WorldWideScience

Sample records for detection accurate identification

  1. Towards an accurate bioimpedance identification

    Science.gov (United States)

    Sanchez, B.; Louarroudi, E.; Bragos, R.; Pintelon, R.

    2013-04-01

    This paper describes the local polynomial method (LPM) for estimating the time-invariant bioimpedance frequency response function (FRF) considering both the output-error (OE) and the errors-in-variables (EIV) identification framework and compare it with the traditional cross— and autocorrelation spectral analysis techniques. The bioimpedance FRF is measured with the multisine electrical impedance spectroscopy (EIS) technique. To show the overwhelming accuracy of the LPM approach, both the LPM and the classical cross— and autocorrelation spectral analysis technique are evaluated through the same experimental data coming from a nonsteady-state measurement of time-varying in vivo myocardial tissue. The estimated error sources at the measurement frequencies due to noise, σnZ, and the stochastic nonlinear distortions, σZNL, have been converted to Ω and plotted over the bioimpedance spectrum for each framework. Ultimately, the impedance spectra have been fitted to a Cole impedance model using both an unweighted and a weighted complex nonlinear least square (CNLS) algorithm. A table is provided with the relative standard errors on the estimated parameters to reveal the importance of which system identification frameworks should be used.

  2. Accurate pose estimation for forensic identification

    Science.gov (United States)

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk

    2010-04-01

    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  3. Efficient Accurate Context-Sensitive Anomaly Detection

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    For program behavior-based anomaly detection, the only way to ensure accurate monitoring is to construct an efficient and precise program behavior model. A new program behavior-based anomaly detection model,called combined pushdown automaton (CPDA) model was proposed, which is based on static binary executable analysis. The CPDA model incorporates the optimized call stack walk and code instrumentation technique to gain complete context information. Thereby the proposed method can detect more attacks, while retaining good performance.

  4. Identification of a 251 gene expression signature that can accurately detect M. tuberculosis in patients with and without HIV co-infection.

    Directory of Open Access Journals (Sweden)

    Noor Dawany

    Full Text Available BACKGROUND: Co-infection with tuberculosis (TB is the leading cause of death in HIV-infected individuals. However, diagnosis of TB, especially in the presence of an HIV co-infection, can be limiting due to the high inaccuracy associated with the use of conventional diagnostic methods. Here we report a gene signature that can identify a tuberculosis infection in patients co-infected with HIV as well as in the absence of HIV. METHODS: We analyzed global gene expression data from peripheral blood mononuclear cell (PBMC samples of patients that were either mono-infected with HIV or co-infected with HIV/TB and used support vector machines to identify a gene signature that can distinguish between the two classes. We then validated our results using publically available gene expression data from patients mono-infected with TB. RESULTS: Our analysis successfully identified a 251-gene signature that accurately distinguishes patients co-infected with HIV/TB from those infected with HIV only, with an overall accuracy of 81.4% (sensitivity = 76.2%, specificity = 86.4%. Furthermore, we show that our 251-gene signature can also accurately distinguish patients with active TB in the absence of an HIV infection from both patients with a latent TB infection and healthy controls (88.9-94.7% accuracy; 69.2-90% sensitivity and 90.3-100% specificity. We also demonstrate that the expression levels of the 251-gene signature diminish as a correlate of the length of TB treatment. CONCLUSIONS: A 251-gene signature is described to (a detect TB in the presence or absence of an HIV co-infection, and (b assess response to treatment following anti-TB therapy.

  5. Accurate detection of differential RNA processing

    Science.gov (United States)

    Drewe, Philipp; Stegle, Oliver; Hartmann, Lisa; Kahles, André; Bohnert, Regina; Wachter, Andreas; Borgwardt, Karsten; Rätsch, Gunnar

    2013-01-01

    Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling data enable identification of novel isoforms, quantification of known isoforms and detection of changes in transcriptional or RNA-processing activity. Existing approaches to detect differential isoform abundance between samples either require a complete isoform annotation or fall short in providing statistically robust and calibrated significance estimates. Here, we propose a suite of statistical tests to address these open needs: a parametric test that uses known isoform annotations to detect changes in relative isoform abundance and a non-parametric test that detects differential read coverages and can be applied when isoform annotations are not available. Both methods account for the discrete nature of read counts and the inherent biological variability. We demonstrate that these tests compare favorably to previous methods, both in terms of accuracy and statistical calibrations. We use these techniques to analyze RNA-Seq libraries from Arabidopsis thaliana and Drosophila melanogaster. The identified differential RNA processing events were consistent with RT–qPCR measurements and previous studies. The proposed toolkit is available from http://bioweb.me/rdiff and enables in-depth analyses of transcriptomes, with or without available isoform annotation. PMID:23585274

  6. Mass spectrometry based protein identification with accurate statistical significance assignment

    OpenAIRE

    Alves, Gelio; Yu, Yi-Kuo

    2014-01-01

    Motivation: Assigning statistical significance accurately has become increasingly important as meta data of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of meta data at any level may propagate to downstream analyses, undermining the validity of scientific conclusions thus drawn. From the perspective of mass spectrometry based proteomics, even though accurate statistics for peptide identification can now be ach...

  7. [A accurate identification method for Chinese materia medica--systematic identification of Chinese materia medica].

    Science.gov (United States)

    Wang, Xue-Yong; Liao, Cai-Li; Liu, Si-Qi; Liu, Chun-Sheng; Shao, Ai-Juan; Huang, Lu-Qi

    2013-05-01

    This paper put forward a more accurate identification method for identification of Chinese materia medica (CMM), the systematic identification of Chinese materia medica (SICMM) , which might solve difficulties in CMM identification used the ordinary traditional ways. Concepts, mechanisms and methods of SICMM were systematically introduced and possibility was proved by experiments. The establishment of SICMM will solve problems in identification of Chinese materia medica not only in phenotypic characters like the mnorphous, microstructure, chemical constituents, but also further discovery evolution and classification of species, subspecies and population in medical plants. The establishment of SICMM will improve the development of identification of CMM and create a more extensive study space.

  8. SNPdetector: a software tool for sensitive and accurate SNP detection.

    Directory of Open Access Journals (Sweden)

    Jinghui Zhang

    2005-10-01

    Full Text Available Identification of single nucleotide polymorphisms (SNPs and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool, and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozygosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov.

  9. SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection.

    Directory of Open Access Journals (Sweden)

    2005-10-01

    Full Text Available Identification of single nucleotide polymorphisms (SNPs and mutations is important for the discovery of genetic predisposition to complex diseases. PCR resequencing is the method of choice for de novo SNP discovery. However, manual curation of putative SNPs has been a major bottleneck in the application of this method to high-throughput screening. Therefore it is critical to develop a more sensitive and accurate computational method for automated SNP detection. We developed a software tool, SNPdetector, for automated identification of SNPs and mutations in fluorescence-based resequencing reads. SNPdetector was designed to model the process of human visual inspection and has a very low false positive and false negative rate. We demonstrate the superior performance of SNPdetector in SNP and mutation analysis by comparing its results with those derived by human inspection, PolyPhred (a popular SNP detection tool, and independent genotype assays in three large-scale investigations. The first study identified and validated inter- and intra-subspecies variations in 4,650 traces of 25 inbred mouse strains that belong to either the Mus musculus species or the M. spretus species. Unexpected heterozgyosity in CAST/Ei strain was observed in two out of 1,167 mouse SNPs. The second study identified 11,241 candidate SNPs in five ENCODE regions of the human genome covering 2.5 Mb of genomic sequence. Approximately 50% of the candidate SNPs were selected for experimental genotyping; the validation rate exceeded 95%. The third study detected ENU-induced mutations (at 0.04% allele frequency in 64,896 traces of 1,236 zebra fish. Our analysis of three large and diverse test datasets demonstrated that SNPdetector is an effective tool for genome-scale research and for large-sample clinical studies. SNPdetector runs on Unix/Linux platform and is available publicly (http://lpg.nci.nih.gov.

  10. Fast and Accurate Residential Fire Detection Using Wireless Sensor Networks

    NARCIS (Netherlands)

    Bahrepour, M.; Meratnia, Nirvana; Havinga, Paul J.M.

    2010-01-01

    Prompt and accurate residential fire detection is important for on-time fire extinguishing and consequently reducing damages and life losses. To detect fire sensors are needed to measure the environmental parameters and algorithms are required to decide about occurrence of fire. Recently, wireless

  11. A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W.; Monroe, Matthew E.; Purvine, Samuel O.; Karpievitch, Yuliya V.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

    2011-07-15

    High-throughput proteomics is rapidly evolving to require high mass measurement accuracy for a variety of different applications. Increased mass measurement accuracy in bottom-up proteomics specifically allows for an improved ability to distinguish and characterize detected MS features, which may in turn be identified by, e.g., matching to entries in a database for both precursor and fragmentation mass identification methods. Many tools exist with which to score the identification of peptides from LC-MS/MS measurements or to assess matches to an accurate mass and time (AMT) tag database, but these two calculations remain distinctly unrelated. Here we present a statistical method, Statistical Tools for AMT tag Confidence (STAC), which extends our previous work incorporating prior probabilities of correct sequence identification from LC-MS/MS, as well as the quality with which LC-MS features match AMT tags, to evaluate peptide identification confidence. Compared to existing tools, we are able to obtain significantly more high-confidence peptide identifications at a given false discovery rate and additionally assign confidence estimates to individual peptide identifications. Freely available software implementations of STAC are available in both command line and as a Windows graphical application.

  12. A novel PCR-based approach for accurate identification of Vibrio parahaemolyticus

    Directory of Open Access Journals (Sweden)

    Ruichao eLi

    2016-01-01

    Full Text Available A PCR-based assay was developed for more accurate identification of Vibrio parahaemolyticus through targeting the blaCARB-17 like element, an intrinsic β-lactamase gene that may also be regarded as a novel species-specific genetic marker of this organism. Phylogenetic analysis showed that blaCARB-17 like genes were more conservative than the tlh, toxR and atpA genes, the genetic markers commonly used as detection targets in identification of V. parahaemolyticus. Our data showed that this blaCARB-17-specific PCR-based detection approach consistently achieved 100% specificity, whereas PCR targeting the tlh, toxR and atpA genes occasionally produced false positive results. Furthermore, a positive result of this test is consistently associated with an intrinsic ampicillin resistance phenotype of the test organism, presumably conferred by the products of blaCARB-17 like genes. We envision that combined analysis of the unique genetic and phenotypic characteristics conferred by blaCARB-17 shall further enhance the detection specificity of this novel yet easy-to-use detection approach to a level superior to the conventional methods used in V. parahaemolyticus detection and identification.

  13. A Novel PCR-Based Approach for Accurate Identification of Vibrio parahaemolyticus.

    Science.gov (United States)

    Li, Ruichao; Chiou, Jiachi; Chan, Edward Wai-Chi; Chen, Sheng

    2016-01-01

    A PCR-based assay was developed for more accurate identification of Vibrio parahaemolyticus through targeting the bla CARB-17 like element, an intrinsic β-lactamase gene that may also be regarded as a novel species-specific genetic marker of this organism. Homologous analysis showed that bla CARB-17 like genes were more conservative than the tlh, toxR and atpA genes, the genetic markers commonly used as detection targets in identification of V. parahaemolyticus. Our data showed that this bla CARB-17-specific PCR-based detection approach consistently achieved 100% specificity, whereas PCR targeting the tlh and atpA genes occasionally produced false positive results. Furthermore, a positive result of this test is consistently associated with an intrinsic ampicillin resistance phenotype of the test organism, presumably conferred by the products of bla CARB-17 like genes. We envision that combined analysis of the unique genetic and phenotypic characteristics conferred by bla CARB-17 shall further enhance the detection specificity of this novel yet easy-to-use detection approach to a level superior to the conventional methods used in V. parahaemolyticus detection and identification.

  14. A fast and accurate FPGA based QRS detection system.

    Science.gov (United States)

    Shukla, Ashish; Macchiarulo, Luca

    2008-01-01

    An accurate Field Programmable Gate Array (FPGA) based ECG Analysis system is described in this paper. The design, based on a popular software based QRS detection algorithm, calculates the threshold value for the next peak detection cycle, from the median of eight previously detected peaks. The hardware design has accuracy in excess of 96% in detecting the beats correctly when tested with a subset of five 30 minute data records obtained from the MIT-BIH Arrhythmia database. The design, implemented using a proprietary design tool (System Generator), is an extension of our previous work and uses 76% resources available in a small-sized FPGA device (Xilinx Spartan xc3s500), has a higher detection accuracy as compared to our previous design and takes almost half the analysis time in comparison to software based approach.

  15. Accurate mobile malware detection and classification in the cloud.

    Science.gov (United States)

    Wang, Xiaolei; Yang, Yuexiang; Zeng, Yingzhi

    2015-01-01

    As the dominator of the Smartphone operating system market, consequently android has attracted the attention of s malware authors and researcher alike. The number of types of android malware is increasing rapidly regardless of the considerable number of proposed malware analysis systems. In this paper, by taking advantages of low false-positive rate of misuse detection and the ability of anomaly detection to detect zero-day malware, we propose a novel hybrid detection system based on a new open-source framework CuckooDroid, which enables the use of Cuckoo Sandbox's features to analyze Android malware through dynamic and static analysis. Our proposed system mainly consists of two parts: anomaly detection engine performing abnormal apps detection through dynamic analysis; signature detection engine performing known malware detection and classification with the combination of static and dynamic analysis. We evaluate our system using 5560 malware samples and 6000 benign samples. Experiments show that our anomaly detection engine with dynamic analysis is capable of detecting zero-day malware with a low false negative rate (1.16 %) and acceptable false positive rate (1.30 %); it is worth noting that our signature detection engine with hybrid analysis can accurately classify malware samples with an average positive rate 98.94 %. Considering the intensive computing resources required by the static and dynamic analysis, our proposed detection system should be deployed off-device, such as in the Cloud. The app store markets and the ordinary users can access our detection system for malware detection through cloud service.

  16. What's in a Name? The Impact of Accurate Staphylococcus pseudintermedius Identification on Appropriate Antimicrobial Susceptibility Testing.

    Science.gov (United States)

    Limbago, Brandi M

    2016-03-01

    Bacteria in the Staphylococcus intermedius group, including Staphylococcus pseudintermedius, often encode mecA-mediated methicillin resistance. Reliable detection of this phenotype for proper treatment and infection control decisions requires that these coagulase-positive staphylococci are accurately identified and specifically that they are not misidentified as S. aureus. As correct species level bacterial identification becomes more commonplace in clinical laboratories, one can expect to see changes in guidance for antimicrobial susceptibility testing and interpretation. The study by Wu et al. in this issue (M. T. Wu, C.-A. D. Burnham, L. F. Westblade, J. Dien Bard, S. D. Lawhon, M. A. Wallace, T. Stanley, E. Burd, J. Hindler, R. M. Humphries, J Clin Microbiol 54:535-542, 2016, http://dx.doi.org/10.1128/JCM.02864-15) highlights the impact of robust identification of S. intermedius group organisms on the selection of appropriate antimicrobial susceptibility testing methods and interpretation.

  17. Virmid: accurate detection of somatic mutations with sample impurity inference.

    Science.gov (United States)

    Kim, Sangwoo; Jeong, Kyowon; Bhutani, Kunal; Lee, Jeong; Patel, Anand; Scott, Eric; Nam, Hojung; Lee, Hayan; Gleeson, Joseph G; Bafna, Vineet

    2013-08-29

    Detection of somatic variation using sequence from disease-control matched data sets is a critical first step. In many cases including cancer, however, it is hard to isolate pure disease tissue, and the impurity hinders accurate mutation analysis by disrupting overall allele frequencies. Here, we propose a new method, Virmid, that explicitly determines the level of impurity in the sample, and uses it for improved detection of somatic variation. Extensive tests on simulated and real sequencing data from breast cancer and hemimegalencephaly demonstrate the power of our model. A software implementation of our method is available at http://sourceforge.net/projects/virmid/.

  18. An Integrative Approach to Accurate Vehicle Logo Detection

    Directory of Open Access Journals (Sweden)

    Hao Pan

    2013-01-01

    required for many applications in intelligent transportation systems and automatic surveillance. The task is challenging considering the small target of logos and the wide range of variability in shape, color, and illumination. A fast and reliable vehicle logo detection approach is proposed following visual attention mechanism from the human vision. Two prelogo detection steps, that is, vehicle region detection and a small RoI segmentation, rapidly focalize a small logo target. An enhanced Adaboost algorithm, together with two types of features of Haar and HOG, is proposed to detect vehicles. An RoI that covers logos is segmented based on our prior knowledge about the logos’ position relative to license plates, which can be accurately localized from frontal vehicle images. A two-stage cascade classier proceeds with the segmented RoI, using a hybrid of Gentle Adaboost and Support Vector Machine (SVM, resulting in precise logo positioning. Extensive experiments were conducted to verify the efficiency of the proposed scheme.

  19. Detection and Identification System of Bacteria and Bacterial Endotoxin Based on Raman Spectroscopy

    National Research Council Canada - National Science Library

    Muhammad Elsayeh; Ahmed H.Kandil

    2016-01-01

    .... Raman spectroscopes represent a q uick and accurate identification and detection method, for bacteria and bacterial endotoxin, which this plays an important role in delivering high quality biomedical...

  20. Accurate Identification of Cancerlectins through Hybrid Machine Learning Technology

    Directory of Open Access Journals (Sweden)

    Jieru Zhang

    2016-01-01

    Full Text Available Cancerlectins are cancer-related proteins that function as lectins. They have been identified through computational identification techniques, but these techniques have sometimes failed to identify proteins because of sequence diversity among the cancerlectins. Advanced machine learning identification methods, such as support vector machine and basic sequence features (n-gram, have also been used to identify cancerlectins. In this study, various protein fingerprint features and advanced classifiers, including ensemble learning techniques, were utilized to identify this group of proteins. We improved the prediction accuracy of the original feature extraction methods and classification algorithms by more than 10% on average. Our work provides a basis for the computational identification of cancerlectins and reveals the power of hybrid machine learning techniques in computational proteomics.

  1. PILER-CR: Fast and accurate identification of CRISPR repeats

    Directory of Open Access Journals (Sweden)

    Edgar Robert C

    2007-01-01

    Full Text Available Abstract Background Sequencing of prokaryotic genomes has recently revealed the presence of CRISPR elements: short, highly conserved repeats separated by unique sequences of similar length. The distinctive sequence signature of CRISPR repeats can be found using general-purpose repeat- or pattern-finding software tools. However, the output of such tools is not always ideal for studying these repeats, and significant effort is sometimes needed to build additional tools and perform manual analysis of the output. Results We present PILER-CR, a program specifically designed for the identification and analysis of CRISPR repeats. The program executes rapidly, completing a 5 Mb genome in around 5 seconds on a current desktop computer. We validate the algorithm by manual curation and by comparison with published surveys of these repeats, finding that PILER-CR has both high sensitivity and high specificity. We also present a catalogue of putative CRISPR repeats identified in a comprehensive analysis of 346 prokaryotic genomes. Conclusion PILER-CR is a useful tool for rapid identification and classification of CRISPR repeats. The software is donated to the public domain. Source code and a Linux binary are freely available at http://www.drive5.com/pilercr.

  2. A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics.

    Science.gov (United States)

    Stanley, Jeffrey R; Adkins, Joshua N; Slysz, Gordon W; Monroe, Matthew E; Purvine, Samuel O; Karpievitch, Yuliya V; Anderson, Gordon A; Smith, Richard D; Dabney, Alan R

    2011-08-15

    Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, because this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referenced as Statistical Tools for AMT Tag Confidence (STAC). STAC additionally provides a uniqueness probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download, as both a command line and a Windows graphical application.

  3. Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

    Science.gov (United States)

    Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y.; Drake, Steven K.; Gucek, Marjan; Suffredini, Anthony F.; Sacks, David B.; Yu, Yi-Kuo

    2016-02-01

    Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple `fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

  4. Accurate single-trial detection of movement intention made possible using adaptive wavelet transform.

    Science.gov (United States)

    Chamanzar, Alireza; Malekmohammadi, Alireza; Bahrani, Masih; Shabany, Mahdi

    2015-01-01

    The outlook of brain-computer interfacing (BCI) is very bright. The real-time, accurate detection of a motor movement task is critical in BCI systems. The poor signal-to-noise-ratio (SNR) of EEG signals and the ambiguity of noise generator sources in brain renders this task quite challenging. In this paper, we demonstrate a novel algorithm for precise detection of the onset of a motor movement through identification of event-related-desynchronization (ERD) patterns. Using an adaptive matched filter technique implemented based on an optimized continues Wavelet transform by selecting an appropriate basis, we can detect single-trial ERDs. Moreover, we use a maximum-likelihood (ML), electrooculography (EOG) artifact removal method to remove eye-related artifacts to significantly improve the detection performance. We have applied this technique to our locally recorded Emotiv(®) data set of 6 healthy subjects, where an average detection selectivity of 85 ± 6% and sensitivity of 88 ± 7.7% is achieved with a temporal precision in the range of -1250 to 367 ms in onset detections of single-trials.

  5. The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

    DEFF Research Database (Denmark)

    Pafilis, Evangelos; Pletscher-Frankild, Sune; Fanini, Lucia

    2013-01-01

    The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary......-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus...

  6. Generic Packing Detection Using Several Complexity Analysis for Accurate Malware Detection

    Directory of Open Access Journals (Sweden)

    Dr. Mafaz Mohsin Khalil Al-Anezi

    2014-01-01

    Full Text Available The attackers do not want their Malicious software (or malwares to be reviled by anti-virus analyzer. In order to conceal their malware, malware programmers are getting utilize the anti reverse engineering techniques and code changing techniques such as the packing, encoding and encryption techniques. Malware writers have learned that signature based detectors can be easily evaded by “packing” the malicious payload in layers of compression or encryption. State-of-the-art malware detectors have adopted both static and dynamic techniques to recover the payload of packed malware, but unfortunately such techniques are highly ineffective. If the malware is packed or encrypted, then it is very difficult to analyze. Therefore, to prevent the harmful effects of malware and to generate signatures for malware detection, the packed and encrypted executable codes must initially be unpacked. The first step of unpacking is to detect the packed executable files. The objective is to efficiently and accurately distinguish between packed and non-packed executables, so that only executables detected as packed will be sent to an general unpacker, thus saving a significant amount of processing time. The generic method of this paper show that it achieves very high detection accuracy of packed executables with a low average processing time. In this paper, a packed file detection technique based on complexity measured by several algorithms, and it has tested using a packed and unpacked dataset of file type .exe. The preliminary results are very promising where achieved high accuracy with enough performance. Where it achieved about 96% detection rate on packed files and 93% detection rate on unpacked files. The experiments also demonstrate that this generic technique can effectively prepared to detect unknown, obfuscated malware and cannot be evaded by known evade techniques.

  7. A fluorescence-based quantitative real-time PCR assay for accurate Pocillopora damicornis species identification

    Science.gov (United States)

    Thomas, Luke; Stat, Michael; Evans, Richard D.; Kennington, W. Jason

    2016-09-01

    Pocillopora damicornis is one of the most extensively studied coral species globally, but high levels of phenotypic plasticity within the genus make species identification based on morphology alone unreliable. As a result, there is a compelling need to develop cheap and time-effective molecular techniques capable of accurately distinguishing P. damicornis from other congeneric species. Here, we develop a fluorescence-based quantitative real-time PCR (qPCR) assay to genotype a single nucleotide polymorphism that accurately distinguishes P. damicornis from other morphologically similar Pocillopora species. We trial the assay across colonies representing multiple Pocillopora species and then apply the assay to screen samples of Pocillopora spp. collected at regional scales along the coastline of Western Australia. This assay offers a cheap and time-effective alternative to Sanger sequencing and has broad applications including studies on gene flow, dispersal, recruitment and physiological thresholds of P. damicornis.

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

    Directory of Open Access Journals (Sweden)

    Kevin R Ramkissoon

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  11. Fundamental problems in fault detection and identification

    DEFF Research Database (Denmark)

    Saberi, Ali; Stoorvogel, Anton A.; Sannuti, Peddapullaiah;

    1999-01-01

    For certain fundamental problems in fault detection and identification, the necessary and sufficient conditions for their solvability are derived. These conditions are weaker than the ones found in the literature, since we do not assume any particular structure for the residual generator...

  12. Detection and identification of novel actinomycetes.

    Science.gov (United States)

    Williams, S T; Locci, R; Beswick, A; Kurtböke, D I; Kuznetsov, V D; Le Monnier, F J; Long, P F; Maycroft, K A; Palma, R A; Petrolini, B

    1993-10-01

    The actinomycetes are well known as a group of filamentous, Gram-positive bacteria that produce many useful secondary metabolites, including antibiotics and enzymes. Although they have been intensively studied for both theoretical and practical objectives, there is much scope for developing our basic knowledge of the means of detection and isolation of these microbes. This session concentrated on new methods for the detection and identification of novel actinomycetes from a range of environments. Approaches to the detection of actinomycetes ranged from investigations of neglected habitats and extreme environments (e.g. alkaline soils and oil drills) to the analysis of DNA extracted from the environment and use of specific phages. The continuing problems of the identification of actinomycete isolates were also considered. Topics discussed included use of phage typing, DNA probes, and correlation between phenetic and genotypic species of Streptomyces.

  13. Camouflage, detection and identification of moving targets

    Science.gov (United States)

    Hall, Joanna R.; Cuthill, Innes C.; Baddeley, Roland; Shohet, Adam J.; Scott-Samuel, Nicholas E.

    2013-01-01

    Nearly all research on camouflage has investigated its effectiveness for concealing stationary objects. However, animals have to move, and patterns that only work when the subject is static will heavily constrain behaviour. We investigated the effects of different camouflages on the three stages of predation—detection, identification and capture—in a computer-based task with humans. An initial experiment tested seven camouflage strategies on static stimuli. In line with previous literature, background-matching and disruptive patterns were found to be most successful. Experiment 2 showed that if stimuli move, an isolated moving object on a stationary background cannot avoid detection or capture regardless of the type of camouflage. Experiment 3 used an identification task and showed that while camouflage is unable to slow detection or capture, camouflaged targets are harder to identify than uncamouflaged targets when similar background objects are present. The specific details of the camouflage patterns have little impact on this effect. If one has to move, camouflage cannot impede detection; but if one is surrounded by similar targets (e.g. other animals in a herd, or moving background distractors), then camouflage can slow identification. Despite previous assumptions, motion does not entirely ‘break’ camouflage. PMID:23486439

  14. Considerations for accurate identification of adult Culex restuans (Diptera: Culicidae) in field studies.

    Science.gov (United States)

    Harrington, Laura C; Poulson, Rebecca L

    2008-01-01

    Understanding the ecology and behavior of different mosquito species (Diptera: Culicidae) is essential for identifying their role in disease transmission cycles and public health risk. Two species of Culex mosquitoes in the northeastern United States, Culex pipiens L. and Culex restuans Theobald, have been implicated in enzootic transmission of West Nile virus (family Flaviviridae, genus Flavivirus, WNV). Despite the difficulty of differentiating these two species as adults, many public health workers and vector biologists collecting adults in the field separate these species based on external morphology. This approach is often used rather than examination of dissected male genitalia or polymerase chain reaction (PCR)-based diagnostics due to time or cost constraints. We evaluated the reliability of seven published morphological characters to differentiate adults of these species by comparing blindly scored morphology with PCR-based confirmations. Our study demonstrates that morphological identification of Cx. pipiens is marginal and often not reliable for Cx. restuans. We also examined error rates with molecular-based approaches. DNA samples were contaminated with as little as one leg from another species. We conclude that to fully understand the respective roles of Culex species in the epidemiology of WNV and other pathogens, more attention should be paid to these considerations for accurate species identification.

  15. T2Candida Provides Rapid and Accurate Species Identification in Pediatric Cases of Candidemia.

    Science.gov (United States)

    Hamula, Camille L; Hughes, Kenneth; Fisher, Brian T; Zaoutis, Theoklis E; Singh, Ila R; Velegraki, Aristea

    2016-06-01

    The goal of this study is to assess the ability of the T2Candida platform (T2 Biosystems, Lexington, MA) to accurately identify Candida species from pediatric blood specimens with low volumes. Whole blood from 15 children with candidemia was collected immediately following blood culture draw. The amount of blood required by the system was reduced by pipetting whole blood directly onto the T2Candida cartridge. Specimens were subsequently run on the T2Dx Instrument (T2 Biosystems). The T2Candida panel provided the appropriate result for each specimen compared with blood culture-based species identification and correctly identified 15 positive and nine negative results in 3 to 5 hours. While the time to species identification for blood culture was not reported, the T2Candida results include species data. T2Candida can be used to efficiently diagnose or rule out candidemia using low-volume blood specimens from pediatric patients. This could result in improved time to appropriate antifungal therapy or reduction in unnecessary empirical antifungal therapy. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Electromagnetic Detection and Identification of Complex Structures

    Science.gov (United States)

    2008-12-01

    1 ELECTROMAGNETIC DETECTION AND IDENTIFICATION OF COMPLEX STRUCTURES I. Kohlberg Kohlberg Associates Reston, Virginia, 20190-4440 S.A...TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Kohlberg Associates Reston, Virginia, 20190-4440 8...Electromagnetic Theory, 2 nd ed. IEEE Press, New York. von Laven, S.A., Albritton, N.G., Baginski, T.A., Hodel, A.S., McMillan, R.W., Kohlberg

  17. DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields

    KAUST Repository

    Shao, Mingfu

    2017-04-20

    Motivation: Reconstructing the full- length expressed transcripts (a. k. a. the transcript assembly problem) from the short sequencing reads produced by RNA-seq protocol plays a central role in identifying novel genes and transcripts as well as in studying gene expressions and gene functions. A crucial step in transcript assembly is to accurately determine the splicing junctions and boundaries of the expressed transcripts from the reads alignment. In contrast to the splicing junctions that can be efficiently detected from spliced reads, the problem of identifying boundaries remains open and challenging, due to the fact that the signal related to boundaries is noisy and weak.

  18. Distributed pedestrian detection alerts based on data fusion with accurate localization.

    Science.gov (United States)

    García, Fernando; Jiménez, Felipe; Anaya, José Javier; Armingol, José María; Naranjo, José Eugenio; de la Escalera, Arturo

    2013-09-04

    Among Advanced Driver Assistance Systems (ADAS) pedestrian detection is a common issue due to the vulnerability of pedestrians in the event of accidents. In the present work, a novel approach for pedestrian detection based on data fusion is presented. Data fusion helps to overcome the limitations inherent to each detection system (computer vision and laser scanner) and provides accurate and trustable tracking of any pedestrian movement. The application is complemented by an efficient communication protocol, able to alert vehicles in the surroundings by a fast and reliable communication. The combination of a powerful location, based on a GPS with inertial measurement, and accurate obstacle localization based on data fusion has allowed locating the detected pedestrians with high accuracy. Tests proved the viability of the detection system and the efficiency of the communication, even at long distances. By the use of the alert communication, dangerous situations such as occlusions or misdetections can be avoided.

  19. Distributed Pedestrian Detection Alerts Based on Data Fusion with Accurate Localization

    Directory of Open Access Journals (Sweden)

    Arturo de la Escalera

    2013-09-01

    Full Text Available Among Advanced Driver Assistance Systems (ADAS pedestrian detection is a common issue due to the vulnerability of pedestrians in the event of accidents. In the present work, a novel approach for pedestrian detection based on data fusion is presented. Data fusion helps to overcome the limitations inherent to each detection system (computer vision and laser scanner and provides accurate and trustable tracking of any pedestrian movement. The application is complemented by an efficient communication protocol, able to alert vehicles in the surroundings by a fast and reliable communication. The combination of a powerful location, based on a GPS with inertial measurement, and accurate obstacle localization based on data fusion has allowed locating the detected pedestrians with high accuracy. Tests proved the viability of the detection system and the efficiency of the communication, even at long distances. By the use of the alert communication, dangerous situations such as occlusions or misdetections can be avoided.

  20. Accurate identification of Culicidae at aquatic developmental stages by MALDI-TOF MS profiling.

    Science.gov (United States)

    Dieme, Constentin; Yssouf, Amina; Vega-Rúa, Anubis; Berenger, Jean-Michel; Failloux, Anna-Bella; Raoult, Didier; Parola, Philippe; Almeras, Lionel

    2014-12-02

    rapid and reliable identification of mosquito species at aquatic stages. With this proteomic tool, it becomes now conceivable to survey mosquito breeding sites prior to the mosquitoes' emergence and to adapt anti-vectorial measures according to the mosquito fauna detected.

  1. An accurate and efficient identification of children with psychosocial problems by means of computerized adaptive testing

    Directory of Open Access Journals (Sweden)

    Reijneveld Symen A

    2011-08-01

    Full Text Available Abstract Background Questionnaires used by health services to identify children with psychosocial problems are often rather short. The psychometric properties of such short questionnaires are mostly less than needed for an accurate distinction between children with and without problems. We aimed to assess whether a short Computerized Adaptive Test (CAT can overcome the weaknesses of short written questionnaires when identifying children with psychosocial problems. Method We used a Dutch national data set obtained from parents of children invited for a routine health examination by Preventive Child Healthcare with 205 items on behavioral and emotional problems (n = 2,041, response 84%. In a random subsample we determined which items met the requirements of an Item Response Theory (IRT model to a sufficient degree. Using those items, item parameters necessary for a CAT were calculated and a cut-off point was defined. In the remaining subsample we determined the validity and efficiency of a Computerized Adaptive Test using simulation techniques, with current treatment status and a clinical score on the Total Problem Scale (TPS of the Child Behavior Checklist as criteria. Results Out of 205 items available 190 sufficiently met the criteria of the underlying IRT model. For 90% of the children a score above or below cut-off point could be determined with 95% accuracy. The mean number of items needed to achieve this was 12. Sensitivity and specificity with the TPS as a criterion were 0.89 and 0.91, respectively. Conclusion An IRT-based CAT is a very promising option for the identification of psychosocial problems in children, as it can lead to an efficient, yet high-quality identification. The results of our simulation study need to be replicated in a real-life administration of this CAT.

  2. A transition radiation detector for RHIC featuring accurate tracking and dE/dx particle identification

    Energy Technology Data Exchange (ETDEWEB)

    O`Brien, E.; Lissauer, D.; McCorkle, S.; Polychronakos, V.; Takai, H. [Brookhaven National Lab., Upton, NY (United States); Chi, C.Y.; Nagamiya, S.; Sippach, W.; Toy, M.; Wang, D.; Wang, Y.F.; Wiggins, C.; Willis, W. [Columbia Univ., New York, NY (United States); Cherniatin, V.; Dolgoshein, B. [Moscow Institute of Physics and Engineering, (Russian Federation); Bennett, M.; Chikanian, A.; Kumar, S.; Mitchell, J.T.; Pope, K. [Yale Univ., New Haven, CT (United States)

    1991-12-31

    We describe the results of a test ran involving a Transition Radiation Detector that can both distinguish electrons from pions which momenta greater titan 0.7 GeV/c and simultaneously track particles passing through the detector. The particle identification is accomplished through a combination of the detection of Transition Radiation from the electron and the differences in electron and pion energy loss (dE/dx) in the detector. The dE/dx particle separation is most, efficient below 2 GeV/c while particle ID utilizing Transition Radiation effective above 1.5 GeV/c. Combined, the electron-pion separation is-better than 5 {times} 10{sup 2}. The single-wire, track-position resolution for the TRD is {approximately}230 {mu}m.

  3. A transition radiation detector which features accurate tracking and dE/dx particle identification

    Energy Technology Data Exchange (ETDEWEB)

    O`Brien, E.; Lissauer, D.; McCorkle, S.; Polychronakos, V.; Takai, H. [Brookhaven National Lab., Upton, NY (United States); Chi, C.Y.; Nagamiya, S.; Sippach, W.; Toy, M.; Wang, D.; Wang, Y.F.; Wiggins, C.; Willis, W. [Columbia Univ., New York, NY (United States); Cherniatin, V.; Dolgoshein, B. [Moscow Inst. of Physics and Engineering, Moscow (Russia Federation); Bennett, M.; Chikanian, A.; Kumar, S.; Mitchell, J.T.; Pope, K. [Yale Univ., New Haven, CT (United States)

    1991-12-31

    We describe the results of a test run involving a Transition Radiation Detector that can both distinguish electrons from pions with momenta greater than 0.7 GeV/c and simultaneously track particles passing through the detector. The particle identification is accomplished through a combination of the detection of Transition Radiation from the electron and the differences in electron and pion energy loss (dE/dx) in the detector. The dE/dx particle separation is most efficient below 2 GeV/c while particle ID utilizing Transition Radiation is effective above 1.5 GeV/c. Combined, the electron-pion separation is better than 5 {times} l0{sup 2}. The single-wire, track-position resolution for the TRD is {approximately}230{mu}m.

  4. A transition radiation detector which features accurate tracking and dE/dx particle identification

    Energy Technology Data Exchange (ETDEWEB)

    O' Brien, E.; Lissauer, D.; McCorkle, S.; Polychronakos, V.; Takai, H. (Brookhaven National Lab., Upton, NY (United States)); Chi, C.Y.; Nagamiya, S.; Sippach, W.; Toy, M.; Wang, D.; Wang, Y.F.; Wiggins, C.; Willis, W. (Columbia Univ., New York, NY (United States)); Cherniatin, V.; Dolgoshein, B. (Moscow Inst. of Physics and Engineering (Russian Federation)); Bennett, M.; Chikanian, A.; Kumar, S.; Mitchell, J.T.; Pope, K. (Yale Univ., New Haven, CT (United States))

    1993-04-01

    The authors describe the results of a test run involving a Transition Radiation Detector that can both distinguish electrons from pions with momenta greater than 0.7 GeV/c and simultaneously track particles passing through the detector. The particle identification is accomplished through a combination of the detection of Transition Radiation from the electron and the differences in electron and pion energy loss (dE/dx) in the detector. The dE/dx particle separation is most efficient below 2 GeV/c while particle ID utilizing Transition Radiation is effective above 1.5 GeV/c. Combined, the electron-pion separation is better than 5 x 10[sup 2]. The single-wire, track-position resolution for the TRD is [approximately] [mu]m.

  5. Identification of "Known Unknowns" Utilizing Accurate Mass Data and ChemSpider

    Science.gov (United States)

    Little, James L.; Williams, Antony J.; Pshenichnov, Alexey; Tkachenko, Valery

    2012-01-01

    In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

  6. Identification of "Known Unknowns" Utilizing Accurate Mass Data and Chemical Abstracts Service Databases

    Science.gov (United States)

    Little, James L.; Cleven, Curtis D.; Brown, Stacy D.

    2011-02-01

    In many cases, an unknown to an investigator is actually known in the chemical literature. We refer to these types of compounds as "known unknowns." Chemical Abstracts Service (CAS) Registry is a particularly good source of these substances as it contains over 54 million entries. Accurate mass measurements can be used to query the CAS Registry by either molecular formulae or average molecular weights. Searching the database by the web-based version of SciFinder is the preferred approach when molecular formulae are available. However, if a definitive molecular formula cannot be ascertained, searching the database with STN Express by average molecular weights is a viable alternative. The results from either approach are refined by employing the number of associated references or minimal sample history as orthogonal filters. These approaches were shown to be successful in identifying "known unknowns" noted in LC-MS and even GC-MS analyses in our laboratory. In addition, they were demonstrated in the identification of a variety of compounds of interest to others.

  7. Identification of "known unknowns" utilizing accurate mass data and chemical abstracts service databases.

    Science.gov (United States)

    Little, James L; Cleven, Curtis D; Brown, Stacy D

    2011-02-01

    In many cases, an unknown to an investigator is actually known in the chemical literature. We refer to these types of compounds as "known unknowns." Chemical Abstracts Service (CAS) Registry is a particularly good source of these substances as it contains over 54 million entries. Accurate mass measurements can be used to query the CAS Registry by either molecular formulae or average molecular weights. Searching the database by the web-based version of SciFinder is the preferred approach when molecular formulae are available. However, if a definitive molecular formula cannot be ascertained, searching the database with STN Express by average molecular weights is a viable alternative. The results from either approach are refined by employing the number of associated references or minimal sample history as orthogonal filters. These approaches were shown to be successful in identifying "known unknowns" noted in LC-MS and even GC-MS analyses in our laboratory. In addition, they were demonstrated in the identification of a variety of compounds of interest to others. © American Society for Mass Spectrometry, 2011

  8. Breaking Snake Camouflage: Humans Detect Snakes More Accurately than Other Animals under Less Discernible Visual Conditions.

    Science.gov (United States)

    Kawai, Nobuyuki; He, Hongshen

    2016-01-01

    Humans and non-human primates are extremely sensitive to snakes as exemplified by their ability to detect pictures of snakes more quickly than those of other animals. These findings are consistent with the Snake Detection Theory, which hypothesizes that as predators, snakes were a major source of evolutionary selection that favored expansion of the visual system of primates for rapid snake detection. Many snakes use camouflage to conceal themselves from both prey and their own predators, making it very challenging to detect them. If snakes have acted as a selective pressure on primate visual systems, they should be more easily detected than other animals under difficult visual conditions. Here we tested whether humans discerned images of snakes more accurately than those of non-threatening animals (e.g., birds, cats, or fish) under conditions of less perceptual information by presenting a series of degraded images with the Random Image Structure Evolution technique (interpolation of random noise). We find that participants recognize mosaic images of snakes, which were regarded as functionally equivalent to camouflage, more accurately than those of other animals under dissolved conditions. The present study supports the Snake Detection Theory by showing that humans have a visual system that accurately recognizes snakes under less discernible visual conditions.

  9. Accurate, noninvasive detection of Helicobacter pylori DNA from stool samples: potential usefulness for monitoring treatment.

    Science.gov (United States)

    Shuber, Anthony P; Ascaño, Jennifer J; Boynton, Kevin A; Mitchell, Anastasia; Frierson, Henry F; El-Rifai, Wa'el; Powell, Steven M

    2002-01-01

    A novel DNA assay demonstrating sensitive and accurate detection of Helicobacter pylori from stool samples is reported. Moreover, in three individuals tested for therapeutic response, the assay showed the disappearance of H. pylori DNA during treatment. Thus, this noninvasive molecular biology-based assay has the potential to be a powerful diagnostic tool given its ability to specifically identify H. pylori DNA.

  10. Accurate, Noninvasive Detection of Helicobacter pylori DNA from Stool Samples: Potential Usefulness for Monitoring Treatment

    OpenAIRE

    Shuber, Anthony P; Ascaño, Jennifer J.; Boynton, Kevin A.; Mitchell, Anastasia; Frierson, Henry F.; El-Rifai, Wa’el; Powell, Steven M

    2002-01-01

    A novel DNA assay demonstrating sensitive and accurate detection of Helicobacter pylori from stool samples is reported. Moreover, in three individuals tested for therapeutic response, the assay showed the disappearance of H. pylori DNA during treatment. Thus, this noninvasive molecular biology-based assay has the potential to be a powerful diagnostic tool given its ability to specifically identify H. pylori DNA.

  11. Innovative Flow Cytometry Allows Accurate Identification of Rare Circulating Cells Involved in Endothelial Dysfunction

    Science.gov (United States)

    Boraldi, Federica; Bartolomeo, Angelica; De Biasi, Sara; Orlando, Stefania; Costa, Sonia; Cossarizza, Andrea; Quaglino, Daniela

    2016-01-01

    Introduction Although rare, circulating endothelial and progenitor cells could be considered as markers of endothelial damage and repair potential, possibly predicting the severity of cardiovascular manifestations. A number of studies highlighted the role of these cells in age-related diseases, including those characterized by ectopic calcification. Nevertheless, their use in clinical practice is still controversial, mainly due to difficulties in finding reproducible and accurate methods for their determination. Methods Circulating mature cells (CMC, CD45-, CD34+, CD133-) and circulating progenitor cells (CPC, CD45dim, CD34bright, CD133+) were investigated by polychromatic high-speed flow cytometry to detect the expression of endothelial (CD309+) or osteogenic (BAP+) differentiation markers in healthy subjects and in patients affected by peripheral vascular manifestations associated with ectopic calcification. Results This study shows that: 1) polychromatic flow cytometry represents a valuable tool to accurately identify rare cells; 2) the balance of CD309+ on CMC/CD309+ on CPC is altered in patients affected by peripheral vascular manifestations, suggesting the occurrence of vascular damage and low repair potential; 3) the increase of circulating cells exhibiting a shift towards an osteoblast-like phenotype (BAP+) is observed in the presence of ectopic calcification. Conclusion Differences between healthy subjects and patients with ectopic calcification indicate that this approach may be useful to better evaluate endothelial dysfunction in a clinical context. PMID:27560136

  12. Accurate band-to-band registration of AOTF imaging spectrometer using motion detection technology

    Science.gov (United States)

    Zhou, Pengwei; Zhao, Huijie; Jin, Shangzhong; Li, Ningchuan

    2016-05-01

    This paper concerns the problem of platform vibration induced band-to-band misregistration with acousto-optic imaging spectrometer in spaceborne application. Registrating images of different bands formed at different time or different position is difficult, especially for hyperspectral images form acousto-optic tunable filter (AOTF) imaging spectrometer. In this study, a motion detection method is presented using the polychromatic undiffracted beam of AOTF. The factors affecting motion detect accuracy are analyzed theoretically, and calculations show that optical distortion is an easily overlooked factor to achieve accurate band-to-band registration. Hence, a reflective dual-path optical system has been proposed for the first time, with reduction of distortion and chromatic aberration, indicating the potential of higher registration accuracy. Consequently, a spectra restoration experiment using additional motion detect channel is presented for the first time, which shows the accurate spectral image registration capability of this technique.

  13. Accurate Detection of Peer-to-Peer Botnet using Multi-Stream Fused Scheme

    Directory of Open Access Journals (Sweden)

    Jian Kang

    2011-05-01

    Full Text Available Nowadays decentralized botnets pose a great threat to Internet. They evolve new features such as P2P Command and Control(C&C, which makes traditional detection methods no longer effective for indicating the existence of the bots. In this paper, based on several of the new P2P botnet characteristic properties, we propose a novel real-time detecting model – MSFM (Multi-Stream Fused Model. MSFM considers multiple types of packets’ unique characteristics and handle them with corresponding strategies. Extensive experiment results show that our model can accurately detect peer-to-peer botnet with relatively low false-positive and false-negative rates.

  14. Analysis of inteins in the Candida parapsilosis complex for simple and accurate species identification.

    Science.gov (United States)

    Prandini, Tâmara Heloísa Rocha; Theodoro, Raquel Cordeiro; Bruder-Nascimento, Ariane C M O; Scheel, Christina M; Bagagli, Eduardo

    2013-09-01

    Inteins are coding sequences that are transcribed and translated with flanking sequences and then are excised by an autocatalytic process. There are two types of inteins in fungi, mini-inteins and full-length inteins, both of which present a splicing domain containing well-conserved amino acid sequences. Full-length inteins also present a homing endonuclease domain that makes the intein a mobile genetic element. These parasitic genetic elements are located in highly conserved genes and may allow for the differentiation of closely related species of the Candida parapsilosis (psilosis) complex. The correct identification of the three psilosis complex species C. parapsilosis, Candida metapsilosis, and Candida orthopsilosis is very important in the clinical setting for improving antifungal therapy and patient care. In this work, we analyzed inteins that are present in the vacuolar ATPase gene VMA and in the threonyl-tRNA synthetase gene ThrRS in 85 strains of the Candida psilosis complex (46 C. parapsilosis, 17 C. metapsilosis, and 22 C. orthopsilosis). Here, we describe an accessible and accurate technique based on a single PCR that is able to differentiate the psilosis complex based on the VMA intein. Although the ThrRS intein does not distinguish the three species of the psilosis complex by PCR product size, it can differentiate them by sequencing and phylogenetic analysis. Furthermore, this intein is unusually present as both mini- and full-length forms in C. orthopsilosis. Additional population studies should be performed to address whether this represents a common intraspecific variability or the presence of subspecies within C. orthopsilosis.

  15. A method to detect landmark pairs accurately between intra-patient volumetric medical images.

    Science.gov (United States)

    Yang, Deshan; Zhang, Miao; Chang, Xiao; Fu, Yabo; Liu, Shi; Li, Harold H; Mutic, Sasa; Duan, Ye

    2017-08-23

    An image processing procedure was developed in this study to detect large quantity of landmark pairs accurately in pairs of volumetric medical images. The detected landmark pairs can be used to evaluate of deformable image registration (DIR) methods quantitatively. Landmark detection and pair matching were implemented in a Gaussian pyramid multi-resolution scheme. A 3D scale-invariant feature transform (SIFT) feature detection method and a 3D Harris-Laplacian corner detection method were employed to detect feature points, i.e., landmarks. A novel feature matching algorithm, Multi-Resolution Inverse-Consistent Guided Matching or MRICGM, was developed to allow accurate feature pairs matching. MRICGM performs feature matching using guidance by the feature pairs detected at the lower resolution stage and the higher confidence feature pairs already detected at the same resolution stage, while enforces inverse consistency. The proposed feature detection and feature pair matching algorithms were optimized to process 3D CT and MRI images. They were successfully applied between the inter-phase abdomen 4DCT images of three patients, between the original and the re-scanned radiation therapy simulation CT images of two head-neck patients, and between inter-fractional treatment MRIs of two patients. The proposed procedure was able to successfully detect and match over 6300 feature pairs on average. The automatically detected landmark pairs were manually verified and the mismatched pairs were rejected. The automatic feature matching accuracy before manual error rejection was 99.4%. Performance of MRICGM was also evaluated using seven digital phantom datasets with known ground truth of tissue deformation. On average, 11855 feature pairs were detected per digital phantom dataset with TRE = 0.77 ± 0.72 mm. A procedure was developed in this study to detect large number of landmark pairs accurately between two volumetric medical images. It allows a semi-automatic way to generate the

  16. Accurate detection of carcinoma cells by use of a cell microarray chip.

    Directory of Open Access Journals (Sweden)

    Shohei Yamamura

    Full Text Available BACKGROUND: Accurate detection and analysis of circulating tumor cells plays an important role in the diagnosis and treatment of metastatic cancer treatment. METHODS AND FINDINGS: A cell microarray chip was used to detect spiked carcinoma cells among leukocytes. The chip, with 20,944 microchambers (105 µm width and 50 µm depth, was made from polystyrene; and the formation of monolayers of leukocytes in the microchambers was observed. Cultured human T lymphoblastoid leukemia (CCRF-CEM cells were used to examine the potential of the cell microarray chip for the detection of spiked carcinoma cells. A T lymphoblastoid leukemia suspension was dispersed on the chip surface, followed by 15 min standing to allow the leukocytes to settle down into the microchambers. Approximately 29 leukocytes were found in each microchamber when about 600,000 leukocytes in total were dispersed onto a cell microarray chip. Similarly, when leukocytes isolated from human whole blood were used, approximately 89 leukocytes entered each microchamber when about 1,800,000 leukocytes in total were placed onto the cell microarray chip. After washing the chip surface, PE-labeled anti-cytokeratin monoclonal antibody and APC-labeled anti-CD326 (EpCAM monoclonal antibody solution were dispersed onto the chip surface and allowed to react for 15 min; and then a microarray scanner was employed to detect any fluorescence-positive cells within 20 min. In the experiments using spiked carcinoma cells (NCI-H1650, 0.01 to 0.0001%, accurate detection of carcinoma cells was achieved with PE-labeled anti-cytokeratin monoclonal antibody. Furthermore, verification of carcinoma cells in the microchambers was performed by double staining with the above monoclonal antibodies. CONCLUSION: The potential application of the cell microarray chip for the detection of CTCs was shown, thus demonstrating accurate detection by double staining for cytokeratin and EpCAM at the single carcinoma cell level.

  17. An accurate assay for HCV based on real-time fluorescence detection of isothermal RNA amplification.

    Science.gov (United States)

    Wu, Xuping; Wang, Jianfang; Song, Jinyun; Li, Jiayan; Yang, Yongfeng

    2016-09-01

    Hepatitis C virus (HCV) is one of the common reasons of liver fibrosis and hepatocellular carcinoma (HCC). Early, rapid and accurate HCV RNA detection is important to prevent and control liver disease. A simultaneous amplification and testing (SAT) assay, which is based on isothermal amplification of RNA and real-time fluorescence detection, was designed to optimize routine HCV RNA detection. In this study, HCV RNA and an internal control (IC) were amplified and analyzed simultaneously by SAT assay and detection of fluorescence using routine real-time PCR equipment. The assay detected as few as 10 copies of HCV RNA transcripts. We tested 705 serum samples with SAT, among which 96.4% (680/705) showed consistent results compared with routine real-time PCR. About 92% (23/25) discordant samples were confirmed to be same results as SAT-HCV by using a second real-time PCR. The sensitivity and specificity of SAT-HCV assay were 99.6% (461/463) and 100% (242/242), respectively. In conclusion, the SAT assay is an accurate test with a high specificity and sensitivity which may increase the detection rate of HCV. It is therefore a promising tool to diagnose HCV infection.

  18. Robust and accurate anomaly detection in ECG artifacts using time series motif discovery.

    Science.gov (United States)

    Sivaraks, Haemwaan; Ratanamahatana, Chotirat Ann

    2015-01-01

    Electrocardiogram (ECG) anomaly detection is an important technique for detecting dissimilar heartbeats which helps identify abnormal ECGs before the diagnosis process. Currently available ECG anomaly detection methods, ranging from academic research to commercial ECG machines, still suffer from a high false alarm rate because these methods are not able to differentiate ECG artifacts from real ECG signal, especially, in ECG artifacts that are similar to ECG signals in terms of shape and/or frequency. The problem leads to high vigilance for physicians and misinterpretation risk for nonspecialists. Therefore, this work proposes a novel anomaly detection technique that is highly robust and accurate in the presence of ECG artifacts which can effectively reduce the false alarm rate. Expert knowledge from cardiologists and motif discovery technique is utilized in our design. In addition, every step of the algorithm conforms to the interpretation of cardiologists. Our method can be utilized to both single-lead ECGs and multilead ECGs. Our experiment results on real ECG datasets are interpreted and evaluated by cardiologists. Our proposed algorithm can mostly achieve 100% of accuracy on detection (AoD), sensitivity, specificity, and positive predictive value with 0% false alarm rate. The results demonstrate that our proposed method is highly accurate and robust to artifacts, compared with competitive anomaly detection methods.

  19. Accurate identification of the six human Plasmodium spp. causing imported malaria, including Plasmodium ovale wallikeri and Plasmodium knowlesi.

    Science.gov (United States)

    Calderaro, Adriana; Piccolo, Giovanna; Gorrini, Chiara; Rossi, Sabina; Montecchini, Sara; Dell'Anna, Maria Loretana; De Conto, Flora; Medici, Maria Cristina; Chezzi, Carlo; Arcangeletti, Maria Cristina

    2013-09-13

    Accurate identification of Plasmodium infections in non-endemic countries is of critical importance with regard to the administration of a targeted therapy having a positive impact on patient health and management and allowing the prevention of the risk of re-introduction of endemic malaria in such countries. Malaria is no longer endemic in Italy where it is the most commonly imported disease, with one of the highest rates of imported malaria among European non-endemic countries including France, the UK and Germany, and with a prevalence of 24.3% at the University Hospital of Parma. Molecular methods showed high sensitivity and specificity and changed the epidemiology of imported malaria in several non-endemic countries, highlighted a higher prevalence of Plasmodium ovale, Plasmodium vivax and Plasmodium malariae underestimated by microscopy and, not least, brought to light both the existence of two species of P. ovale (Plasmodium ovale curtisi and Plasmodium ovale wallikeri) and the infection in humans by Plasmodium knowlesi, otherwise not detectable by microscopy. In this retrospective study an evaluation of two real-time PCR assays able to identify P. ovale wallikeri, distinguishing it from P. ovale curtisi, and to detect P. knowlesi, respectively, was performed applying them on a subset of 398 blood samples belonging to patients with the clinical suspicion of malaria. These assays revealed an excellent analytical sensitivity and no cross-reactivity versus other Plasmodium spp. infecting humans, suggesting their usefulness for an accurate and complete diagnosis of imported malaria. Among the 128 patients with malaria, eight P. ovale curtisi and four P. ovale wallikeri infections were detected, while no cases of P. knowlesi infection were observed. Real-time PCR assays specific for P. ovale wallikeri and P. knowlesi were included in the panel currently used in the University Hospital of Parma for the diagnosis of imported malaria, accomplishing the goal of

  20. A New Skin Detection Approach for Adult Image Identification

    Directory of Open Access Journals (Sweden)

    A. Nadian Ghomsheh

    2012-11-01

    Full Text Available With rapid proliferation of adult content on the internet, development of software to detect and filter this content is gaining more and more attention. In this study, a new method for adult image identification is proposed. Accurate human skin detection and extraction of relative features are the bottlenecks in this regard. In the proposed skin detection method, first, Hue color information is utilized to examine whether skin is present in the image, and if so, using dynamic thresholding an estimate of the skin region is obtained. In the second step, for images that contain skin, an exponential function is fitted to the histogram of the estimated skin area. Based on the parameters of the fitted function, the final skin map of the image is extracted. Area, texture, and a new shape feature are extracted from each region and used for image classification using neural networks. 95% accuracy for skin detection and 93.7% accuracy of adult image detection, compared to other methods showed the significance of the proposed method.

  1. Accurate Target Identification Using Multi-look Fusion of Low Quality Target Signatures

    Science.gov (United States)

    2008-12-01

    qualité, ce qui pourrait avoir des conséquences importantes pour les applications pratiques. D’une part, l’apparition de technologies de capteurs et...identification performance and this is not adequate for many target identification applications . Furthermore, in order for the single-look procedure to...obtenues qu’avec un un seul capteur . Toutefois, force est de constater que le rendement de l’identification correcte d’objectifs par l’approche

  2. Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety.

    Science.gov (United States)

    Mangal, Manisha; Bansal, Sangita; Sharma, Satish K; Gupta, Ram K

    2016-07-03

    Food safety is a global health concern. For the prevention and recognition of problems related to health and safety, detection of foodborne pathogen is of utmost importance at all levels of food production chain. For several decades, a lot of research has been targeted at the development of rapid methodology as reducing the time needed to complete pathogen detection tests has been the primary goal of food microbiologists. With the result, food microbiology laboratories now have a wide array of detection methods and automated technologies such as enzyme immunoassay, polymerase chain reaction, and microarrays, which can cut test times considerably. Nucleic acid amplification strategies and advances in amplicon detection methodologies have been the key factors in the progress of molecular microbiology. A comprehensive literature survey has been carried out to give an overview in the field of foodborne pathogen detection. In this paper, we describe the conventional methods, as well as recent developments in food pathogen detection, identification, and quantification, with a major emphasis on molecular detection methods.

  3. Autonomous system for pathogen detection and identification

    Energy Technology Data Exchange (ETDEWEB)

    Belgrader, P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Benett, W. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bergman, W. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Langlois, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mariella, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Milanovich, F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Miles, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Venkateswaran, K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Long, G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Nelson, W. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    1998-09-24

    This purpose of this project is to build a prototype instrument that will, running unattended, detect, identify, and quantify BW agents. In order to accomplish this, we have chosen to start with the world' s leading, proven, assays for pathogens: surface-molecular recognition assays, such as antibody-based assays, implemented on a high-performance, identification (ID)-capable flow cytometer, and the polymerase chain reaction (PCR) for nucleic-acid based assays. With these assays, we must integrate the capability to: l collect samples from aerosols, water, or surfaces; l perform sample preparation prior to the assays; l incubate the prepared samples, if necessary, for a period of time; l transport the prepared, incubated samples to the assays; l perform the assays; l interpret and report the results of the assays. Issues such as reliability, sensitivity and accuracy, quantity of consumables, maintenance schedule, etc. must be addressed satisfactorily to the end user. The highest possible sensitivity and specificity of the assay must be combined with no false alarms. Today, we have assays that can, in under 30 minutes, detect and identify simulants for BW agents at concentrations of a few hundred colony-forming units per ml of solution. If the bio-aerosol sampler of this system collects 1000 Ymin and concentrates the respirable particles into 1 ml of solution with 70% processing efficiency over a period of 5 minutes, then this translates to a detection/ID capability of under 0.1 agent-containing particle/liter of air.

  4. Rapid identification and detection of pathogenic Fungi by padlock probes

    NARCIS (Netherlands)

    Tsui, C.K.M.; Wang, B.; Schoen, C.D.; Hamelin, R.C.

    2013-01-01

    Fungi are important pathogens of human diseases, as well as to agricultural crop and trees. Molecular diagnostics can detect diseases early, and improve identification accuracy and follow-up disease management. The use of padlock probe is effective to facilitate these detections and pathogen identif

  5. Accurate coronary centerline extraction, caliber estimation and catheter detection in angiographies.

    Science.gov (United States)

    Hernandez-Vela, Antonio; Gatta, Carlo; Escalera, Sergio; Igual, Laura; Martin-Yuste, Victoria; Sabate, Manel; Radeva, Petia

    2012-11-01

    Segmentation of coronary arteries in X-Ray angiography is a fundamental tool to evaluate arterial diseases and choose proper coronary treatment. The accurate segmentation of coronary arteries has become an important topic for the registration of different modalities which allows physicians rapid access to different medical imaging information from Computed Tomography (CT) scans or Magnetic Resonance Imaging (MRI). In this paper, we propose an accurate fully automatic algorithm based on Graph-cuts for vessel centerline extraction, caliber estimation, and catheter detection. Vesselness, geodesic paths, and a new multi-scale edgeness map are combined to customize the Graph-cuts approach to the segmentation of tubular structures, by means of a global optimization of the Graph-cuts energy function. Moreover, a novel supervised learning methodology that integrates local and contextual information is proposed for automatic catheter detection. We evaluate the method performance on three datasets coming from different imaging systems. The method performs as good as the expert observer w.r.t. centerline detection and caliber estimation. Moreover, the method discriminates between arteries and catheter with an accuracy of 96.5%, sensitivity of 72%, and precision of 97.4%.

  6. Parente2: a fast and accurate method for detecting identity by descent

    KAUST Repository

    Rodriguez, Jesse M.

    2014-10-01

    Identity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographic studies to linking genomic variation with phenotype and disease. The problem of accurate IBD detection has become increasingly challenging with the availability of large collections of human genotypes and genomes: Given a cohort\\'s size, a quadratic number of pairwise genome comparisons must be performed. Therefore, computation time and the false discovery rate can also scale quadratically. To enable accurate and efficient large-scale IBD detection, we present Parente2, a novel method for detecting IBD segments. Parente2 is based on an embedded log-likelihood ratio and uses a model that accounts for linkage disequilibrium by explicitly modeling haplotype frequencies. Parente2 operates directly on genotype data without the need to phase data prior to IBD inference. We evaluate Parente2\\'s performance through extensive simulations using real data, and we show that it provides substantially higher accuracy compared to previous state-of-the-art methods while maintaining high computational efficiency.

  7. A highly accurate inclusive cancer screening test using Caenorhabditis elegans scent detection.

    Science.gov (United States)

    Hirotsu, Takaaki; Sonoda, Hideto; Uozumi, Takayuki; Shinden, Yoshiaki; Mimori, Koshi; Maehara, Yoshihiko; Ueda, Naoko; Hamakawa, Masayuki

    2015-01-01

    Early detection and treatment are of vital importance to the successful eradication of various cancers, and development of economical and non-invasive novel cancer screening systems is critical. Previous reports using canine scent detection demonstrated the existence of cancer-specific odours. However, it is difficult to introduce canine scent recognition into clinical practice because of the need to maintain accuracy. In this study, we developed a Nematode Scent Detection Test (NSDT) using Caenorhabditis elegans to provide a novel highly accurate cancer detection system that is economical, painless, rapid and convenient. We demonstrated wild-type C. elegans displayed attractive chemotaxis towards human cancer cell secretions, cancer tissues and urine from cancer patients but avoided control urine; in parallel, the response of the olfactory neurons of C. elegans to the urine from cancer patients was significantly stronger than to control urine. In contrast, G protein α mutants and olfactory neurons-ablated animals were not attracted to cancer patient urine, suggesting that C. elegans senses odours in urine. We tested 242 samples to measure the performance of the NSDT, and found the sensitivity was 95.8%; this is markedly higher than that of other existing tumour markers. Furthermore, the specificity was 95.0%. Importantly, this test was able to diagnose various cancer types tested at the early stage (stage 0 or 1). To conclude, C. elegans scent-based analyses might provide a new strategy to detect and study disease-associated scents.

  8. A highly accurate inclusive cancer screening test using Caenorhabditis elegans scent detection.

    Directory of Open Access Journals (Sweden)

    Takaaki Hirotsu

    Full Text Available Early detection and treatment are of vital importance to the successful eradication of various cancers, and development of economical and non-invasive novel cancer screening systems is critical. Previous reports using canine scent detection demonstrated the existence of cancer-specific odours. However, it is difficult to introduce canine scent recognition into clinical practice because of the need to maintain accuracy. In this study, we developed a Nematode Scent Detection Test (NSDT using Caenorhabditis elegans to provide a novel highly accurate cancer detection system that is economical, painless, rapid and convenient. We demonstrated wild-type C. elegans displayed attractive chemotaxis towards human cancer cell secretions, cancer tissues and urine from cancer patients but avoided control urine; in parallel, the response of the olfactory neurons of C. elegans to the urine from cancer patients was significantly stronger than to control urine. In contrast, G protein α mutants and olfactory neurons-ablated animals were not attracted to cancer patient urine, suggesting that C. elegans senses odours in urine. We tested 242 samples to measure the performance of the NSDT, and found the sensitivity was 95.8%; this is markedly higher than that of other existing tumour markers. Furthermore, the specificity was 95.0%. Importantly, this test was able to diagnose various cancer types tested at the early stage (stage 0 or 1. To conclude, C. elegans scent-based analyses might provide a new strategy to detect and study disease-associated scents.

  9. A simplified and accurate detection of the genetically modified wheat MON71800 with one calibrator plasmid.

    Science.gov (United States)

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

    2015-06-01

    With the increasing number of genetically modified (GM) events, unauthorized GMO releases into the food market have increased dramatically, and many countries have developed detection tools for them. This study described the qualitative and quantitative detection methods of unauthorized the GM wheat MON71800 with a reference plasmid (pGEM-M71800). The wheat acetyl-CoA carboxylase (acc) gene was used as the endogenous gene. The plasmid pGEM-M71800, which contains both the acc gene and the event-specific target MON71800, was constructed as a positive control for the qualitative and quantitative analyses. The limit of detection in the qualitative PCR assay was approximately 10 copies. In the quantitative PCR assay, the standard deviation and relative standard deviation repeatability values ranged from 0.06 to 0.25 and from 0.23% to 1.12%, respectively. This study supplies a powerful and very simple but accurate detection strategy for unauthorized GM wheat MON71800 that utilizes a single calibrator plasmid.

  10. Identification and Damage Detection on Structural Systems

    DEFF Research Database (Denmark)

    Brincker, Rune; Kirkegaard, Poul Henning; Andersen, Palle

    1994-01-01

    A short introduction is given to system identification and damage assessment in civil engineering structures. The most commonly used FFT-based techniques for system identification are mentioned, and the Random decrement technique and parametric methods based on ARMA models are introduced. Speed...

  11. Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium.

    Science.gov (United States)

    Mianzhi, Yao; Shah, Nagendra P

    2017-03-24

    Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.

  12. Accurate Anomaly Detection using Adaptive Monitoring and Fast Switching in SDN

    Directory of Open Access Journals (Sweden)

    Gagandeep Garg

    2015-10-01

    Full Text Available —Software defined networking (SDN is rapidly evolving technology which provides a suitable environment for easily applying efficient monitoring policies on the networks. SDN provides a centralized control of the whole network from which monitoring of network traffic and resources can be done with ease. SDN promises to drastically simplify network monitoring and management and also enable rapid innovation of networks through network programmability. SDN architecture separates the control of the network from the forwarding devices. With the higher innovation provided by the SDN, security threats at open interfaces of SDN also increases significantly as an attacker can target the single centralized point i.e. controller, to attack the network. Hence, efficient adaptive monitoring and measurement is required to detect and prevent malicious activities inside the network. Various such techniques have already been proposed by many researchers. This paper describes a work of applying efficient adaptive monitoring on the network while maintaining the performance of the network considering monitoring overhead over the controller. This work represents effective bandwidth utilization for calculation of threshold range while applying anomaly detection rules for monitoring of the network. Accurate detection of anomalies is implemented and also allows valid users and applications to transfer the data without any restrictions inside the network which otherwise were considered as anomalies in previous technique due to fluctuation of data and narrow threshold window. The concept of fast switching also used to improve the processing speed and performance of the networks.

  13. A highly accurate wireless digital sun sensor based on profile detecting and detector multiplexing technologies

    Science.gov (United States)

    Wei, Minsong; Xing, Fei; You, Zheng

    2017-01-01

    The advancing growth of micro- and nano-satellites requires miniaturized sun sensors which could be conveniently applied in the attitude determination subsystem. In this work, a profile detecting technology based high accurate wireless digital sun sensor was proposed, which could transform a two-dimensional image into two-linear profile output so that it can realize a high update rate under a very low power consumption. A multiple spots recovery approach with an asymmetric mask pattern design principle was introduced to fit the multiplexing image detector method for accuracy improvement of the sun sensor within a large Field of View (FOV). A FOV determination principle based on the concept of FOV region was also proposed to facilitate both sub-FOV analysis and the whole FOV determination. A RF MCU, together with solar cells, was utilized to achieve the wireless and self-powered functionality. The prototype of the sun sensor is approximately 10 times lower in size and weight compared with the conventional digital sun sensor (DSS). Test results indicated that the accuracy of the prototype was 0.01° within a cone FOV of 100°. Such an autonomous DSS could be equipped flexibly on a micro- or nano-satellite, especially for highly accurate remote sensing applications.

  14. Medical Image Watermarking Technique for Accurate Tamper Detection in ROI and Exact Recovery of ROI.

    Science.gov (United States)

    Eswaraiah, R; Sreenivasa Reddy, E

    2014-01-01

    In telemedicine while transferring medical images tampers may be introduced. Before making any diagnostic decisions, the integrity of region of interest (ROI) of the received medical image must be verified to avoid misdiagnosis. In this paper, we propose a novel fragile block based medical image watermarking technique to avoid embedding distortion inside ROI, verify integrity of ROI, detect accurately the tampered blocks inside ROI, and recover the original ROI with zero loss. In this proposed method, the medical image is segmented into three sets of pixels: ROI pixels, region of noninterest (RONI) pixels, and border pixels. Then, authentication data and information of ROI are embedded in border pixels. Recovery data of ROI is embedded into RONI. Results of experiments conducted on a number of medical images reveal that the proposed method produces high quality watermarked medical images, identifies the presence of tampers inside ROI with 100% accuracy, and recovers the original ROI without any loss.

  15. Rapid and accurate identification by real-time PCR of biotoxin-producing dinoflagellates from the family gymnodiniaceae.

    Science.gov (United States)

    Smith, Kirsty F; de Salas, Miguel; Adamson, Janet; Rhodes, Lesley L

    2014-03-07

    The identification of toxin-producing dinoflagellates for monitoring programmes and bio-compound discovery requires considerable taxonomic expertise. It can also be difficult to morphologically differentiate toxic and non-toxic species or strains. Various molecular methods have been used for dinoflagellate identification and detection, and this study describes the development of eight real-time polymerase chain reaction (PCR) assays targeting the large subunit ribosomal RNA (LSU rRNA) gene of species from the genera Gymnodinium, Karenia, Karlodinium, and Takayama. Assays proved to be highly specific and sensitive, and the assay for G. catenatum was further developed for quantification in response to a bloom in Manukau Harbour, New Zealand. The assay estimated cell densities from environmental samples as low as 0.07 cells per PCR reaction, which equated to three cells per litre. This assay not only enabled conclusive species identification but also detected the presence of cells below the limit of detection for light microscopy. This study demonstrates the usefulness of real-time PCR as a sensitive and rapid molecular technique for the detection and quantification of micro-algae from environmental samples.

  16. Application of the antibiotic batumin for accurate and rapid identification of staphylococcal small colony variants

    Directory of Open Access Journals (Sweden)

    Churkina Larisa N

    2012-07-01

    Full Text Available Abstract Background Staphylococcus aureus is a major human pathogen causing significant morbidity and mortality. The S. aureus colonies in osteomyelitis, in patients with cystic fibrosis and patients with endoprosthesis rejection frequently have an atypical morphology, i.e. staphylococcal small-colony variants, which form a naturally occurring subpopulation of clinically important staphylococci. Identification of these small colony variants is difficult, because of the loss of typical phenotypic characteristics of these variants. We wanted to improve and simplify the diagnosis of staphylococcal infection using a diagnostic preparation, consisting of 5 μg batumin paper disks. Batumin possesses a unique selective activity against all studied Staphylococcus spp., whereas all other species tested thus far are batumin resistant. We assessed the efficacy of the batumin diagnostic preparation to identify staphylococcal small colony variants, isolated from osteomyelitis patients. Findings With the batumin diagnostic preparation, all 30 tested staphylococcal small-colony variants had a growth inhibition zone around the disk of minimum 25 mm, accordant with the inhibition zones of the parent strains, isolated from the same patients. Conclusions The batumin diagnostic preparation correctly identified the small-colony variants of S. aureus, S. haemolyticus and S. epidermidis as belonging to the genus Staphylococcus, which differ profoundly from parental strains and are difficult to identify with standard methods. Identification of staphylococcal small-colony variants with the batumin diagnostic preparation is technically simple and can facilitate practical laboratory work.

  17. Retrival experience as an accurate indicator of person identification in line-ups

    Directory of Open Access Journals (Sweden)

    María José Contreras

    2011-07-01

    Full Text Available Responses in eyewitness identification of a person in a line-up may be based on two types of recovery experiences, remember and know experiences. Remember responses involve eyewitness identification of the target person as an episodic memory task, because it implies retrieving information about the target person in the place and at the time of the event. Know responses, in contrast, engage recognition based on familiarity or perceptual facilitation, that is, as a semantic memory task. To explore the relation between retrieval experiences and recognition accuracy, 86 participants took part in a recognition task with two conditions: one with an interpolated target absent line-up and the other only with the target present line-up. Accuracy of recognition and retrieval experience was measured. The results showed that, having previously participated in a target-absent line-up, increased omissions, while the number of hits decreased. Furthermore, participants’ know responses were associated to false recognition, whilst remember responses were associated to hits in recognition. Thus, asking eyewitnesses to inform about the kind of retrieval experience in which they based their recognition responses, may serve as a reliable indicator of accuracy in recognition. Future studies are needed to investigate whether this is also the case in natural settings.

  18. Poisonous or non-poisonous plants? DNA-based tools and applications for accurate identification.

    Science.gov (United States)

    Mezzasalma, Valerio; Ganopoulos, Ioannis; Galimberti, Andrea; Cornara, Laura; Ferri, Emanuele; Labra, Massimo

    2017-01-01

    Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.

  19. On the Accurate Identification of Network Paths Having a Common Bottleneck

    Directory of Open Access Journals (Sweden)

    Muhammad Murtaza Yousaf

    2013-01-01

    Full Text Available We present a new mechanism for detecting shared bottlenecks between end-to-end paths in a network. Our mechanism, which only needs one-way delays from endpoints as an input, is based on the well-known linear algebraic approach: singular value decomposition (SVD. Clusters of flows which share a bottleneck are extracted from SVD results by applying an outlier detection method. Simulations with varying topologies and different network conditions show the high accuracy of our technique.

  20. Structural Acoustic UXO Detection and Identification in Marine Environments

    Science.gov (United States)

    2016-05-01

    FINAL REPORT Structural Acoustic UXO Detection and Identification in Marine Environments SERDP Project MR-2103 MAY 2016 B. H...NUMBER Structural Acoustic UXO Detection and Identification in Marine Environments- Final report for Follow-on Work- MR-2103 Sb. GRANT NUMBER Sc...ADORESSIESI 10- SPONSOR/MONITOR’S ACRUNTMISI SERDP Program Office SER DP 4800 Mark Center Drive, Suite I 7D08 Alexandria, VA 22350-3605 11. SPON:soR

  1. [Accurate detection of a case with Angelman syndrome (type 1) using SNP array].

    Science.gov (United States)

    Shi, Shanshan; Lin, Shaobin; Liao, Yanfen; Li, Weijing

    2016-12-10

    To analyze a case with Angelman syndrome (AS) using single nucleotide polymorphism array (SNP array) and explore its genotype-phenotype correlation. G-banded karyotyping and SNP array were performed on a child featuring congenital malformations, intellectual disability and developmental delay. Mendelian error checking based on the SNP information was used to delineate the parental origin of detected abnormality. Result of the SNP array was validated with fluorescence in situ hybridization (FISH). The SNP array has detected a 6.053 Mb deletion at 15q11.2q13.1 (22,770,421- 28,823,722) which overlapped with the critical region of AS (type 1). The parents of the child showed no abnormal results for G-banded karyotyping, SNP array and FISH analysis, indicating a de novo origin of the deletion. Mendelian error checking based on the SNP information suggested that the 15q11.2q13.1 deletion was of maternal origin. SNP array can accurately define the size, location and parental origin of chromosomal microdeletions, which may facilitate the diagnosis of AS due to 15q11q13 deletion and better understanding of its genotype-phenotype correlation.

  2. Functional neuroimaging of visuospatial working memory tasks enables accurate detection of attention deficit and hyperactivity disorder

    Directory of Open Access Journals (Sweden)

    Rubi Hammer

    2015-01-01

    Full Text Available Finding neurobiological markers for neurodevelopmental disorders, such as attention deficit and hyperactivity disorder (ADHD, is a major objective of clinicians and neuroscientists. We examined if functional Magnetic Resonance Imaging (fMRI data from a few distinct visuospatial working memory (VSWM tasks enables accurately detecting cases with ADHD. We tested 20 boys with ADHD combined type and 20 typically developed (TD boys in four VSWM tasks that differed in feedback availability (feedback, no-feedback and reward size (large, small. We used a multimodal analysis based on brain activity in 16 regions of interest, significantly activated or deactivated in the four VSWM tasks (based on the entire participants' sample. Dimensionality of the data was reduced into 10 principal components that were used as the input variables to a logistic regression classifier. fMRI data from the four VSWM tasks enabled a classification accuracy of 92.5%, with high predicted ADHD probability values for most clinical cases, and low predicted ADHD probabilities for most TDs. This accuracy level was higher than those achieved by using the fMRI data of any single task, or the respective behavioral data. This indicates that task-based fMRI data acquired while participants perform a few distinct VSWM tasks enables improved detection of clinical cases.

  3. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    Science.gov (United States)

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-05-05

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis.

  4. Polarimetric radars and polarimetric SAR data in tasks of detection and identification of marine oil pollution

    Science.gov (United States)

    Sineva, A. A.; Ivanov, A. Yu.

    2016-12-01

    Detecting and distinguishing different kinds of oil pollution, including spills of crude oil on the sea surface, is one important problem of modern remote sensing. The wide use of imaging radars is not always effective. In this review paper, the main principles and methods of polarization radar imaging and radar data processing are discussed based on present theoretical and experimental approaches and ideas. The efficiency of polarimetric methods for oil-spill detection and accurate identification on the sea surface is demonstrated as well. As is shown, modern methods of multipolarimetric radar-signal processing is a powerful means for improving oil-pollution detection and discrimination algorithms.

  5. Accurate Identification of Fatty Liver Disease in Data Warehouse Utilizing Natural Language Processing.

    Science.gov (United States)

    Redman, Joseph S; Natarajan, Yamini; Hou, Jason K; Wang, Jingqi; Hanif, Muzammil; Feng, Hua; Kramer, Jennifer R; Desiderio, Roxanne; Xu, Hua; El-Serag, Hashem B; Kanwal, Fasiha

    2017-08-31

    Natural language processing is a powerful technique of machine learning capable of maximizing data extraction from complex electronic medical records. We utilized this technique to develop algorithms capable of "reading" full-text radiology reports to accurately identify the presence of fatty liver disease. Abdominal ultrasound, computerized tomography, and magnetic resonance imaging reports were retrieved from the Veterans Affairs Corporate Data Warehouse from a random national sample of 652 patients. Radiographic fatty liver disease was determined by manual review by two physicians and verified with an expert radiologist. A split validation method was utilized for algorithm development. For all three imaging modalities, the algorithms could identify fatty liver disease with >90% recall and precision, with F-measures >90%. These algorithms could be used to rapidly screen patient records to establish a large cohort to facilitate epidemiological and clinical studies and examine the clinic course and outcomes of patients with radiographic hepatic steatosis.

  6. Edge detection of iris of the eye for human biometric identification system

    Directory of Open Access Journals (Sweden)

    Kateryna O. Tryfonova

    2015-03-01

    Full Text Available Method of human biometric identification by iris of the eye is considered as one of the most accurate and reliable methods of identification. Aim of the research is to solve the problem of edge detection of digital image of the human eye iris to be able to implement human biometric identification system by means of mobile device. To achieve this aim the algorithm of edge detection by Canny is considered in work. It consists of the following steps: smoothing, finding gradients, non-maximum suppression, double thresholding with hysteresis. The software implementation of the Canny algorithm is carried out for the Android mobile platform with the use of high level programming language Java.

  7. An Immunology-inspired Fault Detection and Identification System

    Directory of Open Access Journals (Sweden)

    Liguo Weng

    2012-09-01

    Full Text Available This paper presents a fault detection and identification (FDI approach inspired by the immune system. The salient features of the immune system, such as adaptability, robustness, flexibility, archival memory and distributed cognition abilities, have been the valuable source of inspiration for fundamentally new methods for fault detection and identification. This research makes use of immunological concepts to develop a robust fault detection and identification mechanism, capable of detecting and classifying diverse system faults dynamically. Such an FDI mechanism also has the ability to learn and classify overlapping faults using distributed sensing. Moreover, its detection accuracy can be continuously improved during system operation. As tested by numerical simulations in which faults are represented by overlapping banana functions, the proposed algorithms are adaptive to new types of faults and overlapping faults.

  8. A tri-stage cluster identification model for accurate analysis of seismic catalogs

    Directory of Open Access Journals (Sweden)

    S. J. Nanda

    2013-02-01

    Full Text Available In this paper we propose a tri-stage cluster identification model that is a combination of a simple single iteration distance algorithm and an iterative K-means algorithm. In this study of earthquake seismicity, the model considers event location, time and magnitude information from earthquake catalog data to efficiently classify events as either background or mainshock and aftershock sequences. Tests on a synthetic seismicity catalog demonstrate the efficiency of the proposed model in terms of accuracy percentage (94.81% for background and 89.46% for aftershocks. The close agreement between lambda and cumulative plots for the ideal synthetic catalog and that generated by the proposed model also supports the accuracy of the proposed technique. There is flexibility in the model design to allow for proper selection of location and magnitude ranges, depending upon the nature of the mainshocks present in the catalog. The effectiveness of the proposed model also is evaluated by the classification of events in three historic catalogs: California, Japan and Indonesia. As expected, for both synthetic and historic catalog analysis it is observed that the density of events classified as background is almost uniform throughout the region, whereas the density of aftershock events are higher near the mainshocks.

  9. Use of Fourier transform infrared spectroscopy (FTIR spectroscopy for rapid and accurate identification of Yeasts isolated from human and animals

    Directory of Open Access Journals (Sweden)

    M. Taha

    2013-06-01

    Full Text Available Rapid and accurate identification of yeast is increasingly important to stipulate the appropriate therapy thus reducing morbidity and mortality related to yeast infections. Vibrational spectroscopic techniques (infrared (IR and Raman could provide potential alternatives to conventional typing methods, because they constitute a rapid, inexpensive and highly specific spectroscopic fingerprint through-which microorganism can be identified. The present study evaluate (FTIR spectroscopy as a sensitive and effective assay for the identification of the most frequent yeast species isolated from human and animals. One hundred and twenty-eight yeasts isolated from infected human mouths/vaginas, chronic diseased cows, crop mycosis in chicken and soil contaminated with pigeon droppings were phenotypically identified. Using universal primers, ITS1/ITS4, we have amplified ITS1-5.8S-ITS2 rDNA regions for 39 yeast isolates as representative samples. The PCR products were digested with restriction enzyme MspI and examined by PCR-RFLP, which was an efficient technique for identification of Candida spp., Cryptococcus neoformans and Trichosporon asahii. Further, identification of the same 39 isolates were done by FTIR spectroscopy and considered as reference for other strains by comparison of their FTIR spectra. The current study has sharply demonstrated the significant spectral differences between the various examined species of Candida, Cryptococcus, Trichosporon, Rhodotorula and Geotrichum isolated from different sources. Decisively, our research has confirmed that FTIR spectroscopy is a promising diagnostic tool, because of its sensitivity, rapidity, high differentiation capacity and simplicity compared to conventional/molecular techniques.

  10. Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification?

    Science.gov (United States)

    Muth, Thilo; Renard, Bernhard Y

    2017-03-21

    While peptide identifications in mass spectrometry (MS)-based shotgun proteomics are mostly obtained using database search methods, high-resolution spectrum data from modern MS instruments nowadays offer the prospect of improving the performance of computational de novo peptide sequencing. The major benefit of de novo sequencing is that it does not require a reference database to deduce full-length or partial tag-based peptide sequences directly from experimental tandem mass spectrometry spectra. Although various algorithms have been developed for automated de novo sequencing, the prediction accuracy of proposed solutions has been rarely evaluated in independent benchmarking studies. The main objective of this work is to provide a detailed evaluation on the performance of de novo sequencing algorithms on high-resolution data. For this purpose, we processed four experimental data sets acquired from different instrument types from collision-induced dissociation and higher energy collisional dissociation (HCD) fragmentation mode using the software packages Novor, PEAKS and PepNovo. Moreover, the accuracy of these algorithms is also tested on ground truth data based on simulated spectra generated from peak intensity prediction software. We found that Novor shows the overall best performance compared with PEAKS and PepNovo with respect to the accuracy of correct full peptide, tag-based and single-residue predictions. In addition, the same tool outpaced the commercial competitor PEAKS in terms of running time speedup by factors of around 12-17. Despite around 35% prediction accuracy for complete peptide sequences on HCD data sets, taken as a whole, the evaluated algorithms perform moderately on experimental data but show a significantly better performance on simulated data (up to 84% accuracy). Further, we describe the most frequently occurring de novo sequencing errors and evaluate the influence of missing fragment ion peaks and spectral noise on the accuracy. Finally

  11. Multislice Computed Tomography Accurately Detects Stenosis in Coronary Artery Bypass Conduits

    Science.gov (United States)

    Duran, Cihan; Sagbas, Ertan; Caynak, Baris; Sanisoglu, Ilhan; Akpinar, Belhhan; Gulbaran, Murat

    2007-01-01

    The aim of this study was to evaluate the accuracy of multislice computed tomography in detecting graft stenosis or occlusion after coronary artery bypass grafting, using coronary angiography as the standard. From January 2005 through May 2006, 25 patients (19 men and 6 women; mean age, 54 ± 11.3 years) underwent diagnostic investigation of their bypass grafts by multislice computed tomography within 1 month of coronary angiography. The mean time elapsed after coronary artery bypass grafting was 6.2 years. In these 25 patients, we examined 65 bypass conduits (24 arterial and 41 venous) and 171 graft segments (the shaft, proximal anastomosis, and distal anastomosis). Compared with coronary angiography, the segment-based sensitivity, specificity, and positive and negative predictive values of multislice computed tomography in the evaluation of stenosis were 89%, 100%, 100%, and 99%, respectively. The patency rate for multislice compu-ted tomography was 85% (55/65: 3 arterial and 7 venous grafts were occluded), with 100% sensitivity and specificity. From these data, we conclude that multislice computed tomography can accurately evaluate the patency and stenosis of bypass grafts during outpatient follow-up. PMID:17948078

  12. Simultaneous three-dimensional tracking of individual signals from multi-trap optical tweezers using fast and accurate photodiode detection.

    Science.gov (United States)

    Ott, Dino; Nader, S; Reihani, S; Oddershede, Lene B

    2014-09-22

    Multiple-beam optical traps facilitate advanced trapping geometries and exciting discoveries. However, the increased manipulation capabilities come at the price of more challenging position and force detection. Due to unrivaled bandwidth and resolution, photodiode based detection is preferred over camera based detection in most single/dual-beam optical traps assays. However, it has not been trivial to implement photodiode based detection for multiple-beam optical traps. Here, we present a simple and efficient method based on spatial filtering for parallel photodiode detection of multiple traps. The technique enables fast and accurate 3D force and distance detection of multiple objects simultaneously manipulated by multiple-beam optical tweezers.

  13. Microarrays for Universal Detection and Identification of Phytoplasmas

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Nyskjold, Henriette; Bertaccini, Assunta

    2013-01-01

    Detection and identification of phytoplasmas is a laborious process often involving nested PCR followed by restriction enzyme analysis and fine-resolution gel electrophoresis. To improve throughput, other methods are needed. Microarray technology offers a generic assay that can potentially detect...

  14. More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing.

    Science.gov (United States)

    Ambers, Angie D; Churchill, Jennifer D; King, Jonathan L; Stoljarova, Monika; Gill-King, Harrell; Assidi, Mourad; Abu-Elmagd, Muhammad; Buhmeida, Abdelbaset; Al-Qahtani, Mohammed; Budowle, Bruce

    2016-10-17

    Although the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. Massively parallel sequencing (MPS) offers an opportunity to provide biometric data in such cases, and these cases provide valuable data on the feasibility of applying MPS for characterization of modern forensic casework samples. In this study, MPS was used to characterize 140-year-old human skeletal remains discovered at a historical site in Deadwood, South Dakota, United States. The remains were in an unmarked grave and there were no records or other metadata available regarding the identity of the individual. Due to the high throughput of MPS, a variety of biometric markers could be typed using a single sample. Using MPS and suitable forensic genetic markers, more relevant information could be obtained from a limited quantity and quality sample. Results were obtained for 25/26 Y-STRs, 34/34 Y SNPs, 166/166 ancestry-informative SNPs, 24/24 phenotype-informative SNPs, 102/102 human identity SNPs, 27/29 autosomal STRs (plus amelogenin), and 4/8 X-STRs (as well as ten regions of mtDNA). The Y-chromosome (Y-STR, Y-SNP) and mtDNA profiles of the unidentified skeletal remains are consistent with the R1b and H1 haplogroups, respectively. Both of these haplogroups are the most common haplogroups in Western Europe. Ancestry-informative SNP analysis also supported European ancestry. The genetic results are consistent with anthropological findings that the remains belong to a male of European ancestry (Caucasian). Phenotype-informative SNP data provided strong support that the individual had light red hair and brown eyes. This study is among the first to genetically characterize historical human remains with forensic genetic marker kits specifically designed for MPS. The outcome demonstrates that substantially more genetic information can be obtained from

  15. Detection and identification of spatial offset: double-judgment psychophysics revisited.

    Science.gov (United States)

    Allik, Jüri; Toom, Mai; Rauk, Marika

    2014-11-01

    In a bull's-eye acuity task, we asked observers to identify in which direction, to the left or the right, a spot had been displaced from the center of a circle and-after that, in the same trial-to detect which of the two presented circles contained the displaced spot. Replicating our previous findings (Allik, Dzhafarov, & Rauk, 1982), the spatial offset direction identification probability was higher than the probability with which the correct observation interval could be detected. All data were explained by a Thurstonian model, according to which the spatial positions of both spots are projected onto an internal axis of representation as two random numbers, x and y, drawn from a random distribution with a fixed standard deviation ς (final sigma). The observed identification and detection probabilities were accurately reproduced, provided that the observer tested two different inequalities: x + y > 0 for the identification, and x (2) - y (2) > 0 for the detection. In order to eliminate small discrepancies between the predicted and the observed data, we proposed that the positional error increases with increasing distance from the center of the annulus. It was concluded that, to explain the superiority of the identification over the detection effect, there is no need to propose separate axes of representation for mono- and bipolar information, as is usually postulated in double-judgment psychophysics.

  16. Rapid, Accurate, and Quantitative Detection of Propranolol in Multiple Human Biofluids via Surface-Enhanced Raman Scattering.

    Science.gov (United States)

    Subaihi, Abdu; Almanqur, Laila; Muhamadali, Howbeer; AlMasoud, Najla; Ellis, David I; Trivedi, Drupad K; Hollywood, Katherine A; Xu, Yun; Goodacre, Royston

    2016-11-15

    There has been an increasing demand for rapid and sensitive techniques for the identification and quantification of pharmaceutical compounds in human biofluids during the past few decades, and surface-enhanced Raman scattering (SERS) is one of a number of physicochemical techniques with the potential to meet these demands. In this study we have developed a SERS-based analytical approach for the assessment of human biofluids in combination with chemometrics. This novel approach has enabled the detection and quantification of the β-blocker propranolol spiked into human serum, plasma, and urine at physiologically relevant concentrations. A range of multivariate statistical analysis techniques, including principal component analysis (PCA), principal component-discriminant function analysis (PC-DFA) and partial least-squares regression (PLSR) were employed to investigate the relationship between the full SERS spectral data and the level of propranolol. The SERS spectra when combined with PCA and PC-DFA demonstrated clear differentiation of neat biofluids and biofluids spiked with varying concentrations of propranolol ranging from 0 to 120 μM, and clear trends in ordination scores space could be correlated with the level of propranolol. Since PCA and PC-DFA are categorical classifiers, PLSR modeling was subsequently used to provide accurate propranolol quantification within all biofluids with high prediction accuracy (expressed as root-mean-square error of predictions) of 0.58, 9.68, and 1.69 for serum, plasma, and urine respectively, and these models also had excellent linearity for the training and test sets between 0 and 120 μM. The limit of detection as calculated from the area under the naphthalene ring vibration from propranolol was 133.1 ng/mL (0.45 μM), 156.8 ng/mL (0.53 μM), and 168.6 ng/mL (0.57 μM) for serum, plasma, and urine, respectively. This result shows a consistent signal irrespective of biofluid, and all are well within the expected physiological

  17. High Specificity in Circulating Tumor Cell Identification Is Required for Accurate Evaluation of Programmed Death-Ligand 1

    Science.gov (United States)

    Schultz, Zachery D.; Warrick, Jay W.; Guckenberger, David J.; Pezzi, Hannah M.; Sperger, Jamie M.; Heninger, Erika; Saeed, Anwaar; Leal, Ticiana; Mattox, Kara; Traynor, Anne M.; Campbell, Toby C.; Berry, Scott M.; Beebe, David J.; Lang, Joshua M.

    2016-01-01

    Background Expression of programmed-death ligand 1 (PD-L1) in non-small cell lung cancer (NSCLC) is typically evaluated through invasive biopsies; however, recent advances in the identification of circulating tumor cells (CTCs) may be a less invasive method to assay tumor cells for these purposes. These liquid biopsies rely on accurate identification of CTCs from the diverse populations in the blood, where some tumor cells share characteristics with normal blood cells. While many blood cells can be excluded by their high expression of CD45, neutrophils and other immature myeloid subsets have low to absent expression of CD45 and also express PD-L1. Furthermore, cytokeratin is typically used to identify CTCs, but neutrophils may stain non-specifically for intracellular antibodies, including cytokeratin, thus preventing accurate evaluation of PD-L1 expression on tumor cells. This holds even greater significance when evaluating PD-L1 in epithelial cell adhesion molecule (EpCAM) positive and EpCAM negative CTCs (as in epithelial-mesenchymal transition (EMT)). Methods To evaluate the impact of CTC misidentification on PD-L1 evaluation, we utilized CD11b to identify myeloid cells. CTCs were isolated from patients with metastatic NSCLC using EpCAM, MUC1 or Vimentin capture antibodies and exclusion-based sample preparation (ESP) technology. Results Large populations of CD11b+CD45lo cells were identified in buffy coats and stained non-specifically for intracellular antibodies including cytokeratin. The amount of CD11b+ cells misidentified as CTCs varied among patients; accounting for 33–100% of traditionally identified CTCs. Cells captured with vimentin had a higher frequency of CD11b+ cells at 41%, compared to 20% and 18% with MUC1 or EpCAM, respectively. Cells misidentified as CTCs ultimately skewed PD-L1 expression to varying degrees across patient samples. Conclusions Interfering myeloid populations can be differentiated from true CTCs with additional staining criteria

  18. High Specificity in Circulating Tumor Cell Identification Is Required for Accurate Evaluation of Programmed Death-Ligand 1.

    Directory of Open Access Journals (Sweden)

    Jennifer L Schehr

    Full Text Available Expression of programmed-death ligand 1 (PD-L1 in non-small cell lung cancer (NSCLC is typically evaluated through invasive biopsies; however, recent advances in the identification of circulating tumor cells (CTCs may be a less invasive method to assay tumor cells for these purposes. These liquid biopsies rely on accurate identification of CTCs from the diverse populations in the blood, where some tumor cells share characteristics with normal blood cells. While many blood cells can be excluded by their high expression of CD45, neutrophils and other immature myeloid subsets have low to absent expression of CD45 and also express PD-L1. Furthermore, cytokeratin is typically used to identify CTCs, but neutrophils may stain non-specifically for intracellular antibodies, including cytokeratin, thus preventing accurate evaluation of PD-L1 expression on tumor cells. This holds even greater significance when evaluating PD-L1 in epithelial cell adhesion molecule (EpCAM positive and EpCAM negative CTCs (as in epithelial-mesenchymal transition (EMT.To evaluate the impact of CTC misidentification on PD-L1 evaluation, we utilized CD11b to identify myeloid cells. CTCs were isolated from patients with metastatic NSCLC using EpCAM, MUC1 or Vimentin capture antibodies and exclusion-based sample preparation (ESP technology.Large populations of CD11b+CD45lo cells were identified in buffy coats and stained non-specifically for intracellular antibodies including cytokeratin. The amount of CD11b+ cells misidentified as CTCs varied among patients; accounting for 33-100% of traditionally identified CTCs. Cells captured with vimentin had a higher frequency of CD11b+ cells at 41%, compared to 20% and 18% with MUC1 or EpCAM, respectively. Cells misidentified as CTCs ultimately skewed PD-L1 expression to varying degrees across patient samples.Interfering myeloid populations can be differentiated from true CTCs with additional staining criteria, thus improving the

  19. Bacteriophage Amplification-Coupled Detection and Identification of Bacterial Pathogens

    Science.gov (United States)

    Cox, Christopher R.; Voorhees, Kent J.

    Current methods of species-specific bacterial detection and identification are complex, time-consuming, and often require expensive specialized equipment and highly trained personnel. Numerous biochemical and genotypic identification methods have been applied to bacterial characterization, but all rely on tedious microbiological culturing practices and/or costly sequencing protocols which render them impractical for deployment as rapid, cost-effective point-of-care or field detection and identification methods. With a view towards addressing these shortcomings, we have exploited the evolutionarily conserved interactions between a bacteriophage (phage) and its bacterial host to develop species-specific detection methods. Phage amplification-coupled matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) was utilized to rapidly detect phage propagation resulting from species-specific in vitro bacterial infection. This novel signal amplification method allowed for bacterial detection and identification in as little as 2 h, and when combined with disulfide bond reduction methods developed in our laboratory to enhance MALDI-TOF-MS resolution, was observed to lower the limit of detection by several orders of magnitude over conventional spectroscopy and phage typing methods. Phage amplification has been combined with lateral flow immunochromatography (LFI) to develop rapid, easy-to-operate, portable, species-specific point-of-care (POC) detection devices. Prototype LFI detectors have been developed and characterized for Yersinia pestis and Bacillus anthracis, the etiologic agents of plague and anthrax, respectively. Comparable sensitivity and rapidity was observed when phage amplification was adapted to a species-specific handheld LFI detector, thus allowing for rapid, simple, POC bacterial detection and identification while eliminating the need for bacterial culturing or DNA isolation and amplification techniques.

  20. Accurate LC peak boundary detection for ¹⁶O/¹⁸O labeled LC-MS data.

    Directory of Open Access Journals (Sweden)

    Jian Cui

    Full Text Available In liquid chromatography-mass spectrometry (LC-MS, parts of LC peaks are often corrupted by their co-eluting peptides, which results in increased quantification variance. In this paper, we propose to apply accurate LC peak boundary detection to remove the corrupted part of LC peaks. Accurate LC peak boundary detection is achieved by checking the consistency of intensity patterns within peptide elution time ranges. In addition, we remove peptides with erroneous mass assignment through model fitness check, which compares observed intensity patterns to theoretically constructed ones. The proposed algorithm can significantly improve the accuracy and precision of peptide ratio measurements.

  1. Identification of feces by detection of Bacteroides genes.

    Science.gov (United States)

    Nakanishi, Hiroaki; Shojo, Hideki; Ohmori, Takeshi; Hara, Masaaki; Takada, Aya; Adachi, Noboru; Saito, Kazuyuki

    2013-01-01

    In forensic science, the identification of feces is very important in a variety of crime investigations. However, no sensitive and simple fecal identification method using molecular biological techniques has been reported. Here, we focused on the fecal bacteria, Bacteroides uniformis, Bacteroides vulgatus and Bacteroides thetaiotaomicron, and developed a novel fecal identification method by detection of the gene sequences specific to these bacteria in various body (feces, blood, saliva, semen, urine, vaginal fluids and skin surfaces) and forensic (anal adhesions) specimens. Bacterial gene detection was performed by real-time PCR using a minor groove binding probe to amplify the RNA polymerase β-subunit gene of B. uniformis and B. vulgatus, and the α-1-6 mannanase gene of B. thetaiotaomicron. At least one of these bacteria was detected in the feces of 20 donors; the proportions of B. uniformis, B. vulgatus and B. thetaiotaomicron were 95, 85 and 60%, respectively. Bacteroides vulgatus was also detected in one of six vaginal fluid samples, but B. thetaiotaomicron and B. uniformis were not detected in body samples other than feces. Further, we applied this method to forensic specimens from 18 donors. Eighteen anal adhesions also contained at least one of three bacteria; B. uniformis, B. vulgatus and B. thetaiotaomicron were detected in 89, 78 and 56%, respectively, of the specimens. Thus, these bacteria were present at a high frequency in the fecal and forensic specimens, while either B. uniformis or B. vulgatus was detected in all samples. Therefore, B. uniformis and B. vulgatus represent more appropriate target species than B. thetaiotaomicron for the identification of fecal material. If B. vulgatus and/or B. uniformis are detected, it is likely that the sample contains feces. Taken together, our results suggest that the use of molecular biological techniques will aid the detection of feces in forensic practice, although it is possible that the samples contained

  2. Detection and Identification System of Bacteria and Bacterial Endotoxin Based on Raman Spectroscopy

    Directory of Open Access Journals (Sweden)

    Muhammad Elsayeh

    2016-03-01

    Full Text Available Sepsis is a global health problem that causes risk of death. In the developing world, about 60 to 80 % of death cases are caused by Sepsis. Rapid methods for detecting its causes, represent one of the major factors that may reduce Sepsis risks. Such methods can provide microbial detection and identification which is critical to determine the right treatment for the patient. Microbial and Pyrogen detection is important for quality control system to ensure the absence of pathogens and Pyrogens in the manufacturing of both medical and food products. Raman spectroscopes represent a q uick and accurate identification and detection method, for bacteria and bacterial endotoxin, which this plays an important role in delivering high quality biomedical products using the power of Raman spectroscopy. It is a rapid method for chemical structure detection that can be used in identifying and classifying bacteria and bacterial endotoxin. Such a method acts as a solution for time and cost effective quality control procedures. This work presents an automatic system based on Raman spectroscopy to detect and identify bacteria and bacterial endotoxin. It uses the frequency properties of Raman scattering through the interaction between organic materials and electromagnetic waves. The scattered intensities are measured and wave number converted into frequency, then the cepstral coefficients are extracted for both the detection and identification. The methodology depends on normalization of Fourier transformed cepstral signal to extract their classification features. Experiments’ results proved effective identification and detection of bacteria and bacterial endotoxin even with concentrations as low as 0.0003 Endotoxin unit (EU/ml and 1 Colony Forming Unit (CFU/ml using signal processing based enhancement technique.

  3. P2P worm detection based on application identification

    Institute of Scientific and Technical Information of China (English)

    XIA Chunhe; SHI Yunping; LI Xiaojian; GAO Wei

    2007-01-01

    P2P worm exploits common vulnerabilities and spreads through peer-to-peer networks.Despite being recognized as a potential and deadly threat to the Internet recently,few relevant countermeasures are found in extant literature.Once it breaks out,a P2P worm could result in unpredictable losses.Based on propagation characteristics of the worm,this paper presents a detection method called PWD (P2P Worm Detection),which is designed based on application identification and unknown worm detection.Simulation result and LAN-environment experiment result both indicate that PWD is an effective method to detect and block P2P worms.

  4. Identification of hidden allergens: detection of pistachio traces in mortadella.

    Science.gov (United States)

    Barbieri, G; Frigeri, G

    2006-12-01

    An analytical method based on the detection of specific DNA was developed and applied to mortadella samples with and without pistachio (Pistacia vera). The method is proposed for the detection of traces of pistachio deriving from previous processes or from accidental contamination, since in predisposed individuals pistachios can cause allergic reactions leading to anaphylactic shock. Three pairs of primers were identified and tested by polymerase chain reaction (PCR) on mortadella samples prepared with pistachio. Accidental contamination was also simulated. The optimized PCR was able to detect the presence of pistachio, even at low concentrations. The primers pair PSTC 1-2 is suggested for unambiguous identification of pistachio in mortadella. The limit of detection for this primers pair was 100 mg kg-1. No interference was observed from other spices or ingredients utilized in the formulation of the mortadella. The method enabled the identification of possible traces of pistachio remaining in the production plant after less than thorough washing.

  5. Phytochip: development of a DNA-microarray for rapid and accurate identification of Pseudo-nitzschia spp and other harmful algal species.

    Science.gov (United States)

    Noyer, Charlotte; Abot, Anne; Trouilh, Lidwine; Leberre, Véronique Anton; Dreanno, Catherine

    2015-05-01

    Detection of harmful algal blooms has become a challenging concern because of the direct impacts on public health and economy. The identification of toxic dinoflagellates and diatoms in monitoring programs requires an extensive taxonomic expertise and is time consuming. Advances in molecular biology have allowed the development of new approaches, more rapid, accurate and cost-effective for detecting these microorganisms. In this context, we developed a new DNA microarray (called, Phytochip) for the simultaneous detection of multiple HAB species with a particular emphasis on Pseudo-nitzschia species. Oligonucleotide probes were designed along the rRNA operon. After DNA extraction, the target rDNA genes were amplified and labeled using an asymmetric PCR; then, the amplicons were hybridized to the oligonucleotide probes present on the chips. The total assay from seawater sampling to data acquisition can be performed within a working day. Specificity and sensitivity were assessed by using monoclonal cultures, mixtures of species and field samples spiked with a known amount of cultured cells. The Phytochip with its 81 validated oligonucleotide probes was able to detect 12 species of Pseudo-nitzschia and 11 species of dinoflagellates among which were 3 species of Karenia and 3 species of Alexandrium. The Phytochip was applied to environmental samples already characterized by light microscopy and cloned into DNA libraries. The hybridizations on the Phytochip were in good agreement with the sequences retrieved from the clone libraries and the microscopic observations. The Phytochip enables a reliable multiplex detection of phytoplankton and can assist a water quality monitoring program as well as more general ecological research.

  6. Low-cost backpack-portable robot system for mine and UXO detection and identification

    Science.gov (United States)

    Nelson, Carl V.; Arabian, Adam K.

    2002-08-01

    The Johns Hopkins University Applied Physics Laboratory (JHU/APL) has developed a prototype backpack-portable robot system for mine and unexploded ordnance (UXO) detection and identification. The robot system is compact, lightweight and is estimated to be inexpensive to construct. The robot has been designed with an inexpensive, highly accurate, wide bandwidth time-domain electromagnetic induction (EMI) sensor for the detection and identification of metal components in mines and UXO. The robot can be configured for autonomous or person-in-the-loop control. The robot system can be configured with additional light-weight and low-cost mine and UXO sensors such as ground penetrating radar (GPR) and chemical explosive detectors.

  7. Explosive Detection and Identification by PGNAA

    Energy Technology Data Exchange (ETDEWEB)

    E.H. Seabury; A.J. Caffrey

    2004-11-01

    The goal of this project was to determine the feasibility of using field-portable prompt gamma-ray neutron activation analysis (PGNAA) to detect and identify explosives in improvised nuclear devices (INDs). The studies were carried out using the Monte Carlo N-Particle (MCNP) code developed at Los Alamos National Laboratory. The model results were tested experimentally using explosive simulants and the PINS PGNAA system developed at Idaho National Engineering and Environmental Laboratory (INEEL). The results of the MCNP calculations and PINS measurements are presented in this report. The calculations and measurements were in good agreement and indicate that most explosives are readily distinguishable from one another.

  8. Model identification for dose response signal detection

    OpenAIRE

    Bretz, Frank; Dette, Holger; Titoff, Stefanie; Volgushev, Stanislav

    2012-01-01

    We consider the problem of detecting a dose response signal if several competing regression models are available to describe the dose response relationship. In particular, we re-analyze the MCP-Mod approach from Bretz et al. (2005), which has become a very popular tool for this problem in recent years. We propose an improvement based on likelihood ratio tests and prove that in linear models this approach is always at least as powerful as the MCP-Mod method. This result remains ...

  9. Explosives Detection and Identification by PGNAA

    Energy Technology Data Exchange (ETDEWEB)

    E. H. Seabury; A. J. Caffrey

    2006-04-01

    The feasibility of using field-portable prompt gamma-ray neutron activation analysis (PGNAA) to detect and identify explosives in improvised nuclear devices has been studied computationally, using the Monte Carlo N-Particle (MCNP) code developed at Los Alamos National Laboratory. The Monte Carlo results, in turn were tested experimentally using explosive simulants and the PINS PGNAA system developed at Idaho National Laboratory (INL). The results of the MCNP calculations and PINS measurements have been previously reported. In this report we describe measurements performed on actual explosives and compare the results with calculations. The calculations and measurements were in good agreement and indicate that most explosives are readily distinguishable from one another by PGNAA

  10. Development of a Rapid and Accurate Identification Method for Citrobacter Species Isolated from Pork Products Using a Matrix-Assisted Laser-Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS).

    Science.gov (United States)

    Kwak, Hye-Lim; Han, Sun-Kyung; Park, Sunghoon; Park, Si Hong; Shim, Jae-Yong; Oh, Mihwa; Ricke, Steven C; Kim, Hae-Yeong

    2015-09-01

    Previous detection methods for Citrobacter are considered time consuming and laborious. In this study, we have developed a rapid and accurate detection method for Citrobacter species in pork products, using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). A total of 35 Citrobacter strains were isolated from 30 pork products and identified by both MALDI-TOF MS and 16S rRNA gene sequencing approaches. All isolates were identified to the species level by the MALDI-TOF MS, while 16S rRNA gene sequencing results could not discriminate them clearly. These results confirmed that MALDI-TOF MS is a more accurate and rapid detection method for the identification of Citrobacter species.

  11. Detecting Children's Lies: Are Parents Accurate Judges of Their Own Children's Lies?

    Science.gov (United States)

    Talwar, Victoria; Renaud, Sarah-Jane; Conway, Lauryn

    2015-01-01

    The current study investigated whether parents are accurate judges of their own children's lie-telling behavior. Participants included 250 mother-child dyads. Children were between three and 11 years of age. A temptation resistance paradigm was used to elicit a minor transgressive behavior from the children involving peeking at a forbidden toy and…

  12. Deep sequencing analyses of low density microbial communities: Working at the boundary of accurate microbiota detection

    NARCIS (Netherlands)

    Biesbroek, G.; Sanders, E.A.M.; Roeselers, G.; Wang, X.; Caspers, M.P.M.; Trzciński, K.; Bogaert, D.; Keijser, B.J.F.

    2012-01-01

    Introduction: Accurate analyses of microbiota composition of low-density communities (103-104 bacteria/sample) can be challenging. Background DNA from chemicals and consumables, extraction biases as well as differences in PCR efficiency can significantly interfere with microbiota assessment. This

  13. Detecting Children's Lies: Are Parents Accurate Judges of Their Own Children's Lies?

    Science.gov (United States)

    Talwar, Victoria; Renaud, Sarah-Jane; Conway, Lauryn

    2015-01-01

    The current study investigated whether parents are accurate judges of their own children's lie-telling behavior. Participants included 250 mother-child dyads. Children were between three and 11 years of age. A temptation resistance paradigm was used to elicit a minor transgressive behavior from the children involving peeking at a forbidden toy and…

  14. LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

    DEFF Research Database (Denmark)

    Will, Sebastian; Joshi, Tejal; Hofacker, Ivo L.

    2012-01-01

    Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of genomic regions containing potential structural ncRNAs. The analysis of these data requires highly accurate prediction of ncRNA boundaries and discrimination of promising candidate ncRNAs from weak predictions. Existing...

  15. Deep sequencing analyses of low density microbial communities: Working at the boundary of accurate microbiota detection

    NARCIS (Netherlands)

    Biesbroek, G.; Sanders, E.A.M.; Roeselers, G.; Wang, X.; Caspers, M.P.M.; Trzciński, K.; Bogaert, D.; Keijser, B.J.F.

    2012-01-01

    Introduction: Accurate analyses of microbiota composition of low-density communities (103-104 bacteria/sample) can be challenging. Background DNA from chemicals and consumables, extraction biases as well as differences in PCR efficiency can significantly interfere with microbiota assessment. This st

  16. Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR.

    Directory of Open Access Journals (Sweden)

    Erin P Price

    Full Text Available Burkholderia ubonensis is an environmental bacterium belonging to the Burkholderia cepacia complex (Bcc, a group of genetically related organisms that are associated with opportunistic but generally nonfatal infections in healthy individuals. In contrast, the near-neighbour species Burkholderia pseudomallei causes melioidosis, a disease that can be fatal in up to 95% of cases if left untreated. B. ubonensis is frequently misidentified as B. pseudomallei from soil samples using selective culturing on Ashdown's medium, reflecting both the shared environmental niche and morphological similarities of these species. Additionally, B. ubonensis shows potential as an important biocontrol agent in B. pseudomallei-endemic regions as certain strains possess antagonistic properties towards B. pseudomallei. Current methods for characterising B. ubonensis are laborious, time-consuming and costly, and as such this bacterium remains poorly studied. The aim of our study was to develop a rapid and inexpensive real-time PCR-based assay specific for B. ubonensis. We demonstrate that a novel B. ubonensis-specific assay, Bu550, accurately differentiates B. ubonensis from B. pseudomallei and other species that grow on selective Ashdown's agar. We anticipate that Bu550 will catalyse research on B. ubonensis by enabling rapid identification of this organism from Ashdown's-positive colonies that are not B. pseudomallei.

  17. Accurate spectroscopic characterization of ethyl mercaptan and dimethyl sulfide isotopologues: a route toward their astrophysical detection

    Energy Technology Data Exchange (ETDEWEB)

    Puzzarini, C. [Dipartimento di Chimica, " Giacomo Ciamician," Università diBologna, Via F. Selmi 2, I-40126 Bologna (Italy); Senent, M. L. [Departamento de Química y Física Teóricas, Institsuto de Estructura de la Materia, IEM-C.S.I.C., Serrano 121, Madrid E-28006 (Spain); Domínguez-Gómez, R. [Doctora Vinculada IEM-CSIC, Departamento de Ingeniería Civil, Cátedra de Química, E.U.I.T. Obras Públicas, Universidad Politécnica de Madrid (Spain); Carvajal, M. [Departamento de Física Aplicada, Facultad de Ciencias Experimentales, Unidad Asociada IEM-CSIC-U.Huelva, Universidad de Huelva, E-21071 Huelva (Spain); Hochlaf, M. [Université Paris-Est, Laboratoire de Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 boulevard Descartes, F-77454 Marne-la-Vallée (France); Al-Mogren, M. Mogren, E-mail: cristina.puzzarini@unibo.it, E-mail: senent@iem.cfmac.csic.es, E-mail: rosa.dominguez@upm.es, E-mail: miguel.carvajal@dfa.uhu.es, E-mail: majdi.hochlaf@u-pem.fr, E-mail: mmogren@ksu.edu.sa [Chemistry Department, Faculty of Science, King Saud University, PO Box 2455, Riyadh 11451 (Saudi Arabia)

    2014-11-20

    Using state-of-the-art computational methodologies, we predict a set of reliable rotational and torsional parameters for ethyl mercaptan and dimethyl sulfide monosubstituted isotopologues. This includes rotational, quartic, and sextic centrifugal-distortion constants, torsional levels, and torsional splittings. The accuracy of the present data was assessed from a comparison to the available experimental data. Generally, our computed parameters should help in the characterization and the identification of these organo-sulfur molecules in laboratory settings and in the interstellar medium.

  18. GPR-Based Landmine Detection and Identification Using Multiple Features

    Directory of Open Access Journals (Sweden)

    Kwang Hee Ko

    2012-01-01

    Full Text Available This paper presents a method to identify landmines in various burial conditions. A ground penetration radar is used to generate data set, which is then processed to reduce the ground effect and noise to obtain landmine signals. Principal components and Fourier coefficients of the landmine signals are computed, which are used as features of each landmine for detection and identification. A database is constructed based on the features of various types of landmines and the ground conditions, including the different levels of moisture and types of ground and the burial depths of the landmines. Detection and identification is performed by searching for features in the database. For a robust decision, the counting method and the Mahalanobis distance-based likelihood ratio test method are employed. Four landmines, different in size and material, are considered as examples that demonstrate the efficiency of the proposed method for detecting and identifying landmines.

  19. Modelling Visual Change Detection and Identification under Free Viewing Conditions.

    Science.gov (United States)

    McAnally, Ken; Martin, Russell

    2016-01-01

    We examined whether the abilities of observers to perform an analogue of a real-world monitoring task involving detection and identification of changes to items in a visual display could be explained better by models based on signal detection theory (SDT) or high threshold theory (HTT). Our study differed from most previous studies in that observers were allowed to inspect the initial display for 3s, simulating the long inspection times typical of natural viewing, and their eye movements were not constrained. For the majority of observers, combined change detection and identification performance was best modelled by a SDT-based process that assumed that memory resources were distributed across all eight items in our displays. Some observers required a parameter to allow for sometimes making random guesses at the identities of changes they had missed. However, the performance of a small proportion of observers was best explained by a HTT-based model that allowed for lapses of attention.

  20. Multistage audiovisual integration of speech: dissociating identification and detection

    DEFF Research Database (Denmark)

    Eskelund, Kasper; Tuomainen, Jyrki; Andersen, Tobias

    2011-01-01

    Speech perception integrates auditory and visual information. This is evidenced by the McGurk illusion where seeing the talking face influences the auditory phonetic percept and by the audiovisual detection advantage where seeing the talking face influences the detectability of the acoustic speech...... signal. Here we show that identification of phonetic content and detection can be dissociated as speech-specific and non-specific audiovisual integration effects. To this end, we employed synthetically modified stimuli, sine wave speech (SWS), which is an impoverished speech signal that only observers...

  1. Robust and accurate detection algorithm for multimode polymer optical FBG sensor system

    DEFF Research Database (Denmark)

    Ganziy, Denis; Jespersen, O.; Rose, B.

    2015-01-01

    We propose a novel dynamic gate algorithm (DGA) for robust and fast peak detection. The algorithm uses a threshold determined detection window and center of gravity algorithm with bias compensation. Our experiment demonstrates that the DGA method is fast and robust with better stability...

  2. Physicochemical property distributions for accurate and rapid pairwise protein homology detection

    Directory of Open Access Journals (Sweden)

    Oehmen Christopher S

    2010-03-01

    Full Text Available Abstract Background The challenge of remote homology detection is that many evolutionarily related sequences have very little similarity at the amino acid level. Kernel-based discriminative methods, such as support vector machines (SVMs, that use vector representations of sequences derived from sequence properties have been shown to have superior accuracy when compared to traditional approaches for the task of remote homology detection. Results We introduce a new method for feature vector representation based on the physicochemical properties of the primary protein sequence. A distribution of physicochemical property scores are assembled from 4-mers of the sequence and normalized based on the null distribution of the property over all possible 4-mers. With this approach there is little computational cost associated with the transformation of the protein into feature space, and overall performance in terms of remote homology detection is comparable with current state-of-the-art methods. We demonstrate that the features can be used for the task of pairwise remote homology detection with improved accuracy versus sequence-based methods such as BLAST and other feature-based methods of similar computational cost. Conclusions A protein feature method based on physicochemical properties is a viable approach for extracting features in a computationally inexpensive manner while retaining the sensitivity of SVM protein homology detection. Furthermore, identifying features that can be used for generic pairwise homology detection in lieu of family-based homology detection is important for applications such as large database searches and comparative genomics.

  3. Towards Accurate Node-Based Detection of P2P Botnets

    Directory of Open Access Journals (Sweden)

    Chunyong Yin

    2014-01-01

    Full Text Available Botnets are a serious security threat to the current Internet infrastructure. In this paper, we propose a novel direction for P2P botnet detection called node-based detection. This approach focuses on the network characteristics of individual nodes. Based on our model, we examine node’s flows and extract the useful features over a given time period. We have tested our approach on real-life data sets and achieved detection rates of 99-100% and low false positives rates of 0–2%. Comparison with other similar approaches on the same data sets shows that our approach outperforms the existing approaches.

  4. Detection and identification of human targets in radar data

    Science.gov (United States)

    Gürbüz, Sevgi Z.; Melvin, William L.; Williams, Douglas B.

    2007-04-01

    Radar offers unique advantages over other sensors, such as visual or seismic sensors, for human target detection. Many situations, especially military applications, prevent the placement of video cameras or implantment seismic sensors in the area being observed, because of security or other threats. However, radar can operate far away from potential targets, and functions during daytime as well as nighttime, in virtually all weather conditions. In this paper, we examine the problem of human target detection and identification using single-channel, airborne, synthetic aperture radar (SAR). Human targets are differentiated from other detected slow-moving targets by analyzing the spectrogram of each potential target. Human spectrograms are unique, and can be used not just to identify targets as human, but also to determine features about the human target being observed, such as size, gender, action, and speed. A 12-point human model, together with kinematic equations of motion for each body part, is used to calculate the expected target return and spectrogram. A MATLAB simulation environment is developed including ground clutter, human and non-human targets for the testing of spectrogram-based detection and identification algorithms. Simulations show that spectrograms have some ability to detect and identify human targets in low noise. An example gender discrimination system correctly detected 83.97% of males and 91.11% of females. The problems and limitations of spectrogram-based methods in high clutter environments are discussed. The SNR loss inherent to spectrogram-based methods is quantified. An alternate detection and identification method that will be used as a basis for future work is proposed.

  5. High Performance and Accurate Change Detection System for HyspIRI Missions Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose novel and high performance change detection algorithms to process HyspIRI data, which have been used for monitoring changes in vegetation, climate,...

  6. CYP450 phenotyping and accurate mass identification of metabolites of the 8-aminoquinoline, anti-malarial drug primaquine

    Directory of Open Access Journals (Sweden)

    Pybus Brandon S

    2012-08-01

    Full Text Available Abstract Background The 8-aminoquinoline (8AQ drug primaquine (PQ is currently the only approved drug effective against the persistent liver stage of the hypnozoite forming strains Plasmodium vivax and Plasmodium ovale as well as Stage V gametocytes of Plasmodium falciparum. To date, several groups have investigated the toxicity observed in the 8AQ class, however, exact mechanisms and/or metabolic species responsible for PQ’s haemotoxic and anti-malarial properties are not fully understood. Methods In the present study, the metabolism of PQ was evaluated using in vitro recombinant metabolic enzymes from the cytochrome P450 (CYP and mono-amine oxidase (MAO families. Based on this information, metabolite identification experiments were performed using nominal and accurate mass measurements. Results Relative activity factor (RAF-weighted intrinsic clearance values show the relative role of each enzyme to be MAO-A, 2C19, 3A4, and 2D6, with 76.1, 17.0, 5.2, and 1.7% contributions to PQ metabolism, respectively. CYP 2D6 was shown to produce at least six different oxidative metabolites along with demethylations, while MAO-A products derived from the PQ aldehyde, a pre-cursor to carboxy PQ. CYPs 2C19 and 3A4 produced only trace levels of hydroxylated species. Conclusions As a result of this work, CYP 2D6 and MAO-A have been implicated as the key enzymes associated with PQ metabolism, and metabolites previously identified as potentially playing a role in efficacy and haemolytic toxicity have been attributed to production via CYP 2D6 mediated pathways.

  7. Identification of Novel Perfluoroalkyl Ether Carboxylic Acids (PFECAs) and Sulfonic Acids (PFESAs) in Natural Waters Using Accurate Mass Time-of-Flight Mass Spectrometry (TOFMS).

    Science.gov (United States)

    Strynar, Mark; Dagnino, Sonia; McMahen, Rebecca; Liang, Shuang; Lindstrom, Andrew; Andersen, Erik; McMillan, Larry; Thurman, Michael; Ferrer, Imma; Ball, Carol

    2015-10-06

    Recent scientific scrutiny and concerns over exposure, toxicity, and risk have led to international regulatory efforts resulting in the reduction or elimination of certain perfluorinated compounds from various products and waste streams. Some manufacturers have started producing shorter chain per- and polyfluorinated compounds to try to reduce the potential for bioaccumulation in humans and wildlife. Some of these new compounds contain central ether oxygens or other minor modifications of traditional perfluorinated structures. At present, there has been very limited information published on these "replacement chemistries" in the peer-reviewed literature. In this study we used a time-of-flight mass spectrometry detector (LC-ESI-TOFMS) to identify fluorinated compounds in natural waters collected from locations with historical perfluorinated compound contamination. Our workflow for discovery of chemicals included sequential sampling of surface water for identification of potential sources, nontargeted TOFMS analysis, molecular feature extraction (MFE) of samples, and evaluation of features unique to the sample with source inputs. Specifically, compounds were tentatively identified by (1) accurate mass determination of parent and/or related adducts and fragments from in-source collision-induced dissociation (CID), (2) in-depth evaluation of in-source adducts formed during analysis, and (3) confirmation with authentic standards when available. We observed groups of compounds in homologous series that differed by multiples of CF2 (m/z 49.9968) or CF2O (m/z 65.9917). Compounds in each series were chromatographically separated and had comparable fragments and adducts produced during analysis. We detected 12 novel perfluoroalkyl ether carboxylic and sulfonic acids in surface water in North Carolina, USA using this approach. A key piece of evidence was the discovery of accurate mass in-source n-mer formation (H(+) and Na(+)) differing by m/z 21.9819, corresponding to the

  8. Hydrogen sulfide detection based on reflection: from a poison test approach of ancient China to single-cell accurate localization.

    Science.gov (United States)

    Kong, Hao; Ma, Zhuoran; Wang, Song; Gong, Xiaoyun; Zhang, Sichun; Zhang, Xinrong

    2014-08-05

    With the inspiration of an ancient Chinese poison test approach, we report a rapid hydrogen sulfide detection strategy in specific areas of live cells using silver needles with good spatial resolution of 2 × 2 μm(2). Besides the accurate-localization ability, this reflection-based strategy also has attractive merits of convenience and robust response when free pretreatment and short detection time are concerned. The success of endogenous H2S level evaluation in cellular cytoplasm and nuclear of human A549 cells promises the application potential of our strategy in scientific research and medical diagnosis.

  9. An accurate and reliable method for identification and quantification of fatty acids and trans fatty acids in food fats samples using gas chromatography

    Directory of Open Access Journals (Sweden)

    Jumat Salimon

    2017-05-01

    Full Text Available A method for the separation, identification and further quantification of fatty acids (FAs and trans fatty acids (TFAs by gas chromatography (GC using the combination of lipid extraction and derivatization with the base-catalysed method followed by trimethylsilyl-diazomethane (TMS-DM was developed. The proposed method was found to allow sensitive and accurate determination of a wide range of different types of FAs, including TFA isomers. The method was validated on real samples of dietary fat from hydrogenated edible oils (margarine and nine standard FAs as representatives of margarines. For this purpose, response linearity, limit of detection (LOD, limit of quantification (LOQ, precision and recovery (R% were all determined. Based on the results obtained, R-values from all the samples were revealed to be close to 100%, repeatability RSD ranged between 0.89% and 2.34%, and reproducibility RSD values ranged between 1.46% and 3.72%. The applicability of this method was demonstrated in four margarine samples and it was compared with the method used as reference. In general, the results proved that the proposed method is suitable for the analysis of FAs since it has shown higher effectiveness in TFA analysis than the classic methods. Thus, it could be an effective tool for analysing dietary fats and oils in complex mixtures of food products for the monitoring of low levels of FAs and TFA, and the control of labelling authenticity.

  10. Modeling inter-signal arrival times for accurate detection of CAN bus signal injection attacks

    Energy Technology Data Exchange (ETDEWEB)

    Moore, Michael Roy [ORNL; Bridges, Robert A [ORNL; Combs, Frank L [ORNL; Starr, Michael S [ORNL; Prowell, Stacy J [ORNL

    2017-01-01

    Modern vehicles rely on hundreds of on-board electronic control units (ECUs) communicating over in-vehicle networks. As external interfaces to the car control networks (such as the on-board diagnostic (OBD) port, auxiliary media ports, etc.) become common, and vehicle-to-vehicle / vehicle-to-infrastructure technology is in the near future, the attack surface for vehicles grows, exposing control networks to potentially life-critical attacks. This paper addresses the need for securing the CAN bus by detecting anomalous traffic patterns via unusual refresh rates of certain commands. While previous works have identified signal frequency as an important feature for CAN bus intrusion detection, this paper provides the first such algorithm with experiments on five attack scenarios. Our data-driven anomaly detection algorithm requires only five seconds of training time (on normal data) and achieves true positive / false discovery rates of 0.9998/0.00298, respectively (micro-averaged across the five experimental tests).

  11. Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing

    Science.gov (United States)

    Poleksic, Aleksandar; Yao, Yuan; Tong, Hanghang; Meng, Patrick; Xie, Lei

    2016-01-01

    Target-based screening is one of the major approaches in drug discovery. Besides the intended target, unexpected drug off-target interactions often occur, and many of them have not been recognized and characterized. The off-target interactions can be responsible for either therapeutic or side effects. Thus, identifying the genome-wide off-targets of lead compounds or existing drugs will be critical for designing effective and safe drugs, and providing new opportunities for drug repurposing. Although many computational methods have been developed to predict drug-target interactions, they are either less accurate than the one that we are proposing here or computationally too intensive, thereby limiting their capability for large-scale off-target identification. In addition, the performances of most machine learning based algorithms have been mainly evaluated to predict off-target interactions in the same gene family for hundreds of chemicals. It is not clear how these algorithms perform in terms of detecting off-targets across gene families on a proteome scale. Here, we are presenting a fast and accurate off-target prediction method, REMAP, which is based on a dual regularized one-class collaborative filtering algorithm, to explore continuous chemical space, protein space, and their interactome on a large scale. When tested in a reliable, extensive, and cross-gene family benchmark, REMAP outperforms the state-of-the-art methods. Furthermore, REMAP is highly scalable. It can screen a dataset of 200 thousands chemicals against 20 thousands proteins within 2 hours. Using the reconstructed genome-wide target profile as the fingerprint of a chemical compound, we predicted that seven FDA-approved drugs can be repurposed as novel anti-cancer therapies. The anti-cancer activity of six of them is supported by experimental evidences. Thus, REMAP is a valuable addition to the existing in silico toolbox for drug target identification, drug repurposing, phenotypic screening, and

  12. Deep Sequencing Analyses of Low Density Microbial Communities: Working at the Boundary of Accurate Microbiota Detection

    Science.gov (United States)

    Biesbroek, Giske; Sanders, Elisabeth A. M.; Roeselers, Guus; Wang, Xinhui; Caspers, Martien P. M.; Trzciński, Krzysztof

    2012-01-01

    Introduction Accurate analyses of microbiota composition of low-density communities (103–104 bacteria/sample) can be challenging. Background DNA from chemicals and consumables, extraction biases as well as differences in PCR efficiency can significantly interfere with microbiota assessment. This study was aiming to establish protocols for accurate microbiota analysis at low microbial density. Methods To examine possible effects of bacterial density on microbiota analyses we compared microbiota profiles of serial diluted saliva and low (nares, nasopharynx) and high-density (oropharynx) upper airway communities in four healthy individuals. DNA was extracted with four different extraction methods (Epicentre Masterpure, Qiagen DNeasy, Mobio Powersoil and a phenol bead-beating protocol combined with Agowa-Mag-mini). Bacterial DNA recovery was analysed by 16S qPCR and microbiota profiles through GS-FLX-Titanium-Sequencing of 16S rRNA gene amplicons spanning the V5–V7 regions. Results Lower template concentrations significantly impacted microbiota profiling results. With higher dilutions, low abundant species were overrepresented. In samples of bacteria per ml, e.g. DNA DNA extraction method determined if DNA levels were below or above 1 pg/µl and, together with lysis preferences per method, had profound impact on microbiota analyses in both relative abundance as well as representation of species. Conclusion This study aimed to interpret microbiota analyses of low-density communities. Bacterial density seemed to interfere with microbiota analyses at bacteria per ml or DNA <1 pg/µl. We therefore recommend this threshold for working with low density materials. This study underlines that bias reduction is crucial for adequate profiling of especially low-density bacterial communities. PMID:22412957

  13. Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection.

    Directory of Open Access Journals (Sweden)

    Giske Biesbroek

    Full Text Available INTRODUCTION: Accurate analyses of microbiota composition of low-density communities (10(3-10(4 bacteria/sample can be challenging. Background DNA from chemicals and consumables, extraction biases as well as differences in PCR efficiency can significantly interfere with microbiota assessment. This study was aiming to establish protocols for accurate microbiota analysis at low microbial density. METHODS: To examine possible effects of bacterial density on microbiota analyses we compared microbiota profiles of serial diluted saliva and low (nares, nasopharynx and high-density (oropharynx upper airway communities in four healthy individuals. DNA was extracted with four different extraction methods (Epicentre Masterpure, Qiagen DNeasy, Mobio Powersoil and a phenol bead-beating protocol combined with Agowa-Mag-mini. Bacterial DNA recovery was analysed by 16S qPCR and microbiota profiles through GS-FLX-Titanium-Sequencing of 16S rRNA gene amplicons spanning the V5-V7 regions. RESULTS: Lower template concentrations significantly impacted microbiota profiling results. With higher dilutions, low abundant species were overrepresented. In samples of <10(5 bacteria per ml, e.g. DNA <1 pg/µl, microbiota profiling deviated from the original sample and other dilutions showing a significant increase in the taxa Proteobacteria and decrease in Bacteroidetes. In similar low density samples, DNA extraction method determined if DNA levels were below or above 1 pg/µl and, together with lysis preferences per method, had profound impact on microbiota analyses in both relative abundance as well as representation of species. CONCLUSION: This study aimed to interpret microbiota analyses of low-density communities. Bacterial density seemed to interfere with microbiota analyses at < than 10(6 bacteria per ml or DNA <1 pg/µl. We therefore recommend this threshold for working with low density materials. This study underlines that bias reduction is crucial for adequate

  14. How Accurately Can Your Wrist Device Recognize Daily Activities and Detect Falls?

    Directory of Open Access Journals (Sweden)

    Martin Gjoreski

    2016-06-01

    Full Text Available Although wearable accelerometers can successfully recognize activities and detect falls, their adoption in real life is low because users do not want to wear additional devices. A possible solution is an accelerometer inside a wrist device/smartwatch. However, wrist placement might perform poorly in terms of accuracy due to frequent random movements of the hand. In this paper we perform a thorough, large-scale evaluation of methods for activity recognition and fall detection on four datasets. On the first two we showed that the left wrist performs better compared to the dominant right one, and also better compared to the elbow and the chest, but worse compared to the ankle, knee and belt. On the third (Opportunity dataset, our method outperformed the related work, indicating that our feature-preprocessing creates better input data. And finally, on a real-life unlabeled dataset the recognized activities captured the subject’s daily rhythm and activities. Our fall-detection method detected all of the fast falls and minimized the false positives, achieving 85% accuracy on the first dataset. Because the other datasets did not contain fall events, only false positives were evaluated, resulting in 9 for the second, 1 for the third and 15 for the real-life dataset (57 days data.

  15. How Accurately Can Your Wrist Device Recognize Daily Activities and Detect Falls?

    Science.gov (United States)

    Gjoreski, Martin; Gjoreski, Hristijan; Luštrek, Mitja; Gams, Matjaž

    2016-06-01

    Although wearable accelerometers can successfully recognize activities and detect falls, their adoption in real life is low because users do not want to wear additional devices. A possible solution is an accelerometer inside a wrist device/smartwatch. However, wrist placement might perform poorly in terms of accuracy due to frequent random movements of the hand. In this paper we perform a thorough, large-scale evaluation of methods for activity recognition and fall detection on four datasets. On the first two we showed that the left wrist performs better compared to the dominant right one, and also better compared to the elbow and the chest, but worse compared to the ankle, knee and belt. On the third (Opportunity) dataset, our method outperformed the related work, indicating that our feature-preprocessing creates better input data. And finally, on a real-life unlabeled dataset the recognized activities captured the subject's daily rhythm and activities. Our fall-detection method detected all of the fast falls and minimized the false positives, achieving 85% accuracy on the first dataset. Because the other datasets did not contain fall events, only false positives were evaluated, resulting in 9 for the second, 1 for the third and 15 for the real-life dataset (57 days data).

  16. A method for accurate detection of genomic microdeletions using real-time quantitative PCR

    Directory of Open Access Journals (Sweden)

    Bassett Anne S

    2005-12-01

    Full Text Available Abstract Background Quantitative Polymerase Chain Reaction (qPCR is a well-established method for quantifying levels of gene expression, but has not been routinely applied to the detection of constitutional copy number alterations of human genomic DNA. Microdeletions or microduplications of the human genome are associated with a variety of genetic disorders. Although, clinical laboratories routinely use fluorescence in situ hybridization (FISH to identify such cryptic genomic alterations, there remains a significant number of individuals in which constitutional genomic imbalance is suspected, based on clinical parameters, but cannot be readily detected using current cytogenetic techniques. Results In this study, a novel application for real-time qPCR is presented that can be used to reproducibly detect chromosomal microdeletions and microduplications. This approach was applied to DNA from a series of patient samples and controls to validate genomic copy number alteration at cytoband 22q11. The study group comprised 12 patients with clinical symptoms of chromosome 22q11 deletion syndrome (22q11DS, 1 patient trisomic for 22q11 and 4 normal controls. 6 of the patients (group 1 had known hemizygous deletions, as detected by standard diagnostic FISH, whilst the remaining 6 patients (group 2 were classified as 22q11DS negative using the clinical FISH assay. Screening of the patients and controls with a set of 10 real time qPCR primers, spanning the 22q11.2-deleted region and flanking sequence, confirmed the FISH assay results for all patients with 100% concordance. Moreover, this qPCR enabled a refinement of the region of deletion at 22q11. Analysis of DNA from chromosome 22 trisomic sample demonstrated genomic duplication within 22q11. Conclusion In this paper we present a qPCR approach for the detection of chromosomal microdeletions and microduplications. The strategic use of in silico modelling for qPCR primer design to avoid regions of repetitive

  17. Multistage audiovisual integration of speech: dissociating identification and detection

    DEFF Research Database (Denmark)

    Eskelund, Kasper; Tuomainen, Jyrki; Andersen, Tobias

    2011-01-01

    Speech perception integrates auditory and visual information. This is evidenced by the McGurk illusion where seeing the talking face influences the auditory phonetic percept and by the audiovisual detection advantage where seeing the talking face influences the detectability of the acoustic speech...... signal. Here we show that identification of phonetic content and detection can be dissociated as speech-specific and non-specific audiovisual integration effects. To this end, we employed synthetically modified stimuli, sine wave speech (SWS), which is an impoverished speech signal that only observers...... informed of its speech-like nature recognize as speech. While the McGurk illusion only occurred for informed observers the audiovisual detection advantage occurred for naïve observers as well. This finding supports a multi-stage account of audiovisual integration of speech in which the many attributes...

  18. Combining computer algorithms with experimental approaches permits the rapid and accurate identification of T cell epitopes from defined antigens.

    Science.gov (United States)

    Schirle, M; Weinschenk, T; Stevanović, S

    2001-11-01

    The identification of T cell epitopes from immunologically relevant antigens remains a critical step in the development of vaccines and methods for monitoring of T cell responses. This review presents an overview of strategies that employ computer algorithms for the selection of candidate peptides from defined proteins and subsequent verification of their in vivo relevance by experimental approaches. Several computer algorithms are currently being used for epitope prediction of various major histocompatibility complex (MHC) class I and II molecules, based either on the analysis of natural MHC ligands or on the binding properties of synthetic peptides. Moreover, the analysis of proteasomal digests of peptides and whole proteins has led to the development of algorithms for the prediction of proteasomal cleavages. In order to verify the generation of the predicted peptides during antigen processing in vivo as well as their immunogenic potential, several experimental approaches have been pursued in the recent past. Mass spectrometry-based bioanalytical approaches have been used specifically to detect predicted peptides among isolated natural ligands. Other strategies employ various methods for the stimulation of primary T cell responses against the predicted peptides and subsequent testing of the recognition pattern towards target cells that express the antigen.

  19. Dynamic Bayesian Network for Accurate Detection of Peptides from Tandem Mass Spectra.

    Science.gov (United States)

    Halloran, John T; Bilmes, Jeff A; Noble, William S

    2016-08-05

    A central problem in mass spectrometry analysis involves identifying, for each observed tandem mass spectrum, the corresponding generating peptide. We present a dynamic Bayesian network (DBN) toolkit that addresses this problem by using a machine learning approach. At the heart of this toolkit is a DBN for Rapid Identification (DRIP), which can be trained from collections of high-confidence peptide-spectrum matches (PSMs). DRIP's score function considers fragment ion matches using Gaussians rather than fixed fragment-ion tolerances and also finds the optimal alignment between the theoretical and observed spectrum by considering all possible alignments, up to a threshold that is controlled using a beam-pruning algorithm. This function not only yields state-of-the art database search accuracy but also can be used to generate features that significantly boost the performance of the Percolator postprocessor. The DRIP software is built upon a general purpose DBN toolkit (GMTK), thereby allowing a wide variety of options for user-specific inference tasks as well as facilitating easy modifications to the DRIP model in future work. DRIP is implemented in Python and C++ and is available under Apache license at http://melodi-lab.github.io/dripToolkit .

  20. Accurate Modeling of The Siemens S7 SCADA Protocol For Intrusion Detection And Digital Forensic

    Directory of Open Access Journals (Sweden)

    Amit Kleinmann

    2014-09-01

    Full Text Available The Siemens S7 protocol is commonly used in SCADA systems for communications between a Human Machine Interface (HMI and the Programmable Logic Controllers (PLCs. This paper presents a model-based Intrusion Detection Systems (IDS designed for S7 networks. The approach is based on the key observation that S7 traffic to and from a specific PLC is highly periodic; as a result, each HMI-PLC channel can be modeled using its own unique Deterministic Finite Automaton (DFA. The resulting DFA-based IDS is very sensitive and is able to flag anomalies such as a message appearing out of its position in the normal sequence or a message referring to a single unexpected bit. The intrusion detection approach was evaluated on traffic from two production systems. Despite its high sensitivity, the system had a very low false positive rate - over 99.82% of the traffic was identified as normal.

  1. QuartetS: A Fast and Accurate Algorithm for Large-Scale Orthology Detection

    Science.gov (United States)

    2011-01-01

    genomic data to reveal the molecular functions of genes, their essentiality to a species survival and their connections to the virulence of pathogenic...i.e. orthologs) across different species often share equivalent molecular func- tions, orthology detection methods have become pivotal in helping...versus proteins. Genetica , 118, 209–216. 4. Serres,M.H., Kerr,A.R., McCormack,T.J. and Riley,M. (2009) Evolution by leaps: gene duplication in bacteria

  2. High resolution melting analysis: a rapid and accurate method to detect CALR mutations.

    Directory of Open Access Journals (Sweden)

    Cristina Bilbao-Sieyro

    Full Text Available The recent discovery of CALR mutations in essential thrombocythemia (ET and primary myelofibrosis (PMF patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN. We tested the feasibility of high-resolution melting (HRM as a screening method for rapid detection of CALR mutations.CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET.Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34, 14% of persistent thrombocytosis suggestive of MPN (3/21 and none of the secondary thrombocytosis (0/98. Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%.This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations.

  3. High Resolution Melting Analysis: A Rapid and Accurate Method to Detect CALR Mutations

    Science.gov (United States)

    Moreno, Melania; Torres, Laura; Santana-Lopez, Gonzalo; Rodriguez-Medina, Carlos; Perera, María; Bellosillo, Beatriz; de la Iglesia, Silvia; Molero, Teresa; Gomez-Casares, Maria Teresa

    2014-01-01

    Background The recent discovery of CALR mutations in essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN). We tested the feasibility of high-resolution melting (HRM) as a screening method for rapid detection of CALR mutations. Methods CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET. Results Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34), 14% of persistent thrombocytosis suggestive of MPN (3/21) and none of the secondary thrombocytosis (0/98). Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%. Conclusions This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations. PMID:25068507

  4. Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA

    Directory of Open Access Journals (Sweden)

    Chan Alan

    2006-06-01

    Full Text Available Abstract Background Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length. Results In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A. Conclusion Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.

  5. Ultrasound detection and identification of cosmetic fillers in the skin

    DEFF Research Database (Denmark)

    Wortsman, X.; Wortsman, J.; Orlandi, C.

    2012-01-01

    Background While the incidence of cosmetic filler injections is rising world-wide, neither exact details of the procedure nor the agent used are always reported or remembered by the patients. Thus, although complications are reportedly rare, availability of a precise diagnostic tool to detect...... cutaneous filler deposits could help clarify the association between the procedure and the underlying pathology. Objectives The aim of this study was to evaluate cutaneous sonography in the detection and identification of cosmetic fillers deposits and, describe dermatological abnormalities found associated...... with the presence of those agents. Methods We used ultrasound in a porcine skin model to determine the sonographic characteristics of commonly available filler agents, and subsequently applied the analysis to detect and identify cosmetic fillers among patients referred for skin disorders. Results Fillers...

  6. Blood Pressure over Height Ratios: Simple and Accurate Method of Detecting Elevated Blood Pressure in Children

    Directory of Open Access Journals (Sweden)

    Ovidiu Galescu

    2012-01-01

    Full Text Available Background. Blood pressure (BP percentiles in childhood are assessed according to age, gender, and height. Objective. To create a simple BP/height ratio for both systolic BP (SBP and diastolic BP (DBP. To study the relationship between BP/height ratios and corresponding BP percentiles in children. Methods. We analyzed data on height and BP from 2006-2007 NHANES data. BP percentiles were calculated for 3775 children. Receiver-operating characteristic (ROC curve analyses were performed to calculate sensitivity and specificity of BP/height ratios as diagnostic tests for elevated BP (>90%. Correlation analysis was performed between BP percentiles and BP/height ratios. Results. The average age was 12.54 ± 2.67 years. SBP/height and DBP/height ratios strongly correlated with SBP & DBP percentiles in both boys (<0.001, 2=0.85, 2=0.86 and girls (<0.001, 2=0.85, 2=0.90. The cutoffs of SBP/height and DBP/height ratios in boys were ≥0.75 and ≥0.46, respectively; in girls the ratios were ≥0.75 and ≥0.48, respectively with sensitivity and specificity in range of 83–100%. Conclusion. BP/height ratios are simple with high sensitivity and specificity to detect elevated BP in children. These ratios can be easily used in routine medical care of children.

  7. A new hybrid intelligent system for accurate detection of Parkinson's disease.

    Science.gov (United States)

    Hariharan, M; Polat, Kemal; Sindhu, R

    2014-03-01

    Elderly people are commonly affected by Parkinson's disease (PD) which is one of the most common neurodegenerative disorders due to the loss of dopamine-producing brain cells. People with PD's (PWP) may have difficulty in walking, talking or completing other simple tasks. Variety of medications is available to treat PD. Recently, researchers have found that voice signals recorded from the PWP is becoming a useful tool to differentiate them from healthy controls. Several dysphonia features, feature reduction/selection techniques and classification algorithms were proposed by researchers in the literature to detect PD. In this paper, hybrid intelligent system is proposed which includes feature pre-processing using Model-based clustering (Gaussian mixture model), feature reduction/selection using principal component analysis (PCA), linear discriminant analysis (LDA), sequential forward selection (SFS) and sequential backward selection (SBS), and classification using three supervised classifiers such as least-square support vector machine (LS-SVM), probabilistic neural network (PNN) and general regression neural network (GRNN). PD dataset was used from University of California-Irvine (UCI) machine learning database. The strength of the proposed method has been evaluated through several performance measures. The experimental results show that the combination of feature pre-processing, feature reduction/selection methods and classification gives a maximum classification accuracy of 100% for the Parkinson's dataset. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  8. Accurate determination of the diffusion coefficient of proteins by Fourier analysis with whole column imaging detection.

    Science.gov (United States)

    Zarabadi, Atefeh S; Pawliszyn, Janusz

    2015-02-17

    Analysis in the frequency domain is considered a powerful tool to elicit precise information from spectroscopic signals. In this study, the Fourier transformation technique is employed to determine the diffusion coefficient (D) of a number of proteins in the frequency domain. Analytical approaches are investigated for determination of D from both experimental and data treatment viewpoints. The diffusion process is modeled to calculate diffusion coefficients based on the Fourier transformation solution to Fick's law equation, and its results are compared to time domain results. The simulations characterize optimum spatial and temporal conditions and demonstrate the noise tolerance of the method. The proposed model is validated by its application for the electropherograms from the diffusion path of a set of proteins. Real-time dynamic scanning is conducted to monitor dispersion by employing whole column imaging detection technology in combination with capillary isoelectric focusing (CIEF) and the imaging plug flow (iPF) experiment. These experimental techniques provide different peak shapes, which are utilized to demonstrate the Fourier transformation ability in extracting diffusion coefficients out of irregular shape signals. Experimental results confirmed that the Fourier transformation procedure substantially enhanced the accuracy of the determined values compared to those obtained in the time domain.

  9. Modelling Visual Change Detection and Identification under Free Viewing Conditions.

    Directory of Open Access Journals (Sweden)

    Ken McAnally

    Full Text Available We examined whether the abilities of observers to perform an analogue of a real-world monitoring task involving detection and identification of changes to items in a visual display could be explained better by models based on signal detection theory (SDT or high threshold theory (HTT. Our study differed from most previous studies in that observers were allowed to inspect the initial display for 3s, simulating the long inspection times typical of natural viewing, and their eye movements were not constrained. For the majority of observers, combined change detection and identification performance was best modelled by a SDT-based process that assumed that memory resources were distributed across all eight items in our displays. Some observers required a parameter to allow for sometimes making random guesses at the identities of changes they had missed. However, the performance of a small proportion of observers was best explained by a HTT-based model that allowed for lapses of attention.

  10. On-line detecting of transformer winding deformation based on parameter identification of leakage inductance

    Institute of Scientific and Technical Information of China (English)

    Hao Zhiguo; Zhang Baohui; Li Peng

    2007-01-01

    Transformers are required to demonstrate the ability to withstand short circuit currents. Over currents caused by short circuit can give rise to windings deformation. In this paper, a novel method is proposed to monitor the state of transformer windings, which is achieved through on-line detecting the leakage inductance of the windings. Specifically, the mathematical model is established for on-line identifying the leakage inductance of the windings by applying least square algorithm (LSA) to the equivalent circuit equations. The effect of measurement and model inaccuracy on the identification error is analyzed, and the corrected model is also given to decrease these adverse effect on the results. Finally, dynamic test is carried out to verify our method. The test results clearly show that our method is very accurate even under the fluctuation of load or power factor. Therefore, our method can be effectively used to on-line detect the windings deformation.

  11. HEASARC Astronomical Archive: GLIESE2MAS - Gliese Catalog Stars with Accurate Coordinates and 2MASS Cross-Identifications

    Data.gov (United States)

    National Aeronautics and Space Administration — This table contains precise epoch 2000 coordinates and cross-identifications to sources in the 2MASS Point Source Catalog for nearly all stars in the Gliese,...

  12. Detection and identification of speech sounds using cortical activity patterns.

    Science.gov (United States)

    Centanni, T M; Sloan, A M; Reed, A C; Engineer, C T; Rennaker, R L; Kilgard, M P

    2014-01-31

    We have developed a classifier capable of locating and identifying speech sounds using activity from rat auditory cortex with an accuracy equivalent to behavioral performance and without the need to specify the onset time of the speech sounds. This classifier can identify speech sounds from a large speech set within 40 ms of stimulus presentation. To compare the temporal limits of the classifier to behavior, we developed a novel task that requires rats to identify individual consonant sounds from a stream of distracter consonants. The classifier successfully predicted the ability of rats to accurately identify speech sounds for syllable presentation rates up to 10 syllables per second (up to 17.9 ± 1.5 bits/s), which is comparable to human performance. Our results demonstrate that the spatiotemporal patterns generated in primary auditory cortex can be used to quickly and accurately identify consonant sounds from a continuous speech stream without prior knowledge of the stimulus onset times. Improved understanding of the neural mechanisms that support robust speech processing in difficult listening conditions could improve the identification and treatment of a variety of speech-processing disorders. Copyright © 2013 IBRO. Published by Elsevier Ltd. All rights reserved.

  13. Rapid and high-throughput pan-Orthopoxvirus detection and identification using PCR and mass spectrometry.

    Science.gov (United States)

    Eshoo, Mark W; Whitehouse, Chris A; Nalca, Aysegul; Zoll, Scott; Ecker, Joseph A; Hall, Thomas A; Pennella, Thuy-Trang D; Duncan, David D; Desai, Anjali; Moradi, Emily K; Rudnick, Karl; Libby, Brian; Ranken, Raymond; Sampath, Rangarajan; Hofstadler, Steven A; Ecker, David J; Blyn, Lawrence B

    2009-07-22

    The genus Orthopoxvirus contains several species of related viruses, including the causative agent of smallpox (Variola virus). In addition to smallpox, several other members of the genus are capable of causing human infection, including monkeypox, cowpox, and other zoonotic rodent-borne poxviruses. Therefore, a single assay that can accurately identify all orthopoxviruses could provide a valuable tool for rapid broad orthopovirus identification. We have developed a pan-Orthopoxvirus assay for identification of all members of the genus based on four PCR reactions targeting Orthopoxvirus DNA and RNA helicase and polymerase genes. The amplicons are detected using electrospray ionization-mass spectrometry (PCR/ESI-MS) on the Ibis T5000 system. We demonstrate that the assay can detect and identify a diverse collection of orthopoxviruses, provide sub-species information and characterize viruses from the blood of rabbitpox infected rabbits. The assay is sensitive at the stochastic limit of PCR and detected virus in blood containing approximately six plaque-forming units per milliliter from a rabbitpox virus-infected rabbit.

  14. Rapid and high-throughput pan-Orthopoxvirus detection and identification using PCR and mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Mark W Eshoo

    Full Text Available The genus Orthopoxvirus contains several species of related viruses, including the causative agent of smallpox (Variola virus. In addition to smallpox, several other members of the genus are capable of causing human infection, including monkeypox, cowpox, and other zoonotic rodent-borne poxviruses. Therefore, a single assay that can accurately identify all orthopoxviruses could provide a valuable tool for rapid broad orthopovirus identification. We have developed a pan-Orthopoxvirus assay for identification of all members of the genus based on four PCR reactions targeting Orthopoxvirus DNA and RNA helicase and polymerase genes. The amplicons are detected using electrospray ionization-mass spectrometry (PCR/ESI-MS on the Ibis T5000 system. We demonstrate that the assay can detect and identify a diverse collection of orthopoxviruses, provide sub-species information and characterize viruses from the blood of rabbitpox infected rabbits. The assay is sensitive at the stochastic limit of PCR and detected virus in blood containing approximately six plaque-forming units per milliliter from a rabbitpox virus-infected rabbit.

  15. Robust Principal Component Test in Gross Error Detection and Identification

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Principle component analysis (PCA) based chi-square test is more sensitive to subtle gross errors and has greater power to correctly detect gross errors than classical chi-square test. However, classical principal component test (PCT) is non-robust and can be very sensitive to one or more outliers. In this paper, a Huber function liked robust weight factor was added in the collective chi-square test to eliminate the influence of gross errors on the PCT. Meanwhile, robust chi-square test was applied to modified simultaneous estimation of gross error (MSEGE) strategy to detect and identify multiple gross errors. Simulation results show that the proposed robust test can reduce the possibility of type Ⅱ errors effectively. Adding robust chi-square test into MSEGE does not obviously improve the power of multiple gross error identification, the proposed approach considers the influence of outliers on hypothesis statistic test and is more reasonable.

  16. New Biometric Approaches for Improved Person Identification Using Facial Detection

    Directory of Open Access Journals (Sweden)

    V.K. NARENDIRA KUMAR

    2012-08-01

    Full Text Available Biometrics is measurable characteristics specific to an individual. Face detection has diverse applications especially as an identification solution which can meet the crying needs in security areas. While traditionally 2D images of faces have been used, 3D scans that contain both 3D data and registered color are becoming easier to acquire. Before 3D face images can be used to identify an individual, they require some form of initial alignment information, typically based on facial feature locations. We follow this by a discussion of the algorithms performance when constrained to frontal images and an analysis of its performance on a more complex dataset with significant head pose variation using 3D face data for detection provides a promising route to improved performance.

  17. Identification of Escherichia coli O157 by using a novel colorimetric detection method with DNA microarrays.

    Science.gov (United States)

    Quiñones, Beatriz; Swimley, Michelle S; Taylor, Amber W; Dawson, Erica D

    2011-06-01

    Shiga toxin-producing Escherichia coli O157 is a leading cause of foodborne illness worldwide. To evaluate better methods to rapidly detect and genotype E. coli O157 strains, the present study evaluated the use of ampliPHOX, a novel colorimetric detection method based on photopolymerization, for pathogen identification with DNA microarrays. A low-density DNA oligonucleotide microarray was designed to target stx1 and stx2 genes encoding Shiga toxin production, the eae gene coding for adherence membrane protein, and the per gene encoding the O157-antigen perosamine synthetase. Results from the validation experiments demonstrated that the use of ampliPHOX allowed the accurate genotyping of the tested E. coli strains, and positive hybridization signals were observed for only probes targeting virulence genes present in the reference strains. Quantification showed that the average signal-to-noise ratio values ranged from 47.73 ± 7.12 to 76.71 ± 8.33, whereas average signal-to-noise ratio values below 2.5 were determined for probes where no polymer was formed due to lack of specific hybridization. Sensitivity tests demonstrated that the sensitivity threshold for E. coli O157 detection was 100-1000 CFU/mL. Thus, the use of DNA microarrays in combination with photopolymerization allowed the rapid and accurate genotyping of E. coli O157 strains.

  18. Patient identification errors: the detective in the laboratory.

    Science.gov (United States)

    Salinas, Maria; López-Garrigós, Maite; Lillo, Rosa; Gutiérrez, Mercedes; Lugo, Javier; Leiva-Salinas, Carlos

    2013-11-01

    The eradication of errors regarding patients' identification is one of the main goals for safety improvement. As clinical laboratory intervenes in 70% of clinical decisions, laboratory safety is crucial in patient safety. We studied the number of Laboratory Information System (LIS) demographic data errors registered in our laboratory during one year. The laboratory attends a variety of inpatients and outpatients. The demographic data of outpatients is registered in the LIS, when they present to the laboratory front desk. The requests from the primary care centers (PCC) are made electronically by the general practitioner. A manual step is always done at the PCC to conciliate the patient identification number in the electronic request with the one in the LIS. Manual registration is done through hospital information system demographic data capture when patient's medical record number is registered in LIS. Laboratory report is always sent out electronically to the patient's electronic medical record. Daily, every demographic data in LIS is manually compared to the request form to detect potential errors. Fewer errors were committed when electronic order was used. There was great error variability between PCC when using the electronic order. LIS demographic data manual registration errors depended on patient origin and test requesting method. Even when using the electronic approach, errors were detected. There was a great variability between PCC even when using this electronic modality; this suggests that the number of errors is still dependent on the personnel in charge of the technology. © 2013.

  19. Creation of an Accurate Algorithm to Detect Snellen Best Documented Visual Acuity from Ophthalmology Electronic Health Record Notes.

    Science.gov (United States)

    Mbagwu, Michael; French, Dustin D; Gill, Manjot; Mitchell, Christopher; Jackson, Kathryn; Kho, Abel; Bryar, Paul J

    2016-05-04

    Visual acuity is the primary measure used in ophthalmology to determine how well a patient can see. Visual acuity for a single eye may be recorded in multiple ways for a single patient visit (eg, Snellen vs. Jäger units vs. font print size), and be recorded for either distance or near vision. Capturing the best documented visual acuity (BDVA) of each eye in an individual patient visit is an important step for making electronic ophthalmology clinical notes useful in research. Currently, there is limited methodology for capturing BDVA in an efficient and accurate manner from electronic health record (EHR) notes. We developed an algorithm to detect BDVA for right and left eyes from defined fields within electronic ophthalmology clinical notes. We designed an algorithm to detect the BDVA from defined fields within 295,218 ophthalmology clinical notes with visual acuity data present. About 5668 unique responses were identified and an algorithm was developed to map all of the unique responses to a structured list of Snellen visual acuities. Visual acuity was captured from a total of 295,218 ophthalmology clinical notes during the study dates. The algorithm identified all visual acuities in the defined visual acuity section for each eye and returned a single BDVA for each eye. A clinician chart review of 100 random patient notes showed a 99% accuracy detecting BDVA from these records and 1% observed error. Our algorithm successfully captures best documented Snellen distance visual acuity from ophthalmology clinical notes and transforms a variety of inputs into a structured Snellen equivalent list. Our work, to the best of our knowledge, represents the first attempt at capturing visual acuity accurately from large numbers of electronic ophthalmology notes. Use of this algorithm can benefit research groups interested in assessing visual acuity for patient centered outcome. All codes used for this study are currently available, and will be made available online at https://phekb.org.

  20. Fast Photon Detection for Particle Identification with COMPASS RICH-1

    CERN Document Server

    Abbon, P; Angerer, H; Apollonio, M; Birsa, R; Bordalo, P; Bradamante, Franco; Bressan, A; Busso, L; Chiosso, M; Ciliberti, P; Colantoni, M L; Costa, S; Dalla Torre, S; Dafni, T; Delagnes, E; Deschamps, H; Díaz, V; Dibiase, N; Duic, V; Eyrich, W; Faso, D; Ferrero, A; Finger, M; Fischer, H; Gerassimov, S; Giorgi, M; Gobbo, B; Hagemann, R; Von Harrach, D; Heinsius, F H; Horikawa, S; Joosten, R; Ketzer, B; Königsmann, K C; Kolosov, V N; Konorov, I; Kramer, Daniel; Kunne, Fabienne; Lehmann, A; Levorato, S; Maggiora, A; Magnon, A; Mann, A; Martin, A; Menon, G; Mutter, A; Nahle, O; Nerling, F; Neyret, D; Pagano, P; Panebianco, S; Panzieri, D; Paul, S; Pesaro, G; Polak, J; Rebourgeard, P; Robinet, F; Rocco, E; Schiavon, Paolo; Schill, C; Schroder, W; Silva, L; Slunecka, M; Sozzi, F; Steiger, L; Sulc, M; Svec, M; Tessarotto, F; Teufel, A; Wollny, H; COMPASS RICH Upgrade Group

    2007-01-01

    Particle identification at high rates is an important challenge for many current and future high-energy physics experiments. The upgrade of the COMPASS RICH-1 detector requires a new technique for Cherenkov photon detection at count rates of several $10^6$ per channel in the central detector region, and a read-out system allowing for trigger rates of up to 100 kHz. To cope with these requirements, the photon detectors in the central region have been replaced with the detection system described in this paper. In the peripheral regions, the existing multi-wire proportional chambers with CsI photocathode are now read out via a new system employing APV pre-amplifiers and flash ADC chips. The new detection system consists of multi-anode photomultiplier tubes (MAPMT) and fast read-out electronics based on the MAD4 discriminator and the F1-TDC chip. The RICH-1 is in operation in its upgraded version for the 2006 CERN SPS run. We present the photon detection design, constructive aspects and the first Cherenkov light ...

  1. Rapid and accurate identification of Mycobacterium tuberculosis complex and common non-tuberculous mycobacteria by multiplex real-time PCR targeting different housekeeping genes.

    Science.gov (United States)

    Nasr Esfahani, Bahram; Rezaei Yazdi, Hadi; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Zarkesh Esfahani, Hamid

    2012-11-01

    Rapid and accurate identification of mycobacteria isolates from primary culture is important due to timely and appropriate antibiotic therapy. Conventional methods for identification of Mycobacterium species based on biochemical tests needs several weeks and may remain inconclusive. In this study, a novel multiplex real-time PCR was developed for rapid identification of Mycobacterium genus, Mycobacterium tuberculosis complex (MTC) and the most common non-tuberculosis mycobacteria species including M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and the M. gordonae in three reaction tubes but under same PCR condition. Genetic targets for primer designing included the 16S rDNA gene, the dnaJ gene, the gyrB gene and internal transcribed spacer (ITS). Multiplex real-time PCR was setup with reference Mycobacterium strains and was subsequently tested with 66 clinical isolates. Results of multiplex real-time PCR were analyzed with melting curves and melting temperature (T (m)) of Mycobacterium genus, MTC, and each of non-tuberculosis Mycobacterium species were determined. Multiplex real-time PCR results were compared with amplification and sequencing of 16S-23S rDNA ITS for identification of Mycobacterium species. Sensitivity and specificity of designed primers were each 100 % for MTC, M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and M. gordonae. Sensitivity and specificity of designed primer for genus Mycobacterium was 96 and 100 %, respectively. According to the obtained results, we conclude that this multiplex real-time PCR with melting curve analysis and these novel primers can be used for rapid and accurate identification of genus Mycobacterium, MTC, and the most common non-tuberculosis Mycobacterium species.

  2. Identification of anabolic steroids and derivatives using bioassay-guided fractionation,UHPLC/TOFMS analysis and accurate mass database searching

    NARCIS (Netherlands)

    Peters, R.J.B.; Rijk, J.C.W.; Bovee, T.F.H.; Nijrolder, A.W.J.M.; Lommen, A.; Nielen, M.W.F.

    2010-01-01

    Biological tests can be used to screen samples for large groups of compounds having a particular effect, but it is often difficult to identify a specific compound when a positive effect is observed. The identification of an unknown compound is a challenge for analytical chemistry in environmental an

  3. Liquid Hybridization and Solid Phase Detection: A Highly Sensitive and Accurate Strategy for MicroRNA Detection in Plants and Animals

    Directory of Open Access Journals (Sweden)

    Fosheng Li

    2016-09-01

    Full Text Available MicroRNAs (miRNAs play important roles in nearly every aspect of biology, including physiological, biochemical, developmental and pathological processes. Therefore, a highly sensitive and accurate method of detection of miRNAs has great potential in research on theory and application, such as the clinical approach to medicine, animal and plant production, as well as stress response. Here, we report a strategic method to detect miRNAs from multicellular organisms, which mainly includes liquid hybridization and solid phase detection (LHSPD; it has been verified in various species and is much more sensitive than traditional biotin-labeled Northern blots. By using this strategy and chemiluminescent detection with digoxigenin (DIG-labeled or biotin-labeled oligonucleotide probes, as low as 0.01–0.25 fmol [for DIG-CDP Star (disodium2-chloro-5-(4-methoxyspiro{1,2-dioxetane-3,2′-(5′-chlorotricyclo[3.3.1.13,7]decan}-4-ylphenyl phosphate system], 0.005–0.1 fmol (for biotin-CDP Star system, or 0.05–0.5 fmol (for biotin-luminol system of miRNA can be detected and one-base difference can be distinguished between miRNA sequences. Moreover, LHSPD performed very well in the quantitative analysis of miRNAs, and the whole process can be completed within about 9 h. The strategy of LHSPD provides an effective solution for rapid, accurate, and sensitive detection and quantitative analysis of miRNAs in plants and animals.

  4. A combined strategy for landmine detection and identification using synthetic GPR responses

    Science.gov (United States)

    Gonzalez-Huici, Maria A.; Giovanneschi, Fabio

    2013-12-01

    Synthetic Ground Penetrating Radar (GPR) target responses may be successfully used for buried landmine classification purposes. This paper demonstrates that accurately simulated one-dimensional temporal signatures can be employed as reference waveforms for efficient clutter suppression and improved target detection/recognition. The proposed methodology is a combined approach consisting of a cross-correlation based identification algorithm and an energy based detection algorithm. The former can be implemented before conducting the detection as an additional filtering step in the form of a similarity constraint between measured and synthetic scattered signals. The application of the combined method to experimental data yields a clear gain in the detection sensitivity, particularly for those mines which are most difficult to detect through scattered energy considerations alone. Moreover, an adapted Inverse Distance Weighted (IDW) averaging has been incorporated to enhance the quality of the imaging and to rise the Signal-to-Clutter ratio (SCR) of the resulting maps. This strategy can help to substantially reduce the number of false alarms and speed up the clearance labors.

  5. Rapid detection and identification of Bacillus anthracis in food using pyrosequencing technology.

    Science.gov (United States)

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

    2013-08-01

    The development of advanced methodologies for the detection of Bacillus anthracis has been evolving rapidly since the release of the anthrax spores in the mail in 2001. Recent advances in detection and identification techniques could prove to be an essential component in the defense against biological attacks. Sequence based such as pyrosequencing, which has the capability to determine short DNA stretches in real-time using biotinylated PCR amplicons, has potential biodefense applications. Using markers from the virulence plasmids (pXO1 and pXO2) and chromosomal regions, we have demonstrated the power of this technology in the rapid, specific and sensitive detection of B. anthracis spores in food matrices including milk, juice, bottled water, and processed meat. The combined use of immunomagnetic separation and pyrosequencing showed positive detection when liquid foods (bottled water, milk, juice), and processed meat were experimentally inoculated with 6CFU/mL and 6CFU/g, respectively, without an enrichment step. Pyrosequencing is completed in about 60min (following PCR amplification) and yields accurate and reliable results with an added layer of confidence. The entire assay (from sample preparation to sequencing information) can be completed in about 7.5h. A typical run on food samples yielded 67-80bp reads with 94-100% identity to the expected sequence. This sequence based approach is a novel application for the detection of anthrax spores in food with potential application in foodborne bioterrorism response and biodefense involving the use of anthrax spores.

  6. Geometric identification and damage detection of structural elements by terrestrial laser scanner

    Science.gov (United States)

    Hou, Tsung-Chin; Liu, Yu-Wei; Su, Yu-Min

    2016-04-01

    In recent years, three-dimensional (3D) terrestrial laser scanning technologies with higher precision and higher capability are developing rapidly. The growing maturity of laser scanning has gradually approached the required precision as those have been provided by traditional structural monitoring technologies. Together with widely available fast computation for massive point cloud data processing, 3D laser scanning can serve as an efficient structural monitoring alternative for civil engineering communities. Currently most research efforts have focused on integrating/calculating the measured multi-station point cloud data, as well as modeling/establishing the 3D meshes of the scanned objects. Very little attention has been spent on extracting the information related to health conditions and mechanical states of structures. In this study, an automated numerical approach that integrates various existing algorithms for geometric identification and damage detection of structural elements were established. Specifically, adaptive meshes were employed for classifying the point cloud data of the structural elements, and detecting the associated damages from the calculated eigenvalues in each area of the structural element. Furthermore, kd-tree was used to enhance the searching efficiency of plane fitting which were later used for identifying the boundaries of structural elements. The results of geometric identification were compared with M3C2 algorithm provided by CloudCompare, as well as validated by LVDT measurements of full-scale reinforced concrete beams tested in laboratory. It shows that 3D laser scanning, through the established processing approaches of the point cloud data, can offer a rapid, nondestructive, remote, and accurate solution for geometric identification and damage detection of structural elements.

  7. Use of Medical Metered Dose Inhalers for Functionality Testing of Bioaerosol Detection and Identification Systems

    Science.gov (United States)

    2012-05-01

    BIOAEROSOL DETECTION AND IDENTIFICATION SYSTEMS ECBC-TR-964 Jana Kesavan Deborah R. Schepers Jerold R. Bottiger RESEARCH AND TECHNOLOGY...Testing Of Bioaerosol Detection And Identification Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...Medical Metered Dose Inhalers for Functionality Testing of Bioaerosol Detection and Identification Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c

  8. The combined-disk boronic acid test as an accurate strategy for the detection of KPC carbapenemase in Central America.

    Science.gov (United States)

    Zúñiga, Julio; Cruz, Gerardo; Pérez, Carlos; Tarajia, Musharaf

    2016-03-31

    Carbapenemase-producing Klebsiella pneumoniae (KPC) outbreaks may cause a huge economical burden on developing countries. Furthermore, KPC can be challenging to detect. We describe the laboratory strategy for the detection of KPC from 2011 to 2013 in a tertiary care hospital in Central America with approximately 1,000 beds. A retrospective analysis of a clinical laboratory database was done to determine the pragmatic application of the combined-disk boronic acid test during a KPC outbreak in Panama. A total of 1,026 Klebsiella pneumoniae isolates were found, of which 133 were positive for KPC. The strategy during two phases was described according to the test employed as a confirmatory test for KPC. After the K. pneumoniae isolates were detected by the VITEK 2 system, blaKPC polymerase chain reaction (PCR) and the combined-disk boronic acid test were employed as a confirmatory test during phase one. The combined-disk boronic acid test was employed as a confirmatory test for KPC during phase two. The sensitivity, specificity, positive predictive value, and negative predictive value of the boronic acid test were 100%, 97%, 91%, and 100%, respectively, when blaKPC PCR was employed as a confirmatory test during the start of the outbreak. Afterwards, modified VITEK 2 system parameters resulted in 116 suspicious KPC samples and the boronic acid test confirmed 102 isolates. The use of an automated bacterial identification system and the boronic acid test for the detection of KPC was an effective and low-cost strategy for a clinical laboratory in Panama during an outbreak.

  9. Applying face identification to detecting hijacking of airplane

    Science.gov (United States)

    Luo, Xuanwen; Cheng, Qiang

    2004-09-01

    That terrorists hijacked the airplanes and crashed the World Trade Center is disaster to civilization. To avoid the happening of hijack is critical to homeland security. To report the hijacking in time, limit the terrorist to operate the plane if happened and land the plane to the nearest airport could be an efficient way to avoid the misery. Image processing technique in human face recognition or identification could be used for this task. Before the plane take off, the face images of pilots are input into a face identification system installed in the airplane. The camera in front of pilot seat keeps taking the pilot face image during the flight and comparing it with pre-input pilot face images. If a different face is detected, a warning signal is sent to ground automatically. At the same time, the automatic cruise system is started or the plane is controlled by the ground. The terrorists will have no control over the plane. The plane will be landed to a nearest or appropriate airport under the control of the ground or cruise system. This technique could also be used in automobile industry as an image key to avoid car stealth.

  10. Wavelet features for failure detection and identification in vibration systems

    Science.gov (United States)

    Deckert, James C.; Rhenals, Alonso E.; Tenney, Robert R.; Willsky, Alan S.

    1992-12-01

    The result of this effort is an extremely flexible and powerful methodology for failure detection and identification (FDI) in vibrating systems. The essential elements of this methodology are: (1) an off-line set of techniques to identify high-energy, statistically significant features in the continuous wavelet transform (CWT); (2) a CWT-based preprocessor to extract the most useful features from the sensor signal; and (3) simple artificial neural networks (incorporating a mechanism to defer any decision if the current feature sample is determined to be ambiguous) for the subsequent classification task. For the helicopter intermediate gearbox test-stand data and centrifugal and fire pump shipboard (mild operating condition) data used, the algorithms designed using this method achieved perfect detection performance (1.000 probability of detection, and 0.000 false alarm probability), with a probability less than 0.04 that a decision would be deferred-based on only 500 milliseconds of data from each sample case. While this effort shows the exceptional promise of our wavelet-based method for FDI in vibrating systems, more demanding applications, which also have other sources of high-energy vibration, raise additional technical issues that could provide the focus for a Phase 2 effort.

  11. Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry.

    Science.gov (United States)

    Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

    2016-01-01

    The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification.

  12. Rapid and accurate identification of Streptococcus equi subspecies by MALDI-TOF MS

    DEFF Research Database (Denmark)

    Kudirkiene, Egle; Welker, Martin; Knudsen, Nanna Reumert

    2015-01-01

    phenotypic and sequence similarity between three subspecies their discrimination remains difficult. In this study, we aimed to design and validate a novel, Superspectra based, MALDI-TOF MS approach for reliable, rapid and cost-effective identification of SEE and SEZ, the most frequent S. equi subspecies.......3±7.5%). This result may be attributed to the highly clonal population structure of SEE, as opposed to the diversity of SEZ seen in horses. Importantly strains with atypical colony appearance both within SEE and SEZ did not affect correct identification of the strains by MALDI-TOF MS. Atypical colony variants...... with spectra analyses using the SARAMIS database. Additionally, first results on subtyping of SEZ indicated that a more refined discrimination, for example for epidemiological surveys, may be possible...

  13. CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation

    Directory of Open Access Journals (Sweden)

    Li Gong-Hua

    2010-08-01

    Full Text Available Abstract Background The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB, thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been developed to predict protein function, but these methods need to be improved further, such as, enhancing the accuracy, sensitivity, and the computational speed. Here, an accurate algorithm, the CMASA (Contact MAtrix based local Structural Alignment algorithm, has been developed to predict unknown functions of proteins based on the local protein structural similarity. This algorithm has been evaluated by building a test set including 164 enzyme families, and also been compared to other methods. Results The evaluation of CMASA shows that the CMASA is highly accurate (0.96, sensitive (0.86, and fast enough to be used in the large-scale functional annotation. Comparing to both sequence-based and global structure-based methods, not only the CMASA can find remote homologous proteins, but also can find the active site convergence. Comparing to other local structure comparison-based methods, the CMASA can obtain the better performance than both FFF (a method using geometry to predict protein function and SPASM (a local structure alignment method; and the CMASA is more sensitive than PINTS and is more accurate than JESS (both are local structure alignment methods. The CMASA was applied to annotate the enzyme catalytic sites of the non-redundant PDB, and at least 166 putative catalytic sites have been suggested, these sites can not be observed by the Catalytic Site Atlas (CSA. Conclusions The CMASA is an accurate algorithm for detecting local protein structural similarity, and it holds several advantages in predicting enzyme active sites. The CMASA can be used in large-scale enzyme active site annotation. The CMASA can be available by the

  14. Accurate and reproducible invasive breast cancer detection in whole-slide images: A Deep Learning approach for quantifying tumor extent

    Science.gov (United States)

    Cruz-Roa, Angel; Gilmore, Hannah; Basavanhally, Ajay; Feldman, Michael; Ganesan, Shridar; Shih, Natalie N. C.; Tomaszewski, John; González, Fabio A.; Madabhushi, Anant

    2017-04-01

    With the increasing ability to routinely and rapidly digitize whole slide images with slide scanners, there has been interest in developing computerized image analysis algorithms for automated detection of disease extent from digital pathology images. The manual identification of presence and extent of breast cancer by a pathologist is critical for patient management for tumor staging and assessing treatment response. However, this process is tedious and subject to inter- and intra-reader variability. For computerized methods to be useful as decision support tools, they need to be resilient to data acquired from different sources, different staining and cutting protocols and different scanners. The objective of this study was to evaluate the accuracy and robustness of a deep learning-based method to automatically identify the extent of invasive tumor on digitized images. Here, we present a new method that employs a convolutional neural network for detecting presence of invasive tumor on whole slide images. Our approach involves training the classifier on nearly 400 exemplars from multiple different sites, and scanners, and then independently validating on almost 200 cases from The Cancer Genome Atlas. Our approach yielded a Dice coefficient of 75.86%, a positive predictive value of 71.62% and a negative predictive value of 96.77% in terms of pixel-by-pixel evaluation compared to manually annotated regions of invasive ductal carcinoma.

  15. Identification of 4th intercostal space using sternal notch to xiphoid length for accurate electrocardiogram lead placement.

    Science.gov (United States)

    Day, Kevin; Oliva, Isabel; Krupinski, Elizabeth; Marcus, Frank

    2015-01-01

    Precordial ECG lead placement is difficult in obese patients with increased chest wall soft tissues due to inaccurate palpation of the intercostal spaces. We investigated whether the length of the sternum (distance between the sternal notch and xiphoid process) can accurately predict the location of the 4th intercostal space, which is the traditional location for V1 lead position. Fifty-five consecutive adult chest computed tomography examinations were reviewed for measurements. The sternal notch to right 4th intercostal space distance was 67% of the sternal notch to xiphoid process length with an overall correlation of r=0.600 (pintercostal space for accurate placement of the precordial electrodes in adults in whom the 4th intercostal space cannot be found by physical exam. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. BlueDetect: An iBeacon-Enabled Scheme for Accurate and Energy-Efficient Indoor-Outdoor Detection and Seamless Location-Based Service.

    Science.gov (United States)

    Zou, Han; Jiang, Hao; Luo, Yiwen; Zhu, Jianjie; Lu, Xiaoxuan; Xie, Lihua

    2016-02-22

    The location and contextual status (indoor or outdoor) is fundamental and critical information for upper-layer applications, such as activity recognition and location-based services (LBS) for individuals. In addition, optimizations of building management systems (BMS), such as the pre-cooling or heating process of the air-conditioning system according to the human traffic entering or exiting a building, can utilize the information, as well. The emerging mobile devices, which are equipped with various sensors, become a feasible and flexible platform to perform indoor-outdoor (IO) detection. However, power-hungry sensors, such as GPS and WiFi, should be used with caution due to the constrained battery storage on mobile device. We propose BlueDetect: an accurate, fast response and energy-efficient scheme for IO detection and seamless LBS running on the mobile device based on the emerging low-power iBeacon technology. By leveraging the on-broad Bluetooth module and our proposed algorithms, BlueDetect provides a precise IO detection service that can turn on/off on-board power-hungry sensors smartly and automatically, optimize their performances and reduce the power consumption of mobile devices simultaneously. Moreover, seamless positioning and navigation services can be realized by it, especially in a semi-outdoor environment, which cannot be achieved by GPS or an indoor positioning system (IPS) easily. We prototype BlueDetect on Android mobile devices and evaluate its performance comprehensively. The experimental results have validated the superiority of BlueDetect in terms of IO detection accuracy, localization accuracy and energy consumption.

  17. BlueDetect: An iBeacon-Enabled Scheme for Accurate and Energy-Efficient Indoor-Outdoor Detection and Seamless Location-Based Service

    Directory of Open Access Journals (Sweden)

    Han Zou

    2016-02-01

    Full Text Available The location and contextual status (indoor or outdoor is fundamental and critical information for upper-layer applications, such as activity recognition and location-based services (LBS for individuals. In addition, optimizations of building management systems (BMS, such as the pre-cooling or heating process of the air-conditioning system according to the human traffic entering or exiting a building, can utilize the information, as well. The emerging mobile devices, which are equipped with various sensors, become a feasible and flexible platform to perform indoor-outdoor (IO detection. However, power-hungry sensors, such as GPS and WiFi, should be used with caution due to the constrained battery storage on mobile device. We propose BlueDetect: an accurate, fast response and energy-efficient scheme for IO detection and seamless LBS running on the mobile device based on the emerging low-power iBeacon technology. By leveraging the on-broad Bluetooth module and our proposed algorithms, BlueDetect provides a precise IO detection service that can turn on/off on-board power-hungry sensors smartly and automatically, optimize their performances and reduce the power consumption of mobile devices simultaneously. Moreover, seamless positioning and navigation services can be realized by it, especially in a semi-outdoor environment, which cannot be achieved by GPS or an indoor positioning system (IPS easily. We prototype BlueDetect on Android mobile devices and evaluate its performance comprehensively. The experimental results have validated the superiority of BlueDetect in terms of IO detection accuracy, localization accuracy and energy consumption.

  18. Medical isotope identification with large mobile detection systems

    Science.gov (United States)

    Mukhopadhyay, Sanjoy; Maurer, Richard

    2012-10-01

    The Remote Sensing laboratory (RSL) of National Security Technologies Inc. has built an array of large (5.08 - cm x 10.16 - cm x 40.6 - cm) thallium doped sodium iodide (NaI: Tl) scintillators to locate and screen gamma-ray emitting radioisotopes that are of interests to radiological emergency responders [1]. These vehicle mounted detectors provide the operators with rapid, simple, specific information for radiological threat assessment. Applications include large area inspection, customs inspection, border protection, emergency response, and monitoring of radiological facilities. These RSL mobile units are currently being upgraded to meet the Defense Threat Reduction Agency mission requirements for a next-generation system capable of detecting and identifying nuclear threat materials. One of the challenging problems faced by these gamma-ray detectors is the unambiguous identification of medical isotopes like 131I (364.49 keV [81.7%], 636.99 keV [7.17%]), 99Tcm (140.51 keV [89.1%]) and 67Ga (184.6 keV [19.7%], 300.2 [16.0%], 393.5 [4.5%] that are used in radionuclide therapy and often have overlapping gamma-ray energy regions of interest (ROI). The problem is made worse by short (about 5 seconds) acquisition time of the spectral data necessary for dynamic mobile detectors. This article describes attempts to identify medical isotopes from data collected from this mobile detection system in a short period of time (not exceeding 5 secs) and a large standoff distance (typically ~ 10 meters) The mobile units offer identification capabilities that are based on hardware auto stabilization of the amplifier gain. The 1461 keV gamma-energy line from 40K is tracked. It uses gamma-ray energy windowing along with embedded mobile Gamma Detector Response and Analysis Software (GADRAS) [2] simultaneously to deconvolve any overlapping gamma-energy ROIs. These high sensitivity detectors are capable of resolving complex masking scenarios and exceed all ANSI N42.34 (2006) requirements

  19. A case of spontaneous cerebrospinal fluid rhinorrhea: Accurate detection of the leak point by magnetic resonance cisternography

    Directory of Open Access Journals (Sweden)

    Teppei Matsubara

    2014-01-01

    Full Text Available Background: Spontaneous cerebrospinal fluid (CSF rhinorrhea is a rare entity. The accurate preoperative localization of the leak point is essential for planning surgical treatment, but is sometimes difficult. To localize the leak point, magnetic resonance cisternography (MRC is the method of choice, but its effectiveness remains unclear. Case Description: A 34-year-old mildly obese female experienced spontaneous CSF rhinorrhea after an attack of bronchial asthma. High-resolution computed tomography (CT failed to reveal the leak point, while MRC demonstrated an arachnoid herniation at the olfactory cleft. The patient underwent endoscopic endonasal repair of the CSF leak with success. There has been no recurrence of CSF rhinorrhea for 14 months after surgery followed by the administration of acetazolamide. Conclusion: We report a rare case of spontaneous CSF rhinorrhea associated with benign intracranial hypertension, in which the leak point was successfully detected by MRC. The CSF leak was completely repaired by minimally invasive endoscopic endonasal surgery. MRC may be a reliable method for detecting CSF leak points.

  20. Accurate spectroscopic characterization of oxirane: A valuable route to its identification in Titan's atmosphere and the assignment of unidentified infrared bands

    Energy Technology Data Exchange (ETDEWEB)

    Puzzarini, Cristina [Dipartimento di Chimica " Giacomo Ciamician," Università di Bologna, Via Selmi 2, I-40126 Bologna (Italy); Biczysko, Malgorzata; Bloino, Julien; Barone, Vincenzo, E-mail: cristina.puzzarini@unibo.it [Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)

    2014-04-20

    In an effort to provide an accurate spectroscopic characterization of oxirane, state-of-the-art computational methods and approaches have been employed to determine highly accurate fundamental vibrational frequencies and rotational parameters. Available experimental data were used to assess the reliability of our computations, and an accuracy on average of 10 cm{sup –1} for fundamental transitions as well as overtones and combination bands has been pointed out. Moving to rotational spectroscopy, relative discrepancies of 0.1%, 2%-3%, and 3%-4% were observed for rotational, quartic, and sextic centrifugal-distortion constants, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for identification of oxirane in Titan's atmosphere and the assignment of unidentified infrared bands. Since oxirane was already observed in the interstellar medium and some astronomical objects are characterized by very high D/H ratios, we also considered the accurate determination of the spectroscopic parameters for the mono-deuterated species, oxirane-d1. For the latter, an empirical scaling procedure allowed us to improve our computed data and to provide predictions for rotational transitions with a relative accuracy of about 0.02% (i.e., an uncertainty of about 40 MHz for a transition lying at 200 GHz).

  1. People Detection and Re-Identification in Complex Environments

    Science.gov (United States)

    Truong Cong, Dung-Nghi; Khoudour, Louahdi; Achard, Catherine; Douadi, Lounis

    This paper presents an automatic system for detecting and re-identifying people moving in different sites with non-overlapping views. We first propose an automatic process for silhouette extraction based on the combination of an adaptive background subtraction algorithm and a motion detection module. Such a combination takes advantage of both approaches and is able to tackle the problem of particular environments. The silhouette extraction results are then clustered based on their spatial belonging and colorimetric characteristics in order to preserve only the key regions that effectively represent the appearance of a person. The next important step consists in characterizing the extracted silhouettes by the appearance-based signatures. Our proposed descriptor, which includes both color and spatial feature of objects, leads to satisfying results compared to other descriptors in the literature. Since the passage of a person needs to be characterized by multiple frames, a large quantity of data has to be processed. Thus, a graph-based algorithm is used to realize the comparison of passages of people in front of cameras and to make the final decision of re-identification. The global system is tested on two real and difficult data sets recorded in very different environments. The experimental results show that our proposed system leads to very satisfactory results.

  2. Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

    Science.gov (United States)

    Li, Yuan; Wang, Mingjun; Wang, Huilin; Tan, Hao; Zhang, Ziding; Webb, Geoffrey I.; Song, Jiangning

    2014-07-01

    Lysine acetylation is a reversible post-translational modification, playing an important role in cytokine signaling, transcriptional regulation, and apoptosis. To fully understand acetylation mechanisms, identification of substrates and specific acetylation sites is crucial. Experimental identification is often time-consuming and expensive. Alternative bioinformatics methods are cost-effective and can be used in a high-throughput manner to generate relatively precise predictions. Here we develop a method termed as SSPKA for species-specific lysine acetylation prediction, using random forest classifiers that combine sequence-derived and functional features with two-step feature selection. Feature importance analysis indicates functional features, applied for lysine acetylation site prediction for the first time, significantly improve the predictive performance. We apply the SSPKA model to screen the entire human proteome and identify many high-confidence putative substrates that are not previously identified. The results along with the implemented Java tool, serve as useful resources to elucidate the mechanism of lysine acetylation and facilitate hypothesis-driven experimental design and validation.

  3. Streptococcus dysgalactiae subsp. equisimilis Isolated From Infections in Dogs and Humans: Are Current Subspecies Identification Criteria accurate?

    Science.gov (United States)

    Ciszewski, Marcin; Zegarski, Kamil; Szewczyk, Eligia M

    2016-11-01

    Streptococcus dysgalactiae is a pyogenic species pathogenic both for humans and animals. Until recently, it has been considered an exclusive animal pathogen causing infections in wild as well as domestic animals. Currently, human infections are being reported with increasing frequency, and their clinical picture is often similar to the ones caused by Streptococcus pyogenes. Due to the fact that S. dysgalactiae is a heterogeneous species, it was divided into two subspecies: S. dysgalactiae subsp. equisimilis (SDSE) and S. dysgalactiae subsp. dysgalactiae (SDSD). The first differentiation criterion, described in 1996, was based on strain isolation source. Currently applied criteria, published in 1998, are based on hemolysis type and Lancefield group classification. In this study, we compared subspecies identification results for 36 strains isolated from clinical cases both in humans and animals. Species differentiation was based on two previously described criteria as well as MALDI-TOF and genetic analyses: RISA and 16S rRNA genes sequencing. Antimicrobial susceptibility profiles were also determined according to CLSI guidelines. The results presented in our study suggest that the subspecies differentiation criteria previously described in the above two literature positions seem to be inaccurate in analyzed group of strains, the hemolysis type on blood agar, and Lancefield classification should not be here longer considered as criteria in subspecies identification. The antimicrobial susceptibility tests indicate emerging of multiresistant human SDSE strains resistant also to vancomycin, linezolid and tigecycline, which might pose a substantial problem in treatment.

  4. Evaluation of different pretreatment protocols to detect accurately clinical carbapenemase-producing Enterobacteriaceae by MALDI-TOF.

    Science.gov (United States)

    Monteferrante, Carmine G; Sultan, Sadaf; Ten Kate, Marian T; Dekker, Lennard J M; Sparbier, Katrin; Peer, Markus; Kostzrewa, Markus; Luider, Theo M; Goessens, Wil H F; Burgers, Peter C

    2016-10-01

    Carbapenemase-resistant bacteria are increasingly spreading worldwide causing public concern due to their ability to elude antimicrobial treatment. Early identification of these bacteria is therefore of high importance. Here, we describe the development of a simple and robust protocol for the detection of carbapenemase activity in clinical isolates of Enterobacteriaceae, suitable for routine and clinical applications. The final protocol involves cellular lysis and enzyme extraction from a defined amount of bacterial cells followed by the addition of a benchmark drug (e.g. the carbapenem antibiotic imipenem or ertapenem). Carbapenem inactivation is mediated by enzymatic hydrolysis (cleavage) of the β-lactam common structural motif, which can be detected using MALDI-TOF MS. A total of 260 strains were studied (208 carbapenemase producers and 52 non-carbapenemase producers) resulting in 100% sensitivity and 100% specificity for the KPC, NDM and OXA-48-like PCR-confirmed positive isolates using imipenem as benchmark. Differences between the benchmark (indicator) antibiotics imipenem and ertapenem, buffer constituents and sample preparation methods have been investigated. Carbapenemase activity was further characterized by performing specific inhibitor experiments. Intraday and interday reproducibility (coefficient of variation) of the observed hydrolysis results were 15% and 30%, respectively. A comparative study of our extraction method and a recently published method using whole bacterial cells is presented and differences are discussed. Using this method, an existing carbapenemase activity can be directly read from the mass spectrum as a ratio of hydrolysed product and substrate, setting an important step towards routine application in clinical laboratories. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. ETHNOPRED: a novel machine learning method for accurate continental and sub-continental ancestry identification and population stratification correction

    Science.gov (United States)

    2013-01-01

    Background Population stratification is a systematic difference in allele frequencies between subpopulations. This can lead to spurious association findings in the case–control genome wide association studies (GWASs) used to identify single nucleotide polymorphisms (SNPs) associated with disease-linked phenotypes. Methods such as self-declared ancestry, ancestry informative markers, genomic control, structured association, and principal component analysis are used to assess and correct population stratification but each has limitations. We provide an alternative technique to address population stratification. Results We propose a novel machine learning method, ETHNOPRED, which uses the genotype and ethnicity data from the HapMap project to learn ensembles of disjoint decision trees, capable of accurately predicting an individual’s continental and sub-continental ancestry. To predict an individual’s continental ancestry, ETHNOPRED produced an ensemble of 3 decision trees involving a total of 10 SNPs, with 10-fold cross validation accuracy of 100% using HapMap II dataset. We extended this model to involve 29 disjoint decision trees over 149 SNPs, and showed that this ensemble has an accuracy of ≥ 99.9%, even if some of those 149 SNP values were missing. On an independent dataset, predominantly of Caucasian origin, our continental classifier showed 96.8% accuracy and improved genomic control’s λ from 1.22 to 1.11. We next used the HapMap III dataset to learn classifiers to distinguish European subpopulations (North-Western vs. Southern), East Asian subpopulations (Chinese vs. Japanese), African subpopulations (Eastern vs. Western), North American subpopulations (European vs. Chinese vs. African vs. Mexican vs. Indian), and Kenyan subpopulations (Luhya vs. Maasai). In these cases, ETHNOPRED produced ensembles of 3, 39, 21, 11, and 25 disjoint decision trees, respectively involving 31, 502, 526, 242 and 271 SNPs, with 10-fold cross validation accuracy of

  6. Visual Detection and Identification Are Not the Same: Evidence from Psychophysics and fMRI

    Science.gov (United States)

    Straube, Sirko; Fahle, Manfred

    2011-01-01

    Sometimes object detection as opposed to identification is sufficient to initiate the appropriate action. To explore the neural origin of behavioural differences between the two tasks, we combine psychophysical measurements and fMRI, specifically contrasting shape detection versus identification of a figure. This figure consisted of Gabor elements…

  7. Application of an Accurate and Validated Method for Identification and Quantification of Acrylamide in Bread, Biscuits and Other Bakery Products Using GC-MS/MS System

    OpenAIRE

    Negoiță,Mioara; Culețu,Alina

    2016-01-01

    A gas chromatography tandem mass spectrometry has been developed and validated for the separation, detection, identification and quantification of acrylamide in bread, biscuits and similar products. The method showed good precision with values lower than 6%. A good sensitivity was achieved for bread with 2.41 and 7.23 µg kg-1 limit of detection (LOD) and limit of quantification (LOQ), respectively, while for biscuits, LOD and LOQ were 4.63 and 13.89 µg kg-1, respectively. Accuracy obtained th...

  8. Identification of novel autoantibodies for detection of malignant mesothelioma.

    Directory of Open Access Journals (Sweden)

    Xufei Zhang

    Full Text Available BACKGROUND: The malignant mesothelioma (MM survival rate has been hampered by the lack of efficient and accurate early detection methods. The immune system may detect the early changes of tumor progression by responding with tumor-associated autoantibody production. Hence, in this study, we translated the humoral immune response to cancer proteins into a potential blood test for MM. METHODOLOGY/PRINCIPAL FINDINGS: A T7 phage MM cDNA library was constructed using MM tumor tissues and biopanned for tumor-associated antigens (TAAs using pooled MM patient and normal serum samples. About 1008 individual phage TAA clones from the biopanned library were subjected to protein microarray construction and tested with 53 MM and 52 control serum samples as a training group. Nine candidate autoantibody markers were selected from the training group using Tclass system and logistic regression statistical analysis, which achieved 94.3% sensitivity and 90.4% specificity with an AUC value of 0.89 in receiver operating characteristic analysis. The classifier was further evaluated with 50 patient and 50 normal serum samples as an independent blind validation, and the sensitivity of 86.0% and the specificity of 86.0% were obtained with an AUC of 0.82. Sequencing and BLASTN analysis of the classifier revealed that five of these nine candidate markers were found to have strong homology to cancer related proteins (PDIA6, MEG3, SDCCAG3, IGHG3, IGHG1. CONCLUSIONS/SIGNIFICANCE: Our results indicated that using a panel of 9 autoantibody markers presented a promising accuracy for MM detection. Although the results need further validation in high-risk groups, they provided the potentials in developing a serum-based assay for MM diagnosis.

  9. Polymerase chain reaction assay for rapid, sensitive detection, and identification of Colletotrichum gloeosporioides causing greater yam anthracnose.

    Science.gov (United States)

    Raj, Mithun; Jeeva, M L; Hegde, V; Vidyadharan, Pravi; Archana, P V; Senthil alias Sankar, M; Nath, S Vishnu

    2012-11-01

    Anthracnose caused by Colletotrichum gloeosporioides is an economically important disease which affects greater yam (Dioscorea alata L.) worldwide. Apart from airborne conidia, the pathogen propagules surviving in soil and planting material are the major sources of inoculum. A nested PCR assay has been developed for specific detection of C. gloeosporioides in soil and planting material. In conventional (single-round) PCR, the limit of detection was 20 pg, whereas in nested PCR the detection limit increased to 0.2 pg of DNA. The primers designed were found to be highly specific and could be used for accurate identification of the pathogen up to species level. The protocol was standardized for detection of the pathogen in artificially and naturally infected field samples.

  10. Evaluation of a pan-serotype point-of-care rapid diagnostic assay for accurate detection of acute dengue infection.

    Science.gov (United States)

    Vivek, Rosario; Ahamed, Syed Fazil; Kotabagi, Shalini; Chandele, Anmol; Khanna, Ira; Khanna, Navin; Nayak, Kaustuv; Dias, Mary; Kaja, Murali-Krishna; Shet, Anita

    2017-03-01

    The catastrophic rise in dengue infections in India and globally has created a need for an accurate, validated low-cost rapid diagnostic test (RDT) for dengue. We prospectively evaluated the diagnostic performance of NS1/IgM RDT (dengue day 1) using 211 samples from a pediatric dengue cohort representing all 4 serotypes in southern India. The dengue-positive panel consisted of 179 dengue real-time polymerase chain reaction (RT-PCR) positive samples from symptomatic children. The dengue-negative panel consisted of 32 samples from dengue-negative febrile children and asymptomatic individuals that were negative for dengue RT-PCR/NS1 enzyme-linked immunosorbent assay/IgM/IgG. NS1/IgM RDT sensitivity was 89.4% and specificity was 93.8%. The NS1/IgM RDT showed high sensitivity throughout the acute phase of illness, in primary and secondary infections, in different severity groups, and detected all 4 dengue serotypes, including coinfections. This NS1/IgM RDT is a useful point-of-care assay for rapid and reliable diagnosis of acute dengue and an excellent surveillance tool in our battle against dengue. Copyright © 2016. Published by Elsevier Inc.

  11. Aptamer-conjugated live human immune cell based biosensors for the accurate detection of C-reactive protein

    Science.gov (United States)

    Hwang, Jangsun; Seo, Youngmin; Jo, Yeonho; Son, Jaewoo; Choi, Jonghoon

    2016-10-01

    C-reactive protein (CRP) is a pentameric protein that is present in the bloodstream during inflammatory events, e.g., liver failure, leukemia, and/or bacterial infection. The level of CRP indicates the progress and prognosis of certain diseases; it is therefore necessary to measure CRP levels in the blood accurately. The normal concentration of CRP is reported to be 1-3 mg/L. Inflammatory events increase the level of CRP by up to 500 times; accordingly, CRP is a biomarker of acute inflammatory disease. In this study, we demonstrated the preparation of DNA aptamer-conjugated peripheral blood mononuclear cells (Apt-PBMCs) that specifically capture human CRP. Live PBMCs functionalized with aptamers could detect different levels of human CRP by producing immune complexes with reporter antibody. The binding behavior of Apt-PBMCs toward highly concentrated CRP sites was also investigated. The immune responses of Apt-PBMCs were evaluated by measuring TNF-alpha secretion after stimulating the PBMCs with lipopolysaccharides. In summary, engineered Apt-PBMCs have potential applications as live cell based biosensors and for in vitro tracing of CRP secretion sites.

  12. Rapid metabolite discovery, identification, and accurate comparison of the stereoselective metabolism of metalaxyl in rat hepatic microsomes.

    Science.gov (United States)

    Wang, Xinru; Qiu, Jing; Xu, Peng; Zhang, Ping; Wang, Yao; Zhou, Zhiqiang; Zhu, Wentao

    2015-01-28

    Metabolite identification and quantitation impose great challenges on risk assessment of agrochemicals, as many metabolite standards are generally unavailable. In this study, metalaxyl metabolites were identified by time-of-flight mass spectrometry and semiquantified by triple quadrupole tandem mass spectrometry with self-prepared (13)C-labeled metalaxyl metabolites as internal standards. Such methodology was employed to characterize the stereoselective metabolism of metalaxyl in rat hepatic microsomes successfully. Metabolites derived from hydroxylation, demethylation, and didemethylation were identified and semiquantified. The results indicated that (+)-S-metalaxyl eliminated preferentially as the enantiomer fraction was 0.32 after 60 min incubation. The amounts of hydroxymetalaxyl and demethylmetalaxyl derived from (-)-R-metalaxyl were 1.76 and 1.82 times higher than that of (+)-S-metalaxyl, whereas didemethylmetalaxyl derived from (+)-S-metalaxyl was 1.44 times larger than that from (-)-R-metalaxyl. This study highlights a new quantitation approach for stereoselective metabolism of chiral agrochemicals and provides more knowledge on metalaxyl risk assessment.

  13. Accurate high-throughput identification of parallel G-quadruplex topology by a new tetraaryl-substituted imidazole.

    Science.gov (United States)

    Hu, Ming-Hao; Chen, Shuo-Bin; Wang, Yu-Qing; Zeng, You-Mei; Ou, Tian-Miao; Li, Ding; Gu, Lian-Quan; Huang, Zhi-Shu; Tan, Jia-Heng

    2016-09-15

    G-quadruplex nucleic acids are four-stranded DNA or RNA secondary structures that are formed in guanine-rich sequences. These structures exhibit extensive structural polymorphism and play a pivotal role in the control of a variety of cellular processes. To date, diverse approaches for high-throughput identification of G-quadruplex structures have been successfully developed, but high-throughput methods for further characterization of their topologies are still lacking. In this study, we report a new tetra-arylimidazole probe psIZCM-1, which was found to display significant and distinctive changes in both the absorption and the fluorescence spectra in the presence of parallel G-quadruplexes but show insignificant changes upon interactions with anti-parallel G-quadruplexes or other non-quadruplex oligonucleotides. In view of this dual-output feature, we used psIZCM-1 to identify the parallel G-quadruplexes from a large set of 314 oligonucleotides (including 300 G-quadruplex-forming oligonucleotides and 14 non-quadruplex oligonucleotides) via a microplate reader and accordingly established a high-throughput method for the characterization of parallel G-quadruplex topologies. The accuracy of this method was greater than 95%, which was much higher than that of the commercial probe NMM. To make the approach more practical, we further combined psIZCM-1 with another G-quadruplex probe IZCM-7 to realize the high-throughput classification of parallel, anti-parallel G-quadruplexes and non-quadruplex structures.

  14. Mass spectrometric detection, identification, and fragmentation of arseno-phytochelatins.

    Science.gov (United States)

    Schmied-Tobies, Maria I H; Arroyo-Abad, Uriel; Mattusch, Jürgen; Reemtsma, Thorsten

    2014-11-01

    Phytochelatins (PC) are cystein-rich oligopeptides in plants for coordination with toxic metals and metalloids via their thiol groups. The composition, structure, and mass spectrometric fragmentation of arseno-PC (As-PC) with PC of different degree of oligomerization (PC2-PC5) in solution were studied using liquid chromatography coupled in parallel to inductively coupled plasma mass spectrometry and electrospray ionization quadrupole time-of-flight mass spectrometry. As-PC were detected from As(PC2) to As(PC5) with an increasing number of isomers that differ in the position of thiol groups bound to As. Thermodynamic modeling supported the identification process in case of these isomers. Mass spectrometric fragmentation of the As-PC does not follow the established pattern of peptides but is governed by the formation of series of As-containing annular cations, which coordinate to As via S, N, or O. Structure proposals for 30 As-PC fragment ions in the range m/z 147.92 to m/z 1290.18 are elaborated. Many of these fragment ions are characteristic to several As-PC and may be suited for a screening for As-PC in plant extracts. The mass spectrometric data offer the perspective for a future more sensitive determination of As-PC by means of liquid chromatography tandem mass spectrometry with multiple reaction monitoring.

  15. Detection And Identification Of Inflammatory Bowel Disease Electronic Nose

    Science.gov (United States)

    Covington, J. A.; Ouaret, N.; Gardner, J. W.; Nwokolo, C.; Bardhan, K. D.; Arasaradnam, R. P.

    2011-11-01

    Inflammatory bowel disease (IBD) is an inflammation of the lining of the human bowel and a major health issue in Europe. IBD carries with it significant morbidity from toxic treatment, surgery and a risk of developing bowel cancer. Thus there is a need for early identification of the disease using non-invasive tests. Present diagnostic techniques are based around invasive tests (i.e. endoscopy) and laboratory culture; the latter is limited as only 50% of the gut bacteria can be identified. Here we explore the use of an e-nose as a tool to detect and identify two IBDs (i.e. Crohn's disease (CD) & Ulcerative Colitis (UC)) based on headspace analysis from urine samples. We believe that the gut bacterial flora is altered by disease (due to fermentation) that in-turn modulates the gas composition within urine samples. 24 samples (9 CD, 6 UC, 9 controls) were analysed with an in-house e-nose and an Owlstone IMS instrument. Data analysis was performed using linear discriminant analysis (LDA and principal components analysis (PCA). Using the e-nose, LDA separates both disease groups and control, whilst PCA shows a small overlap of classes. The IMS data are more complex but shows some disease/control separation. We are presently collecting further samples for a larger study using more advanced data processing methods.

  16. Phevor Combines Multiple Biomedical Ontologies for Accurate Identification of Disease-Causing Alleles in Single Individuals and Small Nuclear Families

    Science.gov (United States)

    Singleton, Marc V.; Guthery, Stephen L.; Voelkerding, Karl V.; Chen, Karin; Kennedy, Brett; Margraf, Rebecca L.; Durtschi, Jacob; Eilbeck, Karen; Reese, Martin G.; Jorde, Lynn B.; Huff, Chad D.; Yandell, Mark

    2014-01-01

    Phevor integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. Phevor works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant-prioritization tools. It does so by using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant-prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single-exome and family-trio-based diagnostic analyses, the most commonly occurring clinical scenarios and ones for which existing personal genome diagnostic tools are most inaccurate and underpowered. Here, we present a series of benchmark analyses illustrating Phevor’s performance characteristics. Also presented are three recent Utah Genome Project case studies in which Phevor was used to identify disease-causing alleles. Collectively, these results show that Phevor improves diagnostic accuracy not only for individuals presenting with established disease phenotypes but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases or known disease-causing alleles. As we demonstrate, Phevor can also use latent information in ontologies to discover genes and disease-causing alleles not previously associated with disease. PMID:24702956

  17. Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

    Science.gov (United States)

    Zacher, Benedikt; Michel, Margaux; Schwalb, Björn; Cramer, Patrick; Tresch, Achim

    2017-01-01

    Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today’s largest compendium of chromatin assays. Extensive benchmarks demonstrate that GenoSTAN generally identifies promoters and enhancers with significantly higher accuracy than previous methods. Moreover, GenoSTAN-derived promoters and enhancers showed significantly higher enrichment of complex trait-associated genetic variants than current annotations. Altogether, GenoSTAN provides an easy-to-use tool to define promoters and enhancers in any system, and our annotation of human transcriptional cis-regulatory elements constitutes a rich resource for future research in biology and medicine. PMID:28056037

  18. A new private communication scheme based on the idea of fault detection and identification

    Energy Technology Data Exchange (ETDEWEB)

    Chen Maoyin [Department of Automation, Tsinghua University, Beijing 100084 (China)]. E-mail: maoyinchen@163.com; Zhou Donghua [Department of Automation, Tsinghua University, Beijing 100084 (China); Shang Yun [College of Mathematics and Information Science, Shaanxi Normal University, Xi' an 710062 (China)

    2006-02-27

    By use of the idea of fault detection and identification, this Letter proposes a new scheme to resolve the problem of chaotic private communication. From the point of view of fault detection and identification the scalar message signal hidden in the chaotic systems can be regarded as the component fault signal, thereby it can be detected and recovered using the model-based methods of fault detection and identification. The famous Duffing oscillator is used to illustrate and verify the effectiveness of this scheme.

  19. Identification and validation of reference genes for accurate normalization of real-time quantitative PCR data in kiwifruit.

    Science.gov (United States)

    Ferradás, Yolanda; Rey, Laura; Martínez, Óscar; Rey, Manuel; González, Ma Victoria

    2016-05-01

    Identification and validation of reference genes are required for the normalization of qPCR data. We studied the expression stability produced by eight primer pairs amplifying four common genes used as references for normalization. Samples representing different tissues, organs and developmental stages in kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) were used. A total of 117 kiwifruit samples were divided into five sample sets (mature leaves, axillary buds, stigmatic arms, fruit flesh and seeds). All samples were also analysed as a single set. The expression stability of the candidate primer pairs was tested using three algorithms (geNorm, NormFinder and BestKeeper). The minimum number of reference genes necessary for normalization was also determined. A unique primer pair was selected for amplifying the 18S rRNA gene. The primer pair selected for amplifying the ACTIN gene was different depending on the sample set. 18S 2 and ACT 2 were the candidate primer pairs selected for normalization in the three sample sets (mature leaves, fruit flesh and stigmatic arms). 18S 2 and ACT 3 were the primer pairs selected for normalization in axillary buds. No primer pair could be selected for use as the reference for the seed sample set. The analysis of all samples in a single set did not produce the selection of any stably expressing primer pair. Considering data previously reported in the literature, we validated the selected primer pairs amplifying the FLOWERING LOCUS T gene for use in the normalization of gene expression in kiwifruit.

  20. A Robust Motion Artifact Detection Algorithm for Accurate Detection of Heart Rates from Photoplethysmographic Signals using Time-Frequency Spectral Features.

    Science.gov (United States)

    Dao, Duy; Salehizadeh, S M A; Noj, Yeon; Chong, Jo Woon; Cho, Chae; Mcmanus, Dave; Darling, Chad E; Mendelson, Yitzhak; Chon, Ki H

    2016-10-21

    Motion and noise artifacts (MNAs) impose limits on the usability of the photoplethysmogram (PPG), particularly in the context of ambulatory monitoring. MNAs can distort PPG, causing erroneous estimation of physiological parameters such as heart rate (HR) and arterial oxygen saturation (SpO2). In this study we present a novel approach, "TifMA," based on using the Time-frequency spectrum of PPG to first detect the MNA-corrupted data and next discard the non-usable part of the corrupted data. The term "non-usable" refers to segments of PPG data from which the HR signal cannot be recovered accurately. Two sequential classification procedures were included in the TifMA algorithm. The first classifier distinguishes between MNA-corrupted and MNA-free PPG data. Once a segment of data is deemed MNA-corrupted, the next classifier determines whether the HR can be recovered from the corrupted segment or not. A support vector machine (SVM) classifier was used to build a decision boundary for the first classification task using data segments from a training data set. Features from time-frequency spectra of PPG were extracted to build the detection model. Five datasets were considered for evaluating TifMA performance: (1) and (2) were lab-controlled PPG recordings from forehead and finger pulse oximeter sensors with subjects making random movements, (3) and (4) were actual patient PPG recordings from UMass Memorial Medical Center with random free movements and (5) was a lab-controlled PPG recording dataset measured at the forehead while the subjects ran on a treadmill. The first dataset was used to analyze the noise sensitivity of the algorithm. Datasets 2-4 were used to evaluate the MNA detection phase of the algorithm. The results from the first phase of the algorithm (MNA detection) were compared to results from three existing MNA detection algorithms: the Hjorth, kurtosis-Shannon Entropy and time-domain variability-SVM approaches. This last is an approach recently developed

  1. SU-E-J-23: An Accurate Algorithm to Match Imperfectly Matched Images for Lung Tumor Detection Without Markers

    Energy Technology Data Exchange (ETDEWEB)

    Rozario, T; Bereg, S [University of Texas at Dallas, Richardson, TX (United States); Chiu, T; Liu, H; Kearney, V; Jiang, L; Mao, W [UT Southwestern Medical Center, Dallas, TX (United States)

    2014-06-01

    Purpose: In order to locate lung tumors on projection images without internal markers, digitally reconstructed radiograph (DRR) is created and compared with projection images. Since lung tumors always move and their locations change on projection images while they are static on DRRs, a special DRR (background DRR) is generated based on modified anatomy from which lung tumors are removed. In addition, global discrepancies exist between DRRs and projections due to their different image originations, scattering, and noises. This adversely affects comparison accuracy. A simple but efficient comparison algorithm is reported. Methods: This method divides global images into a matrix of small tiles and similarities will be evaluated by calculating normalized cross correlation (NCC) between corresponding tiles on projections and DRRs. The tile configuration (tile locations) will be automatically optimized to keep the tumor within a single tile which has bad matching with the corresponding DRR tile. A pixel based linear transformation will be determined by linear interpolations of tile transformation results obtained during tile matching. The DRR will be transformed to the projection image level and subtracted from it. The resulting subtracted image now contains only the tumor. A DRR of the tumor is registered to the subtracted image to locate the tumor. Results: This method has been successfully applied to kV fluoro images (about 1000 images) acquired on a Vero (Brainlab) for dynamic tumor tracking on phantom studies. Radiation opaque markers are implanted and used as ground truth for tumor positions. Although, other organs and bony structures introduce strong signals superimposed on tumors at some angles, this method accurately locates tumors on every projection over 12 gantry angles. The maximum error is less than 2.6 mm while the total average error is 1.0 mm. Conclusion: This algorithm is capable of detecting tumor without markers despite strong background signals.

  2. Human Movement Detection and Identification Using Pyroelectric Infrared Sensors

    Directory of Open Access Journals (Sweden)

    Jaeseok Yun

    2014-05-01

    Full Text Available Pyroelectric infrared (PIR sensors are widely used as a presence trigger, but the analog output of PIR sensors depends on several other aspects, including the distance of the body from the PIR sensor, the direction and speed of movement, the body shape and gait. In this paper, we present an empirical study of human movement detection and identification using a set of PIR sensors. We have developed a data collection module having two pairs of PIR sensors orthogonally aligned and modified Fresnel lenses. We have placed three PIR-based modules in a hallway for monitoring people; one module on the ceiling; two modules on opposite walls facing each other. We have collected a data set from eight subjects when walking in three different conditions: two directions (back and forth, three distance intervals (close to one wall sensor, in the middle, close to the other wall sensor and three speed levels (slow, moderate, fast. We have used two types of feature sets: a raw data set and a reduced feature set composed of amplitude and time to peaks; and passage duration extracted from each PIR sensor. We have performed classification analysis with well-known machine learning algorithms, including instance-based learning and support vector machine. Our findings show that with the raw data set captured from a single PIR sensor of each of the three modules, we could achieve more than 92% accuracy in classifying the direction and speed of movement, the distance interval and identifying subjects. We could also achieve more than 94% accuracy in classifying the direction, speed and distance and identifying subjects using the reduced feature set extracted from two pairs of PIR sensors of each of the three modules.

  3. Amplified protein detection and identification through DNA-conjugated M13 bacteriophage.

    Science.gov (United States)

    Lee, Ju Hun; Domaille, Dylan W; Cha, Jennifer N

    2012-06-26

    Sensitive protein detection and accurate identification continues to be in great demand for disease screening in clinical and laboratory settings. For these diagnostics to be of clinical value, it is necessary to develop sensors that have high sensitivity but favorable cost-to-benefit ratios. However, many of these sensing platforms are thermally unstable or require significant materials synthesis, engineering, or fabrication. Recently, we demonstrated that naturally occurring M13 bacteriophage can serve as biological scaffolds for engineering protein diagnostics. These viruses have five copies of the pIII protein, which can bind specifically to target antigens, and thousands of pVIII coat proteins, which can be genetically or chemically modified to react with signal-producing materials, such as plasmon-shifting gold nanoparticles (Au NPs). In this report, we show that DNA-conjugated M13 bacteriophage can act as inexpensive protein sensors that can rapidly induce a color change in the presence of a target protein yet also offer the ability to identify the detected antigen in a separate step. Many copies of a specific DNA oligonucleotide were appended to each virus to create phage-DNA conjugates that can hybridize with DNA-conjugated gold nanoparticles. In the case of a colorimetric positive result, the identity of the antigen can also be easily determined by using a DNA microarray. This saves precious resources by establishing a rapid, quantitative method to first screen for the presence of antigen followed by a highly specific typing assay if necessary.

  4. Detection and Identification of Probiotic Lactobacillus plantarum Strains by Multiplex PCR Using RAPD-Derived Primers

    Directory of Open Access Journals (Sweden)

    Alex Galanis

    2015-10-01

    Full Text Available Lactobacillus plantarum 2035 and Lactobacillus plantarum ACA-DC 2640 are two lactic acid bacteria (LAB strains that have been isolated from Feta cheese. Both display significant potential for the production of novel probiotic food products. The aim of the present study was the development of an accurate and efficient method for the molecular detection and identification of the above strains in a single reaction. A multiplex PCR assay was designed for each strain, based on specific primers derived from Random Amplified Polymorphic DNA (RAPD Sequenced Characterized Amplified Region (SCAR analysis. The specificity of the assay was tested with a total of 23 different LAB strains, for L. plantarum 2035 and L. plantarum ACA-DC 2640. The multiplex PCR assay was also successfully applied for the detection of the above cultures in yogurt samples prepared in our lab. The proposed methodology may be applied for monitoring the presence of these strains in food products, thus evaluating their probiotic character. Moreover, our strategy may be adapted for other novel LAB strains with probiotic potential, thus providing a powerful tool for molecular discrimination that could be invaluable to the food industry.

  5. Detection and Identification of Probiotic Lactobacillus plantarum Strains by Multiplex PCR Using RAPD-Derived Primers.

    Science.gov (United States)

    Galanis, Alex; Kourkoutas, Yiannis; Tassou, Chrysoula C; Chorianopoulos, Nikos

    2015-10-22

    Lactobacillus plantarum 2035 and Lactobacillus plantarum ACA-DC 2640 are two lactic acid bacteria (LAB) strains that have been isolated from Feta cheese. Both display significant potential for the production of novel probiotic food products. The aim of the present study was the development of an accurate and efficient method for the molecular detection and identification of the above strains in a single reaction. A multiplex PCR assay was designed for each strain, based on specific primers derived from Random Amplified Polymorphic DNA (RAPD) Sequenced Characterized Amplified Region (SCAR) analysis. The specificity of the assay was tested with a total of 23 different LAB strains, for L. plantarum 2035 and L. plantarum ACA-DC 2640. The multiplex PCR assay was also successfully applied for the detection of the above cultures in yogurt samples prepared in our lab. The proposed methodology may be applied for monitoring the presence of these strains in food products, thus evaluating their probiotic character. Moreover, our strategy may be adapted for other novel LAB strains with probiotic potential, thus providing a powerful tool for molecular discrimination that could be invaluable to the food industry.

  6. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems.

    Directory of Open Access Journals (Sweden)

    Ram Samudrala

    2009-04-01

    Full Text Available The type III secretion system is an essential component for virulence in many Gram-negative bacteria. Though components of the secretion system apparatus are conserved, its substrates--effector proteins--are not. We have used a novel computational approach to confidently identify new secreted effectors by integrating protein sequence-based features, including evolutionary measures such as the pattern of homologs in a range of other organisms, G+C content, amino acid composition, and the N-terminal 30 residues of the protein sequence. The method was trained on known effectors from the plant pathogen Pseudomonas syringae and validated on a set of effectors from the animal pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium after eliminating effectors with detectable sequence similarity. We show that this approach can predict known secreted effectors with high specificity and sensitivity. Furthermore, by considering a large set of effectors from multiple organisms, we computationally identify a common putative secretion signal in the N-terminal 20 residues of secreted effectors. This signal can be used to discriminate 46 out of 68 total known effectors from both organisms, suggesting that it is a real, shared signal applicable to many type III secreted effectors. We use the method to make novel predictions of secreted effectors in S. Typhimurium, some of which have been experimentally validated. We also apply the method to predict secreted effectors in the genetically intractable human pathogen Chlamydia trachomatis, identifying the majority of known secreted proteins in addition to providing a number of novel predictions. This approach provides a new way to identify secreted effectors in a broad range of pathogenic bacteria for further experimental characterization and provides insight into the nature of the type III secretion signal.

  7. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems

    Energy Technology Data Exchange (ETDEWEB)

    Samudrala, Ram; Heffron, Fred; McDermott, Jason E.

    2009-04-24

    The type III secretion system is an essential component for virulence in many Gram-negative bacteria. Though components of the secretion system apparatus are conserved, its substrates, effector proteins, are not. We have used a machine learning approach to identify new secreted effectors. The method integrates evolutionary measures, such as the pattern of homologs in a range of other organisms, and sequence-based features, such as G+C content, amino acid composition and the N-terminal 30 residues of the protein sequence. The method was trained on known effectors from Salmonella typhimurium and validated on a corresponding set of effectors from Pseudomonas syringae, after eliminating effectors with detectable sequence similarity. The method was able to identify all of the known effectors in P. syringae with a specificity of 84% and sensitivity of 82%. The reciprocal validation, training on P. syringae and validating on S. typhimurium, gave similar results with a specificity of 86% when the sensitivity level was 87%. These results show that type III effectors in disparate organisms share common features. We found that maximal performance is attained by including an N-terminal sequence of only 30 residues, which agrees with previous studies indicating that this region contains the secretion signal. We then used the method to define the most important residues in this putative secretion signal. Finally, we present novel predictions of secreted effectors in S. typhimurium, some of which have been experimentally validated, and apply the method to predict secreted effectors in the genetically intractable human pathogen Chlamydia trachomatis. This approach is a novel and effective way to identify secreted effectors in a broad range of pathogenic bacteria for further experimental characterization and provides insight into the nature of the type III secretion signal.

  8. Aircraft Abnormal Conditions Detection, Identification, and Evaluation Using Innate and Adaptive Immune Systems Interaction

    Science.gov (United States)

    Al Azzawi, Dia

    Abnormal flight conditions play a major role in aircraft accidents frequently causing loss of control. To ensure aircraft operation safety in all situations, intelligent system monitoring and adaptation must rely on accurately detecting the presence of abnormal conditions as soon as they take place, identifying their root cause(s), estimating their nature and severity, and predicting their impact on the flight envelope. Due to the complexity and multidimensionality of the aircraft system under abnormal conditions, these requirements are extremely difficult to satisfy using existing analytical and/or statistical approaches. Moreover, current methodologies have addressed only isolated classes of abnormal conditions and a reduced number of aircraft dynamic parameters within a limited region of the flight envelope. This research effort aims at developing an integrated and comprehensive framework for the aircraft abnormal conditions detection, identification, and evaluation based on the artificial immune systems paradigm, which has the capability to address the complexity and multidimensionality issues related to aircraft systems. Within the proposed framework, a novel algorithm was developed for the abnormal conditions detection problem and extended to the abnormal conditions identification and evaluation. The algorithm and its extensions were inspired from the functionality of the biological dendritic cells (an important part of the innate immune system) and their interaction with the different components of the adaptive immune system. Immunity-based methodologies for re-assessing the flight envelope at post-failure and predicting the impact of the abnormal conditions on the performance and handling qualities are also proposed and investigated in this study. The generality of the approach makes it applicable to any system. Data for artificial immune system development were collected from flight tests of a supersonic research aircraft within a motion-based flight

  9. Toward optimizing patient-specific IMRT QA techniques in the accurate detection of dosimetrically acceptable and unacceptable patient plans.

    Science.gov (United States)

    McKenzie, Elizabeth M; Balter, Peter A; Stingo, Francesco C; Jones, Jimmy; Followill, David S; Kry, Stephen F

    2014-12-01

    in the performance of any device between gamma criteria of 2%/2 mm, 3%/3 mm, and 5%/3 mm. Finally, optimal cutoffs (e.g., percent of pixels passing gamma) were determined for each device and while clinical practice commonly uses a threshold of 90% of pixels passing for most cases, these results showed variability in the optimal cutoff among devices. IMRT QA devices have differences in their ability to accurately detect dosimetrically acceptable and unacceptable plans. Field-by-field analysis with a MapCheck device and use of the MapCheck with a MapPhan phantom while delivering at planned rotational gantry angles resulted in a significantly poorer ability to accurately sort acceptable and unacceptable plans compared with the other techniques examined. Patient-specific IMRT QA techniques in general should be thoroughly evaluated for their ability to correctly differentiate acceptable and unacceptable plans. Additionally, optimal agreement thresholds should be identified and used as common clinical thresholds typically worked very poorly to identify unacceptable plans.

  10. DETECT: a MATLAB toolbox for event detection and identification in time series, with applications to artifact detection in EEG signals.

    Directory of Open Access Journals (Sweden)

    Vernon Lawhern

    Full Text Available Recent advances in sensor and recording technology have allowed scientists to acquire very large time-series datasets. Researchers often analyze these datasets in the context of events, which are intervals of time where the properties of the signal change relative to a baseline signal. We have developed DETECT, a MATLAB toolbox for detecting event time intervals in long, multi-channel time series. Our primary goal is to produce a toolbox that is simple for researchers to use, allowing them to quickly train a model on multiple classes of events, assess the accuracy of the model, and determine how closely the results agree with their own manual identification of events without requiring extensive programming knowledge or machine learning experience. As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and show the functionality of the tools found in the toolbox. We also discuss the application of DETECT for identifying irregular heartbeat waveforms found in electrocardiogram (ECG data as an additional illustration.

  11. Improving Monaural Speaker Identification by Double-Talk Detection

    DEFF Research Database (Denmark)

    Saeidi, Rahim; Mowlaee, Pejman; Kinnunen, Tomi

    2010-01-01

    This paper describes a novel approach to improve monoaural speaker identification where two speakers are present in a single-microphone recording. The goal is to identify both of the underlying speakers in the given mixture. The proposed approach is composed of a double-talk detector (DTD) as a p......) as a preprocessor and speaker identification back-end. We demonstrate that including the double-talk detector improves the speaker identification accuracy. Experiments on GRID corpus show that including the DTD improves average recognition accuracy from 96.53% to 97.43%....

  12. An innovative method for rapid identification and detection of Vibrio alginolyticus in different infection models

    Directory of Open Access Journals (Sweden)

    Kaifei eFu

    2016-05-01

    Full Text Available Vibrio alginolyticus is one of the most common pathogenic marine Vibrio species, and has been found to cause serious seafood-poisoning or fatal extra-intestinal infections in humans, such as necrotizing soft-tissue infections, bacteremia, septic shock and multiple organ failures. Delayed accurate diagnosis and treatment of most Vibrio infections usually result to high mortality rates. The objective of this study was to establish a rapid diagnostic method to detect and identify the presence of V. alginolyticus in different samples, so as to facilitate timely treatment. The widely employed conventional methods for detection of V. alginolyticus include biochemical identification and a variety of PCR methods. The former is of low specificity and time-consuming (2-3 days, while the latter has improved accuracy and processing time. Despite such advancements, these methods are still complicated, time-consuming, expensive, require expertise and advanced laboratory systems, and are not optimal for field use. With the goal of providing a simple and efficient way to detect V. alginolyticus, we established a rapid diagnostic method based on Loop-mediated Isothermal Amplification (LAMP technology that is feasible to use in both experimental and field environments. Three primer pairs targeting the toxR gene of V. alginolyticus were designed, and amplification was carried out in an ESE tube scanner and Real-Time PCR device. We successfully identified 93 V. alginolyticus strains from a total of 105 different bacterial isolates and confirmed their identity by 16s rDNA sequencing. We also applied this method on infected mouse blood and contaminated scallop samples, and accurate results were both easily and rapidly (20-60min obtained. Therefore, the RT-LAMP assay we developed can be conveniently used to detect the presence of V. alginolyticus in different samples. Furthermore, this method will also fulfill the gap for real-time screening of V. alginolyticus

  13. Accurate and Sensitive Detection of Plasmodium Species in Humans by Use of the Dihydrofolate Reductase-Thymidylate Synthase Linker Region▿ †

    Science.gov (United States)

    Tanomsing, Naowarat; Imwong, Mallika; Theppabutr, Sasikrit; Pukrittayakamee, Sasithon; Day, Nicholas P. J.; White, Nicholas J.; Snounou, Georges

    2010-01-01

    A nested-PCR protocol based on the linker region of the Plasmodium dihydrofolate reductase-thymidylate synthase gene (dhfr-ts) was developed. This provides highly sensitive specific detection and identification of the five parasite species that infect humans. PMID:20702666

  14. Molecular detection and species identification of Enterocytozoon bieneusi isolated from immunocompetent Orang Asli in Malaysia.

    Science.gov (United States)

    Ashikin, Azah; Al-Mekhlafi, Hesham M; Moktar, Norhayati; Anuar, Tengku Shahrul

    2017-04-01

    Most studies of opportunistic infections focus on immunocompromised patients. However, there is a lack of information on microsporidiosis in healthy people (immunocompetent) worldwide. This study aimed to detect and identify microsporidia species in immunocompetent Orang Asli living in Pahang, Malaysia. Orang Asli is a collective term for a group of indigenous people that usually reside in the interior regions of Peninsular Malaysia. They comprise about 0.7% of the total population in Malaysia and 76% of them lived below the poverty line i.e., poor housing conditions with the lack of access to safe drinking water and adequate sanitation, contaminated environment, high illiteracy rate and unhygienic practices by these people. Stool samples were collected from 209 Orang Asli and analyzed for detecting the presence of Enterocytozoon bieneusi and Encephalitozoon intestinalis by polymerase chain reaction assay targeting small subunit ribosomal RNA gene. E. bieneusi was detected in 8 individuals (3.83%). This infection was commonly found in males than females (5.2% vs. 2.7%). All infected Orang Asli were adults, with a mean age of 44years. Diarrhea and other gastrointestinal symptoms were reported in one case (12.5%) among individuals infected with this species. These findings clearly show that exposure to E. bieneusi may actually be common than reported. The accurate detection and identification of microsporidian species by molecular technique will improve therapy, clinical manifestations and prognosis of this infection, as no antiparasitic therapy has been approved for E. bieneusi. It is hoped that these findings will allow the formulation of better health management and disease prevention advisories, and improvement in the standards of health in similar communities.

  15. Accurate sequential detection of primary tumor and metastatic lymphatics using a temperature-induced phase transition nanoparticulate system

    Directory of Open Access Journals (Sweden)

    Oh KS

    2014-06-01

    Full Text Available Keun Sang Oh,1 Ji Young Yhee,2 Dong-Eun Lee,3 Kwangmeyung Kim,2 Ick Chan Kwon,2 Jae Hong Seo,4 Sang Yoon Kim,5 Soon Hong Yuk1,4 1College of Pharmacy, Korea University, Sejong, 2Biomedical Research Center, Korea Institute of Science and Technology, Seoul, 3Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeonbuk, 4Biomedical Research Center, Korea University Guro Hospital, Seoul, 5Department of Otolaryngology, Asan Medical Center, University of Ulsan, College of Medicine, Seoul, Republic of Korea Abstract: Primary tumor and tumor-associated metastatic lymphatics have emerged as new targets for anticancer therapy, given that these are difficult to treat using traditional chemotherapy. In this study, docetaxel-loaded Pluronic nanoparticles with Flamma™ (FPR-675, fluorescence molecular imaging dye; DTX/FPR-675 Pluronic NPs were prepared using a temperature-induced phase transition for accurate detection of metastatic lymphatics. Significant accumulation was seen at the primary tumor and in metastatic lymph nodes within a short time. Particle size, maximum drug loading capacity, and drug encapsulation efficiency of the docetaxel-loaded Pluronic NPs were approximately 10.34±4.28 nm, 3.84 wt%, and 94±2.67 wt%, respectively. Lymphatic tracking after local and systemic delivery showed that DTX/FPR-675 Pluronic NPs were more potent in tumor-bearing mice than in normal mice, and excised mouse lymphatics showed stronger near-infrared fluorescence intensity on the tumor-bearing side than on the non-tumor-bearing side at 60 minutes post-injection. In vivo cytotoxicity and efficacy data for the NPs demonstrated that the systemically administered NPs caused little tissue damage and had minimal side effects in terms of slow renal excretion and prolonged circulation in tumor-bearing mice, and rapid renal excretion in non-tumor-bearing mice using an in vivo real-time near-infrared fluorescence imaging system. These results

  16. Surface Enhanced Raman Spectroscopy for the Rapid Detection and Identification of Microbial Pathogens in Human Serum

    Science.gov (United States)

    2014-12-11

    1): p. 27-32. 14. Lindahl, O., et al. Prostate cancer detection using a combination of raman spectroscopy and stiffness sensing. in 1st Global...identification of leukemia cells [12], diagnosis of dysplasia in Barrett’s esophagus [13], and identification of prostate cancer [14]. The

  17. High-precision topography measurement through accurate in-focus plane detection with hybrid digital holographic microscope and white light interferometer module.

    Science.gov (United States)

    Liżewski, Kamil; Tomczewski, Sławomir; Kozacki, Tomasz; Kostencka, Julianna

    2014-04-10

    High-precision topography measurement of micro-objects using interferometric and holographic techniques can be realized provided that the in-focus plane of an imaging system is very accurately determined. Therefore, in this paper we propose an accurate technique for in-focus plane determination, which is based on coherent and incoherent light. The proposed method consists of two major steps. First, a calibration of the imaging system with an amplitude object is performed with a common autofocusing method using coherent illumination, which allows for accurate localization of the in-focus plane position. In the second step, the position of the detected in-focus plane with respect to the imaging system is measured with white light interferometry. The obtained distance is used to accurately adjust a sample with the precision required for the measurement. The experimental validation of the proposed method is given for measurement of high-numerical-aperture microlenses with subwavelength accuracy.

  18. Detection and identification of bio-threats using MALDI-TOF-MS

    NARCIS (Netherlands)

    Paauw, A.

    2012-01-01

    MALDI-TOF-MS emerged as a new diagnostic tool in established clinical laboratories. Advantages compared to conventional techniques are that it is a fast, cost-effective, accurate method, which is suitable for high-throughput identification of bacteria by less skilled laboratory personnel because pre

  19. Mass and charge identification of fragments detected with the Chimera Silicon-CsI(Tl) telescopes

    Energy Technology Data Exchange (ETDEWEB)

    Le Neindre, N.; Alderighi, M.; Anzalone, A.; Barna, R.; Bartolucci, M.; Berceanu, I.; Borderie, B.; Bougault, R.; Bruno, M.; Cardella, G.; Cavallaro, S.; D' Agostino, M. E-mail: dagostino@bo.infn.it; Dayras, R.; De Filippo, E.; De Pasquale, D.; Geraci, E.; Giustolisi, F.; Grzeszczuk, A.; Guazzoni, P.; Guinet, D.; Iacono-Manno, M.; Italiano, A.; Kowalski, S.; Lanchais, A.; Lanzano, G.; Lanzalone, G.; Li, S.; Lo Nigro, S.; Maiolino, C.; Manfredi, G.; Moisa, D.; Pagano, A.; Papa, M.; Paduszynski, T.; Petrovici, M.; Piasecki, E.; Pirrone, S.; Politi, G.; Pop, A.; Porto, F.; Rivet, M.F.; Rosato, E.; Russo, S.; Sambataro, S.; Sechi, G.; Simion, V.; Sperduto, M.L.; Steckmeyer, J.C.; Sutera, C.; Trifiro, A.; Tassan-Got, L.; Trimarchi, M.; Vannini, G.; Vigilante, M.; Wilczynski, J.; Wu, H.; Xiao, Z.; Zetta, L.; Zipper, W

    2002-09-01

    Mass and charge identification of charged products detected with Silicon-CsI(Tl) telescopes of the Chimera apparatus are presented. An identification function, based on the Bethe-Bloch formula, is used to fit empirical correlations between {delta}E and E ADC readings, in order to determine, event by event, the atomic and mass numbers of the detected charged reaction products prior to energy calibration.

  20. Rapid identification of bio-molecules applied for detection of biosecurity agents using rolling circle amplification.

    Directory of Open Access Journals (Sweden)

    Jenny Göransson

    Full Text Available Detection and identification of pathogens in environmental samples for biosecurity applications are challenging due to the strict requirements on specificity, sensitivity and time. We have developed a concept for quick, specific and sensitive pathogen identification in environmental samples. Target identification is realized by padlock- and proximity probing, and reacted probes are amplified by RCA (rolling-circle amplification. The individual RCA products are labeled by fluorescence and enumerated by an instrument, developed for sensitive and rapid digital analysis. The concept is demonstrated by identification of simili biowarfare agents for bacteria (Escherichia coli and Pantoea agglomerans and spores (Bacillus atrophaeus released in field.

  1. SU-E-J-149: Secondary Emission Detection for Improved Proton Relative Stopping Power Identification

    Energy Technology Data Exchange (ETDEWEB)

    Saunders, J; Musall, B; Erickson, A [Georgia Institute of Technology, Atlanta, GA (Georgia)

    2015-06-15

    Purpose: This research investigates application of secondary prompt gamma (PG) emission spectra, resulting from nuclear reactions induced by protons, to characterize tissue composition along the particle path. The objective of utilizing the intensity of discrete high-energy peaks of PG is to improve the accuracy of relative stopping power (RSP) values available for proton therapy treatment planning on a patient specific basis and to reduce uncertainty in dose depth calculations. Methods: In this research, MCNP6 was used to simulate PG emission spectra generated from proton induced nuclear reactions in medium of varying composition of carbon, oxygen, calcium and nitrogen, the predominant elements found in human tissue. The relative peak intensities at discrete energies predicted by MCNP6 were compared to the corresponding atomic composition of the medium. Results: The results have shown a good general agreement with experimentally measured values reported by other investigators. Unexpected divergence from experimental spectra was noted in the peak intensities for some cases depending on the source of the cross-section data when using compiled proton table libraries vs. physics models built into MCNP6. While the use of proton cross-section libraries is generally recommended when available, these libraries lack data for several less abundant isotopes. This limits the range of their applicability and forces the simulations to rely on physics models for reactions with natural atomic compositions. Conclusion: Current end-of-range proton imaging provides an average RSP for the total estimated track length. The accurate identification of tissue composition along the incident particle path using PG detection and characterization allows for improved determination of the tissue RSP on the local level. While this would allow for more accurate depth calculations resulting in tighter treatment margins, precise understanding of proton beam behavior in tissue of various

  2. Detection and identification of enterohemorrhagic Escherichia coli O157:H7 and Vibrio cholerae O139 using oligonucleotide microarray

    Directory of Open Access Journals (Sweden)

    Zhang Zheng

    2007-12-01

    Full Text Available Abstract Background The rapid and accurate detection and identification of the new subtype of the pathogens is crucial for diagnosis, treatment and control of the contagious disease outbreak. Here, in this study, an approach to detect and identify Escherichia coli O157:H7 and Vibrio cholerae O139 was established using oligonucleotide microarray. We coupled multiplex PCR with oligonucleotide microarray to construct an assay suitable for simultaneous identification of two subtypes of the pathogens. Results The stx1, stx2 gene and uidA gene having the specific mutant spot were chosen as the targets for Escherichia coli O157:H7, and meanwhile the ctxA, tcpA, and LPSgt gene for Vibrio cholerae O139. The oligonucleotide microarray was composed of eight probes including negative control and positive control from 16S rDNA gene. The six primers were designed to amplify target fragments in two triplex PCR, and then hybridized with oligonucleotide microarray. An internal control would be to run a PCR reaction in parallel. Multiplex PCR did not produce any non-specific amplicons when 149 related species or genera of standard bacteria were tested (100% specificity. In addition, Escherichia coli O157:H7 and Escherichia coli O157:non-H7, Vibrio cholerae O139 and Vibrio cholerae O1 had been discriminated respectively. Using recombinant plasmid and target pathogens, we were able to detect positive hybridization signals with 102 copies/μL and 103 cfu/mL per reaction. Conclusion The DNA microarray assay reported here could detect and identify Escherichia coli O157:H7 and Vibrio cholerae O139, and furthermore the subtype was distinguished. This assay was a specific and sensitive tool for simultaneous detection and identification of the new subtype of two pathogens causing diarrhea in human.

  3. Rapid and accurate identification of species belonging to the Candida parapsilosis complex by real-time PCR and melting curve analysis.

    Science.gov (United States)

    Hays, Constantin; Duhamel, Chantal; Cattoir, Vincent; Bonhomme, Julie

    2011-04-01

    Candida parapsilosis is the second most frequent Candida species isolated from blood cultures. Since 2005, C. parapsilosis has been divided into three distinct species based on genetic traits: Candida parapsilosis, Candida metapsilosis and Candida orthopsilosis. The aim of this study was to develop a rapid real-time PCR assay able to distinguish these closely related species via a melting curve analysis. This identification method was optimized by using reference strains and well-characterized clinical isolates of Candida species. A single set of consensus primers was designed to amplify a 184 bp portion of the SADH gene in order to identify species based on the unique melt profile resulting from DNA sequence variations from each species of the complex. PCR products were detected with SYBR Green fluorescent dye and identification was established by melting curve analysis. For validation of the technique, a total of 116 clinical isolates, phenotypically identified as C. parapsilosis, were tested by real-time PCR and results were further compared with PCR-RFLP patterns of the SADH gene, used as the reference method. The melting curve analysis of amplified DNA could differentiate between C. parapsilosis (83.5 °C), C. metapsilosis (82.9 °C) and C. orthopsilosis (82.1 °C), with a sensitivity and specificity comparable to those of the reference method. One hundred and fourteen C. parapsilosis and two C. orthopsilosis isolates were identified among the clinical isolates. This method provides a simple, rapid and reliable identification of species belonging to the C. parapsilosis complex. This novel approach could be helpful for clinical and epidemiological investigations.

  4. microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs.

    Science.gov (United States)

    Georgakilas, Georgios; Vlachos, Ioannis S; Paraskevopoulou, Maria D; Yang, Peter; Zhang, Yuhong; Economides, Aris N; Hatzigeorgiou, Artemis G

    2014-12-10

    A large fraction of microRNAs (miRNAs) are derived from intergenic non-coding loci and the identification of their promoters remains 'elusive'. Here, we present microTSS, a machine-learning algorithm that provides highly accurate, single-nucleotide resolution predictions for intergenic miRNA transcription start sites (TSSs). MicroTSS integrates high-resolution RNA-sequencing data with active transcription marks derived from chromatin immunoprecipitation and DNase-sequencing to enable the characterization of tissue-specific promoters. MicroTSS is validated with a specifically designed Drosha-null/conditional-null mouse model, generated using the conditional by inversion (COIN) methodology. Analyses of global run-on sequencing data revealed numerous pri-miRNAs in human and mouse either originating from divergent transcription at promoters of active genes or partially overlapping with annotated long non-coding RNAs. MicroTSS is readily applicable to any cell or tissue samples and constitutes the missing part towards integrating the regulation of miRNA transcription into the modelling of tissue-specific regulatory networks.

  5. Identification of Bile Duct Paucity in Alagille Syndrome: Using CK7 and EMA Immunohistochemistry as a Reliable Panel for Accurate Diagnosis.

    Science.gov (United States)

    Herman, Haley K; Abramowsky, Carlos R; Caltharp, Shelley; Metry, Diana; Cundiff, Caitlin A; Romero, Rene; Gillespie, Scott E; Shehata, Bahig M

    2016-01-01

    Bile duct paucity is the absence or marked reduction in the number of interlobular bile ducts (ILBD) within portal tracts. Its syndromic variant, Alagille syndrome (ALGS), is a multisystem disorder with effects on the liver, cardiovascular system, skeleton, face, and eyes. It is inherited as an autosomal dominant trait due to defects in NOTCH signaling pathway. ALGS is characterized by vanishing ILBD with subsequent chronic obstructive cholestasis in approximately 89% of cases. Cholestasis stimulates formation of new bile ductules through a process of neoductular reaction, making it difficult to evaluate the presence or absence of ILBD. Therefore, finding a method to differentiate clearly between ILBD and the ductular proliferation is essential for accurate diagnosis. A database search identified 28 patients with confirmed diagnosis of ALGS between 1992 and 2014. Additionally, 7 controls were used. A panel of two immunostains, cytokeratin 7 (CK7) and epithelial membrane antigen (EMA), was performed. CK7 highlighted the bile duct epithelium of ILBD and ductular proliferation, while EMA stained only the brush border of ILBD. In our ALGS group, the ratio of EMA-positive ILBD to identified portal tracts was 12.6% (range, 0%-41%). However, this same ratio was 95.0% (range, 90%-100%) among control cases (P EMA, to differentiate ILBD from ductular proliferation in patients with cholestasis. With this panel, identification of bile duct paucity can be achieved. Additional studies, including molecular confirmation and clinical correlation, would provide a definitive diagnosis of ALGS.

  6. Ambient ionization-accurate mass spectrometry (AMI-AMS) for the identification of nonvisible set-off in food-contact materials.

    Science.gov (United States)

    Bentayeb, Karim; Ackerman, Luke K; Begley, Timothy H

    2012-02-29

    Set-off is the unintentional transfer of substances used in printing from the external printed surface of food packaging to the inner, food-contact surface. Ambient ionization-accurate mass spectrometry (AMI-AMS) detected and identified compounds from print set-off not visible to the human eye. AMI mass spectra from inner and outer surfaces of printed and nonprinted food packaging were compared to detect and identify nonvisible set-off components. A protocol to identify unknowns was developed using a custom open-source database of printing inks and food-packaging compounds. The protocol matched print-related food-contact surface ions with the molecular formulas of common ions, isotopes, and fragments of compounds from the database. AMI-AMS was able to detect print set-off and identify seven different compounds. Set-off on the packaging samples was confirmed using gas chromatographic-mass spectrometric (GC-MS) analysis of single-sided solvent extracts. N-Ethyl-2(and 4)-methylbenzenesulfonamide, 2,4-diphenyl-4-methyl-1(and 2)-pentene, and 2,4,7,9-tetramethyl-5-decyne-4,7-diol were present on the food-contact layer at concentrations from 0.21 to 2.7 ± 1.6 μg dm⁻², corresponding to nearly milligram per kilogram concentrations in the packaged food. Other minor set-off compounds were detected only by AMI-AMS, a fast, simple, and thorough technique to detect and identify set-off in food packaging.

  7. System for identification of microorganism and detection of infectious disorder

    DEFF Research Database (Denmark)

    2013-01-01

    Methods for the identification of microorganisms or infectious disorders are disclosed, comprising obtaining a suitable sample from sources such as persons, animals, plants, food, water or soil. The methods also comprise providing tailored nucleic acid substrate(s) designed to react with a type 1...... topoisomerase from one or more microorganism(s) or infectious agent(s), and incubating said substrate with said sample, or extracts or preparations from the sample, so that the substrate is processed by said topoisomerase if said microorganism(s) or infectious agent(s) is present in the sample. Finally......, processed substrates are identified and potentially quantified by one or more of a range of standard molecular biology methods and read-out systems. The identification and potential quantification of microorganisms and infectious agents, including but not limited to Plasmodium falciparum and Mycobacterium...

  8. System for identification of microorganism and detection of infectious disorder

    DEFF Research Database (Denmark)

    2013-01-01

    Methods for the identification of microorganisms or infectious disorders are disclosed, comprising obtaining a suitable sample from sources such as persons, animals, plants, food, water or soil. The methods also comprise providing tailored nucleic acid substrate(s) designed to react with a type 1......, processed substrates are identified and potentially quantified by one or more of a range of standard molecular biology methods and read-out systems. The identification and potential quantification of microorganisms and infectious agents, including but not limited to Plasmodium falciparum and Mycobacterium...... the technology enables the testing of medical or chemical treatments designed to cure or prevent diseases based upon drugs targeting type 1 topoisomerases. Finally, the reagents and platforms needed for said purposes can be compiled from loose parts or provided as user-friendly kits, potentially enabling home...

  9. A portable analog lock-in amplifier for accurate phase measurement and application in high-precision optical oxygen concentration detection

    Science.gov (United States)

    Chen, Xi; Chang, Jun; Wang, Fupeng; Wang, Zongliang; Wei, Wei; Liu, Yuanyuan; Qin, Zengguang

    2016-10-01

    A portable analog lock-in amplifier capable of accurate phase detection is proposed in this paper. The proposed lock-in amplifier, which uses the dual-channel orthometric signals as the references to build the xy coordinate system, can detect the relative phase between the input and x-axis based on trigonometric function. The sensitivity of the phase measurement reaches 0.014 degree, and a detection precision of 0.1 degree is achieved. At the same time, the performance of the lock-in amplifier is verified in the high precision optical oxygen concentration detection. Experimental results reveal that the portable analog lock-in amplifier is accurate for phase detection applications. In the oxygen sensing experiments, 0.058% oxygen concentration resulted in 0.1 degree phase shift detected by the lock-in amplifier precisely. In addition, the lock-in amplifier is small and economical compared with the commercial lock-in equipments, so it can be easily integrated in many portable devices for industrial applications.

  10. A portable analog lock-in amplifier for accurate phase measurement and application in high-precision optical oxygen concentration detection

    Science.gov (United States)

    Chen, Xi; Chang, Jun; Wang, Fupeng; Wang, Zongliang; Wei, Wei; Liu, Yuanyuan; Qin, Zengguang

    2017-03-01

    A portable analog lock-in amplifier capable of accurate phase detection is proposed in this paper. The proposed lock-in amplifier, which uses the dual-channel orthometric signals as the references to build the xy coordinate system, can detect the relative phase between the input and x-axis based on trigonometric function. The sensitivity of the phase measurement reaches 0.014 degree, and a detection precision of 0.1 degree is achieved. At the same time, the performance of the lock-in amplifier is verified in the high precision optical oxygen concentration detection. Experimental results reveal that the portable analog lock-in amplifier is accurate for phase detection applications. In the oxygen sensing experiments, 0.058% oxygen concentration resulted in 0.1 degree phase shift detected by the lock-in amplifier precisely. In addition, the lock-in amplifier is small and economical compared with the commercial lock-in equipments, so it can be easily integrated in many portable devices for industrial applications.

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

    Science.gov (United States)

    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.

  12. Development of Conductive Polymer Analysis for the Rapid Detection and Identification of Phytopathogenic Microbes

    Science.gov (United States)

    A. Dan Wilson; D.G. Lester; C.S. Oberle

    2004-01-01

    Conductive polymer analysis, a type of electronic aroma detection technology, was evaluated for its efficacy in the detection, identification, and discrimination of plant-pathogenic microorganisms on standardized media and in diseased plant tissues. The method is based on the acquisition of a diagnostic electronic fingerprint derived from multisensor responses to...

  13. Exploration of available feature detection and identification systems and their performance on radiographs

    Science.gov (United States)

    Wantuch, Andrew C.; Vita, Joshua A.; Jimenez, Edward S.; Bray, Iliana E.

    2016-10-01

    Despite object detection, recognition, and identification being very active areas of computer vision research, many of the available tools to aid in these processes are designed with only photographs in mind. Although some algorithms used specifically for feature detection and identification may not take explicit advantage of the colors available in the image, they still under-perform on radiographs, which are grayscale images. We are especially interested in the robustness of these algorithms, specifically their performance on a preexisting database of X-ray radiographs in compressed JPEG form, with multiple ways of describing pixel information. We will review various aspects of the performance of available feature detection and identification systems, including MATLABs Computer Vision toolbox, VLFeat, and OpenCV on our non-ideal database. In the process, we will explore possible reasons for the algorithms' lessened ability to detect and identify features from the X-ray radiographs.

  14. An automatic method for fast and accurate liver segmentation in CT images using a shape detection level set method

    Science.gov (United States)

    Lee, Jeongjin; Kim, Namkug; Lee, Ho; Seo, Joon Beom; Won, Hyung Jin; Shin, Yong Moon; Shin, Yeong Gil

    2007-03-01

    Automatic liver segmentation is still a challenging task due to the ambiguity of liver boundary and the complex context of nearby organs. In this paper, we propose a faster and more accurate way of liver segmentation in CT images with an enhanced level set method. The speed image for level-set propagation is smoothly generated by increasing number of iterations in anisotropic diffusion filtering. This prevents the level-set propagation from stopping in front of local minima, which prevails in liver CT images due to irregular intensity distributions of the interior liver region. The curvature term of shape modeling level-set method captures well the shape variations of the liver along the slice. Finally, rolling ball algorithm is applied for including enhanced vessels near the liver boundary. Our approach are tested and compared to manual segmentation results of eight CT scans with 5mm slice distance using the average distance and volume error. The average distance error between corresponding liver boundaries is 1.58 mm and the average volume error is 2.2%. The average processing time for the segmentation of each slice is 5.2 seconds, which is much faster than the conventional ones. Accurate and fast result of our method will expedite the next stage of liver volume quantification for liver transplantations.

  15. Network Traffic Anomalies Detection and Identification with Flow Monitoring

    CERN Document Server

    Nguyen, Huy; Kim, Dong Il; Choi, Deokjai

    2010-01-01

    Network management and security is currently one of the most vibrant research areas, among which, research on detecting and identifying anomalies has attracted a lot of interest. Researchers are still struggling to find an effective and lightweight method for anomaly detection purpose. In this paper, we propose a simple, robust method that detects network anomalous traffic data based on flow monitoring. Our method works based on monitoring the four predefined metrics that capture the flow statistics of the network. In order to prove the power of the new method, we did build an application that detects network anomalies using our method. And the result of the experiments proves that by using the four simple metrics from the flow data, we do not only effectively detect but can also identify the network traffic anomalies.

  16. Point Mutation Identification Using On-Chip Ligase Detection Reaction

    Institute of Scientific and Technical Information of China (English)

    李艳; 曾令文; 程京

    2004-01-01

    An efficient method was developed to detect point mutations using oligonucleotide microarrays and the ligase detection reaction (LDR).Allele-specific LDR primers were immobilized on polylysine-coated glass slides to perform LDR on a chip.The spotting concentration and detection limit were analyzed using a synthesized oligonucleotide as a template.The optimal primer spotting concentration was 20 (mol/L and the lowest detectable template concentration was 0.33 nmol/L.The method was successfully employed to identify malignant mutations of hypertrophic cardiomyopathy.Asymmetric polymerase chain reaction was employed to prepare single stranded DNA as LDR templates from cloned plasmids.The discrimination ratios for AC,TC,GT,TT,GA,and AA mismatches are 32.82,44.24,17.75,18.34,11.66,and 8.91,respectively.This method may allow construction of multiple mutation detection systems.

  17. Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

    DEFF Research Database (Denmark)

    Pipek, Orsolya; Ribli, Dezső; Molnar, Janos

    2017-01-01

    for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets. We show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup...... are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run....... To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples. Using 30 isogenic samples, reliable cohorts of validated mutations were created...

  18. Fast and Accurate Identification of Cross-Linked Peptides for the Structural Analysis of Large Protein Complexes and Elucidation of Interaction Networks. / Tahir, Salman; Bukowski-Wills, Jimi-Carlo; Rasmussen, Morten; Rappsilber, Juri

    DEFF Research Database (Denmark)

    Rasmussen, Morten

    Fast and Accurate Identification of Cross-Linked Peptides for the structural analysis of large protein complexes and to elucidate interaction networks. Salman Tahir Jimi-Carlo Bukowski-Wills; Morten Rasmussen; Juri RappsilberWellcome Trust Centre for Cell Biology, Edinburgh , United Kingdom   Novel...

  19. Rapid and highly accurate detection of Drosophila suzukii, spotted wing Drosophila (Diptera: Drosophilidae) by loop-mediated isothermal amplification assays

    Science.gov (United States)

    Drosophila suzukii, the spotted wing drosophila (SWD), is currently a major pest that causes severe economic losses to thin-skinned, small fruit growers in North America and Europe. The monitoring and early detection of SWD in the field is of the utmost importance for its proper management. Althou...

  20. Novel and sensitive qPCR assays for the detection and identification of aspergillosis causing species.

    Science.gov (United States)

    Paholcsek, Melinda; Leiter, Eva; Markovics, Arnold; Biró, Sándor

    2014-09-01

    Despite concerted efforts, diagnosis of aspergillosis is still a great challenge to clinical microbiology laboratories. Along with the requirement for high sensitivity and specificity, species-specific identification is important. We developed rapid, sensitive and species-specific qPCR assays using the TaqMan technology for the detection and identification of Aspergillus fumigatus and Aspergillus terreus. The assays were designed to target orthologs of the Streptomyces factor C gene that are only found in a few species of filamentous fungi. Fungi acquired this gene through horizontal gene transfer and divergence of the gene allows identification of species. The assays have potential as a molecular diagnosis tool for the early detection of fungal infection caused by Aspergillus fumigatus and Aspergillus terreus, which merits future diagnostic studies. The assays were sensitive enough to detect a few genomic equivalents in blood samples.

  1. Damage detection in structures through nonlinear excitation and system identification

    Science.gov (United States)

    Hajj, Muhammad R.; Bordonaro, Giancarlo G.; Nayfeh, Ali H.; Duke, John C., Jr.

    2008-03-01

    Variations in parameters representing natural frequency, damping and effective nonlinearities before and after damage initiation in a beam carrying a lumped mass are assessed. The identification of these parameters is performed by exploiting and modeling nonlinear behavior of the beam-mass system and matching an approximate solution of the representative model with quantities obtained from spectral analysis of measured vibrations. The representative model and identified coefficients are validated through comparison of measured and predicted responses. Percentage variations of the identified parameters before and after damage initiation are determined to establish their sensitivities to the state of damage of the beam. The results show that damping and effective nonlinearity parameters are more sensitive to damage initiation than the system's natural frequency. Moreover, the sensitivity of nonlinear parameters to damage is better established using a physically-derived parameter rather than spectral amplitudes of harmonic components.

  2. Development of PCR protocols for specific identification of Clostridium spiroforme and detection of sas and sbs genes.

    Science.gov (United States)

    Drigo, Ilenia; Bacchin, Cosetta; Cocchi, Monia; Bano, Luca; Agnoletti, Fabrizio

    2008-10-15

    Rabbit diarrhoea caused by toxigenic Clostridium spiroforme is responsible for significant losses in commercial rabbitries but the accurate identification of this micro-organism is difficult due to the absence of both a commercial biochemical panel and biomolecular methods. The aim of this study was therefore to develop PCR protocols for specific detection of C. spiroforme and its binary toxin encoding genes. The C. spiroforme specie-specific primers were designed based on its 16S rDNA published sequences and the specificity of these primers was tested with DNA extracted from closely related Clostridium species. The sa/bs_F and sa/bs _R C. spiroforme binary toxin specific primers were designed to be complementary, respectively, to a sequence of 21 bases on the 3' and of sas gene and on the 5' of the sbs gene. The detection limits of in house developed PCR protocols were 25CFU/ml of bacterial suspension and 1.38x10(4)CFU/g of caecal content for specie-specific primers and 80CFU/ml of bacterial suspension and 2.8x10(4)CFU/g of caecal content in case of sa/bs primers. These results indicated that the described PCR assays enable specific identification of C. spiroforme and its binary toxin genes and can therefore be considered a rapid, reliable tool for the diagnosis of C. spiroforme-related enterotoxaemia.

  3. A colorimetric method for highly sensitive and accurate detection of iodide by finding the critical color in a color change process using silver triangular nanoplates

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiu-Hua; Ling, Jian, E-mail: lingjian@ynu.edu.cn; Peng, Jun; Cao, Qiu-E., E-mail: qecao@ynu.edu.cn; Ding, Zhong-Tao; Bian, Long-Chun

    2013-10-10

    Graphical abstract: -- Highlights: •Demonstrated a new colorimetric strategy for iodide detection by silver nanoplates. •The colorimetric strategy is to find the critical color in a color change process. •The colorimetric strategy is more accurate and sensitive than common colorimetry. •Discovered a new morphological transformation phenomenon of silver nanoplates. -- Abstract: In this contribution, we demonstrated a novel colorimetric method for highly sensitive and accurate detection of iodide using citrate-stabilized silver triangular nanoplates (silver TNPs). Very lower concentration of iodide can induce an appreciable color change of silver TNPs solution from blue to yellow by fusing of silver TNPs to nanoparticles, as confirmed by UV–vis absorption spectroscopy and transmission electron microscopy (TEM). The principle of this colorimetric assay is not an ordinary colorimetry, but a new colorimetric strategy by finding the critical color in a color change process. With this strategy, 0.1 μM of iodide can be recognized within 30 min by naked-eyes observation, and lower concentration of iodide down to 8.8 nM can be detected using a spectrophotometer. Furthermore, this high sensitive colorimetric assay has good accuracy, stability and reproducibility comparing with other ordinary colorimetry. We believe this new colorimetric method will open up a fresh insight of simple, rapid and reliable detection of iodide and can find its future application in the biochemical analysis or clinical diagnosis.

  4. Novel real-time simultaneous amplification and testing method to accurately and rapidly detect Mycobacterium tuberculosis complex.

    Science.gov (United States)

    Cui, Zhenling; Wang, Yongzhong; Fang, Liang; Zheng, Ruijuan; Huang, Xiaochen; Liu, Xiaoqin; Zhang, Gang; Rui, Dongmei; Ju, Jinliang; Hu, Zhongyi

    2012-03-01

    The aim of this study was to establish and evaluate a simultaneous amplification and testing method for detection of the Mycobacterium tuberculosis complex (SAT-TB assay) in clinical specimens by using isothermal RNA amplification and real-time fluorescence detection. In the SAT-TB assay, a 170-bp M. tuberculosis 16S rRNA fragment is reverse transcribed to DNA by use of Moloney murine leukemia virus (M-MLV) reverse transcriptase, using specific primers incorporating the T7 promoter sequence, and undergoes successive cycles of amplification using T7 RNA polymerase. Using a real-time PCR instrument, hybridization of an internal 6-carboxyfluorescein-4-[4-(dimethylamino)phenylazo] benzoic acid N-succinimidyl ester (FAM-DABCYL)-labeled fluorescent probe can be used to detect RNA amplification. The SAT-TB assay takes less than 1.5 h to perform, and the sensitivity of the assay for detection of M. tuberculosis H37Rv is 100 CFU/ml. The TB probe has no cross-reactivity with nontuberculous mycobacteria or other common respiratory tract pathogens. For 253 pulmonary tuberculosis (PTB) specimens and 134 non-TB specimens, the SAT-TB results correlated with 95.6% (370/387 specimens) of the Bactec MGIT 960 culture assay results. The sensitivity, specificity, and positive and negative predictive values of the SAT-TB test for the diagnosis of PTB were 67.6%, 100%, 100%, and 62.0%, respectively, compared to 61.7%, 100%, 100%, and 58.0% for Bactec MGIT 960 culture. For PTB diagnosis, the sensitivities of the SAT-TB and Bactec MGIT 960 culture methods were 97.6% and 95.9%, respectively, for smear-positive specimens and 39.2% and 30.2%, respectively, for smear-negative specimens. In conclusion, the SAT-TB assay is a novel, simple test with a high specificity which may enhance the detection rate of TB. It is therefore a promising tool for rapid diagnosis of M. tuberculosis infection in clinical microbiology laboratories.

  5. Comparison of Methodologies to Detect Low Levels of Hemolysis in Serum for Accurate Assessment of Serum microRNAs.

    Science.gov (United States)

    Shah, Jaynish S; Soon, Patsy S; Marsh, Deborah J

    2016-01-01

    microRNAs have emerged as powerful regulators of many biological processes, and their expression in many cancer tissues has been shown to correlate with clinical parameters such as cancer type and prognosis. Present in a variety of biological fluids, microRNAs have been described as a 'gold mine' of potential noninvasive biomarkers. Release of microRNA content of blood cells upon hemolysis dramatically alters the microRNA profile in blood, potentially affecting levels of a significant number of proposed biomarker microRNAs and, consequently, accuracy of serum or plasma-based tests. Several methods to detect low levels of hemolysis have been proposed; however, a direct comparison assessing their sensitivities is currently lacking. In this study, we evaluated the sensitivities of four methods to detect hemolysis in serum (listed in the order of sensitivity): measurement of hemoglobin using a Coulter® AcT diff™ Analyzer, visual inspection, the absorbance of hemoglobin measured by spectrophotometry at 414 nm and the ratio of red blood cell-enriched miR-451a to the reference microRNA miR-23a-3p. The miR ratio detected hemolysis down to approximately 0.001%, whereas the Coulter® AcT diff™ Analyzer was unable to detect hemolysis lower than 1%. The spectrophotometric method could detect down to 0.004% hemolysis, and correlated with the miR ratio. Analysis of hemolysis in a cohort of 86 serum samples from cancer patients and healthy controls showed that 31 of 86 (36%) were predicted by the miR ratio to be hemolyzed, whereas only 8 of these samples (9%) showed visible pink discoloration. Using receiver operator characteristic (ROC) analyses, we identified absorbance cutoffs of 0.072 and 0.3 that could identify samples with low and high levels of hemolysis, respectively. Overall, this study will assist researchers in the selection of appropriate methodologies to test for hemolysis in serum samples prior to quantifying expression of microRNAs.

  6. Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

    KAUST Repository

    Kobayashi, Masaaki

    2017-04-20

    Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)).

  7. The Utility of Specific Markers Based on ITS2 Sequences for Molecular Identification and Detection of Trichogramma spp.

    Institute of Scientific and Technical Information of China (English)

    LI Zheng-xi; SHEN Zuo-rui

    2002-01-01

    The technology based on specific PCR amplification using internal transcribed spacer 2 of nuclear ribosomal DNA for molecular identification and detection of Trichogramma species was studied. Firstly the ITS2s of six Trichogramma species were cloned and sequenced, and the interspecific sequence variation was analyzed. Secondly the ITS2 regions of six geographical populations of T. dendrolimi were cloned and sequenced, and the intraspecific sequence identity was analyzed. The results show that the interspecific variation and intraspecific similarity of ITS2 sequences are very suitable for designation of specific primers at specieslevel. Screening of specific primers for T. dendrolimi leads to final sensitive and stable diagnostic primers. This system lets non-specialists can not only identify adults (males and females), but also identify eggs in parasitized hosts rapidly and accurately, which is impossible by conventional methods. Further development of this protocol can create a complete set of specific primers for different species of the whole genus Trichogramma.

  8. Remote sensing techniques for the detection of soil erosion and the identification of soil conservation practices

    Science.gov (United States)

    Pelletier, R. E.; Griffin, R. H.

    1985-01-01

    The following paper is a summary of a number of techniques initiated under the AgRISTARS (Agriculture and Resources Inventory Surveys Through Aerospace Remote Sensing) project for the detection of soil degradation caused by water erosion and the identification of soil conservation practices for resource inventories. Discussed are methods to utilize a geographic information system to determine potential soil erosion through a USLE (Universal Soil Loss Equation) model; application of the Kauth-Thomas Transform to detect present erosional status; and the identification of conservation practices through visual interpretation and a variety of enhancement procedures applied to digital remotely sensed data.

  9. Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing

    Directory of Open Access Journals (Sweden)

    ElSharawy Abdou

    2012-09-01

    Full Text Available Abstract Background Many hypothesis-driven genetic studies require the ability to comprehensively and efficiently target specific regions of the genome to detect sequence variations. Often, sample availability is limited requiring the use of whole genome amplification (WGA. We evaluated a high-throughput microdroplet-based PCR approach in combination with next generation sequencing (NGS to target 384 discrete exons from 373 genes involved in cancer. In our evaluation, we compared the performance of six non-amplified gDNA samples from two HapMap family trios. Three of these samples were also preamplified by WGA and evaluated. We tested sample pooling or multiplexing strategies at different stages of the tested targeted NGS (T-NGS workflow. Results The results demonstrated comparable sequence performance between non-amplified and preamplified samples and between different indexing strategies [sequence specificity of 66.0% ± 3.4%, uniformity (coverage at 0.2× of the mean of 85.6% ± 0.6%]. The average genotype concordance maintained across all the samples was 99.5% ± 0.4%, regardless of sample type or pooling strategy. We did not detect any errors in the Mendelian patterns of inheritance of genotypes between the parents and offspring within each trio. We also demonstrated the ability to detect minor allele frequencies within the pooled samples that conform to predicted models. Conclusion Our described PCR-based sample multiplex approach and the ability to use WGA material for NGS may enable researchers to perform deep resequencing studies and explore variants at very low frequencies and cost.

  10. Full automatic fiducial marker detection on coil arrays for accurate instrumentation placement during MRI guided breast interventions

    Science.gov (United States)

    Filippatos, Konstantinos; Boehler, Tobias; Geisler, Benjamin; Zachmann, Harald; Twellmann, Thorsten

    2010-02-01

    With its high sensitivity, dynamic contrast-enhanced MR imaging (DCE-MRI) of the breast is today one of the first-line tools for early detection and diagnosis of breast cancer, particularly in the dense breast of young women. However, many relevant findings are very small or occult on targeted ultrasound images or mammography, so that MRI guided biopsy is the only option for a precise histological work-up [1]. State-of-the-art software tools for computer-aided diagnosis of breast cancer in DCE-MRI data offer also means for image-based planning of biopsy interventions. One step in the MRI guided biopsy workflow is the alignment of the patient position with the preoperative MR images. In these images, the location and orientation of the coil localization unit can be inferred from a number of fiducial markers, which for this purpose have to be manually or semi-automatically detected by the user. In this study, we propose a method for precise, full-automatic localization of fiducial markers, on which basis a virtual localization unit can be subsequently placed in the image volume for the purpose of determining the parameters for needle navigation. The method is based on adaptive thresholding for separating breast tissue from background followed by rigid registration of marker templates. In an evaluation of 25 clinical cases comprising 4 different commercial coil array models and 3 different MR imaging protocols, the method yielded a sensitivity of 0.96 at a false positive rate of 0.44 markers per case. The mean distance deviation between detected fiducial centers and ground truth information that was appointed from a radiologist was 0.94mm.

  11. Automatic player detection and identification for sports entertainment applications

    NARCIS (Netherlands)

    Mahmood, Zahid; Ali, Tauseef; Khattak, Shadid; Hasan, Laiq; Khan, Samee U.

    2014-01-01

    In this paper, we develop an augmented reality sports broadcasting application for automatic detection, recognition of players during play, followed by display of personal information of players. The proposed application can be divided into four major steps. In first step, each player in the image i

  12. Hyperspectral Based Skin Detection for Person of Interest Identification

    Science.gov (United States)

    2015-03-01

    pp. 91–98. [8] A.S. Nunez and Michael J. Mendenhall , “Detection of human skin in near infrared hyperspectral imagery,” in Geoscience and Remote Sensing...Symposium, 2008. IGARSS 2008. IEEE International, July 2008, vol. 2, pp. II–621–II–624. [9] A.S. Nunez, Michael J. Mendenhall , and K. Gross

  13. Fluctuation-Enhanced Sensing for Biological Agent Detection and Identification

    CERN Document Server

    Kish, Laszlo B; King, Maria D; Kwan, Chiman; Jensen, James O; Schmera, Gabor; Smulko, Janusz; Gingl, Zoltan; Granqvist, Claes G

    2009-01-01

    We survey and show our earlier results about three different ways of fluctuation-enhanced sensing of bio agent, the phage-based method for bacterium detection published earlier; sensing and evaluating the bacterial odors; and spectral and amplitude distribution analysis of noise in light scattering to identify spores based on their diffusion coefficient.

  14. Automatic player detection and identification for sports entertainment applications

    NARCIS (Netherlands)

    Mahmood, Zahid; Ali, Tauseef; Khattak, Shadid; Hasan, Laiq; Khan, Samee U.

    In this paper, we develop an augmented reality sports broadcasting application for automatic detection, recognition of players during play, followed by display of personal information of players. The proposed application can be divided into four major steps. In first step, each player in the image

  15. The identification and remote detection of alien invasive plants in ...

    African Journals Online (AJOL)

    Kabir Peerbhay

    This paper reviews remote sensing techniques that have been used in ... plant substrates, soil properties, the microclimate, water relations, density and height of vegetation ... the distribution of alien plant invader propagules in support of controlling the spread of alien .... Additionally, a precise weed detection system.

  16. ACCURATE DETECTION OF HIGH-SPEED MULTI-TARGET VIDEO SEQUENCES MOTION REGIONS BASED ON RECONSTRUCTED BACKGROUND DIFFERENCE

    Institute of Scientific and Technical Information of China (English)

    Zhang Wentao; Li Xiaofeng; Li Zaiming

    2001-01-01

    The paper first discusses shortcomings of classical adjacent-frame difference. Sec ondly, based on the image energy and high order statistic(HOS) theory, background reconstruction constraints are setup. Under the help of block-processing technology, background is reconstructed quickly. Finally, background difference is used to detect motion regions instead of adjacent frame difference. The DSP based platform tests indicate the background can be recovered losslessly in about one second, and moving regions are not influenced by moving target speeds. The algorithm has important usage both in theory and applications.

  17. Detection and identification of wild yeasts in lager breweries.

    Science.gov (United States)

    van der Aa Kühle, A; Jespersen, L

    1998-09-08

    Wild yeasts were detected in 41 out of 101 brewery yeast samples investigated using six different selective principles. Malt extract, yeast extract, glucose, peptone (MYGP) agar supplemented with 195 ppm CuSO4 was found to be the most effective selective principle, detecting wild yeasts in 80% of the contaminated samples. Both Saccharomyces and non-Saccharomyces wild yeasts were detected on this medium. Lysine medium, crystal violet medium and incubation of non-selective media at 37 degrees C detected wild yeasts in 46-56% of the contaminated samples. On using actidione medium, only 20% of the wild yeasts were detected. The combined use of MYGP supplemented with 195 ppm CuSO4 and one of the other selective principles did not improve the recovery of the wild yeasts. The wild yeasts found consisted of Saccharomyces cerevisiae (57%), Pichia spp. (28%) and Candida spp. (15%). Using the API ID 32 C kit, 35 different assimilation profiles were obtained for the 124 wild yeast isolates investigated. All isolates were capable of glucose assimilation, whereas only 79% of the isolates assimilated saccharose, 75% maltose, 70% galactose, 65% raffinose and 65% lactate. Lactose, inositol, rhamnose and glucuronate were not assimilated by any of the isolates. The differences in assimilation pattern did not reflect any differences in recovery by the selective principles investigated. The majority of the wild yeast isolates investigated were capable of growth in wort and beer, indicating their possible role as spoilage organisms. The Sacch. cerevisiae isolates were found to be the most hazardous, with some isolates being capable of extensive growth in bottled beer within seventeen days at ambient temperature.

  18. Satellite-Based EMI Detection, Identification, and Mitigation

    Science.gov (United States)

    Stottler, R.; Bowman, C.

    2016-09-01

    Commanding, controlling, and maintaining the health of satellites requires a clear operating spectrum for communications. Electro Magnetic Interference (EMI) from other satellites can interfere with these communications. Determining which satellite is at fault improves space situational awareness and can be used to avoid the problem in the future. The Rfi detection And Prediction Tool, Optimizing Resources (RAPTOR) monitors the satellite communication antenna signals to detect EMI (also called RFI for Radio Frequency Interference) using a neural network trained on past cases of both normal communications and EMI events. RAPTOR maintains a database of satellites that have violated the reserved spectrum in the past. When satellite-based EMI is detected, RAPTOR first checks this list to determine if any are angularly close to the satellite being communicated with. Additionally, RAPTOR checks the Space Catalog to see if any of its active satellites are angularly close. RAPTOR also consults on-line databases to determine if the described operating frequencies of the satellites match the detected EMI and recommends candidates to be added to the known offenders database, accordingly. Based on detected EMI and predicted orbits and frequencies, RAPTOR automatically reschedules satellite communications to avoid current and future satellite-based EMI. It also includes an intuitive display for a global network of satellite communications antennas and their statuses including the status of their EM spectrum. RAPTOR has been prototyped and tested with real data (amplitudes versus frequency over time) for both satellite communication signals and is currently undergoing full-scale development. This paper describes the RAPTOR technologies and results of testing.

  19. Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection.

    Directory of Open Access Journals (Sweden)

    Amel Ghouila

    Full Text Available Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searching for domains in divergent species. Recently, methods for HMM/HMM comparisons have been proposed and proved to be more sensitive than sequence/HMM approaches in certain cases. However, these approaches are usually not used for protein domain discovery at a genome scale, and the benefit that could be expected from their utilization for this problem has not been investigated. Using proteins of P. falciparum and L. major as examples, we investigate the extent to which HMM/HMM comparisons can identify new domain occurrences not already identified by sequence/HMM approaches. We show that although HMM/HMM comparisons are much more sensitive than sequence/HMM comparisons, they are not sufficiently accurate to be used as a standalone complement of sequence/HMM approaches at the genome scale. Hence, we propose to use domain co-occurrence--the general domain tendency to preferentially appear along with some favorite domains in the proteins--to improve the accuracy of the approach. We show that the combination of HMM/HMM comparisons and co-occurrence domain detection boosts protein annotations. At an estimated False Discovery Rate of 5%, it revealed 901 and 1098 new domains in Plasmodium and Leishmania proteins, respectively. Manual inspection of part of these predictions shows that it contains several domain families that were missing in the two organisms. All new domain occurrences have been integrated in the EuPathDomains database, along with the GO annotations that can be deduced.

  20. Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection.

    Science.gov (United States)

    Ghouila, Amel; Florent, Isabelle; Guerfali, Fatma Zahra; Terrapon, Nicolas; Laouini, Dhafer; Yahia, Sadok Ben; Gascuel, Olivier; Bréhélin, Laurent

    2014-01-01

    Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs) have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searching for domains in divergent species. Recently, methods for HMM/HMM comparisons have been proposed and proved to be more sensitive than sequence/HMM approaches in certain cases. However, these approaches are usually not used for protein domain discovery at a genome scale, and the benefit that could be expected from their utilization for this problem has not been investigated. Using proteins of P. falciparum and L. major as examples, we investigate the extent to which HMM/HMM comparisons can identify new domain occurrences not already identified by sequence/HMM approaches. We show that although HMM/HMM comparisons are much more sensitive than sequence/HMM comparisons, they are not sufficiently accurate to be used as a standalone complement of sequence/HMM approaches at the genome scale. Hence, we propose to use domain co-occurrence--the general domain tendency to preferentially appear along with some favorite domains in the proteins--to improve the accuracy of the approach. We show that the combination of HMM/HMM comparisons and co-occurrence domain detection boosts protein annotations. At an estimated False Discovery Rate of 5%, it revealed 901 and 1098 new domains in Plasmodium and Leishmania proteins, respectively. Manual inspection of part of these predictions shows that it contains several domain families that were missing in the two organisms. All new domain occurrences have been integrated in the EuPathDomains database, along with the GO annotations that can be deduced.

  1. An Optimized Method for Accurate Fetal Sex Prediction and Sex Chromosome Aneuploidy Detection in Non-Invasive Prenatal Testing.

    Science.gov (United States)

    Wang, Ting; He, Quanze; Li, Haibo; Ding, Jie; Wen, Ping; Zhang, Qin; Xiang, Jingjing; Li, Qiong; Xuan, Liming; Kong, Lingyin; Mao, Yan; Zhu, Yijun; Shen, Jingjing; Liang, Bo; Li, Hong

    2016-01-01

    Massively parallel sequencing (MPS) combined with bioinformatic analysis has been widely applied to detect fetal chromosomal aneuploidies such as trisomy 21, 18, 13 and sex chromosome aneuploidies (SCAs) by sequencing cell-free fetal DNA (cffDNA) from maternal plasma, so-called non-invasive prenatal testing (NIPT). However, many technical challenges, such as dependency on correct fetal sex prediction, large variations of chromosome Y measurement and high sensitivity to random reads mapping, may result in higher false negative rate (FNR) and false positive rate (FPR) in fetal sex prediction as well as in SCAs detection. Here, we developed an optimized method to improve the accuracy of the current method by filtering out randomly mapped reads in six specific regions of the Y chromosome. The method reduces the FNR and FPR of fetal sex prediction from nearly 1% to 0.01% and 0.06%, respectively and works robustly under conditions of low fetal DNA concentration (1%) in testing and simulation of 92 samples. The optimized method was further confirmed by large scale testing (1590 samples), suggesting that it is reliable and robust enough for clinical testing.

  2. Isothermal microcalorimetry accurately detects bacteria, tumorous microtissues, and parasitic worms in a label-free well-plate assay.

    Science.gov (United States)

    Braissant, Olivier; Keiser, Jennifer; Meister, Isabel; Bachmann, Alexander; Wirz, Dieter; Göpfert, Beat; Bonkat, Gernot; Wadsö, Ingemar

    2015-03-01

    Isothermal microcalorimetry is a label-free assay that allows monitoring of enzymatic and metabolic activities. The technique has strengths, but most instruments have a low throughput, which has limited their use for bioassays. Here, an isothermal microcalorimeter, equipped with a vessel holder similar to a 48-well plate, was used. The increased throughput of this microcalorimeter makes it valuable for biomedical and pharmaceutical applications. Our results show that the sensitivity of the instrument allows the detection of 3 × 10(4) bacteria per vial. Growth of P. mirabilis in Luria Broth medium was detected between 2 and 9 h with decreasing inoculum. The culture released 2.1J with a maximum thermal power of 76 μW. The growth rate calculated using calorimetric and spectrophotometric data were 0.60 and 0.57 h(-1) , respectively. Additional insight on protease activities of P. mirabilis matching the last peak in heat production could be gathered as well. Growth of tumor microtissues releasing a maximum thermal power of 2.1 μW was also monitored and corresponds to a diameter increase of the microtissues from ca. 100 to 428 μm. This opens new research avenues in cancer research, diagnostics, and development of new antitumor drugs. For parasitic worms, the technique allows assessment of parasite survival using motor and metabolic activities even with a single worm.

  3. Establishment of an accurate and fast detection method using molecular beacons in loop-mediated isothermal amplification assay

    Science.gov (United States)

    Liu, Wei; Huang, Simo; Liu, Ningwei; Dong, Derong; Yang, Zhan; Tang, Yue; Ma, Wen; He, Xiaoming; Ao, Da; Xu, Yaqing; Zou, Dayang; Huang, Liuyu

    2017-01-01

    This study established a constant-temperature fluorescence quantitative detection method, combining loop-mediated isothermal amplification (LAMP) with molecular beacons. The advantages of LAMP are its convenience and efficiency, as it does not require a thermocycler and results are easily visualized by the naked eye. However, a major disadvantage of current LAMP techniques is the use of indirect evaluation methods (e.g., electrophoresis, SYBR Green I dye, precipitation, hydroxynaphthol blue dye, the turbidimetric method, calcein/Mn2+ dye, and the composite probe method), which cannot distinguish between the desired products and products of nonspecific amplification, thereby leading to false positives. Use of molecular beacons avoids this problem because molecular beacons produce fluorescence signals only when binding to target DNA, thus acting as a direct indicator of amplification products. Our analyses determined the optimal conditions for molecular beacons as an evaluation tool in LAMP: beacon length of 25–45 bp, beacon concentration of 0.6–1 pmol/μL, and reaction temperature of 60–65 °C. In conclusion, we validated a novel molecular beacon loop-mediated isothermal amplification method (MB-LAMP), realizing the direct detection of LAMP product. PMID:28059137

  4. An Optimized Method for Accurate Fetal Sex Prediction and Sex Chromosome Aneuploidy Detection in Non-Invasive Prenatal Testing.

    Directory of Open Access Journals (Sweden)

    Ting Wang

    Full Text Available Massively parallel sequencing (MPS combined with bioinformatic analysis has been widely applied to detect fetal chromosomal aneuploidies such as trisomy 21, 18, 13 and sex chromosome aneuploidies (SCAs by sequencing cell-free fetal DNA (cffDNA from maternal plasma, so-called non-invasive prenatal testing (NIPT. However, many technical challenges, such as dependency on correct fetal sex prediction, large variations of chromosome Y measurement and high sensitivity to random reads mapping, may result in higher false negative rate (FNR and false positive rate (FPR in fetal sex prediction as well as in SCAs detection. Here, we developed an optimized method to improve the accuracy of the current method by filtering out randomly mapped reads in six specific regions of the Y chromosome. The method reduces the FNR and FPR of fetal sex prediction from nearly 1% to 0.01% and 0.06%, respectively and works robustly under conditions of low fetal DNA concentration (1% in testing and simulation of 92 samples. The optimized method was further confirmed by large scale testing (1590 samples, suggesting that it is reliable and robust enough for clinical testing.

  5. An Optimized Method for Accurate Fetal Sex Prediction and Sex Chromosome Aneuploidy Detection in Non-Invasive Prenatal Testing

    Science.gov (United States)

    Li, Haibo; Ding, Jie; Wen, Ping; Zhang, Qin; Xiang, Jingjing; Li, Qiong; Xuan, Liming; Kong, Lingyin; Mao, Yan; Zhu, Yijun; Shen, Jingjing; Liang, Bo; Li, Hong

    2016-01-01

    Massively parallel sequencing (MPS) combined with bioinformatic analysis has been widely applied to detect fetal chromosomal aneuploidies such as trisomy 21, 18, 13 and sex chromosome aneuploidies (SCAs) by sequencing cell-free fetal DNA (cffDNA) from maternal plasma, so-called non-invasive prenatal testing (NIPT). However, many technical challenges, such as dependency on correct fetal sex prediction, large variations of chromosome Y measurement and high sensitivity to random reads mapping, may result in higher false negative rate (FNR) and false positive rate (FPR) in fetal sex prediction as well as in SCAs detection. Here, we developed an optimized method to improve the accuracy of the current method by filtering out randomly mapped reads in six specific regions of the Y chromosome. The method reduces the FNR and FPR of fetal sex prediction from nearly 1% to 0.01% and 0.06%, respectively and works robustly under conditions of low fetal DNA concentration (1%) in testing and simulation of 92 samples. The optimized method was further confirmed by large scale testing (1590 samples), suggesting that it is reliable and robust enough for clinical testing. PMID:27441628

  6. Rapid and accurate detection of Cyanobacterial toxin microcystin-LR using fiber-optic long-period grating based immunosensor

    CERN Document Server

    Tripathi, Saurabh Mani; Mikulic, Predrag; Mishra, Garima

    2014-01-01

    In this paper we present a label-free, stable and highly sensitive fiber-optic sensor for detection of environmental toxin microcystin-LR (MC-LR). Thiolated MC-LR-targeting aptamer covalently immobilized on dual-resonance long-period fiber gratings (DR-LPFG) is used as MC-LR recognition element and the spectral response of the DR-LPFG is monitored for various concentrations of MC-LR. Sensitivity of the DR-LPFG is optimized by coating an appropriate thickness of gold layer to the fiber surface. Gold coating serves two purposes, first it locally supports a surface-Plasmon mode associated with the modified cladding modes and second it helps covalently immobilize the MC-LR targeting aptamer to the sensor surface. Monitoring both the resonance wavelengths of our ultra sensitive DR-LPFGs (3891.5 nm/RIU) we study the aptamer and MC-LR binding to the sensor surface. Real-time, efficient MC-LR molecular binding to the sensor surface is also confirmed using atomic force microscopy. The detection limit of our sensor, li...

  7. Evaluation of modified Wright-staining of dried urinary sediment as a method for accurate detection of bacteriuria in cats.

    Science.gov (United States)

    Swenson, Cheryl L; Boisvert, Agatha M; Gibbons-Burgener, Suzanne N; Kruger, John M

    2011-06-01

    Urinary sediment examination and quantitative urinary culture results are frequently discordant. The aims of this study were to compare accuracy of light microscopic examination of wet-mounted unstained (wet-unstained) and air-dried modified Wright-stained (dry-stained) sedimented preparations of urine with results of quantitative aerobic bacterial culture for detection and characterization of bacteriuria in cats. In addition, the presence of pyuria detected by urinalysis and potential risk factors were assessed. A blinded prospective study was conducted on 472 urinary samples collected from 410 cats by cystocentesis. The age and sex of each cat were recorded. Complete urinalyses were performed and included quantification of WBCs. Quantity and morphology of bacteria in each specimen were determined by light microscopic examination of wet-unstained (performed by certified medical technologists) and dry-stained (performed by a veterinary clinical pathologist) sedimented preparations of urine and compared with results of quantitative bacterial cultures. Of 472 urinary specimens, 29 were positive for bacteriuria by culture and considered true positives and 443 were considered true negatives. Compared with these results, examination of wet-unstained and dry-stained urines had sensitivities of 75.9% and 82.8%, specificities of 56.7% and 98.7%, and test efficiencies of 57.8% and 97.7%, respectively. Positive likelihood ratios were 1.8 and 63.7 and negative likelihood ratios were 0.42 and 0.17 for wet-unstained and dry-stained examinations, respectively. Compared with 29 culture-positive samples, the wet-unstained method had morphologic concordance and misclassification rates of 37.9% and 62.1%, respectively, whereas the dry-stained method had morphologic concordance and misclassification rates of 65.5% and 34.5%, respectively. Only 34% of samples with bacteriuria had pyuria. Frequency of bacteriuria was not significantly different based on age and sex of the cats, but

  8. DNA extraction techniques compared for accurate detection of genetically modified organisms (GMOs) in maize food and feed products.

    Science.gov (United States)

    Turkec, Aydin; Kazan, Hande; Karacanli, Burçin; Lucas, Stuart J

    2015-08-01

    In this paper, DNA extraction methods have been evaluated to detect the presence of genetically modified organisms (GMOs) in maize food and feed products commercialised in Turkey. All the extraction methods tested performed well for the majority of maize foods and feed products analysed. However, the highest DNA content was achieved by the Wizard, Genespin or the CTAB method, all of which produced optimal DNA yield and purity for different maize food and feed products. The samples were then screened for the presence of GM elements, along with certified reference materials. Of the food and feed samples, 8 % tested positive for the presence of one GM element (NOS terminator), of which half (4 % of the total) also contained a second element (the Cauliflower Mosaic Virus 35S promoter). The results obtained herein clearly demonstrate the presence of GM maize in the Turkish market, and that the Foodproof GMO Screening Kit provides reliable screening of maize food and feed products.

  9. Neutron Interrogation System For Underwater Threat Detection And Identification

    Science.gov (United States)

    Barzilov, Alexander P.; Novikov, Ivan S.; Womble, Phil C.

    2009-03-01

    Wartime and terrorist activities, training and munitions testing, dumping and accidents have generated significant munitions contamination in the coastal and inland waters in the United States and abroad. Although current methods provide information about the existence of the anomaly (for instance, metal objects) in the sea bottom, they fail to identify the nature of the found objects. Field experience indicates that often in excess of 90% of objects excavated during the course of munitions clean up are found to be non-hazardous items (false alarm). The technology to detect and identify waterborne or underwater threats is also vital for protection of critical infrastructures (ports, dams, locks, refineries, and LNG/LPG). We are proposing a compact neutron interrogation system, which will be used to confirm possible threats by determining the chemical composition of the suspicious underwater object. The system consists of an electronic d-T 14-MeV neutron generator, a gamma detector to detect the gamma signal from the irradiated object and a data acquisition system. The detected signal then is analyzed to quantify the chemical elements of interest and to identify explosives or chemical warfare agents.

  10. A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

    Directory of Open Access Journals (Sweden)

    Pique-Regi Roger

    2011-05-01

    Full Text Available Abstract Background Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly defined since it has been only studied systematically in one large-scale study and by using non optimal ad-hoc SNP array data analysis tools, uncovering rather large alterations (> 1 Mb and affecting a high proportion of cells. Here we propose a novel methodology, Mosaic Alteration Detection-MAD, by providing a software tool that is effective for capturing previously described alterations as wells as new variants that are smaller in size and/or affecting a low percentage of cells. Results The developed method identified all previously known mosaic abnormalities reported in SNP array data obtained from controls, bladder cancer and HapMap individuals. In addition MAD tool was able to detect new mosaic variants not reported before that were smaller in size and with lower percentage of cells affected. The performance of the tool was analysed by studying simulated data for different scenarios. Our method showed high sensitivity and specificity for all assessed scenarios. Conclusions The tool presented here has the ability to identify mosaic abnormalities with high sensitivity and specificity. Our results confirm the lack of sensitivity of former methods by identifying new mosaic variants not reported in previously utilised datasets. Our work suggests that the prevalence of mosaic alterations could be higher than initially thought. The use of appropriate SNP array data analysis methods would help in defining the human genome mosaic map.

  11. Accurate X-ray position of the Anomalous X-ray Pulsar XTE J1810-197 and identification of its likely IR counterpart

    CERN Document Server

    Israel, G L; Mangano, V; Testa, V; Perna, R; Hummel, W; Mignani, R P; Ageorges, N; Curto, G L; Marco, O; Angelini, L; Campana, S; Covino, S; Marconi, G; Mereghetti, S; Stella, L

    2004-01-01

    We report the accurate sub-arcsec X-ray position of the new Anomalous X-ray Pulsar (AXP) XTE J1810-197, derived with a Chndra-HRC Target of Opportunity observation carried out in November 2003. We also report the discovery of a likely IR counterpart based on a VLT (IR band) Target of Opportunity observation carried out in October 2003. Our proposed counterpart is the only IR source (Ks=20.8) in the X-ray error circle. Its IR colors as well as the X-ray/IR flux ratio, are consistent with those of the counterparts of all other AXPs (at variance with field star colors). Deep Gunn-i band images obtained at the 3.6m ESO telescope detected no sources down to a limiting magnitude of 24.3. Moreover, we find that the pulsed fraction and count rates of XTE J1810-197 remained nearly unchanged since the previous Chandra and XMM-Newton observations (2003 August 27th and September 8th, respectively). We briefly discuss the implications of these results. In particular, we note that the transient (or at least highly variable...

  12. Accurate Identification of ALK Positive Lung Carcinoma Patients: Novel FDA-Cleared Automated Fluorescence In Situ Hybridization Scanning System and Ultrasensitive Immunohistochemistry

    Science.gov (United States)

    Conde, Esther; Suárez-Gauthier, Ana; Benito, Amparo; Garrido, Pilar; García-Campelo, Rosario; Biscuola, Michele; Paz-Ares, Luis; Hardisson, David; de Castro, Javier; Camacho, M. Carmen; Rodriguez-Abreu, Delvys; Abdulkader, Ihab; Ramirez, Josep; Reguart, Noemí; Salido, Marta; Pijuán, Lara; Arriola, Edurne; Sanz, Julián; Folgueras, Victoria; Villanueva, Noemí; Gómez-Román, Javier; Hidalgo, Manuel; López-Ríos, Fernando

    2014-01-01

    Background Based on the excellent results of the clinical trials with ALK-inhibitors, the importance of accurately identifying ALK positive lung cancer has never been greater. However, there are increasing number of recent publications addressing discordances between FISH and IHC. The controversy is further fuelled by the different regulatory approvals. This situation prompted us to investigate two ALK IHC antibodies (using a novel ultrasensitive detection-amplification kit) and an automated ALK FISH scanning system (FDA-cleared) in a series of non-small cell lung cancer tumor samples. Methods Forty-seven ALK FISH-positive and 56 ALK FISH-negative NSCLC samples were studied. All specimens were screened for ALK expression by two IHC antibodies (clone 5A4 from Novocastra and clone D5F3 from Ventana) and for ALK rearrangement by FISH (Vysis ALK FISH break-apart kit), which was automatically captured and scored by using Bioview's automated scanning system. Results All positive cases with the IHC antibodies were FISH-positive. There was only one IHC-negative case with both antibodies which showed a FISH-positive result. The overall sensitivity and specificity of the IHC in comparison with FISH were 98% and 100%, respectively. Conclusions The specificity of these ultrasensitive IHC assays may obviate the need for FISH confirmation in positive IHC cases. However, the likelihood of false negative IHC results strengthens the case for FISH testing, at least in some situations. PMID:25248157

  13. Accurate identification of ALK positive lung carcinoma patients: novel FDA-cleared automated fluorescence in situ hybridization scanning system and ultrasensitive immunohistochemistry.

    Directory of Open Access Journals (Sweden)

    Esther Conde

    Full Text Available BACKGROUND: Based on the excellent results of the clinical trials with ALK-inhibitors, the importance of accurately identifying ALK positive lung cancer has never been greater. However, there are increasing number of recent publications addressing discordances between FISH and IHC. The controversy is further fuelled by the different regulatory approvals. This situation prompted us to investigate two ALK IHC antibodies (using a novel ultrasensitive detection-amplification kit and an automated ALK FISH scanning system (FDA-cleared in a series of non-small cell lung cancer tumor samples. METHODS: Forty-seven ALK FISH-positive and 56 ALK FISH-negative NSCLC samples were studied. All specimens were screened for ALK expression by two IHC antibodies (clone 5A4 from Novocastra and clone D5F3 from Ventana and for ALK rearrangement by FISH (Vysis ALK FISH break-apart kit, which was automatically captured and scored by using Bioview's automated scanning system. RESULTS: All positive cases with the IHC antibodies were FISH-positive. There was only one IHC-negative case with both antibodies which showed a FISH-positive result. The overall sensitivity and specificity of the IHC in comparison with FISH were 98% and 100%, respectively. CONCLUSIONS: The specificity of these ultrasensitive IHC assays may obviate the need for FISH confirmation in positive IHC cases. However, the likelihood of false negative IHC results strengthens the case for FISH testing, at least in some situations.

  14. Pyrosequencing as a tool for rapid fish species identification and commercial fraud detection.

    Science.gov (United States)

    De Battisti, Cristian; Marciano, Sabrina; Magnabosco, Cristian; Busato, Sara; Arcangeli, Giuseppe; Cattoli, Giovanni

    2014-01-08

    The increased consumption of fish products, as well as the occurrence of exotic fish species in the Mediterranean Sea and in the fish market, has increased the risk of commercial fraud. Furthermore, the great amount of processed seafood products has greatly limited the application of classic identification systems. DNA-based identification allows a clear and unambiguous detection of polymorphisms between species, permitting differentiation and identification of both commercial fraud and introduction of species with potential toxic effects on humans. In this study, a novel DNA-based approach for differentiation of fish species based on pyrosequencing technology has been developed. Raw and processed fish products were tested, and up to 25 species of fish belonging to Clupeiformes and Pleuronectiformes groups were uniquely and rapidly identified. The proper identification based on short and unique genetic sequence signatures demonstrates that this approach is promising and cost-effective for large-scale surveys.

  15. A Subspace Identification Method for Detecting Abnormal Behavior in HVAC Systems

    Directory of Open Access Journals (Sweden)

    Dimitris Sklavounos

    2015-01-01

    Full Text Available A method for the detection of abnormal behavior in HVAC systems is presented. The method combines deterministic subspace identification for each zone independently to create a system model that produces the anticipated zone’s temperature and the sequential test CUSUM algorithm to detect drifts of the rate of change of the difference between the real and the anticipated measurements. Simulation results regarding the detection of infiltration heat losses and the detection of exogenous heat gains such as fire demonstrate the effectiveness of the proposed method.

  16. Species-specific detection and identification of fusarium species complex, the causal agent of sugarcane pokkah boeng in China.

    Directory of Open Access Journals (Sweden)

    Zhenyue Lin

    Full Text Available BACKGROUND: Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. METHODS: A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. RESULT: Two Fusarium species (F. verticillioides and F. proliferatum that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. CONCLUSIONS/SIGNIFICANCE: This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng.

  17. Real-time quantitative PCR for detection and identification of Actinobacillus pleuropneumoniae serotype 2

    Directory of Open Access Journals (Sweden)

    Dors Arkadiusz

    2016-09-01

    Full Text Available Introduction: Porcine pleuropneumonia inflicts important economic losses on most commercial herds. Detection of subclinical or chronic infection in animals still remains a challenge, as isolation and identification of A. pleuropneumoniae serotypes is difficult and quantification of the bacteria on agar plates is often almost impossible. The aim of the study was to develop and evaluate a serotype-specific quantitative TaqMan probe-based PCR for detection of serotype 2 in pig lungs, tonsils, and nasal swabs.

  18. Identification of pathogenic microbial cells and spores by electrochemical detection on a biochip

    OpenAIRE

    Andresen Heiko; Gabig-Ciminska Magdalena; Albers Joerg; Hintsche Rainer; Enfors Sven-Olof

    2004-01-01

    Abstract Background Bacillus cereus constitutes a significant cause of acute food poisoning in humans. Despite the recent development of different detection methods, new effective control measures and better diagnostic tools are required for quick and reliable detection of pathogenic micro-organisms. Thus, the objective of this study was to determine a simple method for rapid identification of enterotoxic Bacillus strains. Here, a special attention is given to an electrochemical biosensor sin...

  19. Rapid and accurate identification of isolates of Candida species by melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA)

    NARCIS (Netherlands)

    Decat, E.; van Mechelen, E.; Saerens, B.; Vermeulen, S.J.T.; Boekhout, T.; de Blaiser, S.; Vaneechoutte, M.; Deschaght, P.

    2013-01-01

    Rapid identification of clinically important yeasts can facilitate the initiation of anti-fungal therapy, since susceptibility is largely species-dependent. We evaluated melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA) as an identification too

  20. Rapid and accurate identification of isolates of Candida species by melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA)

    NARCIS (Netherlands)

    Decat, E.; van Mechelen, E.; Saerens, B.; Vermeulen, S.J.T.; Boekhout, T.; de Blaiser, S.; Vaneechoutte, M.; Deschaght, P.

    2013-01-01

    Rapid identification of clinically important yeasts can facilitate the initiation of anti-fungal therapy, since susceptibility is largely species-dependent. We evaluated melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA) as an identification

  1. Detection of bacterial 16S ribosomal RNA genes for forensic identification of vaginal fluid.

    Science.gov (United States)

    Akutsu, Tomoko; Motani, Hisako; Watanabe, Ken; Iwase, Hirotaro; Sakurada, Koichi

    2012-05-01

    To preliminarily evaluate the applicability of bacterial DNA as a marker for the forensic identification of vaginal fluid, we developed and performed PCR-based detection of 16S ribosomal RNA genes of Lactobacillus spp. dominating the vagina and of bacterial vaginosis-related bacteria from DNA extracted from body fluids and stains. As a result, 16S ribosomal RNA genes of Lactobacillus crispatus, Lactobacillus jensenii and Atopobium vaginae were specifically detected in vaginal fluid and female urine samples. Bacterial genes detected in female urine might have originated from contaminated vaginal fluid. In addition, those of Lactobacillus iners, Lactobacillus gasseri and Gardnerella vaginalis were also detected in non-vaginal body fluids such as semen. Because bacterial genes were successfully amplified in DNA samples extracted by using the general procedure for animal tissues without any optional treatments, DNA samples prepared for the identification of vaginal fluid can also be used for personal identification. In conclusion, 16S ribosomal RNA genes of L. crispatus, L. jensenii and A. vaginae could be effective markers for forensic identification of vaginal fluid.

  2. Molecular techniques for the identification and detection of microorganisms relevant for the food industry

    NARCIS (Netherlands)

    Klijn, N.

    1996-01-01

    The research described in this thesis concerns the development and application in food microbiology of molecular identification and detection techniques based on 16S rRNA sequences. The technologies developed were applied to study the microbial ecology of two groups of bacteria, namely

  3. Molecular techniques for the identification and detection of microorganisms relevant for the food industry.

    NARCIS (Netherlands)

    Klijn, N.

    1996-01-01

    The research described in this thesis concerns the development and application in food microbiology of molecular identification and detection techniques based on 16S rRNA sequences. The technologies developed were applied to study the microbial ecology of two groups of bacteria, namely starter cultu

  4. Molecular techniques for the identification and detection of microorganisms relevant for the food industry

    NARCIS (Netherlands)

    Klijn, N.

    1996-01-01

    The research described in this thesis concerns the development and application in food microbiology of molecular identification and detection techniques based on 16S rRNA sequences. The technologies developed were applied to study the microbial ecology of two groups of bacteria, namely star

  5. Subspace-Based Algorithms for Structural Identification, Damage Detection, and Sensor Data Fusion

    Directory of Open Access Journals (Sweden)

    Goursat Maurice

    2007-01-01

    Full Text Available This paper reports on the theory and practice of covariance-driven output-only and input/output subspace-based identification and detection algorithms. The motivating and investigated application domain is vibration-based structural analysis and health monitoring of mechanical, civil, and aeronautic structures.

  6. Pulsed Photofission Delayed Gamma Ray Detection for Nuclear Material Identification

    Energy Technology Data Exchange (ETDEWEB)

    John Kavouras; Xianfei Wen; Daren R. Norman; Dante R. Nakazawa; Haori Yang

    2012-11-01

    Innovative systems with increased sensitivity and resolution are in great demand to detect diversion and to prevent misuse in support of nuclear materials management for the U.S. fuel cycle. Nuclear fission is the most important multiplicative process involved in non-destructive active interrogation. This process produces the most easily recognizable signature for nuclear materials. High-energy gamma rays can also excite a nucleus and cause fission through a process known as photofission. After photofission reactions, delayed signals are easily distinguishable from the interrogating radiation. Linac-based, advanced inspection techniques utilizing the fission signals after photofission have been extensively studied for homeland security applications. Previous research also showed that a unique delayed gamma ray energy spectrum exists for each fissionable isotope. Isotopic composition measurement methods based on delayed gamma ray spectroscopy will be the primary focus of this work.

  7. Common pharmacophore identification using frequent clique detection algorithm.

    Science.gov (United States)

    Podolyan, Yevgeniy; Karypis, George

    2009-01-01

    The knowledge of a pharmacophore, or the 3D arrangement of features in the biologically active molecule that is responsible for its pharmacological activity, can help in the search and design of a new or better drug acting upon the same or related target. In this paper, we describe two new algorithms based on the frequent clique detection in the molecular graphs. The first algorithm mines all frequent cliques that are present in at least one of the conformers of each (or a portion of all) molecules. The second algorithm exploits the similarities among the different conformers of the same molecule and achieves an order of magnitude performance speedup compared to the first algorithm. Both algorithms are guaranteed to find all common pharmacophores in the data set, which is confirmed by the validation on the set of molecules for which pharmacophores have been determined experimentally. In addition, these algorithms are able to scale to data sets with arbitrarily large number of conformers per molecule and identify multiple ligand binding modes or multiple binding sites of the target.

  8. Detection and Identification of People at a Critical Infrastructure Facilities of Trafic Buildings

    Directory of Open Access Journals (Sweden)

    Rastislav PIRNÍK

    2014-12-01

    Full Text Available This paper focuses on identification of persons entering objects of crucial infrastructure and subsequent detection of movement in parts of objects. It explains some of the technologies and approaches to processing specific image information within existing building apparatus. The article describes the proposed algorithm for detection of persons. It brings a fresh approach to detection of moving objects (groups of persons involved in enclosed areas focusing on securing freely accessible places in buildings. Based on the designed algorithm of identification with presupposed utilisation of 3D application, motion trajectory of persons in delimited space can be automatically identified. The application was created in opensource software tool using the OpenCV library.

  9. An algorithm for image clusters detection and identification based on color for an autonomous mobile robot

    Energy Technology Data Exchange (ETDEWEB)

    Uy, D.L.

    1996-02-01

    An algorithm for detection and identification of image clusters or {open_quotes}blobs{close_quotes} based on color information for an autonomous mobile robot is developed. The input image data are first processed using a crisp color fuszzyfier, a binary smoothing filter, and a median filter. The processed image data is then inputed to the image clusters detection and identification program. The program employed the concept of {open_quotes}elastic rectangle{close_quotes}that stretches in such a way that the whole blob is finally enclosed in a rectangle. A C-program is develop to test the algorithm. The algorithm is tested only on image data of 8x8 sizes with different number of blobs in them. The algorithm works very in detecting and identifying image clusters.

  10. Confidence in word detection predicts word identification: implications for an unconscious perception paradigm.

    Science.gov (United States)

    Haase, S J; Fisk, G

    2001-01-01

    The present experiments extend the scope of the independent observation model based on signal detection theory (Macmillan & Creelman, 1991) to complex (word) stimulus sets. In the first experiment, the model predicts the relationship between uncertain detection and subsequent correct identification, thereby providing an alternative interpretation to a phenomenon often described as unconscious perception. Our second experiment used an exclusion task (Jacoby, Toth, & Yonelinas, 1993), which, according to theories of unconscious perception, should show qualitative differences in performance based on stimulus detection accuracy and provide a relative measure of conscious versus unconscious influences (Merikle, Joordens, & Stoltz, 1995). Exclusion performance was also explained by the model, suggesting that undetected words did not unconsciously influence identification responses.

  11. Identification problem for stochastic models with application to carcinogenesis, cancer detection and radiation biology

    Directory of Open Access Journals (Sweden)

    L. G. Hanin

    2002-01-01

    Full Text Available A general framework for solving identification problem for a broad class of deterministic and stochastic models is discussed. This methodology allows for a unified approach to studying identifiability of various stochastic models arising in biology and medicine including models of spontaneous and induced Carcinogenesis, tumor progression and detection, and randomized hit and target models of irradiated cell survival. A variety of known results on parameter identification for stochastic models is reviewed and several new results are presented with an emphasis on rigorous mathematical development.

  12. MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species.

    Science.gov (United States)

    Kim, Young Jin; Kim, Si Hyun; Park, Hyun-Jung; Park, Hae-Geun; Park, Dongchul; Song, Sae Am; Lee, Hee Joo; Yong, Dongeun; Choi, Jun Yong; Kook, Joong-Ki; Kim, Hye Ran; Shin, Jeong Hwan

    2016-08-01

    All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 0, 2, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively. MALDI-TOF could be used as the primary tool for identification of Clostridium species.

  13. Rapid and accurate detection of Arcobacter contamination in commercial chicken products and wastewater samples by real-time polymerase chain reaction.

    Science.gov (United States)

    González, Ana; Suski, Jan; Ferrús, Maria A

    2010-03-01

    An SYBR Green real-time polymerase chain reaction (PCR) assay was developed for Arcobacter detection in food and wastewater samples. The assay was applied to 36 chicken and 33 wastewater samples, and the results were compared with those obtained for conventional PCR, multiplex PCR, and culture isolation. Isolates were identified by multiplex PCR and restriction fragment length polymorphism analysis of PCR-amplified DNA fragment, and typed by randomly amplified polymorphic DNA. Arcobacter sp. was detected in 25 of the 26 chicken carcasses (96%) and in 4 of the 10 liver samples (40%) by real-time PCR. Twenty-five chicken samples were positive also by conventional PCR, but in most of them the detection was only possible after 48-h enrichment. Arcobacter butzleri was the most frequently detected species. Twenty-four Arcobacter isolates were obtained from chicken samples, where A. butzleri is the only identified species. All the wastewater samples (100%) were positive for Arcobacter sp. by real-time PCR without enrichment. A. butzleri and Arcobacter cryaerophilus were detected by multiplex PCR. Fifteen samples were found to be positive by culture. Thirty-six isolates were obtained; all of them were identified as A. butzleri by multiplex PCR. However, by PCR-restriction fragment length polymorphism, 34 were identified as A. butzleri, 1 as A. cryaerophilus, and another 1 as Arcobacter skirrowii. A great genetic heterogeneity was observed by randomly amplified polymorphic DNA-PCR profiling. The real-time PCR assay developed in this work showed better detection levels than conventional PCR, together with shorter times of testing samples. Therefore, it could be used as a rapid and accurate instrument for monitoring Arcobacter contamination levels in food and water samples.

  14. Detection and identification of bacterial DNA in serum from patients with acute pancreatitis

    Science.gov (United States)

    de Madaria, E; Martínez, J; Lozano, B; Sempere, L; Benlloch, S; Such, J; Uceda, F; Francés, R; Pérez-Mateo, M

    2005-01-01

    Background and aims: Bacterial infections are common complications in patients with acute pancreatitis, and translocation of bacteria from the intestinal lumen is probably the first step in the pathogenesis of these infections. As blood cultures in afebrile patients are usually negative, more sensitive methods to investigate this hypothesis in patients are needed. Our group has recently developed a method to detect the presence of bacterial DNA in biological fluids, and we aimed to detect bacterial DNA in patients with acute pancreatitis, as molecular evidences of bacterial translocation. Methods: Samples of blood were obtained on three consecutive days within the first six days after admission. Bacterial DNA was detected using a polymerase chain reaction based method, and an automated DNA nucleotide sequencing process allowed identification of bacteria species. Results: Thirty one consecutively admitted patients with acute pancreatitis were studied. Bacterial DNA was detected in six patients (19.3%), and the sequencing process allowed identification of Citrobacter freundii and Pseudomonas aeruginosa. In two patients the same bacteria detected at admission was detected 24 hours later (above 99.9% homology of nucleotide sequence). Basic clinical and biochemical characteristics were similar among patients with or without the presence of bacterial DNA. Conclusion: Detection of gram negative bacteria derived bacterial DNA in our series supports the contention that bacterial translocation is a systemic process in approximately 20% of patients with acute pancreatitis that does not seem to be related to the severity of the episode or immediate development of infection. PMID:16099797

  15. PCR applications in identification of saliva samples exposed to different conditions (streptococci detection based).

    Science.gov (United States)

    Ali, M M; Shokry, D A; Zaghloul, H S; Rashed, L A; Nada, M G

    2013-06-15

    Oral streptococci represent about 20% of the total oral bacteria, so if it is possible to detect the presence of oral specific bacteria from a forensic specimen by Polymerase chain reaction, this could be used to verify the presence of saliva. Aim of this study is detection of Streptococcus salivarius which is one of the most common streptococci in oral bacteria and Streptococcus mutans which is common in cases of dental caries in various body fluids and skin swabs and assessment of which one of both organisms is more reliable in saliva identification, cross sectional study on Egypt population. Negative control samples (15 samples) were taken from various body fluids (urine, semen) and skin swabs. Mock forensic samples (85 samples) included fresh saliva, saliva, cotton fabrics contaminated with saliva, cigarette butts, bitten apple and semen mixed with saliva samples). DNA extraction was done using DNeasy blood and tissue kit (Qiagen, Tokyo, Japan). Polymerase chain reaction was done for DNA amplification using Polymerase chain reaction master mix then gel electrophoresis was done for samples qualification. Control bacteria were S. salivarius and Streptococcus mutans. Streptococcus salivarius was detected in 83.5% of all saliva contained samples and S. mutans was detected in 67% of saliva contained samples. Both bacteria were not detected in other body fluids and skin swabs, so S. salivarius is more reliable in saliva identification as well as differentiating it from other body fluids. Polymerase chain reaction is valuable in detection of saliva by detecting S. salivarius.

  16. Accurate detection of the tumor clone in peripheral T-cell lymphoma biopsies by flow cytometric analysis of TCR-Vβ repertoire.

    Science.gov (United States)

    Salameire, Dimitri; Solly, Françoise; Fabre, Blandine; Lefebvre, Christine; Chauvet, Martine; Gressin, Rémy; Corront, Bernadette; Ciapa, Agnès; Pernollet, Martine; Plumas, Joël; Macintyre, Elizabeth; Callanan, Mary B; Leroux, Dominique; Jacob, Marie-Christine

    2012-09-01

    Multiparametric flow cytometry has proven to be a powerful method for detection and immunophenotypic characterization of clonal subsets, particularly in lymphoproliferative disorders of the B-cell lineage. Although in theory promising, this approach has not been comparably fulfilled in mature T-cell malignancies. Specifically, the T-cell receptor-Vβ repertoire analysis in blood can provide strong evidence of clonality, particularly when a single expanded Vß family is detected. The purpose of this study was to determine the relevance of this approach when applied to biopsies, at the site of tumor involvement. To this end, 30 peripheral T-cell lymphoma and 94 control biopsies were prospectively studied. Vβ expansions were commonly detected within CD4+ or CD8+ T cells (97% of peripheral T-cell lymphoma and 54% of non-peripheral T-cell lymphoma cases); thus, not differentiating malignant from reactive processes. Interestingly, we demonstrated that using a standardized evaluation, the detection of a high Vβ expansion was closely associated with diagnosis of peripheral T-cell lymphoma, with remarkable specificity (98%) and sensitivity (90%). This approach also identified eight cases of peripheral T-cell lymphoma that were not detectable by other forms of immunophenotyping. Moreover, focusing Vβ expression analysis to T-cell subsets with aberrant immunophenotypes, we demonstrated that the T-cell clone might be heterogeneous with regard to surface CD7 or CD10 expression (4/11 cases), providing indication on 'phenotypic plasticity'. Finally, among the wide variety of Vβ families, the occurrence of a Vβ17 expansion in five cases was striking. To our knowledge, this is the first report demonstrating the power of T-cell receptor-Vβ repertoire analysis by flow cytometry in biopsies as a basis for peripheral T-cell lymphoma diagnosis and precise T-cell clone identification and characterization.

  17. [A novel method for the identification of illegal cooking oil (1): detection of three capsaicinoids with liquid chromatography-mass spectrometry].

    Science.gov (United States)

    Ang, Longxing; Jin, Jing; Wang, Shuqiu; Wang, Xingfu; Tian, Yuzeng; Chen, Jiping

    2012-11-01

    Illegal cooking oil (ICO, also named swill-cooked dirty oil) has recently become a serious food safety problem in China. Now, the identification method of ICO is also a hot research area. Owning to the special eating habits of Chinese people, cayenne is widely used in catering business. Capsaicinoids are main spicy compounds in cayenne. So, they are potential evaluation indices for the identification of ICO. In this study, a solid phase extraction-liquid chromatography-mass spectrometry (SPE-LC-MS) method has been developed to detect the trace residues of three capsaicinoids (capsaicin, dihydrocapsaicin and nonylic acid vanillylamide) in cooking oil. The oil sample was first extracted with 20 g/L sodium hydroxide, the C18 SPE cartridge was then used to clean-up the sample and enrich the analytes before the liquid chromatography-mass spectrometry (LC-MS) detection. With this method, sixty seven blind samples provided by China National Center for Food Safety Risk Assessment were analyzed. The results showed that the capsaicinoids are good evaluation indices for the identification of ICO. In all the 48 ICO samples, 36 samples were successfully recognized. All the 19 normal oil samples were accurately identified. This method has been chosen and authorized as one of the four standard instrumental identification methods for ICO by the National Ministry of Health of China.

  18. Intraoperative Identification of the Parathyroid Gland with a Fluorescence Detection System.

    Science.gov (United States)

    Shinden, Yoshiaki; Nakajo, Akihiro; Arima, Hideo; Tanoue, Kiyonori; Hirata, Munetsugu; Kijima, Yuko; Maemura, Kosei; Natsugoe, Shoji

    2017-06-01

    Intraoperative identification of the difficult-to-spot parathyroid gland is critical during surgery for thyroid and parathyroid disease. Recently, intrinsic fluorescence of the parathyroid gland was identified, and a new method was developed for intraoperative detection of the parathyroid with an original fluorescent detection apparatus. Here, we describe a method for intraoperative detection of the parathyroid using a ready-made photodynamic eye (PDE) system without any fluorescent dye or contrast agents. Seventeen patients who underwent surgical treatment for thyroid or parathyroid disease at Kagoshima University Hospital were enrolled in this study. Intrinsic fluorescence of various tissues was detected with the PDE system. Intraoperative in vivo and ex vivo intrinsic fluorescence of the parathyroid, thyroid, lymph nodes and fat tissues was measured and analyzed. The parathyroid gland had a significantly higher fluorescence intensity than the other tissues, including the thyroid glands, lymph nodes and fat tissues, and we could identify them during surgery using the fluorescence-guided method. Our method could be applicable for two intraoperative clinical procedures: ex vivo tissue identification of parathyroid tissue and in vivo identification of the location of the parathyroid gland, including ectopic glands. The PDE system may be an easy and highly feasible method to identify the parathyroid gland during surgery.

  19. Helicopter Based Magnetic Detection Of Wells At The Teapot Dome (Naval Petroleum Reserve No. 3 Oilfield: Rapid And Accurate Geophysical Algorithms For Locating Wells

    Science.gov (United States)

    Harbert, W.; Hammack, R.; Veloski, G.; Hodge, G.

    2011-12-01

    In this study Airborne magnetic data was collected by Fugro Airborne Surveys from a helicopter platform (Figure 1) using the Midas II system over the 39 km2 NPR3 (Naval Petroleum Reserve No. 3) oilfield in east-central Wyoming. The Midas II system employs two Scintrex CS-2 cesium vapor magnetometers on opposite ends of a transversely mounted, 13.4-m long horizontal boom located amidships (Fig. 1). Each magnetic sensor had an in-flight sensitivity of 0.01 nT. Real time compensation of the magnetic data for magnetic noise induced by maneuvering of the aircraft was accomplished using two fluxgate magnetometers mounted just inboard of the cesium sensors. The total area surveyed was 40.5 km2 (NPR3) near Casper, Wyoming. The purpose of the survey was to accurately locate wells that had been drilled there during more than 90 years of continuous oilfield operation. The survey was conducted at low altitude and with closely spaced flight lines to improve the detection of wells with weak magnetic response and to increase the resolution of closely spaced wells. The survey was in preparation for a planned CO2 flood to enhance oil recovery, which requires a complete well inventory with accurate locations for all existing wells. The magnetic survey was intended to locate wells that are missing from the well database and to provide accurate locations for all wells. The well location method used combined an input dataset (for example, leveled total magnetic field reduced to the pole), combined with first and second horizontal spatial derivatives of this input dataset, which were then analyzed using focal statistics and finally combined using a fuzzy combination operation. Analytic signal and the Shi and Butt (2004) ZS attribute were also analyzed using this algorithm. A parameter could be adjusted to determine sensitivity. Depending on the input dataset 88% to 100% of the wells were located, with typical values being 95% to 99% for the NPR3 field site.

  20. A colorimetric method for highly sensitive and accurate detection of iodide by finding the critical color in a color change process using silver triangular nanoplates.

    Science.gov (United States)

    Yang, Xiu-Hua; Ling, Jian; Peng, Jun; Cao, Qiu-E; Ding, Zhong-Tao; Bian, Long-Chun

    2013-10-10

    In this contribution, we demonstrated a novel colorimetric method for highly sensitive and accurate detection of iodide using citrate-stabilized silver triangular nanoplates (silver TNPs). Very lower concentration of iodide can induce an appreciable color change of silver TNPs solution from blue to yellow by fusing of silver TNPs to nanoparticles, as confirmed by UV-vis absorption spectroscopy and transmission electron microscopy (TEM). The principle of this colorimetric assay is not an ordinary colorimetry, but a new colorimetric strategy by finding the critical color in a color change process. With this strategy, 0.1 μM of iodide can be recognized within 30 min by naked-eyes observation, and lower concentration of iodide down to 8.8 nM can be detected using a spectrophotometer. Furthermore, this high sensitive colorimetric assay has good accuracy, stability and reproducibility comparing with other ordinary colorimetry. We believe this new colorimetric method will open up a fresh insight of simple, rapid and reliable detection of iodide and can find its future application in the biochemical analysis or clinical diagnosis.

  1. An Application for Driver Drowsiness Identification based on Pupil Detection using IR Camera

    Science.gov (United States)

    Kumar, K. S. Chidanand; Bhowmick, Brojeshwar

    A Driver drowsiness identification system has been proposed that generates alarms when driver falls asleep during driving. A number of different physical phenomena can be monitored and measured in order to detect drowsiness of driver in a vehicle. This paper presents a methodology for driver drowsiness identification using IR camera by detecting and tracking pupils. The face region is first determined first using euler number and template matching. Pupils are then located in the face region. In subsequent frames of video, pupils are tracked in order to find whether the eyes are open or closed. If eyes are closed for several consecutive frames then it is concluded that the driver is fatigued and alarm is generated.

  2. Identification of urine protein biomarkers with the potential for early detection of lung cancer

    OpenAIRE

    Hongjuan Zhang; Jing Cao; Lin Li; Yanbin Liu; Hong Zhao; Nan Li; Bo Li; Aiqun Zhang; Huanwei Huang; She Chen; Mengqiu Dong; Lei Yu; Jian Zhang; Liang Chen

    2015-01-01

    Lung cancer is the leading cause of cancer-related deaths and has an overall 5-year survival rate lower than 15%. Large-scale clinical trials have demonstrated a significant relative reduction in mortality in high-risk individuals with low-dose computed tomography screening. However, biomarkers capable of identifying the most at-risk population and detecting lung cancer before it becomes clinically apparent are urgently needed in the clinic. Here, we report the identification of urine biomark...

  3. Detection and identification of Trichophyton tonsurans from clinical isolates and hairbrush samples by loop-mediated isothermal amplification system.

    Science.gov (United States)

    Yo, Ayaka; Yamamoto, Mikachi; Nakayama, Takako; Ishikawa, Jun; Makimura, Koichi

    2016-09-01

    Since the 1990s, there have been reports of the spread of dermatophytosis caused by Trichophyton tonsurans among contact sports athletes in several countries, including Japan. This study was performed to develop a loop-mediated isothermal amplification (LAMP) system for rapid and accurate detection and identification of T. tonsurans from clinical isolates or hairbrush samples for diagnosis and to prevent the spread of infection. A specific primer set was prepared by comparing the whole genome sequence of T. tonsurans with those of six other closely related dermatophytes. After confirming the sensitivity and specificity of this system, LAMP assay was performed using 37 clinical samples obtained from three healthy volunteers and 24 judo athletes. A total of 155 fungal isolates (56 strains of various standard fungi, 96 identified T. tonsurans isolates, three hairbrush-cultured isolates from judo athletes) and 37 hairbrush samples (34 samples from 24 judo athletes, and three samples from three healthy volunteers) were used for culture and LAMP assay, respectively. The assay showed no cross-reactivity to standard strains other than T. tonsurans. The detection limit was 100 copies of DNA template per tube. All of the 96 T. tonsurans isolates were amplified, and all samples from healthy volunteers showed negative results. Four of the 34 hairbrush samples obtained from judo athletes showed positive results in LAMP assay, and two of the four were positive in both culture and LAMP assay. We developed a rapid LAMP system with high specificity and sensitivity for diagnosis of T. tonsurans infection.

  4. Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes.

    Science.gov (United States)

    Ono, Hanako; Ishii, Kazuo; Kozaki, Toshinori; Ogiwara, Isao; Kanekatsu, Motoki; Yamada, Tetsuya

    2015-12-04

    . To our knowledge, this is the first reported improvement in accurate detection of DEGs via comparative RNA-Seq analysis that involved preparation of a non-redundant reference sequence. This method could be used to rapidly and cost-effectively detect useful genes in unsequenced plants.

  5. Attentive and pre-attentive processes in change detection and identification.

    Directory of Open Access Journals (Sweden)

    Howard C Hughes

    Full Text Available In studies of change blindness, observers often have the phenomenological impression that the blindness is overcome all at once, so that change detection, localization and identification apparently occur together. Three experiments are described that explore dissociations between these processes using a discrete trial procedure in which 2 visual frames are presented sequentially with no intervening inter-frame-interval. The results reveal that change detection and localization are essentially perfect under these conditions regardless of the number of elements in the display, which is consistent with the idea that change detection and localization are mediated by pre-attentive parallel processes.In contrast, identification accuracy for an item before it changes is generally poor, and is heavily dependent on the number of items displayed. Identification accuracy after a change is substantially better, but depends on the new item's duration. This suggests that the change captures attention, which substantially enhances the likelihood of correctly identifying the new item. However, the results also reveal a limited capacity to identify unattended items. Specifically, we provide evidence that strongly suggests that, at least under these conditions, observers were able to identify two items without focused attention. Our results further suggest that spatial pre-cues that attract attention to an item before the change occurs simply ensure that the cued item is one of the two whose identity is encoded.

  6. Application of ARMAV models to the identification and damage detection of mechanical and civil engineering structures

    Science.gov (United States)

    Bodeux, J. B.; Golinval, J. C.

    2001-06-01

    In this paper, the application of auto-regressive moving average vector models to system identification and damage detection is investigated. These parametric models have already been applied for the analysis of multiple input-output systems under ambient excitation. Their main advantage consists in the capability of extracting modal parameters from the recorded time signals, without the requirement of excitation measurement. The excitation is supposed to be a stationary Gaussian white noise. The method also allows the estimation of modal parameter uncertainties. On the basis of these uncertainties, a statistically based damage detection scheme is performed and it becomes possible to assess whether changes of modal parameters are caused by, e.g. some damage or simply by estimation inaccuracies. The paper reports first an example of identification and damage detection applied to a simulated system under random excitation. The `Steel-Quake' benchmark proposed in the framework of COST Action F3 `Structural Dynamics' is also analysed. This structure was defined by the Joint Research Centre in Ispra (Italy) to test steel building performance during earthquakes. The proposed method gives an excellent identification of frequencies and mode shapes, while damping ratios are estimated with less accuracy.

  7. Accurate shadow detection in liver CT images%肝CT图像中阴影部分的精确检测

    Institute of Scientific and Technical Information of China (English)

    张晓峰; 李景辉; 马燕

    2009-01-01

    The shadows in liver are likely to be cancer tissue, so the liver cancers can be detected by detecting the shadows first. The shadows and normal liver tissue are hard to divide for the densities of them are close to each other. An algorithm is proposed to calculate the signed distance function (SDF) in Chan- Vese model. This algorithm makes the initial curve close to the division edge at the beginning, largely decreases the repeating times and improves the speed of target detection of Chan-Vese model. Finally, this algorithm is applied to the accurate detection of shadows in liver CT images and divides the shadows from normal liver tissue successfully.%肝部阴影是肝癌的重要疑似对象,因此检测肝癌可以先将肝部阴影检测出来.但肝部阴影与正常肝组织密度接近,很难分割.为此,提出一种CV分割方法的初始距离函数的设置方法,该方法使初始曲线一开始就接近图像的分割边缘,极大地减少了CV方法的迭代次数,加快了CV方法目标提取的速度.最后将该方法应用于肝部阴影的精确检测,成功地分割了图像中的肝部组织与其中的阴影部分.

  8. Advanced techniques for detection and identification of microbial agents of gastroenteritis.

    Science.gov (United States)

    Dunbar, Sherry A; Zhang, Hongwei; Tang, Yi-Wei

    2013-09-01

    Gastroenteritis persists as a worldwide problem, responsible for approximately 2 million deaths annually. Traditional diagnostic methods used in the clinical microbiology laboratory include a myriad of tests, such as culture, microscopy, and immunodiagnostics, which can be labor intensive and suffer from long turnaround times and, in some cases, poor sensitivity. [corrected]. This article reviews recent advances in genomic and proteomic technologies that have been applied to the detection and identification of gastrointestinal pathogens. These methods simplify and speed up the detection of pathogenic microorganisms, and their implementation in the clinical microbiology laboratory has potential to revolutionize the diagnosis of gastroenteritis.

  9. Health Monitoring of Offshore Wind Turbines Online Fault Detection and Identification Module Test Case: Pitch Offset

    DEFF Research Database (Denmark)

    Perisic, Nevena; Pedersen, Bo Juul; Kirkegaard, Poul Henning

    LACobserver is a model based health monitoring (HM) system for wind turbines (WTGs) which provides an intuitive engineering link between load and strength parameters. The present work demonstrates a newly developed LACobserver Fault Detection and Identification (FDI) module for online detection...... of pitch offset and corresponding root causes. Blade-to-blade pitch offset slowly degrade the WTG performance and results in lower WTG annual energy production and higher structural loads. Thus, a FDI strategy will increase wind turbine efficiency, performance and operational lifetime....

  10. A universal microarray detection method for identification of multiple Phytophthora spp. using padlock probes.

    Science.gov (United States)

    Sikora, Katarzyna; Verstappen, Els; Mendes, Odette; Schoen, Cor; Ristaino, Jean; Bonants, Peter

    2012-06-01

    The genus Phytophthora consists of many species that cause important diseases in ornamental, agronomic, and forest ecosystems worldwide. Molecular methods have been developed for detection and identification of one or several species of Phytophthora in single or multiplex reactions. In this article, we describe a padlock probe (PLP)-based multiplex method of detection and identification for many Phytophthora spp. simultaneously. A generic TaqMan polymerase chain reaction assay, which detects all known Phytophthora spp., is conducted first, followed by a species-specific PLP ligation. A 96-well-based microarray platform with colorimetric readout is used to detect and identify the different Phytophthora spp. PLPs are long oligonucleotides containing target complementary sequence regions at both their 5' and 3' ends which can be ligated on the target into a circular molecule. The ligation is point mutation specific; therefore, closely related sequences can be differentiated. This circular molecule can then be detected on a microarray. We developed 23 PLPs to economically important Phytophthora spp. based upon internal transcribed spacer-1 sequence differences between individual Phytophthora spp. Tests on genomic DNA of many Phytophthora isolates and DNA from environmental samples showed the specificity and utility of PLPs for Phytophthora diagnostics.

  11. Development of damage detection methods in containment building using system identification

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Jeong Moon; Choun, Young Sun; Choi, In Kil

    2001-05-01

    This study presents an SI-based damage detection schemes using minimization of an error function. The singular value decomposition is utilized to investigate the instability of the SI. The Tikhonov regularization scheme is introduced to alleviate oscillations in the solutions of the SI. The optimal regularization factor is determined by the GMS and the GGMS. The characteristics of measurement error are investigated. The regularization effect is estimated by the concept of the error level and the resolution limit. The statistical approach is employed for reliable damage detection. The Monte-Carlo simulation is performed by the artificially perturbed data. The statistical distribution of system parameters obtained by the Monte-Carlo simulation is utilized in the hypothesis test for the damage detection. The validity and effectiveness of the proposed method is demonstrated through three types of numerical examples identification of an inclusion in a plate, determination of prestress losses in a containment building and damage detection in a containment building.

  12. Detection and identification of infectious bronchitis virus by RT-PCR in Iran.

    Science.gov (United States)

    Homayounimehr, Alireza; Pakbin, Ahmad; Momayyez, Reza; Fatemi, Seyyedeh Mahsa Rastegar

    2016-06-01

    Infectious bronchitis virus (IBV) causes severe diseases in poultry with significant economic consequences to the poultry industry in Iran. The aim of this study was the detection and identification of IBV by reverse transcription(RT)-PCR in Iran. Ten IB virus strains were detected by testing trachea, cecal tonsil, and kidney tissues collected from broiler and layer farms in Iran. In order to detect infectious bronchitis virus, an optimized RT-PCR was used. Primers targeting the conserved region of known IBV serotypes were used in the RT-PCR assay. Primers selectively detecting Massachusetts and 793/B type IB viruses were designed to amplify the S1 gene of the virus and used in the nested PCR test. Our findings indicate the circulation of at least three genotypes of IB viruses (Massachusetts, 793/B, and variant 2) among poultry flocks.

  13. Accurate recapture identification for genetic mark-recapture studies with error-tolerant likelihood-based match calling and sample clustering.

    Science.gov (United States)

    Sethi, Suresh A; Linden, Daniel; Wenburg, John; Lewis, Cara; Lemons, Patrick; Fuller, Angela; Hare, Matthew P

    2016-12-01

    Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark-recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering algorithms to group samples into sets of recaptures based upon pairwise match calls, these tools can be used to reconstruct accurate capture histories for mark-recapture modelling. Here, we assess the performance of a recently introduced error-tolerant likelihood-based match-calling model and sample clustering algorithm for genetic mark-recapture studies. We assessed both biallelic (i.e. single nucleotide polymorphisms; SNP) and multiallelic (i.e. microsatellite; MSAT) markers using a combination of simulation analyses and case study data on Pacific walrus (Odobenus rosmarus divergens) and fishers (Pekania pennanti). A novel two-stage clustering approach is demonstrated for genetic mark-recapture applications. First, repeat captures within a sampling occasion are identified. Subsequently, recaptures across sampling occasions are identified. The likelihood-based matching protocol performed well in simulation trials, demonstrating utility for use in a wide range of genetic mark-recapture studies. Moderately sized SNP (64+) and MSAT (10-15) panels produced accurate match calls for recaptures and accurate non-match calls for samples from closely related individuals in the face of low to moderate genotyping error. Furthermore, matching performance remained stable or increased as the number of genetic markers increased, genotyping error notwithstanding.

  14. Electrochemical detection of commercial silver nanoparticles: identification, sizing and detection in environmental media

    Science.gov (United States)

    Stuart, E. J. E.; Tschulik, K.; Omanović, D.; Cullen, J. T.; Jurkschat, K.; Crossley, A.; Compton, R. G.

    2013-11-01

    The electrochemistry of silver nanoparticles contained in a consumer product has been studied. The redox properties of silver particles in a commercially available disinfectant cleaning spray were investigated via cyclic voltammetry before particle-impact voltammetry was used to detect single particles in both a typical aqueous electrolyte and authentic seawater media. We show that particle-impact voltammetry is a promising method for the detection of nanoparticles that have leached into the environment from consumer products, which is an important development for the determination of risks associated with the incorporation of nanotechnology into everyday products.

  15. Enzymic colorimetry-based DNA chip: a rapid and accurate assay for detecting mutations for clarithromycin resistance in the 23S rRNA gene of Helicobacter pylori.

    Science.gov (United States)

    Xuan, Shi-Hai; Zhou, Yu-Gui; Shao, Bo; Cui, Ya-Lin; Li, Jian; Yin, Hong-Bo; Song, Xiao-Ping; Cong, Hui; Jing, Feng-Xiang; Jin, Qing-Hui; Wang, Hui-Min; Zhou, Jie

    2009-11-01

    Macrolide drugs, such as clarithromycin (CAM), are a key component of many combination therapies used to eradicate Helicobacter pylori. However, resistance to CAM is increasing in H. pylori and is becoming a serious problem in H. pylori eradication therapy. CAM resistance in H. pylori is mostly due to point mutations (A2142G/C, A2143G) in the peptidyltransferase-encoding region of the 23S rRNA gene. In this study an enzymic colorimetry-based DNA chip was developed to analyse single-nucleotide polymorphisms of the 23S rRNA gene to determine the prevalence of mutations in CAM-related resistance in H. pylori-positive patients. The results of the colorimetric DNA chip were confirmed by direct DNA sequencing. In 63 samples, the incidence of the A2143G mutation was 17.46 % (11/63). The results of the colorimetric DNA chip were concordant with DNA sequencing in 96.83 % of results (61/63). The colorimetric DNA chip could detect wild-type and mutant signals at every site, even at a DNA concentration of 1.53 x 10(2) copies microl(-1). Thus, the colorimetric DNA chip is a reliable assay for rapid and accurate detection of mutations in the 23S rRNA gene of H. pylori that lead to CAM-related resistance, directly from gastric tissues.

  16. Rapid Electrochemical Detection and Identification of Microbiological and Chemical Contaminants for Manned Spaceflight Project

    Science.gov (United States)

    Pierson, Duane; Botkin, Douglas; Gazda, Daniel

    2014-01-01

    Microbial control in the spacecraft environment is a daunting task, especially in the presence of human crew members. Currently, assessing the potential crew health risk associated with a microbial contamination event requires return of representative environmental samples that are analyzed in a ground-based laboratory. It is therefore not currently possible to quickly identify microbes during spaceflight. This project addresses the unmet need for spaceflight-compatible microbial identification technology. The electrochemical detection and identification platform is expected to provide a sensitive, specific, and rapid sample-to-answer capability for in-flight microbial monitoring that can distinguish between related microorganisms (pathogens and non-pathogens) as well as chemical contaminants. This will dramatically enhance our ability to monitor the spacecraft environment and the health risk to the crew. Further, the project is expected to eliminate the need for sample return while significantly reducing crew time required for detection of multiple targets. Initial work will focus on the optimization of bacterial detection and identification. The platform is designed to release nucleic acids (DNA and RNA) from microorganisms without the use of harmful chemicals. Bacterial DNA or RNA is captured by bacteria-specific probe molecules that are bound to a microelectrode, and that capture event can generate a small change in the electrical current (Lam, et al. 2012. Anal. Chem. 84(1): 21-5.). This current is measured, and a determination is made whether a given microbe is present in the sample analyzed. Chemical detection can be accomplished by directly applying a sample to the microelectrode and measuring the resulting current change. This rapid microbial and chemical detection device is designed to be a low-cost, low-power platform anticipated to be operated independently of an external power source, characteristics optimal for manned spaceflight and areas where power

  17. High effective THz-TDS method for the detection and identification of substances in real conditions

    Science.gov (United States)

    Trofimov, Vyacheslav A.; Varentsova, Svetlana A.; Tikhomirov, Vasiliy V.; Trofimov, Vladislav V.

    2016-05-01

    Low efficiency of the standard THz-TDS method for the detection and identification of substances is demonstrated. For this purpose, we use a few examples. In the first example, we model the noisy THz signals transmitted through the amphetamine-type stimulant in real conditions. Namely, with a temperature 18° C, the relative humidity of about 50 % and the distance between the parabolic mirror and the object about of 3.5 meters. We show that the standard THz-TDS method reveals the spectral features of many neutral substances and explosives in the noisy THz signals from the illicit stimulant MA, at the same time this method is not able to detect the presence of this stimulant in the noisy signals. The second example is the detection and identification of plastids with inhomogeneous surface in reflection mode. We show that inhomogeneous surface distorts spectral characteristics of the reflected THz signal main pulse, which cannot be used for the detection and identification of the plastids by means of the THz TDS method. In the last example we show that even under laboratory conditions (at short distance from the receiver), THz TDS detects in the semiconductors the absorption frequencies, which belong to both hazardous and neutral substances. To overcome this disadvantage, we propose to use the time-dependent spectrum of the THz pulse, transmitted through or reflected from a substance. For quality assessment of the presence of the standard substance absorption frequency in the signal under analysis, we use time-dependent integral correlation criteria. The influence of aperture placed in front of the sample on spectral properties of silicon wafers with different resistivity is demonstrated as well.

  18. Rapid detection and identification of viral and bacterial fish pathogens using a DNA array‐based multiplex assay

    DEFF Research Database (Denmark)

    Lievens, B.; Frans, I.; Heusdens, C.

    2011-01-01

    for the simultaneous detection and identification of all cyprinid herpesviruses (CyHV‐1, CyHV‐2 and CyHV‐3) and some of the most important fish pathogenic Flavobacterium species, including F. branchiophilum, F. columnare and F. psychrophilum. For virus identification, the DNA polymerase and helicase genes were...

  19. Generic RT-PCR tests for detection and identification of tospoviruses.

    Science.gov (United States)

    Hassani-Mehraban, A; Westenberg, M; Verhoeven, J T J; van de Vossenberg, B T L H; Kormelink, R; Roenhorst, J W

    2016-07-01

    A set of tests for generic detection and identification of tospoviruses has been developed. Based on a multiple sequence alignment of the nucleocapsid gene and its 5' upstream untranslated region sequence from 28 different species, primers were designed for RT-PCR detection of tospoviruses from all recognized clades, i.e. the American, Asian and Eurasian clades, and from the small group of distinct and floating species. Pilot experiments on isolates from twenty different species showed that the designed primer sets successfully detected all species by RT-PCR, as confirmed by nucleotide sequence analysis of the amplicons. In a final optimized design, the primers were applied in a setting of five RT-PCR tests. Seven different tospoviruses were successfully identified from diagnostic samples and in addition a non-described tospovirus species from alstroemeria plants. The results demonstrate that the newly developed generic RT-PCR tests provide a relevant tool for broad detection and identification of tospoviruses in plant quarantine and diagnostic laboratories.

  20. Immunity-based detection, identification, and evaluation of aircraft sub-system failures

    Science.gov (United States)

    Moncayo, Hever Y.

    This thesis describes the design, development, and flight-simulation testing of an integrated Artificial Immune System (AIS) for detection, identification, and evaluation of a wide variety of sensor, actuator, propulsion, and structural failures/damages including the prediction of the achievable states and other limitations on performance and handling qualities. The AIS scheme achieves high detection rate and low number of false alarms for all the failure categories considered. Data collected using a motion-based flight simulator are used to define the self for an extended sub-region of the flight envelope. The NASA IFCS F-15 research aircraft model is used and represents a supersonic fighter which include model following adaptive control laws based on non-linear dynamic inversion and artificial neural network augmentation. The flight simulation tests are designed to analyze and demonstrate the performance of the immunity-based aircraft failure detection, identification and evaluation (FDIE) scheme. A general robustness analysis is also presented by determining the achievable limits for a desired performance in the presence of atmospheric perturbations. For the purpose of this work, the integrated AIS scheme is implemented based on three main components. The first component performs the detection when one of the considered failures is present in the system. The second component consists in the identification of the failure category and the classification according to the failed element. During the third phase a general evaluation of the failure is performed with the estimation of the magnitude/severity of the failure and the prediction of its effect on reducing the flight envelope of the aircraft system. Solutions and alternatives to specific design issues of the AIS scheme, such as data clustering and empty space optimization, data fusion and duplication removal, definition of features, dimensionality reduction, and selection of cluster/detector shape are also

  1. Identification of inorganic improvised explosive devices using sequential injection capillary electrophoresis and contactless conductivity detection.

    Science.gov (United States)

    Blanco, Gustavo A; Nai, Yi H; Hilder, Emily F; Shellie, Robert A; Dicinoski, Greg W; Haddad, Paul R; Breadmore, Michael C

    2011-12-01

    A simple sequential injection capillary electrophoresis (SI-CE) instrument with capacitively coupled contactless conductivity detection (C(4)D) has been developed for the rapid separation of anions relevant to the identification of inorganic improvised explosive devices (IEDs). Four of the most common explosive tracer ions, nitrate, perchlorate, chlorate, and azide, and the most common background ions, chloride, sulfate, thiocyanate, fluoride, phosphate, and carbonate, were chosen for investigation. Using a separation electrolyte comprising 50 mM tris(hydroxymethyl)aminomethane, 50 mM cyclohexyl-2-aminoethanesulfonic acid, pH 8.9 and 0.05% poly(ethyleneimine) (PEI) in a hexadimethrine bromide (HDMB)-coated capillary it was possible to partially separate all 10 ions within 90 s. The combination of two cationic polymer additives (PEI and HDMB) was necessary to achieve adequate selectivity with a sufficiently stable electroosmotic flow (EOF), which was not possible with only one polymer. Careful optimization of variables affecting the speed of separation and injection timing allowed a further reduction of separation time to 55 s while maintaining adequate efficiency and resolution. Software control makes high sample throughput possible (60 samples/h), with very high repeatability of migration times [0.63-2.07% relative standard deviation (RSD) for 240 injections]. The separation speed does not compromise sensitivity, with limits of detection ranging from 23 to 50 μg·L(-1) for all the explosive residues considered, which is 10× lower than those achieved by indirect absorbance detection and 2× lower than those achieved by C(4)D using portable benchtop instrumentation. The combination of automation, high sample throughput, high confidence of peak identification, and low limits of detection makes this methodology ideal for the rapid identification of inorganic IED residues.

  2. Development and validation of a multiplex real-time PCR method to simultaneously detect 47 targets for the identification of genetically modified organisms.

    Science.gov (United States)

    Cottenet, Geoffrey; Blancpain, Carine; Sonnard, Véronique; Chuah, Poh Fong

    2013-08-01

    Considering the increase of the total cultivated land area dedicated to genetically modified organisms (GMO), the consumers' perception toward GMO and the need to comply with various local GMO legislations, efficient and accurate analytical methods are needed for their detection and identification. Considered as the gold standard for GMO analysis, the real-time polymerase chain reaction (RTi-PCR) technology was optimised to produce a high-throughput GMO screening method. Based on simultaneous 24 multiplex RTi-PCR running on a ready-to-use 384-well plate, this new procedure allows the detection and identification of 47 targets on seven samples in duplicate. To comply with GMO analytical quality requirements, a negative and a positive control were analysed in parallel. In addition, an internal positive control was also included in each reaction well for the detection of potential PCR inhibition. Tested on non-GM materials, on different GM events and on proficiency test samples, the method offered high specificity and sensitivity with an absolute limit of detection between 1 and 16 copies depending on the target. Easy to use, fast and cost efficient, this multiplex approach fits the purpose of GMO testing laboratories.

  3. STARR: shortwave-targeted agile Raman robot for the detection and identification of emplaced explosives

    Science.gov (United States)

    Gomer, Nathaniel R.; Gardner, Charles W.

    2014-05-01

    In order to combat the threat of emplaced explosives (land mines, etc.), ChemImage Sensor Systems (CISS) has developed a multi-sensor, robot mounted sensor capable of identification and confirmation of potential threats. The system, known as STARR (Shortwave-infrared Targeted Agile Raman Robot), utilizes shortwave infrared spectroscopy for the identification of potential threats, combined with a visible short-range standoff Raman hyperspectral imaging (HSI) system for material confirmation. The entire system is mounted onto a Talon UGV (Unmanned Ground Vehicle), giving the sensor an increased area search rate and reducing the risk of injury to the operator. The Raman HSI system utilizes a fiber array spectral translator (FAST) for the acquisition of high quality Raman chemical images, allowing for increased sensitivity and improved specificity. An overview of the design and operation of the system will be presented, along with initial detection results of the fusion sensor.

  4. Reliable dual-redundant sensor failure detection and identification for the NASA F-8 DFBW aircraft

    Science.gov (United States)

    Deckert, J. C.; Desai, M. N.; Deyst, J. J., Jr.; Willsky, A. S.

    1978-01-01

    A technique was developed which provides reliable failure detection and identification (FDI) for a dual redundant subset of the flight control sensors onboard the NASA F-8 digital fly by wire (DFBW) aircraft. The technique was successfully applied to simulated sensor failures on the real time F-8 digital simulator and to sensor failures injected on telemetry data from a test flight of the F-8 DFBW aircraft. For failure identification the technique utilized the analytic redundancy which exists as functional and kinematic relationships among the various quantities being measured by the different control sensor types. The technique can be used not only in a dual redundant sensor system, but also in a more highly redundant system after FDI by conventional voting techniques reduced to two the number of unfailed sensors of a particular type. In addition the technique can be easily extended to the case in which only one sensor of a particular type is available.

  5. Rapid Detection and Identification of a Pathogen's DNA Using Phi29 DNA Polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Y.; Dunn, J.; Gao, S.; Bruno, J. F.; Luft, B. J.

    2008-10-31

    Zoonotic pathogens including those transmitted by insect vectors are some of the most deadly of all infectious diseases known to mankind. A number of these agents have been further weaponized and are widely recognized as being potentially significant biothreat agents. We describe a novel method based on multiply-primed rolling circle in vitro amplification for profiling genomic DNAs to permit rapid, cultivation-free differential detection and identification of circular plasmids in infectious agents. Using Phi29 DNA polymerase and a two-step priming reaction we could reproducibly detect and characterize by DNA sequencing circular DNA from Borrelia burgdorferi B31 in DNA samples containing as little as 25 pg of Borrelia DNA amongst a vast excess of human DNA. This simple technology can ultimately be adapted as a sensitive method to detect specific DNA from both known and unknown pathogens in a wide variety of complex environments.

  6. [Culture media for the detection and the identification of Streptococcus agalactiae].

    Science.gov (United States)

    de la Rosa, M; Pérez, M; Carazo, C; Pareja, L; Orts, A; Cantudo, P

    1994-01-01

    Streptococcus agalactiae, a Group B streptococcus, is the main cause of bacterial perinatal infection and is also an important opportunistic pathogen. Detection and identification of S. agalactiae are straight forward with special culture media, where Group B streptococci show a specific, typical pink or red pigment. To quickly and easily detect the pigment, culture media should contain: (i) starch; (ii) an inhibitor of the folate pathway; (iii) animal serum; (iv) a pepsic proteic hydrolysate; and (v) glucose, together with a high-capacity buffer. When selective antibiotics are added to culture media designed in this way, it is possible to detect S. agalactiae directly from clinical samples by observation of its pigment after less than 12 hours of aerobic incubation.

  7. Stable isotope-labeled excipients for drug product identification and counterfeit detection.

    Science.gov (United States)

    Felton, Linda A; Shah, Punit P; Sharp, Zachary; Atudorei, Viorel; Timmins, Graham S

    2011-01-01

    Counterfeit drug products have become a major problem worldwide and a number of techniques to detect counterfeit products or reduce the potential for counterfeiting have been investigated. This study examined the use of stable isotope-labeled excipients in solid dosage forms as a method to identify drug products and to detect counterfeits. (2)H- and (13)C-glucose were used as model excipients and incorporated in wet granulated formulations at a variety of different isotopic ratios. The ratios of (2)H/(1)H and (13)C/(12)C in each product were then determined by isotope ratio mass spectrometry. Results demonstrated the ability to detect the isotope-labeled glucose in both granules and tablets. It was possible to use the isotope ratios to differentiate between specific batches of granules, demonstrating the potential of this technique for in-product, batch-specific identification.

  8. Detection and identification of extra virgin olive oil adulteration by GC-MS combined with chemometrics.

    Science.gov (United States)

    Yang, Yang; Ferro, Miguel Duarte; Cavaco, Isabel; Liang, Yizeng

    2013-04-17

    In this study, an analytical method for the detection and identification of extra virgin olive oil adulteration with four types of oils (corn, peanut, rapeseed, and sunflower oils) was proposed. The variables under evaluation included 22 fatty acids and 6 other significant parameters (the ratio of linoleic/linolenic acid, oleic/linoleic acid, total saturated fatty acids (SFAs), polyunsaturated fatty acids (PUFAs), monounsaturated fatty acids (MUFAs), MUFAs/PUFAs). Univariate analyses followed by multivariate analyses were applied to the adulteration investigation. As a result, the univariate analyses demonstrated that higher contents of eicosanoic acid, docosanoic acid, tetracosanoic acid, and SFAs were the peculiarities of peanut adulteration and higher levels of linolenic acid, 11-eicosenoic acid, erucic acid, and nervonic acid the characteristics of rapeseed adulteration. Then, PLS-LDA made the detection of adulteration effective with a 1% detection limit and 90% prediction ability; a Monte Carlo tree identified the type of adulteration with 85% prediction ability.

  9. Detection and identification of platelet antibodies and antigens in the clinical laboratory.

    Science.gov (United States)

    Curtis, B R; McFarland, J G

    2009-01-01

    As a result of the unique functional properties of platelets, more-robust methods were required for detection of antibodies raised against them. Immunofluorescence detection by flow cytometry, solid-phase red cell adherence, and antigen capture ELISAs are some of the current tests that have been developed to meet the challenges of platelet antibody detection and identification and antigen phenotyping. Recently developed protein liquid bead arrays are becoming the next-generation platelet antibody tests. Fueled by development of PCR and determination of the molecular basis of the PlA1 human platelet antigen (HPA), serologic platelet typing has now been replaced by genotyping of DNA. Allele-specific PCR, melting curve analysis, and 5'-nuclease assays are now evolving into more high-throughput molecular tests. Laboratory testing for the diagnosis of immune platelet disorders has advanced considerably from its humble beginnings.

  10. Classification and Identification of Plant Fibrous Material with Different Species Using near Infrared Technique—A New Way to Approach Determining Biomass Properties Accurately within Different Species

    Science.gov (United States)

    Jiang, Wei; Zhou, Chengfeng; Han, Guangting; Via, Brian; Swain, Tammy; Fan, Zhaofei; Liu, Shaoyang

    2017-01-01

    Plant fibrous material is a good resource in textile and other industries. Normally, several kinds of plant fibrous materials used in one process are needed to be identified and characterized in advance. It is easy to identify them when they are in raw condition. However, most of the materials are semi products which are ground, rotted or pre-hydrolyzed. To classify these samples which include different species with high accuracy is a big challenge. In this research, both qualitative and quantitative analysis methods were chosen to classify six different species of samples, including softwood, hardwood, bast, and aquatic plant. Soft Independent Modeling of Class Analogy (SIMCA) and partial least squares (PLS) were used. The algorithm to classify different species of samples using PLS was created independently in this research. Results found that the six species can be successfully classified using SIMCA and PLS methods, and these two methods show similar results. The identification rates of kenaf, ramie and pine are 100%, and the identification rates of lotus, eucalyptus and tallow are higher than 94%. It is also found that spectra loadings can help pick up best wavenumber ranges for constructing the NIR model. Inter material distance can show how close between two species. Scores graph is helpful to choose the principal components numbers during the model construction. PMID:28105037

  11. Performance of a Micro-Strip Gas Chamber for event wise, high rate thermal neutron detection with accurate 2D position determination

    Science.gov (United States)

    Mindur, B.; Alimov, S.; Fiutowski, T.; Schulz, C.; Wilpert, T.

    2014-12-01

    A two-dimensional (2D) position sensitive detector for neutron scattering applications based on low-pressure gas amplification and micro-strip technology was built and tested with an innovative readout electronics and data acquisition system. This detector contains a thin solid neutron converter and was developed for time- and thus wavelength-resolved neutron detection in single-event counting mode, which improves the image contrast in comparison with integrating detectors. The prototype detector of a Micro-Strip Gas Chamber (MSGC) was built with a solid natGd/CsI thermal neutron converter for spatial resolutions of about 100 μm and counting rates up to 107 neutrons/s. For attaining very high spatial resolutions and counting rates via micro-strip readout with centre-of-gravity evaluation of the signal amplitude distributions, a fast, channel-wise, self-triggering ASIC was developed. The front-end chips (MSGCROCs), which are very first signal processing components, are read out into powerful ADC-FPGA boards for on-line data processing and thereafter via Gigabit Ethernet link into the data receiving PC. The workstation PC is controlled by a modular, high performance dedicated software suite. Such a fast and accurate system is crucial for efficient radiography/tomography, diffraction or imaging applications based on high flux thermal neutron beam. In this paper a brief description of the detector concept with its operation principles, readout electronics requirements and design together with the signals processing stages performed in hardware and software are presented. In more detail the neutron test beam conditions and measurement results are reported. The focus of this paper is on the system integration, two dimensional spatial resolution, the time resolution of the readout system and the imaging capabilities of the overall setup. The detection efficiency of the detector prototype is estimated as well.

  12. Development and validation of a high-performance liquid chromatography-fluorescence detection method for the accurate quantification of colistin in human plasma.

    Science.gov (United States)

    Chepyala, Divyabharathi; Tsai, I-Lin; Sun, Hsin-Yun; Lin, Shu-Wen; Kuo, Ching-Hua

    2015-02-01

    Recently, colistin has become one of the most important drugs for treating infections caused by multidrug-resistant Gram-negative bacteria. Therapeutic drug monitoring is recommended to ensure the safety and efficacy of colistin and to improve clinical outcomes. This study developed an accurate and sensitive high-performance liquid chromatography-fluorescence detection (HPLC-FLD) method for the quantification of colistin in human plasma. The sample preparation included protein precipitation using trichloroacetic acid (TCA) and methanol, followed by in-solid phase extraction (In-SPE) derivatization with 9-fluorenylmethyl chloroformate (FMOC-Cl). A Poroshell 120 EC-C18 2.1×100mm (2.7μm) column was used in the HPLC method with a mobile phase composed of acetonitrile (ACN), tetrahydrofuran (THF), and deionized (DI) water (82%, 2%, 16% (v/v), respectively). Polymyxin B1 was used as the internal standard. The total analysis time was 22min under optimal separation conditions. The HPLC-FLD method was validated over a therapeutic range of 0.3-6.0μgmL(-1). The intra-day and inter-day precisions for colistin A and colistin B were below 9.9% and 4.5% relative standard deviations, respectively. The accuracy test results were between 100.2 and 118.4%. The extraction recoveries were between 81.6 and 94.1%. The method was linear over the test range, with a 0.9991 coefficient of determination. The limit of detection was 0.1μgmL(-1). The validated HPLC-FLD method was successfully applied to quantify the colistin concentrations in 2 patient samples for therapeutic drug monitoring.

  13. Extensive Peptide Fractionation and y1 Ion-Based Interference Detection Method for Enabling Accurate Quantification by Isobaric Labeling and Mass Spectrometry.

    Science.gov (United States)

    Niu, Mingming; Cho, Ji-Hoon; Kodali, Kiran; Pagala, Vishwajeeth; High, Anthony A; Wang, Hong; Wu, Zhiping; Li, Yuxin; Bi, Wenjian; Zhang, Hui; Wang, Xusheng; Zou, Wei; Peng, Junmin

    2017-02-22

    Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from coisolated ions, resulting in ratio compression. Here we report that the ratio compression can be essentially resolved by the combination of pre-MS peptide fractionation, MS2-based interference detection, and post-MS computational interference correction. To recapitulate the complexity of biological samples, we pooled tandem mass tag (TMT)-labeled Escherichia coli peptides at 1:3:10 ratios and added in ∼20-fold more rat peptides as background, followed by the analysis of two-dimensional liquid chromatography (LC)-MS/MS. Systematic investigation shows that quantitative interference was impacted by LC fractionation depth, MS isolation window, and peptide loading amount. Exhaustive fractionation (320 × 4 h) can nearly eliminate the interference and achieve results comparable to the MS3-based method. Importantly, the interference in MS2 scans can be estimated by the intensity of contaminated y1 product ions, and we thus developed an algorithm to correct reporter ion ratios of tryptic peptides. Our data indicate that intermediate fractionation (40 × 2 h) and y1 ion-based correction allow accurate and deep TMT profiling of more than 10 000 proteins, which represents a straightforward and affordable strategy in isobaric labeling proteomics.

  14. Active-SWIR signatures for long-range night/day human detection and identification

    Science.gov (United States)

    Martin, Robert B.; Sluch, Mikhail; Kafka, Kristopher M.; Ice, Robert; Lemoff, Brian E.

    2013-05-01

    The capability to detect, observe, and positively identify people at a distance is important to numerous security and defense applications. Traditional solutions for human detection and observation include long-range visible imagers for daytime and thermal infrared imagers for night-time use. Positive identification, through computer face recognition, requires facial imagery that can be repeatably matched to a database of visible facial signatures (i.e. mug shots). Nighttime identification at large distance is not possible with visible imagers, due to lack of light, or with thermal infrared imagers, due to poor correlation with visible facial imagery. An active-SWIR imaging system was developed that is both eye-safe and invisible, capable of producing close-up facial imagery at distances of several hundred meters, even in total darkness. The SWIR facial signatures correlate well to visible signatures, allowing for biometric face recognition night or day. Night-time face recognition results for several distances will be presented. Human detection and observation results at larger distances will also be presented. Example signatures will be presented and discussed.

  15. The genetic-algorithm-enhanced blind system identification for water distribution pipeline leak detection

    Science.gov (United States)

    Yang, Jin; Wen, Yumei; Li, Ping

    2007-07-01

    The conventional leak location is based on the correlation of leak acoustic signals acquired spatially separately. By correlation, the time lag is estimated for localizing the leakage. In these methods, the detection distance is a prerequisite that has to be known beforehand. However, in practice, this prerequisite is not always satisfied. In this case, the correlation-based methods are not feasible. Actually, the acquired signals contain the characteristics related to the acoustic propagation channels; thus the blind system identification strategy is applied to estimate the transmission performances of acoustic channels. Then the times due to the propagation of the leak source signal travelling from the leak point to sensors are determined. In this way, for leak location, the detection distance is no longer a prerequisite. In blind system identification, due to the long impulse responses of the leak acoustic channels, the channels are inevitably ill conditioned and sensitive to the initial values. To overcome the ill conditions, the overlap-save and cross-correlation fitting techniques are utilized to identify the long impulse sequences under a built constraint. In order to avoid converging to the local minima, the genetic algorithm is used to minimize the cost functions. The practical detection results show the validity of the proposed scheme.

  16. Hyperspectral imaging of the crime scene for detection and identification of blood stains

    Science.gov (United States)

    Edelman, G. J.; van Leeuwen, T. G.; Aalders, M. C. G.

    2013-05-01

    Blood stains are an important source of information in forensic investigations. Extraction of DNA may lead to the identification of victims or suspects, while the blood stain pattern may reveal useful information for the reconstruction of a crime. Consequently, techniques for the detection and identification of blood stains are ideally non-destructive in order not to hamper both DNA and the blood stain pattern analysis. Currently, forensic investigators mainly detect and identify blood stains using chemical or optical methods, which are often either destructive or subject to human interpretation. We demonstrated the feasibility of hyperspectral imaging of the crime scene to detect and identify blood stains remotely. Blood stains outside the human body comprise the main chromophores oxy-hemoglobin, methemoglobin and hemichrome. Consequently, the reflectance spectra of blood stains are influenced by the composite of the optical properties of the individual chromophores and the substrate. Using the coefficient of determination between a non-linear least squares multi-component fit and the measured spectra blood stains were successfully distinguished from other substances visually resembling blood (e.g. ketchup, red wine and lip stick) with a sensitivity of 100 % and a specificity of 85 %. The practical applicability of this technique was demonstrated at a mock crime scene, where blood stains were successfully identified automatically.

  17. Chip-based device for parallel sorting, amplification, detection, and identification of nucleic acid subsequences

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Neil Reginald; Colston, Jr, Billy W.

    2016-08-09

    An apparatus for chip-based sorting, amplification, detection, and identification of a sample having a planar substrate. The planar substrate is divided into cells. The cells are arranged on the planar substrate in rows and columns. Electrodes are located in the cells. A micro-reactor maker produces micro-reactors containing the sample. The micro-reactor maker is positioned to deliver the micro-reactors to the planar substrate. A microprocessor is connected to the electrodes for manipulating the micro-reactors on the planar substrate. A detector is positioned to interrogate the sample contained in the micro-reactors.

  18. Routine ribosomal PCR and DNA sequencing for detection and identification of bacteria

    DEFF Research Database (Denmark)

    Kemp, Michael; Jensen, Kristine H; Dargis, Rimtas

    2010-01-01

    Detection and identification of bacteria by PCR and DNA sequencing from clinical sample material has been introduced as a diagnostic routine analysis during the last 5-10 years. Assays analyzing ribosomal genes have been found to be particularly useful. The technique has identified unusual bacteria...... as well as well-known bacteria in unusual infectious foci. Thereby, it has proven its value both in diagnosing infections in individual patients and as a tool to establish the pathogenic potential of bacteria not previously associated with disease. To be of clinical relevance, results from ribosomal PCR...

  19. Sound vibration signal processing for detection and identification detonation (knock) to optimize performance Otto engine

    Science.gov (United States)

    Sujono, A.; Santoso, B.; Juwana, W. E.

    2016-03-01

    Problems of detonation (knock) on Otto engine (petrol engine) is completely unresolved problem until now, especially if want to improve the performance. This research did sound vibration signal processing engine with a microphone sensor, for the detection and identification of detonation. A microphone that can be mounted is not attached to the cylinder block, that's high temperature, so that its performance will be more stable, durable and inexpensive. However, the method of analysis is not very easy, because a lot of noise (interference). Therefore the use of new methods of pattern recognition, through filtration, and the regression function normalized envelope. The result is quite good, can achieve a success rate of about 95%.

  20. Multi-gene detection and identification of mosquito-borne RNA viruses using an oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Nathan D Grubaugh

    Full Text Available BACKGROUND: Arthropod-borne viruses are important emerging pathogens world-wide. Viruses transmitted by mosquitoes, such as dengue, yellow fever, and Japanese encephalitis viruses, infect hundreds of millions of people and animals each year. Global surveillance of these viruses in mosquito vectors using molecular based assays is critical for prevention and control of the associated diseases. Here, we report an oligonucleotide DNA microarray design, termed ArboChip5.1, for multi-gene detection and identification of mosquito-borne RNA viruses from the genera Flavivirus (family Flaviviridae, Alphavirus (Togaviridae, Orthobunyavirus (Bunyaviridae, and Phlebovirus (Bunyaviridae. METHODOLOGY/PRINCIPAL FINDINGS: The assay utilizes targeted PCR amplification of three genes from each virus genus for electrochemical detection on a portable, field-tested microarray platform. Fifty-two viruses propagated in cell-culture were used to evaluate the specificity of the PCR primer sets and the ArboChip5.1 microarray capture probes. The microarray detected all of the tested viruses and differentiated between many closely related viruses such as members of the dengue, Japanese encephalitis, and Semliki Forest virus clades. Laboratory infected mosquitoes were used to simulate field samples and to determine the limits of detection. Additionally, we identified dengue virus type 3, Japanese encephalitis virus, Tembusu virus, Culex flavivirus, and a Quang Binh-like virus from mosquitoes collected in Thailand in 2011 and 2012. CONCLUSIONS/SIGNIFICANCE: We demonstrated that the described assay can be utilized in a comprehensive field surveillance program by the broad-range amplification and specific identification of arboviruses from infected mosquitoes. Furthermore, the microarray platform can be deployed in the field and viral RNA extraction to data analysis can occur in as little as 12 h. The information derived from the ArboChip5.1 microarray can help to establish

  1. Rapid and Accurate Detection of Mycobacterium tuberculosis in Sputum Samples by Cepheid Xpert MTB/RIF Assay—A Clinical Validation Study

    Science.gov (United States)

    Rachow, Andrea; Zumla, Alimuddin; Heinrich, Norbert; Rojas-Ponce, Gabriel; Mtafya, Bariki; Reither, Klaus; Ntinginya, Elias N.; O'Grady, Justin; Huggett, Jim; Dheda, Keertan; Boehme, Catharina; Perkins, Mark; Saathoff, Elmar; Hoelscher, Michael

    2011-01-01

    Background A crucial impediment to global tuberculosis control is the lack of an accurate, rapid diagnostic test for detection of patients with active TB. A new, rapid diagnostic method, (Cepheid) Xpert MTB/RIF Assay, is an automated sample preparation and real-time PCR instrument, which was shown to have good potential as an alternative to current reference standard sputum microscopy and culture. Methods We performed a clinical validation study on diagnostic accuracy of the Xpert MTB/RIF Assay in a TB and HIV endemic setting. Sputum samples from 292 consecutively enrolled adults from Mbeya, Tanzania, with suspected TB were subject to analysis by the Xpert MTB/RIF Assay. The diagnostic performance of Xpert MTB/RIF Assay was compared to standard sputum smear microscopy and culture. Confirmed Mycobacterium tuberculosis in a positive culture was used as a reference standard for TB diagnosis. Results Xpert MTB/RIF Assay achieved 88.4% (95%CI = 78.4% to 94.9%) sensitivity among patients with a positive culture and 99% (95%CI = 94.7% to 100.0%) specificity in patients who had no TB. HIV status did not affect test performance in 172 HIV-infected patients (58.9% of all participants). Seven additional cases (9.1% of 77) were detected by Xpert MTB/RIF Assay among the group of patients with clinical TB who were culture negative. Within 45 sputum samples which grew non-tuberculous mycobacteria the assay's specificity was 97.8% (95%CI = 88.2% to 99.9%). Conclusions The Xpert MTB/RIF Assay is a highly sensitive, specific and rapid method for diagnosing TB which has potential to complement the current reference standard of TB diagnostics and increase its overall sensitivity. Its usefulness in detecting sputum smear and culture negative patients needs further study. Further evaluation in high burden TB and HIV areas under programmatic health care settings to ascertain applicability, cost-effectiveness, robustness and local acceptance are required. PMID:21738575

  2. Rapid and accurate detection of Mycobacterium tuberculosis in sputum samples by Cepheid Xpert MTB/RIF assay--a clinical validation study.

    Directory of Open Access Journals (Sweden)

    Andrea Rachow

    Full Text Available BACKGROUND: A crucial impediment to global tuberculosis control is the lack of an accurate, rapid diagnostic test for detection of patients with active TB. A new, rapid diagnostic method, (Cepheid Xpert MTB/RIF Assay, is an automated sample preparation and real-time PCR instrument, which was shown to have good potential as an alternative to current reference standard sputum microscopy and culture. METHODS: We performed a clinical validation study on diagnostic accuracy of the Xpert MTB/RIF Assay in a TB and HIV endemic setting. Sputum samples from 292 consecutively enrolled adults from Mbeya, Tanzania, with suspected TB were subject to analysis by the Xpert MTB/RIF Assay. The diagnostic performance of Xpert MTB/RIF Assay was compared to standard sputum smear microscopy and culture. Confirmed Mycobacterium tuberculosis in a positive culture was used as a reference standard for TB diagnosis. RESULTS: Xpert MTB/RIF Assay achieved 88.4% (95%CI = 78.4% to 94.9% sensitivity among patients with a positive culture and 99% (95%CI = 94.7% to 100.0% specificity in patients who had no TB. HIV status did not affect test performance in 172 HIV-infected patients (58.9% of all participants. Seven additional cases (9.1% of 77 were detected by Xpert MTB/RIF Assay among the group of patients with clinical TB who were culture negative. Within 45 sputum samples which grew non-tuberculous mycobacteria the assay's specificity was 97.8% (95%CI = 88.2% to 99.9%. CONCLUSIONS: The Xpert MTB/RIF Assay is a highly sensitive, specific and rapid method for diagnosing TB which has potential to complement the current reference standard of TB diagnostics and increase its overall sensitivity. Its usefulness in detecting sputum smear and culture negative patients needs further study. Further evaluation in high burden TB and HIV areas under programmatic health care settings to ascertain applicability, cost-effectiveness, robustness and local acceptance are required.

  3. Evaluation of the AID carbapenemase line probe assay for rapid detection and identification of carbapenemase genes in Gram-negative bacilli.

    Science.gov (United States)

    Bloemberg, Guido V; Braun-Kiewnick, Andrea; Tedrup, Jan; Meijerink, Carla; Durer, Elena; Ritter, Claudia; Keller, Peter M; Hombach, Michael

    2017-04-11

    This study evaluated the AID carbapenemase line probe assay (LPA) for the detection and identification of carbapenem resistance genes in Enterobacteriaceae and other Gram-negative bacilli (GNB) using bacterial cultures and DNA extracts directly from patient urine samples. The AID carbapenemase LPA detects 13 different carbapenemase genes. Test probe accuracy was verified for using clinical Enterobacteriaceae isolates harbouring bla KPC , bla VIM , bla NDM , bla GIM , bla AIM , bla SPM , bla IMP and bla OXA-48 and a well-characterized set of Escherichia coli DH5α strains transformed with the vector plasmid pUC57- kan harbouring bla BIC , bla SIM , bla DIM , bla IMI-3 , bla IMI-1 and bla NMC-A . Sensitivity and specificity was determined by testing 151 clinical GNB strains previously characterized for the production of carbapenemase activity and carbapenemase genes. Direct detection of carbapenemase genes using the LPA was determined using 299 clinical urine specimens. Analytical sensitivity for detection in urine was determined by testing serial dilutions of bla KPC and bla NDM in clinical Klebsiella pneumoniae strains. All carbapenemase gene probes showed 100% accuracy without cross-reactions. Sensitivity and specificity of the LPA using clinical isolates was 100% for each. Analytical sensitivity for detection of bla KPC and bla NDM in urine was 10 1 -10 2 cfu. The LPA detected carbapenemase genes in 20 urines, which were confirmed in 12 samples by conventional multiplex PCR. Remarkably, 0 of the 20 urines grew carbapenemase-suspicious GNB applying EUCAST recommendations. : The AID carbapenemase LPA is an accurate, sensitive and easy-to-use test for the detection and identification of carbapenemase genes, which can readily be implemented in any diagnostic laboratory.

  4. Radio Frequency Identification Sensor Chips with Anticollision Algorithm for Simultaneous Detection of Multiple DNA Targets

    Science.gov (United States)

    Yazawa, Yoshiaki; Oonishi, Tadashi; Watanabe, Kazuki; Nemoto, Ryo; Shiratori, Akiko

    2010-04-01

    A newly developed DNA measurement method for multiple single nucleotide polymorphism (SNP) typing using a radio-frequency identification (RFID) sensor chip was demonstrated. The RFID sensor chip monolithically integrates a sensor, amplifier, analog-to-digital converter (ADC), and a passive wireless communication interface for receiving commands and transmitting data on a 2.5×2.5 mm2 silicon chip. For the simultaneous multitarget measurement, anticollision control and peak-power suppression are essential. To assign a unique identification number (UID) for the identification of multiple sensor chips, a reproducible random number generator circuit (RRG) was designed and installed on the chip. Peak-power consumption was reduced to 1018 µW by a clock gating of functional circuit blocks. Multiple SNP typing was carried out by simultaneously operating five RFID sensor chips (four with photosensors and one with a temperature sensor). The target DNA was captured on the sensor chips, and SNPs were detected by observing bioluminescence. Finally, the observed data were wirelessly transmitted to the reader.

  5. Accurate identification of UDP-glucuronosyltransferase 1A1 (UGT1A1) inhibitors using UGT1A1-overexpressing HeLa cells.

    Science.gov (United States)

    Sun, Hua; Zhou, Xiaotong; Wu, Baojian

    2015-01-01

    1. UDP-glucuronosyltransferase 1A1 (UGT1A1) plays an irreplaceable role in detoxification of bilirubin and many drugs (e.g., SN-38). Here we aimed to explore the potential of UGT1A1-overexpressing HeLa cells (or HeLa1A1 cells) as a tool to accurately identify UGT1A1 inhibitors. 2. Determination of glucuronidation rates (β-estradiol and SN-38 as the substrates) was performed using HeLa1A1 cells and uridine diphosphoglucuronic acid (UDPGA)-supplemented cDNA expressed UGT1A1 enzyme (or microsomes). The inhibitory effects (IC50 values) of 20 structurally diverse compounds on the UGT1A1 activity were determined using HeLa1A1 cells and microsomal incubations. 3. In HeLa1A1 cells, the IC50 values for inhibition of β-estradiol glucuronidation by the tested compounds ranged from 0.33 to 94.6 µM. In the microsomal incubations, the IC50 values ranged from 0.47 to 155 µM. It was found that the IC50 values of all test compounds derived from the cells were well consistent with those from the microsomes (deviated by less than two-fold). Further, the IC50 values from the cells were strongly correlated with those from microsomes (r = 0.944, p HeLa cells were an appropriate tool to accurately depict the inhibition profiles of chemicals against UGT1A1.

  6. Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'

    Directory of Open Access Journals (Sweden)

    Snowdon Stuart

    2009-07-01

    Full Text Available Abstract Background Metabolomics experiments using Mass Spectrometry (MS technology measure the mass to charge ratio (m/z and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensional metabolite 'fingerprint' or metabolite 'profile' data. High resolution MS instruments perform routinely with a mass accuracy of Results Metabolite 'structures' harvested from publicly accessible databases were converted into a common format to generate a comprehensive archive in MZedDB. 'Rules' were derived from chemical information that allowed MZedDB to generate a list of adducts and neutral loss fragments putatively able to form for each structure and calculate, on the fly, the exact molecular weight of every potential ionisation product to provide targets for annotation searches based on accurate mass. We demonstrate that data matrices representing populations of ionisation products generated from different biological matrices contain a large proportion (sometimes > 50% of molecular isotopes, salt adducts and neutral loss fragments. Correlation analysis of ESI-MS data features confirmed the predicted relationships of m/z signals. An integrated isotope enumerator in MZedDB allowed verification of exact isotopic pattern distributions to corroborate experimental data. Conclusion We conclude that although ultra-high accurate mass instruments provide major insight into the chemical diversity of biological extracts, the facile annotation of a large proportion of signals is not possible by simple, automated query of current databases using computed molecular formulae. Parameterising MZedDB to take into account predicted ionisation behaviour and the biological source of any sample improves greatly both the frequency and accuracy of potential annotation 'hits' in ESI-MS data.

  7. Rapid Detection and Identification of Yersinia pestis from Food Using Immunomagnetic Separation and Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Kingsley K. Amoako

    2012-01-01

    Full Text Available Interest has recently been renewed in the possible use of Y. pestis, the causative agent of plague, as a biological weapon by terrorists. The vulnerability of food to intentional contamination coupled with reports of humans having acquired plague through eating infected animals that were not adequately cooked or handling of meat from infected animals makes the possible use of Y. pestis in a foodborne bioterrorism attack a reality. Rapid, efficient food sample preparation and detection systems that will help overcome the problem associated with the complexity of the different matrices and also remove any ambiguity in results will enable rapid informed decisions to be made regarding contamination of food with biothreat agents. We have developed a rapid detection assay that combines the use of immunomagnetic separation and pyrosequencing in generating results for the unambiguous identification of Y. pestis from milk (0.9 CFU/mL, bagged salad (1.6 CFU/g, and processed meat (10 CFU/g. The low detection limits demonstrated in this assay provide a novel tool for the rapid detection and confirmation of Y. pestis in food without the need for enrichment. The combined use of the iCropTheBug system and pyrosequencing for efficient capture and detection of Y. pestis is novel and has potential applications in food biodefence.

  8. Detection and molecular identification protocols for Phyllosticta citricarpa from citrus matter

    Directory of Open Access Journals (Sweden)

    Mariette Truter

    2012-03-01

    Full Text Available Strict quarantine measures for the export of South African citrus fruit to European and US markets require the development of sensitive and accurate detection methods for the pathogen Phyllosticta citricarpa – a fungus causing citrus black spot disease. Because of the presence of other, non-pathogenic Phyllosticta species, rapid and accurate verification of the Phyllosticta species present on exported citrus fruit is important to producers, exporters and regulatory authorities to prevent unnecessary losses. We have analysed over 800 samples collected over 7 years and have compared sample preparation and detection protocols applied in different environments: nurseries, production systems including phytosanitary inspections in orchards, pack houses and export terminals in order to compile protocols for the detection of P. citricarpa. Standard procedures of sample preparation and DNA extraction were adapted to suit diverse inoculum sources. Low pathogen numbers in symptomless green leaves, for example, obliged the use of a wet-dry enrichment technique constituting the stimulation of fungal growth for easier detection. Physical maceration was adapted for sturdy material using liquid nitrogen or bead beating. The use of a two-step polymerase chain reaction (PCR with nested primers significantly increased both the sensitivity and the specificity of the PCR performed on soil samples, overcoming problems with relatively impure DNA extracts and low pathogen numbers. The assays have proven to be highly consistent, thereby providing a reliable, reproducible and highly sensitive detection and diagnostic service to the southern African citrus industries in order to sustain market access.

  9. Closed-loop spontaneous baroreflex transfer function is inappropriate for system identification of neural arc but partly accurate for peripheral arc: predictability analysis.

    Science.gov (United States)

    Kamiya, Atsunori; Kawada, Toru; Shimizu, Shuji; Sugimachi, Masaru

    2011-04-01

    Although the dynamic characteristics of the baroreflex system have been described by baroreflex transfer functions obtained from open-loop analysis, the predictability of time-series output dynamics from input signals, which should confirm the accuracy of system identification, remains to be elucidated. Moreover, despite theoretical concerns over closed-loop system identification, the accuracy and the predictability of the closed-loop spontaneous baroreflex transfer function have not been evaluated compared with the open-loop transfer function. Using urethane and α-chloralose anaesthetized, vagotomized and aortic-denervated rabbits (n = 10), we identified open-loop baroreflex transfer functions by recording renal sympathetic nerve activity (SNA) while varying the vascularly isolated intracarotid sinus pressure (CSP) according to a binary random (white-noise) sequence (operating pressure ± 20 mmHg), and using a simplified equation to calculate closed-loop-spontaneous baroreflex transfer function while matching CSP with systemic arterial pressure (AP). Our results showed that the open-loop baroreflex transfer functions for the neural and peripheral arcs predicted the time-series SNA and AP outputs from measured CSP and SNA inputs, with r2 of 0.8 ± 0.1 and 0.8 ± 0.1, respectively. In contrast, the closed-loop-spontaneous baroreflex transfer function for the neural arc was markedly different from the open-loop transfer function (enhanced gain increase and a phase lead), and did not predict the time-series SNA dynamics (r2; 0.1 ± 0.1). However, the closed-loop-spontaneous baroreflex transfer function of the peripheral arc partially matched the open-loop transfer function in gain and phase functions, and had limited but reasonable predictability of the time-series AP dynamics (r2, 0.7 ± 0.1). A numerical simulation suggested that a noise predominantly in the neural arc under resting conditions might be a possible mechanism responsible for our findings. Furthermore

  10. Fault detection and identification based on combining logic and model in a wall-climbing robot

    Institute of Scientific and Technical Information of China (English)

    Yong JIANG; Hongguang WANG; Lijin FANG; Mingyang ZHAO

    2009-01-01

    A combined logic- and model-based approach to fault detection and identification (FDI) in a suction foot control system of a wall-climbing robot is presented in this paper. For the control system, some fault models are derived by kinematics analysis. Moreover, the logic relations of the system states are known in advance. First, a fault tree is used to analyze the system by evaluating the basic events (elementary causes), which can lead to a root event (a particular fault). Then, a multiple-model adaptive estimation algorithm is used to detect and identify the model-known faults. Finally, based on the system states of the robot and the results of the estimation, the model-unknown faults are also identified using logical reasoning. Experiments show that the proposed approach based on the combination of logical reasoning and model estimating is efficient in the FDI of the robot.

  11. A PCR detection method for rapid identification of Melissococcus pluton in honeybee larvae.

    Science.gov (United States)

    Govan, V A; Brözel, V; Allsopp, M H; Davison, S

    1998-05-01

    Melissococcus pluton is the causative agent of European foulbrood, a disease of honeybee larvae. This bacterium is particularly difficult to isolate because of its stringent growth requirements and competition from other bacteria. PCR was used selectively to amplify specific rRNA gene sequences of M. pluton from pure culture, from crude cell lysates, and directly from infected bee larvae. The PCR primers were designed from M. pluton 16S rRNA sequence data. The PCR products were visualized by agarose gel electrophoresis and confirmed as originating from M. pluton by sequencing in both directions. Detection was highly specific, and the probes did not hybridize with DNA from other bacterial species tested. This method enabled the rapid and specific detection and identification of M. pluton from pure cultures and infected bee larvae.

  12. System identification aided design of observer-based fault detection systems; Prozessidentifikations-basierter Entwurf beobachtergestuetzter Fehlerdetektionssysteme

    Energy Technology Data Exchange (ETDEWEB)

    Ding, S.X. [Fachgebiet Automatisierungstechnik und komplexe Systeme, Univ. Duisburg-Essen, Duisburg (Germany); Zhang Ping; Heyden, D. [Fakultaet Ingenieurwissenschaften an der Univ. Duisburg-Essen (Germany); Huang Biao [Dept. of Chemical and Materials Engineering, Univ. of Alberta (Canada); Ding, E.L. [Fachbereich Technische Physik, Fachhochschule Gelsenkirchen, Gelsenkirchen (Germany)

    2004-07-01

    This paper deals with problems of observer-based fault detection. An approach is presented, which enables the design of observer-based residual generators based on the process measurement or test data. The basic idea behind this approach is integrating the identification of the so-called fault detection model into the design of observer-based residual generators. (orig.)

  13. Authenticity examination of compressed audio recordings using detection of multiple compression and encoders' identification.

    Science.gov (United States)

    Korycki, Rafal

    2014-05-01

    Since the appearance of digital audio recordings, audio authentication has been becoming increasingly difficult. The currently available technologies and free editing software allow a forger to cut or paste any single word without audible artifacts. Nowadays, the only method referring to digital audio files commonly approved by forensic experts is the ENF criterion. It consists in fluctuation analysis of the mains frequency induced in electronic circuits of recording devices. Therefore, its effectiveness is strictly dependent on the presence of mains signal in the recording, which is a rare occurrence. Recently, much attention has been paid to authenticity analysis of compressed multimedia files and several solutions were proposed for detection of double compression in both digital video and digital audio. This paper addresses the problem of tampering detection in compressed audio files and discusses new methods that can be used for authenticity analysis of digital recordings. Presented approaches consist in evaluation of statistical features extracted from the MDCT coefficients as well as other parameters that may be obtained from compressed audio files. Calculated feature vectors are used for training selected machine learning algorithms. The detection of multiple compression covers up tampering activities as well as identification of traces of montage in digital audio recordings. To enhance the methods' robustness an encoder identification algorithm was developed and applied based on analysis of inherent parameters of compression. The effectiveness of tampering detection algorithms is tested on a predefined large music database consisting of nearly one million of compressed audio files. The influence of compression algorithms' parameters on the classification performance is discussed, based on the results of the current study.

  14. Design of microarray probes for virus identification and detection of emerging viruses at the genus level

    Directory of Open Access Journals (Sweden)

    Ho Mei-Shang

    2006-04-01

    Full Text Available Abstract Background Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. To address this issue, we developed a computational method that identifies the conserved viral sequences at the genus level for all viral genomes available in GenBank, and established a virus probe library. The virus probes are used not only to identify known viruses but also for discerning the genera of emerging or uncharacterized ones. Results Using the microarray approach, the identity of the virus in a test sample is determined by the signals of both genus and species-specific probes. The genera of emerging and uncharacterized viruses are determined based on hybridization of the viral sequences to the conserved probes for the existing viral genera. A detection and classification procedure to determine the identity of a virus directly from detection signals results in the rapid identification of the virus. Conclusion We have demonstrated the validity and feasibility of the above strategy with a small number of viral samples. The probe design algorithm can be applied to any publicly available viral sequence database. The strategy of using separate genus and species probe sets enables the use of a straightforward virus identity calculation directly based on the hybridization signals. Our virus identification strategy has great potential in the diagnosis of viral infections. The virus genus and specific probe database and the associated summary tables are available at http://genestamp.sinica.edu.tw/virus/index.htm.

  15. Identification of pathogenic microbial cells and spores by electrochemical detection on a biochip

    Directory of Open Access Journals (Sweden)

    Andresen Heiko

    2004-04-01

    Full Text Available Abstract Background Bacillus cereus constitutes a significant cause of acute food poisoning in humans. Despite the recent development of different detection methods, new effective control measures and better diagnostic tools are required for quick and reliable detection of pathogenic micro-organisms. Thus, the objective of this study was to determine a simple method for rapid identification of enterotoxic Bacillus strains. Here, a special attention is given to an electrochemical biosensor since it meets the requirements of minimal size, lower costs and decreased power consumption. Results A bead-based sandwich hybridization system was employed in conjugation with electric chips for detection of vegetative cells and spores of Bacillus strains based on their toxin-encoding genes. The system consists of a silicon chip based potentiometric cell, and utilizes paramagnetic beads as solid carriers of the DNA probes. The specific signals from 20 amol of bacterial cell or spore DNA were achieved in less than 4 h. The method was also successful when applied directly to unpurified spore and cell extract samples. The assay for the haemolytic enterotoxin genes resulted in reproducible signals from B. cereus and B. thuringiensis while haemolysin-negative B. subtilis strain did not yield any signal. Conclusions The sensitivity, convenience and specificity of the system have shown its potential. In this respect an electrochemical detection on a chip enabling a fast characterization and monitoring of pathogens in food is of interest. This system can offer a contribution in the rapid identification of bacteria based on the presence of specific genes without preceding nucleic acid amplification.

  16. Identification of upper respiratory tract pathogens using electrochemical detection on an oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Michael J Lodes

    Full Text Available Bacterial and viral upper respiratory infections (URI produce highly variable clinical symptoms that cannot be used to identify the etiologic agent. Proper treatment, however, depends on correct identification of the pathogen involved as antibiotics provide little or no benefit with viral infections. Here we describe a rapid and sensitive genotyping assay and microarray for URI identification using standard amplification and hybridization techniques, with electrochemical detection (ECD on a semiconductor-based oligonucleotide microarray. The assay was developed to detect four bacterial pathogens (Bordetella pertussis, Streptococcus pyogenes, Chlamydia pneumoniae and Mycoplasma pneumoniae and 9 viral pathogens (adenovirus 4, coronavirus OC43, 229E and HK, influenza A and B, parainfluenza types 1, 2, and 3 and respiratory syncytial virus. This new platform forms the basis for a fully automated diagnostics system that is very flexible and can be customized to suit different or additional pathogens. Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation. Because ECD uses an enzymatic reaction to create electrical signals that can be read directly from the array, there is no need for image analysis or for expensive and delicate optical scanning equipment. We show assay sensitivity and specificity that are excellent for a multiplexed format.

  17. Colorimetric sensor array for detection and identification of organophosphorus and carbamate pesticides.

    Science.gov (United States)

    Qian, Sihua; Lin, Hengwei

    2015-01-01

    Due to relatively low persistence and high effectiveness for insect and pest eradication, organophosphates (OPs) and carbamates are the two major classes of pesticides that broadly used in agriculture. Hence, the sensitive and selective detection of OPs and carbamates is highly significant. In this current study, a colorimetric sensor array comprising five inexpensive and commercially available thiocholine and H2O2 sensitive indicators for the simultaneous detection and identification of OPs and carbamates is developed. The sensing mechanism of this array is based on the irreversible inhibition capability of OPs and carbamates to the activity of acetylcholinesterase (AChE), preventing production of thiocholine and H2O2 from S-acetylthiocholine and acetylcholine and thus resulting in decreased or no color reactions to thiocholine and H2O2 sensitive indicators. Through recognition patterns and standard statistical methods (i.e., hierarchical clustering analysis and principal component analysis), the as-developed array demonstrates not only discrimination of OPs and carbamates from other kinds of pesticides but, more interestingly, identification of them exactly from each other. Moreover, this array is experimentally confirmed to have high selectivity and sensitivity, good anti-interference capability, and potential applications in real samples for OPs and carbamates.

  18. Multiplex Solid-Phase PCR for Rapid Detection and Identification of Salmonella spp. at Sub-species

    DEFF Research Database (Denmark)

    Cao, Cuong; Høgberg, Jonas; Wolff, Anders

    -PCR gel electrophoresis. The method will be useful for development of point-of-care devices for rapid detection and identification of Salmonella spp. A solid-phase PCR for rapid detection and identification of S. enteritidis, S. typhimurium and S. dublin is developed. The method offers advantages......This study presents a solid-phase PCR (SP-PCR) for rapid detection, identification, and sub-typing of various Salmonella species, the major food-borne cause of salmonellosis. The target DNA is firstly amplified with PCR primers (one primer is labeled with fluorophores) in the liquid phase...... by the liquid phase primer thus generating new templates for the SP-PCR. After the reaction, PCR products labeled with fluorophores remain attached to the substrate and can be visualized directly by fluorescence readout devices. Using this method, S. enteritidis, S. typhimurium and S. dublin can be detected...

  19. The detection of the methylated Wif-1 gene is more accurate than a fecal occult blood test for colorectal cancer screening

    KAUST Repository

    Amiot, Aurelien

    2014-07-15

    Background: The clinical benefit of guaiac fecal occult blood tests (FOBT) is now well established for colorectal cancer screening. Growing evidence has demonstrated that epigenetic modifications and fecal microbiota changes, also known as dysbiosis, are associated with CRC pathogenesis and might be used as surrogate markers of CRC. Patients and Methods: We performed a cross-sectional study that included all consecutive subjects that were referred (from 2003 to 2007) for screening colonoscopies. Prior to colonoscopy, effluents (fresh stools, sera-S and urine-U) were harvested and FOBTs performed. Methylation levels were measured in stools, S and U for 3 genes (Wif1, ALX-4, and Vimentin) selected from a panel of 63 genes; Kras mutations and seven dominant and subdominant bacterial populations in stools were quantified. Calibration was assessed with the Hosmer-Lemeshow chi-square, and discrimination was determined by calculating the C-statistic (Area Under Curve) and Net Reclassification Improvement index. Results: There were 247 individuals (mean age 60.8±12.4 years, 52% of males) in the study group, and 90 (36%) of these individuals were patients with advanced polyps or invasive adenocarcinomas. A multivariate model adjusted for age and FOBT led to a C-statistic of 0.83 [0.77-0.88]. After supplementary sequential (one-by-one) adjustment, Wif-1 methylation (S or U) and fecal microbiota dysbiosis led to increases of the C-statistic to 0.90 [0.84-0.94] (p = 0.02) and 0.81 [0.74-0.86] (p = 0.49), respectively. When adjusted jointly for FOBT and Wif-1 methylation or fecal microbiota dysbiosis, the increase of the C-statistic was even more significant (0.91 and 0.85, p<0.001 and p = 0.10, respectively). Conclusion: The detection of methylated Wif-1 in either S or U has a higher performance accuracy compared to guaiac FOBT for advanced colorectal neoplasia screening. Conversely, fecal microbiota dysbiosis detection was not more accurate. Blood and urine testing could be

  20. Accurate Detection of Adenylation Domain Functions in Nonribosomal Peptide Synthetases by an Enzyme-linked Immunosorbent Assay System Using Active Site-directed Probes for Adenylation Domains.

    Science.gov (United States)

    Ishikawa, Fumihiro; Miyamoto, Kengo; Konno, Sho; Kasai, Shota; Kakeya, Hideaki

    2015-12-18

    A significant gap exists between protein engineering and enzymes used for the biosynthesis of natural products, largely because there is a paucity of strategies that rapidly detect active-site phenotypes of the enzymes with desired activities. Herein, we describe a proof-of-concept study of an enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using a combination of active site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold with a biotin functionality that immobilizes probe molecules onto a streptavidin-coated solid support. The recombinant NRPSs have a C-terminal His-tag motif that is targeted by an anti-6×His mouse antibody as the primary antibody and a horseradish peroxidase-linked goat antimouse antibody as the secondary antibody. These probes can selectively capture the cognate A domains by ligand-directed targeting. In addition, the ELISA technique detected A domains in the crude cell-free homogenates from the Escherichia coli expression systems. When coupled with a chromogenic substrate, the antibody-based ELISA technique can visualize probe-protein binding interactions, which provides accurate readouts of the A-domain functions in NRPS enzymes. To assess the ELISA-based engineering of the A domains of NRPSs, we reprogramed 2,3-dihydroxybenzoic acid (DHB)-activating enzyme EntE toward salicylic acid (Sal)-activating enzymes and investigated a correlation between binding properties for probe molecules and enzyme catalysts. We generated a mutant of EntE that displayed negligible loss in the kcat/Km value with the noncognate substrate Sal and a corresponding 48-fold decrease in the kcat/Km value with the cognate substrate DHB. The resulting 26-fold switch in substrate specificity was achieved by the replacement of a Ser residue in the active site of EntE with a Cys toward the nonribosomal codes of Sal-activating enzymes. Bringing a laboratory ELISA technique

  1. Selective identification and quantification of saccharin by liquid chromatography and fluorescence detection.

    Science.gov (United States)

    Bruno, Sergio N F; Cardoso, Carlos R; Maciel, Márcia Mosca A; Vokac, Lidmila; da Silva Junior, Ademário I

    2014-09-15

    High-pressure liquid chromatography with ultra-violet detection (HPLC-UV) is one of the most commonly used methods to identify and quantify saccharin in non-alcoholic beverages. However, due to the wide variety of interfering UV spectra in saccharin-containing beverage matrices, the same method cannot be used to measure this analyte accurately. We have developed a new, highly effective method to identify and quantify saccharin using HPLC with fluorescence detection (HPLC-FLD). The excitation wavelength (250 nm) and emission wavelength (440 nm) chosen increased selectivity for all matrices and ensured few changes were required in the mobile phase or other parameters. The presence of saccharin in non-diet beverages - a fraud commonly used to replace more expensive sucrose - was confirmed by comparing coincident peaks as well as the emission spectra of standards and samples.

  2. Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays

    Institute of Scientific and Technical Information of China (English)

    Lian-Qun Jin; Jun-Wen Li; Sheng-Qi Wang; Fu-Huan Chao; Xin-Wei Wang; Zheng-Quan Yuan

    2005-01-01

    AIM: To detect the common intestinal pathogenic bacteria quickly and accurately.METHODS: A rapid (<3 h) experimental procedure was set up based upon the gene chip technology. Target genes were amplified and hybridized by oligonucleotide microarrays.RESULTS: One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 (96.2%) were identified.CONCLUSION: Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus,Staphylococcus aureus, Proteus sp., Bacillus cereus,Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range,and discrimination power of this assay can be continually improved by adding further oligonucleotides to the arrays without any significant increase of complexity or cost.

  3. Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification.

    Science.gov (United States)

    Wright, Erik S; Yilmaz, L Safak; Corcoran, Andrew M; Ökten, Hatice E; Noguera, Daniel R

    2014-08-01

    Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as an integral part of the full-cycle rRNA approach. A major challenge in FISH is the design of oligonucleotide probes with high sensitivity and specificity to their target group. The rapidly expanding number of rRNA sequences has increased awareness of the number of potential nontargets for every FISH probe, making the design of new FISH probes challenging using traditional methods. In this study, we conducted a systematic analysis of published probes that revealed that many have insufficient coverage or specificity for their intended target group. Therefore, we developed an improved thermodynamic model of FISH that can be applied at any taxonomic level, used the model to systematically design probes for all recognized genera of bacteria and archaea, and identified potential cross-hybridizations for the selected probes. This analysis resulted in high-specificity probes for 35.6% of the genera when a single probe was used in the absence of competitor probes and for 60.9% when up to two competitor probes were used. Requiring the hybridization of two independent probes for positive identification further increased specificity. In this case, we could design highly specific probe sets for up to 68.5% of the genera without the use of competitor probes and 87.7% when up to two competitor probes were used. The probes designed in this study, as well as tools for designing new probes, are available online (http://DECIPHER.cee.wisc.edu).

  4. Accurate and Practical Identification of 20 Fusarium Species by Seven-Locus Sequence Analysis and Reverse Line Blot Hybridization, and an In Vitro Antifungal Susceptibility Study▿†

    Science.gov (United States)

    Wang, He; Xiao, Meng; Kong, Fanrong; Chen, Sharon; Dou, Hong-Tao; Sorrell, Tania; Li, Ruo-Yu; Xu, Ying-Chun

    2011-01-01

    Eleven reference and 25 clinical isolates of Fusarium were subject to multilocus DNA sequence analysis to determine the species and haplotypes of the fusarial isolates from Beijing and Shandong, China. Seven loci were analyzed: the translation elongation factor 1 alpha gene (EF-1α); the nuclear rRNA internal transcribed spacer (ITS), large subunit (LSU), and intergenic spacer (IGS) regions; the second largest subunit of the RNA polymerase gene (RPB2); the calmodulin gene (CAM); and the mitochondrial small subunit (mtSSU) rRNA gene. We also evaluated an IGS-targeted PCR/reverse line blot (RLB) assay for species/haplotype identification of Fusarium. Twenty Fusarium species and seven species complexes were identified. Of 25 clinical isolates (10 species), the Gibberella (Fusarium) fujikuroi species complex was the commonest (40%) and was followed by the Fusarium solani species complex (FSSC) (36%) and the F. incarnatum-F. equiseti species complex (12%). Six FSSC isolates were identified to the species level as FSSC-3+4, and three as FSSC-5. Twenty-nine IGS, 27 EF-1α, 26 RPB2, 24 CAM, 18 ITS, 19 LSU, and 18 mtSSU haplotypes were identified; 29 were unique, and haplotypes for 24 clinical strains were novel. By parsimony informative character analysis, the IGS locus was the most phylogenetically informative, and the rRNA gene regions were the least. Results by RLB were concordant with multilocus sequence analysis for all isolates. Amphotericin B was the most active drug against all species. Voriconazole MICs were high (>8 μg/ml) for 15 (42%) isolates, including FSSC. Analysis of larger numbers of isolates is required to determine the clinical utility of the seven-locus sequence analysis and RLB assay in species classification of fusaria. PMID:21389150

  5. Dual redundant sensor FDI techniques applied to the NASA F8C DFBW aircraft. [Failure Detection and Identification

    Science.gov (United States)

    Desai, M. N.; Deckert, J. C.; Deyst, J. J.; Willsky, A. S.; Chow, E. Y.

    1976-01-01

    An onboard failure detection and identification (FDI) technique for dual redundant sensors on the NASA F8C digital fly-by-wire (DFBW) aircraft is presented. The failure of one of a pair of sensors of the same type is detected by a direct redundancy trigger which observes the difference between the outputs of these two sensors. Identification of the failed sensor is accomplished utilizing the analytic redundancy that exists as kinematic and functional relationships among the variables being measured by dissimilar instruments. In addition, identification of generic failures, common to both instruments of a given type, is accomplished by using a time trigger to periodically initiate analytic redundancy failure identification tests for individual sensors. The basic form of these tests is the comparison of the measurement of a variable using the suspect instrument with another measurement of the same variable obtained using other instrument types.

  6. Ultrasensitive detection and rapid identification of multiple foodborne pathogens with the naked eyes.

    Science.gov (United States)

    Zhang, Heng; Zhang, Yali; Lin, Yankui; Liang, Tongwen; Chen, Zhihua; Li, Jinfeng; Yue, Zhenfeng; Lv, Jingzhang; Jiang, Qing; Yi, Changqing

    2015-09-15

    In this study, a novel approach for ultrasensitive detection and rapid high-throughput identification of a panel of common foodborne pathogens with the naked eyes is presented. As a proof-of-concept application, a multiple pathogen analysis array is fabricated through immobilizing three specific polyT-capture probes which can respectively recognize rfbE gene (Escherichia coli O157:H7), invA gene (Salmonella enterica), inlA gene (Listeria monocytogenes) on the plastic substrates. PCR has been developed for amplification and labeling target genes of rfbE, invA, inlA with biotin. The biotinated target DNA is then captured onto the surface of plastic strips through specific DNA hybridization. The succeeding staining of biotinated DNA duplexes with avidin-horseradish peroxidise (AV-HRP) and biotinated anti-HRP antibody greatly amplifies the detectable signal through the multiple cycle signal amplification strategy, and thus realizing ultrasensitive and specific detection of the above three pathogens in food samples with the naked eyes. Results showed approximately 5 copies target pathogenic DNA could be detected with the naked eyes. This simple but very efficient colorimetric assay also show excellent anti-interference capability and good stability, and can be readily applied to point-of-care diagnosis.

  7. Instant detection and identification of concealed explosive-related compounds: Induced Stokes Raman versus infrared.

    Science.gov (United States)

    Elbasuney, Sherif; El-Sherif, Ashraf F

    2017-01-01

    The instant detection of explosives and explosive-related compounds has become an urgent priority in recent years for homeland security and counter-terrorism applications. Modern techniques should offer enhancement in selectivity, sensitivity, and standoff distances. Miniaturisation, portability, and field-ruggedisation are crucial requirements. This study reports on instant and standoff identification of concealed explosive-related compounds using customized Raman technique. Stokes Raman spectra of common explosive-related compounds were generated and spectrally resolved to create characteristic finger print spectra. The scattered Raman emissions over the band 400:2000cm(-1) were compared to infrared absorption using FTIR. It has been demonstrated that the two vibrational spectroscopic techniques were opposite and completing each other. Molecular vibrations with strong absorption in infrared (those involve strong change in dipole moments) induced weak signals in Raman and vice versa. The tailored Raman offered instant detection, high sensitivity, and standoff detection capabilities. Raman demonstrated characteristic fingerprint spectra with stable baseline and sharp intense peaks. Complete correlations of absorption/scattered signals to certain molecular vibrations were conducted to generate an entire spectroscopic profile of explosive-related compounds. This manuscript shades the light on Raman as one of the prevailing technologies for instantaneous detection of explosive-related compounds. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. A simple identification method of saliva by detecting Streptococcus salivarius using loop-mediated isothermal amplification.

    Science.gov (United States)

    Nakanishi, Hiroaki; Ohmori, Takeshi; Hara, Masaaki; Takada, Aya; Shojo, Hideki; Adachi, Noboru; Saito, Kazuyuki

    2011-01-01

    We previously reported that detection of Streptococcus salivarius is feasible for proving the presence of saliva in a forensic sample. Here, a simple and rapid method for the detection of S. salivarius in forensic samples was developed that uses loop-mediated isothermal amplification (LAMP). The LAMP primer set was designed using S. salivarius-specific sequences of glucosyltransferase K. To simplify the procedure, the sample was prepared by boiling and mutanolysin treatment only, and the entire analytical process was completed within 2.5 h. The cut-off value was set at 0.1 absorbance units, measured at 660 nm, upon termination of the reaction. S. salivarius was identified in all saliva samples, but was not detected in other body fluids or on the skin surface. Using this method, S. salivarius was successfully detected in various mock forensic samples. We therefore suggest that this approach is useful for the identification of saliva in forensic practice. © 2010 American Academy of Forensic Sciences.

  9. Seismic Event Identification Using Scanning Detection: A Comparison of Denoising and Classification Methods

    Science.gov (United States)

    Rowe, C. A.; MacCarthy, J. K.; Giudicepietro, F.

    2005-12-01

    Automatic detection and classification methods are increasingly important in observatory operations, as the volume and rate of incoming data exceed the capacity of human analysis staff to process the data in near-real-time. We explore the success of scanning detection for similar event identification in a variety of seismic waveform catalogs. Several waveform pre-processing methods are applied to previously recorded events which are scanned through triggered and continuous waveform catalogs to determine the success and false alarm rate for detections of repeating signals. Pre-processing approaches include adaptive, cross-coherency filtering, adaptive, auto-associative neural network filtering, discrete wavelet package decomposition and linear predictive coding as well as suites of standard bandpass filters. Classification / detection methods for the various pre-processed signals are applied to investigate the robustness of the individual and combined approaches. The classifiers as applied to the processed waveforms include dendrogram-based clustering and neural network classifiers. We will present findings for the various combinations of methods as applied to tectonic earthquakes, mine blasts and volcanic seismicity.

  10. Development of damage detection methods in continuum structures using system identification

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hae Sung; Yeo, In Ho; Park, Hyun Woo; Kim, Yong Han [Seoul National University, Seoul (Korea)

    2001-05-01

    This study presents an SI-based damage detection schemes using minimization of an error function. The singular value decomposition is utilized to investigate the instability of SI. The Tikhonov regularization scheme is introduced to alleviate oscillations in the solutions of the SI. The optimal regularization factor is determined by the GMS and the GGMS. The characteristics of measurement error is investigated. The regularization effect is estimated by the concept of the error level and the resolution limit. The statistical approach is employed for reliable damage detection. The Monte-Carlo simulation is performed by the artificially perturbed data. The statistical distribution of system parameters obtained by the Monte-Carlo simulation is utilized in the hypothesis test for the damage detection. The validity and effectiveness of the proposed method is demonstrated through three types of numerical examples -identification of an inclusion in a plate, determination of prestress losses in a containment building and damage detection in a containment building. 50 refs., 29 figs. (Author)

  11. Detection, Identification, Location, and Remote Sensing Using SAW RFID Sensor Tags

    Science.gov (United States)

    Barton, Richard J.; Kennedy, Timothy F.; Williams, Robert M.; Fink, Patrick W.; Ngo, Phong H.

    2009-01-01

    The Electromagnetic Systems Branch (EV4) of the Avionic Systems Division at NASA Johnson Space Center in Houston, TX is studying the utility of surface acoustic wave (SAW) radiofrequency identification (RFID) tags for multiple wireless applications including detection, identification, tracking, and remote sensing of objects on the lunar surface, monitoring of environmental test facilities, structural shape and health monitoring, and nondestructive test and evaluation of assets. For all of these applications, it is anticipated that the system utilized to interrogate the SAW RFID tags may need to operate at fairly long range and in the presence of considerable multipath and multiple-access interference. Towards that end, EV4 is developing a prototype SAW RFID wireless interrogation system for use in such environments called the Passive Adaptive RFID Sensor Equipment (PARSED) system. The system utilizes a digitally beam-formed planar receiving antenna array to extend range and provide direction-of-arrival information coupled with an approximate maximum-likelihood signal processing algorithm to provide near-optimal estimation of both range and temperature. The system is capable of forming a large number of beams within the field of view and resolving the information from several tags within each beam. The combination of both spatial and waveform discrimination provides the capability to track and monitor telemetry from a large number of objects appearing simultaneously within the field of view of the receiving array. In this paper, we will consider the application of the PARSEQ system to the problem of simultaneous detection, identification, localization, and temperature estimation for multiple objects. We will summarize the overall design of the PARSEQ system and present a detailed description of the design and performance of the signal detection and estimation algorithms incorporated in the system. The system is currently configured only to measure temperature

  12. Fast and Accurate Identification of Cross-Linked Peptides for the Structural Analysis of Large Protein Complexes and Elucidation of Interaction Networks. / Tahir, Salman; Bukowski-Wills, Jimi-Carlo; Rasmussen, Morten; Rappsilber, Juri

    DEFF Research Database (Denmark)

    Rasmussen, Morten

    Fast and Accurate Identification of Cross-Linked Peptides for the structural analysis of large protein complexes and to elucidate interaction networks. Salman Tahir Jimi-Carlo Bukowski-Wills; Morten Rasmussen; Juri RappsilberWellcome Trust Centre for Cell Biology, Edinburgh , United Kingdom   Novel...... to investigate protein structure and protein-protein interactions. When applied to single proteins or small purified protein complexes, this methodology works well. However certain challenges arise when applied to more complex samples. One of the main problems is the combinatorial increase in the search space...... Aspect: Our software efficiently and correctly identifies cross-links within large protein complexes, facilitating the construction of low-resolution 3D-models and interaction networks   .Introduction Chemical cross-linking of peptides coupled with mass spectrometry emerges as a powerful method...

  13. [Molecular identification and detection of moon jellyfish (Aurelia sp.) based on partial sequencing of mitochondrial 16S rDNA and COI].

    Science.gov (United States)

    Wang, Jian-Yan; Zhen, Yu; Wang, Guo-shan; Mi, Tie-Zhu; Yu, Zhi-gang

    2013-03-01

    Taking the moon jellyfish Aurelia sp. commonly found in our coastal sea areas as test object, its genome DNA was extracted, the partial sequences of mt-16S rDNA (650 bp) and mt-COI (709 bp) were PCR-amplified, and, after purification, cloning, and sequencing, the sequences obtained were BLASTn-analyzed. The sequences of greater difference with those of the other jellyfish were chosen, and eight specific primers for the mt-16S rDNA and mt-COI of Aurelia sp. were designed, respectively. The specificity test indicated that the primer AS3 for the mt-16S rDNA and the primer AC3 for the mt-COI were excellent in rapidly detecting the target jellyfish from Rhopilema esculentum, Nemopilema nomurai, Cyanea nozakii, Acromitus sp., and Aurelia sp., and thus, the techniques for the molecular identification and detection of moon jellyfish were preliminarily established, which could get rid of the limitations in classical morphological identification of Aurelia sp. , being able to find the Aurelia sp. in the samples more quickly and accurately.

  14. Detection and identification of beta-lactam residues in milk using a hybrid biosensor.

    Science.gov (United States)

    Ferrini, Anna Maria; Mannoni, Veruscka; Carpico, Graziella; Pellegrini, Guido Enrico

    2008-02-13

    A novel application of a hybrid biosensor is here employed as an analytical method for the detection and presumptive identification of beta-lactam residues in milk. The method is based on measurements of carbon dioxide (CO2), the production of which is related to the microbial growth of the test microorganism Bacillus stearothermophilus var. calidolactis. The presence of beta-lactams in milk inhibits microbial growth and, consequently, the CO2 production rate. The analysis is based on the variation of CO2 between a milk sample spiked with beta-lactams and a twin milk sample containing beta-lactams plus a broad spectrum beta-lactamase, using an electrochemical device of biosensor. A blank milk sample is included as control. The result is obtained starting from the first 120 min. Moreover, the ability to recognize all of the beta-lactams speeds the total time of analysis when chemical identification and quantification are required. The analytical method appears to be adequate for milk control for qualitative screening purposes, complying with the requirements stated in Decision 2002/657/EC.

  15. Detection, identification and typing of Acidithiobacillus species and strains: a review.

    Science.gov (United States)

    Nuñez, Harold; Covarrubias, Paulo C; Moya-Beltrán, Ana; Issotta, Francisco; Atavales, Joaquín; Acuña, Lillian G; Johnson, D Barrie; Quatrini, Raquel

    2016-09-01

    The genus Acidithiobacillus comprises several species of Gram-negative acidophilic bacteria that thrive in natural and man-made low pH environments in a variety of geo-climatic contexts. Beyond their fundamental interest as model extreme acidophiles, these bacteria are involved in the processing of minerals and the desulfurization of coal and natural gas, and are also sources of environmental pollution due to their generation of acid mine drainage and corrosion of cement and concrete structures. Acidithiobacillus spp. are therefore considered a biotechnologically relevant group of bacteria, and their identification and screening in natural and industrial environments is of great concern. Several molecular typing methodologies have been instrumental in improving knowledge of the inherent diversity of acidithiobacilli by providing information on the genetic subtypes sampled in public and private culture collections; more recently, they have provided specific insight into the diversity of acidithiobacilli present in industrial and natural environments. The aim of this review is to provide an overview of techniques used in molecular detection, identification and typing of Acidithiobacillus spp. These methods will be discussed in the context of their contribution to the general and specific understanding of the role of the acidithiobacilli in microbial ecology and industrial biotechnology. Emerging opportunities for industrial and environmental surveillance of acidithiobacilli using next-generation molecular typing methodologies are also reviewed.

  16. Detection and identification of dyes in blue writing inks by LC-DAD-orbitrap MS.

    Science.gov (United States)

    Sun, Qiran; Luo, Yiwen; Yang, Xu; Xiang, Ping; Shen, Min

    2016-04-01

    In the field of forensic questioned document examination, to identify dyes detected in inks not only provides a solid foundation for ink discrimination in forged contents identification, but also facilitates the investigation of ink origin or the study regarding ink dating. To detect and identify potential acid and basic dyes in blue writing inks, a liquid chromatography-diode array detection-Orbitrap mass spectrometry (LC-DAD-Orbitrap MS) method was established. Three sulfonic acid dyes (Acid blue 1, Acid blue 9 and Acid red 52) and six triphenylmethane basic dyes (Ethyl violet, Crystal violet, Methyl violet 2B, Basic blue 7, Victoria blue B and Victoria blue R) were employed as reference dyes for method development. Determination of the nine dyes was validated to evaluate the instrument performance, and it turned out to be sensitive and stable enough for quantification. The method was then applied in the screening analysis of ten blue roller ball pen inks and twenty blue ballpoint pen inks. As a result, including TPR (a de-methylated product of Crystal violet), ten known dyes and four unknown dyes were detected in the inks. The latter were further identified as a de-methylated product of Victoria blue B, Acid blue 104, Acid violet 49 and Acid blue 90, through analyzing their characteristic precursor and product ions acquired by Orbitrap MS with good mass accuracy. The results showed that the established method is capable of detecting and identifying potential dyes in blue writing inks. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  17. National equipment of intraoperatory gamma detection in the identification of sentinel lymph node in animal model

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Paula Cristina Fada dos [Universidade Federal de Sao Paulo (UNIFESP-EPM), Sao Paulo, SP (Brazil). Post-graduate Program on Plastic Surgery], e-mail: ppfada@hotmail.com; Santos, Ivan Dunshee de Abranches Oliveira [Universidade Federal de Sao Paulo (UNIFESP-EPM), Sao Paulo, SP (Brazil). Dept. of Surgery; Nahas, Fabio Xerfan; Ferreira, Lydia Masako [Universidade Federal de Sao Paulo (UNIFESP-EPM), Sao Paulo, SP (Brazil). Dept. of Surgery. Div. of Plastic Sugery; Oliveira Filho, Renato Santos de [University of Sao Paulo (USP), SP (Brazil). Faculty of Medicine

    2009-07-01

    Purpose: To investigate a national equipment of intraoperatory gamma detection in the identification of sentinel lymph node. Methods: Thirty young adult male rats were used. After anesthetized, animals were divided into two groups of 15 animals each. Animals from group A received dextram 500 - Tc{sup 99} radiopharmaceutical and patent blue V and those from group B received only patent blue V to map the lymphatic drainage. The presence of radiation in the background area, in the area of injection and of the ex vivo sentinel lymph node of group A were measured. After the exeresis, each lymph node in group A and in group B was mixed forming a new random sequence and the radioactive reading of each lymph node was carried out, using both pieces of equipment. Results: The hottest sentinel lymph node was identified by the national equipment when radiation was measured in the area of lymphatic drainage after the Dextran 500 was injected. Also, the ex vivo sentinel lymph node. The national equipment has also detected radiation in the lymph nodes that had not received radiopharmaceutical, leading to false positive, checked by the application of Mann-Whitney tests and Student's paired t-tests. The Cronbach alpha has shown high internal consistency of data 0,9416. Conclusions: The national equipment of intraoperatory gamma detection identifies the LS and showed false positives LS and needs improvement. (author)

  18. Detection of Sensor Faults in Small Helicopter UAVs Using Observer/Kalman Filter Identification

    Directory of Open Access Journals (Sweden)

    Guillermo Heredia

    2011-01-01

    Full Text Available Reliability is a critical issue in navigation of unmanned aerial vehicles (UAVs since there is no human pilot that can react to any abnormal situation. Due to size and cost limitations, redundant sensor schemes and aeronautical-grade navigation sensors used in large aircrafts cannot be installed in small UAVs. Therefore, other approaches like analytical redundancy should be used to detect faults in navigation sensors and increase reliability. This paper presents a sensor fault detection and diagnosis system for small autonomous helicopters based on analytical redundancy. Fault detection is accomplished by evaluating any significant change in the behaviour of the vehicle with respect to the fault-free behaviour, which is estimated by using an observer. The observer is obtained from input-output experimental data with the Observer/Kalman Filter Identification (OKID method. The OKID method is able to identify the system and an observer with properties similar to a Kalman filter, directly from input-output experimental data. Results are similar to the Kalman filter, but, with the proposed method, there is no need to estimate neither system matrices nor sensor and process noise covariance matrices. The system has been tested with real helicopter flight data, and the results compared with other methods.

  19. Method for rapid detection and identification of chaetomium and evaluation of resistance to peracetic acid.

    Science.gov (United States)

    Nakayama, Motokazu; Hosoya, Kouichi; Tomiyama, Daisuke; Tsugukuni, Takashi; Matsuzawa, Tetsuhiro; Imanishi, Yumi; Yaguchi, Takashi

    2013-06-01

    In the beverage industry, peracetic acid has been increasingly used as a disinfectant for the filling machinery and environment due to merits of leaving no residue, it is safe for humans, and its antiseptic effect against fungi and endospores of bacteria. Recently, Chaetomium globosum and Chaetomium funicola were reported resistant to peracetic acid; however, little is known concerning the detail of peracetic acid resistance. Therefore, we assessed the peracetic acid resistance of the species of Chaetomium and related genera under identical conditions and made a thorough observation of the microstructure of their ascospores by transmission electron microscopy. The results of analyses revealed that C. globosum and C. funicola showed the high resistance to peracetic acid (a 1-D antiseptic effect after 900 s and 3-D antiseptic effect after 900 s) and had thick cell walls of ascospores that can impede the action mechanism of peracetic acid. We also developed specific primers to detect the C. globosum clade and identify C. funicola by using PCR to amplify the β-tubulin gene. PCR with the primer sets designed for C. globosum (Chae 4F/4R) and C. funicola (Cfu 2F/2R) amplified PCR products specific for the C. globosum clade and C. funicola, respectively. PCR with these two primer sets did not detect other fungi involved in food spoilage and environmental contamination. This detection and identification method is rapid and simple, with extremely high specificity.

  20. Noninvasive presymptomatic detection of Cercospora beticola infection and identification of early metabolic responses in sugar beet

    Directory of Open Access Journals (Sweden)

    Hans-Peter Mock

    2016-09-01

    Full Text Available Cercospora beticola is an economically significant fungal pathogen of sugar beet, and is the causative pathogen of Cercospora leaf spot. Selected host genotypes with contrasting degree of susceptibility to the disease have been exploited to characterize the patterns of metabolite responses to fungal infection, and to devise a pre-symptomatic, non-invasive method of detecting the presence of the pathogen. Sugar beet genotypes were analyzed for metabolite profiles and hyperspectral signatures. Correlation of data matrices from both approaches facilitated identification of candidates for metabolic markers. Hyperspectral imaging was highly predictive with a classification accuracy of 98.5-99.9 % in detecting C. beticola. Metabolite analysis revealed metabolites altered by the host as part of a successful defence response: these were L-DOPA, 12-hydroxyjasmonic acid 12-O-β-D-glucoside, pantothenic acid and 5-O-feruloylquinic acid. The accumulation of glucosylvitexin in the resistant cultivar suggests it acts as a constitutively-produced protectant. The study establishes a proof-of-concept for an unbiased, presymptomatic and non-invasive detection system for the presence of C. beticola. The test needs to be validated with a larger set of genotypes, to be scalable to the level of a crop improvement program, aiming to speed up the selection for resistant cultivars of sugar beet. Untargeted metabolic profiling is a valuable tool to identify metabolites which correlate with hyperspectral data.

  1. A numerical study on detecting defects in a plane-stressed body by system identification

    Energy Technology Data Exchange (ETDEWEB)

    Shin, S. [Dong-A Univ., Pusan (Korea, Republic of) Dept. of Civil Eng.; Moo Koh, H. [Department of Civil Engineering, Seoul National University, Seoul (Korea, Republic of)

    1999-06-01

    A parametric system identification algorithm is applied for detecting holes or cracks in an elastic plane-stressed body using measured static response at the boundaries. A linearly constrained nonlinear optimization problem is solved for optimal constitutive parameters by minimizing the error between the measured and computed displacements. Each finite element in the model is parameterized by decomposing its stiffness matrix into constitutive parameters and kernel matrices. Because locations and sizes of actual holes or cracks in a body are not the a priori knowledge, the finite element model for detecting such defects is simply set up for the defect-free state with the assumption of a linear elastic behavior. Defects in a plane-stressed body are predicted by the reduction in the constitutive parameters of each element from their baseline values without modifying the geometry and topology of the defined finite element model. The proposed defect-detection algorithm allows sparse measured data with respect to the number of degrees of freedom of the model and also provides statistical defect indices when considering noise in measurements. An adaptive parameter grouping scheme is applied to localize defects when limited measurements are provided. The proposed method is investigated through numerically simulated examples. (orig.) 9 refs.

  2. Biochemical Detection and Identification False Alarm Rate Dependence on Wavelength Using Laser Induced Fluorescence

    Science.gov (United States)

    Bhartia, R.; Hug, W. F.; Sala, E. C.; Sijapati, K.; Lane, A. L.; Reid, R. D.; Conrad, P. G.

    2006-01-01

    Most organic and many inorganic materials absorb strongly in specific wavelength ranges in the deep UV between about 220nm and 300nm. Excitation within these absorption bands results in native fluorescence emission. Each compound or composite material, such as a bacterial spore, has a unique excitation-emission fingerprint that can be used to provide information about the material. The sensitivity and specificity with which these materials can be detected and identified depends on the excitation wavelength and the number and location of observation wavelengths.We will present data on our deep ultraviolet Targeted Ultraviolet Chemical Sensors that demonstrate the sensitivity and specificity of the sensors. In particular, we will demonstrate the ability to quantitatively differentiate a wide range of biochemical agent targets against a wide range of background materials. We will describe the relationship between spectral resolution and specificity in target identification, as well as simple, fast, algorithms to identify materials.Hand-held, battery operated instruments using a deep UV laser and multi-band detection have been developed and deployed on missions to the Antarctic, the Arctic, and the deep ocean with the capability of detecting a single bacterial spore and to differentiate a wide range of organic and biological compounds.

  3. Structural damage identification using multifunctional Bragg grating sensors: II. Damage detection results and analysis

    Science.gov (United States)

    Betz, Daniel C.; Staszewski, Wieslaw J.; Thursby, Graham; Culshaw, Brian

    2006-10-01

    Damage detection is an important issue in structural health monitoring. Lamb waves are the most widely used acousto-ultrasonic guided waves for damage detection. This paper gives the results of experiments carried out to study the identification of damage using Bragg grating sensors as ultrasonic receivers of Lamb waves. The experiments involve a rectangular aluminium plate. Damage was introduced into the plate by drilling a hole into the centre of the plate. In order to obtain different severity of damage, the hole diameter was increased step by step. Several signal processing tools are presented and then applied to the Lamb wave signals in order to find a parameter that corresponds to the severity of damage. The parameter that serves as the damage index has to have small cross-sensitivity to other physical parameters, e.g. temperature. Therefore, additional experiments have been carried out to study the temperature dependence of the Lamb wave signals. In order to determine the influence of the temperature on the damage detection results, the cross-sensitivity is studied within this paper.

  4. Virtual Sensor for Failure Detection, Identification and Recovery in the Transition Phase of a Morphing Aircraft

    Directory of Open Access Journals (Sweden)

    Guillermo Heredia

    2010-03-01

    Full Text Available The Helicopter Adaptive Aircraft (HADA is a morphing aircraft which is able to take-off as a helicopter and, when in forward flight, unfold the wings that are hidden under the fuselage, and transfer the power from the main rotor to a propeller, thus morphing from a helicopter to an airplane. In this process, the reliable folding and unfolding of the wings is critical, since a failure may determine the ability to perform a mission, and may even be catastrophic. This paper proposes a virtual sensor based Fault Detection, Identification and Recovery (FDIR system to increase the reliability of the HADA aircraft. The virtual sensor is able to capture the nonlinear interaction between the folding/unfolding wings aerodynamics and the HADA airframe using the navigation sensor measurements. The proposed FDIR system has been validated using a simulation model of the HADA aircraft, which includes real phenomena as sensor noise and sampling characteristics and turbulence and wind perturbations.

  5. Preliminary input to the space shuttle reaction control subsystem failure detection and identification software requirements (uncontrolled)

    Science.gov (United States)

    Bergmann, E.

    1976-01-01

    The current baseline method and software implementation of the space shuttle reaction control subsystem failure detection and identification (RCS FDI) system is presented. This algorithm is recommended for conclusion in the redundancy management (RM) module of the space shuttle guidance, navigation, and control system. Supporting software is presented, and recommended for inclusion in the system management (SM) and display and control (D&C) systems. RCS FDI uses data from sensors in the jets, in the manifold isolation valves, and in the RCS fuel and oxidizer storage tanks. A list of jet failures and fuel imbalance warnings is generated for use by the jet selection algorithm of the on-orbit and entry flight control systems, and to inform the crew and ground controllers of RCS failure status. Manifold isolation valve close commands are generated in the event of failed on or leaking jets to prevent loss of large quantities of RCS fuel.

  6. Easier detection of invertebrate "identification-key characters" with light of different wavelengths

    Directory of Open Access Journals (Sweden)

    Koken Marcel HM

    2011-10-01

    Full Text Available Abstract The marine α-taxonomist often encounters two problems. Firstly, the "environmental dirt" that is frequently present on the specimens and secondly the difficulty in distinguishing key-features due to the uniform colours which fixed animals often adopt. Here we show that illuminating animals with deep-blue or ultraviolet light instead of the normal white-light abrogates both difficulties; dirt disappears and important details become clearly visible. This light regime has also two other advantages. It allows easy detection of very small, normally invisible, animals (0.1 μm range. And as these light wavelengths can induce fluorescence, new identification markers may be discovered by this approach.

  7. Detection of Dispersed Radio Pulses: A machine learning approach to candidate identification and classification

    CERN Document Server

    Devine, Thomas; McLaughlin, Maura

    2016-01-01

    Searching for extraterrestrial, transient signals in astronomical data sets is an active area of current research. However, machine learning techniques are lacking in the literature concerning single-pulse detection. This paper presents a new, two-stage approach for identifying and classifying dispersed pulse groups (DPGs) in single-pulse search output. The first stage identified DPGs and extracted features to characterize them using a new peak identification algorithm which tracks sloping tendencies around local maxima in plots of signal-to-noise ratio vs. dispersion measure. The second stage used supervised machine learning to classify DPGs. We created four benchmark data sets: one unbalanced and three balanced versions using three different imbalance treatments.We empirically evaluated 48 classifiers by training and testing binary and multiclass versions of six machine learning algorithms on each of the four benchmark versions. While each classifier had advantages and disadvantages, all classifiers with im...

  8. Rapid, Bioassay-Guided Process for the Detection and Identification of Antibacterial Neem Oil Compounds.

    Science.gov (United States)

    Krüzselyi, Dániel; Nagy, Róbert; Ott, Péter G; Móricz, Ágnes M

    2016-08-01

    Bioassay guidance was used along the whole process including method development, isolation and identification of antibacterial neem (Azadirachta indica) oil compounds. The biomonitoring was performed by direct bioautography (DB), a combination of thin-layer chromatography (TLC) and antimicrobial detection. DB of neem oil showed one antibacterial zone that was not UV-active; therefore, the TLC separation was improved under DB control. The chromatographic zone that exhibited activity against Bacillus subtilis, Xanthomonas euvesicatoria, Aliivibrio fischeri, Staphylococcus aureus and methicillin-resistant Staphylococcus aureus was characterized by TLC reagents, indicating a lipophilic, fatty acid-like chemical feature. Two compounds were found and identified in the active zone by high-performance liquid chromatography-electrospray ionization mass spectrometry as linoleic and oleic acids. Both fatty acids inhibited B. subtilis, but A. fischeri was sensitive only against linoleic acid.

  9. Detection and identification of monaural and binaural pitch contours in dyslexic listeners

    DEFF Research Database (Denmark)

    Santurette, Sébastien; Poelmans, Hanne; Luts, Heleen

    2010-01-01

    as the controls. Both groups also showed comparable results with a similar-sounding, but monaurally detectable, pitch-evoking stimulus. However, nine of the dyslexic subjects were found to have difficulty identifying pitch contours both in the binaural and the monaural conditions. The ability of subjects......The use of binaural pitch stimuli to test for the presence of binaural auditory impairment in reading-disabled subjects has so far led to contradictory outcomes. While some studies found that a majority of dyslexic subjects was unable to perceive binaural pitch, others obtained a clear response...... of dyslexic listeners to Huggins' pitch (HP). The present study clarified whether impaired binaural pitch perception is found in dyslexia. Results from a pitch contour identification test, performed in 31 dyslexic listeners and 31 matched controls, clearly showed that dyslexics perceived HP as well...

  10. Detection and identification of monaural and binaural pitch contours in dyslexic listeners

    DEFF Research Database (Denmark)

    Santurette, Sébastien; Dau, Torsten; Poelmans, Hanne

    2010-01-01

    Binaural pitch stimuli were used in several recent studies to test for the presence of binaural auditory impairment in reading-disabled subjects. The outcome of three of these studies (Dougherty et al., 1998; Edwards et al., 2004; Chait et al., 2007) has been contradictory: Where the former two...... found that a majority of dyslexic subjects were unable to hear binaural pitch, the latter obtained a clear response of dyslexic listeners to Huggins’ pitch (HP) (Cramer and Huggins, 1958). The present study clarified whether impaired binaural pitch perception is found in dyslexia. Results from a pitch...... contour identification test, performed in 31 dyslexic listeners and 31 matched controls, clearly showed that dyslexics perceived HP as well as the controls. Both groups also showed comparable results with a similar-sounding, monaurally-detectable, pitch-evoking stimulus. However, nine of the dyslexic...

  11. Attack Detection and Identification in Cyber-Physical Systems -- Part I: Models and Fundamental Limitations

    CERN Document Server

    Pasqualetti, Fabio; Bullo, Francesco

    2012-01-01

    Cyber-physical systems integrate computation, communication, and physical capabilities to interact with the physical world and humans. Besides failures of components, cyber-physical systems are prone to malignant attacks, and specific analysis tools as well as monitoring mechanisms need to be developed to enforce system security and reliability. This paper proposes a unified framework to analyze the resilience of cyber-physical systems against attacks cast by an omniscient adversary. We model cyber-physical systems as linear descriptor systems, and attacks as exogenous unknown inputs. Despite its simplicity, our model captures various real-world cyber-physical systems, and it includes and generalizes many prototypical attacks, including stealth, (dynamic) false-data injection and replay attacks. First, we characterize fundamental limitations of static, dynamic, and active monitors for attack detection and identification. Second, we provide constructive algebraic conditions to cast undetectable and unidentifia...

  12. Automatic procedure for mass and charge identification of light isotopes detected in CsI(Tl) of the GARFIELD apparatus

    Energy Technology Data Exchange (ETDEWEB)

    Morelli, L.; Bruno, M.; Baiocco, G. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Bardelli, L.; Barlini, S.; Bini, M.; Casini, G. [Dipartimento di Fisica dell' Universita and INFN, Firenze (Italy); D' Agostino, M., E-mail: dagostino@bo.infn.i [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); Degerlier, M.; Gramegna, F. [INFN, Laboratori Nazionali di Legnaro (Italy); Kravchuk, V.L. [Dipartimento di Fisica dell' Universita and INFN, Bologna (Italy); INFN, Laboratori Nazionali di Legnaro (Italy); Marchi, T. [Dipartimento di Fisica dell' Universita, Padova, ItalyNUCL-EX Collaboration (Italy); INFN, Laboratori Nazionali di Legnaro (Italy); Pasquali, G.; Poggi, G. [Dipartimento di Fisica dell' Universita and INFN, Firenze (Italy)

    2010-08-21

    Mass and charge identification of light charged particles detected with the 180 CsI(Tl) detectors of the GARFIELD apparatus is presented. A 'tracking' method to automatically sample the Z and A ridges of 'Fast-Slow' histograms is developed. An empirical analytic identification function is used to fit correlations between Fast and Slow, in order to determine, event by event, the atomic and mass numbers of the detected charged reaction products. A summary of the advantages of the proposed method with respect to 'hand-based' procedures is reported.

  13. Automatic procedure for mass and charge identification of light isotopes detected in CsI(Tl) of the GARFIELD apparatus

    Science.gov (United States)

    Morelli, L.; Bruno, M.; Baiocco, G.; Bardelli, L.; Barlini, S.; Bini, M.; Casini, G.; D'Agostino, M.; Degerlier, M.; Gramegna, F.; Kravchuk, V. L.; Marchi, T.; Pasquali, G.; Poggi, G.

    2010-08-01

    Mass and charge identification of light charged particles detected with the 180 CsI(Tl) detectors of the GARFIELD apparatus is presented. A "tracking" method to automatically sample the Z and A ridges of "Fast-Slow" histograms is developed. An empirical analytic identification function is used to fit correlations between Fast and Slow, in order to determine, event by event, the atomic and mass numbers of the detected charged reaction products. A summary of the advantages of the proposed method with respect to "hand-based" procedures is reported.

  14. Towards metal detection and identification for humanitarian demining using magnetic polarizability tensor spectroscopy

    Science.gov (United States)

    Dekdouk, B.; Ktistis, C.; Marsh, L. A.; Armitage, D. W.; Peyton, A. J.

    2015-11-01

    This paper presents an inversion procedure to estimate the location and magnetic polarizability tensor of metal targets from broadband electromagnetic induction (EMI) data. The solution of this inversion produces a spectral target signature, which may be used in identifying metal targets in landmines from harmless clutter. In this process, the response of the metal target is modelled with dipole moment and fitted to planar EMI data by solving a minimization least squares problem. A computer simulation platform has been developed using a modelled EMI sensor to produce synthetic data for inversion. The reconstructed tensor is compared with an assumed true solution estimated using a modelled tri-axial Helmholtz coil array. Using some test examples including a sphere which has a known analytical solution, results show the inversion routine produces accurate tensors to within 12% error of the true tensor. A good convergence rate is also demonstrated even when the target location is mis-estimated by a few centimeters. Having verified the inversion routine using finite element modelling, a swept frequency EMI experimental setup is used to compute tensors for a set of test samples representing examples of metallic landmine components and clutter for a broadband range of frequencies (kHz to tens of kHz). Results show the reconstructed spectral target signatures are very distinctive and hence potentially offer an efficient physical approach for landmine identification. The accuracy of the evaluated spectra is similarly verified using a uniform field forming sensor.

  15. Molecular identification of nematode larvae different from those of the Trichinella genus detected by muscle digestion.

    Science.gov (United States)

    Marucci, Gianluca; Interisano, Maria; La Rosa, Giuseppe; Pozio, Edoardo

    2013-05-20

    Although larvae of the genus Trichinella are the most common parasite species detected in vertebrate muscles using artificial digestion, nematode larvae belonging to other genera are sometimes detected and incorrectly identified as Trichinella. However, it is often very difficult to identify these larvae at the species, genus or family level using microscopy because of the absence of specific morphological characters or cuticle damage, and the only means of identification is PCR and sequencing of specific molecular markers (12S mtDNA; COI; 18S rDNA; and ITS1). From 2008 to 2011, 18 nematode isolates not belonging to the genus Trichinella were collected from different host species. Eleven of these isolates were successfully identified at the species, genus or superfamily level: larvae from two common kestrels, three hooded crows, a hen harrier and a domestic pig were identified as Toxocara cati; larvae from a badger were identified as Toxocara canis; larvae from a domestic pig were identified as a free-living nematode of the genus Panagrolaimus; larvae from a wild boar were identified as belonging to the Metastrongylus genus; and larvae from a rough-legged buzzard were identified as belonging to the superfamily Filarioidea. The recovery of nematodes belonging to genera other than Trichinella during routine meat inspection suggests that the persons performing the analyses need to be informed of the possibility of false positives and that a molecular-based identification system that allows for a rapid and reliable response must be adopted (i.e., a DNA barcoding-like system).

  16. Detection, Identification, Location, and Remote Sensing using SAW RFID Sensor Tags

    Science.gov (United States)

    Barton, Richard J.

    2009-01-01

    In this presentation, we will consider the problem of simultaneous detection, identification, location estimation, and remote sensing for multiple objects. In particular, we will describe the design and testing of a wireless system capable of simultaneously detecting the presence of multiple objects, identifying each object, and acquiring both a low-resolution estimate of location and a high-resolution estimate of temperature for each object based on wireless interrogation of passive surface acoustic wave (SAW) radiofrequency identification (RFID) sensor tags affixed to each object. The system is being studied for application on the lunar surface as well as for terrestrial remote sensing applications such as pre-launch monitoring and testing of spacecraft on the launch pad and monitoring of test facilities. The system utilizes a digitally beam-formed planar receiving antenna array to extend range and provide direction-of-arrival information coupled with an approximate maximum-likelihood signal processing algorithm to provide near-optimal estimation of both range and temperature. The system is capable of forming a large number of beams within the field of view and resolving the information from several tags within each beam. The combination of both spatial and waveform discrimination provides the capability to track and monitor telemetry from a large number of objects appearing simultaneously within the field of view of the receiving array. In the presentation, we will summarize the system design and illustrate several aspects of the operational characteristics and signal structure. We will examine the theoretical performance characteristics of the system and compare the theoretical results with results obtained from experiments in both controlled laboratory environments and in the field.

  17. [Evaluation of rapid genotype assay for the identification of gram-positive cocci from blood cultures and detection of mecA and van genes].

    Science.gov (United States)

    Gülhan, Barış; Atmaca, Selahattin; Ozekinci, Tuncer; Suay, Adnan

    2011-10-01

    Rapid and accurate identification of bacterial pathogens grown in blood cultures of patients with sepsis is crucial for prompt initiation of appropriate therapy in order to decrease related morbidity and mortality rates. Although current automated blood culture systems led to a significant improvement in bacterial detection time, more rapid identification systems are still needed to optimise the establishment of treatment. Novel genotype technology which is developed for the rapid diagnosis of sepsis, is a molecular genetic assay based on DNA multiplex amplification with biotinylated primers followed by hybridization to membrane bound probes. The aim of this study was to evaluate the performance of "Genotype® BC gram-positive” test for the identification of gram-positive cocci grown in blood cultures and rapid detection of mecA and van genes. This test uses DNA.STRIP® technology which includes a panel of probes for identification of 17 gram-positive bacterial species and is able to determinate the methicillin and vancomycin resistance mediating genes (mecA and vanA, vanB, vanC1, vanC2/C3) simultaneously, in a single test run. A total of 55 positive blood cultures from BACTECTM Plus/F (Becton Dickinson, USA) aerobic and pediatric blood culture vials were included in the study. The isolates which exhibit gram-positive coccus morphology by Gram staining were identified by Genotype ® BC gram-positive test (Hain Life Science, Germany). All of the samples were also identified with the use of Phoenix PMIC/ID Panel (Becton Dickinson, USA) and antibiotic susceptibilities were determined. Of the 55 blood culture isolates, 17 were identified as Staphylococcus epidermidis [all were methicillin-resistant (MR)], 9 were S.aureus (one was MR), 18 were S.hominis (10 were MR), 4 were E.faecalis, 3 were E. faecium (one was vanconycin-resistant), 2 were S.saprophyticus (one was MR), 1 was S.warneri and 1 was S.haemolyticus, by Phoenix automated system. Genotype® BC gram

  18. Circular dichroism sensor based on cadmium sulfide quantum dots for chiral identification and detection of penicillamine

    Energy Technology Data Exchange (ETDEWEB)

    Ngamdee, Kessarin [Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002 (Thailand); Puangmali, Theerapong [Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen, 40002 (Thailand); Tuntulani, Thawatchai [Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330 (Thailand); Ngeontae, Wittaya, E-mail: wittayange@kku.ac.th [Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002 (Thailand)

    2015-10-22

    A new chemical sensor based on the measuring of circular dichroism signal (CD) was fabricated from cysteamine capped cadmium sulfide quantum dots (Cys-CdS QDs). The chiral-thiol molecules, D-penicillamine (DPA) and L-penicillamine (LPA), were used to evaluate potentials of this sensor. Basically, DPA and LPA provide very low CD signals. However, the CD signals of DPA and LPA can be enhanced in the presence of Cys-CdS QDs. The CD spectra of DPA and LPA exhibited a mirror image profile. Parameters affecting the determination of DPA and LPA were thoroughly investigated in details. Under the optimized condition, the CD signals of DPA and LPA displayed a linear relationship with the concentrations of both enantiomers, ranging from 1 to 35 μM. Detection limits of this sensor were 0.49 and 0.74 μM for DPA and LPA, respectively. To demonstrate a potential application of this sensor, the proposed sensor was used to determine DPA and LPA in real urine samples. It was confirmed that the proposed detection technique was reliable and could be utilized in a broad range of applications. - Highlights: • This paper demonstrates a new CD sensor based on cadmium sulfide quantum dots. • Achiral quantum dots are used for the detection and chiral identification of thiol-chiral containing compounds. • The sensor show highest selectivity towards penicillamine. • The detection limits of the sensor less than 1 μM. • The sensor can potentially be used in physiological urine samples.

  19. Rapid detection and identification of bacterial pathogens by using an ATP bioluminescence immunoassay.

    Science.gov (United States)

    Hunter, Dawn M; Lim, Daniel V

    2010-04-01

    Rapid identification of viable bacterial contaminants in food products is important because of their potential to cause disease. This study examined a method for microbial detection by using a combined ATP bioluminescence immunoassay. Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium were selected as target organisms because of their implication in foodborne illness. Various matrices containing the target cells were examined, including ground beef homogenate, apple juice, milk, and phosphate-buffered saline. Specific antibodies were immobilized on the surface of 96-well plates, and then the sample matrices containing target cells in the wells were incubated. Sample matrix (no cells) was used to establish background. The plates were washed, and the wells were incubated with BacTiter-Glo reagent in Mueller-Hinton II broth. Bioluminescent output was measured with the GloMax 96 luminometer. Signal-to-noise ratios were calculated, resulting in a limit of detection of 10(4) CFU/ml for both E. coli O157:H7 and Salmonella Typhimurium. The limit of detection for both species was not affected by the presence of nontarget cells. The various sample matrices did not affect signal-to-noise ratios when E. coli O157:H7 was the target. A weak matrix effect was observed when Salmonella Typhimurium was the target. A strong linear correlation was observed between the number of cells and luminescent output over 4 orders of magnitude for both species. This method provides a means of simultaneously detecting and identifying viable pathogens in complex matrices, and could have wider application in food microbiology.

  20. In situ detection and identification of hesperidin crystals in satsuma mandarin (Citrus unshiu) peel cells.

    Science.gov (United States)

    Inoue, Tsuyoshi; Yoshinaga, Arata; Takabe, Keiji; Yoshioka, Terutaka; Ogawa, Kazunori; Sakamoto, Masahiro; Azuma, Jun-ichi; Honda, Yoichi

    2015-01-01

    Hesperidin, a flavonoid known to have important pharmacological effects, accumulates particularly in the peels of satsuma mandarin (Citrus unshiu). Although histochemical studies have suggested that hesperidin forms crystals in some tissues of the Rutaceae and Umbelliferae, there has been no rigorous in situ detection or identification of hesperidin crystals in C. unshiu. To characterise the chemical component of the crystals found in C. unshiu peels using Raman microscopy. Sections of C. unshiu peels were made. The distribution and morphology of crystals in the sections were analysed microscopically. Raman microscopy was used to detect hesperidin in the sections directly. The crystals were more abundant in immature peel and were observed particularly in areas surrounding vascular bundles, around the border between the flavedo and albedo layers and just below the epidermal cells. In the morphological analysis by scanning electron microscopy, needle-shaped crystals aggregated and formed clusters of spherical crystals. Spectra obtained by Raman microscopy of the crystals in the peel sections were consistent with those of the hesperidin standard. This study showed the detailed distribution of crystals in C. unshiu peels and their main component was identified using Raman microscopy to be hesperidin for the first time. Copyright © 2014 John Wiley & Sons, Ltd.

  1. Rapid Detection and Identification of Infectious Pathogens Based on High-throughput Sequencing

    Institute of Scientific and Technical Information of China (English)

    Pei-Xiang Ni; Xin Ding; Yin-Xin Zhang; Xue Yao; Rui-Xue Sun; Peng Wang; Yan-Ping Gong

    2015-01-01

    Background:The dilemma of pathogens identification in patients with unidentified clinical symptoms such as fever of unknown origin exists,which not only poses a challenge to both the diagnostic and therapeutic process by itself,but also to expert physicians.Methods:In this report,we have attempted to increase the awareness of unidentified pathogens by developing a method to investigate hitherto unidentified infectious pathogens based on unbiased high-throughput sequencing.Results:Our observations show that this method supplements current diagnostic technology that predominantly relies on information derived five cases from the intensive care unit.This methodological approach detects viruses and corrects the incidence of false positive detection rates of pathogens in a much shorter period.Through our method is followed by polymerase chain reaction validation,we could identify infection with Epstein-Barr virus,and in another case,we could identify infection with Streptococcus viridians based on the culture,which was false positive.Conclusions:This technology is a promising approach to revolutionize rapid diagnosis of infectious pathogens and to guide therapy that might result in the improvement of personalized medicine.

  2. Identification of occult breast lesions detected by magnetic resonance imaging with targeted ultrasound: A prospective study

    Energy Technology Data Exchange (ETDEWEB)

    Aracava, Márcia M., E-mail: marcia.aracava@gmail.com; Chojniak, Rubens, E-mail: chojniak@uol.com.br; Souza, Juliana A., E-mail: julianaalves79@hotmail.com; Bitencourt, Almir G.V., E-mail: almirgvb@yahoo.com.br; Marques, Elvira F., E-mail: elvira.marques@ig.com.br

    2014-03-15

    Objective: To verify the capacity of targeted ultrasound (US) to identify additional lesions detected on breast magnetic resonance imaging (MRI), but occult to initial mammography, US and clinical examinations. Methods: This prospective study included 68 additional relevant breast lesions identified on MRI of 49 patients. As an inclusion criterion, breast US and mammography were required and performed up to six months before MRI. These lesions were then subjected to targeted “second-look” US up to 2 weeks after MRI, performed by one or two radiologists with expertise on breast imaging. Lesions were evaluated according to the established Breast Imaging Report and Data System (BI-RADS) lexicon. Results: Targeted US identified 46/68 (67.6%) lesions revealed by MRI. No significant associations were observed between US identification and the type of lesion, dimensions, morphological characteristics and enhancement pattern according to MRI findings. Targeted US identified 100% of BI-RADS category 5 lesions, 90% of category 4 lesions, and just over 50% of category 3 lesions (p < 0.05). There was significant agreement (p < 0.001) between MRI and US BI-RADS classification for all three categories. Conclusion: Targeted US can identify a large proportion of the lesions detected by breast MRI, especially those at high risk of malignancy, when performed by a professional with experience in both breast US and MRI.

  3. Rapid Detection and Identification of Infectious Pathogens Based on High-throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Pei-Xiang Ni

    2015-01-01

    Full Text Available Background: The dilemma of pathogens identification in patients with unidentified clinical symptoms such as fever of unknown origin exists, which not only poses a challenge to both the diagnostic and therapeutic process by itself, but also to expert physicians. Methods: In this report, we have attempted to increase the awareness of unidentified pathogens by developing a method to investigate hitherto unidentified infectious pathogens based on unbiased high-throughput sequencing. Results: Our observations show that this method supplements current diagnostic technology that predominantly relies on information derived five cases from the intensive care unit. This methodological approach detects viruses and corrects the incidence of false positive detection rates of pathogens in a much shorter period. Through our method is followed by polymerase chain reaction validation, we could identify infection with Epstein-Barr virus, and in another case, we could identify infection with Streptococcus viridians based on the culture, which was false positive. Conclusions: This technology is a promising approach to revolutionize rapid diagnosis of infectious pathogens and to guide therapy that might result in the improvement of personalized medicine.

  4. Identification of Achromobacter xylosoxidans by detection of the bla(OXA-114-like) gene intrinsic in this species.

    Science.gov (United States)

    Turton, Jane F; Mustafa, Nazim; Shah, Jayesh; Hampton, Catherine V; Pike, Rachel; Kenna, Dervla T

    2011-07-01

    Achromobacter xylosoxidans is an emerging pathogen among patients with cystic fibrosis. Here we describe a specific PCR for identification of this organism, based on detection of bla(OXA-114-like). Comparison of isolates by pulsed-field gel electrophoresis revealed evidence of cross-infection in some cases, but most patients harbored their own strain.

  5. Detection of Neisseria meningitidis from Negative Blood Cultures and Cerebrospinal Fluid with the FilmArray Blood Culture Identification Panel

    OpenAIRE

    Pardo, Joe; Klinker, Kenneth P.; Borgert, Samuel J.; Butler, Brittany M.; Rand, Kenneth H.; Iovine, Nicole M.

    2014-01-01

    The FilmArray blood culture identification (BCID) panel is a rapid molecular diagnostic test approved for use with positive blood culture material. We describe a fatal case of meningococcemia with central nervous system (CNS) involvement detected using the BCID test with culture-negative blood and cerebrospinal fluid.

  6. Detection of Neisseria meningitidis from negative blood cultures and cerebrospinal fluid with the FilmArray blood culture identification panel.

    Science.gov (United States)

    Pardo, Joe; Klinker, Kenneth P; Borgert, Samuel J; Butler, Brittany M; Rand, Kenneth H; Iovine, Nicole M

    2014-06-01

    The FilmArray blood culture identification (BCID) panel is a rapid molecular diagnostic test approved for use with positive blood culture material. We describe a fatal case of meningococcemia with central nervous system (CNS) involvement detected using the BCID test with culture-negative blood and cerebrospinal fluid.

  7. Multiplex PCR Assay for Identification of Six Different Staphylococcus spp. and Simultaneous Detection of Methicillin and Mupirocin Resistance

    Science.gov (United States)

    Campos-Peña, E.; Martín-Nuñez, E.; Pulido-Reyes, G.; Martín-Padrón, J.; Caro-Carrillo, E.; Donate-Correa, J.; Lorenzo-Castrillejo, I.; Alcoba-Flórez, J.; Machín, F.

    2014-01-01

    We describe a new, efficient, sensitive, and fast single-tube multiple-PCR protocol for the identification of the most clinically significant Staphylococcus spp. and the simultaneous detection of the methicillin and mupirocin resistance loci. The protocol identifies at the species level isolates belonging to S. aureus, S. epidermidis, S. haemolyticus, S. hominis, S. lugdunensis, and S. saprophyticus. PMID:24829244

  8. Multiplex detection and identification of bacterial pathogens causing potato blackleg and soft rot in Europe, using padlock probes

    NARCIS (Netherlands)

    Slawiak, M.; Doorn, van R.; Szemes, M.; Speksnijder, A.G.C.L.; Waleron, M.; Wolf, van der J.M.; Lojkowska, E.; Schoen, C.D.

    2013-01-01

    The objective of this study was to develop a multiplex detection and identification protocol for bacterial soft rot coliforms, namely Pectobacterium wasabiae (Pw), Pectobacterium atrosepticum (Pba) and Dickeya spp., responsible for potato blackleg and tuber soft rot. The procedures were derived from

  9. Detection and Identification of Multiple Stationary Human Targets Via Bio-Radar Based on the Cross-Correlation Method

    Directory of Open Access Journals (Sweden)

    Yang Zhang

    2016-10-01

    Full Text Available Ultra-wideband (UWB radar has been widely used for detecting human physiological signals (respiration, movement, etc. in the fields of rescue, security, and medicine owing to its high penetrability and range resolution. In these applications, especially in rescue after disaster (earthquake, collapse, mine accident, etc., the presence, number, and location of the trapped victims to be detected and rescued are the key issues of concern. Ample research has been done on the first issue, whereas the identification and localization of multi-targets remains a challenge. False positive and negative identification results are two common problems associated with the detection of multiple stationary human targets. This is mainly because the energy of the signal reflected from the target close to the receiving antenna is considerably stronger than those of the targets at further range, often leading to missing or false recognition if the identification method is based on the energy of the respiratory signal. Therefore, a novel method based on cross-correlation is proposed in this paper that is based on the relativity and periodicity of the signals, rather than on the energy. The validity of this method is confirmed through experiments using different scenarios; the results indicate a discernible improvement in the detection precision and identification of the multiple stationary targets.

  10. 40 CFR Table 6 to Subpart IIIii of... - Examples of Techniques for Equipment Problem Identification, Leak Detection and Mercury Vapor

    Science.gov (United States)

    2010-07-01

    ...; cracks or spalling in cell room floors, pillars, or beams; caustic leaks; liquid mercury accumulations or... Problem Identification, Leak Detection and Mercury Vapor 6 Table 6 to Subpart IIIII of Part 63 Protection... Hazardous Air Pollutants: Mercury Emissions From Mercury Cell Chlor-Alkali Plants Pt. 63, Subpt....

  11. Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification

    NARCIS (Netherlands)

    P.F. Mens; G.J. Schoone; P.A. Kager; H.D.F.H. Schallig

    2006-01-01

    Background: Decisions concerning malaria treatment depend on species identification causing disease. Microscopy is most frequently used, but at low parasitaemia (< 20 parasites/mu l) the technique becomes less sensitive and time consuming. Rapid diagnostic tests based on Plasmodium antigen detection

  12. Rapid sample preparation for detection and identification of avian influenza virus from chicken faecal samples using magnetic bead microsystem

    DEFF Research Database (Denmark)

    Dhumpa, Raghuram; Bu, Minqiang; Handberg, Kurt

    2010-01-01

    Avian influenza virus (AIV) is an infectious agent of birds and mammals. AIV is causing huge economic loss and can be a threat to human health. Reverse transcriptase polymerase chain reaction (RT-PCR) has been used as a method for the detection and identification of AIV virus. Although RT...

  13. Multiplex PCR assay for identification of six different Staphylococcus spp. and simultaneous detection of methicillin and mupirocin resistance.

    Science.gov (United States)

    Campos-Peña, E; Martín-Nuñez, E; Pulido-Reyes, G; Martín-Padrón, J; Caro-Carrillo, E; Donate-Correa, J; Lorenzo-Castrillejo, I; Alcoba-Flórez, J; Machín, F; Méndez-Alvarez, S

    2014-07-01

    We describe a new, efficient, sensitive, and fast single-tube multiple-PCR protocol for the identification of the most clinically significant Staphylococcus spp. and the simultaneous detection of the methicillin and mupirocin resistance loci. The protocol identifies at the species level isolates belonging to S. aureus, S. epidermidis, S. haemolyticus, S. hominis, S. lugdunensis, and S. saprophyticus.

  14. Mode identification using stochastic hybrid models with applications to conflict detection and resolution

    Science.gov (United States)

    Naseri Kouzehgarani, Asal

    2009-12-01

    Most models of aircraft trajectories are non-linear and stochastic in nature; and their internal parameters are often poorly defined. The ability to model, simulate and analyze realistic air traffic management conflict detection scenarios in a scalable, composable, multi-aircraft fashion is an extremely difficult endeavor. Accurate techniques for aircraft mode detection are critical in order to enable the precise projection of aircraft conflicts, and for the enactment of altitude separation resolution strategies. Conflict detection is an inherently probabilistic endeavor; our ability to detect conflicts in a timely and accurate manner over a fixed time horizon is traded off against the increased human workload created by false alarms---that is, situations that would not develop into an actual conflict, or would resolve naturally in the appropriate time horizon-thereby introducing a measure of probabilistic uncertainty in any decision aid fashioned to assist air traffic controllers. The interaction of the continuous dynamics of the aircraft, used for prediction purposes, with the discrete conflict detection logic gives rise to the hybrid nature of the overall system. The introduction of the probabilistic element, common to decision alerting and aiding devices, places the conflict detection and resolution problem in the domain of probabilistic hybrid phenomena. A hidden Markov model (HMM) has two stochastic components: a finite-state Markov chain and a finite set of output probability distributions. In other words an unobservable stochastic process (hidden) that can only be observed through another set of stochastic processes that generate the sequence of observations. The problem of self separation in distributed air traffic management reduces to the ability of aircraft to communicate state information to neighboring aircraft, as well as model the evolution of aircraft trajectories between communications, in the presence of probabilistic uncertain dynamics as well

  15. Identification of feigned mental retardation using the new generation of malingering detection instruments: preliminary findings.

    Science.gov (United States)

    Graue, Lili O; Berry, David T R; Clark, Jessica A; Sollman, Myriam J; Cardi, Michelle; Hopkins, Jaclyn; Werline, Dellynda

    2007-12-01

    A recent Supreme Court decision--Atkins v. Virginia, 536 U.S. 304 (2002)--prohibiting the execution of mentally retarded (MR) defendants may have raised the attractiveness of feigning this condition in the criminal justice system. Unfortunately, very few published studies have addressed the detection of feigned MR. The present report compared results from tests of intelligence, psychiatric feigning, and neurocognitive faking in a group of 26 mild MR participants (MR) and 25 demographically matched community volunteers asked to feign MR (CVM). Results showed that the CVM suppressed their IQ scores to approximate closely the level of MR participants. WAIS-III and psychiatric malingering measures were relatively ineffective at discriminating feigned from genuine MR. Although neurocognitive malingering tests were more accurate, their reduced specificity in MR participants was of potential concern. Revised cutting scores, set to maintain a Specificity rate of about .95 in MR clients, were identified, although they require cross-validation. Overall, these results suggest that new cutting scores will likely need to be validated to detect feigned MR using current malingering instruments.

  16. Expanded envelope concepts for aircraft control-element failure detection and identification

    Science.gov (United States)

    Weiss, Jerold L.; Hsu, John Y.

    1988-01-01

    The purpose of this effort was to develop and demonstrate concepts for expanding the envelope of failure detection and isolation (FDI) algorithms for aircraft-path failures. An algorithm which uses analytic-redundancy in the form of aerodynamic force and moment balance equations was used. Because aircraft-path FDI uses analytical models, there is a tradeoff between accuracy and the ability to detect and isolate failures. For single flight condition operation, design and analysis methods are developed to deal with this robustness problem. When the departure from the single flight condition is significant, algorithm adaptation is necessary. Adaptation requirements for the residual generation portion of the FDI algorithm are interpreted as the need for accurate, large-motion aero-models, over a broad range of velocity and altitude conditions. For the decision-making part of the algorithm, adaptation may require modifications to filtering operations, thresholds, and projection vectors that define the various hypothesis tests performed in the decision mechanism. Methods of obtaining and evaluating adequate residual generation and decision-making designs have been developed. The application of the residual generation ideas to a high-performance fighter is demonstrated by developing adaptive residuals for the AFTI-F-16 and simulating their behavior under a variety of maneuvers using the results of a NASA F-16 simulation.

  17. Identification and Analysis of Immunodominant Antigens for ELISA-Based Detection of Theileria annulata

    Science.gov (United States)

    Bakırcı, Serkan; Tait, Andrew; Kinnaird, Jane; Eren, Hasan

    2016-01-01

    Tropical or Mediterranean theileriosis, caused by the protozoan parasite Theileria annulata, remains an economically important bovine disease in North Africa, Southern Europe, India, the Middle East and Asia. The disease affects mainly exotic cattle and imposes serious constraints upon livestock production and breed improvement programmes. While microscopic and molecular methods exist which are capable of detecting T. annulata during acute infection, the identification of animals in the carrier state is more challenging. Serological tests, which detect antibodies that react against parasite-encoded antigens, should ideally have the potential to identify carrier animals with very high levels of sensitivity and specificity. However, assays developed to date have suffered from a lack of sensitivity and/or specificity and it is, therefore, necessary to identify novel parasite antigens, which can be developed for this purpose. In the present study, genes encoding predicted antigens were bioinformatically identified in the T. annulata genome. These proteins, together with a panel of previously described antigens, were assessed by western blot analysis for immunoreactivity, and this revealed that four novel candidates and five previously described antigens were recognised by immune bovine serum. Using a combination of immunoprecipitation and mass spectrophotometric analysis, an immunodominant protein (encoded by TA15705) was identified as Ta9, a previously defined T cell antigen. Western blotting revealed another of the five proteins in the Ta9 family, TA15710, also to be an immunodominant protein. However, validation by Enzyme-Linked Immunosorbent Assay indicated that due to either allelic polymorphism or differential immune responses of individual hosts, none of the novel candidates can be considered ideal for routine detection of T. annulata-infected/carrier animals. PMID:27270235

  18. Lidar and Dial application for detection and identification: a proposal to improve safety and security

    Science.gov (United States)

    Gaudio, P.; Malizia, A.; Gelfusa, M.; Murari, A.; Parracino, S.; Poggi, L. A.; Lungaroni, M.; Ciparisse, J. F.; Di Giovanni, D.; Cenciarelli, O.; Carestia, M.; Peluso, E.; Gabbarini, V.; Talebzadeh, S.; Bellecci, C.

    2017-01-01

    Nowadays the intentional diffusion in air (both in open and confined environments) of chemical contaminants is a dramatic source of risk for the public health worldwide. The needs of a high-tech networks composed by software, diagnostics, decision support systems and cyber security tools are urging all the stakeholders (military, public, research & academic entities) to create innovative solutions to face this problem and improve both safety and security. The Quantum Electronics and Plasma Physics (QEP) Research Group of the University of Rome Tor Vergata is working since the 1960s on the development of laser-based technologies for the stand-off detection of contaminants in the air. Up to now, four demonstrators have been developed (two LIDAR-based and two DIAL-based) and have been used in experimental campaigns during all 2015. These systems and technologies can be used together to create an innovative solution to the problem of public safety and security: the creation of a network composed by detection systems: A low cost LIDAR based system has been tested in an urban area to detect pollutants coming from urban traffic, in this paper the authors show the results obtained in the city of Crotone (south of Italy). This system can be used as a first alarm and can be coupled with an identification system to investigate the nature of the threat. A laboratory dial based system has been used in order to create a database of absorption spectra of chemical substances that could be release in atmosphere, these spectra can be considered as the fingerprints of the substances that have to be identified. In order to create the database absorption measurements in cell, at different conditions, are in progress and the first results are presented in this paper.

  19. Simultaneous identification and quantification of new psychoactive substances in blood by GC-APCI-QTOFMS coupled to nitrogen chemiluminescence detection without authentic reference standards.

    Science.gov (United States)

    Ojanperä, Ilkka; Mesihää, Samuel; Rasanen, Ilpo; Pelander, Anna; Ketola, Raimo A

    2016-05-01

    A novel platform is introduced for simultaneous identification and quantification of new psychoactive substances (NPS) in blood matrix, without the necessity of using authentic reference standards. The instrumentation consisted of gas chromatography (GC) coupled to nitrogen chemiluminescence detection (NCD) and atmospheric pressure chemical ionization quadrupole time-of-flight mass spectrometry (APCI-QTOFMS). In this concept, the GC flow is divided in appropriate proportions between NCD for single-calibrant quantification, utilizing the detector's equimolar response to nitrogen, and QTOFMS for accurate mass-based identification. The principle was proven by analyzing five NPS, bupropion, desoxypipradrol (2-DPMP), mephedrone, methylone, and naphyrone, in sheep blood. The samples were spiked with the analytes post-extraction to avoid recovery considerations at this point. All the NPS studies produced a protonated molecule in APCI resulting in predictable fragmentation with high mass accuracy. The N-equimolarity of quantification by NCD was investigated by using external calibration with the secondary standard caffeine at five concentration levels between 0.17 and 1.7 mg/L in blood matrix as five replicates. The equimolarity was on average 98.7%, and the range of individual equimolarity determinations was 76.7-130.1%. The current analysis platform affords a promising approach to instant simultaneous qualitative and quantitative analysis of drugs in the absence of authentic reference standards, not only in forensic and clinical toxicology but also in other bioanalytical applications.

  20. A Sparse Semi-Blind Source Identification Method and Its Application to Raman Spectroscopy for Explosives Detection

    CERN Document Server

    Sun, Y

    2011-01-01

    Rapid and reliable detection and identification of unknown chemical substances is critical to homeland security. It is challenging to identify chemical components from a wide range of explosives. There are two key steps involved. One is a nondestructive and informative spectroscopic technique for data acquisition. The other is an associated library of reference features along with a computational method for feature matching and meaningful detection within or beyond the library. Recently several experimental techniques based on Raman scattering have been developed to perform standoff detection and identification of explosives, and they prove to be successful under certain idealized conditions. However data analysis is limited to standard least squares method assuming the complete knowledge of the chemical components. In this paper, we develop a new iterative method to identify unknown substances from mixture samples of Raman spectroscopy. In the first step, a constrained least squares method decomposes the dat...

  1. Is a single direct MR arthrography series in ABER position as accurate in detecting anteroinferior labroligamentous lesions as conventional MR arthography?

    NARCIS (Netherlands)

    Schreinemachers, S.A.; van der Hulst, V.P.M.; Willems, W.J.; Bipat, S.; van der Woude, H.J.

    2009-01-01

    The purpose of this study is to retrospectively compare accuracy of single magnetic resonance (MR) arthrography series in Abduction External Rotation (ABER) with conventional MR arthrography for detection and characterisation of anteroinferior labroligamentous lesions, with arthroscopy as reference

  2. Identification of anthocyanins in berries by narrow-bore high-performance liquid chromatography with electrospray ionization detection.

    Science.gov (United States)

    Dugo, P; Mondello, L; Errante, G; Zappia, G; Dugo, G

    2001-08-01

    Qualitative determination of anthocyanins in extracts of red fruits by narrow-bore HPLC/ESI-MS was carried out. This method was used to investigate anthocyanin contents of black bilberry (Vaccinium myrtillus L.), blackberry (Rubus sp.), and mulberry (Morus nigra). An ultraviolet diode array and a mass spectrometer with ESI source were used for detection. Anthocyanin identifications were made by using retention time data and UV-vis and mass spectra and comparing them with those of commercially available standard compounds. The method allowed the identification of fourteen anthocyanins in black bilberry extract, six anthocyanins in blackberry extract, and five anthocyanins in mulberry extract.

  3. Detection and identification of free-living amoeba from aquatic environment in different seasons in Taiwan

    Science.gov (United States)

    Tzeng, K.; Hsu, B.; Tsai, H.; Huang, P.; Tsai, J.; Kao, P.; Huang, K.; Chen, J.

    2013-12-01

    Free-living amoeba includes Acanthamoeba and Naegleria, which are widely distributed in water and soil. Human infection with free-living amoeba leads to serious illness, even lethal. For example, central nervous system infection will cause amoebic meningoencephalitis, and infections will cause amoebic keratitis. The presence of free-living amoeba in environment water can be used as a water quality indicator in ecosystem assessment. In Taiwan, reservoirs are indispensable because of the water source are limited by the steep terrain and the short river flow. Therefore, we need to pay more attention in the quality control of reservoirs water. The aims of this study are to investigate the presence of free-living amoeba in Taiwan reservoirs, and to compare the differences among seasons. At last, the identification and genotyping of Acanthamoeba and Naegleria are investigated. In this study, we use polymerase chain reaction with specific primers to analyze the presence of free-living amoeba in aquatic environment. We collected total 60 samples from reservoirs in Taiwan. The water samples are divided into two parts for both direct concentration method and culture method. The results show the different detection rates among seasons. For Acanthamoeba, the detection rates were 28.3% (17 of 60 water samples), 21.7% (13 of 60 water samples) and 8.3% (5 of 60 water samples) in autumn, winter and spring, respectively. For Naegleria, the detection rates were 6.7% (4 of 60 water samples), 0% (0 of 60 water samples) and 0% (0 of 60 water samples) were detected positive in autumn, winter and spring, respectively. Sequence analysis showed that the major genotypes in Acanthamoeba were T3, T4, T10 and T11 in autumn, T2, T4 and T10 in winter, T4 in spring. Due to the presences of Acanthamoeba and Naegleria in reservoirs, we should pay more attention in water quality monitoring to prevent the potential risks of diseases. Keywords: free-living amoeba, Acanthamoeba, Naegleria, polymerase

  4. Detection of erosion/deposition depth using a low frequency passive Radio Frequency Identification (RFID) technology

    Science.gov (United States)

    Moustakidis, Iordanis Vlasios

    This thesis presents an experimental study both in the laboratory and field to develop and test a method for continuously measuring and monitoring scour using an automated identification technology known as Radio Frequency Identification (RFID). RFID systems consist of three main components, namely (a) the reader which controls the system, (b) the transponder (derived from transmitter/responder) that transmits data to the reader and (c) the excitation antenna that allows the communication between the reader and the transponder. The study provides an insight into the RFID technology and develops the framework for using this technology to eventually address two central themes in river mechanics and sediment transport; (a) the determination of the active layer thickness and (b) the scour/deposition depth around a hydraulic structure. In particular, this study develops the methodology for relating the signal strength of a radio frequency (RF) device with the distance between an excitation antenna and the RF device. The experiments presented herein are classified into two main groups, (1) the laboratory and (2) the RF signal vs. the detection distance experiments (field experiments). The laboratory experiments were designed to understand the effect of key RFID parameters (e.g., transponder orientation with respect to the excitation antenna plane, maximum antenna-transponder detection distance), measured in terms of the transponder return RF signal strength for various antenna-transponder distances, transponder orientations with respect to the excitation antenna plane and different mediums in between the excitation antenna and the transponder, on the overall performance of the RFID system. On the other hand, the RF signal vs. the detection distance experiments were based on the results obtained during the laboratory experiments and focused on developing calibration curves by relating the transponder return RF signal strength with the distance between the excitation

  5. Detection and identification of crowded mirror-image letters in normal peripheral vision.

    Science.gov (United States)

    Chung, Susana T L

    2010-02-01

    Performance for discriminating single mirror-image letters in peripheral vision can be as good as that in central vision, provided that letter size is scaled appropriately [Higgins, K. E., Arditi, A., & Knoblauch, K. (1996). Detection and identification of mirror-image letter pairs in central and peripheral vision. Vision Research, 36, 331-337]. In this study, we asked whether or not there is a reduction in performance for discriminating mirror-image letters when the letters are flanked closely by other letters, compared with unflanked (single) letters; and if so, whether or not this effect is greater in peripheral than in central vision. We compared contrast thresholds for detecting and identifying mirror-image letters "b" and "d" for a range of letter separations, at the fovea and 10 degrees eccentricity, for letters that were scaled in size. For comparison, thresholds were also determined for a pair of non-mirror-image letters "o" and "x". Our principal finding is that there is an additional loss in sensitivity for identifying mirror-image letters ("bd"), compared with non-mirror-image letters ("ox"), when the letters are flanked closely by other letters. The effect is greater in peripheral than central vision. An auxiliary experiment comparing thresholds for letters "d" and "q" vs. "b" and "d" shows that the additional loss in sensitivity for identifying crowded mirror-image letters cannot be attributed to the similarity in letter features between the two letters, but instead, is specific to the axis of symmetry. Our results suggest that in the presence of proximal objects, there is a specific loss in sensitivity for processing broad-band left-right mirror images in peripheral vision.

  6. Connective tissue growth factor in tear film of the horse: detection, identification and origin.

    Science.gov (United States)

    Ollivier, F J; Brooks, D E; Schultz, G S; Blalock, T D; Andrew, S E; Komaromy, A M; Cutler, T J; Lassaline, M E; Kallberg, M E; Van Setten, G B

    2004-02-01

    Healing of corneal ulcers in horses is often associated with profound corneal stromal fibrosis and scar formation resulting in visual impairment. Connective tissue growth factor (CTGF) is a fibrogenic cytokine involved in wound healing and scarring. The purpose of this study was to determine whether CTGF was present in the tear fluid of normal horse eyes and the eyes of horses with corneal ulcers in order to evaluate the role of CTGF in corneal wound healing and corneal scar formation. Tear fluid samples were collected from 65 eyes of 44 horses; 32 samples from normal eyes, 21 samples from eyes with corneal ulceration, and 12 samples from the unaffected contralateral eyes of horses with ulcers. CTGF levels in the tears were determined by enzyme immunoassay using goat IgG against human CTGF. Antigenetic similarity of human and horse CTGF was established in a bio-equivalence assay. The identity of horse CTGF was confirmed by western blot. Lacrimal and nictitating membrane glands were investigated by immunohistochemistry in the attempt to clarify the origin of tear fluid CTGF. CTGF was detected in tear film of 23 normal unaffected eyes (72%) and 8 normal contralateral eyes (67%), with the mean CTGF levels (+/- SEM) being 51.5+/-19.2 and 13.4+/-3.9 ng/ml respectively. CTGF was found in 8 eyes with corneal ulcers (38%) with the mean CTGF concentration of 26.3+/-14.8 ng/ml. Western blot identified the protein detected as CTGF. The identification of CTGF in lacrimal glands suggests a major role of these glands in the presence of CTGF in tears. CTGF is present in horse tear fluid and derives, at least partly, from the lacrimal gland. Equine CTGF has strong antigenic similarity with human CTGF. Corneal disease leads to a decrease of CTGF concentrations in tears. The possible role of CTGF in the healing process of ocular surface requires further investigation.

  7. Detection, identification, and typing of Listeria species from baled silages fed to dairy cows.

    Science.gov (United States)

    Nucera, D M; Grassi, M A; Morra, P; Piano, S; Tabacco, E; Borreani, G

    2016-08-01

    Anaerobiosis, critical for successful ensilage, constitutes a challenge in baled silages. The loss of complete anaerobiosis causes aerobic deterioration and silages undergo dry matter and nutrient losses, pathogen growth, and mycotoxin production. Silage may represent an ideal substrate for Listeria monocytogenes, a pathogen of primary concern in several cheeses. The aim of this research was to investigate the occurrence of Listeria in baled silage fed to cows producing milk for a protected designation of origin cheese, and to characterize isolates by repetitive sequence-based PCR. Listeria spp. were detected in 21 silages and L. monocytogenes in 6 out of 80 of the analyzed silages; 67% of positives were found in molded zones. Results of the PCR typing showed genotypic homogeneity: 72.9 and 78.8% similarity between strains of Listeria spp. (n=56) and L. monocytogenes (n=24), respectively. Identical profiles were recovered in molded and nonmolded areas, indicating that contamination may have occurred during production. The application of PCR allowed the unambiguous identification of Listeria isolated from baled silages, and repetitive sequence-based PCR allowed a rapid and effective typing of isolates. Results disclose the potential of the systematic typing of Listeria in primary production, which is needed for the understanding of its transmission pathways. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  8. Active layer identification of photonic crystal waveguide biosensor chip for the detection of Escherichia coli

    Science.gov (United States)

    Painam, Balveer; Kaler, Rajinder S.; Kumar, Mukesh

    2016-07-01

    This work represents experimental and simulation analysis of photonic crystal waveguide (PCW)-based biosensor structures, which is used for detection of the Escherichia coli (E. coli) cell. A method is adopted for E. coli culture to measure length, diameter, and refractive index to finalize the structural design and to verify the suitability of PCW as a biosensor. This method is tested using DH5α strains of E. coli. The typical precisions of measurements are varied in ranges from 1.132 to 1.825 μm and from 0.447 to 0.66 μm for pathogen's length and diameter, respectively. The measured distribution of samples over length and diameter are in correlation with the measurements performed by scanning electron microscope. After obtaining average length and diameter of cylindrical shaped E. coli cell, we consider these values for simulation analysis of designed PCW biosensor. E. coli cell is trapped in the middle of the PCW biosensor having three different types of waveguides, i.e., gallium arsenide/silicon dioxide (GaAs/SiO2), silicon/silicon dioxide (Si/SiO2), or silicon nitride/silicon dioxide (Si3N4/SiO2) to observe the maximum resonance shift and sensitivity. It is observed from the simulation data analysis that GaAs/SiO2 is the preferred PCW biosensor for the identification of E. coli.

  9. UXO detection and identification based on intrinsic target polarizabilities: A case history

    Energy Technology Data Exchange (ETDEWEB)

    Gasperikova, E.; Smith, J.T.; Morrison, H.F.; Becker, A.; Kappler, K.

    2008-07-15

    Electromagnetic induction data parameterized in time dependent object intrinsic polarizabilities allow discrimination of unexploded ordnance (UXO) from false targets (scrap metal). Data from a cart-mounted system designed for discrimination of UXO with 20 mm to 155 mm diameters are used. Discrimination of UXO from irregular scrap metal is based on the principal dipole polarizabilities of a target. A near-intact UXO displays a single major polarizability coincident with the long axis of the object and two equal smaller transverse polarizabilities, whereas metal scraps have distinct polarizability signatures that rarely mimic those of elongated symmetric bodies. Based on a training data set of known targets, object identification was made by estimating the probability that an object is a single UXO. Our test survey took place on a military base where both 4.2-inch mortar shells and scrap metal were present. The results show that we detected and discriminated correctly all 4.2-inch mortars, and in that process we added 7%, and 17%, respectively, of dry holes (digging scrap) to the total number of excavations in two different survey modes. We also demonstrated a mode of operation that might be more cost effective than the current practice.

  10. Detection and identification of Rickettsia species in Ixodes tick populations from Estonia.

    Science.gov (United States)

    Katargina, Olga; Geller, Julia; Ivanova, Anna; Värv, Kairi; Tefanova, Valentina; Vene, Sirkka; Lundkvist, Åke; Golovljova, Irina

    2015-09-01

    A total of 1640 ticks collected in different geographical parts of Estonia were screened for the presence of Rickettsia species DNA by real-time PCR. DNA of Rickettsia was detected in 83 out of 1640 questing ticks with an overall prevalence of 5.1%. The majority of the ticks infected by rickettsiae were Ixodes ricinus (74 of 83), while 9 of the 83 positive ticks were Ixodes persulcatus. For rickettsial species identification, a part of the citrate synthase gltA gene was sequenced. The majority of the positive samples were identified as Rickettsia helvetica (81 out of 83) and two of the samples were identified as Rickettsia monacensis and Candidatus R. tarasevichiae, respectively. Genetic characterization based on the partial gltA gene showed that the Estonian sequences within the R. helvetica, R. monacensis and Candidatus R. tarasevichiae species demonstrated 100% similarity with sequences deposited in GenBank, originating from Rickettsia species distributed over large territories from Europe to Asia.

  11. Drag detection and identification by whispering gallery mode optical resonance based sensor

    Science.gov (United States)

    Saetchnikov, Vladimir A.; Tcherniavskaia, Elina A.; Saetchnikov, Anton V.; Schweiger, Gustav; Ostendorf, Andreas

    2013-06-01

    Experimental data on optical resonance spectra of whispering gallery modes of dielectric microspheres in antibiotic solutions under varied in wide range concentration are represented. Optical resonance was demonstrated could be detected at a laser power of less than 1 microwatt. Several antibiotics of different generations: Amoxicillin, Azithromycin, Cephazolin, Chloramphenicol, Levofloxacin, Lincomicin Benzylpenicillin, Riphampicon both in deionized water and physiological solution had been used for measurements. Both spectral shift and the structure of resonance spectra were of specific interest in this investigation. Drag identification has been performed by developed multilayer perceptron network. The network topology was designed included: a number of the hidden layers of multilayered perceptron, a number of neurons in each of layers, a method of training of a neural network, activation functions of layers, type and size of a deviation of the received values from required values. For a network training the method of the back propagation error in various modifications has been used. Input vectors correspond to 6 classes of biological substances under investigation. The result of classification was considered as positive when each of the region, representing a certain substance in a space: relative spectral shift of an optical resonance maxima - relative efficiency of excitation of WGM, was singly connected. It was demonstrated that the approach described in the paper can be a promising platform for the development of sensitive, lab-on-chip type sensors that can be used as an express diagnostic tools for different drugs and instrumentation for proteomics, genomics, drug discovery, and membrane studies.

  12. A novel asymmetric-loop molecular beacon-based two-phase hybridization assay for accurate and high-throughput detection of multiple drug resistance-conferring point mutations in Mycobacterium tuberculosis.

    Science.gov (United States)

    Chen, Qinghai; Wu, Nan; Xie, Meng; Zhang, Bo; Chen, Ming; Li, Jianjun; Zhuo, Lisha; Kuang, Hong; Fu, Weiling

    2012-04-01

    The accurate and high-throughput detection of drug resistance-related multiple point mutations remains a challenge. Although the combination of molecular beacons with bio-immobilization technology, such as microarray, is promising, its application is difficult due to the ineffective immobilization of molecular beacons on the chip surface. Here, we propose a novel asymmetric-loop molecular beacon in which the loop consists of 2 parts. One is complementary to a target, while the other is complementary to an oligonucleotide probe immobilized on the chip surface. With this novel probe, a two-phase hybridization assay can be used for simultaneously detecting multiple point mutations. This assay will have advantages, such as easy probe availability, multiplex detection, low background, and high-efficiency hybridization, and may provide a new avenue for the immobilization of molecular beacons and high-throughput detection of point mutations.

  13. HIPPI: highly accurate protein family classification with ensembles of HMMs

    Directory of Open Access Journals (Sweden)

    Nam-phuong Nguyen

    2016-11-01

    Full Text Available Abstract Background Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics. Results We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification. HIPPI uses a novel technique to represent a multiple sequence alignment for a given protein family or superfamily by an ensemble of profile hidden Markov models computed using HMMER. An evaluation of HIPPI on the Pfam database shows that HIPPI has better overall precision and recall than blastp, HMMER, and pipelines based on HHsearch, and maintains good accuracy even for fragmentary query sequences and for protein families with low average pairwise sequence identity, both conditions where other methods degrade in accuracy. Conclusion HIPPI provides accurate protein family identification and is robust to difficult model conditions. Our results, combined with observations from previous studies, show that ensembles of profile Hidden Markov models can better represent multiple sequence alignments than a single profile Hidden Markov model, and thus can improve downstream analyses for various bioinformatic tasks. Further research is needed to determine the best practices for building the ensemble of profile Hidden Markov models. HIPPI is available on GitHub at https://github.com/smirarab/sepp .

  14. Automatic solution for detection, identification and biomedical monitoring of a cow using remote sensing for optimised treatment of cattle

    Directory of Open Access Journals (Sweden)

    Yevgeny Beiderman

    2014-12-01

    Full Text Available In this paper we show how a novel photonic remote sensing system assembled on a robotic platform can extract vital biomedical parameters from cattle including their heart beating, breathing and chewing activity. The sensor is based upon a camera and a laser using selfinterference phenomena. The whole system intends to provide an automatic solution for detection, identification and biomedical monitoring of a cow. The detection algorithm is based upon image processing involving probability map construction. The identification algorithms involve well known image pattern recognition techniques. The sensor is used on top of an automated robotic platform in order to support animal decision making. Field tests and computer simulated results are presented.

  15. Application of exogenous mixture of glutathione and stable isotope labeled glutathione for trapping reactive metabolites in cryopreserved human hepatocytes. Detection of the glutathione conjugates using high resolution accurate mass spectrometry.

    Science.gov (United States)

    Mezine, Igor; Bode, Chris; Raughley, Bethany; Bhoopathy, Sid; Roberts, Kenneth J; Owen, Albert J; Hidalgo, Ismael J

    2013-08-25

    Metabolites (including reactive metabolites) of troglitazone were generated by incubation with cryopreserved human hepatocytes and trapped in the presence of an exogenous mixture of unlabeled and stable isotope labeled (SIL: [1,2-(13)C, (15)N]-glycine) glutathione (GSH/SIL-GSH). The incubation samples were analyzed using liquid chromatography-high resolution accurate mass spectrometry (LC-HRAMS) implemented on a LTQ Orbitrap mass spectrometer. The GSH conjugates of the reactive metabolites were detected via a characteristic mono-isotopic pattern (peaks separated by 3.0037u). Analysis of the incubation samples led to detection of a number of previously described GSH conjugates, as well as two novel methylated GSH conjugates, which were partially characterized based on accurate mass measurements and MS/MS data. The addition of exogenous GSH led to an increase in the apparent level of detected GSH conjugates. Kinetic isotopic measurements showed that the rates of incorporation of exogenous GSH are conjugate-specific. In conclusion, this approach, based on the use of a mixture of GSH/SIL-GSH, allows facile capture and detection of reactive metabolites in human hepatocytes. Moreover, the data suggest that routine addition of glutathione to the assay medium may be advisable for experiments with cryopreserved hepatocytes. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  16. Detection and identification of putative bacterial endosymbionts and endogenous viruses in tick cell lines.

    Science.gov (United States)

    Alberdi, M Pilar; Dalby, Matthew J; Rodriguez-Andres, Julio; Fazakerley, John K; Kohl, Alain; Bell-Sakyi, Lesley

    2012-06-01

    As well as being vectors of many viral, bacterial, and protozoan pathogens of medical and veterinary importance, ticks harbour a variety of microorganisms which are not known to be pathogenic for vertebrate hosts. Continuous cell lines established from ixodid and argasid ticks could be infected with such endosymbiotic bacteria and endogenous viruses, but to date very few cell lines have been examined for their presence. DNA and RNA extracted from over 50 tick cell lines deposited in the Roslin Wellcome Trust Tick Cell Biobank (http://tickcells.roslin.ac.uk) were screened for presence of bacteria and RNA viruses, respectively. Sequencing of PCR products amplified using pan-16S rRNA primers revealed the presence of DNA sequences from bacterial endosymbionts in several cell lines derived from Amblyomma and Dermacentor spp. ticks. Identification to species level was attempted using Rickettsia- and Francisella-specific primers. Pan-Nairovirus primers amplified PCR products of uncertain specificity in cell lines derived from Rhipicephalus, Hyalomma, Ixodes, Carios, and Ornithodoros spp. ticks. Further characterisation attempted with primers specific for Crimean-Congo haemorrhagic fever virus segments confirmed the absence of this arbovirus in the cells. A set of pan-Flavivirus primers did not detect endogenous viruses in any of the cell lines. Transmission electron microscopy revealed the presence of endogenous reovirus-like viruses in many of the cell lines; only 4 of these lines gave positive results with primers specific for the tick Orbivirus St Croix River virus, indicating that there may be additional, as yet undescribed 'tick-only' viruses inhabiting tick cell lines.

  17. Detection and identification of putative bacterial endosymbionts and endogenous viruses in tick cell lines☆

    Science.gov (United States)

    Alberdi, M. Pilar; Dalby, Matthew J.; Rodriguez-Andres, Julio; Fazakerley, John K.; Kohl, Alain; Bell-Sakyi, Lesley

    2012-01-01

    As well as being vectors of many viral, bacterial, and protozoan pathogens of medical and veterinary importance, ticks harbour a variety of microorganisms which are not known to be pathogenic for vertebrate hosts. Continuous cell lines established from ixodid and argasid ticks could be infected with such endosymbiotic bacteria and endogenous viruses, but to date very few cell lines have been examined for their presence. DNA and RNA extracted from over 50 tick cell lines deposited in the Roslin Wellcome Trust Tick Cell Biobank (http://tickcells.roslin.ac.uk) were screened for presence of bacteria and RNA viruses, respectively. Sequencing of PCR products amplified using pan-16S rRNA primers revealed the presence of DNA sequences from bacterial endosymbionts in several cell lines derived from Amblyomma and Dermacentor spp. ticks. Identification to species level was attempted using Rickettsia- and Francisella-specific primers. Pan-Nairovirus primers amplified PCR products of uncertain specificity in cell lines derived from Rhipicephalus, Hyalomma, Ixodes, Carios, and Ornithodoros spp. ticks. Further characterisation attempted with primers specific for Crimean-Congo haemorrhagic fever virus segments confirmed the absence of this arbovirus in the cells. A set of pan-Flavivirus primers did not detect endogenous viruses in any of the cell lines. Transmission electron microscopy revealed the presence of endogenous reovirus-like viruses in many of the cell lines; only 4 of these lines gave positive results with primers specific for the tick Orbivirus St Croix River virus, indicating that there may be additional, as yet undescribed ‘tick-only’ viruses inhabiting tick cell lines. PMID:22743047

  18. Sink detection on tilted terrain for automated identification of glacial cirques

    Science.gov (United States)

    Prasicek, Günther; Robl, Jörg; Lang, Andreas

    2016-04-01

    Glacial cirques are morphologically distinct but complex landforms and represent a vital part of high mountain topography. Their distribution, elevation and relief are expected to hold information on (1) the extent of glacial occupation, (2) the mechanism of glacial cirque erosion, and (3) how glacial in concert with periglacial processes can limit peak altitude and mountain range height. While easily detectably for the expert's eye both in nature and on various representations of topography, their complicated nature makes them a nemesis for computer algorithms. Consequently, manual mapping of glacial cirques is commonplace in many mountain landscapes worldwide, but consistent datasets of cirque distribution and objectively mapped cirques and their morphometrical attributes are lacking. Among the biggest problems for algorithm development are the complexity in shape and the great variability of cirque size. For example, glacial cirques can be rather circular or longitudinal in extent, exist as individual and composite landforms, show prominent topographic depressions or can entirely be filled with water or sediment. For these reasons, attributes like circularity, size, drainage area and topology of landform elements (e.g. a flat floor surrounded by steep walls) have only a limited potential for automated cirque detection. Here we present a novel, geomorphometric method for automated identification of glacial cirques on digital elevation models that exploits their genetic bowl-like shape. First, we differentiate between glacial and fluvial terrain employing an algorithm based on a moving window approach and multi-scale curvature, which is also capable of fitting the analysis window to valley width. We then fit a plane to the valley stretch clipped by the analysis window and rotate the terrain around the center cell until the plane is level. Doing so, we produce sinks of considerable size if the clipped terrain represents a cirque, while no or only very small sinks

  19. Measurement of cooling detection thresholds for identification of diabetic sensorimotor polyneuropathy in type 1 diabetes.

    Directory of Open Access Journals (Sweden)

    Zoe Lysy

    Full Text Available OBJECTIVE: Compared to recently-studied novel morphological measures, conventional small nerve fiber functional tests have not been systematically studied for identification of diabetic sensorimotor polyneuropathy (DSP. We aimed to determine and compare the diagnostic performance of cooling detection thresholds (CDT in a cross-sectional type 1 diabetes cohort. RESEARCH DESIGN AND METHODS: 136 subjects with type 1 diabetes and 52 healthy volunteers underwent clinical and electrophysiological examination for DSP classification concomitantly with the Toronto Clinical Neuropathy Score (TCNS and three small fiber function tests: CDT, heart rate variability (HRV, and laser doppler imaging of axon-mediated neurogenic flare responses to cutaneous heating (LDIFLARE. Area under the curve (AUC and optimal thresholds were determined by receiver operating characteristic (ROC curves in the type 1 diabetes cohort. RESULTS: Type 1 diabetes subjects were 42±17 years of age with mean HbA1c 7.9±1.7%. Fifty-nine (45% met the case definition for DSP. CDT values were lowest in cases with DSP (18.3±8.4°C compared to controls without DSP (28.4±3.5°C and to healthy volunteers (29.6±1.8°C; p-value for both comparisons<0.0001. AUCCDT was 0.863 which was similar to AUCTCNS (0.858, p = 0.24 and AUCHRV (0.788, p = 0.05, but exceeded AUCLDIFLARE (0.750, p = 0.001. The threshold of <25.1°C was equivalent to the lower bound of the healthy volunteer 95% distribution [25.1, 30.8°C] and performed with 83% sensitivity and 82% specificity. CONCLUSIONS: Akin to novel small fiber morphological measures, CDT is a functional test that identifies DSP with very good diagnostic performance. These findings support further research that revisits the role of CDT in early DSP detection.

  20. Laboratory and Field Testing of Commercially Available Detectors for the Identification of Chemicals of Interest in the Nuclear Fuel Cycle for the Detection of Undeclared Activities

    Energy Technology Data Exchange (ETDEWEB)

    Carla Miller; Mary Adamic; Stacey Barker; Barry Siskind; Joe Brady; Warren Stern; Heidi Smartt; Mike McDaniel; Mike Stern; Rollin Lakis

    2014-07-01

    Traditionally, IAEA inspectors have focused on the detection of nuclear indicators as part of infield inspection activities. The ability to rapidly detect and identify chemical as well as nuclear signatures can increase the ability of IAEA inspectors to detect undeclared activities at a site. Identification of chemical indicators have been limited to use in the analysis of environmental samples. Although IAEA analytical laboratories are highly effective, environmental sample processing does not allow for immediate or real-time results to an IAEA inspector at a facility. During a complementary access inspection, under the Additional Protocol, the use of fieldable technologies that can quickly provide accurate information on chemicals that may be indicative of undeclared activities can increase the ability of IAEA to effectively and efficiently complete their mission. The Complementary Access Working Group (CAWG) is a multi-laboratory team with members from Brookhaven National Laboratory, Idaho National Laboratory, Los Alamos National Laboratory, and Sandia National Laboratory. The team identified chemicals at each stage of the nuclear fuel cycle that may provide IAEA inspectors with indications that proliferation activities may be occurring. The group eliminated all indicators related to equipment, technology and training, developing a list of by-products/effluents, non-nuclear materials, nuclear materials, and other observables. These proliferation indicators were prioritized based on detectability from a conduct of operations (CONOPS) perspective of a CA inspection (for example, whether an inspector actually can access the S&O or whether it is in process with no physical access), and the IAEA’s interest in the detection technology in conjunction with radiation detectors. The list was consolidated to general categories (nuclear materials from a chemical detection technique, inorganic chemicals, organic chemicals, halogens, and miscellaneous materials). The team

  1. Rapid identification of mycobacteria and rapid detection of drug resistance in Mycobacterium tuberculosis in cultured isolates and in respiratory specimens.

    Science.gov (United States)

    Yam, Wing-Cheong; Siu, Kit-Hang Gilman

    2013-01-01

    Recent advances in molecular biology and better understanding of the genetic basis of drug resistance have allowed rapid identification of mycobacteria and rapid detection of drug resistance of Mycobacterium tuberculosis present in cultured isolates or in respiratory specimens. In this chapter, several simple nucleic acid amplification-based techniques are introduced as molecular approach for clinical diagnosis of tuberculosis. A one-tube nested IS6110-based polymerase chain reaction (PCR) is used for M. tuberculosis complex identification; the use of a multiplex allele-specific PCR is demonstrated to detect the isoniazid resistance; PCR-sequencing assays are applied for rifampicin and ofloxacin resistance detection and 16S rDNA sequencing is utilized for identification of mycobacterial species from cultures of acid fast bacilli (AFB). Despite the high specificity and sensitivity of the molecular techniques, mycobacterial culture remains the "Gold Standard" for tuberculosis diagnosis. Negative results of molecular tests never preclude the infection or the presence of drug resistance. These technological advancements are, therefore, not intended to replace the conventional tests, but rather have major complementary roles in tuberculosis diagnosis.

  2. ViriChip: a solid phase assay for detection and identification of viruses by atomic force microscopy

    Science.gov (United States)

    Nettikadan, Saju R.; Johnson, James C.; Vengasandra, Srikanth G.; Muys, James; Henderson, Eric

    2004-03-01

    Bionanotechnology can be viewed as the integration of tools and concepts in nanotechnology with the attributes of biomolecules. We report here on an atomic force microscopy-immunosensor assay (AFMIA) that couples AFM with solid phase affinity capture of biological entities for the rapid detection and identification of group B coxsackievirus particles. Virus identification is based on type-specific immunocapture and the morphological properties of the captured viruses as obtained by the AFM. Representatives of the six group B coxsackieviruses have been specifically captured from 1 µl volumes of clarified cell lysates, body fluids and environmental samples. Concentration and kinetic profiles for capture indicate that detection is possible at 103 TCID50 µl-1 and the dynamic range of the assay spans three logs. The results demonstrate that the melding of a nanotechnological tool (AFM) with biotechnology (solid phase immunocapture of virus particles) can create a clinically relevant platform, useful for the detection and identification of enterovirus particles in a variety of samples.

  3. Shell thickness-dependent Raman enhancement for rapid identification and detection of pesticide residues at fruit peels.

    Science.gov (United States)

    Liu, Bianhua; Han, Guangmei; Zhang, Zhongping; Liu, Renyong; Jiang, Changlong; Wang, Suhua; Han, Ming-Yong

    2012-01-03

    Here, we report the shell thickness-dependent Raman enhancement of silver-coated gold nanoparticles (Au@Ag NPs) for the identification and detection of pesticide residues at various fruit peels. The Raman enhancement of Au@Ag NPs to a large family of sulfur-containing pesticides is ~2 orders of magnitude stronger than those of bare Au and Ag NPs, and there is a strong dependence of the Raman enhancement on the Ag shell thickness. It has been shown for the first time that the huge Raman enhancement is contributed by individual Au@Ag NPs rather than aggregated Au@Ag NPs with "hot spots" among the neighboring NPs. Therefore, the Au@Ag NPs with excellent individual-particle enhancement can be exploited as stand-alone-particle Raman amplifiers for the surface identification and detection of pesticide residues at various peels of fruits, such as apple, grape, mango, pear, and peach. By casting the particle sensors onto fruit peels, several types of pesticide residues (e.g., thiocarbamate and organophosphorous compounds) have been reliably/rapidly detected, for example, 1.5 nanograms of thiram per square centimeter at apple peel under the current unoptimized condition. The surface-lifting spectroscopic technique offers great practical potentials for the on-site assessment and identification of pesticide residues in agricultural products.

  4. Microbial agent detection using near-IR electrophoretic and spectral signatures (MADNESS) for rapid identification in detect-to-warn applications.

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, Anthony Lee; Bambha, Ray P.; VanderNoot, Victoria A.; Fruetel, Julia A.; Renzi, Ronald F.; Krafcik, Karen Lee

    2009-10-01

    Rapid identification of aerosolized biological agents following an alarm by particle triggering systems is needed to enable response actions that save lives and protect assets. Rapid identifiers must achieve species level specificity, as this is required to distinguish disease-causing organisms (e.g., Bacillus anthracis) from benign neighbors (e.g., Bacillus subtilis). We have developed a rapid (1-5 minute), novel identification methodology that sorts intact organisms from each other and particulates using capillary electrophoresis (CE), and detects using near-infrared (NIR) absorbance and scattering. We have successfully demonstrated CE resolution of Bacillus spores and vegetative bacteria at the species level. To achieve sufficient sensitivity for detection needs ({approx}10{sup 4} cfu/mL for bacteria), we have developed fiber-coupled cavity-enhanced absorbance techniques. Using this method, we have demonstrated {approx}two orders of magnitude greater sensitivity than published results for absorbing dyes, and single particle (spore) detection through primarily scattering effects. Results of the integrated CE-NIR system for spore detection are presented.

  5. On Identifiability of Bias-Type Actuator-Sensor Faults in Multiple-Model-Based Fault Detection and Identification

    Science.gov (United States)

    Joshi, Suresh M.

    2012-01-01

    This paper explores a class of multiple-model-based fault detection and identification (FDI) methods for bias-type faults in actuators and sensors. These methods employ banks of Kalman-Bucy filters to detect the faults, determine the fault pattern, and estimate the fault values, wherein each Kalman-Bucy filter is tuned to a different failure pattern. Necessary and sufficient conditions are presented for identifiability of actuator faults, sensor faults, and simultaneous actuator and sensor faults. It is shown that FDI of simultaneous actuator and sensor faults is not possible using these methods when all sensors have biases.

  6. An Accurate and Efficient Algorithm for Detection of Radio Bursts with an Unknown Dispersion Measure, for Single-dish Telescopes and Interferometers

    Science.gov (United States)

    Zackay, Barak; Ofek, Eran O.

    2017-01-01

    Astronomical radio signals are subjected to phase dispersion while traveling through the interstellar medium. To optimally detect a short-duration signal within a frequency band, we have to precisely compensate for the unknown pulse dispersion, which is a computationally demanding task. We present the “fast dispersion measure transform” algorithm for optimal detection of such signals. Our algorithm has a low theoretical complexity of 2{N}f{N}t+{N}t{N}{{Δ }}{{log}}2({N}f), where Nf, Nt, and NΔ are the numbers of frequency bins, time bins, and dispersion measure bins, respectively. Unlike previously suggested fast algorithms, our algorithm conserves the sensitivity of brute-force dedispersion. Our tests indicate that this algorithm, running on a standard desktop computer and implemented in a high-level programming language, is already faster than the state-of-the-art dedispersion codes running on graphical processing units (GPUs). We also present a variant of the algorithm that can be efficiently implemented on GPUs. The latter algorithm’s computation and data-transport requirements are similar to those of a two-dimensional fast Fourier transform, indicating that incoherent dedispersion can now be considered a nonissue while planning future surveys. We further present a fast algorithm for sensitive detection of pulses shorter than the dispersive smearing limits of incoherent dedispersion. In typical cases, this algorithm is orders of magnitude faster than enumerating dispersion measures and coherently dedispersing by convolution. We analyze the computational complexity of pulsed signal searches by radio interferometers. We conclude that, using our suggested algorithms, maximally sensitive blind searches for dispersed pulses are feasible using existing facilities. We provide an implementation of these algorithms in Python and MATLAB.

  7. A diagnostic one-step real-time reverse transcription polymerase chain reaction method for accurate detection of influenza virus type A

    Science.gov (United States)

    Behzadi, Mohammad Amin; Alborzi, Abdolvahab

    2016-01-01

    Introduction Influenza A is known as a public health concern worldwide. In this study, a novel one-step real-time reverse transcription polymerase chain reaction (rtRT-PCR) assay was designed and optimized for the detection of influenza A viruses. Material and methods The primers and probe were designed based on the analysis of 90 matrix nucleotide sequence data of influenza type A subtypes from the GenBank database of the National Center for Biotechnology Information (NCBI). The influenza virus A/Tehran/5652/2010 (H1N1 pdm09) was used as a reference. The rtRT-PCR assay was optimized, compared with that of the World Health Organization (WHO), and its analytical sensitivity, specificity and reproducibility were evaluated. In total, 64 nasopharyngeal swabs from patients with influenza-like illness (ILI) and 41 samples without ILI symptoms were tested for the virus, using conventional cell culture, direct immunofluorescence antibody (DFA) methods, and one-step rtRT-PCR with the designed primer set and probe and the WHO’s. Results The optimized assay results were similar to the WHO’s. The optimized assay results were similar to WHO’s, with non-significant differences for 10–103 copies of viral RNA/reaction (p > 0.05). It detected 10 copies of viral RNA/reaction with high reproducibility and no cross reactivity with other respiratory viruses. A specific cytopathic effect was observed in 6/64 (9.37%) of the ILI group using conventional culture and DFA staining methods; however, it was not seen in non-ILI. Also, the results of our assay and the WHO’s were similar to those of viral isolation and DFA staining. Conclusions Given the high specificity, sensitivity and reproducibility of this novel assay, it can serve as a reliable diagnostic tool for the detection of influenza A viruses in clinical specimens and lab experiments. PMID:27904520

  8. 晶闸管变流设备电源精确过零检测技术∗%Thyristor Converter Equipment Supply Accurate Zero Crossing Detection Technology

    Institute of Scientific and Technical Information of China (English)

    姚正武

    2014-01-01

    研究低压交变电压过零脉冲的生成电路在于克服相关专利技术因采用降压变压器、整流或光耦器件、较复杂电子电路等,而使得电路在过零检测的精确性等方面存在的不足。通过分析设计交变电压过零检测环节、微分环节、脉冲整形和输出环节等,采用自建电路并检测各环节波形,可知电路过零脉冲误差低于0.5μs,功耗低于9.4 mW。故与现有技术相比电路具有诸多优点,可应用于晶闸管变流设备的定相和触发控制、交流电源的检测等方面。%It aims to conquer the shortcomings in zero detection accuracy of some related patents etc. to study the low-voltage alternating voltage zero crossing pulse generation circuit because these related patents adopted some step-down transformers,rectifier devices or optical couplers as well as some of more complex circuits. It can be known that the circuit can make the error of zero crossing pulse less than 0.5 μ s,circuit power consumption less than 9.4 mW by some ways to analysis and design the zero crossing detection circuit,differential circuit,shaping and output pulse circuit,to make the circuit and detect each part wave. So,the circuit has more advantages than some circuits of the existing patents and can be widely used in thyristor phase-shifting or zero crossing triggering and the phasing technology,AC power detection etc.

  9. Hexaplex PCR detection system for identification of five human Plasmodium species with an internal control.

    Science.gov (United States)

    Chew, Ching Hoong; Lim, Yvonne Ai Lian; Lee, Ping Chin; Mahmud, Rohela; Chua, Kek Heng

    2012-12-01

    Malaria remains one of the major killers of humankind and persists to threaten the lives of more than one-third of the world's population. Given that human malaria can now be caused by five species of Plasmodium, i.e., Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, Plasmodium ovale, and the recently included Plasmodium knowlesi, there is a critical need not only to augment global health efforts in malaria control but also, more importantly, to develop a rapid, accurate, species-sensitive/species-specific, and economically effective diagnostic method for malaria caused by these five species. Therefore, in the present study, a straightforward single-step hexaplex PCR system targeting five human Plasmodium 18S small-subunit rRNAs (ssu rRNAs) was designed, and the system successfully detected all five human malaria parasites. In addition, this system enables the differentiation of single infection as well as mixed infections up to the two-species level. This assay was validated with 50 randomly blinded test and 184 clinical samples suspected to indicate malaria. This hexaplex PCR system is not only an ideal alternative for routine malaria diagnosis in laboratories with conventional PCR machines but also adds value to diagnoses when there is a lack of an experienced microscopist or/and when the parasite morphology is confusing. Indeed, this system will definitely enhance the accuracy and accelerate the speed in the diagnosis of malaria, as well as improve the efficacy of malaria treatment and control, in addition to providing reliable data from epidemiological surveillance studies.

  10. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    Science.gov (United States)

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-12-01

    Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy.

  11. An accurate and efficient algorithm for detection of radio bursts with an unknown dispersion measure, for single dish telescopes and interferometers

    CERN Document Server

    Zackay, Barak

    2014-01-01

    Astronomical radio bursts disperse while traveling through the interstellar medium. To optimally detect a short-duration signal within a frequency band, we have to precisely compensate for the pulse dispersion, which is a computationally demanding task. We present the Fast Dispersion Measure Transform (FDMT) algorithm for optimal detection of such signals. Our algorithm has a low theoretical complexity of 2N_f N_t+ N_t N_d log_2(N_f) where N_f, N_t and N_d are the numbers of frequency bins, time bins, and dispersion measure bins, respectively. Unlike previously suggested fast algorithms our algorithm conserves the sensitivity of brute force dedispersion. Our tests indicate that this algorithm, running on a standard desktop computer, and implemented in a high-level programming language, is already faster than the state of the art dedispersion codes running on graphical processing units (GPUs). We also present a variant of the algorithm that can be efficiently implemented on GPUs. The latter algorithm's computa...

  12. An epigenetic biomarker combination of PCDH17 and POU4F2 detects bladder cancer accurately by methylation analyses of urine sediment DNA in Han Chinese

    Science.gov (United States)

    Li, Qiaoling; An, Dan; Fang, Lu; Lin, Youcheng; Hou, Yong; Xu, Abai; Fu, Yu; Lu, Wei; Chen, Xin; Chen, Mingwei; Zhang, Meng; Jiang, Huiling; Zhang, Chuanxia; Dong, Pei; Li, Chong; Chen, Jun; Yang, Guosheng; Liu, Chunxiao; Cai, Zhiming; Zhou, Fangjian; Wu, Song

    2016-01-01

    To develop a routine and effectual procedure of detecting bladder cancer (BlCa), an optimized combination of epigenetic biomarkers that work synergistically with high sensitivity and specificity is necessary. In this study, methylation levels of seven biomarkers (EOMES, GDF15, NID2, PCDH17, POU4F2, TCF21, and ZNF154) in 148 individuals—which including 58 urothelial cell carcinoma (UCC) patients, 20 infected urinary calculi (IUC) patients, 20 kidney cancer (KC) patients,20 prostate cancer (PC) patients, and 30 healthy volunteers (HV)—were quantified by qMSP using the urine sediment DNA. Receiver operating characteristic (ROC) curves were generated for each biomarker. The combining predictors of possible combinations were calculated through logistic regression model. Subsequently, ROC curves of the three best performing combinations were constructed. Then, we validated the three best performing combinations and POU4F2 in another 72 UCC, 21 IUC, 26 KC and 22 PC, and 23 HV urine samples. The combination of POU4F2/PCDH17 has yielded the highest sensitivity and specificity of 90.00% and 93.96% in all the 312 individuals, showing the capability of detecting BlCa effectively among pathologically varied sample groups. PMID:26700620

  13. Colorimetric sensor array allows fast detection and simultaneous identification of sepsis-causing bacteria in spiked blood culture.

    Science.gov (United States)

    Lim, Sung H; Mix, Samantha; Xu, Zeyu; Taba, Brian; Budvytiene, Indre; Berliner, Anders N; Queralto, Nuria; Churi, Yair S; Huang, Richard S; Eiden, Michael; Martino, Raymond A; Rhodes, Paul; Banaei, Niaz

    2014-02-01

    Sepsis is a medical emergency demanding early diagnosis and tailored antimicrobial therapy. Every hour of delay in initiating effective therapy measurably increases patient mortality. Blood culture is currently the reference standard for detecting bloodstream infection, a multistep process which may take one to several days. Here, we report a novel paradigm for earlier detection and the simultaneous identification of pathogens in spiked blood cultures by means of a metabolomic "fingerprint" of the volatile mixture outgassed by the organisms. The colorimetric sensor array provided significantly faster detection of positive blood cultures than a conventional blood culture system (12.1 h versus 14.9 h, P detection. The colorimetric sensor array also allowed for discrimination between unrelated strains of methicillin-resistant Staphylococcus aureus, indicating that the metabolomic fingerprint has the potential to track nosocomial transmissions. Altogether, the colorimetric sensor array is a promising tool that offers a new paradigm for diagnosing bloodstream infections.

  14. Development and In silico Evaluation of Large-Scale Metabolite Identification Methods using Functional Group Detection for Metabolomics

    Directory of Open Access Journals (Sweden)

    Joshua M Mitchell

    2014-07-01

    Full Text Available Large-scale identification of metabolites is key to elucidating and modeling metabolism at the systems level. Advances in metabolomics technologies, particularly ultra-high resolution mass spectrometry enable comprehensive and rapid analysis of metabolites. However, a significant barrier to meaningful data interpretation is the identification of a wide range of metabolites including unknowns and the determination of their role(s in various metabolic networks. Chemoselective (CS probes to tag metabolite functional groups combined with high mass accuracy provide additional structural constraints for metabolite identification and quantification. We have developed a novel algorithm, Chemically Aware Substructure Search (CASS that efficiently detects functional groups within existing metabolite databases, allowing for combined molecular formula and functional group (from CS tagging queries to aid in metabolite identification without a priori knowledge. Analysis of the isomeric compounds in both Human Metabolome Database (HMDB and KEGG Ligand demonstrated a high percentage of isomeric molecular formulae (43% and 28% respectively, indicating the necessity for techniques such as CS-tagging. Furthermore, these two databases have only moderate overlap in molecular formulae. Thus, it is prudent to use multiple databases in metabolite assignment, since each major metabolite database represents different portions of metabolism within the biosphere. In silico analysis of various CS-tagging strategies under different conditions for adduct formation demonstrate that combined FT-MS derived molecular formulae and CS-tagging can uniquely identify up to 71% of KEGG and 37% of the combined KEGG/HMDB database versus 41% and 17% respectively without adduct formation. This difference between database isomer disambiguation highlights the strength of CS-tagging for non-lipid metabolite identification. However, unique identification of complex lipids still needs

  15. Rapid Electrochemical Detection and Identification of Microbiological and Chemical Contaminants for Manned Spaceflight Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A great deal of effort has gone into the development of point-of-use methods to meet the challenge of rapid bacterial identification for both environmental...

  16. A robust and accurate approach to automatic blood vessel detection and segmentation from angiography x-ray images using multistage random forests

    Science.gov (United States)

    Gupta, Vipin; Kale, Amit; Sundar, Hari

    2012-03-01

    In this paper we propose a novel approach based on multi-stage random forests to address problems faced by traditional vessel segmentation algorithms on account of image artifacts such as stitches organ shadows etc.. Our approach consists of collecting a very large number of training data consisting of positive and negative examples of valid seed points. The method makes use of a 14x14 window around a putative seed point. For this window three types of feature vectors are computed viz. vesselness, eigenvalue and a novel effective margin feature. A random forest RF is trained for each of the feature vectors. At run time the three RFs are applied in succession to a putative seed point generated by a naiive vessel detection algorithm based on vesselness. Our approach will prune this set of putative seed points to correctly identify true seed points thereby avoiding false positives. We demonstrate the effectiveness of our algorithm on a large dataset of angio images.

  17. 宏基因组中可移动序列的精确检测问题研究%Accurate Detection of Mobile Sequence in Metagenome

    Institute of Scientific and Technical Information of China (English)

    彭超; 王普; 葛瑞泉; 周丰丰

    2016-01-01

    基因组组装是宏基因组分析的主要挑战之一。通常假设所有测序序列均来源于同一个基因组,微生物中非常活跃的可移动元件给这个前提假设提出了重大质疑。文章将该质疑抽象为可移动元件与宿主染色体之间的二分类问题,准确的二分类性能将进一步促进宏基因组学方面的研究。基于宏基因组测序数据的数值化特征,详细考察特征选择算法 ReliefF、卡方检验和 Fisher判别t检验,并结合分类模型逻辑回归、极限学习机、支持向量机和随机森林,验证最优可移动元件检测模型的性能。实验结果表明,ReliefF特征选择算法和随机森林分类算法的融合模型,使用100个特征即可正确分类95%以上的宏基因组测序数据,优于使用全部的690个特征。%Genome assembling is one of the challenges in metagenomic analysis. It is usually assumed that the sequencing reads are from the same genome. However, the mobile elements active in microbial genomes raise a critical question mark on this assumption. This work formulated this issue as a binary classiifcation problem. The accurate discrimination of mobile elements from chromosomes could greatly facilitate the metagenomic analysis. After quantifying the sequencing reads in metagenome, the collaboration of binary classiifcation algorithms with feature selection algorithms, including ReliefF, chi-squared test, and Fisher’st-test was investigated. All feature subsets were tested using the classiifcation algorithms such as logisitic regression, extreme learning machine, support vector machine and random forest. Experimental results demonstrate that the model based on ReliefF algorithm and Random Forest algorithm achieves over 95% in accuracy with only 100 features, which outperforms the model utilizing all 690 features.

  18. Detection of partial-thickness supraspinatus tendon tears: is a single direct MR arthrography series in ABER position as accurate as conventional MR arthrography?

    Energy Technology Data Exchange (ETDEWEB)

    Schreinemachers, Saskia A. [Onze Lieve Vrouwe Gasthuis, Department of Radiology, Amsterdam (Netherlands); Onze Lieve Vrouwe Gasthuis, Amsterdam (Netherlands); Hulst, Victor P.M. van der; Woude, Henk-Jan van der [Onze Lieve Vrouwe Gasthuis, Department of Radiology, Amsterdam (Netherlands); Willems, W.J. [Onze Lieve Vrouwe Gasthuis, Orthopaedic Surgery, Amsterdam (Netherlands); Bipat, Shandra [University of Amsterdam (NL). Department of Radiology, Academic Medical Center (Netherlands)

    2009-10-15

    The purpose of this study was to retrospectively evaluate sensitivity and specificity of a single magnetic resonance (MR) arthrography series in abduction external rotation (ABER) position compared with conventional MR arthrography for detection of supraspinatus tendon tears, with arthroscopy as gold standard, and to assess interobserver variability. Institutional review board approval was obtained; informed consent was waived. MR arthrograms of 250 patients (170 men and 80 women; mean age, 36 years) were retrospectively and independently evaluated by three observers. Oblique coronal T1-weighted fat-suppressed images, proton density, and T2-weighted images and axial T1-weighted images and oblique sagittal T1-weighted fat-suppressed images were analyzed to detect supraspinatus tendon tears. Separately, a single T1-weighted fat-suppressed oblique axial series in ABER position was evaluated. Both protocols were scored randomly without knowledge of patients' clinical history and arthroscopy results. Tears were subclassified, based on articular surface integrity and extension (Lee classification). Interobserver agreement was assessed by kappa statistics for all patients. Ninety-two of 250 patients underwent arthroscopy; sensitivity and specificity of ABER and conventional MR arthrography were calculated and compared using paired McNemar test. Weighted kappa values of ABER and conventional MR arthrography were 0.48-0.65 and 0.60-0.67, respectively. According to arthroscopy, 69 of 92 patients had an intact cuff, and 23 patients had a cuff tear (16 partial thickness and seven full thickness). There were no statistically significant differences between ABER and conventional MR arthrography regarding sensitivity (48-61% and 52-70%, respectively) and specificity (80-94% and 91-95%). Sensitivity and specificity of a single T1-weighted series in ABER position and conventional MR arthrography are comparable for assessment of rotator cuff tears. (orig.)

  19. Is a single direct MR arthrography series in ABER position as accurate in detecting anteroinferior labroligamentous lesions as conventional MR arthography?

    Energy Technology Data Exchange (ETDEWEB)

    Schreinemachers, Saskia A.; Hulst, Victor P.M. van der; Woude, Henk-Jan van der [Onze Lieve Vrouwe Gasthuis, Department of Radiology, Amsterdam (Netherlands); Jaap Willems, W. [Onze Lieve Vrouwe Gasthuis, Orthopaedic Surgery, Amsterdam (Netherlands); Bipat, Shandra [University of Amsterdam, Department of Radiology, Academic Medical Centre, Amsterdam (Netherlands)

    2009-07-15

    The purpose of this study is to retrospectively compare accuracy of single magnetic resonance (MR) arthrography series in Abduction External Rotation (ABER) with conventional MR arthrography for detection and characterisation of anteroinferior labroligamentous lesions, with arthroscopy as reference standard. Inter-observer variability of both protocols was determined. Institutional review board approval was obtained; informed consent was waived. MR arthrograms, including oblique axial fat suppressed T1-weighted images in ABER position and conventional imaging directions of 250 patients (170 men, 80 women; mean age, 36 years), were retrospectively and independently evaluated by three reviewers. Reviewers were blinded to clinical information and arthroscopic results. Labroligamentous lesions were registered in both ABER and MRa. The lesions were sub-classified (Bankart, Perthes, anterior labrum periosteal sleeve avulsion (ALPSA) or lesions not otherwise specified). Inter-observer agreement was assessed by Kappa statistics for all 250 patients. Ninety-two of 250 patients underwent arthroscopy. Sensitivity, specificity and accuracy of ABER versus conventional MR arthrography were calculated and compared using paired McNemar test. Kappa values of the ABER and conventional MR arthrography ranged from 0.44 to 0.56 and 0.44 to 0.62, respectively. According to arthroscopy, 45 of 92 patients had an intact anteroinferior labrum, and in 44 patients, a labroligamentous lesion (eight Bankart, seven Perthes, 29 ALPSA and three lesions not otherwise specified) was diagnosed. There were no statistically significant differences between ABER and conventional MR arthrography regarding sensitivity (85-89%, 89-96%), specificity (82-91%, 84-89%) and overall accuracy (50-62%, 53-63%). The results of a single MR arthrography series in ABER position are comparable with those of conventional MR arthrography for detecting anteroinferior labroligamentous lesions. (orig.)

  20. Detection of multiple mycotoxin occurrences in soy animal feed by traditional mycological identification combined with molecular species identification

    Directory of Open Access Journals (Sweden)

    A.C. Gutleb

    2015-01-01

    Full Text Available Soy products are a main component of animal feed. Because mycotoxins may harm farm animals, undermining productivity and health, a mycological and toxigenic screening was carried out on 36 batches used in animal feed, collected in 2008, 2009 and 2010 in Italy. The investigated mycoflora of a subset of soy seed (n = 6 suggested that Aspergillus spp. and Fusarium spp. frequently colonize soy seeds. Aflatoxins, fumonisins and deoxynivalenol were detected in 88.9%, 72.2% and 30.6% of samples, respectively. Co-occurrence of at least two toxins was observed in 72% of cases. The molecular analysis of the Fusarium spp. population identified Fusarium verticillioides as potential producers of fumonisins, but no known deoxynivalenol producers were detected. It is suggested that the widespread presence of toxins can be due to non-optimal storing conditions of the feed. Moreover, our results suggest that mycotoxin thresholds should be adapted to consider the frequent case of toxin co-occurrence. This approach would better reflect the real toxigenic risk of feedstuffs.

  1. Rapid and accurate detection of the CFTR gene mutation 1811+1.6 kbA>G by real-time fluorescence resonance energy transfer PCR.

    Science.gov (United States)

    Reboul, Marie-Pierre; Higueret, Laurent; Biteau, Nicolas; Iron, Albert

    2005-10-01

    The CFTR gene mutation 1811+1.6 kbA>G has been reported as associated with a severe phenotype of cystic fibrosis with pancreatic insufficiency. This mutation has been identified as a rather common one in the South West of France and in the Iberian Peninsula. Because of the precise geographical origin of the subjects and its frequency, the mutation has to be investigated with accuracy. We have developed an original real-time Fluorescence Resonance Energy Transfer (FRET) PCR assay for genotyping the mutation 1811+1.6 kbA>G. It is based on the amplification of a region spanning the mutation with simultaneous detection of the amplicon by hybridization with a bi-probe followed by a melting curve analysis. The results obtained are identical with those resulting from either restriction fragment length polymorphism analysis or sequencing. The distinction between the wild type and the mutation 1811+1.6 kbA>G is easy because the corresponding melting points shows a difference of 6 or 9.5 degrees C depending on the associated SNP A/T located 16 bp downstream. We demonstrated that a FRET assay showed enough sensitivity to discriminate between two nucleotide polymorphisms (SNPs) in the sequence of the sensor. In conclusion, this method is specific, fast, easy to perform, reproducible, inexpensive as it uses only one bi-probe and well adapted to daily practice.

  2. Kinesiographic recordings of jaw movements are not accurate to detect magnetic resonance-diagnosed temporomandibular joint (TMJ) effusion and disk displacement: findings from a validation study.

    Science.gov (United States)

    Manfredini, Daniele; Favero, Lorenzo; Federzoni, Elvis; Cocilovo, Francesco; Guarda-Nardini, Luca

    2012-10-01

    The aim of this study was to perform a validation study assessing the correlation between magnetic resonance (MR) findings of temporomandibular joint (TMJ) disk displacement and effusion and some parameters drawn from kinesiographic (KG) recordings of jaw motion, i.e., deflection, deviations, incisures. Thirty-one patients with TMJ disorders underwent a kinesiographic recording in the same day in which the MR was performed. Regression analysis was performed to assess the correlation between the MR and KG findings. MR findings were not correlated with KG parameters (P > .05). The accuracy of all KG variables for diagnosing MR-detected signs was low. KG deflection ranged from 38.7% to 54.8%, KG deviation from 42% to 54.8%, and KG incisures from 9.6% to 71%. Specificity and positive predictive values were far from acceptable levels for all KG variables. The findings do not support the usefulness of jaw-tracking devices in dental practices that diagnose and manage temporomandibular disorders. Copyright © 2012 Elsevier Inc. All rights reserved.

  3. The non-contact detection and identification of blood stained fingerprints using visible wavelength reflectance hyperspectral imaging: Part 1.

    Science.gov (United States)

    Cadd, Samuel; Li, Bo; Beveridge, Peter; O'Hare, William T; Campbell, Andrew; Islam, Meez

    2016-05-01

    Blood is one of the most commonly encountered types of biological evidence found at scenes of violent crime and one of the most commonly observed fingerprint contaminants. Current visualisation methods rely on presumptive tests or chemical enhancement methods. Although these can successfully visualise ridge detail, they are destructive, do not confirm the presence of blood and can have a negative impact on DNA sampling. A novel application of visible wavelength reflectance hyperspectral imaging (HSI) has been used for the detection and positive identification of blood stained fingerprints in a non-contact and non-destructive manner on white ceramic tiles. The identification of blood was based on the unique visible absorption spectrum of haemoglobin between 400 and 500 nm. HSI has been used to successfully visualise ridge detail in blood stained fingerprints to the ninth depletion. Ridge detail was still detectable with diluted blood to 20-fold dilutions. Latent blood stains were detectable to 15,000-fold dilutions. Ridge detail was detectable for fingerprints up to 6 months old. HSI was also able to conclusively distinguish blood stained fingerprints from fingerprints in six paints and eleven other red/brown media with zero false positives.

  4. Identification of proliferating cells in chicken embryos using 5-bromo- 2'-deoxyuridine immunohistochemical detection

    Directory of Open Access Journals (Sweden)

    Mário Lúcio Lopes

    2000-03-01

    Full Text Available Chicken embryos were incubated with BrdU, embedded in plastic resin, sectioned and screened immunohistochemically to identify proliferating cells in the neural tube and somites. Fixation in 4% paraformaldehyde for 1 h was essential for detecting specific colorimetric signals of BrdU incorporation into cells during the S phase of the cell cycle. Transverse sections of the neural tube showed that the nuclei of proliferating cells (BrdU positive had a uniform and centralized distribution, whereas unstained nuclei were found only along the extremities of the neural tube. Transverse sections of differentiated somites showed proliferating cells in the scleratome and dermatome. However, no incorporation of BrdU was observed in myotomic cells, which give rise to axial skeletal muscle. In spite of their proximity, the dermatome and myotome showed marked differences in cell proliferation. The excellent preservation of morphological characteristics in the embryonic tissues facilitated identification of variations in BrdU incorporation.Embriões de frango foram incubados na presença de BrdU e montados em resina plástica. A detecção de células em proliferação nos somitos e tubo neural foi feita através de anticorpos contra BrdU. Um ponto essencial para a otimização do método foi a fixação dos embriões por apenas uma hora em paraformaldeído a 4%. Análise de cortes transversais revelou que no tubo neural os núcleos marcados se posicionavam na região central. Cortes transversais em somitos diferenciados revelaram a presença de células em proliferação no dermátomo e esclerótomo, no entanto não foi observado nenhum sinal no miótomo. A metodologia aqui apresentada permitiu identificar com clareza e boa resolução as células em proliferação presentes em tecidos embrionários.

  5. Detection and identification by PCR of Clostridium chauvoei in clinical isolates, bovine faeces and substrates from biogas plant

    Science.gov (United States)

    Bagge, E; Lewerin, S Sternberg; Johansson, K-E

    2009-01-01

    Background Clostridium chauvoei causes blackleg, an acute disease associated with high mortality in ruminants. The apparent primary port of entry is oral, during grazing on pasture contaminated by spores. Cases of blackleg can occur year after year on contaminated pastures. A method to determine the prevalence of C. chauvoei spores on pasture would be useful. The standard method for C. chauvoei detection is culture and biochemical identification, which requires a pure culture. In most muscle samples from cattle dead from blackleg the amount of C. chauvoei in samples is high and the bacterium can easily be cultured, although some samples may be contaminated. Detection by PCR would be faster and independent of contaminating flora. Digested residues from biogas plants provide an excellent fertiliser, but it is known that spore-forming baeria such as Clostridium spp. are not reduced by pasteurisation. The use of digested residues as fertiliser may contribute to the spread of C. chauvoei. Soil, manure and substrate from biogas plants are contaminated with other anaerobic bacteria which outgrow C. chauvoei. Therefore, detection by PCR is would be useful. This study applied a PCR-based method to detect of C. chauvoei in 25 muscle and blood samples, 114 manure samples, 84 soil samples and 33 samples from the biogas process. Methods Muscle tissues from suspected cases of blackleg were analysed both by the standard culture method followed by biochemical identification and by PCR, with and without preculture. To investigate whether muscle tissue samples are necessary, samples taken by swabs were also investigated. Samples from a biogas plant and manure and soil from farms were analysed by culture followed by PCR. The farms had proven cases of blackleg. For detection of C. chauvoei in the samples, a specific PCR primer pair complementary to the spacer region of the 16S-23S rRNA gene was used. Results Clostridium chauvoei was detected in 32% of muscle samples analysed by

  6. A PCR Based Microbial Monitoring Alternative Method of Detection and Identification of Microbes Aboard ISS

    Science.gov (United States)

    Khodadad, Christina; Oubre, Cherie; Castro, Victoria; Flint, Stephanie; Ott, Mark; Roman, Monserrate; Wheeler, Ray; Melendez, Orlando

    2017-01-01

    Previous research has shown that microorganisms and potential human pathogens have been detected on the International Space Station (ISS) with additional introduction of new microflora occurring with every exchange of crew or addition of equipment and supplies. These microbes are readily transferred between crew and subsystems (i.e. ECLSS, environmental control and life support systems). As this can be detrimental to astronaut health and optimal performance of ISS systems, monitoring of systems such as ECLSS to include identification of microbial contaminants could prevent adverse effects on human health and life support systems. Current monitoring on ISS is laborious and utilizes culture based methods followed by sample return to Earth for complete analysis. Future, long-distance spaceflight missions will require real-time monitoring capabilities that enable efficient and rapid assessments of the microbial environment allowing for expedited decisions and more targeted response to cope with anomalies. Polymerase chain reaction (PCR), a molecular microbial monitoring method was chosen and numerous PCR instruments investigated for their potential to perform in microgravity conditions. Using ISS as a test bed for PCR verification in microgravity will enable NASA to assess whether molecular based microbiological sensors may be components of reliable, closed-loop life support and habitation systems in spacecraft, enhancing infrastructure capabilities through increased efficiency, reliability, and time savings by enabling sample analysis on orbit. NASA selected the Water Monitoring Suite as one of the rapid spaceflight hardware demonstration activities utilizing a streamlined process to minimize the time required to fly experimental flight hardware. The RAZOR EX (BioFire Defense, Salt Lake City, UT) system was part of the water monitoring suite and is a commercial off-the-shelf (COTS) real-time PCR instrument designed for field work. The RAZOR EX was originally designed

  7. Detection of impaired renal function. Is the modern serologic marker cystatin C more accurate than the {sup 99m}Tc-MAG{sub 3} clearance?

    Energy Technology Data Exchange (ETDEWEB)

    Reinhardt, M.J.; Weidling, H.; Breuel, H.P.; Biersack, H.J. [Klinik und Poliklinik fuer Nuklearmedizin, Univ. Bonn (Germany)

    2004-12-01

    Aim: Real function is usually determined by means of creatinine-clearance, and of serum Cystatin C, the latter with increasing frequency. The present study analyses, whether the diagnostic accuracy of {sup 99m}Tc-MAG{sub 3} clearance is comparable to that of these modern serologic methods. Patients, methods: 71 consecutive adult Caucasian patients (42 female, 29 male; age 50{+-}16 yrs., range 20-83) who were referred to a nuclear medicine department for determination of bilateral renal function with {sup 99m}Tc-MAG{sub 3} were included. Following sufficient hydration, 10 ml of blood were taken for determination of Cystatin C and creatinine in serum prior to i.v. injection of the radiotracer. According to the recommendations of the National Kidney Foundation, glomerular filtration rate (GFR) was calculated form serum creatinine using either Cockcroft and Gault and Modification of Diet in Renal Disease (MDRD) study equation. These estimates of GFR served as reference. Cystatin C is a low molecular protein produced by all nuclear cells and is eliminated to 85% by glomerular filtration. Analysis of {sup 99m}Tc-MAG{sub 3} clearance was performed by means of Bubeck's formula. Results: Linear regression analysis produced Pearson's correlation coefficients of r=0.68 and r=-0.69 for the comparison of either Cystatin C and {sup 99m}Tc-MAG{sub 3} clearance with the Cockcroft and Gault equation. The comparison of Cystatin C and {sup 99m}Tc-MAG{sub 3} clearance with MDRD study equation resulted in correlation coefficients of r=0.755 and r=-0.77. None of these differences were significant. The exclusion of renal impairment or the detection of an at least moderate renal impairment revealed again no significant differences between Cystatin C and {sup 99m}Tc-MAG{sub 3} clearance. Conclusions: Cystatin C and {sup 99m}Tc-MAG{sub 3} clearance are equally suited to exclude renal impairment or to detect a relevant renal impairment. Differences between both procedures are more

  8. Direct identification and discernment of Mycobacterium avium and Mycobacterium intracellulare using a real-time RNA isothermal amplification and detection method.

    Science.gov (United States)

    Cui, Zhenling; Li, Yuanyuan; Cheng, Song; Yang, Hua; Lu, Junmei; Zhu, Honglei; Hu, Zhongyi

    2015-12-01

    The purpose of this work was to establish a real-time simultaneous amplification and testing method for identification and discernment of Mycobacterium avium and Mycobacterium intracellulare (SAT-MAC assay) and to evaluate the efficiency with which this method can detect isolated strains and clinical sputum specimens. The specific 16S rRNA sequences of M. avium and M. intracellulare were used as targets to design RNA probes and a reverse transcription primer containing T7 promoter. RNA isothermal amplification and real-time fluorescence detection were performed at 42 °C. SAT-MAC assay, culture tests on Lowenstein-Jensen (L-J) culture medium and PCR-sequencing were used to test the clinical isolated strains and sputum specimens. The limit of detection (LOD) of M. avium and M. intracellulare by SAT-MAC was found to be 30 CFU/mL and 20 CFU/mL. SAT-MAC showed high specificity in 21 species of mycobacteria standard strains and 5 species of non-mycobacteria bacteria. Using PCR-sequencing as the reference method, both rates of SAT-MAC assay for identifying M. avium and M. intracellulare from clinical isolates were 100% (259/259). Consistent with the results of L-J culture combined PCR-sequencing, the coincidence rate of SAT-MAC assay in clinical sputum specimens was 100% (369/369) for M. avium and 99.19% (366/369) for Mycobacterium intracellular. The SAT-MAC assay can identify and distinguish M. avium and M. intracellulare rapidly and accurately. It may be suitable for use in clinical microbiology laboratories.

  9. Identification of anti-HPA-1a allo-antibodies using IgG platelet antibody detection and crossmatch system assay with Galileo Echo.

    Science.gov (United States)

    Di Cristofaro, Julie; Frassati, Coralie; Montagnie, Rolande; Basire, Agnes; Merieux, Yves; Picard, Christophe

    2015-01-01

    Fetal/neonatal allo-immune thrombocytopenia is the most frequent and the most dangerous clinical condition involving anti-human platelet antigens (HPA)-1a allo-antibodies. Anti-HPA-1a allo-immunization requires rapid and accurate diagnosis to determine appropriate treatment. The Capture-P Ready-Screen assay (C-PRS) is a new qualitative immunoassay to detect IgG anti-human leukocyte antigen (HLA) and anti-HPA allo-antibodies. The aim of this study is to assess the identification of anti-HPA-1a allo-antibodies using the C-PRS assay, associated with HLA class I stripping reagents, on the automated benchtop analyzer Galileo Echo. Forty-nine sera were analyzed: without anti-HLA class I or anti-HPA allo-antibodies, with anti-HLA class I allo-antibodies, with anti-HPA-1a allo-antibodies, among which with anti-HLA class I allo-antibodies. None of the samples without allo-antibodies were reactive. Only anti-HLA antibodies, detected by cytotoxicity-dependent complement and not by Luminex, remained positive before and after stripping reagents. Of the 13 samples, anti-HPA-1a allo-antibodies that were correctly identified before and after incubation with HLA assassin reagent were 70% and 85%, respectively. Anti-glycoprotein auto-antibodies and anti-HLA allo-antibodies do not interfere with the detection of anti-HPA-1a antibodies. This preliminary study indicates that further improvement of the test will be helpful in developing a clinically useful assay in the future.

  10. Rapid detection and identification of Stachybotrys and Chaetomium species using tissue PCR analysis

    DEFF Research Database (Denmark)

    Lewinska, Anna Malgorzata; Peuhkuri, Ruut Hannele; Rode, Carsten

    2016-01-01

    level is essential for health risk assessment and building remediation. This study focuses on molecular identification of two common indoor fungal genera: Stachybotrys and Chaetomium. This study proposes two new DNA barcode candidates for Stachybotrys and Chaetomium: the gene encoding mitogen activated...... protein kinase (hogA) and the intergenic region between histone 3 and histone 4 (h3-h4) as well as it introduces a rapid - 3.5 h - protocol for direct Stachybotrys and Chaetomium species identification, which bypasses culture cultivation, DNA extraction and DNA sequencing....

  11. Modal Identification and Damage Detection on a Concrete Highway Bridge by Frequency Domain Decomposition

    DEFF Research Database (Denmark)

    Brincker, Rune; Andersen, Palle; Zhang, Lingmi

    2007-01-01

    As a part of a research project co-founded by the European Community, a series of 15 damage tests were performed on a prestressed concrete highway bridge in Switzerland. The ambient response of the bridge was recorded for each damage case. A dense array of instruments allowed the identification...... of a modal model with a total of 408 degrees of freedom. Six modes were identified in the frequency range from 0 to 16.7 Hz. The objective of this paper is to demonstrate the effectiveness of the Frequency Domain Decomposition (FDD) technique for modal identification of large structures. A second objective...

  12. Modal Identification and Damage Detection on a Concrete Highway Bridge by Frequency Domain Decomposition

    DEFF Research Database (Denmark)

    Brincker, Rune; Andersen, P.; Zhang, L.

    2002-01-01

    As a part of a research project co-founded by the European Community, a series of 15 damage tests were performed on a prestressed concrete highway bridge in Switzerland. The ambient response of the bridge was recorded for each damage case. A dense array of instruments allowed the identification...... of a modal model with a total of 408 degrees of freedom. Six modes were identified in the frequency range from 0 to 16.7 Hz. The objective of this paper is to demonstrate the effectiveness of the Frequency Domain Decomposition (FDD) technique for modal identification of large structures. A second objective...

  13. Intelligent detection and identification in fiber-optical perimeter intrusion monitoring system based on the FBG sensor network

    Science.gov (United States)

    Wu, Huijuan; Qian, Ya; Zhang, Wei; Li, Hanyu; Xie, Xin

    2015-12-01

    A real-time intelligent fiber-optic perimeter intrusion detection system (PIDS) based on the fiber Bragg grating (FBG) sensor network is presented in this paper. To distinguish the effects of different intrusion events, a novel real-time behavior impact classification method is proposed based on the essential statistical characteristics of signal's profile in the time domain. The features are extracted by the principal component analysis (PCA), which are then used to identify the event with a K-nearest neighbor classifier. Simulation and field tests are both carried out to validate its effectiveness. The average identification rate (IR) for five sample signals in the simulation test is as high as 96.67%, and the recognition rate for eight typical signals in the field test can also be achieved up to 96.52%, which includes both the fence-mounted and the ground-buried sensing signals. Besides, critically high detection rate (DR) and low false alarm rate (FAR) can be simultaneously obtained based on the autocorrelation characteristics analysis and a hierarchical detection and identification flow.

  14. Detection of orthopoxvirus DNA by real-time PCR and identification of variola virus DNA by melting analysis.

    Science.gov (United States)

    Nitsche, Andreas; Ellerbrok, Heinz; Pauli, Georg

    2004-03-01

    Although variola virus was eradicated by the World Health Organization vaccination program in the 1970s, the diagnosis of smallpox infection has attracted great interest in the context of a possible deliberate release of variola virus in bioterrorist attacks. Obviously, fast and reliable diagnostic tools are required to detect variola virus and to distinguish it from orthopoxviruses that have identical morphological characteristics, including vaccinia virus. The advent of real-time PCR for the clinical diagnosis of viral infections has facilitated the detection of minute amounts of viral nucleic acids in a fast, safe, and precise manner, including the option to quantify and to genotype the target reliably. In this study a complete set of four hybridization probe-based real-time PCR assays for the specific detection of orthopoxvirus DNA is presented. Melting analysis following PCR enables the identification of variola virus by the PCR product's characteristic melting temperature, permitting the discrimination of variola virus from other orthopoxviruses. In addition, an assay for the specific amplification of variola virus DNA is presented. All assays can be performed simultaneously in the same cycler, and results of a PCR run are obtained in less than 1 h. The application of more than one assay for the same organism significantly contributes to the diagnostic reliability, reducing the risk of false-negative results due to unknown sequence variations. In conclusion, the assays presented will improve the speed and reliability of orthopoxvirus diagnostics and variola virus identification.

  15. Application of single-stage Orbitrap mass spectrometry and differential analysis software to nontargeted analysis of contaminants in dog food: detection, identification, and quantification of glycoalkaloids.

    Science.gov (United States)

    Lohne, Jack J; Turnipseed, Sherri B; Andersen, Wendy C; Storey, Joseph; Madson, Mark R

    2015-05-20

    The objective of this study was to perform a preliminary investigation of the nontargeted search and quantitative capabilities of a single-stage Exactive High-Resolution Mass Spectrometer (HRMS). To do this, the instrument and its associated software performed a non-targeted search for deleterious substances in a dog food sample suspected of causing gastrointestinal problems in dogs. A single-stage Orbitrap/high-performance liquid chromatography method and differential expression analysis software (Sieve) was used to detect and identify, and subsequently quantify, nontargeted compounds occurring only in the suspect dog food sample. When combined with an online database (ChemSpider), a preliminary identification of one of the nontargeted compounds was determined to be potato glycoalkaloids. The diagnostic product ion ratios and quantitative data accuracy generated by the single-stage Orbitrap MS were shown to be similar to results obtained using a triple quadrupole LC-MS/MS. Additionally, the ability of the single-stage Orbitrap instrument to provide precursor and product ion accurate masses and isotope patterns was also investigated.

  16. Detection and identification of monaural and binaural pitch contours in dyslexic listeners

    DEFF Research Database (Denmark)

    Santurette, Sébastien; Poelmans, Hanne; Luts, Heleen

    2010-01-01

    of dyslexic listeners to Huggins' pitch (HP). The present study clarified whether impaired binaural pitch perception is found in dyslexia. Results from a pitch contour identification test, performed in 31 dyslexic listeners and 31 matched controls, clearly showed that dyslexics perceived HP as well...

  17. Specific detection and identification of mulberry-infecting strains of Xylella fastidiosa by polymerase chain reaction

    Science.gov (United States)

    X. fastidiosa causes bacterial leaf scorch in many landscape trees including elm, oak, sycamore and mulberry, but methods for specific identification of a particular tree host species-limited strain or differentiation of tree-specific strains are lacking. It is also unknown whether a particular land...

  18. Rapid and High-Throughput pan-Orthopoxvirus Detection and Identification using PCR and Mass Spectrometry

    Science.gov (United States)

    2009-07-01

    ATCC; VR-2379 Vtk-79 ? ? ATCC; VR-2031 A5 ? ? USAMRIID Modified Vaccinia Ankara ( MVA ) 1971 Munich, Germany BEI NR-2634 Lister 1892 Elsetree, London...identification and differentiation of small pox and other orthopoxviruses. J Clin Microbiol 33: 2069–2076. 19. Espy MJ, Cockerill IF, Meyer RF, Bowen MD

  19. Detecting asymmetries in balance control in Parkinson's disease patients with system identification techniques.

    NARCIS (Netherlands)

    Boonstra, Tjitske; van Asseldonk, Edwin H.F.; van Vugt, J.P.P.; van der Kooij, Herman; Bloem, B.B.

    2009-01-01

    Objective: To test the hypothesis that balance control in Parkinson’s disease (PD) is asymmetrically affected using system identification techniques. Background: PD is an asymmetrical disease. It is unknown whether axial symptoms, such as impaired balance, also show asymmetry. Clinical scales used t

  20. A signal detection theory analysis of an unconscious perception effect.

    Science.gov (United States)

    Haase, S J; Theios, J; Jenison, R

    1999-07-01

    The independent observation model (Macmillan & Creelman, 1991) is fitted to detection-identification data collected under conditions of heavy masking. The model accurately predicts a quantitative relationship between stimulus detection and stimulus identification over a wide range of detection performance. This model can also be used to offer a signal detection interpretation of the common finding of above-chance identification following a missed signal. While our finding is not a new one, the stimuli used in this experiment (redundant three-letter strings) differ slightly from those used in traditional signal detection work. Also, the stimuli were presented very briefly and heavily masked, conditions typical in the study of unconscious perception effects.

  1. Simultaneous detection and identification of Aspergillus and mucorales species in tissues collected from patients with fungal rhinosinusitis.

    Science.gov (United States)

    Zhao, Zuotao; Li, Lili; Wan, Zhe; Chen, Wei; Liu, Honggang; Li, Ruoyu

    2011-04-01

    Rapid detection and differentiation of Aspergillus and Mucorales species in fungal rhinosinusitis diagnosis are desirable, since the clinical management and prognosis associated with the two taxa are fundamentally different. We describe an assay based on a combination of broad-range PCR amplification and reverse line blot hybridization (PCR/RLB) to detect and differentiate the pathogens causing fungal rhinosinusitis, which include five Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. nidulans) and seven Mucorales species (Mucor heimalis, Mucor racemosus, Mucor cercinelloidea, Rhizopus arrhizus, Rhizopus microsporus, Rhizomucor pusillus, and Absidia corymbifera). The assay was validated with 98 well-characterized clinical isolates and 41 clinical tissue specimens. PCR/RLB showed high sensitivity and specificity, with 100% correct identifications of 98 clinical isolates and no cross-hybridization between the species-specific probes. Results for five control isolates, Candida albicans, Fusarium solani, Scedosporium apiospermum, Penicillium marneffei, and Exophiala verrucosa, were negative as judged by PCR/RLB. The analytical sensitivity of PCR/RLB was found to be 1.8 × 10(-3) ng/μl by 10-fold serial dilution of Aspergillus genomic DNA. The assay identified 35 of 41 (85.4%) clinical specimens, exhibiting a higher sensitivity than fungal culture (22 of 41; 53.7%) and direct sequencing (18 of 41; 43.9%). PCR/RLB similarly showed high specificity, with correct identification 16 of 18 specimens detected by internal transcribed spacer (ITS) sequencing and 16 of 22 detected by fungal culture, but it also has the additional advantage of being able to detect mixed infection in a single clinical specimen. The PCR/RLB assay thus provides a rapid and reliable option for laboratory diagnosis of fungal rhinosinusitis.

  2. Simultaneous Detection and Identification of Aspergillus and Mucorales Species in Tissues Collected from Patients with Fungal Rhinosinusitis▿

    Science.gov (United States)

    Zhao, Zuotao; Li, Lili; Wan, Zhe; Chen, Wei; Liu, Honggang; Li, Ruoyu

    2011-01-01

    Rapid detection and differentiation of Aspergillus and Mucorales species in fungal rhinosinusitis diagnosis are desirable, since the clinical management and prognosis associated with the two taxa are fundamentally different. We describe an assay based on a combination of broad-range PCR amplification and reverse line blot hybridization (PCR/RLB) to detect and differentiate the pathogens causing fungal rhinosinusitis, which include five Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, and A. nidulans) and seven Mucorales species (Mucor heimalis, Mucor racemosus, Mucor cercinelloidea, Rhizopus arrhizus, Rhizopus microsporus, Rhizomucor pusillus, and Absidia corymbifera). The assay was validated with 98 well-characterized clinical isolates and 41 clinical tissue specimens. PCR/RLB showed high sensitivity and specificity, with 100% correct identifications of 98 clinical isolates and no cross-hybridization between the species-specific probes. Results for five control isolates, Candida albicans, Fusarium solani, Scedosporium apiospermum, Penicillium marneffei, and Exophiala verrucosa, were negative as judged by PCR/RLB. The analytical sensitivity of PCR/RLB was found to be 1.8 × 10−3 ng/μl by 10-fold serial dilution of Aspergillus genomic DNA. The assay identified 35 of 41 (85.4%) clinical specimens, exhibiting a higher sensitivity than fungal culture (22 of 41; 53.7%) and direct sequencing (18 of 41; 43.9%). PCR/RLB similarly showed high specificity, with correct identification 16 of 18 specimens detected by internal transcribed spacer (ITS) sequencing and 16 of 22 detected by fungal culture, but it also has the additional advantage of being able to detect mixed infection in a single clinical specimen. The PCR/RLB assay thus provides a rapid and reliable option for laboratory diagnosis of fungal rhinosinusitis. PMID:21325541

  3. Astrophysical limitations to the identification of dark matter: indirect neutrino signals vis-a-vis direct detection recoil rates

    CERN Document Server

    Serpico, Pasquale D

    2010-01-01

    A convincing identification of dark matter (DM) particles can probably be achieved only through a combined analysis of different detections strategies, which provides an effective way of removing degeneracies in the parameter space of DM models. In practice, however, this program is made complicated by the fact that different strategies depend on different physical quantities, or on the same quantities but in a different way, making the treatment of systematic errors rather tricky. We discuss here the uncertainties on the recoil rate in direct detection experiments and on the muon rate induced by neutrinos from dark matter annihilations in the Sun, and we show that, contrarily to the local DM density or overall cross section scale, irreducible astrophysical uncertainties affect the two rates in a different fashion, therefore limiting our ability to reconstruct the parameters of the dark matter particle. By varying within their respective errors astrophysical parameters such as the escape velocity and the velo...

  4. Detection and Identification of the First Viruses in Chia (Salvia hispanica)

    OpenAIRE

    Celli, Marcos G.; Perotto, Maria C.; Martino, Julia A.; Flores, Ceferino R.; Vilma C. Conci; Patricia Rodriguez Pardina

    2014-01-01

    Chia (Salvia hispanica), an herbaceous plant native to Latin America, has become important in the last 20 years due to its beneficial effects on health. Here, we present the first record and identification of two viruses in chia plants. The comparison of the complete nucleotide sequences showed the presence of two viral species with the typical genome organization of bipartite New World begomovirus, identified as Sida mosaic Bolivia virus 2 and Tomato yellow spot virus, according to the ICT...

  5. Application of Advanced Methods for Identification and Detection of Nuclear Explosions from the Asian Continent

    Science.gov (United States)

    1975-12-01

    enhancement and identification. The MARS code now accepts from one up to three components of seismic data and applies a series of narrow band... seismic event data to determine its effectiveness as a discriminant between earthquakes and underground explosions. In Section III we discuss the results...remove signal distortion due to instrumental factors, and to perform polarization filtering on multicomponent data . Improvements have also been imple

  6. Routine use of CHROMagar Candida medium for presumptive identification of Candida yeast species and detection of mixed fungal populations.

    Science.gov (United States)

    Bouchara, Jean-Philippe; Declerck, Philippe; Cimon, Bernard; Planchenault, Claire; de Gentile, Ludovic; Chabasse, Dominique

    1996-02-01

    OBJECTIVE: To assess the value of the new differential culture medium CHROMagar Candida for routine investigation of clinical specimens. METHODS: During a whole year, 6150 clinical samples were plated on CHROMagar Candida medium. After incubation, the green colonies were considered to be Candida albicans. The colonies of other colors were identified using Bichrolatex-krusei, or by their assimilation pattern on ID 32C test strips and their morphology on rice cream-agar-Tween. RESULTS: Among the 6150 clinical samples, 1643 were positive for fungi. Aspergillus fumigatus and Geotrichum sp. were the predominant filamentous fungi isolated. Candida albicans was the most common species isolated (1274 of the positive samples; 77.5%), and Candida glabrata was the second most common yeast isolated (174 positive samples; 10.6%). Other yeast species were detected at lower frequencies, mainly Candida tropicalis (3.8%), Candida krusei (2.7%), Saccharomyces cerevisiae (2.7%) and Candida kefyr (2.3%), and 16 samples revealed a lipophilic species, Malassezia furfur. Mixed fungal populations accounted for 14.7% of the positive samples. Two or more yeast species were detected in 206 of the 242 specimens containing mixed fungal populations, and five yeast species were detected in one sample. Additionally, we did not observe significant differences in the isolation of yeasts or filamentous fungi from the 366 samples simultaneously plated on CHROMagar Candida and Sabouraud dextrose agar. Close agreement between the two culture media was observed for 89.9% of these samples. CONCLUSIONS: CHROMagar Candida medium was shown to be extremely helpful in a routine clinical mycology service, facilitating the detection of mixed cultures of yeasts and allowing direct identification of C. albicans, as well as rapid presumptive identification of the other yeasts: C. glabrata, C. tropicalis, C. krusei and S. cerevisiae. This chromogenic medium thus appears to be suitable as a primary culture medium

  7. Explosives trace detection in the process of biometrical fingerprint identification for access control

    Science.gov (United States)

    Bertseva, Elena V.; Savin, Andrey V.

    2007-02-01

    A method for trace detection of explosives on the surface of biometric fingerprint scanner is proposed and its sensitivity explored. The method is based on attenuated total reflection mid-infrared spectroscopy. The detection limit is about several microgram and the detectivity increases with the wavelength used for scanning. The advantages of the proposed method include high selectivity and thus low false alarm level, applicability to low vapor pressure explosives and low cost.

  8. Three-dimensional surface-enhanced Raman scattering hotspots in spherical colloidal superstructure for identification and detection of drugs in human urine.

    Science.gov (United States)

    Han, Zhenzhen; Liu, Honglin; Wang, Bin; Weng, Shizhuang; Yang, Liangbao; Liu, Jinhuai

    2015-01-01

    Rapid component separation and robust surface-enhanced Raman scattering (SERS) identification of drugs in real human urine remain an attractive challenge because of the sample complexity, low molecular affinity for metal surface, and inefficient use of hotspots in one- or two-dimensional (2D) geometries. Here, we developed a 5 min strategy of cyclohexane (CYH) extraction for separating amphetamines from human urine. Simultaneously, an oil-in-water emulsion method is used to assemble monodisperse Ag nanoparticles in the CYH phase into spherical colloidal superstructures in the aqueous phase. These superstructures create three-dimensional (3D) SERS hotspots which exist between every two adjacent particles in 3D space, break the traditional 2D limitation, and extend the hotspots into the third dimension along the z-axis. In this platform, a conservative estimate of Raman enhancement factor is larger than 10(7), and the same CYH extraction processing results in a high acceptability and enrichment of drug molecules in 3D hotspots which demonstrates excellent stability and reproducibility and is suitable for the quantitative examination of amphetamines in both aqueous and organic phases. Parallel ultraperformance liquid chromatography (UPLC) examinations corroborate an excellent performance of our SERS platform for the quantitative analysis of methamphetamine (MA) in both aqueous solution and real human urine, of which the detection limits reach 1 and 10 ppb, respectively, with tolerable signal-to-noise ratios. Moreover, SERS examinations on different proportions of MA and 3,4-methylenedioxymethamphetamine (MDMA) in human urine demonstrate an excellent capability of multiplex quantification of ultratrace analytes. By virtue of a spectral classification algorithm, we realize the rapid and accurate recognition of weak Raman signals of amphetamines at trace levels and also clearly distinguish various proportions of multiplex components. Our platform for detecting drugs

  9. Identification of acoustic wave propagation in a duct line and its application to detection of impact source location based on signal processing

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Yong Woo; Kim, Min Soo; Lee, Sang Kwon [Inha University, Seoul (Korea, Republic of)

    2010-12-15

    For the detection of the impact location in a pipeline system, the correlation method has been the conventional method. For the application of the correlation method, the diameter of a duct should be small so that the acoustic wave inside the duct can propagate with nondispersive characteristics, in the form of, for example, a plane wave. This correlation method calculates the cross-correlation between acoustic waves measured at two acceleration sensors attached to a buried duct. It also gives information about the arrival time delay of an acoustic wave between two sensors. These arrival time delays are used for the estimation of the impact location. However, when the diameter of the duct is large, the acousti