacterial density estimation by fluorescent microscopy in dynamic of several 30-days experiments. The purpose of research was estimation of changes in soil bacterial community on the different soil horizons under aerobic and anaerobic conditions with adding nutrients in two experimental sets: cellulose and chitin. Was modified the nalidixic acid method for inhibition of DNA division of gram-negative bacteria, and the method provides the quantification of this bacterial group by fluorescent microscopy. Established approach allowed to estimate 3-4 times more cells of gram-negative bacteria in soil. The functions of actinomyces in soil polymer destruction are traditionally considered as dominant in comparison to gram-negative bacterial group. However, quantification of gram-negative bacteria in chernozem and peatland provides underestimation of classical notion for this bacterial group. Chitin introduction had no positive effect to gram-negative bacterial population density changes in chernozem but concurrently this nutrient provided the fast growing dynamics at the first 3 days of experiment both under aerobic and anaerobic conditions. This is confirming chitinolytic activity of gram-negative bacteria in soil organic matter decomposition. At the next part of research modified method for soil gram-negative bacteria quantification was compared to fluorescent in situ

  2. Simultaneous imaging of locus coeruleus and substantia nigra with a quantitative neuromelanin MRI approach.

    PubMed

    Chen, Xiangchuan; Huddleston, Daniel E; Langley, Jason; Ahn, Sinyeob; Barnum, Christopher J; Factor, Stewart A; Levey, Allan I; Hu, Xiaoping

    2014-12-01

    Quantitative MRI of neuromelanin (NM) containing structures (referred to as NM-MRI) in the brainstem, namely the locus coeruleus (LC) and substantia nigra (SN), may assist with the early detection of Parkinson's disease (PD) and Alzheimer's disease (AD) as well as differential diagnosis in the early disease stages. In this study, two gradient echo (GRE) sequences with magnetization transfer contrast (MTC) preparation pulses were developed to simultaneously image the LC and SN. This has been a challenge with NM-MRI techniques used in previous studies due to the relatively high specific absorption rate (SAR) induced by these techniques. In addition, a semi-automated quantitative analysis scheme was applied to estimate volumes and contrast-to-noise ratios (CNR) of the LC and SN based on segmentation of both structures. Compared to a T1-weighted turbo spin echo (TSE) sequence typically used for simultaneous imaging of the LC and SN, the two GRE-MTC sequences exhibited improved performance in terms of higher sensitivity (in CNR) in imaging the SN and lower SAR during the scans. A multiple-measurement protocol was adopted as well so that motion degraded measurements could be removed and artifacts associated with motion could be corrected. The present approach has demonstrated advantages in image acquisition (lower SAR and higher sensitivity), image pre-processing (with motion correction) and quantitative image analysis (segmentation-based estimation of volume and CNR) when compared with existing NM-MRI approaches. This approach has potential for detection and monitoring of neurodegeneration in LC and SN in disease states including AD and PD.

  3. Novel image processing approach to detect malaria

    NASA Astrophysics Data System (ADS)

    Mas, David; Ferrer, Belen; Cojoc, Dan; Finaurini, Sara; Mico, Vicente; Garcia, Javier; Zalevsky, Zeev

    2015-09-01

    In this paper we present a novel image processing algorithm providing good preliminary capabilities for in vitro detection of malaria. The proposed concept is based upon analysis of the temporal variation of each pixel. Changes in dark pixels mean that inter cellular activity happened, indicating the presence of the malaria parasite inside the cell. Preliminary experimental results involving analysis of red blood cells being either healthy or infected with malaria parasites, validated the potential benefit of the proposed numerical approach.

  4. Using multiple PCR and CE with chemiluminescence detection for simultaneous qualitative and quantitative analysis of genetically modified organism.

    PubMed

    Guo, Longhua; Qiu, Bin; Chi, Yuwu; Chen, Guonan

    2008-09-01

    In this paper, an ultrasensitive CE-CL detection system coupled with a novel double-on-column coaxial flow detection interface was developed for the detection of PCR products. A reliable procedure based on this system had been demonstrated for qualitative and quantitative analysis of genetically modified organism-the detection of Roundup Ready Soy (RRS) samples was presented as an example. The promoter, terminator, function and two reference genes of RRS were amplified with multiplex PCR simultaneously. After that, the multiplex PCR products were labeled with acridinium ester at the 5'-terminal through an amino modification and then analyzed by the proposed CE-CL system. Reproducibility of analysis times and peak heights for the CE-CL analysis were determined to be better than 0.91 and 3.07% (RSD, n=15), respectively, for three consecutive days. It was shown that this method could accurately and qualitatively detect RRS standards and the simulative samples. The evaluation in terms of quantitative analysis of RRS provided by this new method was confirmed by comparing our assay results with those of the standard real-time quantitative PCR (RT-QPCR) using SYBR Green I dyes. The results showed a good coherence between the two methods. This approach demonstrated the possibility for accurate qualitative and quantitative detection of GM plants in a single run.

  5. Could animals detect the approaching tsunami?

    NASA Astrophysics Data System (ADS)

    Jagannathan, Srinivasan; Makris, Nicholas; Ratilal, Purnima

    2005-04-01

    A number of sources report the phenomenon of animals running to safety well before the recent southeast Asian tsunami struck. The phenomenon was apparently observed on both sides of the Bay of Bengal, from Thailand to Sri Lanka. The latter is far from the epicenter of the earthquake. Did the earthquake supply the only warning or is it possible that the tsunami radiated seismo-acoustic signals of sufficient amplitude and frequency for animals to detect and interpret it long before it struck shore? This possibility is quantitatively investigated by solving the coupled hydrodynamic-acoustic equations with a tsunami driving term in a range-dependent ocean acoustic waveguide. Cases where the tsunami is in deep water and on the continental shelf are considered. [The general topic of this research follows from a suggestion made by Herman Medwin.

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

    SciTech Connect

    Xie, Hongzhi; Mukundan, Harshini; Martinez, Jennifer S; Swanson, Basil I; Anderson, Aaron S; Grace, Kevin

    2009-01-01

    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

  7. Wave propagation models for quantitative defect detection by ultrasonic methods

    NASA Astrophysics Data System (ADS)

    Srivastava, Ankit; Bartoli, Ivan; Coccia, Stefano; Lanza di Scalea, Francesco

    2008-03-01

    Ultrasonic guided wave testing necessitates of quantitative, rather than qualitative, information on flaw size, shape and position. This quantitative diagnosis ability can be used to provide meaningful data to a prognosis algorithm for remaining life prediction, or simply to generate data sets for a statistical defect classification algorithm. Quantitative diagnostics needs models able to represent the interaction of guided waves with various defect scenarios. One such model is the Global-Local (GL) method, which uses a full finite element discretization of the region around a flaw to properly represent wave diffraction, and a suitable set of wave functions to simulate regions away from the flaw. Displacement and stress continuity conditions are imposed at the boundary between the global and the local regions. In this paper the GL method is expanded to take advantage of the Semi-Analytical Finite Element (SAFE) method in the global portion of the waveguide. The SAFE method is efficient because it only requires the discretization of the cross-section of the waveguide to obtain the wave dispersion solutions and it can handle complex structures such as multilayered sandwich panels. The GL method is applied to predicting quantitatively the interaction of guided waves with defects in aluminum and composites structural components.

  8. A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization

    PubMed Central

    Dreger, Mathias; Leung, Bo Wah; Brownlee, George G; Deng, Tao

    2009-01-01

    We describe a method for studying quantitative changes in accessibility of surface lysine residues of the PB1 subunit of the influenza RNA polymerase as a result of association with the PA subunit to form a PB1-PA heterodimer. Our method combines two established methods: (i) the chemical modification of surface lysine residues of native proteins by N-hydroxysuccinimidobiotin (NHS-biotin) and (ii) the stable isotope labeling of amino acids in cell culture (SILAC) followed by tryptic digestion and mass spectrometry. By linking the chemical modification with the SILAC methodology for the first time, we obtain quantitative data on chemical modification allowing subtle changes in accessibility to be described. Five regions in the PB1 monomer showed altered reactivity to NHS-biotin when compared with the [PB1-PA] heterodimer. Mutational analysis of residues in two such regions—at K265 and K481 of PB1, which were about three- and twofold, respectively, less accessible to biotinylation in the PB1-PA heterodimer compared with the PB1 monomer, demonstrated that both K265 and K481 were crucial for polymerase function. This novel assay of quantitative profiling of biotinylation patterns (Q-POP assay) highlights likely conformational changes at important functional sites, as observed here for PB1, and may provide information on protein–protein interaction interfaces. The Q-POP assay should be a generally applicable approach and may detect novel functional sites suitable for targeting by drugs. PMID:19517532

  9. Quantitation of dissolved gas content in emulsions and in blood using mass spectrometric detection.

    PubMed

    Grimley, Everett; Turner, Nicole; Newell, Clayton; Simpkins, Cuthbert; Rodriguez, Juan

    2011-06-01

    Quantitation of dissolved gases in blood or in other biological media is essential for understanding the dynamics of metabolic processes. Current detection techniques, while enabling rapid and convenient assessment of dissolved gases, provide only direct information on the partial pressure of gases dissolved in the aqueous fraction of the fluid. The more relevant quantity known as gas content, which refers to the total amount of the gas in all fractions of the sample, can be inferred from those partial pressures, but only indirectly through mathematical modeling. Here we describe a simple mass spectrometric technique for rapid and direct quantitation of gas content for a wide range of gases. The technique is based on a mass spectrometer detector that continuously monitors gases that are rapidly extracted from samples injected into a purge vessel. The accuracy and sample processing speed of the system is demonstrated with experiments that reproduce within minutes literature values for the solubility of various gases in water. The capability of the technique is further demonstrated through accurate determination of O(2) content in a lipid emulsion and in whole blood, using as little as 20 μL of sample. The approach to gas content quantitation described here should greatly expand the range of animals and conditions that may be used in studies of metabolic gas exchange, and facilitate the development of artificial oxygen carriers and resuscitation fluids. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Quantitation of dissolved gas content in emulsions and in blood using mass spectrometric detection

    PubMed Central

    Grimley, Everett; Turner, Nicole; Newell, Clayton; Simpkins, Cuthbert; Rodriguez, Juan

    2011-01-01

    Quantitation of dissolved gases in blood or in other biological media is essential for understanding the dynamics of metabolic processes. Current detection techniques, while enabling rapid and convenient assessment of dissolved gases, provide only direct information on the partial pressure of gases dissolved in the aqueous fraction of the fluid. The more relevant quantity known as gas content, which refers to the total amount of the gas in all fractions of the sample, can be inferred from those partial pressures, but only indirectly through mathematical modeling. Here we describe a simple mass spectrometric technique for rapid and direct quantitation of gas content for a wide range of gases. The technique is based on a mass spectrometer detector that continuously monitors gases that are rapidly extracted from samples injected into a purge vessel. The accuracy and sample processing speed of the system is demonstrated with experiments that reproduce within minutes literature values for the solubility of various gases in water. The capability of the technique is further demonstrated through accurate determination of O2 content in a lipid emulsion and in whole blood, using as little as 20 μL of sample. The approach to gas content quantitation described here should greatly expand the range of animals and conditions that may be used in studies of metabolic gas exchange, and facilitate the development of artificial oxygen carriers and resuscitation fluids. PMID:21497566

  11. Column precipitation chromatography: an approach to quantitative analysis of eigencolloids.

    PubMed

    Breynaert, E; Maes, A

    2005-08-01

    A new column precipitation chromatography (CPC) technique, capable of quantitatively measuring technetium eigencolloids in aqueous solutions, is presented. The CPC technique is based on the destabilization and precipitation of eigencolloids by polycations in a confined matrix. Tc(IV) colloids can be quantitatively determined from their precipitation onto the CPC column (separation step) and their subsequent elution upon oxidation to pertechnetate by peroxide (elution step). A clean-bed particle removal model was used to explain the experimental results.

  12. [Research progress of real-time quantitative PCR method for group A rotavirus detection].

    PubMed

    Guo, Yan-Qing; Li, Dan-Di; Duan, Zhao-Jun

    2013-11-01

    Group A rotavirus is one of the most significant etiological agents which causes acute gastroenteritis among infants and young children worldwide. So far, several method which includes electron microscopy (EM), enzyme immunoassay (EIA), reverse transcription-polymerase chain reaction (RT-PCR)and Real-time Quantitative PCR has been established for the detection of rotavirus. Compared with other methods, Real-time quantitative PCR have advantages in specificity, sensitivity, genotyping and quantitative accuracy. This article shows a overview of the application of real-time quantitative PCR technique to detecte group A rotavirus.

  13. Detection of yellow fever virus: a comparison of quantitative real-time PCR and plaque assay.

    PubMed

    Bae, Hi-Gung; Nitsche, Andreas; Teichmann, Anette; Biel, Stefan S; Niedrig, Matthias

    2003-06-30

    Yellow fever virus quantitation is performed routinely by cultivation of virus containing samples using susceptible cells. Counting of the resulting plaques provides a marker for the number of infectious particles present in the sample. This assay usually takes up to 5 days before results are obtained and must be carried out under L2 or L3 laboratory conditions, depending on the yellow fever virus strain used. For clinical diagnosis of yellow fever virus infections the cell culture-based approach takes too long and is of limited practical relevance. Recently, due to its considerable sensitivity, PCR has become a promising method for virus detection. However, whilst PCR can detect virus-specific nucleic acids, it does not allow conclusions to be drawn regarding the infectious potential of the virus detected. Nonetheless, for diagnostic purposes, a rapid, specific and sensitive virus PCR is preferable. Therefore, two independent yellow fever virus-specific real-time PCR assays were established and compared the viral RNA loads to the results of a traditional plaque assay. The estimated ratio of yellow fever virus genomes to infectious particles was between 1000:1 and 5000:1; both approaches displayed a comparable precision of <45%. A significant correlation between genome number as determined by real-time PCR and the corresponding number of plaques in paired samples was found with a Pearson coefficient of correlation of r=0.88 (P<0.0001).

  14. Quantitative validation of anti-PTBP1 antibody for diagnostic neuropathology use: Image analysis approach.

    PubMed

    Goceri, Evgin; Goksel, Behiye; Elder, James B; Puduvalli, Vinay K; Otero, Jose J; Gurcan, Metin N

    2016-12-26

    Traditional diagnostic neuropathology relies on subjective interpretation of visual data obtained from a brightfield microscopy. This approach causes high variability, unsatisfactory reproducibility, and inability for multiplexing even among experts. These problems may affect patient outcomes and confound clinical decision-making. Also, standard histological processing of pathological specimens leads to auto-fluorescence and other artifacts, a reason why fluorescent microscopy is not routinely implemented in diagnostic pathology. To overcome these problems, objective and quantitative methods are required to help neuropathologists in their clinical decision-making. Therefore, we propose a computerized image analysis method to validate anti-PTBP1 antibody for its potential use in diagnostic neuropathology. Images were obtained from standard neuropathological specimens stained with anti-PTBP1 antibody. First, the noise characteristics of the images were modeled and images are de-noised according to the noise model. Next, images are filtered with sigma-adaptive Gaussian filtering for normalization, and cell nuclei are detected and segmented with a k-means-based deterministic approach. Experiments on 29 data sets from 3 cases of brain tumor and reactive gliosis show statistically significant differences between the number of positively stained nuclei in images stained with and without anti-PTBP1 antibody. The experimental analysis of specimens from 3 different brain tumor groups and 1 reactive gliosis group indicates the feasibility of using anti-PTBP1 antibody in diagnostic neuropathology, and computerized image analysis provides a systematic and quantitative approach to explore feasibility.

  15. Surface-enhanced Raman scattering for quantitative detection of ethyl carbamate in alcoholic beverages.

    PubMed

    Yang, Danting; Zhou, Haibo; Ying, Yibin; Niessner, Reinhard; Haisch, Christoph

    2013-11-01

    Ethyl carbamate, a by-product of fermentation and storage with widespread occurrence in fermented food and alcoholic beverages, is a compound potentially toxic to humans. In this work, a new approach for quantitative detection of ethyl carbamate in alcoholic beverages, based on surface-enhanced Raman scattering (SERS), is reported. Individual silver-coated gold nanoparticle colloids are used as SERS amplifiers, yielding high Raman enhancement of ethyl carbamate in three kinds of alcoholic beverages (vodka, Obstler, and white rum). The characteristic band at 1,003 cm(-1), which is the strongest and best reproducible peak in the SERS spectra, was used for quantitative evaluation of ethyl carbamate. The limit of detection, which corresponds to a signal-to-noise ratio of 3, was 9.0 × 10(-9) M (0.8 μg · L(-1)), 1.3 × 10(-7) M (11.6 μg · L(-1)), and 7.8 × 10(-8) M (6.9 μg · L(-1)), respectively. Surface-enhanced Raman spectroscopy offers great practical potential for the in situ assessment and identification of ethyl carbamate in the alcoholic beverage industry.

  16. Fast wide-field photothermal and quantitative phase cell imaging with optical lock-in detection

    PubMed Central

    Eldridge, Will J.; Meiri, Amihai; Sheinfeld, Adi; Rinehart, Matthew T.; Wax, Adam

    2014-01-01

    We present a fast, wide-field holography system for detecting photothermally excited gold nanospheres with combined quantitative phase imaging. An interferometric photothermal optical lock-in approach (POLI) is shown to improve SNR for detecting nanoparticles (NPs) on multiple substrates, including a monolayer of NPs on a silanized coverslip, and NPs bound to live cells. Furthermore, the set up allowed for co-registered quantitative phase imaging (QPI) to be acquired in an off-axis holographic set-up. An SNR of 103 was obtained for NP-tagging of epidermal growth factor receptor (EGFR) in live cells with a 3 second acquisition, while an SNR of 47 was seen for 20 ms acquisition. An analysis of improvements in SNR due to averaging multiple frames is presented, which suggest that residual photothermal signal can be a limiting factor. The combination of techniques allows for high resolution imaging of cell structure via QPI with the ability to identify receptor expression via POLI. PMID:25136482

  17. Quantum dots assisted laser desorption/ionization mass spectrometric detection of carbohydrates: qualitative and quantitative analysis.

    PubMed

    Bibi, Aisha; Ju, Huangxian

    2016-04-01

    A quantum dots (QDs) assisted laser desorption/ionization mass spectrometric (QDA-LDI-MS) strategy was proposed for qualitative and quantitative analysis of a series of carbohydrates. The adsorption of carbohydrates on the modified surface of different QDs as the matrices depended mainly on the formation of hydrogen bonding, which led to higher MS intensity than those with conventional organic matrix. The effects of QDs concentration and sample preparation method were explored for improving the selective ionization process and the detection sensitivity. The proposed approach offered a new dimension to the application of QDs as matrices for MALDI-MS research of carbohydrates. It could be used for quantitative measurement of glucose concentration in human serum with good performance. The QDs served as a matrix showed the advantages of low background, higher sensitivity, convenient sample preparation and excellent stability under vacuum. The QDs assisted LDI-MS approach has promising application to the analysis of carbohydrates in complex biological samples. Copyright © 2016 John Wiley & Sons, Ltd.

  18. Real-time PCR for quantitative detection of bovine tissues in food and feed.

    PubMed

    Martín, Irene; García, Teresa; Fajardo, Violeta; Rojas, María; Hernández, Pablo E; González, Isabel; Martín, Rosario

    2008-03-01

    A real-time PCR approach with the SYBR Green detection system has been developed for the quantitative detection of bovine tissues in food and feedstuffs. The method combines the use of bovine-specific primers, which amplify an 84-bp fragment of the mitochondrial 12S rRNA gene, and universal primers, which amplify a 140-bp fragment of the nuclear 18S rRNA gene from eukaryotic DNA. The 18S rRNA primers are used as endogenous controls for the total content of PCR-amplifiable DNA in the sample. The specificity of the primers was tested against 18 animal species, including mammals, birds, and fish, as well as 6 plant species. Analysis of experimental bovine tissues-oats mixtures demonstrated the suitability of the assay for the detection of bovine DNA in mixtures containing as low as 0.1% of bovine tissues. The performance of the method is not affected by severe heat treatment (up to 133 degrees C for 20 min at 300 kPa). The reported PCR assay could be very useful for detecting bovine-derived ingredients in raw and heat-treated food and feedstuffs.

  19. Identification and quantitation of Bacillus globigii using metal enhanced electrochemical detection and capillary biosensor.

    PubMed

    Mwilu, Samuel K; Aluoch, Austin O; Miller, Seth; Wong, Paula; Sadik, Omowunmi A; Fatah, Alim A; Arcilesi, Richard D

    2009-09-15

    Presented herein are two detection strategies for the identification and quantification of Bacillus globigii, a spore forming nonpathogenic simulant of Bacillus anthracis. The first strategy involves a label-free, metal-enhanced electrochemical immunosensor for the quantitative detection of Bacillus globigii (atrophaeus). The immunosensor comprises of antibacillus globigii (BG) antibody self-assembled onto a gold quartz crystal electrode via cystamine bond. A solid-phase monolayer of silver underpotentially deposited onto the cystamine modified-Au-electrode surface is used as the redox probe. The monolayer was also generated by adsorbing silver nanoparticles on the gold electrode. When the antibody-modified electrode is exposed to BG spores, the antibody-antigen (Ab-Ag) complex formed insulated the electrode surface toward the silver redox probe. The variation of redox current was found to be proportional to the concentration of the BG spores between 1 x 10(2)-3.5 x 10(4) spores/mL. A detection limit of 602 spores/mL was obtained, which is well-below the infectious dose of anthrax spores at 2.5 x 10(5) spores/mL. The second approach involves the use of ultrasensitive portable capillary biosensor (UPAC) to detect the spores. The capillary is an enclosed system that acts as the flow cell, the waveguide, and the solid support for immobilized bimolecular probes. An evanescent excitation generates a signal from an antigen-antibody-fluorophore complex, which propagates along the capillary and is guided to the detector. A limit of detection of 112 spores/mL was reported using the UPAC sensor. Both methods showed lower detection limits compared to the conventional ELISA. The effect of potential interferants tested using Bacillus pumilus confirmed the selectivity for the analyte. This work should allow the first responders to rapidly detect and quantify Bacillus globigii spores at concentrations that are well-below the infectious dose.

  20. Theoretical foundations for a quantitative approach to paleogenetics. I, II.

    NASA Technical Reports Server (NTRS)

    Holmquist, R.

    1972-01-01

    It is shown that by neglecting the phenomena of multiple hits, back mutation, and chance coincidence errors larger than 100% can be introduced in the calculated value of the average number of nucleotide base differences to be expected between two homologous polynucleotides. Mathematical formulas are derived to correct quantitatively for these effects. It is pointed out that the effects change materially the quantitative aspects of phylogenics, such as the length of the legs of the trees. A number of problems are solved without approximation.-

  1. Attenuated Total Internal Reflectance Infrared Spectroscopy (ATR-FTIR): A Quantitative Approach for Kidney Stone Analysis

    PubMed Central

    Gulley-Stahl, Heather J.; Haas, Jennifer A.; Schmidt, Katherine A.; Evan, Andrew P.; Sommer, André J.

    2011-01-01

    The impact of kidney stone disease is significant worldwide, yet methods for quantifying stone components remain limited. A new approach requiring minimal sample preparation for the quantitative analysis of kidney stone components has been investigated utilizing attenuated total internal reflectance infrared spectroscopy (ATR-FTIR). Calcium oxalate monohydrate (COM) and hydroxylapatite (HAP), two of the most common constituents of urinary stones, were used for quantitative analysis. Calibration curves were constructed using integrated band intensities of four infrared absorptions versus concentration (weight %). The correlation coefficients of the calibration curves range from 0.997 to 0.93. The limits of detection range from 0.07 ± 0.02% COM/HAP where COM is the analyte and HAP the matrix to 0.26 ± 0.07% HAP/COM where HAP is the analyte and COM the matrix. This study shows that linear calibration curves can be generated for the quantitative analysis of stone mixtures provided the system is well understood especially with respect to particle size. PMID:19589213

  2. Quantitative Detection of Pharmaceuticals Using a Combination of Paper Microfluidics and Wavelength Modulated Raman Spectroscopy

    PubMed Central

    Craig, Derek; Mazilu, Michael; Dholakia, Kishan

    2015-01-01

    Raman spectroscopy has proven to be an indispensable technique for the identification of various types of analytes due to the fingerprint vibration spectrum obtained. Paper microfluidics has also emerged as a low cost, easy to fabricate and portable approach for point of care testing. However, due to inherent background fluorescence, combining Raman spectroscopy with paper microfluidics is to date an unmet challenge in the absence of using surface enhanced mechanisms. We describe the first use of wavelength modulated Raman spectroscopy (WMRS) for analysis on a paper microfluidics platform. This study demonstrates the ability to suppress the background fluorescence of the paper using WMRS and the subsequent implementation of this technique for pharmaceutical analysis. The results of this study demonstrate that it is possible to discriminate between both paracetamol and ibuprofen, whilst, also being able to detect the presence of each analyte quantitatively at nanomolar concentrations. PMID:25938464

  3. Quantitative detection of pharmaceuticals using a combination of paper microfluidics and wavelength modulated Raman spectroscopy.

    PubMed

    Craig, Derek; Mazilu, Michael; Dholakia, Kishan

    2015-01-01

    Raman spectroscopy has proven to be an indispensable technique for the identification of various types of analytes due to the fingerprint vibration spectrum obtained. Paper microfluidics has also emerged as a low cost, easy to fabricate and portable approach for point of care testing. However, due to inherent background fluorescence, combining Raman spectroscopy with paper microfluidics is to date an unmet challenge in the absence of using surface enhanced mechanisms. We describe the first use of wavelength modulated Raman spectroscopy (WMRS) for analysis on a paper microfluidics platform. This study demonstrates the ability to suppress the background fluorescence of the paper using WMRS and the subsequent implementation of this technique for pharmaceutical analysis. The results of this study demonstrate that it is possible to discriminate between both paracetamol and ibuprofen, whilst, also being able to detect the presence of each analyte quantitatively at nanomolar concentrations.

  4. Quantitative Raman Spectroscopy when the Signal-to-Noise is Below the Limit of Quantitation due to Fluorescence Interference: Advantages of a Moving Window Sequentially Shifted Excitation Approach.

    PubMed

    Marshall, Sarah; Cooper, John B

    2016-09-01

    Raman spectroscopy is a useful analytical tool. However, its application is often limited because shot noise from fluorescence obscures the Raman signal. In such cases, quantitative analysis is not possible when the signal-to-noise ratio (SNR) drops below two. A method is described for performing quantitative Raman spectroscopy that not only removes fluorescence backgrounds, but also results in a significant improvement in the SNR. The Raman data is extracted using a moving window sequentially shifted excitation algorithm. To demonstrate the capabilities of the method, a binary mixture of two analytes at varying concentrations is quantified in the presence of a highly fluorescent dye. Linear calibration plots were constructed and validated for the binary model using individual Raman peaks with SNR ranging from 0.073-12.6; r(2) values are greater than 0.96 in all cases, with all but the weakest peaks yielding values greater than 0.997. The presented method demonstrates a universal and autonomous approach for the quantitative analysis of highly fluorescent samples via Raman spectroscopy. The lower limit on the SNR ratio for quantitative Raman analysis with the described method is 0.1. In order to assess the effectiveness of the presented method, the entire set of experiments was also processed using the more common shifted excitation Raman difference spectroscopy (SERDS) approach. The advantages of the proposed method over SERDS are demonstrated for both the detection limit and the SNR of the processed spectra. © The Author(s) 2016.

  5. A Quantitative Approach to the Design of School Bus Routes.

    ERIC Educational Resources Information Center

    Tracz, George S.

    A number of factors--including the reorganization of school administrative structures, the availability of new technology, increased competition among groups for limited resources, and changing patterns of communication--suggest an increased need for quantitative analysis in the school district decision-making process. One area of school…

  6. Improving Library Performance: Quantitative Approaches to Library Planning.

    ERIC Educational Resources Information Center

    Webster, Duane E.

    The use of analytical models and quantitative methods for both short- and long-range problem solving offer library managers an excellent opportunity to improve and rationalize decision-making for strategic and organizational planning. The first step is to identify the problems confronting the library and understand its current capabilities.…

  7. Quantitative and sensitive RNA based detection of Bacillus spores

    PubMed Central

    Osmekhina, Ekaterina; Shvetsova, Antonina; Ruottinen, Maria; Neubauer, Peter

    2014-01-01

    The fast and reliable detection of bacterial spores is of great importance and still remains a challenge. Here we describe a direct RNA-based diagnostic method for the specific detection of viable bacterial spores which does not depends on an enzymatic amplification step and therefore is directly appropriate for quantification. The procedure includes the following steps: (i) heat activation of spores, (ii) germination and enrichment cultivation, (iii) cell lysis, and (iv) analysis of 16S rRNA in crude cell lysates using a sandwich hybridization assay. The sensitivity of the method is dependent on the cultivation time and the detection limit; it is possible to detect 10 spores per ml when the RNA analysis is performed after 6 h of enrichment cultivation. At spore concentrations above 106 spores per ml the cultivation time can be shortened to 30 min. Total analysis times are in the range of 2–8 h depending on the spore concentration in samples. The developed procedure is optimized at the example of Bacillus subtilis spores but should be applicable to other organisms. The new method can easily be modified for other target RNAs and is suitable for specific detection of spores from known groups of organisms. PMID:24653718

  8. Some new approaches to the detection of programmed cell death

    NASA Astrophysics Data System (ADS)

    Bilyy, Rostyslav O.; Bilyi, Alexander I.; Getman, Vasyl B.; Kit, Yuriy Ya.; Mayor, Christina Ya.; Antonyuk, Volodmyr O.; Stoika, Rostyslav S.

    2006-08-01

    Apoptosis, or programmed cell death, is a form of cell death occurring during normal physiological processes and is used by the multicellular organism for elimination of "old" and impaired cells. Apoptosis is characterized by specific morphological changes such as plasma membrane blebbing, nucleus condensation, and cell wrinkling with further destruction into apoptotic bodies. Apoptosis detection is in focus of instrumental methods used in modern biomedical sciences. The available methods for such purpose are either very expensive, or require time-consuming operations. Their specificity and sensitivity are frequently not sufficient for biomedical diagnostics. We propose to use light scattering analysis for evaluation of apoptosis in cell population, especially for the detection of physical changes of cells, such as cell condensation and degradation into apoptotic bodies. The method proved to be very effective, providing quantitative estimation and high precision, simplicity and low costs of analysis (UA Patent No.64090). Another approach for the detection of apoptosis is based on the recently discovered fact (Bilyy, Stoika 2003; Bilyy et al, 2004; 2005) that apoptotic cells are characterized by increased expression levels of specific glycoproteins in the plasma membrane, which were proved to be selective and specific markers of apoptotic cells. Specific carbohydrate-binding proteins - lectins - were used for identification of mentioned glycoproteins; fluorescent conjugates of lectins were proved to be another novel tool for apoptosis identification using approaches of biophotonics.

  9. An electrochemical immunosensor for quantitative detection of ficolin-3

    NASA Astrophysics Data System (ADS)

    San, Lili; Zeng, Dongdong; Song, Shiping; Zuo, Xiaolei; Zhang, Huan; Wang, Chenguang; Wu, Jiarui; Mi, Xianqiang

    2016-06-01

    Diabetes mellitus (DM) is one of the most common metabolic disorders in the world, of which more than 90% is type-2 diabetes mellitus (T2DM). There is a rather urgent need for reliable, sensitive and quick detection techniques in clinical application of T2DM. Ficolin-3 is a potential biomarker of T2DM, because serum ficolin-3 levels are associated with insulin resistance and predict the incidence of T2DM. Herein, a sandwich-type electrochemical immunosensor was developed for the detection of ficolin-3 in human serum. Cyclic voltammetry and the amperometric current versus time were used to characterize the performance of the immunosensor. Under optimal conditions, the detection limitation of ficolin-3 was 100 ng ml-1 and the linear dynamic range was between 2 and 50 μg ml-1. The method has ideal accuracy, excellent stability and selectivity and has wide application prospects in clinical research.

  10. Magnetic Ligation Method for Quantitative Detection of MicroRNAs

    PubMed Central

    Liong, Monty; Im, Hyungsoon; Majmudar, Maulik D.; Aguirre, Aaron D.; Sebas, Matthew; Lee, Hakho; Weissleder, Ralph

    2014-01-01

    A magnetic ligation method is utilized for the detection of microRNAs amongst a complex biological background without polymerase chain reaction or nucleotide modification. The sandwich probes assay can be adapted to analyze a panel of microRNAs associated with cardiovascular diseases in heart tissue samples. PMID:24532323

  11. The colorimetric detection and quantitation of total protein.

    PubMed

    Krohn, Randall I

    2011-09-01

    Protein quantification is an important step for handling protein samples for isolation and characterization; it is a prerequisite step before submitting proteins for chromatographic, electrophoretic, or immunochemical analysis and separation. Colorimetric methods are fast, simple, and not laborious. This unit describes a number of assays able to detect protein concentrations in the low microgram to milligram per milliliter ranges in a variety of formats.

  12. High dynamic range detection of Chlamydia trachomatis growth by direct quantitative PCR of the infected cells.

    PubMed

    Eszik, Ildikó; Lantos, Ildikó; Önder, Kamil; Somogyvári, Ferenc; Burián, Katalin; Endrész, Valéria; Virok, Dezső P

    2016-01-01

    Chlamydiae are obligate intracellular bacteria developing in an intracytoplasmic niche, the inclusion. Chlamydia growth measurement by inclusion counting is a key task in the development of novel antichlamydial antibiotics and in vaccine studies. Most of the current counting methods rely on the immunofluorescent staining of the inclusions and either manual or automatic microscopy detection and enumeration. The manual method is highly labor intensive, while the automatic methods are either medium-throughput or require automatic microscopy. The sensitive and specific PCR technology could be an effective method for growth related chlamydial DNA detection; however the currently described PCR approaches have a major limitation, the requirement of purification of DNA or RNA from the infected cells. This limitation makes this approach unfeasible for high-throughput screenings. To overcome this, we developed a quantitative PCR (qPCR) method for the detection of Chlamydia trachomatis DNA directly from the infected HeLa cells. With our method we were able to detect the bacterial growth in a 4 log scale (multiplicity of infection (MOI): 64 to 0.0039), with high correlation between the biological and technical replicates. As a further proof of the method, we applied the direct qPCR for antibiotic minimum inhibitory concentration (MIC) measurements. The measured MICs of moxifloxacin, tetracycline, clarithromycin and compound PCC00213 were 0.031 μg/ml, 0.031 μg/ml, 0.0039 μg/ml and 6.2 μg/ml respectively, identical or close to the already published MIC values. Our direct qPCR method for chlamydial growth and antibiotic MIC determination is less time-consuming, more objective and more sensitive than the currently applied manual or automatic fluorescent microscopy- based methods.

  13. Groundtruth approach to accurate quantitation of fluorescence microarrays

    SciTech Connect

    Mascio-Kegelmeyer, L; Tomascik-Cheeseman, L; Burnett, M S; van Hummelen, P; Wyrobek, A J

    2000-12-01

    To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.

  14. From DNA sequence to transcriptional behaviour: a quantitative approach.

    PubMed

    Segal, Eran; Widom, Jonathan

    2009-07-01

    Complex transcriptional behaviours are encoded in the DNA sequences of gene regulatory regions. Advances in our understanding of these behaviours have been recently gained through quantitative models that describe how molecules such as transcription factors and nucleosomes interact with genomic sequences. An emerging view is that every regulatory sequence is associated with a unique binding affinity landscape for each molecule and, consequently, with a unique set of molecule-binding configurations and transcriptional outputs. We present a quantitative framework based on existing methods that unifies these ideas. This framework explains many experimental observations regarding the binding patterns of factors and nucleosomes and the dynamics of transcriptional activation. It can also be used to model more complex phenomena such as transcriptional noise and the evolution of transcriptional regulation.

  15. Gravity driven high throughput phase detecting cytometer based on quantitative interferometric microscopy

    NASA Astrophysics Data System (ADS)

    Xue, Liang; Wang, Shouyu; Yan, Keding; Sun, Nan; Ferraro, Pietro; Li, Zhenhua; Liu, Fei

    2014-04-01

    Phase distribution detection of cells and tissues is concerned since it is an important auxiliary method for observing biological samples. High speed and large amount cell detection is needed for its high detecting efficiency. In this paper, we have proposed a simple large scale biological sample phase detection device called gravity driven high throughput phase detecting cytometer based on quantitative interferometric microscopy to obtain flowing red blood cells phase. The system could realize high throughput phase detecting and statistical analysis with high detecting speed and in real time. The statistical characteristics of red blood cells could be obtained which might be helpful for biological analysis and disease detection. We believe this method is a powerful tool to quantitatively measure the phase distribution of biological samples.

  16. Tools for the Quantitative Analysis of Sedimentation Boundaries Detected by Fluorescence Optical Analytical Ultracentrifugation

    PubMed Central

    Zhao, Huaying; Casillas, Ernesto; Shroff, Hari; Patterson, George H.; Schuck, Peter

    2013-01-01

    Fluorescence optical detection in sedimentation velocity analytical ultracentrifugation allows the study of macromolecules at nanomolar concentrations and below. This has significant promise, for example, for the study of systems of high-affinity protein interactions. Here we describe adaptations of the direct boundary modeling analysis approach implemented in the software SEDFIT that were developed to accommodate unique characteristics of the confocal fluorescence detection system. These include spatial gradients of signal intensity due to scanner movements out of the plane of rotation, temporal intensity drifts due to instability of the laser and fluorophores, and masking of the finite excitation and detection cone by the sample holder. In an extensive series of experiments with enhanced green fluorescent protein ranging from low nanomolar to low micromolar concentrations, we show that the experimental data provide sufficient information to determine the parameters required for first-order approximation of the impact of these effects on the recorded data. Systematic deviations of fluorescence optical sedimentation velocity data analyzed using conventional sedimentation models developed for absorbance and interference optics are largely removed after these adaptations, resulting in excellent fits that highlight the high precision of fluorescence sedimentation velocity data, thus allowing a more detailed quantitative interpretation of the signal boundaries that is otherwise not possible for this system. PMID:24204779

  17. DETECTION AND QUANTITATION OF FALLOUT PARTICLES IN A HUMAN LUNG.

    PubMed

    WEGST, A V; PELLETIER, C A; WHIPPLE, G H

    1964-02-28

    Portions of an adult human lung were studied by autoradiography in order to detect the presence of fallout particles. The radioactivity in the remainder of the tissue was determined with a gamma-ray spectrometer. Four particles were found and their activities were determined. From the measurement for total-fission-product activity in the lung tissue it was calculated that there were approximately 264 particles in the right lung at the time of death.

  18. Optimization of Quantitative PCR Methods for Enteropathogen Detection.

    PubMed

    Liu, Jie; Gratz, Jean; Amour, Caroline; Nshama, Rosemary; Walongo, Thomas; Maro, Athanasia; Mduma, Esto; Platts-Mills, James; Boisen, Nadia; Nataro, James; Haverstick, Doris M; Kabir, Furqan; Lertsethtakarn, Paphavee; Silapong, Sasikorn; Jeamwattanalert, Pimmada; Bodhidatta, Ladaporn; Mason, Carl; Begum, Sharmin; Haque, Rashidul; Praharaj, Ira; Kang, Gagandeep; Houpt, Eric R

    2016-01-01

    Detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. Here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. First, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized with diarrhea in Tanzania. Swabs generally yielded a higher quantification cycle (Cq) (average 29.7, standard deviation 3.5 vs. 25.3 ± 2.9 from stool, P<0.001) but were still able to detect 80% of pathogens with a Cq < 30 in stool. Second, a simplified total nucleic acid (TNA) extraction procedure was compared to separate DNA and RNA extractions and showed 92% (318/344) sensitivity and 98% (951/968) specificity, with no difference in Cq value for the positive results (ΔCq(DNA+RNA-TNA) = -0.01 ± 1.17, P = 0.972, N = 318). Third, we devised a quantification scheme that adjusts pathogen quantity to the specimen's extraction and amplification efficiency, and show that this better estimates the quantity of spiked specimens than the raw target Cq. In sum, these methods for enteropathogen quantification, stool sample collection, and nucleic acid extraction will be useful for laboratories studying enteric disease.

  19. Optimization of Quantitative PCR Methods for Enteropathogen Detection

    PubMed Central

    Liu, Jie; Gratz, Jean; Amour, Caroline; Nshama, Rosemary; Walongo, Thomas; Maro, Athanasia; Mduma, Esto; Platts-Mills, James; Boisen, Nadia; Nataro, James; Haverstick, Doris M.; Kabir, Furqan; Lertsethtakarn, Paphavee; Silapong, Sasikorn; Jeamwattanalert, Pimmada; Bodhidatta, Ladaporn; Mason, Carl; Begum, Sharmin; Haque, Rashidul; Praharaj, Ira; Kang, Gagandeep; Houpt, Eric R.

    2016-01-01

    Detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. Here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. First, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized with diarrhea in Tanzania. Swabs generally yielded a higher quantification cycle (Cq) (average 29.7, standard deviation 3.5 vs. 25.3 ± 2.9 from stool, P<0.001) but were still able to detect 80% of pathogens with a Cq < 30 in stool. Second, a simplified total nucleic acid (TNA) extraction procedure was compared to separate DNA and RNA extractions and showed 92% (318/344) sensitivity and 98% (951/968) specificity, with no difference in Cq value for the positive results (ΔCq(DNA+RNA-TNA) = -0.01 ± 1.17, P = 0.972, N = 318). Third, we devised a quantification scheme that adjusts pathogen quantity to the specimen’s extraction and amplification efficiency, and show that this better estimates the quantity of spiked specimens than the raw target Cq. In sum, these methods for enteropathogen quantification, stool sample collection, and nucleic acid extraction will be useful for laboratories studying enteric disease. PMID:27336160

  20. Critical considerations in the immunochemical detection and quantitation of antigenic biomarkers.

    PubMed

    Roberts, D W; Benson, R W; Hinson, J A; Kadlubar, F F

    1991-06-01

    The formation of covalent adducts as a result of the interaction of metabolically activated chemicals with host macromolecules is a common critical event in mutagenic, carcinogenic, and immunologic phenomena. Because of their antigenicity and their immunogenicity, covalent adducts may be detected using sensitive immunochemical techniques. The immunochemical approaches to biomonitoring and molecular dosimetry of DNA damage are particularly attractive because they allow sensitive quantitation of specific DNA adducts present in small samples and do not rely on the use of radiolabeled adducts. Two examples of biomarker immunoassay development are presented: an avidin/biotin-amplified ELISA for the major DNA adduct of the human bladder carcinogen 4-aminobiphenyl (ABP), and a particle concentration fluorescent immunoassay (PCFIA) for the major protein adduct associated with toxicity by the prototype hepatotoxin acetaminophen. The examples illustrate critical steps in the development of biomarker immunoassays which include selection of the relevant adduct, preparation of an appropriate immunogen, immunization, characterization of antisera, and development of application-specific sample processing techniques for biomarker quantitation. Immunochemical procedures may be combined with other analytical techniques to form hybrid systems which take advantage of both the antigenicity and the physical or chemical properties of a biomarker to achieve greater specificity and/or sensitivity. The future usefulness of these new tools of molecular epidemiology will depend on a compound-by-compound validation of methods and critical evaluation of the biologic importance of the particular antigenic biomarker as an indicator of exposure and as an indicator of risk.

  1. Dual core quantum dots for highly quantitative ratiometric detection of trypsin activity in cystic fibrosis patients

    NASA Astrophysics Data System (ADS)

    Castelló Serrano, Iván; Stoica, Georgiana; Matas Adams, Alba; Palomares, Emilio

    2014-10-01

    We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L-1). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for recessive genetic diseases like human cystic fibrosis. In a screening program in which the goal is to detect disease and also the carrier status, early diagnosis could be of great help.We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L-1). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for

  2. A framework for organizing and selecting quantitative approaches for benefit-harm assessment

    PubMed Central

    2012-01-01

    Background Several quantitative approaches for benefit-harm assessment of health care interventions exist but it is unclear how the approaches differ. Our aim was to review existing quantitative approaches for benefit-harm assessment and to develop an organizing framework that clarifies differences and aids selection of quantitative approaches for a particular benefit-harm assessment. Methods We performed a review of the literature to identify quantitative approaches for benefit-harm assessment. Our team, consisting of clinicians, epidemiologists, and statisticians, discussed the approaches and identified their key characteristics. We developed a framework that helps investigators select quantitative approaches for benefit-harm assessment that are appropriate for a particular decisionmaking context. Results Our framework for selecting quantitative approaches requires a concise definition of the treatment comparison and population of interest, identification of key benefit and harm outcomes, and determination of the need for a measure that puts all outcomes on a single scale (which we call a benefit and harm comparison metric). We identified 16 quantitative approaches for benefit-harm assessment. These approaches can be categorized into those that consider single or multiple key benefit and harm outcomes, and those that use a benefit-harm comparison metric or not. Most approaches use aggregate data and can be used in the context of single studies or systematic reviews. Although the majority of approaches provides a benefit and harm comparison metric, only four approaches provide measures of uncertainty around the benefit and harm comparison metric (such as a 95 percent confidence interval). None of the approaches considers the actual joint distribution of benefit and harm outcomes, but one approach considers competing risks when calculating profile-specific event rates. Nine approaches explicitly allow incorporating patient preferences. Conclusion The choice of

  3. A framework for organizing and selecting quantitative approaches for benefit-harm assessment.

    PubMed

    Puhan, Milo A; Singh, Sonal; Weiss, Carlos O; Varadhan, Ravi; Boyd, Cynthia M

    2012-11-19

    Several quantitative approaches for benefit-harm assessment of health care interventions exist but it is unclear how the approaches differ. Our aim was to review existing quantitative approaches for benefit-harm assessment and to develop an organizing framework that clarifies differences and aids selection of quantitative approaches for a particular benefit-harm assessment. We performed a review of the literature to identify quantitative approaches for benefit-harm assessment. Our team, consisting of clinicians, epidemiologists, and statisticians, discussed the approaches and identified their key characteristics. We developed a framework that helps investigators select quantitative approaches for benefit-harm assessment that are appropriate for a particular decisionmaking context. Our framework for selecting quantitative approaches requires a concise definition of the treatment comparison and population of interest, identification of key benefit and harm outcomes, and determination of the need for a measure that puts all outcomes on a single scale (which we call a benefit and harm comparison metric). We identified 16 quantitative approaches for benefit-harm assessment. These approaches can be categorized into those that consider single or multiple key benefit and harm outcomes, and those that use a benefit-harm comparison metric or not. Most approaches use aggregate data and can be used in the context of single studies or systematic reviews. Although the majority of approaches provides a benefit and harm comparison metric, only four approaches provide measures of uncertainty around the benefit and harm comparison metric (such as a 95 percent confidence interval). None of the approaches considers the actual joint distribution of benefit and harm outcomes, but one approach considers competing risks when calculating profile-specific event rates. Nine approaches explicitly allow incorporating patient preferences. The choice of quantitative approaches depends on the

  4. Detection of cardiomyopathy in an animal model using quantitative autoradiography

    SciTech Connect

    Kubota, K.; Som, P.; Oster, Z.H.; Brill, A.B.; Goodman, M.M.; Knapp, F.F. Jr.; Atkins, H.L.; Sole, M.J.

    1988-10-01

    A fatty acid analog (15-p-iodophenyl)-3,3 dimethyl-pentadecanoic acid (DMIPP) was studied in cardiomyopathic (CM) and normal age-matched Syrian hamsters. Dual tracer quantitative wholebody autoradiography (QARG) with DMIPP and 2-(/sup 14/C(U))-2-deoxy-2-fluoro-D-glucose (FDG) or with FDG and /sup 201/Tl enabled comparison of the uptake of a fatty acid and a glucose analog with the blood flow. These comparisons were carried out at the onset and mid-stage of the disease before congestive failure developed. Groups of CM and normal animals were treated with verapamil from the age of 26 days, before the onset of the disease for 41 days. In CM hearts, areas of decreased DMIPP uptake were seen. These areas were much larger than the decrease in uptake of FDG or /sup 201/Tl. In early CM only minimal changes in FDG or /sup 201/Tl uptake were observed as compared to controls. Treatment of CM-prone animals with verapamil prevented any changes in DMIPP, FDG, or /sup 201/Tl uptake. DMIPP seems to be a more sensitive indicator of early cardiomyopathic changes as compared to /sup 201/Tl or FDG. The trial of DMIPP and SPECT in the diagnosis of human disease, as well as for monitoring the effects of drugs which may prevent it seems to be warranted.

  5. Detection of microcystin-producing cyanobacteria in Missisquoi Bay, Quebec, Canada, using quantitative PCR.

    PubMed

    Fortin, Nathalie; Aranda-Rodriguez, Rocio; Jing, Hongmei; Pick, Frances; Bird, David; Greer, Charles W

    2010-08-01

    Toxic cyanobacterial blooms, as well as their increasing global occurrence, pose a serious threat to public health, domestic animals, and livestock. In Missisquoi Bay, Lake Champlain, public health advisories have been issued from 2001 to 2009, and local microcystin concentrations found in the lake water regularly exceeded the Canadian drinking water guideline of 1.5 microg liter(-1). A quantitative PCR (Q-PCR) approach was developed for the detection of blooms formed by microcystin-producing cyanobacteria. Primers were designed for the beta-ketoacyl synthase (mcyD(KS)) and the first dehydratase domain (mcyD(DH)) of the mcyD gene, involved in microcystin synthesis. The Q-PCR method was used to track the toxigenic cyanobacteria in Missisquoi Bay during the summers of 2006 and 2007. Two toxic bloom events were detected in 2006: more than 6.5 x 10(4) copies of the mcyD(KS) gene ml(-1) were detected in August, and an average of 4.0 x 10(4) copies ml(-1) were detected in September, when microcystin concentrations were more than 4 microg liter(-1) and approximately 2 microg liter(-1), respectively. Gene copy numbers and total microcystin concentrations (determined by enzyme-linked immunosorbent assay [ELISA]) were highly correlated in the littoral (r = 0.93, P < 0.001) and the pelagic station (r = 0.87, P < 0.001) in 2006. In contrast to the situation in 2006, a cyanobacterial bloom occurred only in late summer-early fall of 2007, reaching only 3 x 10(2) mcyD(KS) copies ml(-1), while the microcystin concentration was barely detectable. The Q-PCR method allowed the detection of microcystin-producing cyanobacteria when toxins and toxigenic cyanobacterial abundance were still below the limit of detection by high-pressure liquid chromatography (HPLC) and microscopy. Toxin gene copy numbers grew exponentially at a steady rate over a period of 7 weeks. Onshore winds selected for cells with a higher cell quota of microcystin. This technique could be an effective approach for

  6. Quantitative and qualitative approaches to identifying migration chronology in a continental migrant

    USGS Publications Warehouse

    Beatty, William S.; Kesler, Dylan C.; Webb, Elisabeth B.; Raedeke, Andrew H.; Naylor, Luke W.; Humburg, Dale D.

    2013-01-01

    The degree to which extrinsic factors influence migration chronology in North American waterfowl has not been quantified, particularly for dabbling ducks. Previous studies have examined waterfowl migration using various methods, however, quantitative approaches to define avian migration chronology over broad spatio-temporal scales are limited, and the implications for using different approaches have not been assessed. We used movement data from 19 female adult mallards (Anas platyrhynchos) equipped with solar-powered global positioning system satellite transmitters to evaluate two individual level approaches for quantifying migration chronology. The first approach defined migration based on individual movements among geopolitical boundaries (state, provincial, international), whereas the second method modeled net displacement as a function of time using nonlinear models. Differences in migration chronologies identified by each of the approaches were examined with analysis of variance. The geopolitical method identified mean autumn migration midpoints at 15 November 2010 and 13 November 2011, whereas the net displacement method identified midpoints at 15 November 2010 and 14 November 2011. The mean midpoints for spring migration were 3 April 2011 and 20 March 2012 using the geopolitical method and 31 March 2011 and 22 March 2012 using the net displacement method. The duration, initiation date, midpoint, and termination date for both autumn and spring migration did not differ between the two individual level approaches. Although we did not detect differences in migration parameters between the different approaches, the net displacement metric offers broad potential to address questions in movement ecology for migrating species. Ultimately, an objective definition of migration chronology will allow researchers to obtain a comprehensive understanding of the extrinsic factors that drive migration at the individual and population levels. As a result, targeted

  7. Quantitative and qualitative approaches to identifying migration chronology in a continental migrant.

    PubMed

    Beatty, William S; Kesler, Dylan C; Webb, Elisabeth B; Raedeke, Andrew H; Naylor, Luke W; Humburg, Dale D

    2013-01-01

    The degree to which extrinsic factors influence migration chronology in North American waterfowl has not been quantified, particularly for dabbling ducks. Previous studies have examined waterfowl migration using various methods, however, quantitative approaches to define avian migration chronology over broad spatio-temporal scales are limited, and the implications for using different approaches have not been assessed. We used movement data from 19 female adult mallards (Anas platyrhynchos) equipped with solar-powered global positioning system satellite transmitters to evaluate two individual level approaches for quantifying migration chronology. The first approach defined migration based on individual movements among geopolitical boundaries (state, provincial, international), whereas the second method modeled net displacement as a function of time using nonlinear models. Differences in migration chronologies identified by each of the approaches were examined with analysis of variance. The geopolitical method identified mean autumn migration midpoints at 15 November 2010 and 13 November 2011, whereas the net displacement method identified midpoints at 15 November 2010 and 14 November 2011. The mean midpoints for spring migration were 3 April 2011 and 20 March 2012 using the geopolitical method and 31 March 2011 and 22 March 2012 using the net displacement method. The duration, initiation date, midpoint, and termination date for both autumn and spring migration did not differ between the two individual level approaches. Although we did not detect differences in migration parameters between the different approaches, the net displacement metric offers broad potential to address questions in movement ecology for migrating species. Ultimately, an objective definition of migration chronology will allow researchers to obtain a comprehensive understanding of the extrinsic factors that drive migration at the individual and population levels. As a result, targeted

  8. Quantitative and Qualitative Approaches to Identifying Migration Chronology in a Continental Migrant

    PubMed Central

    Beatty, William S.; Kesler, Dylan C.; Webb, Elisabeth B.; Raedeke, Andrew H.; Naylor, Luke W.; Humburg, Dale D.

    2013-01-01

    The degree to which extrinsic factors influence migration chronology in North American waterfowl has not been quantified, particularly for dabbling ducks. Previous studies have examined waterfowl migration using various methods, however, quantitative approaches to define avian migration chronology over broad spatio-temporal scales are limited, and the implications for using different approaches have not been assessed. We used movement data from 19 female adult mallards (Anas platyrhynchos) equipped with solar-powered global positioning system satellite transmitters to evaluate two individual level approaches for quantifying migration chronology. The first approach defined migration based on individual movements among geopolitical boundaries (state, provincial, international), whereas the second method modeled net displacement as a function of time using nonlinear models. Differences in migration chronologies identified by each of the approaches were examined with analysis of variance. The geopolitical method identified mean autumn migration midpoints at 15 November 2010 and 13 November 2011, whereas the net displacement method identified midpoints at 15 November 2010 and 14 November 2011. The mean midpoints for spring migration were 3 April 2011 and 20 March 2012 using the geopolitical method and 31 March 2011 and 22 March 2012 using the net displacement method. The duration, initiation date, midpoint, and termination date for both autumn and spring migration did not differ between the two individual level approaches. Although we did not detect differences in migration parameters between the different approaches, the net displacement metric offers broad potential to address questions in movement ecology for migrating species. Ultimately, an objective definition of migration chronology will allow researchers to obtain a comprehensive understanding of the extrinsic factors that drive migration at the individual and population levels. As a result, targeted

  9. Target-responsive DNAzyme cross-linked hydrogel for visual quantitative detection of lead.

    PubMed

    Huang, Yishun; Ma, Yanli; Chen, Yahong; Wu, Xuemeng; Fang, Luting; Zhu, Zhi; Yang, Chaoyong James

    2014-11-18

    Because of the severe health risks associated with lead pollution, rapid, sensitive, and portable detection of low levels of Pb(2+) in biological and environmental samples is of great importance. In this work, a Pb(2+)-responsive hydrogel was prepared using a DNAzyme and its substrate as cross-linker for rapid, sensitive, portable, and quantitative detection of Pb(2+). Gold nanoparticles (AuNPs) were first encapsulated in the hydrogel as an indicator for colorimetric analysis. In the absence of lead, the DNAzyme is inactive, and the substrate cross-linker maintains the hydrogel in the gel form. In contrast, the presence of lead activates the DNAzyme to cleave the substrate, decreasing the cross-linking density of the hydrogel and resulting in dissolution of the hydrogel and release of AuNPs for visual detection. As low as 10 nM Pb(2+) can be detected by the naked eye. Furthermore, to realize quantitative visual detection, a volumetric bar-chart chip (V-chip) was used for quantitative readout of the hydrogel system by replacing AuNPs with gold-platinum core-shell nanoparticles (Au@PtNPs). The Au@PtNPs released from the hydrogel upon target activation can efficiently catalyze the decomposition of H2O2 to generate a large volume of O2. The gas pressure moves an ink bar in the V-chip for portable visual quantitative detection of lead with a detection limit less than 5 nM. The device was able to detect lead in digested blood with excellent accuracy. The method developed can be used for portable lead quantitation in many applications. Furthermore, the method can be further extended to portable visual quantitative detection of a variety of targets by replacing the lead-responsive DNAzyme with other DNAzymes.

  10. New quantitative detection of pathogens in heterogeneous environmental samples

    NASA Astrophysics Data System (ADS)

    Lee, Eun-Hee; Wang, Xiaofang; Mitchell, Kristi; Chae, Seon-Ha; Son, Ahjeong

    2015-04-01

    Quantum dots and magnetic beads based genomic assay (NanoGene assay) has been developed for sensitive and inhibition resistant gene quantification to achieve in-situ bacteria monitoring in environmental samples. In this study, eaeA gene of pathogenic E. coli O157:H7 was quantified. The result demonstrated the excellent sensitivity (i.e., limit of detection: 87 gene copies for dsDNA and 890 zeptomolar for ssDNA) in the presence of nonspecific microbial populations (Kim et al., 2010; 2011a). The feasibility of the developed gene quantification for non-laboratory environment usage (in-situ use) was investigated. Therefore, DNA hybridization was achieved at ambient temperature and minimum agitation, and the analysis was completed within hours. Most importantly, the NanoGene assay demonstrated the resistance to the presence of naturally occurring inhibitors (humic acids, cations) and residual reagents (surfactants, alcohols) from DNA extraction (Kim et al., 2011b). The assay was also applied to humic acids laden soils (7 types of soils with various amount of organic matters) and successfully quantified 105 to 108 CFU of E. coli O157:H7 per gram soil (R2 = 0.99). The results indicate that the presented NanoGene assay is suitable for further development as an in-situ bacteria monitoring method for working with heterogeneous environmental samples (Wang et al., 2013). Another aspect of the method is to transform the NanoGene assay into a portable device that can be used as a pathogenic bacteria detector in environment. The project consisted of the first inline fluidic components development and characterization as well as the first integration effort on a briefcase platform for the in-situ pathogen detection system (IPDS) (Mitchell et al., 2014). Our long term vision is to further miniaturize the briefcase platform implementation of the IPDS and to commercialize the handheld version of the IPDS.

  11. Analytical bioconjugates, aptamers, enable specific quantitative detection of Listeria monocytogenes.

    PubMed

    Lee, Sang-Hee; Ahn, Ji-Young; Lee, Kyeong-Ah; Um, Hyun-Ju; Sekhon, Simranjeet Singh; Sun Park, Tae; Min, Jiho; Kim, Yang-Hoon

    2015-06-15

    As a major human pathogen in the Listeria genus, Listeria monocytogenes causes the bacterial disease listeriosis, which is a serious infection caused by eating food contaminated with the bacteria. We have developed an aptamer-based sandwich assay (ABSA) platform that demonstrates a promising potential for use in pathogen detection using aptamers as analytical bioconjugates. The whole-bacteria SELEX (WB-SELEX) strategy was adopted to generate aptamers with high affinity and specificity against live L. monocytogenes. Of the 35 aptamer candidates tested, LMCA2 and LMCA26 reacted to L. monocytogenes with high binding, and were consequently chosen as sensing probes. The ABSA platform can significantly enhance the sensitivity by employing a very specific aptamer pair for the sandwich complex. The ABSA platform exhibited a linear response over a wide concentration range of L. monocytogenes from 20 to 2×10(6) CFU per mL and was closely correlated with the following relationship: y=9533.3x+1542.3 (R(2)=0.99). Our proposed ABSA platform also provided excellent specificity for the tests to distinguish L. monocytogenes from other Listeria species and other bacterial genera (3 Listeria spp., 4 Salmonella spp., 2 Vibrio spp., 3 Escherichia coli and 3 Shigella spp.). Improvements in the sensitivity and specificity have not only facilitated the reliable detection of L. monocytogenes at extremely low concentrations, but also allowed for the development of a 96-well plate-based routine assay platform for multivalent diagnostics. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Quantitative detection of bovine and porcine gelatin difference using surface plasmon resonance based biosensor

    NASA Astrophysics Data System (ADS)

    Wardani, Devy P.; Arifin, Muhammad; Suharyadi, Edi; Abraha, Kamsul

    2015-05-01

    Gelatin is a biopolymer derived from collagen that is widely used in food and pharmaceutical products. Due to some religion restrictions and health issues regarding the gelatin consumption which is extracted from certain species, it is necessary to establish a robust, reliable, sensitive and simple quantitative method to detect gelatin from different parent collagen species. To the best of our knowledge, there has not been a gelatin differentiation method based on optical sensor that could detect gelatin from different species quantitatively. Surface plasmon resonance (SPR) based biosensor is known to be a sensitive, simple and label free optical method for detecting biomaterials that is able to do quantitative detection. Therefore, we have utilized SPR-based biosensor to detect the differentiation between bovine and porcine gelatin in various concentration, from 0% to 10% (w/w). Here, we report the ability of SPR-based biosensor to detect difference between both gelatins, its sensitivity toward the gelatin concentration change, its reliability and limit of detection (LOD) and limit of quantification (LOQ) of the sensor. The sensor's LOD and LOQ towards bovine gelatin concentration are 0.38% and 1.26% (w/w), while towards porcine gelatin concentration are 0.66% and 2.20% (w/w), respectively. The results show that SPR-based biosensor is a promising tool for detecting gelatin from different raw materials quantitatively.

  13. A sandwich assay for quantitative detection of transcription factors in cell lysate.

    PubMed

    Fang, Zhiyuan; Zhang, Wenjuan; Ge, Chenchen; Liu, Jie; Lie, Puchang; Zeng, Lingwen

    2012-09-21

    A double-stranded DNA (dsDNA) mediated sandwich assay was developed for quantitative detection of transcription factors. The detection limit for human recombinant c-jun protein is 2.5 ng, and for c-jun protein the limit is as low as 0.625 μg of cell lysate.

  14. Rapid Detection and Quantitative Estimation of Type A Botulinum Toxin by Electroimmunodiffusion

    PubMed Central

    Miller, Carol A.; Anderson, Arthur W.

    1971-01-01

    An experimental system is described for the detection and quantitative estimation of type A botulinum toxin by electroimmunodiffusion. The method is shown to be rapid, specific, and quantitative. As little as 14 mouse LD50 per 0.1 ml of type A toxin was detected within 2 hr. When applied to experimentally contaminated foods such as canned tuna, pumpkin, spinach, green beans, and sausage, the technique detected botulinum toxin rapidly and identified it as to type and quantity. A specific rabbit type A antitoxin was produced for this in vitro system since the equine antitoxin (Center for Disease Control) tested in this experiment was found to be unsuitable. Images PMID:5005291

  15. Quantitative aspects of rare earth metal determinations using capillary electrophoresis with indirect absorbance detection

    SciTech Connect

    Colburn, B.A.; Starnes, S.D.; Sepaniak, M.J.

    1995-04-01

    The practical utility of capillary zone electrophoresis with indirect absorbance detection is examined for the separation and quantitation of rare earth metals. Various imidazole derivatives are investigated as to their suitability as running buffer (displaceable) detection ions with {alpha}-hydroxyisobutyric acid functioning as a chelating agent to enhance separations. Parameters important for quantitative analysis, such as limits of detection, relative standard deviation of peak areas, efficiency, resolution, peak shape and linear dynamic range are presented. The influence of sample matrix, method of injection, and background ion identity on these parameters are investigated and discussed.

  16. A quantitative approach to recommendations on malaria prophylaxis

    PubMed Central

    Pappaioanou, M.; Lobel, H. O.; Campbell, C. C.

    1988-01-01

    In order to develop recommendations for malaria prophylaxis, a quantitative method is needed to balance the risk of Plasmodium falciparum malaria infections against the toxicity of antimalarial drugs. Using decision analysis, we estimated the expected mortality associated with three alternative regimens of prophylactic drugs for visitors to three areas with different risks of infection with chloroquine-resistant P. falciparum. The model used took into account the risks of malaria and of adverse reactions to antimalarial drugs. Estimates of the parameters used in the analysis were based on observations made on U.S. travellers. Reducing the risk of malaria infection was found to have a far greater impact on lowering the expected mortality than that of increasing the chemoprophylactic efficacy of the drugs used, thereby emphasizing the need for travellers to use anti-mosquito measures in malarious areas. The analytical method described can be used to define optimal malaria prevention strategies. PMID:3048761

  17. Detecting distortion: bridging visual and quantitative reasoning on similarity tasks

    NASA Astrophysics Data System (ADS)

    Cox, Dana C.; Lo, Jane-Jane

    2014-03-01

    This study is focused on identifying and describing the reasoning patterns of middle grade students when examining potentially similar figures. Described here is a framework that includes 11 strategies that students used during clinical interview to differentiate similar and non-similar figures. Two factors were found to influence the strategies students selected: the complexity of the figures being compared and the type of distortion present in nonsimilar pairings. Data from this study support the theory that distortions are identified as a dominant property of figures and that students use the presence and absence of distortion to visually decide if two figures are similar. Furthermore, this study shows that visual reasoning is not as primitive or nonconstructive as represented in earlier literature and supports students who are developing numeric reasoning strategies. This illuminates possible pathways students may take when advancing from using visual and additive reasoning strategies to using multiplicative proportional reasoning on similarity tasks. In particular, distortion detection is a visual activity that enables students to reflect upon and evaluate the validity and accuracy of differentiation and quantify perceived relationships leading to ratio. This study has implications for curriculum developers as well as future research.

  18. Optical aptasensors for quantitative detection of small biomolecules: a review.

    PubMed

    Feng, Chunjing; Dai, Shuang; Wang, Lei

    2014-09-15

    Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.

  19. Detection and Quantification of Bremia lactucae by Spore Trapping and Quantitative PCR.

    PubMed

    Kunjeti, Sridhara G; Anchieta, Amy; Martin, Frank N; Choi, Young-Joon; Thines, Marco; Michelmore, Richard W; Koike, Steven T; Tsuchida, Cayla; Mahaffee, Walt; Subbarao, Krishna V; Klosterman, Steven J

    2016-11-01

    Bremia lactucae is an obligate, oomycete pathogen of lettuce that causes leaf chlorosis and necrosis and adversely affects marketability. The disease has been managed with a combination of host resistance and fungicide applications with success over the years. Fungicide applications are routinely made under the assumption that inoculum is always present during favorable environmental conditions. This approach often leads to fungicide resistance in B. lactucae populations. Detection and quantification of airborne B. lactucae near lettuce crops provides an estimation of the inoculum load, enabling more judicious timing of fungicide applications. We developed a quantitative polymerase chain reaction (qPCR)-based assay using a target sequence in mitochondrial DNA for specific detection of B. lactucae. Validation using amplicon sequencing of DNA from 83 geographically diverse isolates, representing 14 Bremia spp., confirmed that the primers developed for the TaqMan assays are species specific and only amplify templates from B. lactucae. DNA from a single sporangium could be detected at a quantification cycle (Cq) value of 32, and Cq values >35 were considered to be nonspecific. The coefficient of determination (R(2)) for regression between sporangial density derived from flow cytometry and Cq values derived from the qPCR was 0.86. The assay was deployed using spore traps in the Salinas Valley, where nearly half of U.S. lettuce is produced. The deployment of this sensitive B. lactucae-specific assay resulted in the detection of the pathogen during the 2-week lettuce-free period as well as during the cropping season. These results demonstrate that this assay will be useful for quantifying inoculum load in and around the lettuce fields for the purpose of timing fungicide applications based on inoculum load.

  20. Quantitation of faecal Fusobacterium improves faecal immunochemical test in detecting advanced colorectal neoplasia

    PubMed Central

    Kwong, Thomas N Y; Chow, Tai-Cheong; Luk, Arthur K C; Dai, Rudin Z W; Nakatsu, Geicho; Lam, Thomas Y T; Zhang, Lin; Wu, Justin C Y; Chan, Francis K L; Ng, Simon S M; Wong, Martin C S; Ng, Siew C; Wu, William K K; Yu, Jun; Sung, Joseph J Y

    2017-01-01

    Objective There is a need for an improved biomarker for colorectal cancer (CRC) and advanced adenoma. We evaluated faecal microbial markers for clinical use in detecting CRC and advanced adenoma. Design We measured relative abundance of Fusobacterium nucleatum (Fn), Peptostreptococcus anaerobius (Pa) and Parvimonas micra (Pm) by quantitative PCR in 309 subjects, including 104 patients with CRC, 103 patients with advanced adenoma and 102 controls. We evaluated the diagnostic performance of these biomarkers with respect to faecal immunochemical test (FIT), and validated the results in an independent cohort of 181 subjects. Results The abundance was higher for all three individual markers in patients with CRC than controls (p<0.001), and for marker Fn in patients with advanced adenoma than controls (p=0.022). The marker Fn, when combined with FIT, showed superior sensitivity (92.3% vs 73.1%, p<0.001) and area under the receiver-operating characteristic curve (AUC) (0.95 vs 0.86, p<0.001) than stand-alone FIT in detecting CRC in the same patient cohort. This combined test also increased the sensitivity (38.6% vs 15.5%, p<0.001) and AUC (0.65 vs 0.57, p=0.007) for detecting advanced adenoma. The performance gain for both CRC and advanced adenoma was confirmed in the validation cohort (p=0.0014 and p=0.031, respectively). Conclusions This study identified marker Fn as a valuable marker to improve diagnostic performance of FIT, providing a complementary role to detect lesions missed by FIT alone. This simple approach may improve the clinical utility of the current FIT, and takes one step further towards a non-invasive, potentially more accurate and affordable diagnosis of advanced colorectal neoplasia. PMID:27797940

  1. A new quantitative in vitro for the detection of latex-specific IgE antibodies.

    PubMed

    Moussadeh, M; Hamedi, N; Alem, N; Alem, M

    1999-12-01

    Immediate-type hypersensitivity to latex allergens has resulted in anaphylactic shock and death in numerous reported cases. The allergenic proteins of latex are contained within the natural rubber extract of Hevea brasiliensis and are eluted into the final product during the manufacturing process. The quantity and types of latex allergens found in different latex products depends on the manufacturing process. Not all of these allergens are available for use in the latex prick skin test, and as a result, such tests may not be conclusive. Furthermore, application of such allergens to the skin of undiagnosed hypersensitive individuals may have harmful effects on their health. Therefore, it is important to be able to utilize in vitro methods, which reliably identify latex allergy without placing hypersensitive individuals at risk. We have developed a relatively simple and new enzyme immuno-assay (EIA) method for the detection of latex allergy. This in vitro method is quantitative and allows for the classification of allergy to latex in a short time. In comparative studies, ninety-nine serum specimens with documented clinical history of latex allergy were tested by this method, and the results paralleled those of the skin prick test performed by an independent group. The data showed that the specificity and sensitivity of our assay approaches 97.5% and 100%, respectively. We conclude that, by using a simple assay, the detection of specific IgE to latex proteins may be valuable for screening individuals and for the diagnosis of allergy to latex.

  2. Rapid Detection and Quantitation of BRAF Mutations in Hairy Cell Leukemia Using a Sensitive Pyrosequencing Assay

    PubMed Central

    Verma, Shalini; Greaves, Wesley O.; Ravandi, Farhad; Reddy, Neelima; Bueso-Ramos, Carlos E.; O’Brien, Susan; Thomas, Deborah A.; Kantarjian, Hagop; Medeiros, L. Jeffrey; Luthra, Rajyalakshmi; Patel, Keyur P.

    2017-01-01

    BRAF proto-oncogene is an important mediator of cell proliferation and survival signals via the RAS-RAF-MEK-ERK signaling pathway. BRAF p.V600E mutation was recently described as a molecular marker of hairy cell leukemia (HCL). We developed and validated a pyrosequencing-based approach that covers BRAF mutational hotspots in exons 11 (codon 468) and 15 (codons 595 to 600) and detects BRAF mutations at an analytical sensitivity of 5%. We screened 16 unenriched archived bone marrow aspirate samples from patients with diagnosis of HCL (n=12) and hairy cell leukemia-variant (HCL-v) (n=4) using pyrosequencing. BRAF p.V600E mutation was present in all HCL cases and absent in all HCL-v. Our data support the recent finding that BRAF p.V600E mutation is universally present in HCL. Moreover, our pyrosequencing based assay provides a convenient, rapid, sensitive and quantitative tool for the detection of BRAF p.V600E mutations in HCL in clinical setting. PMID:22706871

  3. A quantitative confidence signal detection model: 1. Fitting psychometric functions

    PubMed Central

    Yi, Yongwoo

    2016-01-01

    Perceptual thresholds are commonly assayed in the laboratory and clinic. When precision and accuracy are required, thresholds are quantified by fitting a psychometric function to forced-choice data. The primary shortcoming of this approach is that it typically requires 100 trials or more to yield accurate (i.e., small bias) and precise (i.e., small variance) psychometric parameter estimates. We show that confidence probability judgments combined with a model of confidence can yield psychometric parameter estimates that are markedly more precise and/or markedly more efficient than conventional methods. Specifically, both human data and simulations show that including confidence probability judgments for just 20 trials can yield psychometric parameter estimates that match the precision of those obtained from 100 trials using conventional analyses. Such an efficiency advantage would be especially beneficial for tasks (e.g., taste, smell, and vestibular assays) that require more than a few seconds for each trial, but this potential benefit could accrue for many other tasks. PMID:26763777

  4. A quantitative confidence signal detection model: 1. Fitting psychometric functions.

    PubMed

    Yi, Yongwoo; Merfeld, Daniel M

    2016-04-01

    Perceptual thresholds are commonly assayed in the laboratory and clinic. When precision and accuracy are required, thresholds are quantified by fitting a psychometric function to forced-choice data. The primary shortcoming of this approach is that it typically requires 100 trials or more to yield accurate (i.e., small bias) and precise (i.e., small variance) psychometric parameter estimates. We show that confidence probability judgments combined with a model of confidence can yield psychometric parameter estimates that are markedly more precise and/or markedly more efficient than conventional methods. Specifically, both human data and simulations show that including confidence probability judgments for just 20 trials can yield psychometric parameter estimates that match the precision of those obtained from 100 trials using conventional analyses. Such an efficiency advantage would be especially beneficial for tasks (e.g., taste, smell, and vestibular assays) that require more than a few seconds for each trial, but this potential benefit could accrue for many other tasks. Copyright © 2016 the American Physiological Society.

  5. Detection and quantitation of Agrotis baculoviruses in mixed infections.

    PubMed

    Wennmann, Jörg T; Jehle, Johannes A

    2014-03-01

    At least four distinct baculoviruses, namely the Agrotis segetum nucleopolyhedrovirus A (AgseNPV-A), the A. segetum nucleopolyhedrovirus B (AgseNPV-B), the Agrotis ipsilon nucleopolyhedrovirus (AgipNPV) and the A. segetum granulovirus (AgseGV) have been isolated from larval stages (cutworms) of the species A. segetum and A. ipsilon (Lepidoptera: Noctuidae), which are serious soil pests in agriculture. Cutworms can become infected by at least one of these four baculoviruses and also co-infections of A. segetum larvae with AgseNPV-B and AgseGV are observed under laboratory conditions. Because of their adaption to common hosts and the occurrence in mixed infections, these viruses have a considerable potential as biological control agents of cutworms and are suitable objects to decipher the co-evolution and population dynamics of baculoviruses in mixed infections. However, to facilitate studies on these viruses a reliable tool for detection and identification is essential. A method based on highly specific oligonucleotide primers for multiplex polymerase chain reaction (PCR) that led to the amplification of discriminating fragments of the polyhedrin (polh) and granulin (gran) gene of AgseNPV-A, AgseNPV-B, AgipNPV and AgseGV, was established. Furthermore, the AgseNPV-B and AgseGV specific pairs of primers were applied in real-time PCR (qPCR) for AgseNPV-B/AgseGV ratio determination in samples of mixed infections. It is demonstrated further that for quantifying NPVs and GVs in mixed infections, the method of occlusion body isolation is most crucial and significantly influences the results. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Agreement experiments: a method for quantitatively testing new medical image display approaches

    NASA Astrophysics Data System (ADS)

    Johnston, Richard E.; Yankaskas, Bonnie C.; Perry, John R.; Pizer, Stephen M.; Delany, David J.; Parker, L. A.

    1990-08-01

    New medical image display devices or processes are commonly evaluated by anecdotal reports or subjective evaluations which are informative and relatively easy to acquire but do not provide quantitative nieasures. On the other hand, experinients eniploying ROC analysis, yield quantitative measurements but are very laborious and demand pathological proof of outcome. We have designed and are employing a new approach, which we have termed "agreement experiments," to quantitatively test the equivalence of observer performance on two systems. This was specifically developed to test whether a radiologist using a new display technique, which has some clear advantages over the standard technique, will detect and interpret diagnostic signs as he would with the standard display technique. Agreement experiments use checklists and confidence ratings to measure how well two radiologists agree on the presence of diagnostic signs when both view images on the standard display. This yields a baseline measure of agreement. Agreement measurements are then obtained when the two radiologists view cases using the new display, or display method, compared to the standard technique. If the levels of agreement when one reads from the new and one reads from the standard display are not statistically different from the baseline measures of agreement, we conclude the two systems are equivalent in conveying diagnostic signs. We will report on an experiment using this test. The experiment compares the agreement of radiological findings for chest CT studies viewed on the conventional multiformat film/lightbox to agreement of radiological findings from chest CT images presented on a multiple screen video system. The study consists of 80 chest CT studies. The results were an 86% to 81% agreement between the two viewing modalities which fell within our criteria of showing agreement.

  7. Furfural as a marker of cellulose degradation. A quantitative approach

    NASA Astrophysics Data System (ADS)

    Łojewski, Tomasz; Sawoszczuk, Tomasz; Łagan, Janusz Marek; Zięba, Katarzyna; Barański, Andrzej; Łojewska, Joanna

    2010-09-01

    Non-destructive methods of sampling during the physicochemical studies of historical objects such as old books and manuscripts seem to be an obvious choice. Since furfural has been shown to be one of the most abundant gaseous products of cellulose degradation, it can be considered as a convenient marker of degradation progress. The number of quantitative data concerning correlations between the emission of furfural and physicochemical and mechanical properties of paper is rather scarce in the literature. In the present studies, a model paper containing more than 99% of cellulose was aged inside closed vials at 90°C. Gaseous products of paper degradation were measured using sorption tubes filled with Tenax TA sorbent and GC-MS. The method has proved to be sufficiently sensitive for measuring furfural emission not only in accelerated degradation at 90°C but also during natural ageing of paper at room temperature even in relatively short time intervals of 2-28 days. The correlations between furfural emission and polymerization degree, pH, color, tear index, number of double folds and breaking length have been statistically confirmed at confidence level α=0.001. Basing on them it was possible to estimate the number of broken glycosidic bonds per one molecule of furfural formed during degradation—we found a value equal to 9.2.

  8. Biological evolution of replicator systems: towards a quantitative approach.

    PubMed

    Martin, Osmel; Horvath, J E

    2013-04-01

    The aim of this work is to study the features of a simple replicator chemical model of the relation between kinetic stability and entropy production under the action of external perturbations. We quantitatively explore the different paths leading to evolution in a toy model where two independent replicators compete for the same substrate. To do that, the same scenario described originally by Pross (J Phys Org Chem 17:312-316, 2004) is revised and new criteria to define the kinetic stability are proposed. Our results suggest that fast replicator populations are continually favored by the effects of strong stochastic environmental fluctuations capable to determine the global population, the former assumed to be the only acting evolution force. We demonstrate that the process is continually driven by strong perturbations only, and that population crashes may be useful proxies for these catastrophic environmental fluctuations. As expected, such behavior is particularly enhanced under very large scale perturbations, suggesting a likely dynamical footprint in the recovery patterns of new species after mass extinction events in the Earth's geological past. Furthermore, the hypothesis that natural selection always favors the faster processes may give theoretical support to different studies that claim the applicability of maximum principles like the Maximum Metabolic Flux (MMF) or Maximum Entropy Productions Principle (MEPP), seen as the main goal of biological evolution.

  9. Biological Evolution of Replicator Systems: Towards a Quantitative Approach

    NASA Astrophysics Data System (ADS)

    Martin, Osmel; Horvath, J. E.

    2013-04-01

    The aim of this work is to study the features of a simple replicator chemical model of the relation between kinetic stability and entropy production under the action of external perturbations. We quantitatively explore the different paths leading to evolution in a toy model where two independent replicators compete for the same substrate. To do that, the same scenario described originally by Pross (J Phys Org Chem 17:312-316, 2004) is revised and new criteria to define the kinetic stability are proposed. Our results suggest that fast replicator populations are continually favored by the effects of strong stochastic environmental fluctuations capable to determine the global population, the former assumed to be the only acting evolution force. We demonstrate that the process is continually driven by strong perturbations only, and that population crashes may be useful proxies for these catastrophic environmental fluctuations. As expected, such behavior is particularly enhanced under very large scale perturbations, suggesting a likely dynamical footprint in the recovery patterns of new species after mass extinction events in the Earth's geological past. Furthermore, the hypothesis that natural selection always favors the faster processes may give theoretical support to different studies that claim the applicability of maximum principles like the Maximum Metabolic Flux (MMF) or Maximum Entropy Productions Principle (MEPP), seen as the main goal of biological evolution.

  10. Measuring Filament Orientation: A New Quantitative, Local Approach

    NASA Astrophysics Data System (ADS)

    Green, C.-E.; Dawson, J. R.; Cunningham, M. R.; Jones, P. A.; Novak, G.; Fissel, L. M.

    2017-09-01

    The relative orientation between filamentary structures in molecular clouds and the ambient magnetic field provides insight into filament formation and stability. To calculate the relative orientation, a measurement of filament orientation is first required. We propose a new method to calculate the orientation of the one-pixel-wide filament skeleton that is output by filament identification algorithms such as filfinder. We derive the local filament orientation from the direction of the intensity gradient in the skeleton image using the Sobel filter and a few simple post-processing steps. We call this the “Sobel-gradient method.” The resulting filament orientation map can be compared quantitatively on a local scale with the magnetic field orientation map to then find the relative orientation of the filament with respect to the magnetic field at each point along the filament. It can also be used for constructing radial profiles for filament width fitting. The proposed method facilitates automation in analyses of filament skeletons, which is imperative in this era of “big data.”

  11. Vertebral scalloping in neurofibromatosis type 1: a quantitative approach

    PubMed Central

    Kwok, Edmund S.H.; Sawatzky, Bonita; Birch, Patricia; Friedman, Jan M.; Tredwell, Stephen J.

    2002-01-01

    Objective To investigate quantitative differences in vertebral scalloping between children who have scoliosis with and without neurofibromatosis type 1 (NF1). Design A retrospective study. Setting A university-affiliated children’s hospital. Patients Twenty-seven children with scoliosis, 13 of whom had NF1 and 14 of whom did not. Method Existing radiographs of the lumbar vertebrae were used to measure and compare the degree of vertebral scalloping. Main outcome measures The distribution of posterior scalloping ratios in the 2 groups and the most extreme ratio in each subject in each group were compared. Results Scalloping ratios from the children with NF1 were not normally distributed: 31% had ratios greater than 1.20. Scalloping ratios from the non-NF1 children were normally distributed, with a mean ratio (and standard deviation) of 1.13 (0.03). The distribution between the 2 groups was significantly different (p < 0.05). Conclusions In children who have scoliosis but no NF1 there was a range of mild scalloping whereas those with NF1 has severe scalloping. Further studies are needed to determine the possible role of vertebral scalloping in scoliosis severity and progression in children who have NF1. PMID:12067169

  12. Calculation of measurement uncertainty in quantitative analysis of genetically modified organisms using intermediate precision--a practical approach.

    PubMed

    Zel, Jana; Gruden, Kristina; Cankar, Katarina; Stebih, Dejan; Blejec, Andrej

    2007-01-01

    Quantitative characterization of nucleic acids is becoming a frequently used method in routine analysis of biological samples, one use being the detection of genetically modified organisms (GMOs). Measurement uncertainty is an important factor to be considered in these analyses, especially where precise thresholds are set in regulations. Intermediate precision, defined as a measure between repeatability and reproducibility, is a parameter describing the real situation in laboratories dealing with quantitative aspects of molecular biology methods. In this paper, we describe the top-down approach to calculating measurement uncertainty, using intermediate precision, in routine GMO testing of food and feed samples. We illustrate its practicability in defining compliance of results with regulations. The method described is also applicable to other molecular methods for a variety of laboratory diagnostics where quantitative characterization of nucleic acids is needed.

  13. A Discriminative Approach to EEG Seizure Detection

    PubMed Central

    Johnson, Ashley N.; Sow, Daby; Biem, Alain

    2011-01-01

    Seizures are abnormal sudden discharges in the brain with signatures represented in electroencephalograms (EEG). The efficacy of the application of speech processing techniques to discriminate between seizure and non-seizure states in EEGs is reported. The approach accounts for the challenges of unbalanced datasets (seizure and non-seizure), while also showing a system capable of real-time seizure detection. The Minimum Classification Error (MCE) algorithm, which is a discriminative learning algorithm with wide-use in speech processing, is applied and compared with conventional classification techniques that have already been applied to the discrimination between seizure and non-seizure states in the literature. The system is evaluated on 22 pediatric patients multi-channel EEG recordings. Experimental results show that the application of speech processing techniques and MCE compare favorably with conventional classification techniques in terms of classification performance, while requiring less computational overhead. The results strongly suggests the possibility of deploying the designed system at the bedside. PMID:22195192

  14. Quantitative detection and differentiation of free-living amoeba species using SYBR green-based real-time PCR melting curve analysis.

    PubMed

    Behets, Jonas; Declerck, Priscilla; Delaedt, Yasmine; Verelst, Lieve; Ollevier, Frans

    2006-12-01

    Real-time polymerase chain reaction melting curve analysis (MCA) allows differentiation of several free-living amoebae species. Distinctive characteristics were found for Naegleria fowleri, N. lovaniensis, N. australiensis, N. gruberi, Hartmanella vermiformis, and Willaertia magna. Species specificity of the amplicons was confirmed using agarose gel electrophoresis and sequence-based approaches. Amplification efficiency ranged from 91% to 98%, indicating the quantitative potential of the assay. This MCA approach can be used for quantitative detection of free-living amoebae after cultivation but also as a culture-independent detection method.

  15. Introduction to Focus Issue: Quantitative Approaches to Genetic Networks

    NASA Astrophysics Data System (ADS)

    Albert, Réka; Collins, James J.; Glass, Leon

    2013-06-01

    All cells of living organisms contain similar genetic instructions encoded in the organism's DNA. In any particular cell, the control of the expression of each different gene is regulated, in part, by binding of molecular complexes to specific regions of the DNA. The molecular complexes are composed of protein molecules, called transcription factors, combined with various other molecules such as hormones and drugs. Since transcription factors are coded by genes, cellular function is partially determined by genetic networks. Recent research is making large strides to understand both the structure and the function of these networks. Further, the emerging discipline of synthetic biology is engineering novel gene circuits with specific dynamic properties to advance both basic science and potential practical applications. Although there is not yet a universally accepted mathematical framework for studying the properties of genetic networks, the strong analogies between the activation and inhibition of gene expression and electric circuits suggest frameworks based on logical switching circuits. This focus issue provides a selection of papers reflecting current research directions in the quantitative analysis of genetic networks. The work extends from molecular models for the binding of proteins, to realistic detailed models of cellular metabolism. Between these extremes are simplified models in which genetic dynamics are modeled using classical methods of systems engineering, Boolean switching networks, differential equations that are continuous analogues of Boolean switching networks, and differential equations in which control is based on power law functions. The mathematical techniques are applied to study: (i) naturally occurring gene networks in living organisms including: cyanobacteria, Mycoplasma genitalium, fruit flies, immune cells in mammals; (ii) synthetic gene circuits in Escherichia coli and yeast; and (iii) electronic circuits modeling genetic networks

  16. Introduction to focus issue: quantitative approaches to genetic networks.

    PubMed

    Albert, Réka; Collins, James J; Glass, Leon

    2013-06-01

    All cells of living organisms contain similar genetic instructions encoded in the organism's DNA. In any particular cell, the control of the expression of each different gene is regulated, in part, by binding of molecular complexes to specific regions of the DNA. The molecular complexes are composed of protein molecules, called transcription factors, combined with various other molecules such as hormones and drugs. Since transcription factors are coded by genes, cellular function is partially determined by genetic networks. Recent research is making large strides to understand both the structure and the function of these networks. Further, the emerging discipline of synthetic biology is engineering novel gene circuits with specific dynamic properties to advance both basic science and potential practical applications. Although there is not yet a universally accepted mathematical framework for studying the properties of genetic networks, the strong analogies between the activation and inhibition of gene expression and electric circuits suggest frameworks based on logical switching circuits. This focus issue provides a selection of papers reflecting current research directions in the quantitative analysis of genetic networks. The work extends from molecular models for the binding of proteins, to realistic detailed models of cellular metabolism. Between these extremes are simplified models in which genetic dynamics are modeled using classical methods of systems engineering, Boolean switching networks, differential equations that are continuous analogues of Boolean switching networks, and differential equations in which control is based on power law functions. The mathematical techniques are applied to study: (i) naturally occurring gene networks in living organisms including: cyanobacteria, Mycoplasma genitalium, fruit flies, immune cells in mammals; (ii) synthetic gene circuits in Escherichia coli and yeast; and (iii) electronic circuits modeling genetic networks

  17. Ecohydrology of agroecosystems: quantitative approaches towards sustainable irrigation.

    PubMed

    Vico, Giulia; Porporato, Amilcare

    2015-02-01

    Irrigation represents one of the main strategies to enhance and stabilize agricultural productivity, by mitigating the effects of rainfall vagaries. In the face of the projected growth in population and in biofuel demands, as well as shifts in climate and dietary habits, a more sustainable management of water resources in agroecosystems is needed. The field of ecohydrology, traditionally focusing on natural ecosystems, has the potential to offer the necessary quantitative tools to assess and compare agricultural enterprises across climates, soil types, crops, and irrigation strategies, accounting for the unpredictability of the hydro-climatic forcing. Here, agricultural sustainability and productivity are assessed with reference to water productivity (defined as the ratio between yield and total supplied water), yields, water requirements, and their variability-a crucial element for food security and resource allocation planning. These synthetic indicators are quantified by means of a probabilistic description of the soil water balance and crop development. The model results allow the interpretation of patterns of water productivity observed in Zea mays (maize) and Triticum aestivum (wheat), grown under a variety of soils, climates, and irrigation strategies. Employing the same modeling framework, the impact of rainfall pattern and irrigation strategy on yield and water requirements is further explored. The obtained standard deviations of yield and water requirements suggest the existence of a nonlinear tradeoff between yield stabilization and variability of water requirements, which in turn is strongly impacted by irrigation strategy. Moreover, intermediate rainfall amounts are associated to the highest variability in yields and irrigation requirements, although allowing the maximum water productivity. The existence of these tradeoffs between productivity, reliability, and sustainability poses a problem for water management, in particular in mesic climates.

  18. Application of quantitative signal detection in the Dutch spontaneous reporting system for adverse drug reactions.

    PubMed

    van Puijenbroek, Eugène; Diemont, Willem; van Grootheest, Kees

    2003-01-01

    The primary aim of spontaneous reporting systems (SRSs) is the timely detection of unknown adverse drug reactions (ADRs), or signal detection. Generally this is carried out by a systematic manual review of every report sent to an SRS. Statistical analysis of the data sets of an SRS, or quantitative signal detection, can provide additional information concerning a possible relationship between a drug and an ADR. We describe the role of quantitative signal detection and the way it is applied at the Netherlands Pharmacovigilance Centre Lareb. Results of the statistical analysis are implemented in the traditional case-by-case analysis. In addition, for data-mining purposes, a list of associations of ADRs and suspected drugs that are disproportionally present in the database is periodically generated. Finally, quantitative signal generation can be used to study more complex relationships, such as drug-drug interactions and syndromes. The results of quantitative signal detection should be considered as an additional source of information, complementary to the traditional analysis. Techniques for the detection of drug interactions and syndromes offer a new challenge for pharmacovigilance in the near future.

  19. Quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories.

    PubMed

    Wu, C-H; Kong, L; Bialecka-Fornal, M; Park, S; Thompson, A L; Kulkarni, G; Conway, S J; Newman, D K

    2015-07-01

    external diplopterol standards. These new quantitative approaches permit meaningful comparisons between studies, allowing more accurate hopanoid pattern detection in both laboratory and environmental samples.

  20. Quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories

    PubMed Central

    Wu, C-H; Kong, L; Bialecka-Fornal, M; Park, S; Thompson, A L; Kulkarni, G; Conway, S J; Newman, D K

    2015-01-01

    external diplopterol standards. These new quantitative approaches permit meaningful comparisons between studies, allowing more accurate hopanoid pattern detection in both laboratory and environmental samples. PMID:25865768

  1. A quantitative neural network approach to understanding aging phenotypes

    PubMed Central

    Ash, Jessica A.; Rapp, Peter R.

    2015-01-01

    Basic research on neurocognitive aging has traditionally adopted a reductionist approach in the search for the basis of cognitive preservation versus decline. However, increasing evidence suggests that a network level understanding of the brain can provide additional novel insight into the structural and functional organization from which complex behavior and dysfunction emerge. Using graph theory as a mathematical framework to characterize neural networks, recent data suggest that alterations in structural and functional networks may contribute to individual differences in cognitive phenotypes in advanced aging. This paper reviews literature that defines network changes in healthy and pathological aging phenotypes, while highlighting the substantial overlap in key features and patterns observed across aging phenotypes. Consistent with current efforts in this area, here we outline one analytic strategy that attempts to quantify graph theory metrics more precisely, with the goal of improving diagnostic sensitivity and predictive accuracy for differential trajectories in neurocognitive aging. Ultimately, such an approach may yield useful measures for gauging the efficacy of potential preventative interventions and disease modifying treatments early in the course of aging. PMID:24548925

  2. Evaluation of urine for Leishmania infantum DNA detection by real-time quantitative PCR.

    PubMed

    Pessoa-E-Silva, Rômulo; Mendonça Trajano-Silva, Lays Adrianne; Lopes da Silva, Maria Almerice; da Cunha Gonçalves-de-Albuquerque, Suênia; de Goes, Tayná Correia; Silva de Morais, Rayana Carla; Lopes de Melo, Fábio; de Paiva-Cavalcanti, Milena

    2016-12-01

    The availability of some sorts of biological samples which require noninvasive collection methods has led to an even greater interest in applying molecular biology on visceral leishmaniasis (VL) diagnosis, since these samples increase the safety and comfort of both patients and health professionals. In this context, this work aimed to evaluate the suitability of the urine as a specimen for Leishmania infantum kinetoplast DNA detection by real-time quantitative PCR (qPCR). Subsequent to the reproducibility analysis, the detection limit of the qPCR assay was set at 5fg (~0.025 parasites) per μL of urine. From the comparative analysis performed with a set of diagnostic criteria (serological and molecular reference tests), concordance value of 96.08% was obtained (VL-suspected and HIV/AIDS patients, n=51) (P>0.05). Kappa coefficient (95% CI) indicated a good agreement between the test and the set of diagnostic criteria (k=0.778±0.151). The detection of Leishmania DNA in urine by qPCR was possible in untreated individuals, and in those with or without suggestive renal impairment. Fast depletion of the parasite's DNA in urine after treatment (from one dose of meglumine antimoniate) was suggested by negative qPCR results, thus indicating it as a potential alternative specimen to follow up the efficacy of therapeutic approaches. Even when evaluated in a clinically heterogeneous set of patients, the urine showed good prospect as sample for VL diagnosis by qPCR, also indicating a good negative predictive value for untreated suspected patients. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Liquid crystal-based sensors for selective and quantitative detection of nitrogen dioxide

    PubMed Central

    Sen, Avijit; Kupcho, Kurt A.; Grinwald, Bart A.; VanTreeck, Heidi J.; Acharya, Bharat R.

    2013-01-01

    A highly sensitive nitrogen dioxide (NO2) sensor based on orientational transition of a thin film of liquid crystal (LC) supported on a gold surface is reported. Transport of NO2 molecules through the LC film to the LC-gold interface induces an orientation transition in the LC film. The dynamic behavior of the sensor response exhibits a concentration-dependent response rate that is employed to generate an algorithm for quantitative determination of unknown concentrations. Sensitive, selective and reversible detection with minimal effects of environmental fluctuations suggest that these sensors can be used for quantitative NO2 detection for a number of applications. PMID:23526230

  4. Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem.

    PubMed

    Gurcan, Metin N; Tomaszewski, John; Overton, James A; Doyle, Scott; Ruttenberg, Alan; Smith, Barry

    2017-02-01

    Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology - QHIO. We apply QHIO to breast cancer hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts.

  5. Quantitative analysis of gene expression by reverse transcription polymerase chain reaction and capillary electrophoresis with laser-induced fluorescence detection.

    PubMed

    Richards, Mark P; Poch, Stephen M

    2002-05-01

    There has been a dramatic expansion of DNA sequence information compiled over the past several years for a variety of eukaryotic and prokaryotic genomes. Accompanying this increase in knowledge of genomic structure and organization has been a growing interest in studying the function of individual genes including regulation of their expression. A number of methods such as Northern blotting, ribonuclease protection assay, and hybridization arrays have been developed to analyze gene expression at the transcriptional (mRNA) level. Although quantitative estimates of mRNA transcripts can be obtained from each of these methods, oftentimes they lack sufficient sensitivity or the methodology is too costly or too labor-intensive to be applied to the analysis of a large number of samples. The most sensitive method for analyzing gene expression at the mRNA level involves the combination of reverse transcription and polymerase chain reaction (RT-PCR). However, in order to provide accurate quantitative estimates of gene expression, a rapid and efficient method is required for separation and detection of the double-stranded DNA (dsDNA) products of RT-PCR. Recent advances in capillary electrophoresis with laser-induced fluorescence detection (CE/LIF) have made this method suitable for the automated analysis of large numbers of RT-PCR samples. An overview of the application of CE/LIF to quantitative analysis of gene expression by RT-PCR is presented along with selected protocols and examples. Both relative-quantitative (RQ) and quantitative-competitive (QC) approaches to RT-PCR are discussed in conjunction with the use of CE/LIF for rapid and accurate quantitative analysis of PCR products.

  6. A quantitative approach to nonlinear IC process design rule scaling

    NASA Astrophysics Data System (ADS)

    Gold, Spencer Montgomery

    As minimum dimensions in integrated circuit technologies are reduced beyond 0.1 m m, linear process scaling becomes more difficult and costly. Exponentially rising manufacturing facility and process scaling costs can be better managed by performing nonlinear process shrinks. Nonlinear scaling allows the horizontal design rules to be reduced by different factors according to their ability to provide area and performance improvement in a cost effective manner. This thesis describes a methodology and CAD tools for use in selecting nonlinear design rule reduction ratios that make effective tradeoffs between die cost and performance. The cost effectiveness of nonlinear scaling is demonstrated for a complementary GaAs (CGaAsTM) process. CGaAs is a young technology with coarse design rules that would benefit significantly from a nonlinear shrink. The cost/benefit analysis for scaling the design rules is based on a process-independent optimizing SRAM compiler which was developed as part of this work. The methodology for nonlinear scaling includes identifying the rules which have the greatest impact on circuit area and analyzing the area and performance improvements as these rules are scaled through a range of practical scale factors. Benefit data (product of power and delay improvement ratios) is then combined with die cost estimates at each step to yield the cost/benefit ratio, a quantitative metric for design rule reduction. The slopes and inflection points of cost/benefit vs. scale factor plots guide process engineers in selecting reduction ratios for the various design rules. This procedure should be repeated, using the results of one pass as the starting point for the next. The cost/benefit analysis methodology compares embedded static RAMs that are generated by the PUMA process-independent SRAM compiler. This compiler, which is based on Duet's MasterPortTM layout compactor, can create optimized SRAM cell libraries for any complementary technology. It is capable of

  7. A quantitative real-time approach for discriminating apoptosis and necrosis

    PubMed Central

    Lekshmi, Asha; Varadarajan, Shankara Narayanan; Lupitha, Santhik Subhasingh; Indira, Deepa; Mathew, Krupa Ann; Chandrasekharan Nair, Aneesh; Nair, Mydhily; Prasad, Tilak; Sekar, Hari; Gopalakrishnan, Anurup Kochucherukkan; Murali, Abitha; Santhoshkumar, Thankayyan Retnabai

    2017-01-01

    Apoptosis and necrosis are the two major forms of cell death mechanisms. Both forms of cell death are involved in several physiological and pathological conditions and also in the elimination of cancer cells following successful chemotherapy. Large number of cellular and biochemical assays have evolved to determine apoptosis or necrosis for qualitative and quantitative purposes. A closer analysis of the assays and their performance reveal the difficulty in using any of these methods as a confirmatory approach, owing to the secondary induction of necrosis in apoptotic cells. This highlights the essential requirement of an approach with a real-time analysis capability for discriminating the two forms of cell death. This paper describes a sensitive live cell-based method for distinguishing apoptosis and necrosis at single-cell level. The method uses cancer cells stably expressing genetically encoded FRET-based active caspase detection probe and DsRed fluorescent protein targeted to mitochondria. Caspase activation is visualized by loss of FRET upon cleavage of the FRET probe, while retention of mitochondrial fluorescence and loss of FRET probe before its cleavage confirms necrosis. The absence of cleavage as well as the retention of mitochondrial fluorescence indicates live cells. The method described here forms an extremely sensitive tool to visualize and quantify apoptosis and necrosis, which is adaptable for diverse microscopic, flow cytometric techniques and high-throughput imaging platforms with potential application in diverse areas of cell biology and oncology drug screening. PMID:28179996

  8. Quaternary coastal evolution of Oman (Arabian Peninsula) - a quantitative approach

    NASA Astrophysics Data System (ADS)

    Hoffmann, G.; Rupprechter, M.; Roepert, A.; Quraishi, K. Al; Balushi, N. Al; Grützner, C.; Reicherter, K.

    2012-04-01

    The paper reviews the Quaternary coastal evolution of Oman. Emphasise is put on quantifying the different forcing factors. The plate tectonic setting, the Quaternary climate evolution, the sea-level history and the impact of natural hazards are identified as key factors of coastal evolution. The Arabian Plate is characterized by a northward movement forming a continent-continent collision zone in the west and the Makran Subduction Zone in the east. As a result differential land movement is observable in Oman. The Quaternary climate evolution is well understood. Besides other proxies notably spelothems and aeolian deposits allow to draw a consistent picture. It is understood that changes in the position of the intertropical convergence zone result in intensity-changes of the summer monsoon. These changes are related to global atmospheric circulation patterns. Data on the sea-level history are sparse; despite general assumptions of a sea-level lowstand, correlating with the last glacial maximum, resulting in terrestrial conditions within the Arabian Gulf. Furthermore, a mid-Holocene sea level highstand in the range of +2m is documented in several locations. The coastlines of Oman are affected by tsunami and hurricanes. However, almost no instrumental or historical data on the impact of such natural hazards are available due to the isolation of the country in the past. Several Quaternary deposits have been investigated in a reconnaissance survey. There is sound geological evidence for a tsunami to have affected the coastline in 1945, with the possibility of older tsunami events being also recorded in the geological record. There is strong evidence of differential land movement along the coastline; locally indicated by marine terraces in elevations of up to 400m (Rupprechter at al. 2012). By quantifying the differential land movement for numerous sites, the sea-level history will be revealed. Ultimately the data will be utilized to form the base of a modeling approach

  9. A quantitative approach to identifying predators from nest remains

    USGS Publications Warehouse

    Anthony, R. Michael; Grand, J.B.; Fondell, T.F.; Manly, B.F.

    2004-01-01

    Nesting success of Dusky Canada Geese (Branta canadensis occidentalis) has declined greatly since a major earthquake affected southern Alaska in 1964. To identify nest predators, we collected predation data at goose nests and photographs of predators at natural nests containing artificial eggs in 1997-2000. To document feeding behavior by nest predators, we compiled the evidence from destroyed nests with known predators on our study site and from previous studies. We constructed a profile for each predator group and compared the evidence from 895 nests with unknown predators to our predator profiles using mixture-model analysis. This analysis indicated that 72% of destroyed nests were depredated by Bald Eagles and 13% by brown bears, and also yielded the probability that each nest was correctly assigned to a predator group based on model fit. Model testing using simulations indicated that the proportion estimated for eagle predation was unbiased and the proportion for bear predation was slightly overestimated. This approach may have application whenever there are adequate data on nests destroyed by known predators and predators exhibit different feeding behavior at nests.

  10. Conspicuous Strategies in Teaching Expressive Writing: A Quantitative Study Comparing Two Approaches to Process Writing

    ERIC Educational Resources Information Center

    Fontenot, Jennifer; Carney, Karen J.; Hansen, Kay

    2015-01-01

    A process-writing approach (BW) with novel concepts was developed by the authors to teach writing to elementary-level students. They believed the BW approach was effective but was particularly effective for special-needs students. Consequently, they decided to quantitatively test these assertions. Instead of testing students taught using the BW…

  11. Force Design Analysis of the Army Aeromedical Evacuation Company: A Quantitative Approach

    DTIC Science & Technology

    2012-01-01

    Army materiel solutions. Keywords force design, capability assessment, mixed - methods , aeromedical evacuation 1. Introduction 1.1. Background In this...incorporates primary data in a unique mixed - methods (quantitative and qualita- tive) approach to force design. Mixed methods add value in that both... mixed - methods approach to evaluating MEDEVAC DOTMLPF considerations provides a baseline for assessing future Army materiel solutions. Acknowledgment

  12. Application of Person-Centered Approaches to Critical Quantitative Research: Exploring Inequities in College Financing Strategies

    ERIC Educational Resources Information Center

    Malcom-Piqueux, Lindsey

    2014-01-01

    This chapter discusses the utility of person-centered approaches to critical quantitative researchers. These techniques, which identify groups of individuals who share similar attributes, experiences, or outcomes, are contrasted with more commonly used variable-centered approaches. An illustrative example of a latent class analysis of the college…

  13. A Hybrid Approach for Fault Detection in Autonomous Physical Agents

    DTIC Science & Technology

    2014-05-01

    A Hybrid Approach for Fault Detection in Autonomous Physical Agents Eliahu Khalastchi, Meir Kalech, Lior Rokach Information Systems Engineering...Experimentation Keywords Fault detection, Model-Based Diagnosis , Robotics, UAV. 1. INTRODUCTION Autonomous physical agents such as Unmanned Vehicles (UVs...then a crash. To continue operate autonomously, the agent must have an accurate fault detection mechanism. Upon fault detection a diagnosis process

  14. A quantitative epigenetic approach for the assessment of cigarette consumption

    PubMed Central

    Philibert, Robert; Hollenbeck, Nancy; Andersen, Eleanor; Osborn, Terry; Gerrard, Meg; Gibbons, Frederick X.; Wang, Kai

    2015-01-01

    Smoking is the largest preventable cause of morbidity and mortality in the world. Despite the development of numerous preventive and treatment interventions, the rate of daily smoking in the United States is still approximately 22%. Effective psychosocial interventions and pharmacologic agents exist for the prevention and treatment of smoking. Unfortunately, both approaches are hindered by our inability to accurately quantify amount of cigarette consumption from the point of initial experimentation to the point of total dependency. Recently, we and others have demonstrated that smoking is associated with genome-wide changes in DNA methylation. However, whether this advance in basic science can be employed as a reliable assay that is useful for clinical diagnosis and treatment has not been shown. In this communication, we determine the sensitivity and specificity of five of the most consistently replicated CpG loci with respect to smoking status using data from a publically available dataset. We show that methylation status at a CpG locus in the aryl hydrocarbon receptor repressor, cg05575921, is both sensitive and specific for smoking status in adults with a receiver operated curve characteristic area under the curve of 0.99. Given recent demonstrations that methylation at this locus reflects both intensity of smoking and the degree of smoking cessation, we conclude that a methylation-based diagnostic at this locus could have a prominent role in understanding the impact of new products, such as e-cigarettes on initiation of cigarette smoking among adolescents, while improving the prevention and treatment of smoking, and smoking related disorders. PMID:26082730

  15. QUANTITATIVE VS. CONVENTIONAL PCR FOR DETECTION OF HUMAN ADENOVIRUSES IN WATER AND SEDIMENT SAMPLES

    PubMed Central

    STAGGEMEIER, Rodrigo; BORTOLUZZI, Marina; HECK, Tatiana Moraes da Silva; SPILKI, Fernando Rosado; ALMEIDA, Sabrina Esteves de Matos

    2015-01-01

    SUMMARY Human Adenoviruses (HAdV) are notably resistant in the environment. These agents may serve as effective indicators of fecal contamination, and may act as causative agents of a number of different diseases in human beings. Conventional polymerase chain reaction (PCR) and, more recently, quantitative PCR (qPCR) are widely used for detection of viral agents in environmental matrices. In the present study PCR and SYBR(r)Green qPCR assays were compared for detection of HAdV in water (55) and sediments (20) samples of spring and artesian wells, ponds and streams, collected from dairy farms. By the quantitative methodology HAdV were detected in 87.3% of the water samples and 80% of the sediments, while by the conventional PCR 47.3% and 35% were detected in water samples and sediments, respectively. PMID:26422153

  16. QUANTITATIVE VS. CONVENTIONAL PCR FOR DETECTION OF HUMAN ADENOVIRUSES IN WATER AND SEDIMENT SAMPLES.

    PubMed

    Staggemeier, Rodrigo; Bortoluzzi, Marina; Heck, Tatiana Moraes da Silva; Spilki, Fernando Rosado; Almeida, Sabrina Esteves de Matos

    2015-01-01

    Human Adenoviruses (HAdV) are notably resistant in the environment. These agents may serve as effective indicators of fecal contamination, and may act as causative agents of a number of different diseases in human beings. Conventional polymerase chain reaction (PCR) and, more recently, quantitative PCR (qPCR) are widely used for detection of viral agents in environmental matrices. In the present study PCR and SYBR(r)Green qPCR assays were compared for detection of HAdV in water (55) and sediments (20) samples of spring and artesian wells, ponds and streams, collected from dairy farms. By the quantitative methodology HAdV were detected in 87.3% of the water samples and 80% of the sediments, while by the conventional PCR 47.3% and 35% were detected in water samples and sediments, respectively.

  17. [Quantitative specific detection of Staphylococcus aureus based on recombinant lysostaphin and ATP bioluminescence].

    PubMed

    Li, Yuyuan; Mi, Zhiqiang; An, Xiaoping; Zhou, Yusen; Tong, Yigang

    2014-08-01

    Quantitative specific detection of Staphylococcus aureus is based on recombinant lysostaphin and ATP bioluminescence. To produce recombinant lysostaphin, the lysostaphin gene was chemically synthesized and inserted it into prokaryotic expression vector pQE30, and the resulting expression plasmid pQE30-Lys was transformed into E. coli M15 for expressing lysostaphin with IPTG induction. The recombinant protein was purified by Ni(2+)-NTA affinity chromatography. Staphylococcus aureus was detected by the recombinant lysostaphin with ATP bioluminescence, and plate count method. The results of the two methods were compared. The recombinant lysostaphin was successfully expressed, and a method of quantitative specific detection of S. aureus has been established, which showed a significant linear correlation with the colony counting. The detection method developed has good perspective to quantify S. aureus.

  18. Evaluation of a quantitative plasma PCR plate assay for detecting cytomegalovirus infection in marrow transplant recipients.

    PubMed Central

    Gallez-Hawkins, G M; Tegtmeier, B R; ter Veer, A; Niland, J C; Forman, S J; Zaia, J A

    1997-01-01

    A plasma PCR test, using a nonradioactive PCR plate assay, was evaluated for detection of human cytomegalovirus reactivation. This assay was compared to Southern blotting and found to perform well. As a noncompetitive method of quantitation, it was similar to a competitive method for detecting the number of genome copies per milliliter of plasma in marrow transplant recipients. This is a technically simplified assay with potential for adaptation to automation. PMID:9041438

  19. Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud.

    PubMed

    Burns, Malcolm; Wiseman, Gordon; Knight, Angus; Bramley, Peter; Foster, Lucy; Rollinson, Sophie; Damant, Andrew; Primrose, Sandy

    2016-01-07

    Following a report on a significant amount of horse DNA being detected in a beef burger product on sale to the public at a UK supermarket in early 2013, the Elliott report was published in 2014 and contained a list of recommendations for helping ensure food integrity. One of the recommendations included improving laboratory testing capacity and capability to ensure a harmonised approach for testing for food authenticity. Molecular biologists have developed exquisitely sensitive methods based on the polymerase chain reaction (PCR) or mass spectrometry for detecting the presence of particular nucleic acid or peptide/protein sequences. These methods have been shown to be specific and sensitive in terms of lower limits of applicability, but they are largely qualitative in nature. Historically, the conversion of these qualitative techniques into reliable quantitative methods has been beset with problems even when used on relatively simple sample matrices. When the methods are applied to complex sample matrices, as found in many foods, the problems are magnified resulting in a high measurement uncertainty associated with the result which may mean that the assay is not fit for purpose. However, recent advances in the technology and the understanding of molecular biology approaches have further given rise to the re-assessment of these methods for their quantitative potential. This review focuses on important issues for consideration when validating a molecular biology assay and the various factors that can impact on the measurement uncertainty of a result associated with molecular biology approaches used in detection of food fraud, with a particular focus on quantitative PCR-based and proteomics assays.

  20. Quantitative evaluation of image processing algorithms for ill-structured road detection and tracking

    NASA Astrophysics Data System (ADS)

    Dufourd, Delphine; Dalgalarrondo, Andre

    2003-09-01

    In a previous presentation at AeroSense 2002, we described a methodology to assess the results of image processing algorithms for ill-structured road detection and tracking. In this paper, we present our first application of this methodology on sixedge detectors and a database counting about 20,000 images. Our evaluation approach is based on the use of video image sequences, ground truth - reference results established by human experts - and assessment metrics which measure the quality of the image processing results. We need a quantitative, comparative and repetitive evaluation of many algorithms in order to direct future developments. The main scope of this paper consists in presenting the lessons learned from applying our methodology. More precisely, we describe the assessment metrics, the algorithms and the database. Then we describe how we manage to extract the qualities and weaknesses of each algorithm and to establish a global scoring. The insight we gain for the definition of assessment metrics is also presented. Finally, we suggest some promising directions for the development of road tracking algorithms and complementarities that must be sought after. To conclude, we describe future improvements for the database constitution, the assessment tools and the overall methodology.

  1. Tomographic thallium-201 myocardial perfusion scintigrams after maximal coronary artery vasodilation with intravenous dipyridamole: comparison of qualitative and quantitative approaches

    SciTech Connect

    Francisco, D.A.; Collins, S.M.; Go, R.T.; Ehrhardt, J.C.; Van Kirk, O.C.; Marcus, M.L.

    1982-08-01

    Eighty-six patients had thallium-201 (/sup 201/Tl) myocardial perfusion scintigrams after intense coronary artery dilation with i.v. dipyridamole. Tomographic and planar /sup 201/Tl scintigrams were obtained in each patient. Tomographic scintigrams were interpreted using quantitative or visual criteria; planar scintigrams were assessed using visual criteria only. When visual criteria were used, interobserver variability was 40% for tomographic scintigrams and 44% for planar scintigrams. In the 24 patients with normal or nonsignificant CAD, quantitative analysis of the tomograms (range approach) indicated that one of 24 (4%) had a positive image (specificity 96%%); in contrast, when visual criteria were used to interpret the tomographic or planar /sup 201/Tl scintigrams, eight of 24 (33%) had positive scintigrams (specificity 67%). In the 51 abnormal patients, the sensitivity of detecting CAD was 46 of 51 (90%) for tomographic scintigrams interpreted quantitatively, 39 of 51 (76%) for tomographic scintigrams interpreted visually and 41 of 51 (80%) for planar scintigrams assessed visually. The tomographic imaging procedure (quantitative interpretation) also demonstrated a high sensitivity (89%) and specificity (100%) in 28 patients (10 normal and 18 CAD), with a clinical diagnosis of unstable angina pectoris. Overall, the predictive accuracy of an abnormal scintigram with quantitative tomographic imaging (98%) was significantly better (p<0.05) than either qualitative planar or pinhole imaging. (JMT)

  2. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

    EPA Science Inventory

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  3. Comparative analysis of techniques for detection of quiescent Botrytis cinerea in grapes by quantitative PCR

    USDA-ARS?s Scientific Manuscript database

    Quantitative PCR (qPCR) can be used to detect and monitor pathogen colonization, but early attempts to apply the technology to quiescent Botrytis cinerea infections of grape berries identified some specific limitations. In this study, four DNA extraction methods, two tissue-grinding methods, two gra...

  4. NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs.

    PubMed

    Morisset, Dany; Dobnik, David; Hamels, Sandrine; Zel, Jana; Gruden, Kristina

    2008-10-01

    We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1-25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification.

  5. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

    EPA Science Inventory

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  6. A new molecular diagnostic tool for quantitatively detecting and genotyping “Candidatus Liberibacter species”

    USDA-ARS?s Scientific Manuscript database

    A new molecular diagnostic method was developed for quantitative detection of “Candidatus Liberibacter” species associated with citrus Huanglongbing (“Ca. Liberibacter asiaticus”, “Ca. Liberibacter africanus” and “Ca. Liberibacter americanus”) and potato zebra chip disorder (“Ca. Liberibacter solana...

  7. A visual volumetric hydrogel sensor enables quantitative and sensitive detection of copper ions.

    PubMed

    Wu, Rui; Zhang, Shenghai; Lyu, Jitong; Lu, Fang; Yue, Xuanfeng; Lv, Jiagen

    2015-05-11

    We propose a visual volumetric sensor with 5,6-dicarboxylic fluorescein cross-linked amine-functionalized polyacrylamide hydrogel. The sensor undergoes volume response to Cu(2+) ions at the μM level, which enables naked-eye quantitative detection by reading the graduation on a pipette.

  8. QUANTITATIVE DETECTION OF ENVIRONMENTALLY IMPORTANT DYES USING DIODE LASER/FIBER-OPTIC RAMAN

    EPA Science Inventory

    A compact diode laser/fiber-optic Raman spectrometer is used for quantitative detection of environmentally important dyes. This system is based on diode laser excitation at 782 mm, fiber optic probe technology, an imaging spectrometer, and state-of-the-art scientific CCD camera. ...

  9. Single Laboratory Comparison of Quantitative Real-time PCR Assays for the Detection of Fecal Pollution

    EPA Science Inventory

    There are numerous quantitative real-time PCR (qPCR) assays available to detect and enumerate fecal pollution in ambient waters. Each assay employs distinct primers and probes that target different rRNA genes and microorganisms leading to potential variations in concentration es...

  10. NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs

    PubMed Central

    Morisset, Dany; Dobnik, David; Hamels, Sandrine; Žel, Jana; Gruden, Kristina

    2008-01-01

    We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1–25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification. PMID:18710880

  11. QUANTITATIVE DETECTION OF ENVIRONMENTALLY IMPORTANT DYES USING DIODE LASER/FIBER-OPTIC RAMAN

    EPA Science Inventory

    A compact diode laser/fiber-optic Raman spectrometer is used for quantitative detection of environmentally important dyes. This system is based on diode laser excitation at 782 mm, fiber optic probe technology, an imaging spectrometer, and state-of-the-art scientific CCD camera. ...

  12. Quantitative Framework and Management Expectation Tool for the Selection of Bioremediation Approaches at Chlorinated Solvent Sites

    DTIC Science & Technology

    2015-03-19

    Bioremediation Approaches at Chlorinated Solvent Sites March 19, 2015 SERDP & ESTCP Webinar Series (#11) SERDP & ESTCP Webinar Series Welcome and...Expectation Tool for the Selection of Bioremediation Approaches at Chlorinated Solvent Sites Ms. Carmen Lebrón, Independent Consultant (20 minutes + Q&A) Dr...ESTCP Webinar Series Quantitative Framework and Management Expectation Tool for the Selection of Bioremediation Approaches at Chlorinated

  13. Quantitative electrochemiluminescence detection of proteins: Avidin-based sensor and tris(2,2'-bipyridine) ruthenium(II) label.

    PubMed

    Fang, Lanyun; Lü, Zhaozi; Wei, Hui; Wang, Erkang

    2008-06-15

    Quantitative electrochemiluminescence (ECL) detection of a model protein, bovine serum albumin (BSA) was achieved via biotin-avidin interaction using an avidin-based sensor and a well-developed ECL system of tris(2,2'-bipyridine) ruthenium(II) derivative as label and tri-n-propylamine (TPA) as coreactant. To detect the protein, avidin was linked to the glassy carbon electrode through passive adsorptions and covalent interaction with carboxylate-terminated carbon nanotubes that was used as binder to immobilize avidin onto the electrode. Then, biotinylated BSA tagged with tris(2,2'-bipyridine) ruthenium(II) label was attached to the prepared avidin surface. After binding of BSA labeled with tris(2,2'-bipyridine) ruthenium(II) derivative to the surface-immobilized avidin through biotin, ECL response was generated when the self-assembled modified electrode was immersed in a TPA-containing electrolyte solution. Such double protein labeling protocol with a biotin label for biorecognition and ruthenium label for ECL detection facilitated the detection of protein compared to the classical double antibody sandwich format. The ECL intensity was linearly proportional to the feed concentration of BSA over two orders of magnitude in the range of 15nM to 7.5microM. The detection limit was estimated to be 1.5nM. Further application to the lysozyme analysis was carried out to validate the present approach for an effective and favorable protocol for the quantitative detection of proteins. The dynamic range of lysozyme was from 0.001gL(-1) to 0.1gL(-1) and the detection limit was 0.1mgL(-1). Electrochemical impedance and cyclic voltammetric measurements along with some necessary control experiments were conducted to characterize the successful formation of self-assembled modified electrodes and to grant the whole detection process.

  14. Application of quantitative PCR for the detection of microorganisms in water.

    PubMed

    Botes, Marelize; de Kwaadsteniet, Michéle; Cloete, Thomas Eugene

    2013-01-01

    The occurrence of microorganisms in water due to contamination is a health risk and control thereof is a necessity. Conventional detection methods may be misleading and do not provide rapid results allowing for immediate action. The quantitative polymerase chain reaction (qPCR) method has proven to be an effective tool to detect and quantify microorganisms in water within a few hours. Quantitative PCR assays have recently been developed for the detection of specific adeno- and polyomaviruses, bacteria and protozoa in different water sources. The technique is highly sensitive and able to detect low numbers of microorganisms. Quantitative PCR can be applied for microbial source tracking in water sources, to determine the efficiency of water and wastewater treatment plants and act as a tool for risk assessment. Different qPCR assays exist depending on whether an internal control is used or whether measurements are taken at the end of the PCR reaction (end-point qPCR) or in the exponential phase (real-time qPCR). Fluorescent probes are used in the PCR reaction to hybridise within the target sequence to generate a signal and, together with specialised systems, quantify the amount of PCR product. Quantitative reverse transcription polymerase chain reaction (q-RT-PCR) is a more sensitive technique that detects low copy number RNA and can be applied to detect, e.g. enteric viruses and viable microorganisms in water, and measure specific gene expression. There is, however, a need to standardise qPCR protocols if this technique is to be used as an analytical diagnostic tool for routine monitoring. This review focuses on the application of qPCR in the detection of microorganisms in water.

  15. Statistical modeling approach for detecting generalized synchronization

    NASA Astrophysics Data System (ADS)

    Schumacher, Johannes; Haslinger, Robert; Pipa, Gordon

    2012-05-01

    Detecting nonlinear correlations between time series presents a hard problem for data analysis. We present a generative statistical modeling method for detecting nonlinear generalized synchronization. Truncated Volterra series are used to approximate functional interactions. The Volterra kernels are modeled as linear combinations of basis splines, whose coefficients are estimated via l1 and l2 regularized maximum likelihood regression. The regularization manages the high number of kernel coefficients and allows feature selection strategies yielding sparse models. The method's performance is evaluated on different coupled chaotic systems in various synchronization regimes and analytical results for detecting m:n phase synchrony are presented. Experimental applicability is demonstrated by detecting nonlinear interactions between neuronal local field potentials recorded in different parts of macaque visual cortex.

  16. Fraud detection in medicare claims: A multivariate outlier detection approach

    SciTech Connect

    Burr, T.; Hale, C.; Kantor, M.

    1997-04-01

    We apply traditional and customized multivariate outlier detection methods to detect fraud in medicare claims. We use two sets of 11 derived features, and one set of the 22 combined features. The features are defined so that fraudulent medicare providers should tend to have larger features values than non-fraudulent providers. Therefore we have an apriori direction ({open_quotes}large values{close_quotes}) in high dimensional feature space to search for the multivariate outliers. We focus on three issues: (1) outlier masking (Example: the presence of one outlier can make it difficult to detect a second outlier), (2) the impact of having an apriori direction to search for fraud, and (3) how to compare our detection methods. Traditional methods include Mahalanobis distances, (with and without dimension reduction), k-nearest neighbor, and density estimation methods. Some methods attempt to mitigate the outlier masking problem (for example: minimum volume ellipsoid covariance estimator). Customized methods include ranking methods (such as Spearman rank ordering) that exploit the {open_quotes}large is suspicious{close_quotes} notion. No two methods agree completely which providers are most suspicious so we present ways to compare our methods. One comparison method uses a list of known-fraudulent providers. All comparison methods restrict attention to the most suspicious providers.

  17. DRIFTSEL: an R package for detecting signals of natural selection in quantitative traits.

    PubMed

    Karhunen, M; Merilä, J; Leinonen, T; Cano, J M; Ovaskainen, O

    2013-07-01

    Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (DRIFTSEL) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three-spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. DRIFTSEL can also be used to perform usual quantitative genetic analyses in common-garden study designs. © 2013 John Wiley & Sons Ltd.

  18. Quantitative risk assessment & leak detection criteria for a subsea oil export pipeline

    NASA Astrophysics Data System (ADS)

    Zhang, Fang-Yuan; Bai, Yong; Badaruddin, Mohd Fauzi; Tuty, Suhartodjo

    2009-06-01

    A quantitative risk assessment (QRA) based on leak detection criteria (LDC) for the design of a proposed subsea oil export pipeline is presented in this paper. The objective of this QRA/LDC study was to determine if current leak detection methodologies were sufficient, based on QRA results, while excluding the use of statistical leak detection; if not, an appropriate LDC for the leak detection system would need to be established. The famous UK PARLOC database was used for the calculation of pipeline failure rates, and the software POSVCM from MMS was used for oil spill simulations. QRA results revealed that the installation of a statistically based leak detection system (LDS) can significantly reduce time to leak detection, thereby mitigating the consequences of leakage. A sound LDC has been defined based on QRA study results and comments from various LDS vendors to assist the emergency response team (ERT) to quickly identify and locate leakage and employ the most effective measures to contain damage.

  19. Qualitative and Quantitative Detection of Botulinum Neurotoxins from Complex Matrices: Results of the First International Proficiency Test.

    PubMed

    Worbs, Sylvia; Fiebig, Uwe; Zeleny, Reinhard; Schimmel, Heinz; Rummel, Andreas; Luginbühl, Werner; Dorner, Brigitte G

    2015-11-26

    In the framework of the EU project EQuATox, a first international proficiency test (PT) on the detection and quantification of botulinum neurotoxins (BoNT) was conducted. Sample materials included BoNT serotypes A, B and E spiked into buffer, milk, meat extract and serum. Different methods were applied by the participants combining different principles of detection, identification and quantification. Based on qualitative assays, 95% of all results reported were correct. Successful strategies for BoNT detection were based on a combination of complementary immunological, MS-based and functional methods or on suitable functional in vivo/in vitro approaches (mouse bioassay, hemidiaphragm assay and Endopep-MS assay). Quantification of BoNT/A, BoNT/B and BoNT/E was performed by 48% of participating laboratories. It turned out that precise quantification of BoNT was difficult, resulting in a substantial scatter of quantitative data. This was especially true for results obtained by the mouse bioassay which is currently considered as "gold standard" for BoNT detection. The results clearly demonstrate the urgent need for certified BoNT reference materials and the development of methods replacing animal testing. In this context, the BoNT PT provided the valuable information that both the Endopep-MS assay and the hemidiaphragm assay delivered quantitative results superior to the mouse bioassay.

  20. Qualitative and quantitative detection of DNA amplified with HRP-modified SiO2 nanoparticles using scanning electrochemical microscopy.

    PubMed

    Fan, Huajun; Jiao, Fang; Chen, Hong; Zhang, Fan; Wang, Qingjiang; He, Pingang; Fang, Yuzhi

    2013-09-15

    Qualitative and quantitative detection of DNA was achieved by a "sandwich" DNA sensor through SG/TC (substrate generation and tip collection) mode of scanning electrochemical microscopy (SECM). The "sandwich" DNA structure was formed by the hybridization of thiol-tethered oligodeoxynucleotide probes (capture probe), assembled on the gold substrate surface, with target DNA and biotinylated indicator probe. HRP (horseradish peroxidase)-wrapped SiO2 nanoparticles were linked to the sandwich structure through biotin-streptavidin interaction. Hydroquinone (H2Q) was oxidized to benzoquinone (BQ) at the modified substrate surface where sequence-specific hybridization had occurred through the HRP-catalyzed reaction in the presence of H2O2. The detection was based on the reduction of BQ generated on the modified substrate by SECM tip. For SECM imaging experiment, we structured the microsensor platform through localized desorption of 1-dodecanethiol monolayer. Approach curves were employed for quantitative detection of DNA concentration. The detection limit of complementary DNA was as low as 0.8pM. This technique is promising for the application on electrochemical DNA chip.

  1. Qualitative and Quantitative Detection of Botulinum Neurotoxins from Complex Matrices: Results of the First International Proficiency Test

    PubMed Central

    Worbs, Sylvia; Fiebig, Uwe; Zeleny, Reinhard; Schimmel, Heinz; Rummel, Andreas; Luginbühl, Werner; Dorner, Brigitte G.

    2015-01-01

    In the framework of the EU project EQuATox, a first international proficiency test (PT) on the detection and quantification of botulinum neurotoxins (BoNT) was conducted. Sample materials included BoNT serotypes A, B and E spiked into buffer, milk, meat extract and serum. Different methods were applied by the participants combining different principles of detection, identification and quantification. Based on qualitative assays, 95% of all results reported were correct. Successful strategies for BoNT detection were based on a combination of complementary immunological, MS-based and functional methods or on suitable functional in vivo/in vitro approaches (mouse bioassay, hemidiaphragm assay and Endopep-MS assay). Quantification of BoNT/A, BoNT/B and BoNT/E was performed by 48% of participating laboratories. It turned out that precise quantification of BoNT was difficult, resulting in a substantial scatter of quantitative data. This was especially true for results obtained by the mouse bioassay which is currently considered as “gold standard” for BoNT detection. The results clearly demonstrate the urgent need for certified BoNT reference materials and the development of methods replacing animal testing. In this context, the BoNT PT provided the valuable information that both the Endopep-MS assay and the hemidiaphragm assay delivered quantitative results superior to the mouse bioassay. PMID:26703724

  2. Lateral flow immunoassay for quantitative detection of ractopamine in swine urine.

    PubMed

    Ren, Mei Ling; Chen, Xue Lan; Li, Chao Hui; Xu, Bo; Liu, Wen Juan; Xu, Heng Yi; Xiong, Yong Hua

    2014-02-01

    A strip reader based lateral flow immunoassay (LFIA) was established for the rapid and quantitative detection of ractopamine (RAC) in swine urine. The ratio of the optical densities (ODs) of the test line (AT) to that of the control line (AC) was used to effectively minimize interference among strips and sample variations. The linear range for the quantitative detection of RAC was 0.2 ng/mL to 3.5 ng/mL with a median inhibitory concentration (IC50) of 0.59 ± 0.06 ng/mL. The limit of detection (LOD) of the LFIA was 0.13 ng/mL. The intra-assay recovery rates were 92.97%, 97.25%, and 107.41%, whereas the inter-assay rates were 80.07%, 108.17%, and 93.7%, respectively.

  3. Western blot assay for quantitative and qualitative antigen detection in vaccine development.

    PubMed

    Kumar, Sanjai; Zheng, Hong; Mahajan, Babita; Kozakai, Yukiko; Morin, Merribeth; Locke, Emily

    2014-05-01

    Immunological methods for quantitative measurement, antigenic characterization, and monitoring the stability of active immunogenic component(s) are a critical need in the vaccine development process. This unit describes an enhanced chemiluminescence-based western blot for quantitative detection of Plasmodium falciparum circumsporozoite protein (PfCSP), a major malaria candidate vaccine antigen. The most salient features of this assay are its high sensitivity and reproducibility; it can reliably detect ∼5 to 10 pg PfCSP expressed on native parasites or recombinantly expressed in Escherichia coli. Although described for a specific vaccine antigen, this assay should be applicable for any antigen-antibody combination for which relevant detection reagents are available. Detailed stepwise experimental procedures and methods for data acquisition and analysis are described. Copyright © 2014 John Wiley & Sons, Inc.

  4. Application of image processing for terahertz time domain spectroscopy imaging quantitative detection

    NASA Astrophysics Data System (ADS)

    Li, Li-juan; Wang, Sheng; Ren, Jiao-jiao; Zhou, Ming-xing; Zhao, Duo

    2015-03-01

    According to nondestructive testing principle for the terahertz time domain spectroscopy Imaging, using digital image processing techniques, through Terahertz time-domain spectroscopy system collected images and two-dimensional datas and using a range of processing methods, including selecting regions of interest, contrast enhancement, edge detection, and defects being detected. In the paper, Matlab programming is been use to defect recognition of Terahertz, by figuring out the pixels to determine defects defect area and border length, roundness, diameter size. Through the experiment of the qualitative analysis and quantitative calculation of Matlab image processing, this method of detection of defects of geometric dimension of the sample to get a better result.

  5. Paper diagnostic device for quantitative electrochemical detection of ricin at picomolar levels.

    PubMed

    Cunningham, Josephine C; Scida, Karen; Kogan, Molly R; Wang, Bo; Ellington, Andrew D; Crooks, Richard M

    2015-01-01

    We report a paper-based assay platform for detection of ricin a chain. The paper platform is assembled by simple origami paper folding. The sensor is based on quantitative, electrochemical detection of silver nanoparticle labels linked to a magnetic microbead support via a ricin immunosandwich. Importantly, ricin was detected at concentrations as low as 34 pM. Additionally, the assay is robust, even in the presence of 100-fold excess hoax materials. Finally, the device is easily remediated after use by incineration. The cost of the device, not including reagents, is just $0.30. The total assay time, including formation of the immunosandwich, is 9.5 min.

  6. Augmenting Amyloid PET Interpretations With Quantitative Information Improves Consistency of Early Amyloid Detection.

    PubMed

    Harn, Nicholas R; Hunt, Suzanne L; Hill, Jacqueline; Vidoni, Eric; Perry, Mark; Burns, Jeffrey M

    2017-08-01

    Establishing reliable methods for interpreting elevated cerebral amyloid-β plaque on PET scans is increasingly important for radiologists, as availability of PET imaging in clinical practice increases. We examined a 3-step method to detect plaque in cognitively normal older adults, focusing on the additive value of quantitative information during the PET scan interpretation process. Fifty-five F-florbetapir PET scans were evaluated by 3 experienced raters. Scans were first visually interpreted as having "elevated" or "nonelevated" plaque burden ("Visual Read"). Images were then processed using a standardized quantitative analysis software (MIMneuro) to generate whole brain and region of interest SUV ratios. This "Quantitative Read" was considered elevated if at least 2 of 6 regions of interest had an SUV ratio of more than 1.1. The final interpretation combined both visual and quantitative data together ("VisQ Read"). Cohen kappa values were assessed as a measure of interpretation agreement. Plaque was elevated in 25.5% to 29.1% of the 165 total Visual Reads. Interrater agreement was strong (kappa = 0.73-0.82) and consistent with reported values. Quantitative Reads were elevated in 45.5% of participants. Final VisQ Reads changed from initial Visual Reads in 16 interpretations (9.7%), with most changing from "nonelevated" Visual Reads to "elevated." These changed interpretations demonstrated lower plaque quantification than those initially read as "elevated" that remained unchanged. Interrater variability improved for VisQ Reads with the addition of quantitative information (kappa = 0.88-0.96). Inclusion of quantitative information increases consistency of PET scan interpretations for early detection of cerebral amyloid-β plaque accumulation.

  7. Detection of nonauthorized genetically modified organisms using differential quantitative polymerase chain reaction: application to 35S in maize.

    PubMed

    Cankar, Katarina; Chauvensy-Ancel, Valérie; Fortabat, Marie-Noelle; Gruden, Kristina; Kobilinsky, André; Zel, Jana; Bertheau, Yves

    2008-05-15

    Detection of nonauthorized genetically modified organisms (GMOs) has always presented an analytical challenge because the complete sequence data needed to detect them are generally unavailable although sequence similarity to known GMOs can be expected. A new approach, differential quantitative polymerase chain reaction (PCR), for detection of nonauthorized GMOs is presented here. This method is based on the presence of several common elements (e.g., promoter, genes of interest) in different GMOs. A statistical model was developed to study the difference between the number of molecules of such a common sequence and the number of molecules identifying the approved GMO (as determined by border-fragment-based PCR) and the donor organism of the common sequence. When this difference differs statistically from zero, the presence of a nonauthorized GMO can be inferred. The interest and scope of such an approach were tested on a case study of different proportions of genetically modified maize events, with the P35S promoter as the Cauliflower Mosaic Virus common sequence. The presence of a nonauthorized GMO was successfully detected in the mixtures analyzed and in the presence of (donor organism of P35S promoter). This method could be easily transposed to other common GMO sequences and other species and is applicable to other detection areas such as microbiology.

  8. Event-specific qualitative and quantitative detection of five genetically modified rice events using a single standard reference molecule.

    PubMed

    Kim, Jae-Hwan; Park, Saet-Byul; Roh, Hyo-Jeong; Shin, Min-Ki; Moon, Gui-Im; Hong, Jin-Hwan; Kim, Hae-Yeong

    2017-07-01

    One novel standard reference plasmid, namely pUC-RICE5, was constructed as a positive control and calibrator for event-specific qualitative and quantitative detection of genetically modified (GM) rice (Bt63, Kemingdao1, Kefeng6, Kefeng8, and LLRice62). pUC-RICE5 contained fragments of a rice-specific endogenous reference gene (sucrose phosphate synthase) as well as the five GM rice events. An existing qualitative PCR assay approach was modified using pUC-RICE5 to create a quantitative method with limits of detection correlating to approximately 1-10 copies of rice haploid genomes. In this quantitative PCR assay, the square regression coefficients ranged from 0.993 to 1.000. The standard deviation and relative standard deviation values for repeatability ranged from 0.02 to 0.22 and 0.10% to 0.67%, respectively. The Ministry of Food and Drug Safety (Korea) validated the method and the results suggest it could be used routinely to identify five GM rice events.

  9. Functionalized Magnetic Nanoparticles for the Detection and Quantitative Analysis of Cell Surface Antigen

    PubMed Central

    Shahbazi-Gahrouei, Daryoush; Abdolahi, Mohammad; Zarkesh-Esfahani, Sayyed Hamid; Laurent, Sophie; Sermeus, Corine; Gruettner, Cordula

    2013-01-01

    Cell surface antigens as biomarkers offer tremendous potential for early diagnosis, prognosis, and therapeutic response in a variety of diseases such as cancers. In this research, a simple, rapid, accurate, inexpensive, and easily available in vitro assay based on magnetic nanoparticles and magnetic cell separation principle was applied to identify and quantitatively analyze the cell surface antigen expression in the case of prostate cancer cells. Comparing the capability of the assay with flow cytometry as a gold standard method showed similar results. The results showed that the antigen-specific magnetic cell separation with antibody-coated magnetic nanoparticles has high potential for quantitative cell surface antigen detection and analysis. PMID:23484112

  10. Detection of Prostate Cancer: Quantitative Multiparametric MR Imaging Models Developed Using Registered Correlative Histopathology.

    PubMed

    Metzger, Gregory J; Kalavagunta, Chaitanya; Spilseth, Benjamin; Bolan, Patrick J; Li, Xiufeng; Hutter, Diane; Nam, Jung W; Johnson, Andrew D; Henriksen, Jonathan C; Moench, Laura; Konety, Badrinath; Warlick, Christopher A; Schmechel, Stephen C; Koopmeiners, Joseph S

    2016-06-01

    Purpose To develop multiparametric magnetic resonance (MR) imaging models to generate a quantitative, user-independent, voxel-wise composite biomarker score (CBS) for detection of prostate cancer by using coregistered correlative histopathologic results, and to compare performance of CBS-based detection with that of single quantitative MR imaging parameters. Materials and Methods Institutional review board approval and informed consent were obtained. Patients with a diagnosis of prostate cancer underwent multiparametric MR imaging before surgery for treatment. All MR imaging voxels in the prostate were classified as cancer or noncancer on the basis of coregistered histopathologic data. Predictive models were developed by using more than one quantitative MR imaging parameter to generate CBS maps. Model development and evaluation of quantitative MR imaging parameters and CBS were performed separately for the peripheral zone and the whole gland. Model accuracy was evaluated by using the area under the receiver operating characteristic curve (AUC), and confidence intervals were calculated with the bootstrap procedure. The improvement in classification accuracy was evaluated by comparing the AUC for the multiparametric model and the single best-performing quantitative MR imaging parameter at the individual level and in aggregate. Results Quantitative T2, apparent diffusion coefficient (ADC), volume transfer constant (K(trans)), reflux rate constant (kep), and area under the gadolinium concentration curve at 90 seconds (AUGC90) were significantly different between cancer and noncancer voxels (P < .001), with ADC showing the best accuracy (peripheral zone AUC, 0.82; whole gland AUC, 0.74). Four-parameter models demonstrated the best performance in both the peripheral zone (AUC, 0.85; P = .010 vs ADC alone) and whole gland (AUC, 0.77; P = .043 vs ADC alone). Individual-level analysis showed statistically significant improvement in AUC in 82% (23 of 28) and 71% (24 of 34

  11. Eigenstructure assignment approach for structural damage detection

    NASA Technical Reports Server (NTRS)

    Zimmerman, David C.; Kaouk, Mohamed

    1992-01-01

    In this work, a methodology for incorporating measured modal data into an existing refined finite element model is examined with the objective of detecting and locating structural damage. The algorithm is based on the partial inverse problem, in that only partial spectral information is required. The technique utilizes a symmetric eigenstructure assignment algorithm to perform the partial spectral assignment. Algorithms to enhance mode shape assignability and to preserve sparsity in the damaged FEM are developed. The sparsity preservation is of particular importance when considering damage detection in trusslike structures. Several examples are presented to highlight the key points made within the paper.

  12. Estimating background-subtracted fluorescence transients in calcium imaging experiments: a quantitative approach.

    PubMed

    Joucla, Sébastien; Franconville, Romain; Pippow, Andreas; Kloppenburg, Peter; Pouzat, Christophe

    2013-08-01

    Calcium imaging has become a routine technique in neuroscience for subcellular to network level investigations. The fast progresses in the development of new indicators and imaging techniques call for dedicated reliable analysis methods. In particular, efficient and quantitative background fluorescence subtraction routines would be beneficial to most of the calcium imaging research field. A background-subtracted fluorescence transients estimation method that does not require any independent background measurement is therefore developed. This method is based on a fluorescence model fitted to single-trial data using a classical nonlinear regression approach. The model includes an appropriate probabilistic description of the acquisition system's noise leading to accurate confidence intervals on all quantities of interest (background fluorescence, normalized background-subtracted fluorescence time course) when background fluorescence is homogeneous. An automatic procedure detecting background inhomogeneities inside the region of interest is also developed and is shown to be efficient on simulated data. The implementation and performances of the proposed method on experimental recordings from the mouse hypothalamus are presented in details. This method, which applies to both single-cell and bulk-stained tissues recordings, should help improving the statistical comparison of fluorescence calcium signals between experiments and studies. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. A New Approach for Quantitative Evaluation of Ultrasonic Wave Attenuation in Composites

    NASA Astrophysics Data System (ADS)

    Ni, Qing-Qing; Li, Ran; Xia, Hong

    2017-02-01

    When ultrasonic waves propagate in composite materials, the propagation behaviors result from the combination effects of various factors, such as material anisotropy and viscoelastic property, internal microstructure and defects, incident wave characteristics and interface condition between composite components. It is essential to make it clear how these factors affect the ultrasonic wave propagation and attenuation characteristics, and how they mutually interact on each other. In the present paper, based on a newly developed time-domain finite element analysis code, PZflex, a unique approach for clarifying the detailed influence mechanism of aforementioned factors is proposed, in which each attenuation component can be extracted from the overall attenuation and analyzed respectively. By taking into consideration the interrelation between each individual attenuation component, the variation behaviors of each component and internal dynamic stress distribution against material anisotropy and matrix viscosity are separately and quantitatively evaluated. From the detailed analysis results of each attenuation component, the energy dissipation at interface is a major component in ultrasonic wave attenuation characteristics, which can provide a maximum contribution rate of 68.2 % to the overall attenuation, and each attenuation component is closely related to the material anisotropy and viscoelasticity. The results clarify the correlation between ultrasonic wave propagation characteristics and material viscoelastic properties, which will be useful in the further development of ultrasonic technology in defect detection.

  14. Europium doping of superparamagnetic iron oxide nanoparticles enables their detection by fluorescence microscopy and for quantitative analytics.

    PubMed

    Kobayashi, Yuske; Hauptmann, Ralf; Kratz, Harald; Ebert, Monika; Wagner, Susanne; Taupitz, Matthias

    2017-01-01

    Pharmacokinetic studies and histological detection of superparamagnetic iron oxide nanoparticles (SPIO) in biomedical research are limited due to a high iron background especially in pathological tissues. The suitability of doping the iron oxide cores of SPIO with europium (Eu) was tested for improved histologic detection and for quantitative analysis without changing their properties as probes for magnetic resonance imaging (MRI). A special variant of SPIO, so called very small superparamagnetic iron oxide nanoparticles (VSOP), was used for this approach. VSOP, stabilized by a citrate coating, were synthesized with and without addition of Eu (Eu-VSOP and VSOP, respectively). MR signal enhancing effects of Eu-VSOP and VSOP were studied in vitro. Cellular uptake of Eu-VSOP and VSOP was examined in RAW264.7 cells. For Eu-VSOP, fluorescence microscopy and spectrophotometry were used. Eu fluorescence was enhanced by means of an antenna system. For VSOP, Prussian blue staining and photometry using the phenanthroline method were applied. Results for both VSOP variants were compared. Eu-VSOP and VSOP did not differ with respect to MR signal enhancing effects nor to uptake characteristics in the RAW264.7 cell experiments. Fluorescence microscopy detects Eu-VSOP with higher sensitivity compared to light microscopy using Prussian blue staining. In microscopy as well as in the analytical quantification using fluorescence, detection of Eu-VSOP is not contaminated by Fe background. Doping the VSOP with Eu allows for their improved detection by fluorescence microscopy and quantitative analysis without changing their cellular uptake characteristics or their MR signal enhancing effects and thus would allow for a multimodal approach for studying their pharmacokinetics and biodistribution in experimental research.

  15. Object-Oriented Change Detection Based on Multi-Scale Approach

    NASA Astrophysics Data System (ADS)

    Jia, Yonghong; Zhou, Mingting; Jinshan, Ye

    2016-06-01

    The change detection of remote sensing images means analysing the change information quantitatively and recognizing the change types of the surface coverage data in different time phases. With the appearance of high resolution remote sensing image, object-oriented change detection method arises at this historic moment. In this paper, we research multi-scale approach for high resolution images, which includes multi-scale segmentation, multi-scale feature selection and multi-scale classification. Experimental results show that this method has a stronger advantage than the traditional single-scale method of high resolution remote sensing image change detection.

  16. RABA (Reductive Alkylation By Acetone): A novel stable isotope labeling approach for quantitative proteomics

    PubMed Central

    Zhai, Jianjun; Liu, Xiaoyan; Huang, Zhenyu; Zhu, Haining

    2009-01-01

    Quantitative proteomics is challenging and various stable isotope based approaches have been developed to meet the challenge.. Hereby we describe a simple, efficient, reliable and inexpensive method named RABA (reductive alkylation by acetone) to introduce stable isotopes to peptides for quantitative analysis. The RABA method leads to alkylation of N-terminal and lysine amino groups with isopropyl moiety. Using unlabeled (d0) and deuterium labeled (d6) acetone, a 6 Da mass split is introduced to each isopropyl modification between the light and heavy isotope labeled peptides, which is ideally suited for quantitative analysis. The reaction specificity, stoichoimetry, labeling efficiency and linear range of the RABA method has been thoroughly evaluated in this study using standard peptides, tryptic digest of proteins as well as human cell lysate. Reliable quantitative results have been consistently obtained in all experiments. We also applied the RABA method to quantitative analysis of proteins in spinal cords of transgenic mouse models of amyotrophic lateral sclerosis. Highly homologous proteins (transgenic human SOD1 and endogenous mouse SOD1) were distinguished and quantified using the method developed in this study. In addition, the quantitative results using the RABA approach were independently validated by Western blot. PMID:19419886

  17. Data Mining Approaches for Intrusion Detection

    DTIC Science & Technology

    2000-10-12

    In this paper we discuss our research in developing general and systematic methods for intrusion detection. The key ideas are to use data mining techniques...two general data mining algorithms that we have implemented: the association rules algorithm and the frequent episodes algorithm. These algorithms can

  18. Approaches to mycotoxin detection using biosensors

    USDA-ARS?s Scientific Manuscript database

    The number of toxins of concern has continued to rise as emerging toxins have taken on new significance and as interest has increased in detecting metabolites of established toxins (including masked mycotoxins). Of course while the desire exists to monitor for more compounds, resources for such moni...

  19. A Pedagogical Approach to Detective Fiction

    ERIC Educational Resources Information Center

    Reyes-Torres, Agustín

    2011-01-01

    One of the main concerns when teaching a foreign language is how to encourage students to read and become interested in its literature. This article presents detective fiction as a pedagogical tool that provides the key elements to make it appealing for young readers. In this way, the mystery, the action and the suspense in the story; the figure…

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  1. Sensitive and quantitative detection of botulinum neurotoxin in neurons derived from mouse embryonic stem cells

    PubMed Central

    Pellett, Sabine; Du, Zhong-wei; Pier, Christina L.; Tepp, William H.; Zhang, Su-chun; Johnson, Eric A.

    2010-01-01

    Botulinum neurotoxins (BoNTs), the most poisonous protein toxins known, represent a serious bioterrorism threat but are also used as a unique and important bio-pharmaceutical to treat an increasing myriad of neurological disorders. The only currently accepted detection method by the United States Food and Drug Administration for biological activity of BoNTs and for potency determination of pharmaceutical preparations is the mouse bioassay (MBA). Recent advances have indicated that cell-based assays using primary neuronal cells can provide an equally sensitive and robust detection platform as the MBA to reliably and quantitatively detect biologically active BoNTs. This study reports for the first time a BoNT detection assay using mouse embryonic stem cells to produce a neuronal cell culture. The data presented indicate that this assaycan reliably detect BoNT/A with a similar sensitivity as the MBA. PMID:21130748

  2. Qualitative and quantitative PCR methods for detection of three lines of genetically modified potatoes.

    PubMed

    Rho, Jae Kyun; Lee, Theresa; Jung, Soon-Il; Kim, Tae-San; Park, Yong-Hwan; Kim, Young-Mi

    2004-06-02

    Qualitative and quantitative polymerase chain reaction (PCR) methods have been developed for the detection of genetically modified (GM) potatoes. The combination of specific primers for amplification of the promoter region of Cry3A gene, potato leafroll virus replicase gene, and potato virus Y coat protein gene allows to identify each line of NewLeaf, NewLeaf Y, and NewLeaf Plus GM potatoes. Multiplex PCR method was also established for the simple and rapid detection of the three lines of GM potato in a mixture sample. For further quantitative detection, the realtime PCR method has been developed. This method features the use of a standard plasmid as a reference molecule. Standard plasmid contains both a specific region of the transgene Cry3A and an endogenous UDP-glucose pyrophosphorylase gene of the potato. The test samples containing 0.5, 1, 3, and 5% GM potatoes were quantified by this method. At the 3.0% level of each line of GM potato, the relative standard deviations ranged from 6.0 to 19.6%. This result shows that the above PCR methods are applicable to detect GM potatoes quantitatively as well as qualitatively.

  3. Rapid and quantitative detection of C-reactive protein based on quantum dots and immunofiltration assay

    PubMed Central

    Zhang, Pengfei; Bao, Yan; Draz, Mohamed Shehata; Lu, Huiqi; Liu, Chang; Han, Huanxing

    2015-01-01

    Convenient and rapid immunofiltration assays (IFAs) enable on-site “yes” or “no” determination of disease markers. However, traditional IFAs are commonly qualitative or semi-quantitative and are very limited for the efficient testing of samples in field diagnostics. Here, we overcome these limitations by developing a quantum dots (QDs)-based fluorescent IFA for the quantitative detection of C-reactive proteins (CRP). CRP, the well-known diagnostic marker for acute viral and bacterial infections, was used as a model analyte to demonstrate performance and sensitivity of our developed QDs-based IFA. QDs capped with both polyethylene glycol (PEG) and glutathione were used as fluorescent labels for our IFAs. The presence of the surface PEG layer, which reduced the non-specific protein interactions, in conjunction with the inherent optical properties of QDs, resulted in lower background signal, increased sensitivity, and ability to detect CRP down to 0.79 mg/L with only 5 µL serum sample. In addition, the developed assay is simple, fast and can quantitatively detect CRP with a detection limit up to 200 mg/L. Clinical test results of our QD-based IFA are well correlated with the traditional latex enhance immune-agglutination aggregation. The proposed QD-based fluorescent IFA is very promising, and potentially will be adopted for multiplexed immunoassay and in field point-of-care test. PMID:26491289

  4. Rapid and quantitative detection of C-reactive protein based on quantum dots and immunofiltration assay.

    PubMed

    Zhang, Pengfei; Bao, Yan; Draz, Mohamed Shehata; Lu, Huiqi; Liu, Chang; Han, Huanxing

    2015-01-01

    Convenient and rapid immunofiltration assays (IFAs) enable on-site "yes" or "no" determination of disease markers. However, traditional IFAs are commonly qualitative or semi-quantitative and are very limited for the efficient testing of samples in field diagnostics. Here, we overcome these limitations by developing a quantum dots (QDs)-based fluorescent IFA for the quantitative detection of C-reactive proteins (CRP). CRP, the well-known diagnostic marker for acute viral and bacterial infections, was used as a model analyte to demonstrate performance and sensitivity of our developed QDs-based IFA. QDs capped with both polyethylene glycol (PEG) and glutathione were used as fluorescent labels for our IFAs. The presence of the surface PEG layer, which reduced the non-specific protein interactions, in conjunction with the inherent optical properties of QDs, resulted in lower background signal, increased sensitivity, and ability to detect CRP down to 0.79 mg/L with only 5 µL serum sample. In addition, the developed assay is simple, fast and can quantitatively detect CRP with a detection limit up to 200 mg/L. Clinical test results of our QD-based IFA are well correlated with the traditional latex enhance immune-agglutination aggregation. The proposed QD-based fluorescent IFA is very promising, and potentially will be adopted for multiplexed immunoassay and in field point-of-care test.

  5. Application of droplet digital PCR for quantitative detection of Spiroplasma citri in comparison with real time PCR.

    PubMed

    Maheshwari, Yogita; Selvaraj, Vijayanandraj; Hajeri, Subhas; Yokomi, Raymond

    2017-01-01

    Droplet digital polymerase chain reaction (ddPCR) is a method for performing digital PCR that is based on water-oil emulsion droplet technology. It is a unique approach to measure the absolute copy number of nucleic acid targets without the need of external standards. This study evaluated the applicability of ddPCR as a quantitative detection tool for the Spiroplasma citri, causal agent of citrus stubborn disease (CSD) in citrus. Two sets of primers, SP1, based on the spiral in housekeeping gene, and a multicopy prophage gene, SpV1 ORF1, were used to evaluate ddPCR in comparison with real time (quantitative) PCR (qPCR) for S. citri detection in citrus tissues. Standard curve analyses on tenfold dilution series showed that both ddPCR and qPCR exhibited good linearity and efficiency. However, ddPCR had a tenfold greater sensitivity than qPCR and accurately quantified up to one copy of spiralin gene. Receiver operating characteristic analysis indicated that the ddPCR methodology was more robust for diagnosis of CSD and the area under the curve was significantly broader compared to qPCR. Field samples were used to validate ddPCR efficacy and demonstrated that it was equal or better than qPCR to detect S. citri infection in fruit columella due to a higher pathogen titer. The ddPCR assay detected both the S. citri spiralin and the SpV1 ORF1 targets quantitatively with high precision and accuracy compared to qPCR assay. The ddPCR was highly reproducible and repeatable for both the targets and showed higher resilience to PCR inhibitors in citrus tissue extract for the quantification of S. citri compare to qPCR.

  6. Application of droplet digital PCR for quantitative detection of Spiroplasma citri in comparison with real time PCR

    PubMed Central

    Hajeri, Subhas

    2017-01-01

    Droplet digital polymerase chain reaction (ddPCR) is a method for performing digital PCR that is based on water-oil emulsion droplet technology. It is a unique approach to measure the absolute copy number of nucleic acid targets without the need of external standards. This study evaluated the applicability of ddPCR as a quantitative detection tool for the Spiroplasma citri, causal agent of citrus stubborn disease (CSD) in citrus. Two sets of primers, SP1, based on the spiral in housekeeping gene, and a multicopy prophage gene, SpV1 ORF1, were used to evaluate ddPCR in comparison with real time (quantitative) PCR (qPCR) for S. citri detection in citrus tissues. Standard curve analyses on tenfold dilution series showed that both ddPCR and qPCR exhibited good linearity and efficiency. However, ddPCR had a tenfold greater sensitivity than qPCR and accurately quantified up to one copy of spiralin gene. Receiver operating characteristic analysis indicated that the ddPCR methodology was more robust for diagnosis of CSD and the area under the curve was significantly broader compared to qPCR. Field samples were used to validate ddPCR efficacy and demonstrated that it was equal or better than qPCR to detect S. citri infection in fruit columella due to a higher pathogen titer. The ddPCR assay detected both the S. citri spiralin and the SpV1 ORF1 targets quantitatively with high precision and accuracy compared to qPCR assay. The ddPCR was highly reproducible and repeatable for both the targets and showed higher resilience to PCR inhibitors in citrus tissue extract for the quantification of S. citri compare to qPCR. PMID:28910375

  7. Quantitative and sensitive detection of GNAS mutations causing mccune-albright syndrome with next generation sequencing.

    PubMed

    Narumi, Satoshi; Matsuo, Kumihiro; Ishii, Tomohiro; Tanahashi, Yusuke; Hasegawa, Tomonobu

    2013-01-01

    Somatic activating GNAS mutations cause McCune-Albright syndrome (MAS). Owing to low mutation abundance, mutant-specific enrichment procedures, such as the peptide nucleic acid (PNA) method, are required to detect mutations in peripheral blood. Next generation sequencing (NGS) can analyze millions of PCR amplicons independently, thus it is expected to detect low-abundance GNAS mutations quantitatively. In the present study, we aimed to develop an NGS-based method to detect low-abundance somatic GNAS mutations. PCR amplicons encompassing exons 8 and 9 of GNAS, in which most activating mutations occur, were sequenced on the MiSeq instrument. As expected, our NGS-based method could sequence the GNAS locus with very high read depth (approximately 100,000) and low error rate. A serial dilution study with use of cloned mutant and wildtype DNA samples showed a linear correlation between dilution and measured mutation abundance, indicating the reliability of quantification of the mutation. Using the serially diluted samples, the detection limits of three mutation detection methods (the PNA method, NGS, and combinatory use of PNA and NGS [PNA-NGS]) were determined. The lowest detectable mutation abundance was 1% for the PNA method, 0.03% for NGS and 0.01% for PNA-NGS. Finally, we analyzed 16 MAS patient-derived leukocytic DNA samples with the three methods, and compared the mutation detection rate of them. Mutation detection rate of the PNA method, NGS and PNA-NGS in 16 patient-derived peripheral blood samples were 56%, 63% and 75%, respectively. In conclusion, NGS can detect somatic activating GNAS mutations quantitatively and sensitively from peripheral blood samples. At present, the PNA-NGS method is likely the most sensitive method to detect low-abundance GNAS mutation.

  8. Noninvasive imaging of hemoglobin concentration and oxygen saturation for detection of osteoarthritis in the finger joints using multispectral three-dimensional quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Sun, Yao; Sobel, Eric; Jiang, Huabei

    2013-05-01

    We present quantitative imaging of hemoglobin concentration and oxygen saturation in in vivo finger joints and evaluate the feasibility of detecting osteoarthritis (OA) in the hand using three-dimensional (3D) multispectral quantitative photoacoustic tomography (3D qPAT). The results show that both the anatomical structures and quantitative chromophore concentrations (oxy-hemoglobin and deoxy-hemoglobin) of different joint tissues (hard phalanges and soft cartilage/synovial fluid between phalanges) can be imaged in vivo with the multispectral 3D qPAT. Enhanced hemoglobin concentrations and dropped oxygen saturations in osteoarthritic phalanges and soft joint tissues in joint cavities have been observed. This study indicates that the multispectral 3D qPAT is a promising approach to detect the angiogenesis and hypoxia associated with OA disease and a potential clinical tool for early OA detection in the finger joints.

  9. Quantitative Detection of Trace Explosive Vapors by Programmed Temperature Desorption Gas Chromatography-Electron Capture Detector

    PubMed Central

    Field, Christopher R.; Lubrano, Adam; Woytowitz, Morgan; Giordano, Braden C.; Rose-Pehrsson, Susan L.

    2014-01-01

    The direct liquid deposition of solution standards onto sorbent-filled thermal desorption tubes is used for the quantitative analysis of trace explosive vapor samples. The direct liquid deposition method yields a higher fidelity between the analysis of vapor samples and the analysis of solution standards than using separate injection methods for vapors and solutions, i.e., samples collected on vapor collection tubes and standards prepared in solution vials. Additionally, the method can account for instrumentation losses, which makes it ideal for minimizing variability and quantitative trace chemical detection. Gas chromatography with an electron capture detector is an instrumentation configuration sensitive to nitro-energetics, such as TNT and RDX, due to their relatively high electron affinity. However, vapor quantitation of these compounds is difficult without viable vapor standards. Thus, we eliminate the requirement for vapor standards by combining the sensitivity of the instrumentation with a direct liquid deposition protocol to analyze trace explosive vapor samples. PMID:25145416

  10. Quantitative detection of trace explosive vapors by programmed temperature desorption gas chromatography-electron capture detector.

    PubMed

    Field, Christopher R; Lubrano, Adam; Woytowitz, Morgan; Giordano, Braden C; Rose-Pehrsson, Susan L

    2014-07-25

    The direct liquid deposition of solution standards onto sorbent-filled thermal desorption tubes is used for the quantitative analysis of trace explosive vapor samples. The direct liquid deposition method yields a higher fidelity between the analysis of vapor samples and the analysis of solution standards than using separate injection methods for vapors and solutions, i.e., samples collected on vapor collection tubes and standards prepared in solution vials. Additionally, the method can account for instrumentation losses, which makes it ideal for minimizing variability and quantitative trace chemical detection. Gas chromatography with an electron capture detector is an instrumentation configuration sensitive to nitro-energetics, such as TNT and RDX, due to their relatively high electron affinity. However, vapor quantitation of these compounds is difficult without viable vapor standards. Thus, we eliminate the requirement for vapor standards by combining the sensitivity of the instrumentation with a direct liquid deposition protocol to analyze trace explosive vapor samples.

  11. 3D change detection - Approaches and applications

    NASA Astrophysics Data System (ADS)

    Qin, Rongjun; Tian, Jiaojiao; Reinartz, Peter

    2016-12-01

    Due to the unprecedented technology development of sensors, platforms and algorithms for 3D data acquisition and generation, 3D spaceborne, airborne and close-range data, in the form of image based, Light Detection and Ranging (LiDAR) based point clouds, Digital Elevation Models (DEM) and 3D city models, become more accessible than ever before. Change detection (CD) or time-series data analysis in 3D has gained great attention due to its capability of providing volumetric dynamics to facilitate more applications and provide more accurate results. The state-of-the-art CD reviews aim to provide a comprehensive synthesis and to simplify the taxonomy of the traditional remote sensing CD techniques, which mainly sit within the boundary of 2D image/spectrum analysis, largely ignoring the particularities of 3D aspects of the data. The inclusion of 3D data for change detection (termed 3D CD), not only provides a source with different modality for analysis, but also transcends the border of traditional top-view 2D pixel/object-based analysis to highly detailed, oblique view or voxel-based geometric analysis. This paper reviews the recent developments and applications of 3D CD using remote sensing and close-range data, in support of both academia and industry researchers who seek for solutions in detecting and analyzing 3D dynamics of various objects of interest. We first describe the general considerations of 3D CD problems in different processing stages and identify CD types based on the information used, being the geometric comparison and geometric-spectral analysis. We then summarize relevant works and practices in urban, environment, ecology and civil applications, etc. Given the broad spectrum of applications and different types of 3D data, we discuss important issues in 3D CD methods. Finally, we present concluding remarks in algorithmic aspects of 3D CD.

  12. Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data.

    PubMed

    Ning, Zhibin; Zhang, Xu; Mayne, Janice; Figeys, Daniel

    2016-02-16

    Quantitative proteomics can provide rich information on changes in biological functions and processes. However, its accuracy is affected by the inherent information degeneration found in bottom-up proteomics. Therefore, the precise protein inference from identified peptides can be mistaken since an ad hoc rule is used for generating a list of protein groups that depends on both the sample type and the sampling depth. Herein, we propose an alternative approach for examining quantitative proteomic data which is peptide-centric instead of protein-centric. We discuss the feasibility of the peptide-centric approach which was tested on several quantitative proteomic data sets. We show that peptide-centric quantification has several advantages over protein level analysis: (1) it is more sensitive for sample segregation, (2) it avoids the issues associated with protein inference, and (3) it can retrieve significant peptides lost in protein-centric quantification for further downstream analysis.

  13. Liquid Chromatography-Selected Reaction Monitoring (LC-SRM) Approach for the Separation and Quantitation of Sialylated N-Glycans Linkage Isomers

    PubMed Central

    2015-01-01

    The study of N-linked glycans is among the most challenging bioanalytical tasks because of their complexity and variety. The presence of glycoform families that differ only in branching and/or linkage position makes the identification and quantitation of individual glycans exceedingly difficult. Quantitation of these individual glycans is important because changes in the abundance of these isomers are often associated with significant biomedical events. For instance, previous studies have shown that the ratio of α2-3 to α2-6 linked sialic acid (SA) plays an important role in cancer biology. Consequently, quantitative methods to detect alterations in the ratios of glycans based on their SA linkages could serve as a diagnostic tool in oncology, yet traditional glycomic profiling cannot readily differentiate between these linkage isomers. Here, we present a liquid chromatography-selected reaction monitoring (LC-SRM) approach that we demonstrate is capable of quantitating the individual SA linkage isomers. The LC method is capable of separating sialylated N-glycan isomers differing in α2-3 and α2-6 linkages using a novel superficially porous particle (Fused-Core) Penta-HILIC (hydrophilic interaction liquid chromatography) column. SRM detection provides the relative quantitation of each SA linkage isomer, and minimizes interferences from coeluting glycans that are problematic for UV/Fluorescence based quantitation. With our approach, the relative quantitation of each SA linkage isomer is obtained from a straightforward liquid chromatography-mass spectrometry (LC-MS) experiment. PMID:25299151

  14. Comparison of Droplet Digital PCR to Real-Time PCR for Quantitative Detection of Cytomegalovirus

    PubMed Central

    Gu, Z.; Ingersoll, J.; Abdul-Ali, D.; Shi, L.; Pounds, S.; Caliendo, A. M.

    2013-01-01

    Quantitative real-time PCR (QRT-PCR) has been widely implemented for clinical viral load testing, but a lack of standardization and relatively poor precision have hindered its usefulness. Digital PCR offers highly precise, direct quantification without requiring a calibration curve. Performance characteristics of real-time PCR were compared to those of droplet digital PCR (ddPCR) for cytomegalovirus (CMV) load testing. Tenfold serial dilutions of the World Health Organization (WHO) and the National Institute of Standards and Technology (NIST) CMV quantitative standards were tested, together with the AcroMetrix CMV tc panel (Life Technologies, Carlsbad, CA) and 50 human plasma specimens. Each method was evaluated using all three standards for quantitative linearity, lower limit of detection (LOD), and accuracy. Quantitative correlation, mean viral load, and variability were compared. Real-time PCR showed somewhat higher sensitivity than ddPCR (LODs, 3 log10 versus 4 log10 copies/ml and IU/ml for NIST and WHO standards, respectively). Both methods showed a high degree of linearity and quantitative correlation for standards (R2 ≥ 0.98 in each of 6 regression models) and clinical samples (R2 = 0.93) across their detectable ranges. For higher concentrations, ddPCR showed less variability than QRT-PCR for the WHO standards and AcroMetrix standards (P < 0.05). QRT-PCR showed less variability and greater sensitivity than did ddPCR in clinical samples. Both digital and real-time PCR provide accurate CMV load data over a wide linear dynamic range. Digital PCR may provide an opportunity to reduce the quantitative variability currently seen using real-time PCR, but methods need to be further optimized to match the sensitivity of real-time PCR. PMID:23224089

  15. Pro-Social Behavior Amongst Students of Tertiary Institutions: An Explorative and a Quantitative Approach

    ERIC Educational Resources Information Center

    Quain, Samuel; Yidana, Xiaaba Dantallah; Ambotumah, Bernard Baba; Mensah-Livivnstone, Ike Joe Nii Annang

    2016-01-01

    The purpose of this paper was to explore antecedents of pro-social behavior amongst university students, using a private university as a case study. Following an explorative research, the study was guided by some theories relating to the phenomenon, focusing on gender and location factors. A quantitative approach was used in the follow up to the…

  16. A Novel Approach to Teach the Generation of Bioelectrical Potentials from a Descriptive and Quantitative Perspective

    ERIC Educational Resources Information Center

    Rodriguez-Falces, Javier

    2013-01-01

    In electrophysiology studies, it is becoming increasingly common to explain experimental observations using both descriptive methods and quantitative approaches. However, some electrophysiological phenomena, such as the generation of extracellular potentials that results from the propagation of the excitation source along the muscle fiber, are…

  17. A Quantitative Corpus-Based Approach to English Spatial Particles: Conceptual Symmetry and Its Pedagogical Implications

    ERIC Educational Resources Information Center

    Chen, Alvin Cheng-Hsien

    2014-01-01

    The present study aims to investigate how conceptual symmetry plays a role in the use of spatial particles in English and to further examine its pedagogical implications via a corpus-based evaluation of the course books in senior high schools in Taiwan. More specifically, we adopt a quantitative corpus-based approach to investigate whether bipolar…

  18. Qualitative and Quantitative Approaches to the Study of Poverty: Taming the Tensions and Appreciating the Complementarities

    ERIC Educational Resources Information Center

    Balarabe Kura, Sulaiman Y.

    2012-01-01

    There is a germane relationship between qualitative and quantitative approaches to social science research. The relationship is empirically and theoretically demonstrated by poverty researchers. The study of poverty, as argued in this article, is a study of both numbers and contextualities. This article provides a general overview of qualitative…

  19. A Novel Approach to Teach the Generation of Bioelectrical Potentials from a Descriptive and Quantitative Perspective

    ERIC Educational Resources Information Center

    Rodriguez-Falces, Javier

    2013-01-01

    In electrophysiology studies, it is becoming increasingly common to explain experimental observations using both descriptive methods and quantitative approaches. However, some electrophysiological phenomena, such as the generation of extracellular potentials that results from the propagation of the excitation source along the muscle fiber, are…

  20. Poem Generator: A Comparative Quantitative Evaluation of a Microworlds-Based Learning Approach for Teaching English

    ERIC Educational Resources Information Center

    Jenkins, Craig

    2015-01-01

    This paper is a comparative quantitative evaluation of an approach to teaching poetry in the subject domain of English that employs a "guided discovery" pedagogy using computer-based microworlds. It uses a quasi-experimental design in order to measure performance gains in computational thinking and poetic thinking following a…

  1. Rapid and quantitative detection of prostate specific antigen with a quantum dot nanobeads-based immunochromatography test strip.

    PubMed

    Li, Xue; Li, Wenbin; Yang, Qiuhua; Gong, Xiaoqun; Guo, Weisheng; Dong, Chunhong; Liu, Junqing; Xuan, Lixue; Chang, Jin

    2014-05-14

    Convenient and fast testing using an immunochromatography test strip (ICTS) enables rapid yes/no decisions regarding a disease to be made. However, the fundamental limitations of an ICTS, such as a lack of quantitative and sensitive analysis, severely hampers its application in reliable medical testing for the early detection of cancer. Herein, we overcame these limitations by integrating an ICTS with quantum dot nanobeads (QD nanobeads), which were fabricated by encapsulating QDs within modified poly(tert-butyl acrylate-co-ethyl acrylate-co-methacrylic acid) and served as a robust signal-generating reagent for the ICTS. Prostate specific antigen (PSA) was used as a model analyte to demonstrate the performance of the QD nanobeads-based ICTS platform. Under optimized conditions, the concentration of PSA could be determined within 15 min with high sensitivity and specificity using only 40 μL of sample. The detection limit was enhanced by ∼12-fold compared with that of an ICTS that used QDs encapsulated by commercial 11-mercaptoundecanoic acid (QDs@MUA) as the signal-generating reagent. At the same time, the possible clinical utility of this approach was demonstrated by measurements recorded from PSA-positive patient specimens. Our data suggest that the QD nanobeads-based ICTS platform is not only rapid and low-cost but also highly sensitive and specific for use in quantitative point-of-care diagnostics; thus, it holds promise for becoming a part of routine medical testing for the early cancer of detection.

  2. A novel quantitative real-time polymerase chain reaction method for detecting toxigenic Pasteurella multocida in nasal swabs from swine.

    PubMed

    Scherrer, Simone; Frei, Daniel; Wittenbrink, Max Michael

    2016-12-01

    Progressive atrophic rhinitis (PAR) in pigs is caused by toxigenic Pasteurella multocida. In Switzerland, PAR is monitored by selective culture of nasal swabs and subsequent polymerase chain reaction (PCR) screening of bacterial colonies for the P. multocida toxA gene. A panel of 203 nasal swabs from a recent PAR outbreak were used to evaluate a novel quantitative real-time PCR for toxigenic P. multocida in porcine nasal swabs. In comparison to the conventional PCR with a limit of detection of 100 genome equivalents per PCR reaction, the real-time PCR had a limit of detection of 10 genome equivalents. The real-time PCR detected toxA-positive P. multocida in 101 samples (49.8%), whereas the conventional PCR was less sensitive with 90 toxA-positive samples (44.3%). In comparison to the real-time PCR, 5.4% of the toxA-positive samples revealed unevaluable results by conventional PCR. The approach of culture-coupled toxA PCR for the monitoring of PAR in pigs is substantially improved by a novel quantitative real-time PCR.

  3. Methods to determine limit of detection and limit of quantification in quantitative real-time PCR (qPCR).

    PubMed

    Forootan, Amin; Sjöback, Robert; Björkman, Jens; Sjögreen, Björn; Linz, Lucas; Kubista, Mikael

    2017-06-01

    Quantitative Real-Time Polymerase Chain Reaction, better known as qPCR, is the most sensitive and specific technique we have for the detection of nucleic acids. Even though it has been around for more than 30 years and is preferred in research applications, it has yet to win broad acceptance in routine practice. This requires a means to unambiguously assess the performance of specific qPCR analyses. Here we present methods to determine the limit of detection (LoD) and the limit of quantification (LoQ) as applicable to qPCR. These are based on standard statistical methods as recommended by regulatory bodies adapted to qPCR and complemented with a novel approach to estimate the precision of LoD.

  4. Detection of quantitative trait loci for mineral content of Nelore longissimus dorsi muscle.

    PubMed

    Tizioto, Polyana C; Taylor, Jeremy F; Decker, Jared E; Gromboni, Caio F; Mudadu, Mauricio A; Schnabel, Robert D; Coutinho, Luiz L; Mourão, Gerson B; Oliveira, Priscila S N; Souza, Marcela M; Reecy, James M; Nassu, Renata T; Bressani, Flavia A; Tholon, Patricia; Sonstegard, Tad S; Alencar, Mauricio M; Tullio, Rymer R; Nogueira, Ana R A; Regitano, Luciana C A

    2015-03-11

    Beef cattle require dietary minerals for optimal health, production and reproduction. Concentrations of minerals in tissues are at least partly genetically determined. Mapping genomic regions that affect the mineral content of bovine longissimus dorsi muscle can contribute to the identification of genes that control mineral balance, transportation, absorption and excretion and that could be associated to metabolic disorders. We applied a genome-wide association strategy and genotyped 373 Nelore steers from 34 half-sib families with the Illumina BovineHD BeadChip. Genome-wide association analysis was performed for mineral content of longissimus dorsi muscle using a Bayesian approach implemented in the GenSel software. Muscle mineral content in Bos indicus cattle was moderately heritable, with estimates ranging from 0.29 to 0.36. Our results suggest that variation in mineral content is influenced by numerous small-effect QTL (quantitative trait loci) but a large-effect QTL that explained 6.5% of the additive genetic variance in iron content was detected at 72 Mb on bovine chromosome 12. Most of the candidate genes present in the QTL regions for mineral content were involved in signal transduction, signaling pathways via integral (also called intrinsic) membrane proteins, transcription regulation or metal ion binding. This study identified QTL and candidate genes that affect the mineral content of skeletal muscle. Our findings provide the first step towards understanding the molecular basis of mineral balance in bovine muscle and can also serve as a basis for the study of mineral balance in other organisms.

  5. Quantitative Magnetic Resonance Imaging Detects Changes in Meniscal Volume in Vivo After Partial Meniscectomy

    PubMed Central

    Bowers, Megan E.; Tung, Glenn A.; Oksendahl, Heidi L.; Hulstyn, Michael J.; Fadale, Paul D.; Machan, Jason T.; Fleming, Braden C.

    2010-01-01

    Background Quantifying changes in meniscal volume in vivo before and after partial meniscectomy (PM) could help elucidate the mechanisms involved in osteoarthritis development after meniscal injury and its surgical treatment. Purpose/Hypothesis To determine whether quantitative MRI (qMRI) could detect the immediate reduction in meniscal volume created by PM, while ruling out changes in unresected structures. We hypothesized that qMRI would be reliable for determining meniscal volume within the repeated images of unresected menisci. Additionally, we expected no significant difference in volume between the uninjured menisci of the injured knees and the same menisci of the uninjured knees. Study Design Controlled laboratory study. Methods Ten subjects with meniscal tears were evaluated with 3T MRI before and after arthroscopic PM. Manual segmentation was used to create models of the menisci and to determine the pre- and post-operative meniscal volumes for each subject. The responsiveness and reliability of qMRI for determining meniscal volume in vivo were evaluated using these measurements. We expected a decrease in volume of the resected menisci, but not in the uninjured menisci, after surgery. Results The mean pre-operative volume of the injured menisci was significantly greater than the mean post-operative volume (2896±277mm3 vs. 2480±277mm3; p=0.000). There was no significant difference between the mean pre- and post-operative volumes of the uninjured menisci (2687±256mm3 vs. 2694±256mm3; p=1.000). Conclusions Manual segmentation demonstrated a significant reduction in the volume of the surgically resected menisci after PM, but no significant change in the volume of unresected meniscal tissue, indicating that the manual segmentation method is responsive. Clinical Relevance This approach offers a novel, reliable method to study the relationship between the volume of meniscal tissue removed during PM and subsequent patient outcomes during long-term clinical

  6. Quantitative magnetic resonance imaging detects changes in meniscal volume in vivo after partial meniscectomy.

    PubMed

    Bowers, Megan E; Tung, Glenn A; Oksendahl, Heidi L; Hulstyn, Michael J; Fadale, Paul D; Machan, Jason T; Fleming, Braden C

    2010-08-01

    Quantifying changes in meniscal volume in vivo before and after partial meniscectomy (PM) could help elucidate the mechanisms involved in osteoarthritis development after meniscal injury and its surgical treatment. Purpose/ To determine whether quantitative magnetic resonance imaging (qMRI) can detect the immediate reduction in meniscal volume created by PM, while ruling out changes in unresected structures. We hypothesized that qMRI would be reliable for determining meniscal volume within the repeated images of unresected menisci. Additionally, we expected no significant difference in volume between the uninjured menisci of the injured knees and the same menisci of the uninjured knees. Cohort study (Diagnosis); Level of evidence, 2. Ten subjects with meniscal tears were evaluated with 3-T MRI before and after arthroscopic PM. Manual segmentation was used to create models of the menisci and to determine the preoperative and postoperative meniscal volumes for each subject. The responsiveness and reliability of qMRI for determining meniscal volume in vivo were evaluated using these measurements. We expected a decrease in volume of the resected menisci, but not in the uninjured menisci, after surgery. The mean preoperative volume of the injured menisci was significantly greater than the mean postoperative volume (2896 +/- 277 vs 2480 +/- 277 mm(3); P = .000). There was no significant difference between the mean preoperative and postoperative volumes of the uninjured menisci (2687 +/- 256 vs 2694 +/- 256 mm(3); P = 1.000). Manual segmentation demonstrated a significant reduction in the volume of the surgically resected menisci after PM, but no significant change in the volume of unresected meniscal tissue, indicating that the manual segmentation method is responsive. This approach offers a novel, reliable method to study the relationship between the volume of meniscal tissue removed during PM and subsequent patient outcomes during long-term clinical studies.

  7. Quantitative surface acoustic wave detection based on colloidal gold nanoparticles and their bioconjugates.

    PubMed

    Chiu, Chi-Shun; Gwo, Shangjr

    2008-05-01

    The immobilization scheme of monodispersed gold nanoparticles (10-nm diameter) on piezoelectric substrate surfaces using organosilane molecules as cross-linkers has been developed for lithium niobate (LiNbO3) and silicon oxide (SiO2)/gold-covered lithium tantalate (LiTaO3) of Rayleigh and guided shear horizontal- (guided SH) surface acoustic wave (SAW) sensors. In this study, comparative measurements of gold nanoparticle adsorption kinetics using high-resolution field-emission scanning electron microscopy and SAW sensors allow the frequency responses of SAW sensors to be quantitatively correlated with surface densities of adsorbed nanoparticles. Using this approach, gold nanoparticles are used as the "nanosized mass standards" to scale the mass loading in a wide dynamical range. Rayleigh-SAW and guided SH-SAW sensors are employed here to monitor the surface mass changes on the device surfaces in gas and liquid phases, respectively. The mass sensitivity ( approximately 20 Hz.cm2/ng) of Rayleigh-SAW device (fundamental oscillation frequency of 113.3 MHz in air) is more than 2 orders of magnitude higher than that of conventional 9-MHz quartz crystal microbalance sensors. Furthermore, in situ (aqueous solutions), real-time measurements of adsorption kinetics for both citrate-stabilized gold nanoparticles and DNA-gold nanoparticle conjugates are also demonstrated by guided SH-SAW (fundamental oscillation frequency of 121.3 MHz). By comparing frequency shifts between the adsorption cases of gold nanoparticles and DNA-gold nanoparticle conjugates, the average number of bound oligonucleotides per gold nanoparticle can also be determined. The high mass sensitivity ( approximately 6 Hz.cm2/ng) of guided SH-SAW sensors and successful detection of DNA-gold nanoparticle conjugates paves the way for real-time biosensing in liquids using nanoparticle-enhanced SAW devices.

  8. Quantitative surface enhanced Raman scattering detection based on the ``sandwich'' structure substrate

    NASA Astrophysics Data System (ADS)

    Zhang, Junmeng; Qu, Shengchun; Zhang, Lisheng; Tang, Aiwei; Wang, Zhanguo

    2011-08-01

    A sandwich structured substrate was designed for quantitative molecular detection using surface enhanced Raman scattering (SERS), in which the probe molecule was sandwiched between silver nanoparticles (SNPs) and silver nanoarrays. The SNPs was prepared using Lee-Meisel method, and the silver nanoarrays was fabricated on porous anodic aluminum oxide (AAO) using electrodepositing method. The SERS studies show that the sandwich structured substrate exhibits good stability and reproducibility, and the detection sensitivity of Rhodamine 6G (R6G) and Melamine can respectively reach up to 10 -19 M and 10 -9 M, which is improved greatly as compared to other SERS substrates. The improved SERS sensitivity is closely associated with the stronger electromagnetic field enhancement, which stems from localized surface plasmon (LSP) coupling between the two silver nanostructures. Furthermore, the SERS intensity increased almost linearly as the mother concentration increased, which indicates that such a sandwich structure may be used as a good SERS substrate for quantitative analysis.

  9. Quantitative detection of defects based on Markov-PCA-BP algorithm using pulsed infrared thermography technology

    NASA Astrophysics Data System (ADS)

    Tang, Qingju; Dai, Jingmin; Liu, Junyan; Liu, Chunsheng; Liu, Yuanlin; Ren, Chunping

    2016-07-01

    Quantitative detection of debonding defects' diameter and depth in TBCs has been carried out using pulsed infrared thermography technology. By combining principal component analysis with neural network theory, the Markov-PCA-BP algorithm was proposed. The principle and realization process of the proposed algorithm was described. In the prediction model, the principal components which can reflect most characteristics of the thermal wave signal were set as the input, and the defect depth and diameter was set as the output. The experimental data from pulsed infrared thermography tests of TBCs with flat bottom hole defects was selected as the training and testing sample. Markov-PCA-BP predictive system was arrived, based on which both the defect depth and diameter were identified accurately, which proved the effectiveness of the proposed method for quantitative detection of debonding defects in TBCs.

  10. Detection and quantitation of proteoglycans extracted from cell culture medium and cultured cartilage slices

    SciTech Connect

    Hronowski, L.J.; Anastassiades, T.P.

    1988-11-01

    Detection and quantitation of extracted proteoglycans, by staining with the dye Alcian blue on cellulose acetate followed by dissolution of the stained cellulose acetate strips in dimethyl sulfoxide containing 0.5% (v/v) sulfuric acid for absorbance measurement, is described. It is shown that, in the present system, the dye uptake by the proteoglycan is dependent only on the glycosaminoglycan content of the proteoglycan. The method is applied to the quantitation and characterization of proteoglycans and glycosaminoglycans, which have been extracted from radiolabeled bovine ankle cartilage and from mononuclear cell supernatant and which have been separated by DEAE-Sephacel column chromatography. The high sensitivity of the method allows detection of proteoglycans in 25-microliters samples of solutions containing as little as 1 microgram of glycosaminoglycan per milliliter of solution.

  11. Detection of Mycobacterium avium subsp. paratuberculosis in Drinking Water and Biofilms by Quantitative PCR ▿ †

    PubMed Central

    Beumer, Amy; King, Dawn; Donohue, Maura; Mistry, Jatin; Covert, Terry; Pfaller, Stacy

    2010-01-01

    It has been suggested that Mycobacterium avium subspecies paratuberculosis has a role in Crohn's disease. The organism may be acquired but is difficult to culture from the environment. We describe a quantitative PCR (qPCR) method to detect M. avium subsp. paratuberculosis in drinking water and the results of its application to drinking water and faucet biofilm samples collected in the United States. PMID:20817803

  12. Quantitative determination of Closantel residues in milk by high-performance liquid chromatography with fluorescence detection.

    PubMed

    Stoev, G; Dakova, T; Michailova, A

    1999-06-18

    A HPLC method with fluorescence detection for quantitative determination of Closantel residues in milk has been developed and validated. The proposed cleaning procedure with acetonitrile and acetone extraction, and solid-phase clean-up with Florisil enables concentrations of Closantel below 50 micrograms/l to be determined. The method was shown to be sufficient, precise, accurate, selective and rugged. The method was applied in the regular monitoring of Closantel residues in milk and of the pharmacokinetic behavior of Closantel in sheep.

  13. Design of an Evolutionary Approach for Intrusion Detection

    PubMed Central

    2013-01-01

    A novel evolutionary approach is proposed for effective intrusion detection based on benchmark datasets. The proposed approach can generate a pool of noninferior individual solutions and ensemble solutions thereof. The generated ensembles can be used to detect the intrusions accurately. For intrusion detection problem, the proposed approach could consider conflicting objectives simultaneously like detection rate of each attack class, error rate, accuracy, diversity, and so forth. The proposed approach can generate a pool of noninferior solutions and ensembles thereof having optimized trade-offs values of multiple conflicting objectives. In this paper, a three-phase, approach is proposed to generate solutions to a simple chromosome design in the first phase. In the first phase, a Pareto front of noninferior individual solutions is approximated. In the second phase of the proposed approach, the entire solution set is further refined to determine effective ensemble solutions considering solution interaction. In this phase, another improved Pareto front of ensemble solutions over that of individual solutions is approximated. The ensemble solutions in improved Pareto front reported improved detection results based on benchmark datasets for intrusion detection. In the third phase, a combination method like majority voting method is used to fuse the predictions of individual solutions for determining prediction of ensemble solution. Benchmark datasets, namely, KDD cup 1999 and ISCX 2012 dataset, are used to demonstrate and validate the performance of the proposed approach for intrusion detection. The proposed approach can discover individual solutions and ensemble solutions thereof with a good support and a detection rate from benchmark datasets (in comparison with well-known ensemble methods like bagging and boosting). In addition, the proposed approach is a generalized classification approach that is applicable to the problem of any field having multiple conflicting

  14. A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture.

    PubMed

    Ibarrola, Nieves; Kalume, Dario E; Gronborg, Mads; Iwahori, Akiko; Pandey, Akhilesh

    2003-11-15

    Posttranslational modifications are major mechanisms of regulating protein activity and function in vertebrate cells. It is essential to obtain qualitative information about posttranslational modification patterns of proteins to understand signal transduction mechanisms in greater detail. However, it is equally important to measure the dynamics of posttranslational modifications such as phosphorylation to approach signaling networks from a systems biology perspective. Despite a number of advances, methods to quantitate posttranslational modifications remain difficult to implement due to a number of factors including lack of a generic method, elaborate chemical steps, and requirement for large amounts of sample. We have previously shown that stable isotope-containing amino acids in cell culture (SILAC) can be used to differentially label growing cell populations for quantitation of protein levels. In this report, we extend the use of SILAC as a novel proteomic approach for the relative quantitation of posttranslational modifications such as phosphorylation. We have used SILAC to quantitate the extent of known phosphorylation sites as well as to identify and quantitate novel phosphorylation sites.

  15. 'Stories' or 'snapshots'? A study directed at comparing qualitative and quantitative approaches to curriculum evaluation.

    PubMed

    Pateman, B; Jinks, A M

    1999-01-01

    The focus of this paper is a study designed to explore the validity of quantitative approaches of student evaluation in a pre-registration degree programme. As managers of the students' education we were concerned that the quantitative method, which used lecturer criteria, may not fully represent students' views. The approach taken is that of a process-type strategy for curriculum evaluation as described by Parlett and Hamilton (1972). The aim of the study is to produce illuminative data, or students' 'stories' of their educational experiences through use of semi-structured interviews. The results are then compared to the current quantitative measurement tools designed to obtain 'snapshots' of the educational effectiveness of the curriculum. The quantitative measurement tools use Likert scale measurements of teacher-devised criterion statements. The results of the study give a rich source of qualitative data which can be used to inform future curriculum development. However, complete validation of the current quantitative instruments used was not achieved in this study. Student and teacher agendas in respect of important issues pertaining to the course programme were found to differ. Limitations of the study are given. There is discussion of the options open to the management team with regard to future development of curriculum evaluation systems.

  16. Detection, characterization and quantitation of coxsackievirus A16 using polyclonal antibodies against recombinant capsid subunit proteins.

    PubMed

    Liu, Qingwei; Ku, Zhiqiang; Cai, Yicun; Sun, Bing; Leng, Qibin; Huang, Zhong

    2011-04-01

    Coxsackievirus A16 (CVA16), together with enterovirus type 71 (EV71), is responsible for most cases of hand, foot and mouth disease (HFMD) worldwide. Recent findings suggest that the recombination between CVA16 and EV71, and co-circulation of these two viruses may have contributed to the increase of HFMD cases in China over the past few years. Thus, for CVA16, further understanding of its virology, epidemiology and development of diagnostic tests and vaccines are of importance. The present study aimed to develop reagents and protocols for the detection, characterization and quantitation of CVA16. Recombinant CVA16 capsid subunit proteins VP0, VP3 and truncated VP1, were produced in Escherichia coli and used to immunize guinea pigs to generate polyclonal antibodies. The resultant three antisera detected specifically CVA16 propagated in Vero cells by immunostaining, ELISA and Western blotting. The antisera was used to show that CVA16 capsids were composed of correctly processed VP0, VP1 and VP3 subunits, and were present in the form of efficiently assembled particles. A method for the quantitation of the yield of CVA16 in Vero cells was established based on a Western blotting protocol using the recombinant VP0 as a reference standard and anti-VP0 as the detection antibody. This study shows the development and validation of reagents and methods, for qualitative and quantitative determination of CVA16, which are essential for the development of vaccines.

  17. Microfluidic bead trap as a visual bar for quantitative detection of oligonucleotides.

    PubMed

    Zhao, Zichen; Bao, Yuanye; Chu, Lok Ting; Ho, John Kin Lim; Chieng, Ching-Chang; Chen, Ting-Hsuan

    2017-09-04

    We demonstrate a microfluidic bead trap capable of forming a dipstick-type bar visible to the naked eye for simple and quantitative detection of oligonucleotides. We use magnetic microparticles (MMPs) and polystyrene microparticles (PMPs) that are connected and form MMPs-targets-PMPs when target oligonucleotides are present, leaving free PMPs with a number inversely proportional to the amount of targets. Using a capillary flow-driven microfluidic circuitry consisting of a magnetic separator to remove the MMPs-targets-PMPs, the free PMPs can be trapped at the narrowing nozzle downstream, forming a visual bar quantifiable based on the length of PMP accumulation. Such a power-free and instrument-free platform enables a limit of detection at 13 fmol (0.65 nM in 20 μl, S/N = 3) of oligonucleotides and is compatible with single-nucleotide polymorphisms and operation in a complex bio-fluid. Moreover, using DNAzyme as the target oligonucleotide that catalyzes a specific hydrolytic cleavage in the presence of lead ions, we demonstrate a model application that detects lead ions with a limit of detection of 12.2 nM (2.5 μg l(-1)), providing quantitative and visual detection of lead contamination at resource-limited sites.

  18. Microwave-accelerated bioassay technique for rapid and quantitative detection of biological and environmental samples.

    PubMed

    Mohammed, Muzaffer; Syed, Maleeha F; Aslan, Kadir

    2016-01-15

    Quantitative detection of molecules of interest from biological and environmental samples in a rapid manner, particularly with a relevant concentration range, is imperative to the timely assessment of human diseases and environmental issues. In this work, we employed the microwave-accelerated bioassay (MAB) technique, which is based on the combined use of circular bioassay platforms and microwave heating, for rapid and quantitative detection of Glial Fibrillary Acidic Protein (GFAP) and Shiga like toxin (STX 1). The proof-of-principle use of the MAB technique with the circular bioassay platforms for the rapid detection of GFAP in buffer based on colorimetric and fluorescence readouts was demonstrated with a 900W kitchen microwave. We also employed the MAB technique with a new microwave system (called the iCrystal system) for the detection of GFAP from mice with brain injuries and STX 1 from a city water stream. Control bioassays included the commercially available gold standard bioassay kits run at room temperature. Our results show that the lower limit of detection (LLOD) of the colorimetric and fluorescence based bioassays for GFAP was decreased by ~1000 times using the MAB technique and our circular bioassay platforms as compared to the commercially available bioassay kits. The overall bioassay time for GFAP and STX 1 was reduced from 4h using commercially available bioassay kits to 10min using the MAB technique.

  19. Comparison of standard, quantitative and digital PCR in the detection of enterotoxigenic Bacteroides fragilis.

    PubMed

    Purcell, Rachel V; Pearson, John; Frizelle, Frank A; Keenan, Jacqueline I

    2016-09-30

    Gut colonization with enterotoxigenic Bacteroides fragilis (ETBF) appears to be associated with the development of colorectal cancer. However, differences in carriage rates are seen with various testing methods and sampling sites. We compared standard PCR, SYBR green and TaqMan quantitative PCR (qPCR) and digital PCR (dPCR) in detecting the B. fragilis toxin (bft) gene from cultured ETBF, and from matched luminal and faecal stool samples from 19 colorectal cancer patients. Bland-Altman analysis found that all three quantitative methods performed comparably in detecting bft from purified bacterial DNA, with the same limits of detection (<1 copy/μl). However, SYBR qPCR under-performed compared to TaqMan qPCR and dPCR in detecting bft in clinical stool samples; 13/38 samples were reported positive by SYBR, compared to 35 and 36 samples by TaqMan and dPCR, respectively. TaqMan qPCR and dPCR gave bft copy numbers that were 48-fold and 75-fold higher for the same samples than SYBR qPCR, respectively (p < 0.001). For samples that were bft-positive in both fecal and luminal stools, there was no difference in relative abundance between the sites, by any method tested. From our findings, we recommend the use of TaqMan qPCR as the preferred method to detect ETBF from clinical stool samples.

  20. A web-based quantitative signal detection system on adverse drug reaction in China.

    PubMed

    Li, Chanjuan; Xia, Jielai; Deng, Jianxiong; Chen, Wenge; Wang, Suzhen; Jiang, Jing; Chen, Guanquan

    2009-07-01

    To establish a web-based quantitative signal detection system for adverse drug reactions (ADRs) based on spontaneous reporting to the Guangdong province drug-monitoring database in China. Using Microsoft Visual Basic and Active Server Pages programming languages and SQL Server 2000, a web-based system with three software modules was programmed to perform data preparation and association detection, and to generate reports. Information component (IC), the internationally recognized measure of disproportionality for quantitative signal detection, was integrated into the system, and its capacity for signal detection was tested with ADR reports collected from 1 January 2002 to 30 June 2007 in Guangdong. A total of 2,496 associations including known signals were mined from the test database. Signals (e.g., cefradine-induced hematuria) were found early by using the IC analysis. In addition, 291 drug-ADR associations were alerted for the first time in the second quarter of 2007. The system can be used for the detection of significant associations from the Guangdong drug-monitoring database and could be an extremely useful adjunct to the expert assessment of very large numbers of spontaneously reported ADRs for the first time in China.

  1. Validation of quantitative and qualitative methods for detecting allergenic ingredients in processed foods in Japan.

    PubMed

    Sakai, Shinobu; Adachi, Reiko; Akiyama, Hiroshi; Teshima, Reiko

    2013-06-19

    A labeling system for food allergenic ingredients was established in Japan in April 2002. To monitor the labeling, the Japanese government announced official methods for detecting allergens in processed foods in November 2002. The official methods consist of quantitative screening tests using enzyme-linked immunosorbent assays (ELISAs) and qualitative confirmation tests using Western blotting or polymerase chain reactions (PCR). In addition, the Japanese government designated 10 μg protein/g food (the corresponding allergenic ingredient soluble protein weight/food weight), determined by ELISA, as the labeling threshold. To standardize the official methods, the criteria for the validation protocol were described in the official guidelines. This paper, which was presented at the Advances in Food Allergen Detection Symposium, ACS National Meeting and Expo, San Diego, CA, Spring 2012, describes the validation protocol outlined in the official Japanese guidelines, the results of interlaboratory studies for the quantitative detection method (ELISA for crustacean proteins) and the qualitative detection method (PCR for shrimp and crab DNAs), and the reliability of the detection methods.

  2. An ECL-PCR method for quantitative detection of point mutation

    NASA Astrophysics Data System (ADS)

    Zhu, Debin; Xing, Da; Shen, Xingyan; Chen, Qun; Liu, Jinfeng

    2005-04-01

    A new method for identification of point mutations was proposed. Polymerase chain reaction (PCR) amplification of a sequence from genomic DNA was followed by digestion with a kind of restriction enzyme, which only cut the wild-type amplicon containing its recognition site. Reaction products were detected by electrochemiluminescence (ECL) assay after adsorption of the resulting DNA duplexes to the solid phase. One strand of PCR products carries biotin to be bound on a streptavidin-coated microbead for sample selection. Another strand carries Ru(bpy)32+ (TBR) to react with tripropylamine (TPA) to emit light for ECL detection. The method was applied to detect a specific point mutation in H-ras oncogene in T24 cell line. The results show that the detection limit for H-ras amplicon is 100 fmol and the linear range is more than 3 orders of magnitude, thus, make quantitative analysis possible. The genotype can be clearly discriminated. Results of the study suggest that ECL-PCR is a feasible quantitative method for safe, sensitive and rapid detection of point mutation in human genes.

  3. Microwave-Accelerated Bioassay Technique for Rapid and Quantitative Detection of Biological and Environmental Samples

    PubMed Central

    Mohammed, Muzaffer; Syed, Maleeha F.; Aslan, Kadir

    2015-01-01

    Quantitative detection of molecules of interest from biological and environmental samples in a rapid manner, particularly with a relevant concentration range, is imperative to the timely assessment of human diseases and environmental issues. In this work, we employed the microwave-accelerated bioassay (MAB) technique, which is based on the combined use of circular bioassay platforms and microwave heating, for rapid and quantitative detection of Glial Fibrillary Acidic Protein (GFAP) and Shiga like toxin (STX 1). The proof-of-principle use of the MAB technique with the circular bioassay platforms for the rapid detection of GFAP in buffer based on colorimetric and fluorescence readouts was demonstrated with a 900 W kitchen microwave. We also employed the MAB technique with a new microwave system (called the iCrystal system) for the detection of GFAP from mice with brain injuries and STX 1 from a city water stream. Control bioassays included the commercially available gold standard bioassay kits run at room temperature. Our results show that the lower limit of detection (LLOD) of the colorimetric and fluorescence based bioassays for GFAP was decreased by ~1,000 times using the MAB technique and our circular bioassay platforms as compared to the commercially available bioassay kits. The overall bioassay time for GFAP and STX 1 was reduced from 4 hours using commercially available bioassay kits to 10 minutes using the MAB technique. PMID:26356762

  4. Quantitative Ultrasound Assessment of Duchenne Muscular Dystrophy Using Edge Detection Analysis.

    PubMed

    Koppaka, Sisir; Shklyar, Irina; Rutkove, Seward B; Darras, Basil T; Anthony, Brian W; Zaidman, Craig M; Wu, Jim S

    2016-09-01

    The purpose of this study was to investigate the ability of quantitative ultrasound (US) using edge detection analysis to assess patients with Duchenne muscular dystrophy (DMD). After Institutional Review Board approval, US examinations with fixed technical parameters were performed unilaterally in 6 muscles (biceps, deltoid, wrist flexors, quadriceps, medial gastrocnemius, and tibialis anterior) in 19 boys with DMD and 21 age-matched control participants. The muscles of interest were outlined by a tracing tool, and the upper third of the muscle was used for analysis. Edge detection values for each muscle were quantified by the Canny edge detection algorithm and then normalized to the number of edge pixels in the muscle region. The edge detection values were extracted at multiple sensitivity thresholds (0.01-0.99) to determine the optimal threshold for distinguishing DMD from normal. Area under the receiver operating curve values were generated for each muscle and averaged across the 6 muscles. The average age in the DMD group was 8.8 years (range, 3.0-14.3 years), and the average age in the control group was 8.7 years (range, 3.4-13.5 years). For edge detection, a Canny threshold of 0.05 provided the best discrimination between DMD and normal (area under the curve, 0.96; 95% confidence interval, 0.84-1.00). According to a Mann-Whitney test, edge detection values were significantly different between DMD and controls (P < .0001). Quantitative US imaging using edge detection can distinguish patients with DMD from healthy controls at low Canny thresholds, at which discrimination of small structures is best. Edge detection by itself or in combination with other tests can potentially serve as a useful biomarker of disease progression and effectiveness of therapy in muscle disorders.

  5. Quantitative nucleation and growth kinetics of gold nanoparticles via model-assisted dynamic spectroscopic approach.

    PubMed

    Zhou, Yao; Wang, Huixuan; Lin, Wenshuang; Lin, Liqin; Gao, Yixian; Yang, Feng; Du, Mingming; Fang, Weiping; Huang, Jiale; Sun, Daohua; Li, Qingbiao

    2013-10-01

    Lacking of quantitative experimental data and/or kinetic models that could mathematically depict the redox chemistry and the crystallization issue, bottom-to-up formation kinetics of gold nanoparticles (GNPs) remains a challenge. We measured the dynamic regime of GNPs synthesized by l-ascorbic acid (representing a chemical approach) and/or foliar aqueous extract (a biogenic approach) via in situ spectroscopic characterization and established a redox-crystallization model which allows quantitative and separate parameterization of the nucleation and growth processes. The main results were simplified as the following aspects: (I) an efficient approach, i.e., the dynamic in situ spectroscopic characterization assisted with the redox-crystallization model, was established for quantitative analysis of the overall formation kinetics of GNPs in solution; (II) formation of GNPs by the chemical and the biogenic approaches experienced a slow nucleation stage followed by a growth stage which behaved as a mixed-order reaction, and different from the chemical approach, the biogenic method involved heterogeneous nucleation; (III) also, biosynthesis of flaky GNPs was a kinetic-controlled process favored by relatively slow redox chemistry; and (IV) though GNPs formation consists of two aspects, namely the redox chemistry and the crystallization issue, the latter was the rate-determining event that controls the dynamic regime of the whole physicochemical process.

  6. Quantitative Systems Pharmacology Approaches Applied to Microphysiological Systems (MPS): Data Interpretation and Multi-MPS Integration

    PubMed Central

    Yu, J; Cilfone, NA; Large, EM; Sarkar, U; Wishnok, JS; Tannenbaum, SR; Hughes, DJ; Lauffenburger, DA; Griffith, LG; Stokes, CL; Cirit, M

    2015-01-01

    Our goal in developing Microphysiological Systems (MPS) technology is to provide an improved approach for more predictive preclinical drug discovery via a highly integrated experimental/computational paradigm. Success will require quantitative characterization of MPSs and mechanistic analysis of experimental findings sufficient to translate resulting insights from in vitro to in vivo. We describe herein a systems pharmacology approach to MPS development and utilization that incorporates more mechanistic detail than traditional pharmacokinetic/pharmacodynamic (PK/PD) models. A series of studies illustrates diverse facets of our approach. First, we demonstrate two case studies: a PK data analysis and an inflammation response––focused on a single MPS, the liver/immune MPS. Building on the single MPS modeling, a theoretical investigation of a four-MPS interactome then provides a quantitative way to consider several pharmacological concepts such as absorption, distribution, metabolism, and excretion in the design of multi-MPS interactome operation and experiments. PMID:26535159

  7. Quantitative Systems Pharmacology Approaches Applied to Microphysiological Systems (MPS): Data Interpretation and Multi-MPS Integration.

    PubMed

    Yu, J; Cilfone, N A; Large, E M; Sarkar, U; Wishnok, J S; Tannenbaum, S R; Hughes, D J; Lauffenburger, D A; Griffith, L G; Stokes, C L; Cirit, M

    2015-10-01

    Our goal in developing Microphysiological Systems (MPS) technology is to provide an improved approach for more predictive preclinical drug discovery via a highly integrated experimental/computational paradigm. Success will require quantitative characterization of MPSs and mechanistic analysis of experimental findings sufficient to translate resulting insights from in vitro to in vivo. We describe herein a systems pharmacology approach to MPS development and utilization that incorporates more mechanistic detail than traditional pharmacokinetic/pharmacodynamic (PK/PD) models. A series of studies illustrates diverse facets of our approach. First, we demonstrate two case studies: a PK data analysis and an inflammation response--focused on a single MPS, the liver/immune MPS. Building on the single MPS modeling, a theoretical investigation of a four-MPS interactome then provides a quantitative way to consider several pharmacological concepts such as absorption, distribution, metabolism, and excretion in the design of multi-MPS interactome operation and experiments.

  8. [High output stoma: detection and approach].

    PubMed

    Arenas Villafranca, Jose Javier; Abilés, Jimena; Moreno, Gloria; Tortajada Goitia, Begoña; Utrilla Navarro, Pilar; Gándara Adán, Norberto

    2014-12-01

    High output stoma is a frequent complication in patients with ileostomies that is not well identified and is not often properly addressed by clinicians. It has not been described properly, and can vary between debits of 2.000ml in 24 h to 1.500 ml in 3-5 days, according to different authors. Frequently presents both short-term and long-term negative implications for patients and is associated with readmissions. We present a review of published literature focusing in surgical resection-related factors that influence a later appearance of this complication, causes involved in its development, the need to establish a clear and objective concept of high ouput as well as the negative implications it presents. Also we develop how should we the management of these patients regarding treatment and nutritional approach.

  9. A Quantitative Real-Time PCR Approach for Assessing Campylobacter jejuni and Campylobacter coli Colonization in Broiler Herds.

    PubMed

    Haas, Katrin; Overesch, Gudrun; Kuhnert, Peter

    2017-04-01

    Human campylobacteriosis is a major public health concern in developed countries, with Campylobacter jejuni and Campylobacter coli from poultry recognized as the main source of human infection. Identification of Campylobacter-positive broiler herds before slaughter is essential for implementing measures to avoid carryover of pathogens via the slaughter process into the food chain. However, appropriate methods that have been validated for testing poultry flocks antemortem are lacking for Campylobacter. A quantitative real-time PCR (qPCR) that allows simultaneous detection and quantification of C. jejuni and C. coli was adapted and optimized to be applied on boot socks. The adjusted qPCR serves as an easy, sensitive, and quantitative method for Campylobacter detection in poultry flocks antemortem by analysis of boot socks. An adequate correlation was found between qPCR and culture, as well as between boot socks and cecal samples, which are regarded as the "gold standard." Therefore, boot sock sampling followed by qPCR analysis provides a reliable and simple method for assessing Campylobacter load within a flock prior to slaughter. The approach allows categorization of broiler herds into negative, low, moderate, or high Campylobacter colonization. Based on the results of this new approach, risk assessment models, such as evaluating the possible effect of sorting flocks before slaughter, can be easily implemented. Similarly, targeted identification of highly colonized flocks for improvement of biosecurity measures at the farm level will become feasible, presenting an opportunity to increase food safety.

  10. Application of Programmable Bio-Nano-Chip System for the Quantitative Detection of Drugs of Abuse in Oral Fluids*

    PubMed Central

    Christodoulides, Nicolaos; De La Garza, Richard; Simmons, Glennon W.; McRae, Michael P.; Wong, Jorge; Newton, Thomas F.; Smith, Regina; Mahoney, James J.; Hohenstein, Justin; Gomez, Sobeyda; Floriano, Pierre N.; Talavera, Humberto; Sloan, Daniel J.; Moody, David E.; Andrenyak, David M.; Kosten, Thomas R.; Haque, Ahmed; McDevitt, John T.

    2015-01-01

    Objective There is currently a gap in on-site drug of abuse monitoring. Current detection methods involve invasive sampling of blood and urine specimens, or collection of oral fluid, followed by qualitative screening tests using immunochromatographic cartridges. While remote laboratories then may provide confirmation and quantitative assessment of a presumptive positive, this instrumentation is expensive and decoupled from the initial sampling making the current drug-screening program inefficient and costly. The authors applied a noninvasive oral fluid sampling approach integrated with the in-development chip-based Programmable Bio-Nano-Chip (p-BNC) platform for the detection of drugs of abuse. Method The p-BNC assay methodology was applied for the detection of tetrahydrocannabinol, morphine, amphetamine, methamphetamine, cocaine, methadone and benzodiazepines, initially using spiked buffered samples and, ultimately, using oral fluid specimen collected from consented volunteers. Results Rapid (~10 minutes), sensitive detection (~ng/ml) and quantitation of 12 drugs of abuse was demonstrated on the p-BNC platform. Furthermore, the system provided visibility to time-course of select drug and metabolite profiles in oral fluids; for the drug cocaine, three regions of slope were observed that, when combined with concentration measurements from this and prior impairment studies, information about cocaine-induced impairment may be revealed. Conclusions This chip-based p-BNC detection modality has significant potential to be used in the future by law enforcement officers for roadside drug testing and to serve a variety of other settings, including outpatient and inpatient drug rehabilitation centers, emergency rooms, prisons, schools, and in the workplace. PMID:26048639

  11. Quantitative subpixel spectral detection of targets in multispectral images. [terrestrial and planetary surfaces

    NASA Technical Reports Server (NTRS)

    Sabol, Donald E., Jr.; Adams, John B.; Smith, Milton O.

    1992-01-01

    The conditions that affect the spectral detection of target materials at the subpixel scale are examined. Two levels of spectral mixture analysis for determining threshold detection limits of target materials in a spectral mixture are presented, the cases where the target is detected as: (1) a component of a spectral mixture (continuum threshold analysis) and (2) residuals (residual threshold analysis). The results of these two analyses are compared under various measurement conditions. The examples illustrate the general approach that can be used for evaluating the spectral detectability of terrestrial and planetary targets at the subpixel scale.

  12. Quantitative subpixel spectral detection of targets in multispectral images. [terrestrial and planetary surfaces

    NASA Technical Reports Server (NTRS)

    Sabol, Donald E., Jr.; Adams, John B.; Smith, Milton O.

    1992-01-01

    The conditions that affect the spectral detection of target materials at the subpixel scale are examined. Two levels of spectral mixture analysis for determining threshold detection limits of target materials in a spectral mixture are presented, the cases where the target is detected as: (1) a component of a spectral mixture (continuum threshold analysis) and (2) residuals (residual threshold analysis). The results of these two analyses are compared under various measurement conditions. The examples illustrate the general approach that can be used for evaluating the spectral detectability of terrestrial and planetary targets at the subpixel scale.

  13. A new systematic and quantitative approach to characterization of surface nanostructures using fuzzy logic

    NASA Astrophysics Data System (ADS)

    Al-Mousa, Amjed A.

    Thin films are essential constituents of modern electronic devices and have a multitude of applications in such devices. The impact of the surface morphology of thin films on the device characteristics where these films are used has generated substantial attention to advanced film characterization techniques. In this work, we present a new approach to characterize surface nanostructures of thin films by focusing on isolating nanostructures and extracting quantitative information, such as the shape and size of the structures. This methodology is applicable to any Scanning Probe Microscopy (SPM) data, such as Atomic Force Microscopy (AFM) data which we are presenting here. The methodology starts by compensating the AFM data for some specific classes of measurement artifacts. After that, the methodology employs two distinct techniques. The first, which we call the overlay technique, proceeds by systematically processing the raster data that constitute the scanning probe image in both vertical and horizontal directions. It then proceeds by classifying points in each direction separately. Finally, the results from both the horizontal and the vertical subsets are overlaid, where a final decision on each surface point is made. The second technique, based on fuzzy logic, relies on a Fuzzy Inference Engine (FIE) to classify the surface points. Once classified, these points are clustered into surface structures. The latter technique also includes a mechanism which can consistently distinguish crowded surfaces from those with sparsely distributed structures and then tune the fuzzy technique system uniquely for that surface. Both techniques have been applied to characterize organic semiconductor thin films of pentacene on different substrates. Also, we present a case study to demonstrate the effectiveness of our methodology to identify quantitatively particle sizes of two specimens of gold nanoparticles of different nominal dimensions dispersed on a mica surface. A comparison

  14. Localization of Epileptogenic Zone on Pre-surgical Intracranial EEG Recordings: Toward a Validation of Quantitative Signal Analysis Approaches.

    PubMed

    Andrzejak, Ralph G; David, Olivier; Gnatkovsky, Vadym; Wendling, Fabrice; Bartolomei, Fabrice; Francione, Stefano; Kahane, Philippe; Schindler, Kaspar; de Curtis, Marco

    2015-11-01

    In patients diagnosed with pharmaco-resistant epilepsy, cerebral areas responsible for seizure generation can be defined by performing implantation of intracranial electrodes. The identification of the epileptogenic zone (EZ) is based on visual inspection of the intracranial electroencephalogram (IEEG) performed by highly qualified neurophysiologists. New computer-based quantitative EEG analyses have been developed in collaboration with the signal analysis community to expedite EZ detection. The aim of the present report is to compare different signal analysis approaches developed in four different European laboratories working in close collaboration with four European Epilepsy Centers. Computer-based signal analysis methods were retrospectively applied to IEEG recordings performed in four patients undergoing pre-surgical exploration of pharmaco-resistant epilepsy. The four methods elaborated by the different teams to identify the EZ are based either on frequency analysis, on nonlinear signal analysis, on connectivity measures or on statistical parametric mapping of epileptogenicity indices. All methods converge on the identification of EZ in patients that present with fast activity at seizure onset. When traditional visual inspection was not successful in detecting EZ on IEEG, the different signal analysis methods produced highly discordant results. Quantitative analysis of IEEG recordings complement clinical evaluation by contributing to the study of epileptogenic networks during seizures. We demonstrate that the degree of sensitivity of different computer-based methods to detect the EZ in respect to visual EEG inspection depends on the specific seizure pattern.

  15. Quantitative Detection Method of Hydroxyapatite Nanoparticles Based on Eu(3+) Fluorescent Labeling in Vitro and in Vivo.

    PubMed

    Xie, Yunfei; Perera, Thalagalage Shalika Harshani; Li, Fang; Han, Yingchao; Yin, Meizhen

    2015-11-04

    One major challenge for application of hydroxyapatite nanoparticles (nHAP) in nanomedicine is the quantitative detection method. Herein, we exploited one quantitative detection method for nHAP based on the Eu(3+) fluorescent labeling via a simple chemical coprecipitation method. The trace amount of nHAP in cells and tissues can be quantitatively detected on the basis of the fluorescent quantitative determination of Eu(3+) ions in nHAP crystal lattice. The lowest concentration of Eu(3+) ions that can be quantitatively detected is 0.5 nM using DELFIA enhancement solution. This methodology can be broadly applicable for studying the tissue distribution and metabolization of nHAP in vivo.

  16. Detection of human brain tumor infiltration with quantitative stimulated Raman scattering microscopy.

    PubMed

    Ji, Minbiao; Lewis, Spencer; Camelo-Piragua, Sandra; Ramkissoon, Shakti H; Snuderl, Matija; Venneti, Sriram; Fisher-Hubbard, Amanda; Garrard, Mia; Fu, Dan; Wang, Anthony C; Heth, Jason A; Maher, Cormac O; Sanai, Nader; Johnson, Timothy D; Freudiger, Christian W; Sagher, Oren; Xie, Xiaoliang Sunney; Orringer, Daniel A

    2015-10-14

    Differentiating tumor from normal brain is a major barrier to achieving optimal outcome in brain tumor surgery. New imaging techniques for visualizing tumor margins during surgery are needed to improve surgical results. We recently demonstrated the ability of stimulated Raman scattering (SRS) microscopy, a nondestructive, label-free optical method, to reveal glioma infiltration in animal models. We show that SRS reveals human brain tumor infiltration in fresh, unprocessed surgical specimens from 22 neurosurgical patients. SRS detects tumor infiltration in near-perfect agreement with standard hematoxylin and eosin light microscopy (κ = 0.86). The unique chemical contrast specific to SRS microscopy enables tumor detection by revealing quantifiable alterations in tissue cellularity, axonal density, and protein/lipid ratio in tumor-infiltrated tissues. To ensure that SRS microscopic data can be easily used in brain tumor surgery, without the need for expert interpretation, we created a classifier based on cellularity, axonal density, and protein/lipid ratio in SRS images capable of detecting tumor infiltration with 97.5% sensitivity and 98.5% specificity. Quantitative SRS microscopy detects the spread of tumor cells, even in brain tissue surrounding a tumor that appears grossly normal. By accurately revealing tumor infiltration, quantitative SRS microscopy holds potential for improving the accuracy of brain tumor surgery.

  17. Portable SERS-enabled micropipettes for microarea sampling and reliably quantitative detection of surface organic residues.

    PubMed

    Fang, Wei; Zhang, Xinwei; Chen, Yong; Wan, Liang; Huang, Weihua; Shen, Aiguo; Hu, Jiming

    2015-09-15

    We report the first microsampling device for reliably quantitative, label-free and separation-free detection of multicomponents of surface organic residues (SORs) by means of a quality controllable surface-enhanced Raman scattering (SERS)-enabled micropipette. The micropipette is comprised of a drawn glass capillary with a tiny orifice (∼50 μm) at the distal tip, where the specially designed nanorattles (NRs) are compactly coated on the inner wall surface. SERS signals of 4-mercapto benzoic acid (MBA) anchored inside the internal gap of NRs could be used to evaluate and control the quality of micropipettes and, therefore, allow us to overcome the limitations of a reliably quantitative SERS assay using traditional substrates without an internal standard. By dropping a trace extraction agent on targeting SORs located on a narrow surface, the capillary and SERS functionalities of these micropipettes allow on-site microsampling via capillary action and subsequent multiplex distinction/detection due to their molecularly narrow Raman peaks. For example, 8 nM thiram (TMTD), 8 nM malachite green (MG), and 1.5 μM (400 ppb) methyl parathion (MPT) on pepper and cucumber peels have been simultaneously detected in a wide detection range. The portable SERS-enabled device could potentially be facilely incorporated with liquid-liquid or solid phase micro-extracting devices for a broader range of applications in rapid and field analysis of food/public/environment security related SORs.

  18. Quantitative electromyography in the detection of the carriers in Duchenne type muscular dystrophy.

    PubMed

    Valli, G; Scarlato, G; Contartese, M

    1976-04-23

    The quantitative EMG technique was used to detect Duchenne muscular dystrophy carriers. The tests were carried out, measuring the parameters of M.U. potentials (the duration, the phase, and the 0 index according to Van den Bosch, modified by Gardner-Medwin), and using the Willison analyzer, in a group of carriers and normal subjects. Ten M.U. potentials from the deltoid, biceps brachii and quadriceps muscles were photographed and measured in each subject, and the right and the left biceps were examined with the Willison analyzer. An high detection rate was obtained by manual EMG, measuring traditional values such as mean number of phases, A.P. duration and 0 index. The Willison analyzer was significant in 2 known carriers. The total EMG detection rate was higher than the CPK tests both in the known carriers and the possible carriers. It is concluded that the quantitative EMG technique is an useful and specific test to detect carriers of the gene of Duchenne muscular dystrophy.

  19. Detection of human brain tumor infiltration with quantitative stimulated Raman scattering microscopy

    PubMed Central

    Ji, Minbiao; Lewis, Spencer; Camelo-Piragua, Sandra; Ramkissoon, Shakti H.; Snuderl, Matija; Venneti, Sriram; Fisher-Hubbard, Amanda; Garrard, Mia; Fu, Dan; Wang, Anthony C.; Heth, Jason A.; Maher, Cormac O.; Sanai, Nader; Johnson, Timothy D.; Freudiger, Christian W.; Sagher, Oren; Xie, Xiaoliang Sunney; Orringer, Daniel A.

    2016-01-01

    Differentiating tumor from normal brain is a major barrier to achieving optimal outcome in brain tumor surgery. New imaging techniques for visualizing tumor margins during surgery are needed to improve surgical results. We recently demonstrated the ability of stimulated Raman scattering (SRS) microscopy, a non-destructive, label-free optical method, to reveal glioma infiltration in animal models. Here we show that SRS reveals human brain tumor infiltration in fresh, unprocessed surgical specimens from 22 neurosurgical patients. SRS detects tumor infiltration in near-perfect agreement with standard hematoxylin and eosin light microscopy (κ=0.86). The unique chemical contrast specific to SRS microscopy enables tumor detection by revealing quantifiable alterations in tissue cellularity, axonal density and protein:lipid ratio in tumor-infiltrated tissues. To ensure that SRS microscopic data can be easily used in brain tumor surgery, without the need for expert interpretation, we created a classifier based on cellularity, axonal density and protein:lipid ratio in SRS images capable of detecting tumor infiltration with 97.5% sensitivity and 98.5% specificity. Importantly, quantitative SRS microscopy detects the spread of tumor cells, even in brain tissue surrounding a tumor that appears grossly normal. By accurately revealing tumor infiltration, quantitative SRS microscopy holds potential for improving the accuracy of brain tumor surgery. PMID:26468325

  20. A Bayesian quantitative nondestructive evaluation (QNDE) approach to estimating remaining life of aging pressure vessels and piping*

    NASA Astrophysics Data System (ADS)

    Fong, J. T.; Filliben, J. J.; Heckert, N. A.; Guthrie, W. F.

    2013-01-01

    In this paper, we use a Bayesian quantitative nondestructive evaluation (QNDE) approach to estimating the remaining life of aging structures and components. Our approach depends on in-situ NDE measurements of detectable crack lengths and crack growth rates in a multi-crack region of an aging component as a basis for estimating the mean and standard deviation of its remaining life. We introduce a general theory of crack growth involving multiple cracks such that the mean and standard deviation of the initial crack lengths can be directly estimated from NDEmeasured crack length data over a period of several inspection intervals. A numerical example using synthetic NDE data for high strength steels is presented to illustrate this new methodology.

  1. A retrospective cross-sectional quantitative molecular approach in biological samples from patients with syphilis.

    PubMed

    Pinto, Miguel; Antelo, Minia; Ferreira, Rita; Azevedo, Jacinta; Santo, Irene; Borrego, Maria José; Gomes, João Paulo

    2017-03-01

    Syphilis is the sexually transmitted disease caused by Treponema pallidum, a pathogen highly adapted to the human host. As a multistage disease, syphilis presents distinct clinical manifestations that pose different implications for diagnosis. Nevertheless, the inherent factors leading to diverse disease progressions are still unknown. We aimed to assess the association between treponemal loads and dissimilar disease outcomes, to better understand syphilis. We retrospectively analyzed 309 DNA samples distinct anatomic sites associated with particular syphilis manifestations. All samples had previously tested positive by a PCR-based diagnostic kit. An absolute quantitative real-time PCR procedure was used to precisely quantify the number of treponemal and human cells to determine T. pallidum loads in each sample. In general, lesion exudates presented the highest T. pallidum loads in contrast with blood-derived samples. Within the latter, a higher dispersion of T. pallidum quantities was observed for secondary syphilis. T. pallidum was detected in substantial amounts in 37 samples of seronegative individuals and in 13 cases considered as syphilis-treated. No association was found between treponemal loads and serological results or HIV status. This study suggests a scenario where syphilis may be characterized by: i) heterogeneous and high treponemal loads in primary syphilis, regardless of the anatomic site, reflecting dissimilar duration of chancres development and resolution; ii) high dispersion of bacterial concentrations in secondary syphilis, potentially suggesting replication capability of T. pallidum while in the bloodstream; and iii) bacterial evasiveness, either to the host immune system or antibiotic treatment, while remaining hidden in privileged niches. This work highlights the importance of using molecular approaches to study uncultivable human pathogens, such as T. pallidum, in the infection process. Copyright © 2017 Elsevier Ltd. All rights

  2. A new algorithmic approach for fingers detection and identification

    NASA Astrophysics Data System (ADS)

    Mubashar Khan, Arslan; Umar, Waqas; Choudhary, Taimoor; Hussain, Fawad; Haroon Yousaf, Muhammad

    2013-03-01

    Gesture recognition is concerned with the goal of interpreting human gestures through mathematical algorithms. Gestures can originate from any bodily motion or state but commonly originate from the face or hand. Hand gesture detection in a real time environment, where the time and memory are important issues, is a critical operation. Hand gesture recognition largely depends on the accurate detection of the fingers. This paper presents a new algorithmic approach to detect and identify fingers of human hand. The proposed algorithm does not depend upon the prior knowledge of the scene. It detects the active fingers and Metacarpophalangeal (MCP) of the inactive fingers from an already detected hand. Dynamic thresholding technique and connected component labeling scheme are employed for background elimination and hand detection respectively. Algorithm proposed a new approach for finger identification in real time environment keeping the memory and time constraint as low as possible.

  3. Quantitative ultrasound imaging detects degenerative changes in articular cartilage surface and subchondral bone

    NASA Astrophysics Data System (ADS)

    Saarakkala, Simo; Laasanen, Mikko S.; Jurvelin, Jukka S.; Töyräs, Juha

    2006-10-01

    Previous studies have suggested that quantitative ultrasound imaging could sensitively diagnose degeneration of the articular surface and changes in the subchondral bone during the development of osteoarthrosis (OA). We have recently introduced a new parameter, ultrasound roughness index (URI), for the quantification of cartilage surface roughness, and successfully tested it with normal and experimentally degraded articular surfaces. In this in vitro study, the applicability of URI was tested in bovine cartilage samples with spontaneously developed tissue degeneration. Simultaneously, we studied the sensitivity of quantitative ultrasound imaging to detect degenerative changes in the cartilage-bone interface. For reference, histological degenerative grade of the cartilage samples was determined. Mechanical reference measurements were also conducted. Cartilage surface roughness (URI) was significantly (p < 0.05) higher in histologically degenerated samples with inferior mechanical properties. Ultrasound reflection at the cartilage-bone interface was also significantly (p < 0.05) increased in degenerated samples. Furthermore, it was quantitatively confirmed that ultrasound attenuation in the overlying cartilage significantly affects the measured ultrasound reflection values from the cartilage-bone interface. To conclude, the combined ultrasound measurement of the cartilage surface roughness and ultrasound reflection at the cartilage-bone interface complement each other, and may together enable more sensitive and quantitative diagnosis of early OA or follow up after surgical cartilage repair.

  4. Comparison of antigen detection and quantitative PCR in the detection of chlamydial infection in koalas (Phascolarctos cinereus).

    PubMed

    Hanger, Jon; Loader, Joanne; Wan, Charles; Beagley, Kenneth W; Timms, Peter; Polkinghorne, Adam

    2013-03-01

    The gold standard method for detecting chlamydial infection in domestic and wild animals is PCR, but the technique is not suited to testing animals in the field when a rapid diagnosis is frequently required. The objective of this study was to compare the results of a commercially available enzyme immunoassay test for Chlamydia against a quantitative Chlamydia pecorum-specific PCR performed on swabs collected from the conjunctival sac, nasal cavity and urogenital sinuses of naturally infected koalas (Phascolarctos cinereus). The level of agreement for positive results between the two assays was low (43.2%). The immunoassay detection cut-off was determined as approximately 400 C. pecorum copies, indicating that the test was sufficiently sensitive to be used for the rapid diagnosis of active chlamydial infections. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Quantitation of HIV-1 by real-time amplification and detection

    NASA Astrophysics Data System (ADS)

    Jung, Paul M.; Yang, Naiquan; Kroeger, Paul E.

    1998-04-01

    A model assay for HIV-1 using a non-competitive internal standard in quantitative RT-PCR was coupled with real-time detection of both analyte and internal standard (IS) signals in a closed system. Real-time detection by the PE-ABI Prism 7700 relied on TaqMan probes specific for HIV and IS. The exogenous, non-competitive IS RNA was added in the same, known amount to a series of HIV RNA standards. The threshold cycle ratio from this internal standard calibration curve was used in the quantitation of HIV. Two configurations of reporter labels were compared. The HEX-HIV:FAM-IS system was the most precise, with nearly half-log discrimination over a range of 102 through 105 copies HIV-1 RNA. The FAM- HIV:HEX-IS system was less precise, but more sensitive and resistant to sample inhibition. The analysis of these signals and their impact on the range and precision of HIV quantitation is discussed. The design and synthesis of the fluorescently-labelled probes is also described.

  6. Suitability of two-dimensional electrophoretic protein separations for quantitative detection of mutations

    SciTech Connect

    Taylor, J.; Anderson, N.L.; Anderson, N.G.; Gemmell, A.; Giometti, C.S.; Nance, S.L.; Tollaksen, S.L.

    1986-01-01

    Separation of proteins by two-dimensional electrophoresis (2DE) provides a powerful method for mutagenesis studies, since hundreds of proteins can be monitored simultaneously. In previous mutation studies in which 2DE has been used, only qualitative protein differences were monitored; quantitative protein variations were not evaluated. Although significant differences in protein abundance can be detected by eye, the large number of protein spots present in 2DE patterns together with the large number of individual patterns required for a mutagenesis study would necessitate the use of a computerized analysis system to detect the rare quantitative protein changes indicative of gene deletions or inactivation of genes by point mutations in regulatory genes. A pilot study to search for heritable mutations induced by treatment of mice with either ethylnitrosourea or gamma radiation is underway. Samples are being monitored for quantitative changes that reduce the amount of protein by about 50%. The results of this study indicate that the key methods to improve the application of 2DE to mutation screening are to increase the number of measurable spots (i.e., improve stain sensitivity) and to decrease the spread of values for the volume measurements. Even small improvements in these areas could greatly increase the number of monitorable spots. 9 refs., 4 figs.

  7. Comparison of salivary collection and processing methods for quantitative HHV-8 detection.

    PubMed

    Speicher, D J; Johnson, N W

    2014-10-01

    Saliva is a proved diagnostic fluid for the qualitative detection of infectious agents, but the accuracy of viral load determinations is unknown. Stabilising fluids impede nucleic acid degradation, compared with collection onto ice and then freezing, and we have shown that the DNA Genotek P-021 prototype kit (P-021) can produce high-quality DNA after 14 months of storage at room temperature. Here we evaluate the quantitative capability of 10 collection/processing methods. Unstimulated whole mouth fluid was spiked with a mixture of HHV-8 cloned constructs, 10-fold serial dilutions were produced, and samples were extracted and then examined with quantitative PCR (qPCR). Calibration curves were compared by linear regression and qPCR dynamics. All methods extracted with commercial spin columns produced linear calibration curves with large dynamic range and gave accurate viral loads. Ethanol precipitation of the P-021 does not produce a linear standard curve, and virus is lost in the cell pellet. DNA extractions from the P-021 using commercial spin columns produced linear standard curves with wide dynamic range and excellent limit of detection. When extracted with spin columns, the P-021 enables accurate viral loads down to 23 copies μl(-1) DNA. The quantitative and long-term storage capability of this system makes it ideal for study of salivary DNA viruses in resource-poor settings. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Quantitative detection of residual porcine host cell DNA by real-time PCR.

    PubMed

    Chang, Jen-Ting; Chen, Yu-Chen; Chou, Yu-Chi; Wang, Shih-Rong

    2014-03-01

    All biological products are derived from complex living systems and are often mixed with large numbers of impurities. For reasons of safety, residual host-cell DNA must be eliminated during processing. To assay host-cell DNA content in biopharmaceutical products derived from porcine sources, this study applies the quantitative real-time polymerase chain reaction (Q-PCR) method. The optimized assay in this study is based on the pol region of the porcine endogenous retrovirus (PERV). Assay validation results demonstrate that the proposed assay has appropriate accuracy, preciseness, reproducibility, and sensitivity. Primer and probe specificity are evaluated in real-time Q-PCR reactions using genomic DNA from rabbit, mouse, cat, hamster, monkey, human cell, yeast, and Escherichia coli as templates. The sensitivity of real-time Q-PCR is determined using genomic DNA from the porcine kidney cell line. The reliable detection range is within 0.5-10(5) pg/reaction. The limit of quantitation is 500 fg. The sensitivity of the assay meets the authority criterion. Moreover, the assay is applied to determine the level of host-cell DNA in recombinant human coagulation factor IX (rhFIX) from transgenic pigs. The real-time Q-PCR assay is thus a promising new tool for quantitative detection and clearance validation of residual porcine DNA when manufacturing recombinant therapeutics.

  9. Methods for Quantitative Detection of Antibody-induced Complement Activation on Red Blood Cells

    PubMed Central

    Meulenbroek, Elisabeth M.; Wouters, Diana; Zeerleder, Sacha

    2014-01-01

    Antibodies against red blood cells (RBCs) can lead to complement activation resulting in an accelerated clearance via complement receptors in the liver (extravascular hemolysis) or leading to intravascular lysis of RBCs. Alloantibodies (e.g. ABO) or autoantibodies to RBC antigens (as seen in autoimmune hemolytic anemia, AIHA) leading to complement activation are potentially harmful and can be - especially when leading to intravascular lysis - fatal1. Currently, complement activation due to (auto)-antibodies on RBCs is assessed in vitro by using the Coombs test reflecting complement deposition on RBC or by a nonquantitative hemolytic assay reflecting RBC lysis1-4. However, to assess the efficacy of complement inhibitors, it is mandatory to have quantitative techniques. Here we describe two such techniques. First, an assay to detect C3 and C4 deposition on red blood cells that is induced by antibodies in patient serum is presented. For this, FACS analysis is used with fluorescently labeled anti-C3 or anti-C4 antibodies. Next, a quantitative hemolytic assay is described. In this assay, complement-mediated hemolysis induced by patient serum is measured making use of spectrophotometric detection of the released hemoglobin. Both of these assays are very reproducible and quantitative, facilitating studies of antibody-induced complement activation. PMID:24514151

  10. Calibration-free quantitation in microchip zone electrophoresis with conductivity detection.

    PubMed

    Noblitt, Scott D; Henry, Charles S

    2015-08-01

    The relationship between electrophoretic mobility and molar conductivity has previously led to speculation on achieving quantitation in zone electrophoresis without calibration curves when using conductivity detection. However, little work in this area has been pursued, possibly because of the breakdown of simple sensitivity-mobility relationships when working with partially protonated species. This topic is revisited with the aid of electrophoretic simulation software that produces facile predictions of analyte sensitivity relative to an internal standard. Calibration curve slopes for over 50 analyte/internal standard/BGE combinations were measured with both unbiased and electrokinetically biased injections using microchip electrophoresis with conductivity detection. The results were compared to theoretical expectations as computed with PeakMaster software. Good agreement was observed, with some systems being predicted with quantitative accuracy while others showed significant deviations. Some mechanisms that can lead to deviations from theory are demonstrated, but the causes for some discrepancies are still not understood. Overall, this work exhibits another useful application for simulation software, particularly for disposable devices where device-specific calibration curves cannot be collected. It also serves as quantitative validation for some outputs of PeakMaster simulation software.

  11. Development of an effective method for recovery of viral genomic RNA from environmental silty sediments for quantitative molecular detection.

    PubMed

    Miura, Takayuki; Masago, Yoshifumi; Sano, Daisuke; Omura, Tatsuo

    2011-06-01

    Nine approaches to recover viral RNA from environmental silty sediments were newly developed and compared to quantify RNA viruses in sediments using molecular methods. Four of the nine approaches employed direct procedures for extracting RNA from sediments (direct methods), and the remaining five approaches used indirect methods wherein viral particles were recovered before RNA extraction. A direct method using an SDS buffer with EDTA to lyse viral capsids in sediments, phenol-chloroform-isoamyl alcohol to extract RNA, isopropanol to concentrate RNA, and magnetic beads to purify RNA resulted in the highest rate of recovery (geometric mean of 11%, with a geometric standard deviation of 0.02; n = 7) of poliovirus 1 (PV1) inoculated in an environmental sediment sample. The direct method exhibiting the highest rate of PV1 recovery was applied to environmental sediment samples. One hundred eight sediment samples were collected from the Takagi River, Miyagi, Japan, and its estuary from November 2007 to April 2009, and the genomic RNAs of enterovirus and human norovirus in these samples were quantified by reverse transcription (RT)-quantitative PCR (qPCR). The human norovirus genome was detected in one sample collected at the bay, although its concentration was below the quantification limit. Meanwhile, the enterovirus genome was detected in two samples at the river mouth and river at concentrations of 8.6 × 10(2) and 2.4 × 10(2) copies/g (wet weight), respectively. This is the first report to obtain quantitative data for a human pathogenic virus in a river and in estuarine sediments using RT-qPCR.

  12. Incremental diagnostic value of combined quantitative and qualitative parameters of magnetocardiography to detect coronary artery disease.

    PubMed

    Shin, Eun-Seok; Lam, Yat-Yin; Her, Ae-Young; Brachmann, Johannes; Jung, Friedrich; Park, Jai-Wun

    2017-02-01

    Magnetocardiography (MCG) has been proposed as a non-invasive and functional technique with high accuracy for diagnosis of myocardial ischemia. This study sought to investigate the incremental diagnostic value of combined quantitative and qualitative parameters of MCG to detect coronary artery disease (CAD). Ninety six patients with suspected CAD who underwent coronary angiography were enrolled in the analysis to test the diagnostic accuracy of 2 MCG parameters (a quantitative parameter of the percent change of ST-segment fluctuation score and a qualitative parameter of non-dipole phenomenon). The best cut-off value for the percent change of ST-segment fluctuation score was -51.0%. The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value were 78.1, 73.9, 82.0, 79.1, and 77.4, in the percent change of ST-segment fluctuation score and 86.5, 84.8, 88.0, 86.7, and 86.3 in non-dipole phenomenon. The area under the curve of receiver-operating characteristics was 0.79 for the percent change of ST-segment fluctuation score and 0.86 for non-dipole phenomenon (p<0.001). However, the incorporation of non-dipole phenomenon into a model with the percent change of ST-segment fluctuation score significantly improved C-statistics, indicating the enhancement of diagnostic performance in the detection of significant CAD (0.790 to 0.930; p<0.001). Qualitative assessment of non-dipole phenomenon has a better diagnostic value than the quantitative parameter of percent change of ST-segment fluctuation score in the detection of significant CAD. Furthermore, this study found that the incorporation of non-dipole phenomenon into the percent change of ST-segment fluctuation score significantly improved the diagnostic performance of CAD detection. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells.

    PubMed

    Park, Han Sang; Rinehart, Matthew T; Walzer, Katelyn A; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection

  14. Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells

    PubMed Central

    Park, Han Sang; Rinehart, Matthew T.; Walzer, Katelyn A.; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection

  15. Quantitative Genetics and Functional–Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization

    PubMed Central

    Letort, Véronique; Mahe, Paul; Cournède, Paul-Henry; de Reffye, Philippe; Courtois, Brigitte

    2008-01-01

    Background and Aims Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype × environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional–structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods The GREENLAB model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings of the species-specific parameters of the model. The QTL Cartographer software was used to study QTL detection of simulated plant traits. A genetic algorithm was implemented to define the ideotype for yield maximization based on the model parameters and the associated allelic combination. Key Results and Conclusions By keeping the environmental factors constant and using a virtual population with a large number of individuals generated by a Mendelian genetic model, results for an ideal case could be simulated. Virtual QTL detection was compared in the case of phenotypic traits – such as cob weight – and when traits were model parameters, and was found to be more accurate in the latter case. The practical interest of this approach is illustrated by calculating the parameters (and the corresponding genotype) associated with yield optimization of a GREENLAB maize model. The paper discusses the potentials of GREENLAB to represent environment × genotype

  16. Endotoxin Detection in Pharmaceuticals and Medical Devices with Kinetic-QCL, a Kinetic-Quantitative Chromogenic Limulus Amebocyte Lysate Assay.

    PubMed

    Berzofsky, Ronald N.

    1995-01-01

    The observation that endotoxin caused gelation in extracts of Limulus amebocytes has been expanded to the development of an in vitro kinetic, quantitative chromogenic LAL assay (Kinetic-QCL) for the detection of endotoxin in aqueous fluids. Within the last 15 years, the use of Limulus amebocyte lysate to detect and control the presence of pyrogenic substances in pharmaceuticals and medical devices has gained wide international acceptance. Both the United States and European Pharmacopoeias contain descriptions of and requirements for the LAL Bacterial Endotoxin Test. Both pharmacopoeias have begun to remove the rabbit pyrogen test requirement in a majority of drug monographs and have substituted endotoxin limits to be determined by LAL. The use of LAL has proved invaluable in controlling the level of endotoxin in finished product. The endotoxin contribution of raw materials and packaging material can be monitored as well. In-process testing at critical production steps can identify additional sources of endotoxin contamination, and depyrogenation processes can be validated by quantitating the degradation of endotoxin challenges. The speed, reproducibility, sensitivity, and economics of the Kinetic-QCL assay, in conjunction with the ppropriate equipment and software, over both the in vivo rabbit pyrogen test and the more traditional LAL gel-clot assay allow a more in-depth approach to the control of endotoxin in pharmaceuticals and medical devices.

  17. Quantitative evaluation of in vivo vital-dye fluorescence endoscopic imaging for the detection of Barrett’s-associated neoplasia

    PubMed Central

    Thekkek, Nadhi; Lee, Michelle H.; Polydorides, Alexandros D.; Rosen, Daniel G.; Anandasabapathy, Sharmila; Richards-Kortum, Rebecca

    2015-01-01

    Abstract. Current imaging tools are associated with inconsistent sensitivity and specificity for detection of Barrett’s-associated neoplasia. Optical imaging has shown promise in improving the classification of neoplasia in vivo. The goal of this pilot study was to evaluate whether in vivo vital dye fluorescence imaging (VFI) has the potential to improve the accuracy of early-detection of Barrett’s-associated neoplasia. In vivo endoscopic VFI images were collected from 65 sites in 14 patients with confirmed Barrett’s esophagus (BE), dysplasia, or esophageal adenocarcinoma using a modular video endoscope and a high-resolution microendoscope (HRME). Qualitative image features were compared to histology; VFI and HRME images show changes in glandular structure associated with neoplastic progression. Quantitative image features in VFI images were identified for objective image classification of metaplasia and neoplasia, and a diagnostic algorithm was developed using leave-one-out cross validation. Three image features extracted from VFI images were used to classify tissue as neoplastic or not with a sensitivity of 87.8% and a specificity of 77.6% (AUC=0.878). A multimodal approach incorporating VFI and HRME imaging can delineate epithelial changes present in Barrett’s-associated neoplasia. Quantitative analysis of VFI images may provide a means for objective interpretation of BE during surveillance. PMID:25950645

  18. Quantitative evaluation of in vivo vital-dye fluorescence endoscopic imaging for the detection of Barrett's-associated neoplasia

    NASA Astrophysics Data System (ADS)

    Thekkek, Nadhi; Lee, Michelle H.; Polydorides, Alexandros D.; Rosen, Daniel G.; Anandasabapathy, Sharmila; Richards-Kortum, Rebecca

    2015-05-01

    Current imaging tools are associated with inconsistent sensitivity and specificity for detection of Barrett's-associated neoplasia. Optical imaging has shown promise in improving the classification of neoplasia in vivo. The goal of this pilot study was to evaluate whether in vivo vital dye fluorescence imaging (VFI) has the potential to improve the accuracy of early-detection of Barrett's-associated neoplasia. In vivo endoscopic VFI images were collected from 65 sites in 14 patients with confirmed Barrett's esophagus (BE), dysplasia, or esophageal adenocarcinoma using a modular video endoscope and a high-resolution microendoscope (HRME). Qualitative image features were compared to histology; VFI and HRME images show changes in glandular structure associated with neoplastic progression. Quantitative image features in VFI images were identified for objective image classification of metaplasia and neoplasia, and a diagnostic algorithm was developed using leave-one-out cross validation. Three image features extracted from VFI images were used to classify tissue as neoplastic or not with a sensitivity of 87.8% and a specificity of 77.6% (AUC=0.878). A multimodal approach incorporating VFI and HRME imaging can delineate epithelial changes present in Barrett's-associated neoplasia. Quantitative analysis of VFI images may provide a means for objective interpretation of BE during surveillance.

  19. A quantitative immunopolymerase chain reaction method for detection of vegetative insecticidal protein in genetically modified crops.

    PubMed

    Kumar, Rajesh

    2011-10-12

    Vegetative insecticidal protein (Vip) is being employed for transgenic expression in selected crops such as cotton, brinjal, and corn. For regulatory compliance, there is a need for a sensitive and reliable detection method, which can distinguish between approved and nonapproved genetically modified (GM) events and quantify GM contents as well. A quantitative immunopolymerase chain reaction (IPCR) method has been developed for the detection and quantification of Vip protein in GM crops. The developed assay displayed a detection limit of 1 ng/mL (1 ppb) and linear quantification range between 10 and 1000 ng/mL of Vip-S protein. The sensitivity of the assay was found to be 10 times higher than an analogous enzyme-linked immunosorbent assay for Vip-S protein. The results suggest that IPCR has the potential to become a standard method to quantify GM proteins.

  20. Fast real-time polymerase chain reaction for quantitative detection of Lactobacillus delbrueckii bacteriophages in milk.

    PubMed

    Martín, Maria Cruz; del Rio, Beatriz; Martínez, Noelia; Magadán, Alfonso H; Alvarez, Miguel A

    2008-12-01

    One of the main microbiological problems of the dairy industry is the susceptibility of starter bacteria to virus infections. Lactobacillus delbrueckii, a component of thermophilic starter cultures used in the manufacture of several fermented dairy products, including yogurt, is also sensitive to bacteriophage attacks. To avoid the problems associated with these viruses, quick and sensitive detection methods are necessary. In the present study, a fast real-time quantitative polymerase chain reaction assay for the direct detection and quantification of L. delbrueckii phages in milk was developed. A set of primers and a TaqMan MGB probe was designed, based on the lysin gene sequence of different L. delbrueckii phages. The results show the proposed method to be a rapid (total processing time 30 min), specific and highly sensitive technique for detecting L. delbrueckii phages in milk.

  1. A self-referential outlier detection method for quantitative motor unit action potential analysis.

    PubMed

    Sheean, Geoffrey L

    2012-04-01

    Quantitative MUAP analysis is often based on outlier detection, in the case of neurogenic conditions, the finding of MUAPs that are larger than the limit determined from a reference normal population. Such reference data is available from only a few sources and for only a few muscles. It would be desirable if muscles could serve as their own controls. The Henneman size principle determines the order of recruitment, following an exponential distribution of twitch force, motor neurone, motor unit, and MUAP size. Therefore, an outlier could be detected by being too large for the level of recruitment, as judged by its size relative to the other MUAPs. This would improve the sensitivity of detecting neurogenic muscles and obviate the need for external reference data.

  2. Nanomolar colorimetric quantitative detection of Fe3 + and PPi with high selectivity

    NASA Astrophysics Data System (ADS)

    Li, Zhanxian; Li, Haixia; Shi, Caixia; Yu, Mingming; Wei, Liuhe; Ni, Zhonghai

    2016-04-01

    A novel rhodamine and 8-hydroxyquinoline-based derivative was synthesized, which is shown to act as a colorimetric chemosensor for Fe3 + in aqueous solution with high selectivity over various environmentally and biologically relevant metal ions and anions with a distinct color change from colorless to pink in very fast response time (< 1 min). Fe3 + can be detected quantitatively in the concentration range from 6.7 to 16 μM and the detection limit (LOD) on UV-vis response of the sensor can be as low as 15 nM. The 'in situ' prepared Fe3 + complex (1 ṡ Fe) showed high selectivity toward PPi against many common anions, and sensitivity (the LOD can be as low as 71 nM). In addition, both the chemosensor and the 'in situ' prepared Fe3 + complex are reusable for the detection of Fe3 + and PPi respectively.

  3. Quantitative molecular sensing in biological tissues: an approach to non-invasive optical characterization

    NASA Astrophysics Data System (ADS)

    Chandra, Malavika; Vishwanath, Karthik; Fichter, Greg D.; Liao, Elly; Hollister, Scott J.; Mycek, Mary-Ann

    2006-06-01

    A method to non-invasively and quantitatively characterize thick biological tissues by combining both experimental and computational approaches in tissue optical spectroscopy was developed and validated on fifteen porcine articular cartilage (AC) tissue samples. To the best of our knowledge, this study is the first to couple non-invasive reflectance and fluorescence spectroscopic measurements on freshly harvested tissues with Monte Carlo computational modeling of time-resolved propagation of both excitation light and multi-fluorophore emission. For reflectance, quantitative agreement between simulation and experiment was achieved to better than 11%. Fluorescence data and simulations were used to extract the ratio of the absorption coefficients of constituent fluorophores for each measured AC tissue sample. This ratio could be used to monitor relative changes in concentration of the constituent fluorophores over time. The samples studied possessed the complexity and variability not found in artificial tissue-simulating phantoms and serve as a model for future optical molecular sensing studies on tissue engineered constructs intended for use in human therapeutics. An optical technique that could non-invasively and quantitatively assess soft tissue composition or physiologic status would represent a significant advance in tissue engineering. Moreover, the general approach described here for optical characterization should be broadly applicable to quantitative, non-invasive molecular sensing applications in complex, three-dimensional biological tissues.

  4. Molecular detection of Mikrocytos mackini in Pacific oysters using quantitative PCR.

    PubMed

    Polinski, Mark; Lowe, Geoff; Meyer, Gary; Corbeil, Serge; Colling, Axel; Caraguel, Charles; Abbott, Cathryn L

    2015-01-01

    Mikrocytos mackini is an internationally regulated pathogen and causative agent of Denman Island disease in Pacific oysters Crassostrea gigas. Recent phylogenetic breakthroughs have placed this parasite within a highly divergent and globally distributed eukaryotic lineage that has been designated a new taxonomic order, Mikrocytida. The discovery of this new radiation of parasites is accompanied by a heightened awareness of the many knowledge gaps that exist with respect to the general biology, epizootiology, and potential impact of mikrocytid parasites on hosts, ecosystems, and commercial fisheries. It has also highlighted current shortcomings regarding our ability to detect these organisms. In this study, we developed a species-specific, sensitive, and quantitative method for detecting M. mackini DNA from host tissues using probe-based real-time qPCR technology. A limit of sensitivity between 2 and 5 genome copy equivalents was achieved in a reaction matrix containing ≥ 40 ng/μL host gDNA without inhibition. This detection proved superior to existing methods based on conventional PCR, histology or gross pathology and is the first species-specific diagnostic test for M. mackini. Quantitative assessment of parasite DNA using this assay remained accurate to between 10 and 50 copies identifying that during infection, M. mackini DNA was significantly more prevalent in hemolymph, labial palp, and mid-body cross-sections compared to mantle or adductor muscle. DNA extracted from a mid-body cross-section also provided the highest likelihood for detection during diagnostic screening of infected oysters. Taken together, these findings provide strong analytical evidence for the adoption of qPCR as the new reference standard for detecting M. mackini and give preliminary insight into the distribution of the parasite within host tissues. Standardised operating methodologies for sample collection and qPCR testing are provided to aid in the international regulatory diagnosis of

  5. Qualitative and Quantitative Assays for Detection and Characterization of Protein Antimicrobials

    PubMed Central

    Farris, M. Heath; Ford, Kara A.; Doyle, Richard C.

    2016-01-01

    Initial evaluations of large microbial libraries for potential producers of novel antimicrobial proteins require both qualitative and quantitative methods to screen for target enzymes prior to investing greater research effort and resources. The goal of this protocol is to demonstrate two complementary assays for conducting these initial evaluations. The microslide diffusion assay provides an initial or simple detection screen to enable the qualitative and rapid assessment of proteolytic activity against an array of both viable and heat-killed bacterial target substrates. As a counterpart, the increased sensitivity and reproducibility of the dye-release assay provides a quantitative platform for evaluating and comparing environmental influences affecting the hydrolytic activity of protein antimicrobials. The ability to label specific heat-killed cell culture substrates with Remazol brilliant blue R dye expands this capability to tailor the dye-release assay to characterize enzymatic activity of interest. PMID:27166738

  6. A novel tolerance range approach for the quantitative assessment of ecosystems.

    PubMed

    Hearnshaw, Edward J S; Hughey, Kenneth F D

    2012-03-15

    This paper develops a novel tolerance range approach that allows for the quantitative assessment of ecosystems with only a minimum amount of information. The quantitative assessment is achieved through the determination of tolerance range scores and indices that indicate the vulnerability of species. For the purposes of demonstrating the tolerance range approach an ecosystem assessment is performed on Te Waihora/Lake Ellesmere, a large shallow lake found in the Canterbury region of New Zealand. From the analysis of tolerance range scores and indices it was found that brown trout and lake-margin vegetation are the most vulnerable species of value to further degradation. This information implies that management actions should prioritize towards preserving these species to maintain all valued species along sustainable pathways.

  7. [Development and application of TaqMan MGB probe fluorescence quantitative PCR method for rapid detection of Clostridium piliforme].

    PubMed

    Gao, Zheng-qin; Yue, Bing-fei; He, Zheng-ming

    2012-02-01

    To develop a TaqMan MGB probe-based, sensitive and specific fluorescence quantitative PCR assay method for rapid detection of Clostridium piliforme. Primers and probes specific to 16S rRNA gene of Clostridium piliforme were designed. A TaqMan MGB probe-based, fluorescence quantitative PCR method was established. Specificity, sensitivity and stability of the method were assessed, followed by real-time quantitative PCR assay to detect Clostridium piliforme on 1156 clinical specimens during 2008-2011 and compared with conventional PCR assay. The specificity of TaqMan MGB probe-based fluorescence quantitative PCR was high and did not show cross-reactivity with Helicobacter hepaticus, Helicobacter pylori, Campylobacter jejuni, Pasteurella pneumotropica, Escherichia coli or Pseudomonas aeruginosa. The detection limit was 2.2 copies/µl. The correlation coefficient and slope value of standard curve were 0.999 and -3.204, respectively and the efficiency of TaqMan MGB-based probe fluorescence quantitative PCR assay was 100%. When the TaqMan MGB-based probe fluorescence quantitative PCR assay was preformed to detect Clostridium piliforme on 1156 clinical specimens, a total of 101 specimens showed positive on Clostridium piliforme. However, only 44 specimens showed positive when conventional PCR was used. The real-time quantitative PCR for Clostridium piliforme could be completed within 2 hours. The TaqMan MGB-based probe fluorescence quantitative PCR assay method was a reliable, specific, sensitive and useful tool for rapid detection of Clostridium piliforme.

  8. Event-specific quantitative detection of nine genetically modified maizes using one novel standard reference molecule.

    PubMed

    Yang, Litao; Guo, Jinchao; Pan, Aihu; Zhang, Haibo; Zhang, Kewei; Wang, Zhengming; Zhang, Dabing

    2007-01-10

    With the development of genetically modified organism (GMO) detection techniques, the Polymerase Chain Reaction (PCR) technique has been the mainstay for GMO detection, and real-time PCR is the most effective and important method for GMO quantification. An event-specific detection strategy based on the unique and specific integration junction sequences between the host plant genome DNA and the integrated gene is being developed for its high specificity. This study establishes the event-specific detection methods for TC1507 and CBH351 maizes. In addition, the event-specific TaqMan real-time PCR detection methods for another seven GM maize events (Bt11, Bt176, GA21, MON810, MON863, NK603, and T25) were systematically optimized and developed. In these PCR assays, the fluorescent quencher, TAMRA, was dyed on the T-base of the probe at the internal position to improve the intensity of the fluorescent signal. To overcome the difficulties in obtaining the certified reference materials of these GM maizes, one novel standard reference molecule containing all nine specific integration junction sequences of these GM maizes and the maize endogenous reference gene, zSSIIb, was constructed and used for quantitative analysis. The limits of detection of these methods were 20 copies for these different GM maizes, the limits of quantitation were about 20 copies, and the dynamic ranges for quantification were from 0.05 to 100% in 100 ng of DNA template. Furthermore, nine groups of the mixed maize samples of these nine GM maize events were quantitatively analyzed to evaluate the accuracy and precision. The accuracy expressed as bias varied from 0.67 to 28.00% for the nine tested groups of GM maize samples, and the precision expressed as relative standard deviations was from 0.83 to 26.20%. All of these indicated that the established event-specific real-time PCR detection systems and the reference molecule in this study are suitable for the identification and quantification of these GM

  9. Quantitative analysis of PEG-functionalized colloidal gold nanoparticles using charged aerosol detection.

    PubMed

    Smith, Mackensie C; Crist, Rachael M; Clogston, Jeffrey D; McNeil, Scott E

    2015-05-01

    Surface characteristics of a nanoparticle, such as functionalization with polyethylene glycol (PEG), are critical to understand and achieve optimal biocompatibility. Routine physicochemical characterization such as UV-vis spectroscopy (for gold nanoparticles), dynamic light scattering, and zeta potential are commonly used to assess the presence of PEG. However, these techniques are merely qualitative and are not sensitive enough to distinguish differences in PEG quantity, density, or presentation. As an alternative, two methods are described here which allow for quantitative measurement of PEG on PEGylated gold nanoparticles. The first, a displacement method, utilizes dithiothreitol to displace PEG from the gold surface. The dithiothreitol-coated gold nanoparticles are separated from the mixture via centrifugation, and the excess dithiothreitol and dissociated PEG are separated through reversed-phase high-performance liquid chromatography (RP-HPLC). The second, a dissolution method, utilizes potassium cyanide to dissolve the gold nanoparticles and liberate PEG. Excess CN(-), Au(CN)2 (-), and free PEG are separated using RP-HPLC. In both techniques, the free PEG can be quantified against a standard curve using charged aerosol detection. The displacement and dissolution methods are validated here using 2-, 5-, 10-, and 20-kDa PEGylated 30-nm colloidal gold nanoparticles. Further value in these techniques is demonstrated not only by quantitating the total PEG fraction but also by being able to be adapted to quantitate the free unbound PEG and the bound PEG fractions. This is an important distinction, as differences in the bound and unbound PEG fractions can affect biocompatibility, which would not be detected in techniques that only quantitate the total PEG fraction.

  10. Evaluation of various real-time reverse transcription quantitative PCR assays for norovirus detection.

    PubMed

    Yoo, Ju Eun; Lee, Cheonghoon; Park, SungJun; Ko, GwangPyo

    2017-02-01

    Human noroviruses are widespread and contagious viruses causing nonbacterial gastroenteritis. Real-time reverse transcription quantitative PCR (real-time RT-qPCR) is currently the gold standard for sensitive and accurate detection for these pathogens and serves as a critical tool in outbreak prevention and control. Different surveillance teams, however, may use different assays and variability in specimen conditions may lead to disagreement in results. Furthermore, the norovirus genome is highly variable and continuously evolving. These issues necessitate the re-examination of the real-time RT-qPCR's robustness in the context of accurate detection as well as the investigation of practical strategies to enhance assay performance. Four widely referenced real-time RT-qPCR assays (Assay A-D) were simultaneously performed to evaluate characteristics such as PCR efficiency, detection limit, as well as sensitivity and specificity with RT-PCR, and to assess the most accurate method for detecting norovirus genogroups I and II. Overall, Assay D was evaluated to be the most precise and accurate assay in this study. A Zen internal quencher, which decreases nonspecific fluorescence during the PCR reaction, was added to Assay D's probe which further improved assay performance. This study compared several detection assays for noroviruses and an improvement strategy based on such comparisons provided useful characterizations of a highly optimized real-time RT-qPCR assay for norovirus detection.

  11. Comparison of nine different real-time PCR chemistries for qualitative and quantitative applications in GMO detection.

    PubMed

    Buh Gasparic, Meti; Tengs, Torstein; La Paz, Jose Luis; Holst-Jensen, Arne; Pla, Maria; Esteve, Teresa; Zel, Jana; Gruden, Kristina

    2010-03-01

    Several techniques have been developed for detection and quantification of genetically modified organisms, but quantitative real-time PCR is by far the most popular approach. Among the most commonly used real-time PCR chemistries are TaqMan probes and SYBR green, but many other detection chemistries have also been developed. Because their performance has never been compared systematically, here we present an extensive evaluation of some promising chemistries: sequence-unspecific DNA labeling dyes (SYBR green), primer-based technologies (AmpliFluor, Plexor, Lux primers), and techniques involving double-labeled probes, comprising hybridization (molecular beacon) and hydrolysis (TaqMan, CPT, LNA, and MGB) probes, based on recently published experimental data. For each of the detection chemistries assays were included targeting selected loci. Real-time PCR chemistries were subsequently compared for their efficiency in PCR amplification and limits of detection and quantification. The overall applicability of the chemistries was evaluated, adding practicability and cost issues to the performance characteristics. None of the chemistries seemed to be significantly better than any other, but certain features favor LNA and MGB technology as good alternatives to TaqMan in quantification assays. SYBR green and molecular beacon assays can perform equally well but may need more optimization prior to use.

  12. Detection of exogenous gene doping of IGF-I by a real-time quantitative PCR assay.

    PubMed

    Zhang, Jin-Ju; Xu, Jing-Feng; Shen, Yong-Wei; Ma, Shi-Jiao; Zhang, Ting-Ting; Meng, Qing-Lin; Lan, Wen-Jun; Zhang, Chun; Liu, Xiao-Mei

    2017-07-01

    Gene doping can be easily concealed since its product is similar to endogenous protein, making its effective detection very challenging. In this study, we selected insulin-like growth factor I (IGF-I) exogenous gene for gene doping detection. First, the synthetic IGF-I gene was subcloned to recombinant adeno-associated virus (rAAV) plasmid to produce recombinant rAAV2/IGF-I-GFP vectors. Second, in an animal model, rAAV2/IGF-I-GFP vectors were injected into the thigh muscle tissue of mice, and then muscle and blood specimens were sampled at different time points for total DNA isolation. Finally, real-time quantitative PCR was employed to detect the exogenous gene doping of IGF-I. In view of the characteristics of endogenous IGF-I gene sequences, a TaqMan probe was designed at the junction of exons 2 and 3 of IGF-I gene to distinguish it from the exogenous IGF-I gene. In addition, an internal reference control plasmid and its probe were used in PCR to rule out false-positive results through comparison of their threshold cycle (Ct) values. Thus, an accurate exogenous IGF-I gene detection approach was developed in this study. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  13. Anticancer Activity of Estradiol Derivatives: A Quantitative Structure--Activity Relationship Approach

    NASA Astrophysics Data System (ADS)

    Muranaka, Ken

    2001-10-01

    Commercial packages to implement modern QSAR (quantitative structure-activity relationship) techniques are highly priced; however, the essence of QSAR can be taught without them. Microsoft Excel was used to analyze published data on anticancer activities of estradiol analogs by a QSAR approach. The resulting QSAR equations highly correlate the structural features and physicochemical properties of the analogs with the observed biological activities by multiple linear regression.

  14. Quantitative angiography during coronary angioplasty with a single angiographic view: a comparison of automated edge detection and videodensitometric techniques.

    PubMed

    Escaned, J; Foley, D P; Haase, J; Di Mario, C; Hermans, W R; de Feyter, P J; Serruys, P W

    1993-12-01

    Little information is available on the reliability of coronary luminal measurements obtained from quantitative analysis of a single angiographic view, an approach that is central to the practical use of on-line quantitative angiography. In the present study we investigated the contribution of two different techniques of quantitative angiography, edge detection (ED) and videodensitometry (VD), to the application of this concept during coronary angioplasty. Forty-six balloon angioplasty procedures were included in this study, all of them performed in a stenosis located in the mid right coronary segment. This coronary location was chosen to optimize data collection on luminal morphology and to minimize the number of factors that may adversely affect quantitative analysis with both techniques. In all cases two orthogonal angiographic projections were obtained before, after balloon dilatation, and at follow-up. Correlation coefficients and differences between orthogonal measurements obtained with each technique were used to evaluate the agreement between orthogonal readings at every stage of the procedure. The obtained correlation coefficients and mean differences (MD) between orthogonal measurements were as follows: before percutaneous transluminal coronary angiography (PTCA), 0.67 (MD 0.01 +/- 0.47 mm2) and 0.57 (MD 0.05 +/- 0.64 mm2) for ED and VD, respectively (Pitman's test for SD, p < 0.05); after balloon dilatation, 0.32 (MD -0.56 +/- 1.53 mm2) and 0.53 (MD -0.15 +/- 1.43 mm2) for ED and VD, respectively (paired t test for MD, p < 0.05); and at follow-up 0.79 (MD -0.15 +/- 0.97 mm2) and 0.73 (MD 0.17 +/- 1.16 mm2) for ED and VD, respectively (p = NS).(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Standoff detection of explosives: a challenging approach for optical technologies

    NASA Astrophysics Data System (ADS)

    Désilets, S.; Hô, N.; Mathieu, P.; Simard, J. R.; Puckrin, E.; Thériault, J. M.; Lavoie, H.; Théberge, F.; Babin, F.; Gay, D.; Forest, R.; Maheux, J.; Roy, G.; Châteauneuf, M.

    2011-06-01

    Standoff detection of explosives residues on surfaces at few meters was made using optical technologies based on Raman scattering, Laser-Induced Breakdown Spectroscopy (LIBS) and passive standoff FTIR radiometry. By comparison, detection and analysis of nanogram samples of different explosives was made with a microscope system where Raman scattering from a micron-size single point illuminated crystal of explosive was observed. Results from standoff detection experiments using a telescope were compared to experiments using a microscope to find out important parameters leading to the detection. While detection and spectral identification of the micron-size explosive particles was possible with a microscope, standoff detection of these particles was very challenging due to undesired light reflected and produced by the background surface or light coming from other contaminants. Results illustrated the challenging approach of detecting at a standoff distance the presence of low amount of micron or submicron explosive particles.

  16. Quantitative detection of the colloidal gold immunochromatographic strip in HSV color space

    NASA Astrophysics Data System (ADS)

    Wu, Yuanshu; Gao, Yueming; Du, Min

    2014-09-01

    In this paper, a fast, reliable and accurate quantitative detection method for the colloidal gold immunochromatographic strip(GICA) is presented. An image acquisition device which is mainly composed of annular LED source, zoom ratio lens, and 10bit CMOS image sensors with 54.5dB SNR is designed for the detection. Firstly, the test line is extracted from the strip window through using the H component peak points of the HSV space as the clustering centers via the Fuzzy C-Means(FCM) clustering method. Then, a two dimensional eigenvalue composed with the hue(H) and saturation(S) of HSV space was proposed to improve the accuracy of the quantitative detection. At last, the experiment of human chorionic gonadotropin(HCG) with the concentration range 0-500mIU/mL is carried out. The results show that the linear correlation coefficient between this method and optical density(OD) values measured by the fiber optical sensor reach 96.74%. Meanwhile, the linearity of fitting curve constructed with concentration was greater than 95.00%.

  17. Development of Multiplexed Real-Time Quantitative PCR Assay for Detecting Human Adenoviruses

    PubMed Central

    Huang, Meei-Li; Nguy, Long; Ferrenberg, James; Boeckh, Michael; Cent, Anne; Corey, Lawrence

    2008-01-01

    Adenoviruses (AdV) have been associated with a wide variety of human disease and are increasingly recognized as viral pathogens that can cause significant morbidity and mortality in immunocompromised patients. Early detection of AdV DNA in plasma and sterile fluids has been shown to be useful for identifying patients at risk for invasive AdV disease. Due to the large number of existing Adv types, few real-time quantitative AdV PCR assays published effectively cover all AdV types. We designed a series of AdV PCR primers and probes and empirically multiplexed them into two separate real-time PCR assays to quantitatively detect all 49 serotypes of human AdV (Types 1-49) available from ATCC. We then subsequently multiplexed all the primers and probes into one reaction. The sensitivity of these assays was determined to be less than 10 copies per reaction (500 copies/ml plasma). In a retrospective evaluation we detected all 84 clinical AdV isolates isolated in cell culture from patients undergoing hematopoietic stem cell transplant (HSCT) between 1981 and 1987. Prospective analysis of 46 consecutive clinical samples submitted for adenovirus testing showed greater sensitivity and equal specificity of the AdV PCR than viral culture. This real time PCR assay allows rapid, sensitive and specific quantification of all currently defined adenoviruses into either two or one multiplex assay for clinical samples. PMID:18707838

  18. Quantitation of tetrahydrocannabinol in hair using immunoassay and liquid chromatography with tandem mass spectrometric detection.

    PubMed

    Coulter, Cynthia; Taruc, Margaux; Tuyay, James; Moore, Christine

    2009-05-01

    A quantitative analytical procedure for the determination of Delta(9)-tetrahydrocannabinol (THC) in hair has been developed and validated using liquid chromatography with tandem mass spectral detection (LC-MS/MS). Specimens that were determined as containing cannabinoids following immunoassay testing were quantified using solid-phase extraction followed by liquid chromatographic separation and tandem mass spectral detection in positive electrospray ionization mode. For confirmation, two transitions were monitored and one ratio determined. Samples being reported as positive were required to have both transitions present, the ratio of quantifying transition to qualifying transition being within 20% of that determined from known calibration standards. The limit of quantitation and the limit of detection was 10 pg/mg. The percentage recovery of the THC from hair at 20 pg/mg was 56% and a matrix effect of the hair showed an ion suppression percentage of -51%. The immunochemical screening method was performed following a rapid aqueous extraction, requiring only 10 mg of hair; the confirmatory procedure required 20 mg of hair. The methods were applied to proficiency specimens from the Society of Hair Testing, which had been received in August 2008.

  19. Semi-quantitative real-time PCR: A useful approach to identify persons with low replicative chronic hepatitis B.

    PubMed

    Castéra-Guy, Joany; Rubbo, Pierre-Alain; Kania, Dramane; Lemoine, Maud; Van de Perre, Philippe; Tuaillon, Edouard

    2017-06-01

    Antiviral therapy can be avoided during the low replicative phase of chronic Hepatitis B virus (HBV) infection which is characterized notably by HBV DNA concentration below 2000IU/ml. Simplified diagnostic tests can improve access to HBV DNA monitoring in resource-limited settings. The capacity of a new semi-quantitative real-time PCR approach based on sample-to-standard relative detection of the target to discriminate samples with HBV DNA levels above or below the clinical threshold of 2000IU/ml was compared to a quantitative assay (Roche CobasAmpliPrep/CobasTaqMan HBV Test v2.0). The semi-quantitative assay correctly identified 40/40 (100%) low replicative HBV DNA patients and 58/61 (95%) samples from HBV-infected subjects with moderate/high levels of viral DNA. Our results suggested that this alternative PCR test is efficient to guide therapeutic decision based on identification of low replicative HBV infection from all of the chronic hepatitis B carriers requiring treatment, and may be useful in resource-limited settings where the vast majority of cases live. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. High resolution quantitative phase imaging of live cells with constrained optimization approach

    NASA Astrophysics Data System (ADS)

    Pandiyan, Vimal Prabhu; Khare, Kedar; John, Renu

    2016-03-01

    Quantitative phase imaging (QPI) aims at studying weakly scattering and absorbing biological specimens with subwavelength accuracy without any external staining mechanisms. Use of a reference beam at an angle is one of the necessary criteria for recording of high resolution holograms in most of the interferometric methods used for quantitative phase imaging. The spatial separation of the dc and twin images is decided by the reference beam angle and Fourier-filtered reconstructed image will have a very poor resolution if hologram is recorded below a minimum reference angle condition. However, it is always inconvenient to have a large reference beam angle while performing high resolution microscopy of live cells and biological specimens with nanometric features. In this paper, we treat reconstruction of digital holographic microscopy images as a constrained optimization problem with smoothness constraint in order to recover only complex object field in hologram plane even with overlapping dc and twin image terms. We solve this optimization problem by gradient descent approach iteratively and the smoothness constraint is implemented by spatial averaging with appropriate size. This approach will give excellent high resolution image recovery compared to Fourier filtering while keeping a very small reference angle. We demonstrate this approach on digital holographic microscopy of live cells by recovering the quantitative phase of live cells from a hologram recorded with nearly zero reference angle.

  1. Quantitative multiplexed detection of common pulmonary fungal pathogens by labeled primer polymerase chain reaction.

    PubMed

    Gu, Zhengming; Buelow, Daelynn R; Petraitiene, Ruta; Petraitis, Vidmantas; Walsh, Thomas J; Hayden, Randall T

    2014-11-01

    Invasive fungal infections are an important cause of morbidity and mortality among immunocompromised patients. To design and evaluate a multiplexed assay aimed at quantitative detection and differentiation of the 5 molds that are most commonly responsible for pulmonary infections. Using labeled primer polymerase chain reaction chemistry, an assay was designed to target the 5.8S and 28S ribosomal RNA genes of Aspergillus spp, Fusarium spp, Scedosporium spp, and members of the order Mucorales ( Rhizopus oryzae , Rhizopus microsporus, Cunninghamella bertholletiae, Mucor circinelloides, Lichtheimia corymbifera, and Rhizomucor pusillus). This assay was split into 2 multiplexed reactions and was evaluated using both samples seeded with purified nucleic acid from 42 well-characterized clinical fungal isolates and 105 archived samples (47 blood [45%], 42 bronchoalveolar lavage fluid [40%], and 16 tissue [15%]) collected from rabbit models of invasive pulmonary fungal infections. Assay detection sensitivity was less than 25 copies of the target sequence per reaction for Aspergillus spp, 5 copies for Fusarium spp and Scedosporium spp, and 10 copies for the Mucorales. The assay showed quantitative linearity from 5 × 10(1) to 5 × 10(5) copies of target sequence per reaction. Sensitivities and specificities for bronchoalveolar lavage fluid, tissue, and blood samples were 0.86 and 0.99, 0.60 and 1.00, and 0.46 and 1.00, respectively. Labeled primer polymerase chain reaction permits rapid, quantitative detection and differentiation of common agents of invasive fungal infection. The assay described herein shows promise for clinical implementation that may have a significant effect on the rapid diagnosis and treatment of patients' severe infections caused by these pulmonary fungal pathogens.

  2. Quantum dot-based immunochromatography test strip for rapid, quantitative and sensitive detection of alpha fetoprotein.

    PubMed

    Yang, Qiuhua; Gong, Xiaoqun; Song, Tao; Yang, Jiumin; Zhu, Shengjiang; Li, Yunhong; Cui, Ye; Li, Yingxin; Zhang, Bingbo; Chang, Jin

    2011-12-15

    Rapid, quantitative detection of tumor markers with high sensitivity and specificity is critical to clinical diagnosis and treatment of cancer. We describe here a novel portable fluorescent biosensor that integrates quantum dot (QD) with an immunochromatography test strip (ICTS) and a home-made test strip reader for detection of tumor markers in human serum. Alpha fetoprotein (AFP), which is valuable for diagnosis of primary hepatic carcinoma, is used as a model tumor marker to demonstrate the performance of the proposed immunosensor. The principle of this sensor is on the basis of a sandwich immunoreaction that was performed on an ICTS. The fluorescence intensity of captured QD labels on the test line and control line served as signals was determined by the home-made test strip reader. The strong luminescence and robust photostability of QDs combined with the promising advantages of an ICTS and sensitive detection with the test strip reader result in good performance. Under optimal conditions, this biosensor is capable of detecting as low as 1 ng/mL AFP standard analyte in 10 min with only 50 μL sample volume. Furthermore, 1000 clinical human serum samples were tested by both the QD-based ICTS and a commercial electrochemiluminescence immunoassay AFP kit simultaneously to estimate the sensitivity, specificity and concordance of the assays. Results showed high consistency except for 24 false positive cases (false positive rate 3.92%) and 17 false negative cases (false negative rate 4.38%); the error rate was 4.10% in all. This demonstrates that the QD-based ICTS is capable of rapid, sensitive, and quantitative detection of AFP and shows a great promise for point-of-care testing of other tumor markers. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Detection, monitoring, and quantitative analysis of wildfires with the BIRD satellite

    NASA Astrophysics Data System (ADS)

    Oertel, Dieter A.; Briess, Klaus; Lorenz, Eckehard; Skrbek, Wolfgang; Zhukov, Boris

    2004-02-01

    Increasing concern about environment and interest to avoid losses led to growing demands on space borne fire detection, monitoring and quantitative parameter estimation of wildfires. The global change research community intends to quantify the amount of gaseous and particulate matter emitted from vegetation fires, peat fires and coal seam fires. The DLR Institute of Space Sensor Technology and Planetary Exploration (Berlin-Adlershof) developed a small satellite called BIRD (Bi-spectral Infrared Detection) which carries a sensor package specially designed for fire detection. BIRD was launched as a piggy-back satellite on October 22, 2001 with ISRO"s Polar Satellite Launch Vehicle (PSLV). It is circling the Earth on a polar and sun-synchronous orbit at an altitude of 572 km and it is providing unique data for detailed analysis of high temperature events on Earth surface. The BIRD sensor package is dedicated for high resolution and reliable fire recognition. Active fire analysis is possible in the sub-pixel domain. The leading channel for fire detection and monitoring is the MIR channel at 3.8 μm. The rejection of false alarms is based on procedures using MIR/NIR (Middle Infra Red/Near Infra Red) and MIR/TIR (Middle Infra Red/Thermal Infra Red) radiance ratio thresholds. Unique results of BIRD wildfire detection and analysis over fire prone regions in Australia and Asia will be presented. BIRD successfully demonstrates innovative fire recognition technology for small satellites which permit to retrieve quantitative characteristics of active burning wildfires, such as the equivalent fire temperature, fire area, radiative energy release, fire front length and fire front strength.

  4. Quantitative detection of Vibrio cholera toxin by real-time and dynamic cytotoxicity monitoring.

    PubMed

    Jin, Dazhi; Luo, Yun; Zheng, Min; Li, Haijing; Zhang, Jing; Stampfl, Melinda; Xu, Xiao; Ding, Gangqiang; Zhang, Yanjun; Tang, Yi-Wei

    2013-12-01

    We report here the quantitative detection of Vibrio cholerae toxin (CT) in isolates and stool specimens by dynamic monitoring of the full course of CT-mediated cytotoxicity in a real-time cell analysis (RTCA) system. Four cell lines, including Y-1 mouse adrenal tumor cells, Chinese hamster ovary (CHO) cells, small intestine epithelial (FHs74Int) cells, and mouse adrenal gland (PC12-Adh) cells, were evaluated for their suitability for CT-induced cytotoxicity testing. Among them, the Y-1 line was demonstrated to be the most sensitive for CT-mediated cytotoxicity, with limits of detection of 7.0 pg/ml for purified CT and 0.11 ng/ml for spiked CT in pooled negative stool specimens. No CT-mediated cytotoxicity was observed for nontoxigenic V. cholerae, non-V. cholerae species, or non-V. cholerae enterotoxins. The CT-RTCA assay was further validated with 100 stool specimens consecutively collected from patients with diarrhea and 200 V. cholerae isolates recovered from patients and the environment, in comparison to a reference using three detection methods. The CT-RTCA assay had sensitivities and specificities of 97.5% and 100.0%, respectively, for V. cholerae isolates and 90.0% and 97.2% for stool specimens. For stool specimens spiked with CT concentrations ranging from 3.5 pg/ml to 1.8 ng/ml, the inoculation-to-detection time was 1.12 ± 0.38 h, and the values were inversely correlated with CT concentrations (ρ = -1; P = 0.01). The results indicate that the CT-RTCA assay with the Y-1 cell line provides a rapid and sensitive tool for the quantitative detection of CT activities in clinical specimens.

  5. Detection and differentiation of human parvovirus variants by commercial quantitative real-time PCR tests.

    PubMed

    Hokynar, Kati; Norja, Päivi; Laitinen, Harri; Palomäki, Pekka; Garbarg-Chenon, Antoine; Ranki, Annamari; Hedman, Klaus; Söderlund-Venermo, Maria

    2004-05-01

    Parvovirus B19 causes a variety of diseases in humans, with outcomes ranging from asymptomatic to severe, such as chronic anemia in immunocompromised patients or fetal hydrops and death after maternal infection during pregnancy. The virus may be transmitted via plasma-derived products. According to the results of solvent-detergent safety studies, an upper limit of B19 DNA in plasma pools was recently defined. To restrict the input of B19 virus into production pools, a quantitative nucleic acid test is a prerequisite. We examined the suitability of the two commercial quantitative B19 PCR tests, LightCycler-Parvovirus B19 quantification kit (Roche Diagnostics) and RealArt Parvo B19 LC PCR (Artus) for detection, quantification, and differentiation of the three known B19 genotypes, including the newly described erythrovirus variants (genotypes 2 and 3). The former kit was highly sensitive for genotype 1 but was not suitable for detection of genotype 2 or one of two genotype 3 strains. The latter kit detected and differentiated all three genotypes, albeit with lower sensitivity for one of the genotype-3 strains. We furthermore assessed the prevalence of the three B19 virus genotypes in blood donors, by screening pooled plasma samples derived from 140,160 Finnish blood-donor units. None of the pools contained detectable levels of B19 virus genotypes 2 or 3. The origin, mode of transmission, and clinical significance of these genotypes are unknown and deserve further study. The RealArt Parvo B19 LC PCR is suitable for detection, quantification, and differentiation of all three B19 virus genotypes in molecular and clinical research.

  6. Detection of earth-approaching asteroids in near real time

    NASA Technical Reports Server (NTRS)

    Rabinowitz, D. L.

    1991-01-01

    Computer software, called the Moving Object Detection Program (MODP), is described which detects earth-approaching asteroids in near real time. The software runs on a workstation linked to the output of the drift-scanning CCD camera of the Spacewatch Telescope. MOPD recognizes trailed images, detects motion, and accurately determines angular positions and rates of motion for moving objects in the scan images. The results are obtained a few seconds after the image signals are shifted out of the CCD. During 2 months of trial observations with this system, 304 asteroids were detected down to a limiting apparent magnitude for untrailed images of V = 20.5.

  7. Mapping genetic determinants of viral traits with FST and quantitative trait locus (QTL) approaches.

    PubMed

    Doumayrou, Juliette; Thébaud, Gaël; Vuillaume, Florence; Peterschmitt, Michel; Urbino, Cica

    2015-10-01

    The genetic determinism of viral traits can generally be dissected using either forward or reverse genetics because the clonal reproduction of viruses does not require the use of approaches based on laboratory crosses. Nevertheless, we hypothesized that recombinant viruses could be analyzed as sexually reproducing organisms, using either a quantitative trait loci (QTL) approach or a locus-by-locus fixation index (FST). Locus-by-locus FST analysis, and four different regressions and interval mapping algorithms of QTL analysis were applied to a phenotypic and genotypic dataset previously obtained from 47 artificial recombinant genomes generated between two begomovirus species. Both approaches assigned the determinant of within-host accumulation-previously identified using standard virology approaches-to a region including the 5׳ end of the replication-associated protein (Rep) gene and the upstream intergenic region. This study provides a proof of principle that QTL and population genetics tools can be extended to characterize the genetic determinants of viral traits.

  8. Quantitative detection of chemical compounds in human hair with coherent anti-Stokes Raman scattering microscopy

    PubMed Central

    Zimmerley, Maxwell; Lin, Chia-Yu; Oertel, David C.; Marsh, Jennifer M.; Ward, Jimmie L.; Potma, Eric Olaf

    2010-01-01

    Coherent anti-Stokes Raman scattering (CARS) microscopy is used to determine the distribution and concentration of selected compounds in intact human hair. By generating images based on ratiometric CARS contrast, quantitative concentration maps of both water and externally applied d-glycine are produced in the cortex of human hair fibers. Both water and d-glycine are found to homogeneously distribute throughout the cortical regions of the hair. The ability to selectively detect molecular agents in hair fibers is of direct relevance to understanding the chemical and physical mechanisms that underlie the performance of hair-care products. PMID:19725730

  9. Quantitative PCR detection of Batrachochytrium dendrobatidis DNA from sediments and water

    USGS Publications Warehouse

    Kirshtein, J.D.; Anderson, C.W.; Wood, J.S.; Longcore, J.E.; Voytek, M.A.

    2007-01-01

    The fungal pathogen Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a disease implicated in amphibian declines on 5 continents. Polymerase chain reaction (PCR) primer sets exist with which amphibians can be tested for this disease, and advances in sampling techniques allow non-invasive testing of animals. We developed filtering and PCR based quantitative methods by modifying existing PCR assays to detect Bd DNA in water and sediments, without the need for testing amphibians; we tested the methods at 4 field sites. The SYBR based assay using Boyle primers (SYBR/Boyle assay) and the Taqman based assay using Wood primers performed similarly with samples generated in the laboratory (Bd spiked filters), but the SYBR/Boyle assay detected Bd DNA in more field samples. We detected Bd DNA in water from 3 of 4 sites tested, including one pond historically negative for chytridiomycosis. Zoospore equivalents in sampled water ranged from 19 to 454 l-1 (nominal detection limit is 10 DNA copies, or about 0.06 zoospore). We did not detect DNA of Bd from sediments collected at any sites. Our filtering and amplification methods provide a new tool to investigate critical aspects of Bd in the environment. ?? Inter-Research 2007.

  10. Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water.

    PubMed

    Acosta Soto, Lucrecia; Santísima-Trinidad, Ana Belén; Bornay-Llinares, Fernando Jorge; Martín González, Marcos; Pascual Valero, José Antonio; Ros Muñoz, Margarita

    2017-01-01

    The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation. We present two new protocols of DNA extraction from large volumes of reclaimed water. Quantitative PCR (qPCR) and digital PCR (dPCR) were able to detect low amounts of A. lumbricoides eggs. By using the first extraction protocol, which processes 500 mL of reclaimed water, qPCR can detect DNA concentrations as low as one A. lumbricoides egg equivalent, while dPCR can detect DNA concentrations as low as five A. lumbricoides egg equivalents. By using the second protocol, which processes 10 L of reclaimed water, qPCR was able to detect DNA concentrations equivalent to 20 A. lumbricoides eggs. This fact indicated the importance of developing new methodologies to detect helminth eggs with higher sensitivity and precision avoiding possible human infection risks.

  11. Accurate detection and quantitation of heteroplasmic mitochondrial point mutations by pyrosequencing.

    PubMed

    White, Helen E; Durston, Victoria J; Seller, Anneke; Fratter, Carl; Harvey, John F; Cross, Nicholas C P

    2005-01-01

    Disease-causing mutations in mitochondrial DNA (mtDNA) are typically heteroplasmic and therefore interpretation of genetic tests for mitochondrial disorders can be problematic. Detection of low level heteroplasmy is technically demanding and it is often difficult to discriminate between the absence of a mutation or the failure of a technique to detect the mutation in a particular tissue. The reliable measurement of heteroplasmy in different tissues may help identify individuals who are at risk of developing specific complications and allow improved prognostic advice for patients and family members. We have evaluated Pyrosequencing technology for the detection and estimation of heteroplasmy for six mitochondrial point mutations associated with the following diseases: Leber's hereditary optical neuropathy (LHON), G3460A, G11778A, and T14484C; mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS), A3243G; myoclonus epilepsy with ragged red fibers (MERRF), A8344G, and neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP)/Leighs: T8993G/C. Results obtained from the Pyrosequencing assays for 50 patients with presumptive mitochondrial disease were compared to those obtained using the commonly used diagnostic technique of polymerase chain reaction (PCR) and restriction enzyme digestion. The Pyrosequencing assays provided accurate genotyping and quantitative determination of mutational load with a sensitivity and specificity of 100%. The MELAS A3243G mutation was detected reliably at a level of 1% heteroplasmy. We conclude that Pyrosequencing is a rapid and robust method for detecting heteroplasmic mitochondrial point mutations.

  12. [Quantitative analysis method of natural gas combustion process combining wavelength selection and outlier spectra detection].

    PubMed

    Cao, Hui; Hu, Luo-Na; Zhou, Yan

    2012-10-01

    The present paper uses a combination method of wavelength selection and outlier spectra detection for quantitative analysis of nature gas combustion process based on its near infrared spectra. According to the statistical distribution of partial least squares (PLS) model coefficients and prediction errors, the method realized wavelength selection and outlier spectra detection, respectively. In contrast with PLS, PLS after leave-one-out for outlier detection (LOO-PLS), uninformative variable elimination by PLS (UVE-PLS) and UVE-PLS after leave-one-out for outlier detection (LOO-UVE-PLS), the root-mean-squared error of prediction (RMSEP) based on the method for CH4 prediction model is reduced by 14.33%, 14.33%, 10.96% and 12.21%; the RMSEP value for CO prediction model is reduced by 67.26%, 72.58%, 11.32% and 4.52%; the RMSEP value for CO2 prediction model is reduced by 5.95%, 19.7%, 36.71% and 4.04% respectively. Experimental results demonstrate that the method can significantly decrease the number of selected wavelengths, reduce model complexity and effectively detect outlier spectra. The established prediction model of analytes is more accurate as well as robust.

  13. Enzyme-Based Test Strips for Visual or Photographic Detection and Quantitation of Gaseous Sulfur Mustard.

    PubMed

    Bidmanova, Sarka; Steiner, Mark-Steven; Stepan, Martin; Vymazalova, Kamila; Gruber, Michael A; Duerkop, Axel; Damborsky, Jiri; Prokop, Zbynek; Wolfbeis, Otto S

    2016-06-07

    Sulfur mustard is a chemical agent of high military and terroristic significance. No effective antidote exists, and sulfur mustard can be fairly easily produced in large quantity. Rapid field testing of sulfur mustard is highly desirable. Existing analytical devices for its detection are available but can suffer from low selectivity, laborious sample preparation, and/or the need for complex instrumentation. We describe a new kind of test strip for rapid detection of gaseous sulfur mustard that is based on its degradation by the enzyme haloalkane dehalogenase that is accompanied by a change of local pH. This change can be detected using pH indicators contained in the strips whose color changes from blue-green to yellow within 10 min. In addition to visual read-out, we also demonstrate quantitative reflectometric readout by using a conventional digital camera based on red-green-blue data acquisition. Organic haloalkanes, such as 1,2-dichloroethane, have a negligible interfering effect. The visual limit of detection is 20 μg/L, and the one for red-green-blue read-out is as low as 3 μg/L. The assays have good reproducibility ±6% and ±2% for interday assays and intraday assays, respectively. The strips can be stored for at least 6 months without loss of function. They are disposable and can be produced fairly rapidly and at low costs. Hence, they represent a promising tool for in-field detection of sulfur mustard.

  14. A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus)

    PubMed Central

    Kistler, Whitney M.; Parlos, Julie A.; Peper, Steven T.; Dunham, Nicholas R.; Kendall, Ronald J.

    2016-01-01

    Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53–0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population. PMID:27893772

  15. Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water

    PubMed Central

    Santísima-Trinidad, Ana Belén; Bornay-Llinares, Fernando Jorge; Martín González, Marcos; Pascual Valero, José Antonio; Ros Muñoz, Margarita

    2017-01-01

    The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation. We present two new protocols of DNA extraction from large volumes of reclaimed water. Quantitative PCR (qPCR) and digital PCR (dPCR) were able to detect low amounts of A. lumbricoides eggs. By using the first extraction protocol, which processes 500 mL of reclaimed water, qPCR can detect DNA concentrations as low as one A. lumbricoides egg equivalent, while dPCR can detect DNA concentrations as low as five A. lumbricoides egg equivalents. By using the second protocol, which processes 10 L of reclaimed water, qPCR was able to detect DNA concentrations equivalent to 20 A. lumbricoides eggs. This fact indicated the importance of developing new methodologies to detect helminth eggs with higher sensitivity and precision avoiding possible human infection risks. PMID:28377928

  16. Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs

    PubMed Central

    Wong, Wilson; Farr, Ryan; Joglekar, Mugdha; Januszewski, Andrzej; Hardikar, Anandwardhan

    2015-01-01

    Probe-based quantitative PCR (qPCR) is a favoured method for measuring transcript abundance, since it is one of the most sensitive detection methods that provides an accurate and reproducible analysis. Probe-based chemistry offers the least background fluorescence as compared to other (dye-based) chemistries. Presently, there are several platforms available that use probe-based chemistry to quantitate transcript abundance. qPCR in a 96 well plate is the most routinely used method, however only a maximum of 96 samples or miRNAs can be tested in a single run. This is time-consuming and tedious if a large number of samples/miRNAs are to be analyzed. High-throughput probe-based platforms such as microfluidics (e.g. TaqMan Array Card) and nanofluidics arrays (e.g. OpenArray) offer ease to reproducibly and efficiently detect the abundance of multiple microRNAs in a large number of samples in a short time. Here, we demonstrate the experimental setup and protocol for miRNA quantitation from serum or plasma-EDTA samples, using probe-based chemistry and three different platforms (96 well plate, microfluidics and nanofluidics arrays) offering increasing levels of throughput. PMID:25938938

  17. Image-based quantitative analysis of gold immunochromatographic strip via cellular neural network approach.

    PubMed

    Zeng, Nianyin; Wang, Zidong; Zineddin, Bachar; Li, Yurong; Du, Min; Xiao, Liang; Liu, Xiaohui; Young, Terry

    2014-05-01

    Gold immunochromatographic strip assay provides a rapid, simple, single-copy and on-site way to detect the presence or absence of the target analyte. This paper aims to develop a method for accurately segmenting the test line and control line of the gold immunochromatographic strip (GICS) image for quantitatively determining the trace concentrations in the specimen, which can lead to more functional information than the traditional qualitative or semi-quantitative strip assay. The canny operator as well as the mathematical morphology method is used to detect and extract the GICS reading-window. Then, the test line and control line of the GICS reading-window are segmented by the cellular neural network (CNN) algorithm, where the template parameters of the CNN are designed by the switching particle swarm optimization (SPSO) algorithm for improving the performance of the CNN. It is shown that the SPSO-based CNN offers a robust method for accurately segmenting the test and control lines, and therefore serves as a novel image methodology for the interpretation of GICS. Furthermore, quantitative comparison is carried out among four algorithms in terms of the peak signal-to-noise ratio. It is concluded that the proposed CNN algorithm gives higher accuracy and the CNN is capable of parallelism and analog very-large-scale integration implementation within a remarkably efficient time.

  18. Qualitative and quantitative approaches in the dose-response assessment of genotoxic carcinogens.

    PubMed

    Fukushima, Shoji; Gi, Min; Kakehashi, Anna; Wanibuchi, Hideki; Matsumoto, Michiharu

    2016-05-01

    Qualitative and quantitative approaches are important issues in field of carcinogenic risk assessment of the genotoxic carcinogens. Herein, we provide quantitative data on low-dose hepatocarcinogenicity studies for three genotoxic hepatocarcinogens: 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and N-nitrosodiethylamine (DEN). Hepatocarcinogenicity was examined by quantitative analysis of glutathione S-transferase placental form (GST-P) positive foci, which are the preneoplastic lesions in rat hepatocarcinogenesis and the endpoint carcinogenic marker in the rat liver medium-term carcinogenicity bioassay. We also examined DNA damage and gene mutations which occurred through the initiation stage of carcinogenesis. For the establishment of points of departure (PoD) from which the cancer-related risk can be estimated, we analyzed the above events by quantitative no-observed-effect level and benchmark dose approaches. MeIQx at low doses induced formation of DNA-MeIQx adducts; somewhat higher doses caused elevation of 8-hydroxy-2'-deoxyquanosine levels; at still higher doses gene mutations occurred; and the highest dose induced formation of GST-P positive foci. These data indicate that early genotoxic events in the pathway to carcinogenesis showed the expected trend of lower PoDs for earlier events in the carcinogenic process. Similarly, only the highest dose of IQ caused an increase in the number of GST-P positive foci in the liver, while IQ-DNA adduct formation was observed with low doses. Moreover, treatment with DEN at low doses had no effect on development of GST-P positive foci in the liver. These data on PoDs for the markers contribute to understand whether genotoxic carcinogens have a threshold for their carcinogenicity. The most appropriate approach to use in low dose-response assessment must be approved on the basis of scientific judgment.

  19. A quantitative microscopic approach to predict local recurrence based on in vivo intraoperative imaging of sarcoma tumor margins.

    PubMed

    Mueller, Jenna L; Fu, Henry L; Mito, Jeffrey K; Whitley, Melodi J; Chitalia, Rhea; Erkanli, Alaattin; Dodd, Leslie; Cardona, Diana M; Geradts, Joseph; Willett, Rebecca M; Kirsch, David G; Ramanujam, Nimmi

    2015-11-15

    The goal of resection of soft tissue sarcomas located in the extremity is to preserve limb function while completely excising the tumor with a margin of normal tissue. With surgery alone, one-third of patients with soft tissue sarcoma of the extremity will have local recurrence due to microscopic residual disease in the tumor bed. Currently, a limited number of intraoperative pathology-based techniques are used to assess margin status; however, few have been widely adopted due to sampling error and time constraints. To aid in intraoperative diagnosis, we developed a quantitative optical microscopy toolbox, which includes acriflavine staining, fluorescence microscopy, and analytic techniques called sparse component analysis and circle transform to yield quantitative diagnosis of tumor margins. A series of variables were quantified from images of resected primary sarcomas and used to optimize a multivariate model. The sensitivity and specificity for differentiating positive from negative ex vivo resected tumor margins was 82 and 75%. The utility of this approach was tested by imaging the in vivo tumor cavities from 34 mice after resection of a sarcoma with local recurrence as a bench mark. When applied prospectively to images from the tumor cavity, the sensitivity and specificity for differentiating local recurrence was 78 and 82%. For comparison, if pathology was used to predict local recurrence in this data set, it would achieve a sensitivity of 29% and a specificity of 71%. These results indicate a robust approach for detecting microscopic residual disease, which is an effective predictor of local recurrence. © 2015 UICC.

  20. A quantitative microscopic approach to predict local recurrence based on in vivo intraoperative imaging of sarcoma tumor margins

    PubMed Central

    Mueller, Jenna L.; Fu, Henry L.; Mito, Jeffrey K.; Whitley, Melodi J.; Chitalia, Rhea; Erkanli, Alaattin; Dodd, Leslie; Cardona, Diana M.; Geradts, Joseph; Willett, Rebecca M.; Kirsch, David G.; Ramanujam, Nimmi

    2015-01-01

    The goal of resection of soft tissue sarcomas located in the extremity is to preserve limb function while completely excising the tumor with a margin of normal tissue. With surgery alone, one-third of patients with soft tissue sarcoma of the extremity will have local recurrence due to microscopic residual disease in the tumor bed. Currently, a limited number of intraoperative pathology-based techniques are used to assess margin status; however, few have been widely adopted due to sampling error and time constraints. To aid in intraoperative diagnosis, we developed a quantitative optical microscopy toolbox, which includes acriflavine staining, fluorescence microscopy, and analytic techniques called sparse component analysis and circle transform to yield quantitative diagnosis of tumor margins. A series of variables were quantified from images of resected primary sarcomas and used to optimize a multivariate model. The sensitivity and specificity for differentiating positive from negative ex vivo resected tumor margins was 82% and 75%. The utility of this approach was tested by imaging the in vivo tumor cavities from 34 mice after resection of a sarcoma with local recurrence as a bench mark. When applied prospectively to images from the tumor cavity, the sensitivity and specificity for differentiating local recurrence was 78% and 82%. For comparison, if pathology was used to predict local recurrence in this data set, it would achieve a sensitivity of 29% and a specificity of 71%. These results indicate a robust approach for detecting microscopic residual disease, which is an effective predictor of local recurrence. PMID:25994353

  1. [Identification of risk factors for work-related stress in a hospital: a qualitative and quantitative approach].

    PubMed

    Cortese, C G; Gerbaudo, Laura; Manconi, Maria Paola; Violante, B

    2013-01-01

    Italian legislation establishes the obligation for the employer to assess any risks to the safety and health of workers, including those relating to work-related stress (WRS). Several studies have proved the existence of a link between WRS and both individual diseases and organizational results. The research aimed at detecting WRS risk factors in a hospital consisting of 53 departments employing 2334 workers. A qualitative and quantitative approach was adopted divided into six steps: 1) analysis of the hospital indicators; 2) semistructured interviews of the 53 department heads; 3) preparation of a checklist including 42 WRS risk indicators; 4) observation by shadowing of the 53 departments; 5) setting up of 53 focus groups with staff from each department; 6) distribution of the check-list to a representative sample of 747 employees. Data analysis showed a "low" level of WRS risk regarding the hospital as a whole, a "medium" level regarding six transversal indicators and eight departments. Three indicators considered particularly significant were examined in detail: "workplace and ergonomic conditions", "shift work", "interruptions in work flow". The results helped to identifj a series of best practices aimed at reducing WRS risk that are applicable to other health care settings. The qualitative and quantitative approach produced a keen involvement of the employees of the hospital which will positively encourage the real efficacy of the measures taken.

  2. Towards a quantitative SERS approach--online monitoring of analytes in a microfluidic system with isotope-edited internal standards.

    PubMed

    März, Anne; Ackermann, Katrin R; Malsch, Daniéll; Bocklitz, Thomas; Henkel, Thomas; Popp, Jürgen

    2009-04-01

    In this contribution a new approach for quantitative measurements using surface-enhanced Raman spectroscopy (SERS) is presented. Combining the application of isotope-edited internal standard with the advantages of the liquid-liquid segmented-flow-based approach for flow-through SERS detection seems to be a promising means for quantitative SERS analysis. For the investigations discussed here a newly designed flow cell, tested for ideal mixing efficiency on the basis of grayscale-value measurements, is implemented. Measurements with the heteroaromatics nicotine and pyridine using their respective deuterated isotopomers as internal standards show that the integration of an isotopically labeled internal standard in the used liquid-liquid two-phase segmented flow leads to reproducible and comparable SERS spectra independent from the used colloid. With the implementation of an internal standard into the microfluidic device the influence of the properties of the colloid on the SERS activity can be compensated. Thus, the problem of a poor batch-to-batch reproducibility of the needed nanoparticle solutions is solved. To the best of our knowledge these are the first measurements combining the above mentioned concepts in order to correct for differences in the enhancement behaviour of the respective colloid. (c) 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. A preamplification approach to GMO detection in processed foods.

    PubMed

    Del Gaudio, S; Cirillo, A; Di Bernardo, G; Galderisi, U; Cipollaro, M

    2010-03-01

    DNA is widely used as a target for GMO analysis because of its stability and high detectability. Real-time PCR is the method routinely used in most analytical laboratories due to its quantitative performance and great sensitivity. Accurate DNA detection and quantification is dependent on the specificity and sensitivity of the amplification protocol as well as on the quality and quantity of the DNA used in the PCR reaction. In order to enhance the sensitivity of real-time PCR and consequently expand the number of analyzable target genes, we applied a preamplification technique to processed foods where DNA can be present in low amounts and/or in degraded forms thereby affecting the reliability of qualitative and quantitative results. The preamplification procedure utilizes a pool of primers targeting genes of interest and is followed by real-time PCR reactions specific for each gene. An improvement of Ct values was found comparing preamplified vs. non-preamplified DNA. The strategy reported in the present study will be also applicable to other fields requiring quantitative DNA testing by real-time PCR.

  4. Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

    PubMed Central

    Yee, Jaeyong; Kwon, Min-Seok; Park, Taesung; Park, Mira

    2015-01-01

    A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait. PMID:26339620

  5. Rapid, specific and quantitative assays for the detection of the endophytic bacterium Methylobacterium mesophilicum in plants.

    PubMed

    Lacava, P T; Li, W B; Araújo, W L; Azevedo, J L; Hartung, J S

    2006-06-01

    Xylella fastidiosa is a xylem-limited bacterium that causes citrus variegated chlorosis disease in sweet orange. There is evidence that X. fastidiosa interacts with endophytic bacteria present in the xylem of sweet orange, and that these interactions, particularly with Methylobacterium mesophilicum, may affect disease progress. However, these interactions cannot be evaluated in detail until efficient methods for detection and enumeration of these bacteria in planta are developed. We have previously developed standard and quantitative PCR-based assays specific for X. fastidiosa using the LightCycler system [Li, W.B., Pria Jr., L.P.M.W.D., X. Qin, and J.S. Hartung, 2003. Presence of Xylella fastidiosa in sweet orange fruit and seeds and its transmission to seedlings. Phytopathology 93:953-958.], and now report the development of both standard and quantitative PCR assays for M. mesophilicum. The assays are specific for M. mesophilicum and do not amplify DNA from other species of Methylobacterium or other bacteria commonly associated with citrus or plant tissue. Other bacteria tested included Curtobacterium flaccumfaciens, Pantoea agglomerans, Enterobacter cloacae, Bacillus sp., X. fastidiosa, Xanthomonas axonopodis pv. citri, and Candidatus Liberibacter asiaticus. We have demonstrated that with these methods we can quantitatively monitor the colonization of xylem by M. mesophilicum during the course of disease development in plants artificially inoculated with both bacteria.

  6. Quantitative detection of astaxanthin and cantaxanthin in Atlantic salmon by resonance Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Ermakov, Igor V.; Ermakova, Maia R.; Gellermann, Werner

    2006-02-01

    Two major carotenoids species found in salmonids muscle tissues are astaxanthin and cantaxanthin. They are taken up from fish food and are responsible for the attractive red-orange color of salmon filet. Since carotenoids are powerful antioxidants and biomarkers of nutrient consumption, they are thought to indicate fish health and resistance to diseases in fish farm environments. Therefore, a rapid, accurate, quantitative optical technique for measuring carotenoid content in salmon tissues is of economic interest. We demonstrate the possibility of using fast, selective, quantitative detection of astaxanthin and cantaxanthin in salmon muscle tissues, employing resonance Raman spectroscopy. Analyzing strong Raman signals originating from the carbon-carbon double bond stretch vibrations of the carotenoid molecules under blue laser excitation, we are able to characterize quantitatively the concentrations of carotenoids in salmon muscle tissue. To validate the technique, we compared Raman data with absorption measurements of carotenoid extracts in acetone. A close correspondence was observed in absorption spectra for tissue extract in acetone and a pure astaxanthin solution. Raman results show a linear dependence between Raman and absorption data. The proposed technique holds promise as a method of rapid screening of carotenoid levels in fish muscle tissues and may be attractive for the fish farm industry to assess the dietary status of salmon, risk for infective diseases, and product quality control.

  7. Detection and quantitation of HPV DNA replication by Southern blotting and real-time PCR.

    PubMed

    Morgan, Iain M; Taylor, Ewan R

    2005-01-01

    This provides a brief introduction into the mechanism of DNA replication by the E1 and E2 proteins and describes the traditional Southern blotting technique that is used to monitor E1- and E2-mediated DNA replication. It also includes a novel real-time polymerase chain reaction (PCR) approach for monitoring E1- and E2-mediated DNA replication that has enhanced sensitivity and quantitation compared with Southern blotting, and a discussion of when to use the Southern blotting and real-time PCR techniques.

  8. Development and application of quantitative detection method for viral hemorrhagic septicemia virus (VHSV) genogroup IVa.

    PubMed

    Kim, Jong-Oh; Kim, Wi-Sik; Kim, Si-Woo; Han, Hyun-Ja; Kim, Jin Woo; Park, Myoung Ae; Oh, Myung-Joo

    2014-05-23

    Viral hemorrhagic septicemia virus (VHSV) is a problematic pathogen in olive flounder (Paralichthys olivaceus) aquaculture farms in Korea. Thus, it is necessary to develop a rapid and accurate diagnostic method to detect this virus. We developed a quantitative RT-PCR (qRT-PCR) method based on the nucleocapsid (N) gene sequence of Korean VHSV isolate (Genogroup IVa). The slope and R² values of the primer set developed in this study were -0.2928 (96% efficiency) and 0.9979, respectively. Its comparison with viral infectivity calculated by traditional quantifying method (TCID₅₀) showed a similar pattern of kinetic changes in vitro and in vivo. The qRT-PCR method reduced detection time compared to that of TCID₅₀, making it a very useful tool for VHSV diagnosis.

  9. Development and Application of Quantitative Detection Method for Viral Hemorrhagic Septicemia Virus (VHSV) Genogroup IVa

    PubMed Central

    Kim, Jong-Oh; Kim, Wi-Sik; Kim, Si-Woo; Han, Hyun-Ja; Kim, Jin Woo; Park, Myoung Ae; Oh, Myung-Joo

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) is a problematic pathogen in olive flounder (Paralichthys olivaceus) aquaculture farms in Korea. Thus, it is necessary to develop a rapid and accurate diagnostic method to detect this virus. We developed a quantitative RT-PCR (qRT-PCR) method based on the nucleocapsid (N) gene sequence of Korean VHSV isolate (Genogroup IVa). The slope and R2 values of the primer set developed in this study were −0.2928 (96% efficiency) and 0.9979, respectively. Its comparison with viral infectivity calculated by traditional quantifying method (TCID50) showed a similar pattern of kinetic changes in vitro and in vivo. The qRT-PCR method reduced detection time compared to that of TCID50, making it a very useful tool for VHSV diagnosis. PMID:24859343

  10. Rapid method for glutathione quantitation using high-performance liquid chromatography with coulometric electrochemical detection.

    PubMed

    Bayram, Banu; Rimbach, Gerald; Frank, Jan; Esatbeyoglu, Tuba

    2014-01-15

    A rapid, sensitive, and direct method (without derivatization) was developed for the detection of reduced glutathione (GSH) in cultured hepatocytes (HepG2 cells) using high-performance liquid chromatography with electrochemical detection (HPLC-ECD). The method was validated according to the guidelines of the U.S. Food and Drug Administration in terms of linearity, lower limit of quantitation (LOQ), lower limit of detection (LOD), precision, accuracy, recovery, and stabilities of GSH standards and quality control samples. The total analysis time was 5 min, and the retention time of GSH was 1.78 min. Separation was carried out isocratically using 50 mM sodium phosphate (pH 3.0) as a mobile phase with a fused-core column. The detector response was linear between 0.01 and 80 μmol/L, and the regression coefficient (R(2)) was >0.99. The LOD for GSH was 15 fmol, and the intra- and interday recoveries ranged between 100.7 and 104.6%. This method also enabled the rapid detection (in 4 min) of other compounds involved in GSH metabolism such as uric acid, ascorbic acid, and glutathione disulfite. The optimized and validated HPLC-ECD method was successfully applied for the determination of GSH levels in HepG2 cells treated with buthionine sulfoximine (BSO), an inhibitor, and α-lipoic acid (α-LA), an inducer of GSH synthesis. As expected, the amount of GSH concentration-dependently decreased with BSO and increased with α-LA treatments in HepG2 cells. This method could also be useful for the quantitation of GSH, uric acid, ascorbic acid, and glutathione disulfide in other biological matrices such as tissue homogenates and blood.

  11. Development of a quantitative PCR for detection of Lactobacillus plantarum starters during wine malolactic fermentation.

    PubMed

    Cho, Gyu-Sung; Krauss, Sabrina; Huch, Melanie; Du Toit, Maret; Franz, Charles M A P

    2011-12-01

    A quantitative, real-time PCR method was developed to enumerate Lactobacillus plantarum IWBT B 188 during the malolactic fermentation (MLF) in Grauburgunder wine. The qRT-PCR was strain-specific, as it was based on primers targeting a plasmid DNA sequence, or it was L. plantarum-specific, as it targeted a chromosomally located plantaricin gene sequence. Two 50 l wine fermentations were prepared. One was inoculated with 15 g/hl Saccharomyces cerevisiae, followed by L. plantarum IWBT B 188 at 3.6 × 10(6) CFU/ml, whereas the other was not inoculated (control). Viable cell counts were performed for up to 25 days on MRS agar, and the same cells were enumerated by qRT-PCR with both the plasmid or chromosomally encoded gene primers. The L. plantarum strain survived under the harsh conditions in the wine fermentation at levels above 10(5)/ml for approx. 10 days, after which cell numbers decreased to levels of 10(3) CFU/ml at day 25, and to below the detection limit after day 25. In the control, no lactic acid bacteria could be detected throughout the fermentation, with the exception of two sampling points where ca. 1 × 10(2) CFU/ml was detected. The minimum detection level for quantitative PCR in this study was 1 × 10(2) to 1 × 10(3) CFU/ml. The qRT-PCR results determined generally overestimated the plate count results by about 1 log unit, probably as a result of the presence of DNA from dead cells. Overall, qRT-PCR appeared to be well suited for specifically enumerating Lactobacillus plantarum starter cultures in the MLF in wine.

  12. Passive mass transport for direct and quantitative SERS detection using purified silica encapsulated metal nanoparticles

    NASA Astrophysics Data System (ADS)

    Shrestha, Binaya Kumar

    This thesis focuses on understanding implications of nanomaterial quality control and mass transport through internally etched silica coated nanoparticles for direct and quantitative molecular detection using surface enhanced Raman scattering (SERS). Prior to use, bare nanoparticles (partially or uncoated with silica) are removal using column chromatography to improve the quality of these nanomaterials and their SERS reproducibility. Separation of silica coated nanoparticles with two different diameters is achieved using Surfactant-free size exclusion chromatography with modest fractionation. Next, selective molecular transport is modeled and monitored using SERS and evaluated as a function of solution ionic strength, pH, and polarity. Molecular detection is achieved when the analytes first partition through the silica membrane then interact with the metal surface at short distances (i.e., less than 2 nm). The SERS intensities of unique molecular vibrational modes for a given molecule increases as the number of molecules that bind to the metal surface increases and are enhanced via both chemical and electromagnetic enhancement mechanisms as long as the vibrational mode has a component of polarizability tensor along the surface normal. SERS signals increase linearly with molecular concentration until the three-dimensional SERS-active volume is saturated with molecules. Implications of molecular orientation as well as surface selection rules on SERS intensities of molecular vibrational modes are studied to improve quantitative and reproducible SERS detection using internally etched Ag Au SiO2 nanoparticles. Using the unique vibrational modes, SERS intensities for p-aminothiophenol as a function of metal core compositions and plasmonics are studied. By understanding molecular transport mechanisms through internally etched silica matrices coated on metal nanoparticles, important experimental and materials design parameters are learned, which can be subsequently applied

  13. New approach in features extraction for EEG signal detection.

    PubMed

    Guerrero-Mosquera, Carlos; Vazquez, Angel Navia

    2009-01-01

    This paper describes a new approach in features extraction using time-frequency distributions (TFDs) for detecting epileptic seizures to identify abnormalities in electroencephalogram (EEG). Particularly, the method extracts features using the Smoothed Pseudo Wigner-Ville distribution combined with the McAulay-Quatieri sinusoidal model and identifies abnormal neural discharges. We propose a new feature based on the length of the track that, combined with energy and frequency features, allows to isolate a continuous energy trace from another oscillations when an epileptic seizure is beginning. We evaluate our approach using data consisting of 16 different seizures from 6 epileptic patients. The results show that our extraction method is a suitable approach for automatic seizure detection, and opens the possibility of formulating new criteria to detect and analyze abnormal EEGs.

  14. A hybrid approach for efficient anomaly detection using metaheuristic methods.

    PubMed

    Ghanem, Tamer F; Elkilani, Wail S; Abdul-Kader, Hatem M

    2015-07-01

    Network intrusion detection based on anomaly detection techniques has a significant role in protecting networks and systems against harmful activities. Different metaheuristic techniques have been used for anomaly detector generation. Yet, reported literature has not studied the use of the multi-start metaheuristic method for detector generation. This paper proposes a hybrid approach for anomaly detection in large scale datasets using detectors generated based on multi-start metaheuristic method and genetic algorithms. The proposed approach has taken some inspiration of negative selection-based detector generation. The evaluation of this approach is performed using NSL-KDD dataset which is a modified version of the widely used KDD CUP 99 dataset. The results show its effectiveness in generating a suitable number of detectors with an accuracy of 96.1% compared to other competitors of machine learning algorithms.

  15. A hybrid approach for efficient anomaly detection using metaheuristic methods

    PubMed Central

    Ghanem, Tamer F.; Elkilani, Wail S.; Abdul-kader, Hatem M.

    2014-01-01

    Network intrusion detection based on anomaly detection techniques has a significant role in protecting networks and systems against harmful activities. Different metaheuristic techniques have been used for anomaly detector generation. Yet, reported literature has not studied the use of the multi-start metaheuristic method for detector generation. This paper proposes a hybrid approach for anomaly detection in large scale datasets using detectors generated based on multi-start metaheuristic method and genetic algorithms. The proposed approach has taken some inspiration of negative selection-based detector generation. The evaluation of this approach is performed using NSL-KDD dataset which is a modified version of the widely used KDD CUP 99 dataset. The results show its effectiveness in generating a suitable number of detectors with an accuracy of 96.1% compared to other competitors of machine learning algorithms. PMID:26199752

  16. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants.

    PubMed

    Kujur, Alice; Saxena, Maneesha S; Bajaj, Deepak; Laxmi; Parida, Swarup K

    2013-12-01

    The enormous population growth, climate change and global warming are now considered major threats to agriculture and world's food security. To improve the productivity and sustainability of agriculture, the development of highyielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern -omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties.

  17. Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

    PubMed Central

    Abdallah, Cosette; Dumas-Gaudot, Eliane; Renaut, Jenny; Sergeant, Kjell

    2012-01-01

    Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed. PMID:23213324

  18. Detection of parent-of-origin effects for quantitative traits using general pedigree data.

    PubMed

    He, Hai-Qiang; Mao, Wei-Gao; Pan, Dongdong; Zhou, Ji-Yuan; Chen, Ping-Yan; Fung, Wing Kam

    2014-08-01

    Genomic imprinting is a genetic phenomenon in which certain alleles are differentially expressed in a parent-of-origin-specific manner, and plays an important role in the study of complex traits. For a diallelic marker locus in human, the parentalasymmetry tests Q-PAT(c) with any constant c were developed to detect parent-of-origin effects for quantitative traits. However, these methods can only be applied to deal with nuclear families and thus are not suitable for extended pedigrees. In this study, by making no assumption about the distribution of the quantitative trait, we first propose the pedigree parentalasymmetry tests Q-PPAT(c) with any constant c for quantitative traits to test for parent-of-origin effects based on nuclear families with complete information from general pedigree data, in the presence of association between marker alleles under study and quantitative traits. When there are any genotypes missing in pedigrees, we utilize Monte Carlo (MC) sampling and estimation and develop the Q-MCPPAT(c) statistics to test for parent-of-origin effects. Various simulation studies are conducted to assess the performance of the proposed methods, for different sample sizes, genotype missing rates, degrees of imprinting effects and population models. Simulation results show that the proposed methods control the size well under the null hypothesis of no parent-of-origin effects and Q-PPAT(c) are robust to population stratification. In addition, the power comparison demonstrates that Q-PPAT(c) and Q-MCPPAT(c) for pedigree data are much more powerful than Q-PAT(c) only using two-generation nuclear families selected from extended pedigrees.

  19. Quantitative detection of tetracycline residues in honey by a simple sensitive immunoassay.

    PubMed

    Jeon, Moonsun; Rhee Paeng, Insook

    2008-09-26

    Tetracyclines (TCs) are widely used for prevention and control of infectious diseases and have a great activity against variety of Gram-positive and Gram-negative bacteria. Due to the widespread use of TCs in animal husbandry, it can lead to an increase the risk of TCs remaining in human food. To protect consumers, many countries have set acceptable tolerance levels for these drugs. Therefore, it is necessary to establish a suitable analytical technique with specificity, sensitivity and simplicity. The biotin-avidin mediated ELISA method was performed to determine TC residues in honey quantitatively. By using PBS-EDTA assay buffer at pH 7.2, a honey solution of TC standard was prepared and diluted. And no additional pre-treatment of sample was required in this method. The limit of detection and limit of quantitation of the optimized method were 3.98 x 10(-10)M (0.19 mugL(-1)) and 7.94 x 10(-10)M (0.38 mugL(-1)), respectively, and the dynamic range was from 1.52 mugL(-1) to 152 mugL(-1) of TC in honey. No cross-reactivity was observed with the structurally similar compounds, and mean percent recoveries of TC spiked in honey ranged from 95% to 101%. Compared to other methods, this method was superior in terms of detection limit, dynamic range, and % recovery with simple sample-preparation.

  20. A Room Temperature Ultrasensitive Magnetoelectric Susceptometer for Quantitative Tissue Iron Detection

    PubMed Central

    Xi, Hao; Qian, Xiaoshi; Lu, Meng-Chien; Mei, Lei; Rupprecht, Sebastian; Yang, Qing X.; Zhang, Q. M.

    2016-01-01

    Iron is a trace mineral that plays a vital role in the human body. However, absorbing and accumulating excessive iron in body organs (iron overload) can damage or even destroy an organ. Even after many decades of research, progress on the development of noninvasive and low-cost tissue iron detection methods is very limited. Here we report a recent advance in a room-temperature ultrasensitive biomagnetic susceptometer for quantitative tissue iron detection. The biomagnetic susceptometer exploits recent advances in the magnetoelectric (ME) composite sensors that exhibit an ultrahigh AC magnetic sensitivity under the presence of a strong DC magnetic field. The first order gradiometer based on piezoelectric and magnetostrictive laminate (ME composite) structure shows an equivalent magnetic noise of 0.99 nT/rt Hz at 1 Hz in the presence of a DC magnetic field of 0.1 Tesla and a great common mode noise rejection ability. A prototype magnetoelectric liver susceptometry has been demonstrated with liver phantoms. The results indicate its output signals to be linearly responsive to iron concentrations from normal iron dose (0.05 mg Fe/g liver phantom) to 5 mg Fe/g liver phantom iron overload (100X overdose). The results here open up many innovative possibilities for compact-size, portable, cost-affordable, and room-temperature operated medical systems for quantitative determinations of tissue iron. PMID:27465206

  1. A Room Temperature Ultrasensitive Magnetoelectric Susceptometer for Quantitative Tissue Iron Detection.

    PubMed

    Xi, Hao; Qian, Xiaoshi; Lu, Meng-Chien; Mei, Lei; Rupprecht, Sebastian; Yang, Qing X; Zhang, Q M

    2016-07-28

    Iron is a trace mineral that plays a vital role in the human body. However, absorbing and accumulating excessive iron in body organs (iron overload) can damage or even destroy an organ. Even after many decades of research, progress on the development of noninvasive and low-cost tissue iron detection methods is very limited. Here we report a recent advance in a room-temperature ultrasensitive biomagnetic susceptometer for quantitative tissue iron detection. The biomagnetic susceptometer exploits recent advances in the magnetoelectric (ME) composite sensors that exhibit an ultrahigh AC magnetic sensitivity under the presence of a strong DC magnetic field. The first order gradiometer based on piezoelectric and magnetostrictive laminate (ME composite) structure shows an equivalent magnetic noise of 0.99 nT/rt Hz at 1 Hz in the presence of a DC magnetic field of 0.1 Tesla and a great common mode noise rejection ability. A prototype magnetoelectric liver susceptometry has been demonstrated with liver phantoms. The results indicate its output signals to be linearly responsive to iron concentrations from normal iron dose (0.05 mg Fe/g liver phantom) to 5 mg Fe/g liver phantom iron overload (100X overdose). The results here open up many innovative possibilities for compact-size, portable, cost-affordable, and room-temperature operated medical systems for quantitative determinations of tissue iron.

  2. Quantitative single-molecule detection of protein based on DNA tetrahedron fluorescent nanolabels.

    PubMed

    Ding, Yongshun; Liu, Xingti; Zhu, Jing; Wang, Lei; Jiang, Wei

    2014-07-01

    A highly sensitive method for single-molecule quantitative detection of human IgG is presented by the employment of a new fluorescent nanolabel. In this method, fluorescent nanolabels were assembled by inserting SYBR Green I into DNA tetrahedron nanostructure. The bio-nanolabels were attached to the streptavidin-antihuman antibody by a specific reaction between biotin and streptavidin. The antibody was combined with the target antigen, human IgG, which was immobilized on the silanized glass subtrate surface. Finally, epi-fluorescence microscopy (EFM) coupled with an electron multiplying charge-coupled device was employed for fluorescence imaging. The fluorescent spots corresponding to single protein molecule on images were counted and further used for the quantitative detection. It was found that the new nanolabel shows good photostability, biocompatiblity and exhibits no blinking compared to traditional labels like fluorescence dyes and quantum dot (QDs). In addition, the number of fluorescence spots on the images has a linear relationship with the concentration of human IgG in the range of 3.0×10(-14) to 1.0×10(-12)mol L(-1). What is more, this method showed an excellent specificity and a low matrix effect.

  3. Early detection of high-grade squamous intraepithelial lesions in the cervix with quantitative spectroscopic imaging

    PubMed Central

    Mirkovic, Jelena; Yu, Chung-Chieh; O’Donoghue, Geoff P.; Galindo, Luis; Dasari, Ramachandra; de las Morenas, Antonio; Feld, Michael; Stier, Elizabeth

    2013-01-01

    Abstract. Quantitative spectroscopy has recently been extended from a contact-probe to wide-area spectroscopic imaging to enable mapping of optical properties across a wide area of tissue. We train quantitative spectroscopic imaging (QSI) to identify cervical high-grade squamous intraepithelial lesions (HSILs) in 34 subjects undergoing the loop electrosurgical excision procedure (LEEP subjects). QSI’s performance is then prospectively evaluated on the clinically suspicious biopsy sites from 47 subjects undergoing colposcopic-directed biopsy. The results show the per-subject normalized reduced scattering coefficient at 700 nm (An) and the total hemoglobin concentration are significantly different (p<0.05) between HSIL and non-HSIL sites in LEEP subjects. An alone retrospectively distinguishes HSIL from non-HSIL with 89% sensitivity and 83% specificity. It alone applied prospectively on the biopsy sites distinguishes HSIL from non-HSIL with 81% sensitivity and 78% specificity. The findings of this study agree with those of an earlier contact-probe study, validating the robustness of QSI, and specifically An, for identifying HSIL. The performance of An suggests an easy to use and an inexpensive to manufacture monochromatic instrument is capable of early cervical cancer detection, which could be used as a screening and diagnostic tool for detecting cervical cancer in low resource countries. PMID:23843090

  4. A Room Temperature Ultrasensitive Magnetoelectric Susceptometer for Quantitative Tissue Iron Detection

    NASA Astrophysics Data System (ADS)

    Xi, Hao; Qian, Xiaoshi; Lu, Meng-Chien; Mei, Lei; Rupprecht, Sebastian; Yang, Qing X.; Zhang, Q. M.

    2016-07-01

    Iron is a trace mineral that plays a vital role in the human body. However, absorbing and accumulating excessive iron in body organs (iron overload) can damage or even destroy an organ. Even after many decades of research, progress on the development of noninvasive and low-cost tissue iron detection methods is very limited. Here we report a recent advance in a room-temperature ultrasensitive biomagnetic susceptometer for quantitative tissue iron detection. The biomagnetic susceptometer exploits recent advances in the magnetoelectric (ME) composite sensors that exhibit an ultrahigh AC magnetic sensitivity under the presence of a strong DC magnetic field. The first order gradiometer based on piezoelectric and magnetostrictive laminate (ME composite) structure shows an equivalent magnetic noise of 0.99 nT/rt Hz at 1 Hz in the presence of a DC magnetic field of 0.1 Tesla and a great common mode noise rejection ability. A prototype magnetoelectric liver susceptometry has been demonstrated with liver phantoms. The results indicate its output signals to be linearly responsive to iron concentrations from normal iron dose (0.05 mg Fe/g liver phantom) to 5 mg Fe/g liver phantom iron overload (100X overdose). The results here open up many innovative possibilities for compact-size, portable, cost-affordable, and room-temperature operated medical systems for quantitative determinations of tissue iron.

  5. A metabolomics approach to identify and quantify the phytochemicals in watermelons by quantitative (1)HNMR.

    PubMed

    Jayaprakasha, G K; Patil, Bhimanagouda S

    2016-06-01

    Watermelon (Citrullus vulgaris) contains many health-promoting compounds, such as ascorbic acid, carotenoids, phenolic acids and amino acids including l-citrulline, arginine, and glutathione. Reported HPLC method for quantification of l-citrulline and sugars in watermelon involves, time-consuming sample preparation, post-column color development and detection with fluorescence and refractive index detectors. The present study describes development of a method to identify and quantify amino acids and sugars simultaneously from watermelon samples using quantitative proton NMR. Lyophilized watermelon samples (30-50mg) were extracted with deuterium oxide (D2O) by sonication and the centrifuged extract was directly used for quantification and identification with (1)HNMR. An external coaxial insert containing a 65µL of 0.012% 3-(trimethylsilyl) propionic-(2,2,3,3-d4) acid sodium salt (TSP-d4) in D2O was used as a quantitative reference. The levels of l-citrulline and sugars were measured in less than 6min. This rapid quantitation method was validated for specificity, linearity, accuracy, precision, reproducibility, and robustness. The limit of detection for l-citrulline was 38µg/mL and the limit of quantification was 71µg/mL; for sugars, the limits were 59-94µg/mL and 120µg/mL, respectively. This method can be used widely for confirmation and rapid quantitation of multiple compounds in large number of biological or breeding samples for routine analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. A new approach to microcalcification detection in digital mammograms

    SciTech Connect

    Cheng, Heng-Da; Liu, Yui Man; Freimanis, R.I.

    1996-12-31

    Computer-aided mammography is an important and challenging task in automated diagnosis. It has great potential over the traditional x-ray mammography in terms of efficiency and accuracy. Microcalcifications are the earliest sign of breast carcinomas and their accurate detection is one of the key issues for breast cancer control. In this study, a novel approach to detecting microcalcifications in digital mammograms is presented. The essential idea of the proposed approach is to apply a fuzzified image of a mammogram to locate the regions of interest and to interact the fuzzified image with the original image to preserve the fidelity. The major advantage of the proposed method is its ability to detect microcalcifications in very dense breast mammograms. A series of clinical mammograms are employed to test the proposed algorithm. The experiments aptly show that the microcalcifications are not only accurately detected but their features are also well preserved.

  7. A change detection approach to moving object detection in low frame-rate video

    SciTech Connect

    Porter, Reid B; Harvey, Neal R; Theiler, James P

    2009-01-01

    Moving object detection is of significant interest in temporal image analysis since it is a first step in many object identification and tracking applications. A key component in almost all moving object detection algorithms is a pixel-level classifier, where each pixel is predicted to be either part of a moving object or part of the background. In this paper we investigate a change detection approach to the pixel-level classification problem and evaluate its impact on moving object detection. The change detection approach that we investigate was previously applied to multi-and hyper-spectral datasets, where images were typically taken several days, or months apart. In this paper, we apply the approach to low-frame rate (1-2 frames per second) video datasets.

  8. Application of Western blot analysis for the diagnosis of Encephalitozoon cuniculi infection in rabbits: example of a quantitative approach.

    PubMed

    Desoubeaux, Guillaume; Pantin, Ana; Peschke, Roman; Joachim, Anja; Cray, Carolyn

    2017-02-01

    Diagnosis of Encephalitozoon cuniculi infection in rabbits remains a major veterinary issue. ELISA or immunofluorescence assays are the current reference standards of serological tests. However, these conventional techniques suffer from a lack of accuracy for distinguishing active from past infections, as a positive serostatus is common in clinically normal rabbits. In this study, we assessed the diagnostic performance of Western blot (WB) to detect both anti-E. cuniculi immunoglobulin G (IgG) and immunoglobulin M (IgM) in comparison with ELISA and to address the intensity of the immune response through a quantitative approach. Positive WB results were highly correlated with the E. cuniculi-related diseased status (P < 0.0001). Although it was more labor intensive and less standardized, quantitative WB provided detailed comparable analysis regarding the humoral response and diagnostic performance similar to ELISA testing with statistically higher sensitivity (88.4 vs. 76.1% for IgG detection and 84.3 vs. 70.4% for IgM, P < 0.01). Several specific WB bands were shown to be significantly associated with concomitant clinical signs, like the one located at 50 kDa (OR = 8.2, [2.4-27.7], P = 0.0008) for IgG and (OR = 27.9, [4.2-187.9], P = 0.0006) for IgM. Therefore, the quantitative WB may have application in veterinary diagnostic laboratories to increase the accuracy of the clinical diagnosis of E. cuniculi infection. In addition, this tool may help to further understand the development and function of the humoral immune response to this infectious agent.

  9. Detection of Aspergillus fumigatus by quantitative polymerase chain reaction in air samples impacted on low-melt agar.

    PubMed

    Bellanger, Anne-Pauline; Reboux, Gabriel; Murat, Jean-Benjamin; Bex, Valerie; Millon, Laurence

    2010-04-01

    The standard procedure for routine environmental sampling for the prevention of invasive aspergillosis outbreaks is culturing of Aspergillus fumigatus after impaction of air. Time to results is usually 7 days. A preliminary study was carried out to compare the time to results and sensitivity of culturing and quantitative polymerase chain reaction (QPCR) in the detection of airborne A fumigatus. Fungal DNA was extracted from 43 samples of impacted low-melt agar by a 3-step extraction method and amplified by QPCR. Identification was made using a specific A fumigatus probe. With QPCR, 19 of the 43 samples were positive for A fumigatus; with culturing, 7 of these 19 samples were positive, and 12 were negative. The cycle threshold (Ct) values for the 12 culture-negative samples were between 39 and 43 cycles, and the Ct values for 6 of the 7 culture-positive samples were <38 cycles, suggesting that the amount of DNA detected by QPCR was higher in the presence of viable conidia. QPCR detection of airborne A fumigatus in impacted low-melt agar significantly reduces the period of time between sample collection and results (48 hours), suggesting that this new approach can be beneficial for routine environmental sampling. 2010 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

  10. Proteome-wide detection and quantitative analysis of irreversible cysteine oxidation using long column UPLC-pSRM

    PubMed Central

    Lee, Chia-Fang; Paull, Tanya T.; Person, Maria D.

    2013-01-01

    Reactive oxygen species (ROS) play an important role in normal biological functions and pathological processes. ROS is one of the driving forces for oxidizing proteins, especially on cysteine thiols. The labile, transient, and dynamic nature of oxidative modifications poses enormous technical challenges for both accurate modification site determination and quantitation of cysteine thiols. The present study describes a mass spectrometry-based approach that allows effective discovery and quantification of irreversible cysteine modifications. The utilization of a long reverse phase column provides high-resolution chromatography to separate different forms of modified cysteine thiols from protein complexes or cell lysates. This FT-MS approach enabled detection and quantitation of ATM complex cysteine sulfoxidation states using Skyline MS1 filtering. When we applied the long column UPLC-MS/MS analysis, 61 and 44 peptides from cell lysates and cell were identified with cysteine modifications in response to in vitro and in vivo H2O2 oxidation, respectively. Long column Ultra High Pressure Liquid Chromatography -pseudo Selected Reaction Monitoring (UPLC-pSRM) was then developed to monitor the oxidative level of cysteine thiols in cell lysate under varying concentrations of H2O2 treatment. From UPLC-pSRM analysis, the dynamic conversion of sulfinic (S-O2H) and sulfonic acid (S-O3H) was observed within nucleoside diphosphate kinase (Nm23-H1) and heat shock 70 kDa protein 8 (Hsc70). These methods are suitable for proteome-wide studies, providing a highly sensitive, straight-forward approach to identify proteins containing redox-sensitive cysteine thiols in biological systems. PMID:23964713

  11. Chemical approaches to detect and analyze protein sulfenic acids

    PubMed Central

    Furdui, Cristina M.; Poole, Leslie B.

    2013-01-01

    Orchestration of many processes relying on intracellular signal transduction is recognized to require the generation of hydrogen peroxide as a second messenger, yet relatively few molecular details of how this oxidant acts to regulate protein function are currently understood. This review describes emerging chemical tools and approaches that can be applied to study protein oxidation in biological systems, with a particular emphasis on a key player in protein redox regulation, cysteine sulfenic acid. While sulfenic acids (within purified proteins or simple mixtures) are detectable by physical approaches like X-ray crystallography, nuclear magnetic resonance and mass spectrometry, the propensity of these moieties to undergo further modification in complex biological systems has necessitated the development of chemical probes, reporter groups and analytical approaches to allow for their selective detection and quantification. Provided is an overview of techniques that are currently available for the study of sulfenic acids, and some of the biologically meaningful data that have been collected using such approaches. PMID:24105931

  12. The Appeal to Expert Opinion: Quantitative Support for a Bayesian Network Approach.

    PubMed

    Harris, Adam J L; Hahn, Ulrike; Madsen, Jens K; Hsu, Anne S

    2016-08-01

    The appeal to expert opinion is an argument form that uses the verdict of an expert to support a position or hypothesis. A previous scheme-based treatment of the argument form is formalized within a Bayesian network that is able to capture the critical aspects of the argument form, including the central considerations of the expert's expertise and trustworthiness. We propose this as an appropriate normative framework for the argument form, enabling the development and testing of quantitative predictions as to how people evaluate this argument, suggesting that such an approach might be beneficial to argumentation research generally. We subsequently present two experiments as an example of the potential for future research in this vein, demonstrating that participants' quantitative ratings of the convincingness of a proposition that has been supported with an appeal to expert opinion were broadly consistent with the predictions of the Bayesian model.

  13. An efficient approach to the quantitative analysis of humic acid in water.

    PubMed

    Wang, Xue; Li, Bao Qiong; Zhai, Hong Lin; Xiong, Meng Yi; Liu, Ying

    2016-01-01

    Rayleigh and Raman scatterings inevitably appear in fluorescence measurements, which make the quantitative analysis more difficult, especially in the overlap of target signals and scattering signals. Based on the grayscale images of three-dimensional fluorescence spectra, the linear model with two selected Zernike moments was established for the determination of humic acid, and applied to the quantitative analysis of the real sample taken from the Yellow River. The correlation coefficient (R(2)) and leave-one-out cross validation correlation coefficient (R(2)cv) were up to 0.9994 and 0.9987, respectively. The average recoveries were reached 96.28%. Compared with N-way partial least square and alternating trilinear decomposition methods, our approach was immune from the scattering and noise signals owing to its powerful multi-resolution characteristic and the obtained results were more reliable and accurate, which could be applied in food analyses.

  14. New approaches for the analysis of confluent cell layers with quantitative phase digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Pohl, L.; Kaiser, M.; Ketelhut, S.; Pereira, S.; Goycoolea, F.; Kemper, Björn

    2016-03-01

    Digital holographic microscopy (DHM) enables high resolution non-destructive inspection of technical surfaces and minimally-invasive label-free live cell imaging. However, the analysis of confluent cell layers represents a challenge as quantitative DHM phase images in this case do not provide sufficient information for image segmentation, determination of the cellular dry mass or calculation of the cell thickness. We present novel strategies for the analysis of confluent cell layers with quantitative DHM phase contrast utilizing a histogram based-evaluation procedure. The applicability of our approach is illustrated by quantification of drug induced cell morphology changes and it is shown that the method is capable to quantify reliable global morphology changes of confluent cell layers.

  15. Genetic algorithm based image binarization approach and its quantitative evaluation via pooling

    NASA Astrophysics Data System (ADS)

    Hu, Huijun; Liu, Ya; Liu, Maofu

    2015-12-01

    The binarized image is very critical to image visual feature extraction, especially shape feature, and the image binarization approaches have been attracted more attentions in the past decades. In this paper, the genetic algorithm is applied to optimizing the binarization threshold of the strip steel defect image. In order to evaluate our genetic algorithm based image binarization approach in terms of quantity, we propose the novel pooling based evaluation metric, motivated by information retrieval community, to avoid the lack of ground-truth binary image. Experimental results show that our genetic algorithm based binarization approach is effective and efficiency in the strip steel defect images and our quantitative evaluation metric on image binarization via pooling is also feasible and practical.

  16. Utility of Real-Time Quantitative Polymerase Chain Reaction in Detecting Mycobacterium tuberculosis

    PubMed Central

    Zhang, Mingxin; Zhang, Hui

    2017-01-01

    This study aimed to assess the value of real-time quantitative polymerase chain reaction (RT-qPCR) for the detection of Mycobacterium tuberculosis (MTB). Samples from 192 patients with suspected MTB were examined by RT-qPCR and an improved Löwenstein–Jensen (L-J) culture method. To evaluate the diagnostic usefulness of RT-qPCR in detecting MTB, a receiver operating characteristic (ROC) curve for RT-qPCR was generated, and the area under the curve (AUC) as well as a cutoff value was calculated. Using the L-J culture method as the gold standard, accuracy of the RT-qPCR method for detecting MTB was 92.7%, with sensitivity and specificity of 62.5% and 97.02%, respectively. In comparison with the improved L-J culture method, the AUC of RT-qPCR ROC curve was 0.957, which was statistically significant (p < 0.001). The Youden Index reached the maximum value (0.88) for gene copy number of 794.5 IU/mL, which was used as the cutoff value. RT-qPCR detection of MTB yielded results consistent with those of the improved L-J culture method, with high accuracy. RT-qPCR may be used as an auxiliary method for etiological diagnosis of tuberculosis. PMID:28168192

  17. Real-time PCR assay for rapid qualitative and quantitative detection of Entamoeba histolytica.

    PubMed

    Orosz, Erika; Perkátai, Katalin; Kapusinszky, Beatrix; Farkas, Agnes; Kucsera, István

    2012-12-01

    Simple real-time PCR assay with one set of primer and probe for rapid, sensitive qualitative and quantitative detection of Entamoeba histolytica has been used. Consensus sequences were used to amplify a species-specific region of the 16S rRNA gene, and fluorescence resonance energy transfer hybridization probes were used for detection in a LightCycler platform (Roche). The anchor probe sequence was designed to be a perfect match for the 16S rRNA gene of Entamoeba species, while the acceptor probe sequence was designed for Entamoeba histolytica, which allowed differentiation. The performed characteristics of the real-time PCR assay were compared with ELISA antigen and microscopical detection from 77 samples of individuals with suspected clinical diagnosis of imported E. histolytica infection. Stool and liver abscess pus samples were examined with analytical sensitivity of 5 parasites per PCR reaction. The melting curve means Tms (standard deviation) in clinical isolates were 54°C. The real-time assay was 100% sensitive and specific for differentiation of Entamoeba histolytica, compared with conventional ELISA or microscopy. This real-time PCR assay with melting curve analysis is rapid, and specific for the detection and differentiation of Entamoeba histolytica. The suitability for routine use of this assay in clinical diagnostic laboratories is discussed.

  18. Detection of Nanophyetus salmincola in water, snails, and fish tissues by quantitative polymerase chain reaction

    USGS Publications Warehouse

    Purcell, Maureen K.; Powers, Rachel L.; Besijn, Bonnie; Hershberger, Paul K.

    2017-01-01

    We report the development and validation of two quantitative PCR (qPCR) assays to detect Nanophyetus salmincola DNA in water samples and in fish and snail tissues. Analytical and diagnostic validation demonstrated good sensitivity, specificity, and repeatability of both qPCR assays. The N. salmincola DNA copy number in kidney tissue was significantly correlated with metacercaria counts based on microscopy. Extraction methods were optimized for the sensitive qPCR detection of N. salmincola DNA in settled water samples. Artificially spiked samples suggested that the 1-cercaria/L threshold corresponded to an estimated log10 copies per liter ≥ 6.0. Significant correlation of DNA copy number per liter and microscopic counts indicated that the estimated qPCR copy number was a good predictor of the number of waterborne cercariae. However, the detection of real-world samples below the estimated 1-cercaria/L threshold suggests that the assays may also detect other N. salmincola life stages, nonintact cercariae, or free DNA that settles with the debris. In summary, the qPCR assays reported here are suitable for identifying and quantifying all life stages of N. salmincola that occur in fish tissues, snail tissues, and water.

  19. Quantitative GSTP1 methylation and the detection of prostate adenocarcinoma in sextant biopsies.

    PubMed

    Harden, Susan V; Sanderson, Harriette; Goodman, Steven N; Partin, Alan A W; Walsh, Patrick C; Epstein, Jonathan I; Sidransky, David

    2003-11-05

    Hypermethylation of the 5' promoter region of the glutathione S-transferase pi gene (GSTP1) occurs at a very high frequency in prostate adenocarcinoma. We compared the results of blinded histologic review of sextant biopsy samples from 72 excised prostates with those obtained using a quantitative methylation-specific polymerase chain reaction assay (QMSP) for GSTP1. Formal surgical pathologic review of the resected prostates was used to determine the number of patients with (n = 61) and without (n = 11) prostate cancer. Histology alone detected prostate carcinoma with 64% sensitivity (95% confidence interval [CI] = 51% to 76%) and 100% specificity (95% CI = 72% to 100%), whereas the combination of histology and GSTP1 QMSP at an assay threshold greater than 10 detected prostate carcinoma with 75% sensitivity (95% CI = 63% to 86%) and 100% specificity (95% CI = 72% to 100%), an 11% improvement (95% CI = 5% to 22%) in sensitivity over histology alone. The combination of histology and GSTP1 QMSP at an assay threshold greater than 5 detected prostate adenocarcinoma with 79% sensitivity (95% CI = 68% to 89%), a 15% improvement (95% CI = 7% to 26%) over histology alone. Thus, GSTP1 QMSP improved the sensitivity of histologic review of random needle biopsies for prostate cancer diagnosis. Further studies should determine whether detection of GSTP1 hypermethylation in a biopsy sample with normal histology indicates the need for an early repeat biopsy at the same site.

  20. Simultaneous detection and fine mapping of quantitative trait loci in mice using heterogeneous stocks.

    PubMed Central

    Mott, Richard; Flint, Jonathan

    2002-01-01

    We describe a method to simultaneously detect and fine map quantitative trait loci (QTL) that is especially suited to the mapping of modifier loci in mouse mutant models. The method exploits the high level of historical recombination present in a heterogeneous stock (HS), an outbred population of mice derived from known founder strains. The experimental design is an F(2) cross between the HS and a genetically distinct line, such as one carrying a knockout or transgene. QTL detection is performed by a standard genome scan with approximately 100 markers and fine mapping by typing the same animals using densely spaced markers over those candidate regions detected by the scan. The analysis uses an extension of the dynamic-programming technique employed previously to fine map QTL in HS mice. We show by simulation that a QTL accounting for 5% of the total variance can be detected and fine mapped with >50% probability to within 3 cM by genotyping approximately 1500 animals. PMID:11973314

  1. Immunomagnetic quantitative immuno-PCR for detection of less than one HIV-1 virion.

    PubMed

    Barletta, Janet; Bartolome, Amelita; Constantine, Niel T

    2009-05-01

    Methods that allow the accurate and reliable detection of ultra-low molecular levels of proteins using techniques such as quantitative immuno-PCR (qIPCR) have demonstrated numerous technical difficulties. Protein detection methods lose specificity when the protein target is immersed within a matrix of thousands of molecules having wide ranges of concentrations. In addition, sensitivities are limited because of high background signals. To validate the performance of an immunomagnetic bead qIPCR method designed to remove the 'matrix' effect for HIV-1 p24 antigen detection, regression analyses were performed using samples from patients infected with HIV-1 diluted to approximately 100-1000, 10-100, 1-10, and 0.1-1.0 HIV-1 p24 Ag molecules/reaction. The number of HIV-1 p24 Ag molecules was derived from quantified HIV-1 RNA determinations. The modified immunomagnetic qIPCR bead assay demonstrated a limit of quantification of 10-100 HIV-1 p24 molecules per reaction, with an average correlation coefficient of 0.948+/-0.028 over a 4-log dynamic range. This method detects less than one HIV-1 virion (a limit of detection unreported previously for HIV-1), and thus, has the potential to identify HIV-1 infection and monitor the dynamics of the disease course earlier than nucleic acid methods. The immunomagnetic qIPCR bead assay is a simple and inexpensive method for ultra-low protein detection of infectious agents, toxins, and cancer markers at a level unrecognized previously using any enzymatic or molecular method.

  2. Development of one-step quantitative reverse transcription PCR for the rapid detection of flaviviruses.

    PubMed

    Patel, Pranav; Landt, Olfert; Kaiser, Marco; Faye, Oumar; Koppe, Tanja; Lass, Ulrich; Sall, Amadou A; Niedrig, Matthias

    2013-02-14

    The genus Flavivirus includes several pathogenic agents that cause severe illness in humans. Re-emergence of West Nile virus in Europe and continuous spread of certain flaviviruses such as dengue, yellow fever and Japanese encephalitis viruses represent a global danger to public health. Therefore, a rapid and accurate molecular method is required for diagnostics and epidemiological surveillance of flaviviruses. A Pan-Flavi quantitative RT-PCR assay using a Locked-Nucleic Acid probe targeting the flavivirus NS5 gene was developed and optimized to detect a wide range of flaviviruses simultaneously. The specificity and sensitivity of the Pan-Flavi assay were tested using RNA of different flaviviruses and non-flaviviruses. Furthermore, the assay was compared directly to flavivirus species-specific assays for the ability to detect flaviviruses sensitively. Two degenerate primers and one Locked-Nucleic Acids probe were designed to amplify most of the flaviviruses. To increase the specificity and fluorescence signal of the Pan-Flavi assay for detection of yellow fever virus and dengue virus 4, additional primers and probes were included. Viral RNA of thirty different flaviviruses was detected, verifying the broad range specificity. The testing of this assay was successful, using standard plasmid and RNA dilutions of yellow fever virus vaccine strain, dengue virus 1 and tick-borne encephalitis virus, with a sensitivity limit of 10-100 genome copies/reaction. Also comparatively good results were achieved for detecting different flaviviruses by the Pan-Flavi assay when compared to the flavivirus species-specific assays. The assay is rapid, broad-range flavivirus-specific and highly sensitive making it a valuable tool for rapid detection of flaviviruses in livestock samples, epidemiological studies or as useful complement to single flavivirus-specific assays for clinical diagnosis.

  3. A competitive enzyme immunoassay for the quantitative detection of cocaine from banknotes and latent fingermarks.

    PubMed

    van der Heide, Susan; Garcia Calavia, Paula; Hardwick, Sheila; Hudson, Simon; Wolff, Kim; Russell, David A

    2015-05-01

    A sensitive and versatile competitive enzyme immunoassay (cEIA) has been developed for the quantitative detection of cocaine in complex forensic samples. Polyclonal anti-cocaine antibody was purified from serum and deposited onto microtiter plates. The concentration of the cocaine antibody adsorbed onto the plates, and the dilution of the cocaine-HRP hapten were both studied to achieve an optimised immunoassay. The method was successfully used to quantify cocaine in extracts taken from both paper currency and latent fingermarks. The limit of detection (LOD) of 0.162ngmL(-1) achieved with the assay compares favourably to that of conventional chromatography-mass spectroscopy techniques, with an appropriate sensitivity for the quantification of cocaine at the low concentrations present in some forensic samples. The cEIA was directly compared to LC-MS for the analysis of ten UK banknote samples. The results obtained from both techniques were statistically similar, suggesting that the immunoassay was unaffected by cross-reactivity with potentially interfering compounds. The cEIA was used also for the detection of cocaine in extracts from latent fingermarks. The results obtained were compared to the cocaine concentrations detected in oral fluid sampled from the same individual. Using the cEIA, we have shown, for the first time, that endogeneously excreted cocaine can be detected and quantified from a single latent fingermark. Additionally, it has been shown that the presence of cocaine, at similar concentrations, in more than one latent fingermark from the same individual can be linked with those concentrations found in oral fluid. These results show that detection of drugs in latent fingermarks could directly indicate whether an individual has consumed the drug. The specificity and feasibility of measuring low concentrations of cocaine in complex forensic samples demonstrate the effectiveness and robustness of the assay. The immunoassay presents a simple and cost

  4. Sequential Bayesian Detection: A Model-Based Approach

    SciTech Connect

    Sullivan, E J; Candy, J V

    2007-08-13

    Sequential detection theory has been known for a long time evolving in the late 1940's by Wald and followed by Middleton's classic exposition in the 1960's coupled with the concurrent enabling technology of digital computer systems and the development of sequential processors. Its development, when coupled to modern sequential model-based processors, offers a reasonable way to attack physics-based problems. In this chapter, the fundamentals of the sequential detection are reviewed from the Neyman-Pearson theoretical perspective and formulated for both linear and nonlinear (approximate) Gauss-Markov, state-space representations. We review the development of modern sequential detectors and incorporate the sequential model-based processors as an integral part of their solution. Motivated by a wealth of physics-based detection problems, we show how both linear and nonlinear processors can seamlessly be embedded into the sequential detection framework to provide a powerful approach to solving non-stationary detection problems.

  5. Sequential Bayesian Detection: A Model-Based Approach

    SciTech Connect

    Candy, J V

    2008-12-08

    Sequential detection theory has been known for a long time evolving in the late 1940's by Wald and followed by Middleton's classic exposition in the 1960's coupled with the concurrent enabling technology of digital computer systems and the development of sequential processors. Its development, when coupled to modern sequential model-based processors, offers a reasonable way to attack physics-based problems. In this chapter, the fundamentals of the sequential detection are reviewed from the Neyman-Pearson theoretical perspective and formulated for both linear and nonlinear (approximate) Gauss-Markov, state-space representations. We review the development of modern sequential detectors and incorporate the sequential model-based processors as an integral part of their solution. Motivated by a wealth of physics-based detection problems, we show how both linear and nonlinear processors can seamlessly be embedded into the sequential detection framework to provide a powerful approach to solving non-stationary detection problems.

  6. An axial approach to detection in capillary electrophoresis

    SciTech Connect

    Taylor, John Aaron

    1993-05-01

    Our approach involves on-axis illumination of the compounds inside the capillary detection region and is applied to absorbance and fluorescence detection. Absorbance measurements were made by focussing an incident laser beam into one capillary end; by using signals collected over the entire length of analyte band, this enhances the analytical path length of conventional absorbance detection 60x. This instrument offers a 15x improvement in detection limits. Three fluorescence detection experiments are discussed, all of which involve insertion of an optical fiber into capillary. The first uses a high refractive index liquid phase to obtain total internal reflectance along capillary axis, this reducing light scatter. The second uses a charge-coupled device camera for simultaneous imaging of a capillary array (this may be useful in genome sequencing, etc.). The third is a study of fluid motion inside the capillary under pressure-driven and electroosmotic flow. The thesis is divided into four parts. Figs, tabs.

  7. Quantitative Detection of Trace Malachite Green in Aquiculture Water Samples by Extractive Electrospray Ionization Mass Spectrometry

    PubMed Central

    Fang, Xiaowei; Yang, Shuiping; Chingin, Konstantin; Zhu, Liang; Zhang, Xinglei; Zhou, Zhiquan; Zhao, Zhanfeng

    2016-01-01

    Exposure to malachite green (MG) may pose great health risks to humans; thus, it is of prime importance to develop fast and robust methods to quantitatively screen the presence of malachite green in water. Herein the application of extractive electrospray ionization mass spectrometry (EESI-MS) has been extended to the trace detection of MG within lake water and aquiculture water, due to the intensive use of MG as a biocide in fisheries. This method has the advantage of obviating offline liquid-liquid extraction or tedious matrix separation prior to the measurement of malachite green in native aqueous medium. The experimental results indicate that the extrapolated detection limit for MG was ~3.8 μg·L−1 (S/N = 3) in lake water samples and ~0.5 μg·L−1 in ultrapure water under optimized experimental conditions. The signal intensity of MG showed good linearity over the concentration range of 10–1000 μg·L−1. Measurement of practical water samples fortified with MG at 0.01, 0.1 and 1.0 mg·L−1 gave a good validation of the established calibration curve. The average recoveries and relative standard deviation (RSD) of malachite green in lake water and Carassius carassius fish farm effluent water were 115% (6.64% RSD), 85.4% (9.17% RSD) and 96.0% (7.44% RSD), respectively. Overall, the established EESI-MS/MS method has been demonstrated suitable for sensitive and rapid (<2 min per sample) quantitative detection of malachite green in various aqueous media, indicating its potential for online real-time monitoring of real life samples. PMID:27529262

  8. Detection of Leishmania infantum DNA in conjunctival swabs of cats by quantitative real-time PCR.

    PubMed

    Benassi, Julia Cristina; Benvenga, Graziella U; Ferreira, Helena Lage; Pereira, Vanessa F; Keid, Lara B; Soares, Rodrigo; Oliveira, Tricia Maria Ferreira de Sousa

    2017-06-01

    Although some studies have investigated the potential role of cats as a reservoir for Leishmania, their role in the epidemiology of visceral leishmaniasis (VL) is still poorly understood. Molecular diagnostic techniques are an important tool in VL diagnosis, and PCR shows high sensitivity and specificity for Leishmania spp. detection. Quantitative real-time PCR (qPCR) is a method that permits quantitative analysis of a large number of samples, resulting in more sensitive, accurate, and reproducible measurements of specific DNA present in the sample. This study compared real-time PCR (qPCR) and conventional PCR (cPCR) for detection of Leishmania spp. in blood and conjunctival swab (CS) samples of healthy cats from a non-endemic area in the state of São Paulo, Brazil. Of all CS samples, 1.85% (2/108) were positive for Leishmania spp. by both cPCR as qPCR (kappa index = 1), indicating excellent agreement between the two methods. The DNA from the two CS-cPCR- and CS-qPCR-positive samples was further tested with a PCR test amplifying the Leishmania spp. discriminative rRNA internal transcribed spacer 1 (ITS 1), of which one sample generated a 300-350-bp DNA fragment whose size varies according to the Leishmania species. Following sequencing, the fragment showed 100% similarity to a GenBank L. infantum sequence obtained from a cat in Italy. In conclusion, the association of qPCR and CS proved to be effective for detection of Leishmania in cats. Conjunctival swab samples were shown to be a practical and better alternative to blood samples and may be useful in the diagnosis and studies of feline leishmaniasis. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Subtle Sensory Abnormalities Detected by Quantitative Sensory Testing in Patients with Trigeminal Neuralgia.

    PubMed

    Flor, Herta; Rasche, Dirk; Islamian, Ariyan Pirayesh; Rolko, Claudia; Yilmaz, Pinar; Ruppolt, Marc; Capelle, H Holger; Tronnier, Volker; Krauss, Joachim K

    2016-01-01

    Trigeminal neuralgia (TN) is characterized by paroxysmal pain attacks affecting the somatosensory distributions of the trigeminal nerve. It is thought to be associated with a neurovascular conflict most frequently, but pathomechanisms have not been fully elucidated. In general, no sensory deficit is found in routine clinical examination. There is limited data available, however, showing subtle subclinical sensory deficits upon extensive testing. We used quantitative sensory testing (QST) to detect abnormalities in sensory processing in patients with TN by comparing the affected and non-affected nerve branches with their contralateral counterparts and by comparing the results of the patients with those of controls. Observational study. University Hospital, Departments of Neurosurgery, Institute for Cognitive and Clinical Neuroscience. QST was conducted on 48 patients with idiopathic TN and 27 controls matched for age and gender using the standardized protocol of the German Neuropathic Pain Network. Stimulations were performed bilaterally in the distribution of the trigeminal branches. The patients had no prior invasive treatment, and medications at the time of examination were noted. In patients with TN deficits in warm and cold sensory detection thresholds in the affected and also the non-affected nerve branches were found. Tactile sensation thresholds were elevated in the involved nerve branches compared to the contralateral side. More data are needed on the correlation of such findings with the length of history of TN and with changes of the morphology of the trigeminal nerve. QST shows subtle sensory abnormalities in patients with TN despite not being detected in routine clinical examination. Our data may provide a basis for further research on the development of TN and also on improvement after treatment. Quantitative sensory testing, trigeminal neuralgia, facial pain, neuropathic pain, microvascular decompression, cranial nerve.

  10. Quantitative Detection of Trace Malachite Green in Aquiculture Water Samples by Extractive Electrospray Ionization Mass Spectrometry.

    PubMed

    Fang, Xiaowei; Yang, Shuiping; Chingin, Konstantin; Zhu, Liang; Zhang, Xinglei; Zhou, Zhiquan; Zhao, Zhanfeng

    2016-08-11

    Exposure to malachite green (MG) may pose great health risks to humans; thus, it is of prime importance to develop fast and robust methods to quantitatively screen the presence of malachite green in water. Herein the application of extractive electrospray ionization mass spectrometry (EESI-MS) has been extended to the trace detection of MG within lake water and aquiculture water, due to the intensive use of MG as a biocide in fisheries. This method has the advantage of obviating offline liquid-liquid extraction or tedious matrix separation prior to the measurement of malachite green in native aqueous medium. The experimental results indicate that the extrapolated detection limit for MG was ~3.8 μg·L(-1) (S/N = 3) in lake water samples and ~0.5 μg·L(-1) in ultrapure water under optimized experimental conditions. The signal intensity of MG showed good linearity over the concentration range of 10-1000 μg·L(-1). Measurement of practical water samples fortified with MG at 0.01, 0.1 and 1.0 mg·L(-1) gave a good validation of the established calibration curve. The average recoveries and relative standard deviation (RSD) of malachite green in lake water and Carassius carassius fish farm effluent water were 115% (6.64% RSD), 85.4% (9.17% RSD) and 96.0% (7.44% RSD), respectively. Overall, the established EESI-MS/MS method has been demonstrated suitable for sensitive and rapid (<2 min per sample) quantitative detection of malachite green in various aqueous media, indicating its potential for online real-time monitoring of real life samples.

  11. Enhanced Detection of Surface-Associated Bacteria in Indoor Environments by Quantitative PCR

    PubMed Central

    Buttner, Mark P.; Cruz-Perez, Patricia; Stetzenbach, Linda D.

    2001-01-01

    Methods for detecting microorganisms on surfaces are needed to locate biocontamination sources and to relate surface and airborne concentrations. Research was conducted in an experimental room to evaluate surface sampling methods and quantitative PCR (QPCR) for enhanced detection of a target biocontaminant present on flooring materials. QPCR and culture analyses were used to quantitate Bacillus subtilis (Bacillus globigii) endospores on vinyl tile, commercial carpet, and new and soiled residential carpet with samples obtained by four surface sampling methods: a swab kit, a sponge swipe, a cotton swab, and a bulk method. The initial data showed that greater overall sensitivity was obtained with the QPCR than with culture analysis; however, the QPCR results for bulk samples from residential carpet were negative. The swab kit and the sponge swipe methods were then tested with two levels of background biological contamination consisting of Penicillium chrysogenum spores. The B. subtilis values obtained by the QPCR method were greater than those obtained by culture analysis. The differences between the QPCR and culture data were significant for the samples obtained with the swab kit for all flooring materials except soiled residential carpet and with the sponge swipe for commercial carpet. The QPCR data showed that there were no significant differences between the swab kit and sponge swipe sampling methods for any of the flooring materials. Inhibition of QPCR due solely to biological contamination of flooring materials was not evident. However, some degree of inhibition was observed with the soiled residential carpet, which may have been caused by the presence of abiotic contaminants, alone or in combination with biological contaminants. The results of this research demonstrate the ability of QPCR to enhance detection and enumeration of biocontaminants on surface materials and provide information concerning the comparability of currently available surface sampling

  12. Two approaches to improving mental health care: positivist/quantitative versus skill-based/qualitative.

    PubMed

    Luchins, Daniel

    2012-01-01

    The quality improvement model currently used in medicine and mental health was adopted from industry, where it developed out of early 20th-century efforts to apply a positivist/quantitative agenda to improving manufacturing. This article questions the application of this model to mental health care. It argues that (1) developing "operational definitions" for something as value-laden as "quality" risks conflating two realms, what we measure with what we value; (2) when measurements that are tied to individuals are aggregated to establish benchmarks and goals, unwarranted mathematical assumptions are made; (3) choosing clinical outcomes is problematic; (4) there is little relationship between process measures and clinical outcomes; and (5) since changes in quality indices do not relate to improved clinical care, management's reliance on such indices provides an illusory sense of control. An alternative model is the older, skill-based/qualitative approach to knowing, which relies on "implicit/ expert" knowledge. These two approaches offer a series of contrasts: quality versus excellence, competence versus expertise, management versus leadership, extrinsic versus intrinsic rewards. The article concludes that we need not totally dispense with the current quality improvement model, but rather should balance quantitative efforts with the older qualitative approach in a mixed methods model.

  13. A Systematic Approach for Quantitative Analysis of Multidisciplinary Design Optimization Framework

    NASA Astrophysics Data System (ADS)

    Kim, Sangho; Park, Jungkeun; Lee, Jeong-Oog; Lee, Jae-Woo

    An efficient Multidisciplinary Design and Optimization (MDO) framework for an aerospace engineering system should use and integrate distributed resources such as various analysis codes, optimization codes, Computer Aided Design (CAD) tools, Data Base Management Systems (DBMS), etc. in a heterogeneous environment, and need to provide user-friendly graphical user interfaces. In this paper, we propose a systematic approach for determining a reference MDO framework and for evaluating MDO frameworks. The proposed approach incorporates two well-known methods, Analytic Hierarchy Process (AHP) and Quality Function Deployment (QFD), in order to provide a quantitative analysis of the qualitative criteria of MDO frameworks. Identification and hierarchy of the framework requirements and the corresponding solutions for the reference MDO frameworks, the general one and the aircraft oriented one were carefully investigated. The reference frameworks were also quantitatively identified using AHP and QFD. An assessment of three in-house frameworks was then performed. The results produced clear and useful guidelines for improvement of the in-house MDO frameworks and showed the feasibility of the proposed approach for evaluating an MDO framework without a human interference.

  14. Quantitative Detection of Combustion Species using Ultra-Violet Diode Lasers

    NASA Technical Reports Server (NTRS)

    Pilgrim, J. S.; Peterson, K. A.

    2001-01-01

    Southwest Sciences is developing a new microgravity combustion diagnostic based on UV diode lasers. The instrument will allow absolute concentration measurements of combustion species on a variety of microgravity combustion platforms including the Space Station. Our approach uses newly available room temperature UV diode lasers, thereby keeping the instrument compact, rugged and energy efficient. The feasibility of the technique was demonstrated by measurement of CH radicals in laboratory flames. Further progress in fabrication technology of UV diode lasers at shorter wavelengths and higher power will result in detection of transient species in the deeper UV. High sensitivity detection of combustion radicals is provided with wavelength modulation absorption spectroscopy.

  15. Icing detection from geostationary satellite data using machine learning approaches

    NASA Astrophysics Data System (ADS)

    Lee, J.; Ha, S.; Sim, S.; Im, J.

    2015-12-01

    Icing can cause a significant structural damage to aircraft during flight, resulting in various aviation accidents. Icing studies have been typically performed using two approaches: one is a numerical model-based approach and the other is a remote sensing-based approach. The model based approach diagnoses aircraft icing using numerical atmospheric parameters such as temperature, relative humidity, and vertical thermodynamic structure. This approach tends to over-estimate icing according to the literature. The remote sensing-based approach typically uses meteorological satellite/ground sensor data such as Geostationary Operational Environmental Satellite (GOES) and Dual-Polarization radar data. This approach detects icing areas by applying thresholds to parameters such as liquid water path and cloud optical thickness derived from remote sensing data. In this study, we propose an aircraft icing detection approach which optimizes thresholds for L1B bands and/or Cloud Optical Thickness (COT) from Communication, Ocean and Meteorological Satellite-Meteorological Imager (COMS MI) and newly launched Himawari-8 Advanced Himawari Imager (AHI) over East Asia. The proposed approach uses machine learning algorithms including decision trees (DT) and random forest (RF) for optimizing thresholds of L1B data and/or COT. Pilot Reports (PIREPs) from South Korea and Japan were used as icing reference data. Results show that RF produced a lower false alarm rate (1.5%) and a higher overall accuracy (98.8%) than DT (8.5% and 75.3%), respectively. The RF-based approach was also compared with the existing COMS MI and GOES-R icing mask algorithms. The agreements of the proposed approach with the existing two algorithms were 89.2% and 45.5%, respectively. The lower agreement with the GOES-R algorithm was possibly due to the high uncertainty of the cloud phase product from COMS MI.

  16. Gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of Japanese encephalitis virus

    NASA Astrophysics Data System (ADS)

    Huang, Su-Hua; Yang, Tsuey-Ching; Tsai, Ming-Hong; Tsai, I.-Shou; Lu, Huang-Chih; Chuang, Pei-Hsin; Wan, Lei; Lin, Ying-Ju; Lai, Chih-Ho; Lin, Cheng-Wen

    2008-10-01

    Virus isolation and antibody detection are routinely used for diagnosis of Japanese encephalitis virus (JEV) infection, but the low level of transient viremia in some JE patients makes JEV isolation from clinical and surveillance samples very difficult. We describe the use of gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of JEV from its RNA genome. We tested the effect of gold nanoparticles on four different PCR systems, including conventional PCR, reverse-transcription PCR (RT-PCR), and SYBR green real-time PCR and RT-PCR assays for diagnosis in the acute phase of JEV infection. Gold nanoparticles increased the amplification yield of the PCR product and shortened the PCR time compared to the conventional reaction. In addition, nanogold-based real-time RT-PCR showed a linear relationship between Ct and template amount using ten-fold dilutions of JEV. The nanogold-based RT-PCR and real-time quantitative RT-PCR assays were able to detect low levels (1-10 000 copies) of the JEV RNA genomes extracted from culture medium or whole blood, providing early diagnostic tools for the detection of low-level viremia in the acute-phase infection. The assays described here were simple, sensitive, and rapid approaches for detection and quantitation of JEV in tissue cultured samples as well as clinical samples.

  17. LC-MS/MS-based targeted proteomics quantitatively detects the interaction between p53 and MDM2 in breast cancer.

    PubMed

    Zhang, Wen; Zhong, Ting; Chen, Yun

    2017-01-30

    extent of PPI so far. The major issue of current available approaches is the trade-off between sensitivity and specificity. Thus, techniques with the ability to quantify PPIs with both high sensitivity (low false-negative rate) and high specificity (low false-positive rate) are eagerly desired. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics has shown its potential to study biomolecules because of its high sensitivity, high selectivity and wide dynamic range. In this study, we made an effort to develop a LC-MS/MS-based targeted proteomics assay for the quantitative detection of p53-MDM2 interaction in breast cells and tissue samples. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Transrectal quantitative shear wave elastography in the detection and characterisation of prostate cancer.

    PubMed

    Ahmad, Sarfraz; Cao, Rui; Varghese, Tomy; Bidaut, Luc; Nabi, Ghulam

    2013-09-01

    Shear wave imaging (SWI) is a new ultrasound technique whose application facilitates quantitative tissue elasticity assessment during transrectal ultrasound biopsies of the prostate gland. The aim of this study was to determine whether SWI quantitative data can differentiate between benign and malignant areas within prostate glands in men suspected of prostate cancer (PCa). We conducted a protocol-based, prospective, prebiopsy quantitative SWI of prostate glands in 50 unscreened men suspected of prostate cancer between July 2011 and May 2012. The ultrasound image of whole prostate gland was arbitrarily divided into 12 zones for sampling biopsies, as is carried out in routine clinical practice. Each region was imaged by grey scale and SWI imaging techniques. Each region was further biopsied irrespective of findings of grey scale or SWI on ultrasound. Additional biopsies were taken if SWI abnormal area was felt to be outside of these 12 zones. Quantitative assessment of SWI abnormal areas was obtained in kilopascals (kPa) from abnormal regions shown by SWI and compared with histopathology. Sensitivity, specificity, positive and negative predictive values, and likelihood ratios were calculated for SWI (histopathology was a reference standard). Fifty patients, with a mean age of 69 ± 6.2 years, were recruited into the study. Thirty-three (66%) patients were diagnosed with PCa, while an additional 4 (8%) had atypia in at least one of the 12 prostate biopsies. Thirteen (26%) patients had a benign biopsy. Data analysed per core for SWI findings showed that for patients with PSA <20 μg/L, the sensitivity and specificity of SWI for PCa detection were 0.9 and 0.88, respectively, while in patients with PSA >20 μg/L, the sensitivity and specificity were 0.93 and 0.93, respectively. In addition, PCa had significantly higher stiffness values compared to benign tissues (p <0.05), with a trend toward stiffness differences in different Gleason grades. SWI provides quantitative

  19. Quantitative structure carcinogenicity relationship for detecting structural alerts in nitroso-compounds

    SciTech Connect

    Helguera, Aliuska Morales; Gonzalez, Maykel Perez . E-mail: mpgonzalez76@yahoo.es; Cordeiro, Maria Natalia D.S.; Perez, Miguel Angel Cabrera

    2007-06-01

    Prevention of environmentally induced cancers is a major health problem of which solutions depend on the rapid and accurate screening of potential chemical hazards. Lately, theoretical approaches such as the one proposed here - Quantitative Structure-Activity Relationship (QSAR) - are increasingly used for assessing the risks of environmental chemicals, since they can markedly reduce costs, avoid animal testing, and speed up policy decisions. This paper reports a QSAR study based on the Topological Substructural Molecular Design (TOPS-MODE) approach, aiming at predicting the rodent carcinogenicity of a set of nitroso-compounds selected from the Carcinogenic Potency Data Base (CPDB). The set comprises nitrosoureas (14 chemicals), N-nitrosamines (18 chemicals) C-nitroso-compounds (1 chemical), nitrosourethane (1 chemical) and nitrosoguanidine (1 chemical), which have been bioassayed in male rat using gavage as the route of administration. Here we are especially concerned in gathering the role of both parameters on the carcinogenic activity of this family of compounds. First, the regression model was derived, upon removal of one identified nitrosamine outlier, and was able to account for more than 84% of the variance in the experimental activity. Second, the TOPS-MODE approach afforded the bond contributions - expressed as fragment contributions to the carcinogenic activity - that can be interpreted and provide tools for better understanding the mechanisms of carcinogenesis. Finally, and most importantly, we demonstrate the potentialities of this approach towards the recognition of structural alerts for carcinogenicity predictions.

  20. [Quantitative study of encephalic components in 3 tinamid species, with an ecoethological approach (birds: Tinamidae)].

    PubMed

    Bee de Speroni, N; Carezzano, F

    1993-01-01

    The encephalon of three tinamids: Eudromia elegans, Nothura maculosa, and Rhynchotus rufescens are quantitatively analyzed. Both relative volumes and cerebral indexes are calculated for eleven encephalic components. Results are discussed from an eco-etiological approach. The relative size of encephalic components in Eudromia, Rhynchotus, and Nothura indicate a close relationship among brain components and some behavioral patterns and the environment. Marked differences in the cerebral organization of these tinamid genera are not evident. A greater development of the wulst and low values of olfactory bulbs suggest that Eudromia and Rhynchotus are progressive species. Nothura is considered primitive.

  1. Combination and Boundary Detection Approaches on Chinese Indexing.

    ERIC Educational Resources Information Center

    Yang, Christopher C.; Luk, Johnny W. K.; Yung, Stanley K.; Yen, Jerome

    2000-01-01

    Discussion of information retrieval and automatic indexing in digital libraries focuses on Chinese indexing and cross-lingual information retrieval. Investigates the combination and boundary detection approaches based on mutual information for word segmentation, using lexical and statistical information. Reports results of experiments that…

  2. Combination and Boundary Detection Approaches on Chinese Indexing.

    ERIC Educational Resources Information Center

    Yang, Christopher C.; Luk, Johnny W. K.; Yung, Stanley K.; Yen, Jerome

    2000-01-01

    Discussion of information retrieval and automatic indexing in digital libraries focuses on Chinese indexing and cross-lingual information retrieval. Investigates the combination and boundary detection approaches based on mutual information for word segmentation, using lexical and statistical information. Reports results of experiments that…

  3. Multidimensional Approach to Detecting Creative Potential in Managers

    ERIC Educational Resources Information Center

    Caroff, Xavier; Lubart, Todd

    2012-01-01

    Creativity is increasingly recognized as a key component to success in the workplace. This article explores the detection of creative potential in managers. In a first part, creative potential is defined and a multivariate approach concerning the psychological resources for creativity is presented. Then, in a second part, an application of this…

  4. Detection of Differential Item Functioning Using the Lasso Approach

    ERIC Educational Resources Information Center

    Magis, David; Tuerlinckx, Francis; De Boeck, Paul

    2015-01-01

    This article proposes a novel approach to detect differential item functioning (DIF) among dichotomously scored items. Unlike standard DIF methods that perform an item-by-item analysis, we propose the "LR lasso DIF method": logistic regression (LR) model is formulated for all item responses. The model contains item-specific intercepts,…

  5. Multidimensional Approach to Detecting Creative Potential in Managers

    ERIC Educational Resources Information Center

    Caroff, Xavier; Lubart, Todd

    2012-01-01

    Creativity is increasingly recognized as a key component to success in the workplace. This article explores the detection of creative potential in managers. In a first part, creative potential is defined and a multivariate approach concerning the psychological resources for creativity is presented. Then, in a second part, an application of this…

  6. Quantitative detection of powdered activated carbon in wastewater treatment plant effluent by thermogravimetric analysis (TGA).

    PubMed

    Krahnstöver, Therese; Plattner, Julia; Wintgens, Thomas

    2016-09-15

    For the elimination of potentially harmful micropollutants, powdered activated carbon (PAC) adsorption is applied in many wastewater treatment plants (WWTP). This holds the risk of PAC leakage into the WWTP effluent and desorption of contaminants into natural water bodies. In order to assess a potential PAC leakage, PAC concentrations below several mg/L have to be detected in the WWTP effluent. None of the methods that are used for water analysis today are able to differentiate between activated carbon and solid background matrix. Thus, a selective, quantitative and easily applicable method is still needed for the detection of PAC residues in wastewater. In the present study, a method was developed to quantitatively measure the PAC content in wastewater by using filtration and thermogravimetric analysis (TGA), which is a well-established technique for the distinction between different solid materials. For the sample filtration, quartz filters with a temperature stability up to 950 °C were used. This allowed for sensitive and well reproducible measurements, as the TGA was not affected by the presence of the filter. The sample's mass fractions were calculated by integrating the mass decrease rate obtained by TGA in specific, clearly identifiable peak areas. A two-step TGA heating method consisting of N2 and O2 atmospheres led to a good differentiation between PAC and biological background matrix, thanks to the reduction of peak overlapping. A linear correlation was found between a sample's PAC content and the corresponding peak areas under N2 and O2, the sample volume and the solid mass separated by filtration. Based on these findings, various wastewater samples from different WWTPs were then analyzed by TGA with regard to their PAC content. It was found that, compared to alternative techniques such as measurement of turbidity or total suspended solids, the newly developed TGA method allows for a quantitative and selective detection of PAC concentrations down to 0

  7. Pedestrian detection from thermal images: A sparse representation based approach

    NASA Astrophysics Data System (ADS)

    Qi, Bin; John, Vijay; Liu, Zheng; Mita, Seiichi

    2016-05-01

    Pedestrian detection, a key technology in computer vision, plays a paramount role in the applications of advanced driver assistant systems (ADASs) and autonomous vehicles. The objective of pedestrian detection is to identify and locate people in a dynamic environment so that accidents can be avoided. With significant variations introduced by illumination, occlusion, articulated pose, and complex background, pedestrian detection is a challenging task for visual perception. Different from visible images, thermal images are captured and presented with intensity maps based objects' emissivity, and thus have an enhanced spectral range to make human beings perceptible from the cool background. In this study, a sparse representation based approach is proposed for pedestrian detection from thermal images. We first adopted the histogram of sparse code to represent image features and then detect pedestrian with the extracted features in an unimodal and a multimodal framework respectively. In the unimodal framework, two types of dictionaries, i.e. joint dictionary and individual dictionary, are built by learning from prepared training samples. In the multimodal framework, a weighted fusion scheme is proposed to further highlight the contributions from features with higher separability. To validate the proposed approach, experiments were conducted to compare with three widely used features: Haar wavelets (HWs), histogram of oriented gradients (HOG), and histogram of phase congruency (HPC) as well as two classification methods, i.e. AdaBoost and support vector machine (SVM). Experimental results on a publicly available data set demonstrate the superiority of the proposed approach.

  8. Multistage optical smoke detection approach for smoke alarm systems

    NASA Astrophysics Data System (ADS)

    Nguyen, Truc Kim Thi; Kim, Jong-Myon

    2013-05-01

    We propose a novel multistage smoke detection algorithm based on inherent optical characteristics such as diffusion, color, and texture of smoke. Moving regions in a video frame are detected by an approximate median background subtraction method using the diffusion behavior of smoke. These moving regions are segmented by a fuzzy C-means (FCM) clustering algorithm that uses the hue and saturation components of moving pixels in the hue-saturation-intensity color space. A decision rule is used to select candidate smoke regions from smoke-colored FCM clusters. An object tracking approach is employed in the candidate smoke region to detect candidate smoke objects in the video frame, and image texture parameters are extracted from these objects using a gray level co-occurrence matrix (GLCM). The thirteen GLCM features are selected to constitute the feature vector by applying principal components analysis, resulting in high-accuracy smoke detection. Finally, a back propagation neural network is utilized as a classifier to discriminate smoke and nonsmoke using the selected feature vector. Experimental results using a standard experimental dataset of video clips demonstrate that the proposed approach outperforms state-of-the-art smoke detection approaches in terms of accuracy, making real-life implementation feasible.

  9. Rapid and quantitative detection of Fusarium oxysporum f. sp. cubense race 4 in soil by real-time fluorescence loop-mediated isothermal amplification.

    PubMed

    Peng, Jun; Zhang, He; Chen, Fengping; Zhang, Xin; Xie, Yixian; Hou, Xianwen; Li, Guangyi; Pu, Jinji

    2014-12-01

    In this study, a real-time fluorescence loop-mediated isothermal amplification (RealAmp) was developed and evaluated for the rapid and quantitative detection of Fusarium oxysporum f. sp. cubense race 4 (R4) in soil. The LAMP primer set was designed based on previously verified RAPD marker sequences, and the RealAmp assay could specifically detect and distinguish R4 isolates from other related species. The detection sensitivity of the RealAmp assay was approx. 3·82 × 10(3) copies of plasmid DNA or 10(3) of spores per gram in artificially infested soil, indicating that the method is highly tolerant to inhibitor substances in soil compared to real-time PCR. Combining previously published TR4-specific detection methods with the newly established R4-specific RealAmp assay, an indirect approach to detect and differentiate ST4 isolates was achieved by comparing the detection results of R4 and TR4 simultaneously. The existence of ST4 isolates in China was subsequently confirmed through the developed approach. The developed RealAmp assay has been confirmed to be a simple, rapid and effective method to detect R4 in soil, which facilitates to further identify and distinguish ST4 isolates through the comparative analysis of detection results between TR4 and R4 simultaneously. The technique is an alternative quantitative detection method, which will be used for a routine detection service for the soil-borne pathogen in China. © 2014 The Society for Applied Microbiology.

  10. Simultaneous detection of influenza viruses A and B using real-time quantitative PCR.

    PubMed

    van Elden, L J; Nijhuis, M; Schipper, P; Schuurman, R; van Loon, A M

    2001-01-01

    Since influenza viruses can cause severe illness, timely diagnosis is important for an adequate intervention. The available rapid detection methods either lack sensitivity or require complex laboratory manipulation. This study describes a rapid, sensitive detection method that can be easily applied to routine diagnosis. This method simultaneously detects influenza viruses A and B in specimens of patients with respiratory infections using a TaqMan-based real-time PCR assay. Primers and probes were selected from highly conserved regions of the matrix protein gene of influenza virus A and the hemagglutinin gene segment of influenza virus B. The applicability of this multiplex PCR was evaluated with 27 influenza virus A and 9 influenza virus B reference strains and isolates. In addition, the specificity of the assay was assessed using eight reference strains of other respiratory viruses (parainfluenza viruses 1 to 3, respiratory syncytial virus Long strain, rhinoviruses 1A and 14, and coronaviruses OC43 and 229E) and 30 combined nose and throat swabs from asymptomatic subjects. Electron microscopy-counted stocks of influenza viruses A and B were used to develop a quantitative PCR format. Thirteen copies of viral RNA were detected for influenza virus A, and 11 copies were detected for influenza virus B, equaling 0.02 and 0.006 50% tissue culture infective doses, respectively. The diagnostic efficacy of the multiplex TaqMan-based PCR was determined by testing 98 clinical samples. This real-time PCR technique was found to be more sensitive than the combination of conventional viral culturing and shell vial culturing.

  11. Quantitative analysis of electrically detected Ramsey fringes in P-doped Si

    NASA Astrophysics Data System (ADS)

    Greenland, P. T.; Matmon, G.; Villis, B. J.; Bowyer, E. T.; Li, Juerong; Murdin, B. N.; van der Meer, A. F. G.; Redlich, B.; Pidgeon, C. R.; Aeppli, G.

    2015-10-01

    This work describes detection of the laser preparation and subsequent coherent manipulation of the quantum states of orbital levels of donors in doped Si, by measuring the voltage drop across an irradiated Si sample. This electrical signal, which arises from thermal ionization of excited orbital states, and which is detected on a millisecond time scale by a voltmeter, leads to much more sensitive detection than can be had using optical methods, but has not before been quantitatively described from first principles. We present here a unified theory which relates the voltage drop across the sample to the wave function of the excited donors, and compare its predictions to experiments in which pairs of picosecond pulses from the Dutch free-electron laser FELIX are used to resonantly and coherently excite P donors in Si. Although the voltage drop varies on a millisecond time scale we are able to measure Ramsey oscillation of the excitation on a picosecond time scale, thus confirming that the donor wave function, and not just its excited state population, is crucial in determining the electrical signal. We are also able to extract the recombination rate coefficient to the ground state of the donor as well as the photoionization cross section of the excited state and phonon induced thermal ionization rate from the excited state. These quantities, which were previously of limited interest, are here shown to be important in the description of electrical detection, which, in our unoptimized configuration, is sensitive enough to enable us to detect the excitation of ˜107 donors.

  12. A new approach for DNA detection by SERRS.

    PubMed

    Faulds, Karen; Fruk, Ljiljana; Robson, David C; Thompson, David G; Enright, Alexis; Smith, W Ewen; Graham, Duncan

    2006-01-01

    A new approach for the detection of DNA using surface enhance resonance Raman scattering (SERRS) is reported. The majority of existing techniques use fluorescence spectroscopy with advanced probe design to provide information on the identity of specific DNA sequences down to single base resolution. A new approach to the labelling of DNA is discussed which uses Michael addition to couple thiolated DNA to dye labels specifically designed to attach to silver surfaces. When combined with existing strategies for sensitive detection of DNA using commercially available labels, a new class of biomolecular probe known as a SERRS Beacon was produced. The detection techniques of fluorescence and surface enhanced resonance Raman scattering (SERRS) are combined to give a sensitive and selective system for use in the development and creation of novel assays for specifically defined targets. It demonstrates improved potential for multiplexing analysis.

  13. Ensemble spontaneous activity alterations detected by CISA approach.

    PubMed

    Boudaoud, Sofiane; Rix, Hervé; Meste, Olivier; Cazals, Yves

    2007-01-01

    In this paper, we propose a method for detecting alterations in the Ensemble Spontaneous Activity (ESA), a random signal representing the composite spontaneous contribution of the auditory nerve recorded on the round window. The proposed method is based on shape analysis of the ESA amplitude histogram. For this task, we use a recent approach, the Corrected Integral Shape Averaging (CISA). Using this approach, a shape clustering algorithm is proposed to classify healthy and pathological ESA signals generated by a recent ESA model. This model allows a precise simulation of neural mechanisms occurring in the auditory nerve. The obtained results demonstrate that this shape analysis is very sensitive for detecting a small number of fibers with correlated firing, supposed to occur during a particular type of tinnitus. In comparison, the classical spectral index fails in this detection.

  14. A Bayesian approach to traffic light detection and mapping

    NASA Astrophysics Data System (ADS)

    Hosseinyalamdary, Siavash; Yilmaz, Alper

    2017-03-01

    Automatic traffic light detection and mapping is an open research problem. The traffic lights vary in color, shape, geolocation, activation pattern, and installation which complicate their automated detection. In addition, the image of the traffic lights may be noisy, overexposed, underexposed, or occluded. In order to address this problem, we propose a Bayesian inference framework to detect and map traffic lights. In addition to the spatio-temporal consistency constraint, traffic light characteristics such as color, shape and height is shown to further improve the accuracy of the proposed approach. The proposed approach has been evaluated on two benchmark datasets and has been shown to outperform earlier studies. The results show that the precision and recall rates for the KITTI benchmark are 95.78 % and 92.95 % respectively and the precision and recall rates for the LARA benchmark are 98.66 % and 94.65 % .

  15. Quantitative assessment of lesion detection accuracy, resolution, and reconstruction algorithms in neutron stimulated emission computed tomography.

    PubMed

    Lakshmanan, Manu N; Kapadia, Anuj J

    2012-07-01

    We present a quantitative analysis o