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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.
An Integrative Approach to Accurate Vehicle Logo Detection

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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.
Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

Energy Technology Data Exchange (ETDEWEB)

Cui, Yi; Hu, Dehong; Markillie, Lye Meng; Chrisler, William B.; Gaffrey, Matthew J.; Ansong, Charles; Sussel, Lori; Orr, Galya

2017-10-04

Quantitative gene expression analysis in intact single cells can be achieved using single molecule- based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple FISH sub-probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific binding of sub-probes and tissue autofluorescence, limiting its accuracy. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on blinking frequencies of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses blinking frequency patterns, emitted from a transcript bound to multiple sub-probes, which are distinct from blinking patterns emitted from partial or nonspecifically bound sub-probes and autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2, and their ratio (Nkx2-2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct blinking frequency patterns, laying the foundation for reliable single-cell transcriptomics.
Novel Damage Detection Techniques for Structural Health Monitoring Using a Hybrid Sensor

Directory of Open Access Journals (Sweden)

Dengjiang Wang

2016-01-01

Full Text Available This study presents a technique for detecting fatigue cracks based on a hybrid sensor monitoring system consisting of a combination of intelligent coating monitoring (ICM and piezoelectric transducer (PZT sensors. An experimental procedure using this hybrid sensor system was designed to monitor the cracks generated by fatigue testing in plate structures. A probability of detection (POD model that quantifies the reliability of damage detection for a specific sensor or the nondestructive testing (NDT method was used to evaluate the weight factor for the ICM and PZT sensors. To estimate the uncertainty of model parameters in this study, the Bayesian method was employed. Realistic data from fatigue testing was used to validate the overall method, and the results show that the novel damage detection technique using a hybrid sensor can quantify fatigue cracks more accurately than results obtained by conventional sensor methods.
Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes.

Science.gov (United States)

Cao, Jing; Feng, Chao; Liu, Yan; Wang, Shouyu; Liu, Fei

2014-07-15

Since many diseases are caused by pathogenic bacterial infections, accurate and rapid detection of pathogenic bacteria is in urgent need to timely apply appropriate treatments and to reduce economic costs. To end this, we designed molecular beacon-Au nanoparticle hybrid nanoprobes to improve the bacterial detection efficiency and sensitivity. Here, we show that the designed molecular beacon modified Au nanoparticles could specifically recognize synthetic DNAs targets and can readily detect targets in clinical samples. Moreover, the hybrid nanoprobes can recognize Escherichia coli within an hour at a concentration of 10(2) cfu/ml, which is 1000-folds sensitive than using molecular beacon directly. Our results show that the molecular beacon-Au nanoparticle hybrid nanoprobes have great potential in medical and biological applications. Copyright © 2014 Elsevier B.V. All rights reserved.
Highly specific detection of genetic modification events using an enzyme-linked probe hybridization chip.

Science.gov (United States)

Zhang, M Z; Zhang, X F; Chen, X M; Chen, X; Wu, S; Xu, L L

2015-08-10

The enzyme-linked probe hybridization chip utilizes a method based on ligase-hybridizing probe chip technology, with the principle of using thio-primers for protection against enzyme digestion, and using lambda DNA exonuclease to cut multiple PCR products obtained from the sample being tested into single-strand chains for hybridization. The 5'-end amino-labeled probe was fixed onto the aldehyde chip, and hybridized with the single-stranded PCR product, followed by addition of a fluorescent-modified probe that was then enzymatically linked with the adjacent, substrate-bound probe in order to achieve highly specific, parallel, and high-throughput detection. Specificity and sensitivity testing demonstrated that enzyme-linked probe hybridization technology could be applied to the specific detection of eight genetic modification events at the same time, with a sensitivity reaching 0.1% and the achievement of accurate, efficient, and stable results.
A hybrid method for accurate star tracking using star sensor and gyros.

Science.gov (United States)

Lu, Jiazhen; Yang, Lie; Zhang, Hao

2017-10-01

Star tracking is the primary operating mode of star sensors. To improve tracking accuracy and efficiency, a hybrid method using a star sensor and gyroscopes is proposed in this study. In this method, the dynamic conditions of an aircraft are determined first by the estimated angular acceleration. Under low dynamic conditions, the star sensor is used to measure the star vector and the vector difference method is adopted to estimate the current angular velocity. Under high dynamic conditions, the angular velocity is obtained by the calibrated gyros. The star position is predicted based on the estimated angular velocity and calibrated gyros using the star vector measurements. The results of the semi-physical experiment show that this hybrid method is accurate and feasible. In contrast with the star vector difference and gyro-assisted methods, the star position prediction result of the hybrid method is verified to be more accurate in two different cases under the given random noise of the star centroid.
A Motion-Adaptive Deinterlacer via Hybrid Motion Detection and Edge-Pattern Recognition

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He-Yuan Lin

2008-03-01

Full Text Available A novel motion-adaptive deinterlacing algorithm with edge-pattern recognition and hybrid motion detection is introduced. The great variety of video contents makes the processing of assorted motion, edges, textures, and the combination of them very difficult with a single algorithm. The edge-pattern recognition algorithm introduced in this paper exhibits the flexibility in processing both textures and edges which need to be separately accomplished by line average and edge-based line average before. Moreover, predicting the neighboring pixels for pattern analysis and interpolation further enhances the adaptability of the edge-pattern recognition unit when motion detection is incorporated. Our hybrid motion detection features accurate detection of fast and slow motion in interlaced video and also the motion with edges. Using only three fields for detection also renders higher temporal correlation for interpolation. The better performance of our deinterlacing algorithm with higher content-adaptability and less memory cost than the state-of-the-art 4-field motion detection algorithms can be seen from the subjective and objective experimental results of the CIF and PAL video sequences.
A Motion-Adaptive Deinterlacer via Hybrid Motion Detection and Edge-Pattern Recognition

Directory of Open Access Journals (Sweden)

Li Hsin-Te

2008-01-01

Full Text Available Abstract A novel motion-adaptive deinterlacing algorithm with edge-pattern recognition and hybrid motion detection is introduced. The great variety of video contents makes the processing of assorted motion, edges, textures, and the combination of them very difficult with a single algorithm. The edge-pattern recognition algorithm introduced in this paper exhibits the flexibility in processing both textures and edges which need to be separately accomplished by line average and edge-based line average before. Moreover, predicting the neighboring pixels for pattern analysis and interpolation further enhances the adaptability of the edge-pattern recognition unit when motion detection is incorporated. Our hybrid motion detection features accurate detection of fast and slow motion in interlaced video and also the motion with edges. Using only three fields for detection also renders higher temporal correlation for interpolation. The better performance of our deinterlacing algorithm with higher content-adaptability and less memory cost than the state-of-the-art 4-field motion detection algorithms can be seen from the subjective and objective experimental results of the CIF and PAL video sequences.
Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors

Science.gov (United States)

Star, Alexander; Tu, Eugene; Niemann, Joseph; Gabriel, Jean-Christophe P.; Joiner, C. Steve; Valcke, Christian

2006-01-01

We report carbon nanotube network field-effect transistors (NTNFETs) that function as selective detectors of DNA immobilization and hybridization. NTNFETs with immobilized synthetic oligonucleotides have been shown to specifically recognize target DNA sequences, including H63D single-nucleotide polymorphism (SNP) discrimination in the HFE gene, responsible for hereditary hemochromatosis. The electronic responses of NTNFETs upon single-stranded DNA immobilization and subsequent DNA hybridization events were confirmed by using fluorescence-labeled oligonucleotides and then were further explored for label-free DNA detection at picomolar to micromolar concentrations. We have also observed a strong effect of DNA counterions on the electronic response, thus suggesting a charge-based mechanism of DNA detection using NTNFET devices. Implementation of label-free electronic detection assays using NTNFETs constitutes an important step toward low-cost, low-complexity, highly sensitive and accurate molecular diagnostics. hemochromatosis | SNP | biosensor
ANOMALY DETECTION IN NETWORKING USING HYBRID ARTIFICIAL IMMUNE ALGORITHM

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D. Amutha Guka

2012-01-01

Full Text Available Especially in today’s network scenario, when computers are interconnected through internet, security of an information system is very important issue. Because no system can be absolutely secure, the timely and accurate detection of anomalies is necessary. The main aim of this research paper is to improve the anomaly detection by using Hybrid Artificial Immune Algorithm (HAIA which is based on Artificial Immune Systems (AIS and Genetic Algorithm (GA. In this research work, HAIA approach is used to develop Network Anomaly Detection System (NADS. The detector set is generated by using GA and the anomalies are identified using Negative Selection Algorithm (NSA which is based on AIS. The HAIA algorithm is tested with KDD Cup 99 benchmark dataset. The detection rate is used to measure the effectiveness of the NADS. The results and consistency of the HAIA are compared with earlier approaches and the results are presented. The proposed algorithm gives best results when compared to the earlier approaches.
Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays

Science.gov (United States)

Jin, Lian-Qun; Li, Jun-Wen; Wang, Sheng-Qi; Chao, Fu-Huan; Wang, Xin-Wei; Yuan, Zheng-Quan

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. PMID:16437687
Hybrid Intrusion Detection System for DDoS Attacks

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Özge Cepheli

2016-01-01

Full Text Available Distributed denial-of-service (DDoS attacks are one of the major threats and possibly the hardest security problem for today’s Internet. In this paper we propose a hybrid detection system, referred to as hybrid intrusion detection system (H-IDS, for detection of DDoS attacks. Our proposed detection system makes use of both anomaly-based and signature-based detection methods separately but in an integrated fashion and combines the outcomes of both detectors to enhance the overall detection accuracy. We apply two distinct datasets to our proposed system in order to test the detection performance of H-IDS and conclude that the proposed hybrid system gives better results than the systems based on nonhybrid detection.
Rapid detection of the CYP2A6*12 hybrid allele by Pyrosequencing® technology

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Gallagher Margaret L

2009-08-01

Full Text Available Abstract Background Identification of CYP2A6 alleles associated with reduced enzyme activity is important in the study of inter-individual differences in drug metabolism. CYP2A6*12 is a hybrid allele that results from unequal crossover between CYP2A6 and CYP2A7 genes. The 5' regulatory region and exons 1–2 are derived from CYP2A7, and exons 3–9 are derived from CYP2A6. Conventional methods for detection of CYP2A6*12 consist of two-step PCR protocols that are laborious and unsuitable for high-throughput genotyping. We developed a rapid and accurate method to detect the CYP2A6*12 allele by Pyrosequencing technology. Methods A single set of PCR primers was designed to specifically amplify both the CYP2A6*1 wild-type allele and the CYP2A6*12 hybrid allele. An internal Pyrosequencing primer was used to generate allele-specific sequence information, which detected homozygous wild-type, heterozygous hybrid, and homozygous hybrid alleles. We first validated the assay on 104 DNA samples that were also genotyped by conventional two-step PCR and by cycle sequencing. CYP2A6*12 allele frequencies were then determined using the Pyrosequencing assay on 181 multi-ethnic DNA samples from subjects of African American, European Caucasian, Pacific Rim, and Hispanic descent. Finally, we streamlined the Pyrosequencing assay by integrating liquid handling robotics into the workflow. Results Pyrosequencing results demonstrated 100% concordance with conventional two-step PCR and cycle sequencing methods. Allele frequency data showed slightly higher prevalence of the CYP2A6*12 allele in European Caucasians and Hispanics. Conclusion This Pyrosequencing assay proved to be a simple, rapid, and accurate alternative to conventional methods, which can be easily adapted to the needs of higher-throughput studies.
An Efficient Hybrid DSMC/MD Algorithm for Accurate Modeling of Micro Gas Flows

KAUST Repository

Liang, Tengfei

2013-01-01

Aiming at simulating micro gas flows with accurate boundary conditions, an efficient hybrid algorithmis developed by combining themolecular dynamics (MD) method with the direct simulationMonte Carlo (DSMC)method. The efficiency comes from the fact that theMD method is applied only within the gas-wall interaction layer, characterized by the cut-off distance of the gas-solid interaction potential, to resolve accurately the gas-wall interaction process, while the DSMC method is employed in the remaining portion of the flow field to efficiently simulate rarefied gas transport outside the gas-wall interaction layer. A unique feature about the present scheme is that the coupling between the two methods is realized by matching the molecular velocity distribution function at the DSMC/MD interface, hence there is no need for one-toone mapping between a MD gas molecule and a DSMC simulation particle. Further improvement in efficiency is achieved by taking advantage of gas rarefaction inside the gas-wall interaction layer and by employing the "smart-wall model" proposed by Barisik et al. The developed hybrid algorithm is validated on two classical benchmarks namely 1-D Fourier thermal problem and Couette shear flow problem. Both the accuracy and efficiency of the hybrid algorithm are discussed. As an application, the hybrid algorithm is employed to simulate thermal transpiration coefficient in the free-molecule regime for a system with atomically smooth surface. Result is utilized to validate the coefficients calculated from the pure DSMC simulation with Maxwell and Cercignani-Lampis gas-wall interaction models. ©c 2014 Global-Science Press.
Effect of sample storage time on detection of hybridization signals in Checkerboard DNA-DNA hybridization.

Science.gov (United States)

do Nascimento, Cássio; Muller, Katia; Sato, Sandra; Albuquerque Junior, Rubens Ferreira

2012-04-01

Long-term sample storage can affect the intensity of the hybridization signals provided by molecular diagnostic methods that use chemiluminescent detection. The aim of this study was to evaluate the effect of different storage times on the hybridization signals of 13 bacterial species detected by the Checkerboard DNA-DNA hybridization method using whole-genomic DNA probes. Ninety-six subgingival biofilm samples were collected from 36 healthy subjects, and the intensity of hybridization signals was evaluated at 4 different time periods: (1) immediately after collecting (n = 24) and (2) after storage at -20 °C for 6 months (n = 24), (3) for 12 months (n = 24), and (4) for 24 months (n = 24). The intensity of hybridization signals obtained from groups 1 and 2 were significantly higher than in the other groups (p 0.05). The Checkerboard DNA-DNA hybridization method was suitable to detect hybridization signals from all groups evaluated, and the intensity of signals decreased significantly after long periods of sample storage.
In situ hybridization at the electron microscope level: hybrid detection by autoradiography and colloidal gold.

Science.gov (United States)

Hutchison, N J; Langer-Safer, P R; Ward, D C; Hamkalo, B A

1982-11-01

In situ hybridization has become a standard method for localizing DNA or RNA sequences in cytological preparations. We developed two methods to extend this technique to the transmission electron microscope level using mouse satellite DNA hybridization to whole mount metaphase chromosomes as the test system. The first method devised is a direct extension of standard light microscope level using mouse satellite DNA hybridization to whole mount metaphase chromosomes as the test system. The first method devised is a direct extension of standard light microscope in situ hybridization. Radioactively labeled complementary RNA (cRNA) is hybridized to metaphase chromosomes deposited on electron microscope grids and fixed in 70 percent ethanol vapor; hybridixation site are detected by autoradiography. Specific and intense labeling of chromosomal centromeric regions is observed even after relatively short exposure times. Inerphase nuclei present in some of the metaphase chromosome preparations also show defined paatterms of satellite DNA labeling which suggests that satellite-containing regions are associate with each other during interphase. The sensitivity of this method is estimated to at least as good as that at the light microscope level while the resolution is improved at least threefold. The second method, which circumvents the use of autoradiogrphic detection, uses biotin-labeled polynucleotide probes. After hybridization of these probes, either DNA or RNA, to fixed chromosomes on grids, hybrids are detected via reaction is improved at least threefold. The second method, which circumvents the use of autoradiographic detection, uses biotin-labeled polynucleotide probes. After hybridization of these probes, either DNA or RNA, to fixed chromosomes on grids, hybrids are detected via reaction with an antibody against biotin and secondary antibody adsorbed to the surface of over centromeric heterochromatin and along the associated peripheral fibers. Labeling is on average
Accurate Energies and Structures for Large Water Clusters Using the X3LYP Hybrid Density Functional

OpenAIRE

Su, Julius T.; Xu, Xin; Goddard, William A., III

2004-01-01

We predict structures and energies of water clusters containing up to 19 waters with X3LYP, an extended hybrid density functional designed to describe noncovalently bound systems as accurately as covalent systems. Our work establishes X3LYP as the most practical ab initio method today for calculating accurate water cluster structures and energies. We compare X3LYP/aug-cc-pVTZ energies to the most accurate theoretical values available (n = 2−6, 8), MP2 with basis set superposition error (BSSE)...
Automated DNA electrophoresis, hybridization and detection

International Nuclear Information System (INIS)

Zapolski, E.J.; Gersten, D.M.; Golab, T.J.; Ledley, R.S.

1986-01-01

A fully automated, computer controlled system for nucleic acid hybridization analysis has been devised and constructed. In practice, DNA is digested with restriction endonuclease enzyme(s) and loaded into the system by pipette; 32 P-labelled nucleic acid probe(s) is loaded into the nine hybridization chambers. Instructions for all the steps in the automated process are specified by answering questions that appear on the computer screen at the start of the experiment. Subsequent steps are performed automatically. The system performs horizontal electrophoresis in agarose gel, fixed the fragments to a solid phase matrix, denatures, neutralizes, prehybridizes, hybridizes, washes, dries and detects the radioactivity according to the specifications given by the operator. The results, printed out at the end, give the positions on the matrix to which radioactivity remains hybridized following stringent washing
Mode identification using stochastic hybrid models with applications to conflict detection and resolution

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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

Accurate modeling and maximum power point detection of ...

African Journals Online (AJOL)

Accurate modeling and maximum power point detection of photovoltaic ... Determination of MPP enables the PV system to deliver maximum available power. ..... adaptive artificial neural network: Proposition for a new sizing procedure.
Hybridization-Based Detection of Helicobacter pylori at Human Body Temperature Using Advanced Locked Nucleic Acid (LNA) Probes

Science.gov (United States)

Fontenete, Sílvia; Guimarães, Nuno; Leite, Marina; Figueiredo, Céu; Wengel, Jesper; Filipe Azevedo, Nuno

2013-01-01

The understanding of the human microbiome and its influence upon human life has long been a subject of study. Hence, methods that allow the direct detection and visualization of microorganisms and microbial consortia (e.g. biofilms) within the human body would be invaluable. In here, we assessed the possibility of developing a variant of fluorescence in situ hybridization (FISH), named fluorescence in vivo hybridization (FIVH), for the detection of Helicobacter pylori. Using oligonucleotide variations comprising locked nucleic acids (LNA) and 2’-O-methyl RNAs (2’OMe) with two types of backbone linkages (phosphate or phosphorothioate), we were able to successfully identify two probes that hybridize at 37 °C with high specificity and sensitivity for H. pylori, both in pure cultures and in gastric biopsies. Furthermore, the use of this type of probes implied that toxic compounds typically used in FISH were either found to be unnecessary or could be replaced by a non-toxic substitute. We show here for the first time that the use of advanced LNA probes in FIVH conditions provides an accurate, simple and fast method for H. pylori detection and location, which could be used in the future for potential in vivo applications either for this microorganism or for others. PMID:24278398
Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

Science.gov (United States)

Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

2016-06-21

We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results.
Detection of DNA hybridizations using solid-state nanopores

International Nuclear Information System (INIS)

Balagurusamy, Venkat S K; Weinger, Paul; Sean Ling, Xinsheng

2010-01-01

We report an experimental study of using DNA translocation through solid-state nanopores to detect the sequential arrangement of two double-stranded 12-mer hybridization segments on a single-stranded DNA molecule. The sample DNA is a trimer molecule formed by hybridizing three single-stranded oligonucleotides. A polystyrene bead is attached to the end of the trimer DNA, providing a mechanism in slowing down the translocation and suppressing the thermal diffusion, thereby allowing the detection of short features of DNA by standard patch-clamp electronics. The electrical signature of the translocation of a trimer molecule through a nanopore has been identified successfully in the temporal traces of ionic current. The results reported here represent the first successful attempt in using a solid-state nanopore as an ionic scanning device in resolving individual hybridization segments (or 'probes') on a DNA molecule.
Detection of DNA hybridizations using solid-state nanopores

Energy Technology Data Exchange (ETDEWEB)

Balagurusamy, Venkat S K; Weinger, Paul; Sean Ling, Xinsheng, E-mail: Xinsheng_Ling@brown.edu [Department of Physics, Brown University, Providence, RI 02912 (United States)

2010-08-20

We report an experimental study of using DNA translocation through solid-state nanopores to detect the sequential arrangement of two double-stranded 12-mer hybridization segments on a single-stranded DNA molecule. The sample DNA is a trimer molecule formed by hybridizing three single-stranded oligonucleotides. A polystyrene bead is attached to the end of the trimer DNA, providing a mechanism in slowing down the translocation and suppressing the thermal diffusion, thereby allowing the detection of short features of DNA by standard patch-clamp electronics. The electrical signature of the translocation of a trimer molecule through a nanopore has been identified successfully in the temporal traces of ionic current. The results reported here represent the first successful attempt in using a solid-state nanopore as an ionic scanning device in resolving individual hybridization segments (or 'probes') on a DNA molecule.
Thermodynamic framework to assess low abundance DNA mutation detection by hybridization

Science.gov (United States)

Willems, Hanny; Jacobs, An; Hadiwikarta, Wahyu Wijaya; Venken, Tom; Valkenborg, Dirk; Van Roy, Nadine; Vandesompele, Jo; Hooyberghs, Jef

2017-01-01

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine. PMID:28542229
HyDe: a Python Package for Genome-Scale Hybridization Detection.

Science.gov (United States)

Blischak, Paul D; Chifman, Julia; Wolfe, Andrea D; Kubatko, Laura S

2018-03-19

The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this paper we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python, and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde).
Clinical Utility of Array Comparative Genomic Hybridization for Detection of Chromosomal Abnormalities in Pediatric Acute Lymphoblastic Leukemia

Science.gov (United States)

Rabin, Karen R.; Man, Tsz-Kwong; Yu, Alexander; Folsom, Matthew R.; Zhao, Yi-Jue; Rao, Pulivarthi H.; Plon, Sharon E.; Naeem, Rizwan C.

2014-01-01

Background Accurate detection of recurrent chromosomal abnormalities is critical to assign patients to risk-based therapeutic regimens for pediatric acute lymphoblastic leukemia (ALL). Procedure We investigated the utility of array comparative genomic hybridization (aCGH) for detection of chromosomal abnormalities compared to standard clinical evaluation with karyotype and fluorescent in-situ hybridization (FISH). Fifty pediatric ALL diagnostic bone marrows were analyzed by bacterial artificial chromosome (BAC) array, and findings compared to standard clinical evaluation. Results Sensitivity of aCGH was 79% to detect karyotypic findings other than balanced translocations, which cannot be detected by aCGH because they involve no copy number change. aCGH also missed abnormalities occurring in subclones constituting less than 25% of cells. aCGH detected 44 additional abnormalities undetected or misidentified by karyotype, 21 subsequently validated by FISH, including abnormalities in 4 of 10 cases with uninformative cytogenetics. aCGH detected concurrent terminal deletions of both 9p and 20q in three cases, in two of which the 20q deletion was undetected by karyotype. A narrow region of loss at 7p21 was detected in two cases. Conclusions An array with increased BAC density over regions important in ALL, combined with PCR for fusion products of balanced translocations, could minimize labor- and time-intensive cytogenetic assays and provide key prognostic information in the approximately 35% of cases with uninformative cytogenetics. PMID:18253961
Fast and Accurate Residential Fire Detection Using Wireless Sensor Networks

NARCIS (Netherlands)

Bahrepour, Majid; 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
Towers of hybrid mesons

International Nuclear Information System (INIS)

Semay, Claude; Buisseret, Fabien; Silvestre-Brac, Bernard

2009-01-01

A hybrid meson is a quark-antiquark pair in which, contrary to ordinary mesons, the gluon field is in an excited state. In the framework of constituent models, the interaction potential is assumed to be the energy of an excited string. An approximate, but accurate, analytical solution of the Schroedinger equation with such a potential is presented. When applied to hybrid charmonia and bottomonia, towers of states are predicted in which the masses are a linear function of a harmonic oscillator band number for the quark-antiquark pair. Such a formula could be a reliable guide for the experimental detection of heavy hybrid mesons.
Comparisons of hybrid radiosity-diffusion model and diffusion equation for bioluminescence tomography in cavity cancer detection

Science.gov (United States)

Chen, Xueli; Yang, Defu; Qu, Xiaochao; Hu, Hao; Liang, Jimin; Gao, Xinbo; Tian, Jie

2012-06-01

Bioluminescence tomography (BLT) has been successfully applied to the detection and therapeutic evaluation of solid cancers. However, the existing BLT reconstruction algorithms are not accurate enough for cavity cancer detection because of neglecting the void problem. Motivated by the ability of the hybrid radiosity-diffusion model (HRDM) in describing the light propagation in cavity organs, an HRDM-based BLT reconstruction algorithm was provided for the specific problem of cavity cancer detection. HRDM has been applied to optical tomography but is limited to simple and regular geometries because of the complexity in coupling the boundary between the scattering and void region. In the provided algorithm, HRDM was first applied to three-dimensional complicated and irregular geometries and then employed as the forward light transport model to describe the bioluminescent light propagation in tissues. Combining HRDM with the sparse reconstruction strategy, the cavity cancer cells labeled with bioluminescent probes can be more accurately reconstructed. Compared with the diffusion equation based reconstruction algorithm, the essentiality and superiority of the HRDM-based algorithm were demonstrated with simulation, phantom and animal studies. An in vivo gastric cancer-bearing nude mouse experiment was conducted, whose results revealed the ability and feasibility of the HRDM-based algorithm in the biomedical application of gastric cancer detection.
Detection of cardiovascular anomalies: Hybrid systems approach

KAUST Repository

Ledezma, Fernando; Laleg-Kirati, Taous-Meriem

2012-01-01

In this paper, we propose a hybrid interpretation of the cardiovascular system. Based on a model proposed by Simaan et al. (2009), we study the problem of detecting cardiovascular anomalies that can be caused by variations in some physiological
Accurately Detecting Students' Lies regarding Relational Aggression by Correctional Instructions

Science.gov (United States)

Dickhauser, Oliver; Reinhard, Marc-Andre; Marksteiner, Tamara

2012-01-01

This study investigates the effect of correctional instructions when detecting lies about relational aggression. Based on models from the field of social psychology, we predict that correctional instruction will lead to a less pronounced lie bias and to more accurate lie detection. Seventy-five teachers received videotapes of students' true denial…
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.
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.
Hybrid inorganic/organic photonic crystal biochips for cancer biomarkers detection

Science.gov (United States)

Sinibaldi, Alberto; Danz, Norbert; Munzert, Peter; Michelotti, Francesco

2018-06-01

We report on hybrid inorganic/organic one-dimensional photonic crystal biochips sustaining Bloch surface waves. The biochips were used, together with an optical platform operating in a label-free and fluorescence configuration simultaneously, to detect the cancer biomarker Angiopoietin 2 in a protein base buffer. The hybrid photonic crystals embed in their geometry a thin functionalization poly-acrylic acid layer deposited by plasma polymerization, which is used to immobilize a monoclonal antibody for highly specific biological recognition. The fluorescence operation mode is described in detail, putting into evidence the role of field enhancement and localization at the photonic crystal surface in the shaping and intensification of the angular fluorescence pattern. In the fluorescence operation mode, the hybrid biochips can attain the limit of detection 6 ng/ml.
Graphene-Plasmonic Hybrid Platform for Label-Free SERS Biomedical Detection

Science.gov (United States)

Wang, Pu

Surface Enhanced Raman Scattering (SERS) has attracted explosive interest for the wealth of vibrational information it provides with minimal invasive effects to target analyte. Nanotechnology, especially in the form of noble metal nanoparticles exhibit unique electromagnetic and chemical characteristics that are explored to realize ultra-sensitive SERS detection in chemical and biological analysis. Graphene, atom-thick carbon monolayer, exhibits superior chemical stability and bio-compatibility. A combination of SERS-active metal nanostructures and graphene will create various synergies in SERS. The main objective of this research was to exploit the applications of the graphene-Au tip hybrid platform in SERS. The hybrid platform consists of a periodic Au nano-pyramid substrate to provide reproducible plasmonic enhancement, and the superimposed monolayer graphene sheet, serving as "built-in" Raman marker. Extensive theoretical and experimental studies were conducted to determine the potentials of the hybrid platform as SERS substrate. Results from both Finite-Domain Time-Domain (FDTD) numerical simulation and Raman scattering of graphene suggested that the hybrid platform boosted a high density of hotspots yielding 1000 times SERS enhancement of graphene bands. Ultra-high sensitivity of the hybrid platform was demonstrated by bio-molecules including dye, protein and neurotransmitters. Dopamine and serotonin can be detected and distinguished at 10-9 M concentration in the presence of human body fluid. Single molecule detection was obtained using a bi-analyte technique. Graphene supported a vibration mode dependent SERS chemical enhancement of ˜10 to the analyte. Quantitative evaluation of hotspots was presented using spatially resolved Raman mapping of graphene SERS enhancement. Graphene plays a crucial role in quantifying SERS hotspots and paves the path for defining SERS EF that could be universally applied to various SERS systems. A reproducible and statistically
Going With the Flow: An Aid in Detecting and Differentiating Bronchopulmonary Sequestrations and Hybrid Lesions.

Science.gov (United States)

Oliver, Edward R; DeBari, Suzanne E; Giannone, Mariann M; Pogoriler, Jennifer E; Johnson, Ann M; Horii, Steven C; Gebb, Juliana S; Howell, Lori J; Adzick, N Scott; Coleman, Beverly G

2018-02-01

68 of 73 hybrid lesions. Ultrasound is most accurate for systemic feeding artery detection in bronchopulmonary sequestrations and hybrid lesions and can also type the lesions as intralobar or extralobar when draining veins are evaluated. © 2017 by the American Institute of Ultrasound in Medicine.
Detection of Food Spoilage and Pathogenic Bacteria Based on Ligation Detection Reaction Coupled to Flow-Through Hybridization on Membranes

Directory of Open Access Journals (Sweden)

K. Böhme

2014-01-01

Full Text Available Traditional culturing methods are still commonly applied for bacterial identification in the food control sector, despite being time and labor intensive. Microarray technologies represent an interesting alternative. However, they require higher costs and technical expertise, making them still inappropriate for microbial routine analysis. The present study describes the development of an efficient method for bacterial identification based on flow-through reverse dot-blot (FT-RDB hybridization on membranes, coupled to the high specific ligation detection reaction (LDR. First, the methodology was optimized by testing different types of ligase enzymes, labeling, and membranes. Furthermore, specific oligonucleotide probes were designed based on the 16S rRNA gene, using the bioinformatic tool Oligonucleotide Retrieving for Molecular Applications (ORMA. Four probes were selected and synthesized, being specific for Aeromonas spp., Pseudomonas spp., Shewanella spp., and Morganella morganii, respectively. For the validation of the probes, 16 reference strains from type culture collections were tested by LDR and FT-RDB hybridization using universal arrays spotted onto membranes. In conclusion, the described methodology could be applied for the rapid, accurate, and cost-effective identification of bacterial species, exhibiting special relevance in food safety and quality.
Fuzzy Based Advanced Hybrid Intrusion Detection System to Detect Malicious Nodes in Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Rupinder Singh

2017-01-01

Full Text Available In this paper, an Advanced Hybrid Intrusion Detection System (AHIDS that automatically detects the WSNs attacks is proposed. AHIDS makes use of cluster-based architecture with enhanced LEACH protocol that intends to reduce the level of energy consumption by the sensor nodes. AHIDS uses anomaly detection and misuse detection based on fuzzy rule sets along with the Multilayer Perceptron Neural Network. The Feed Forward Neural Network along with the Backpropagation Neural Network are utilized to integrate the detection results and indicate the different types of attackers (i.e., Sybil attack, wormhole attack, and hello flood attack. For detection of Sybil attack, Advanced Sybil Attack Detection Algorithm is developed while the detection of wormhole attack is done by Wormhole Resistant Hybrid Technique. The detection of hello flood attack is done by using signal strength and distance. An experimental analysis is carried out in a set of nodes; 13.33% of the nodes are determined as misbehaving nodes, which classified attackers along with a detection rate of the true positive rate and false positive rate. Sybil attack is detected at a rate of 99,40%; hello flood attack has a detection rate of 98, 20%; and wormhole attack has a detection rate of 99, 20%.

Microfluidic Arrayed Lab-On-A-Chip for Electrochemical Capacitive Detection of DNA Hybridization Events.

Science.gov (United States)

Ben-Yoav, Hadar; Dykstra, Peter H; Bentley, William E; Ghodssi, Reza

2017-01-01

A microfluidic electrochemical lab-on-a-chip (LOC) device for DNA hybridization detection has been developed. The device comprises a 3 × 3 array of microelectrodes integrated with a dual layer microfluidic valved manipulation system that provides controlled and automated capabilities for high throughput analysis of microliter volume samples. The surface of the microelectrodes is functionalized with single-stranded DNA (ssDNA) probes which enable specific detection of complementary ssDNA targets. These targets are detected by a capacitive technique which measures dielectric variation at the microelectrode-electrolyte interface due to DNA hybridization events. A quantitative analysis of the hybridization events is carried out based on a sensing modeling that includes detailed analysis of energy storage and dissipation components. By calculating these components during hybridization events the device is able to demonstrate specific and dose response sensing characteristics. The developed microfluidic LOC for DNA hybridization detection offers a technology for real-time and label-free assessment of genetic markers outside of laboratory settings, such as at the point-of-care or in-field environmental monitoring.
Detection of cardiovascular anomalies: Hybrid systems approach

KAUST Repository

Ledezma, Fernando

2012-06-06

In this paper, we propose a hybrid interpretation of the cardiovascular system. Based on a model proposed by Simaan et al. (2009), we study the problem of detecting cardiovascular anomalies that can be caused by variations in some physiological parameters, using an observerbased approach. We present the first numerical results obtained. © 2012 IFAC.
Detection of DNA hybridization using graphene-coated black phosphorus surface plasmon resonance sensor

Science.gov (United States)

Pal, Sarika; Verma, Alka; Raikwar, S.; Prajapati, Y. K.; Saini, J. P.

2018-05-01

In this paper, graphene-coated black phosphorus at the metal surface for the detection of DNA hybridization event is numerically demonstrated. The strategy consists of placing the sensing medium on top of black phosphorus-graphene-coated SPR which interfaces with phosphate-buffered saline solution carrying single-stranded DNA. Upon hybridization with its complementary DNA, desorption of the nanostructures takes place and thus enables the sensitive detection of the DNA hybridization event. The proposed sensor exhibits a sensitivity (125 ο/RIU), detection accuracy (0.95) and quality factor (13.62 RIU-1) for complementary DNA. In comparison with other reported papers, our suggested sensor provides much better performance. Thus, this label-free DNA detection platform should spur off new interest towards the use of black phosphorus-graphene-coated SPR interfaces.
Hybrid silica materials for detection of toxic species and clinical diagnosis

OpenAIRE

Pascual Vidal, Lluís

2017-01-01

The present PhD thesis entitled "Silica Hybrid Materials for detection of toxic species and clinical diagnosis" is focused on the design and synthesis of new hybrid materials, using different silica supports as inorganic scaffolds, with applications in recognition, sensing and diagnostic protocols. The first chapter of the PhD thesis is devoted to the definition and classification of hybrid materials, relying on concepts of Nanotechnology, Supramolecular and Materials Chemistry. State o...
A self-interaction-free local hybrid functional: Accurate binding energies vis-à-vis accurate ionization potentials from Kohn-Sham eigenvalues

International Nuclear Information System (INIS)

Schmidt, Tobias; Kümmel, Stephan; Kraisler, Eli; Makmal, Adi; Kronik, Leeor

2014-01-01

We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potentials is not yet satisfactory, and if we choose to optimize their prediction, a rather different value of the functional's parameter is obtained. We put this finding in a larger context by discussing similar observations for other functionals and possible directions for further functional development that our findings suggest
A novel hybridization approach for detection of citrus viroids.

Science.gov (United States)

Murcia, N; Serra, P; Olmos, A; Duran-Vila, N

2009-04-01

Citrus plants are natural hosts of several viroid species all belonging to the family Pospiviroidae. Previous attempts to detect viroids from field-grown species and cultivars yielded erratic results unless analyses were performed using Etrog citron a secondary bio-amplification host. To overcome the use of Etrog citron a number of RT-PCR approaches have been proposed with different degrees of success. Here we report the suitability of an easy to handle northern hybridization protocol for viroid detection of samples collected from field-grown citrus species and cultivars. The protocol involves: (i) Nucleic acid preparations from bark tissue samples collected from field-grown trees regardless of the growing season and storage conditions; (ii) Separation in 5% PAGE or 1% agarose, blotting to membrane and fixing; (iii) Hybridization with viroid-specific DIG-labelled probes and detection with anti-DIG-alkaline phosphatase conjugate and autoradiography with the CSPD substrate. The method has been tested with viroid-infected trees of sweet orange, lemon, mandarin, grapefruit, sour orange, Swingle citrumello, Tahiti lime and Mexican lime. This novel hybridization approach is extremely sensitive, easy to handle and shortens the time needed for reliable viroid indexing tests. The suitability of PCR generated DIG-labelled probes and the sensitivity achieved when the samples are separated and blotted from non-denaturing gels are discussed.
A novel fluorescent in situ hybridization technique for detection of Rickettsia spp. in archival samples

DEFF Research Database (Denmark)

Svendsen, Claus Bo; Boye, Mette; Struve, Carsten

2009-01-01

A novel, sensitive and specific method for detecting Rickettsia spp. in archival samples is described. The method involves the use of fluorescently marked oligonucleotide probes for in situ hybridization. Specific hybridization of Ricekttsia was found without problems of cross-reactions with bact......A novel, sensitive and specific method for detecting Rickettsia spp. in archival samples is described. The method involves the use of fluorescently marked oligonucleotide probes for in situ hybridization. Specific hybridization of Ricekttsia was found without problems of cross...
A PDMS-based cylindrical hybrid lens for enhanced fluorescence detection in microfluidic systems.

Science.gov (United States)

Lin, Bor-Shyh; Yang, Yu-Ching; Ho, Chong-Yi; Yang, Han-Yu; Wang, Hsiang-Yu

2014-02-13

Microfluidic systems based on fluorescence detection have been developed and applied for many biological and chemical applications. Because of the tiny amount of sample in the system; the induced fluorescence can be weak. Therefore, most microfluidic systems deploy multiple optical components or sophisticated equipment to enhance the efficiency of fluorescence detection. However, these strategies encounter common issues of complex manufacturing processes and high costs. In this study; a miniature, cylindrical and hybrid lens made of polydimethylsiloxane (PDMS) to improve the fluorescence detection in microfluidic systems is proposed. The hybrid lens integrates a laser focusing lens and a fluorescence collecting lens to achieve dual functions and simplify optical setup. Moreover, PDMS has advantages of low-cost and straightforward fabrication compared with conventional optical components. The performance of the proposed lens is first examined with two fluorescent dyes and the results show that the lens provides satisfactory enhancement for fluorescence detection of Rhodamine 6G and Nile Red. The overall increments in collected fluorescence signal and detection sensitivity are more than 220% of those without lens, and the detection limits of Rhodamine 6G and Nile red are lowered to 0.01 μg/mL and 0.05 μg/mL, respectively. The hybrid lens is further applied to the detection of Nile red-labeled Chlorella vulgaris cells and it increases both signal intensity and detection sensitivity by more than 520%. The proposed hybrid lens also dramatically reduces the variation in detected signal caused by the deviation in incident angle of excitation light.
Stochastic linear hybrid systems: Modeling, estimation, and application

Science.gov (United States)

Seah, Chze Eng

Hybrid systems are dynamical systems which have interacting continuous state and discrete state (or mode). Accurate modeling and state estimation of hybrid systems are important in many applications. We propose a hybrid system model, known as the Stochastic Linear Hybrid System (SLHS), to describe hybrid systems with stochastic linear system dynamics in each mode and stochastic continuous-state-dependent mode transitions. We then develop a hybrid estimation algorithm, called the State-Dependent-Transition Hybrid Estimation (SDTHE) algorithm, to estimate the continuous state and discrete state of the SLHS from noisy measurements. It is shown that the SDTHE algorithm is more accurate or more computationally efficient than existing hybrid estimation algorithms. Next, we develop a performance analysis algorithm to evaluate the performance of the SDTHE algorithm in a given operating scenario. We also investigate sufficient conditions for the stability of the SDTHE algorithm. The proposed SLHS model and SDTHE algorithm are illustrated to be useful in several applications. In Air Traffic Control (ATC), to facilitate implementations of new efficient operational concepts, accurate modeling and estimation of aircraft trajectories are needed. In ATC, an aircraft's trajectory can be divided into a number of flight modes. Furthermore, as the aircraft is required to follow a given flight plan or clearance, its flight mode transitions are dependent of its continuous state. However, the flight mode transitions are also stochastic due to navigation uncertainties or unknown pilot intents. Thus, we develop an aircraft dynamics model in ATC based on the SLHS. The SDTHE algorithm is then used in aircraft tracking applications to estimate the positions/velocities of aircraft and their flight modes accurately. Next, we develop an aircraft conformance monitoring algorithm to detect any deviations of aircraft trajectories in ATC that might compromise safety. In this application, the SLHS
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 and accur...
Fast and Accurate Hybrid Stream PCRTMSOLAR Radiative Transfer Model for Reflected Solar Spectrum Simulation in the Cloudy Atmosphere

Science.gov (United States)

Yang, Qiguang; Liu, Xu; Wu, Wan; Kizer, Susan; Baize, Rosemary R.

2016-01-01

A hybrid stream PCRTM-SOLAR model has been proposed for fast and accurate radiative transfer simulation. It calculates the reflected solar (RS) radiances with a fast coarse way and then, with the help of a pre-saved matrix, transforms the results to obtain the desired high accurate RS spectrum. The methodology has been demonstrated with the hybrid stream discrete ordinate (HSDO) radiative transfer (RT) model. The HSDO method calculates the monochromatic radiances using a 4-stream discrete ordinate method, where only a small number of monochromatic radiances are simulated with both 4-stream and a larger N-stream (N = 16) discrete ordinate RT algorithm. The accuracy of the obtained channel radiance is comparable to the result from N-stream moderate resolution atmospheric transmission version 5 (MODTRAN5). The root-mean-square errors are usually less than 5x10(exp -4) mW/sq cm/sr/cm. The computational speed is three to four-orders of magnitude faster than the medium speed correlated-k option MODTRAN5. This method is very efficient to simulate thousands of RS spectra under multi-layer clouds/aerosols and solar radiation conditions for climate change study and numerical weather prediction applications.
Vehicle surge detection and pathway discrimination by pedestrians who are blind: Effect of adding an alert sound to hybrid electric vehicles on performance.

Science.gov (United States)

Kim, Dae Shik; Emerson, Robert Wall; Naghshineh, Koorosh; Pliskow, Jay; Myers, Kyle

2012-05-01

This study examined the effect of adding an artificially generated alert sound to a quiet vehicle on its detectability and localizability with 15 visually impaired adults. When starting from a stationary position, the hybrid electric vehicle with an alert sound was significantly more quickly and reliably detected than either the identical vehicle without such added sound or the comparable internal combustion engine vehicle. However, no significant difference was found between the vehicles in respect to how accurately the participants could discriminate the path of a given vehicle (straight vs. right turn). These results suggest that adding an artificial sound to a hybrid electric vehicle may help reduce delay in street crossing initiation by a blind pedestrian, but the benefit of such alert sound may not be obvious in determining whether the vehicle in his near parallel lane proceeds straight through the intersection or turns right in front of him.
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.
Population genetic diversity and hybrid detection in captive zebras.

Science.gov (United States)

Ito, Hideyuki; Langenhorst, Tanya; Ogden, Rob; Inoue-Murayama, Miho

2015-08-21

Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy's zebra E. grevyi and the mountain zebra E. zebra. The Grevy's zebra and the mountain zebra are endangered, and hybridization between the Grevy's zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy's zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy's and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy's zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy's zebra.
Directional genomic hybridization for chromosomal inversion discovery and detection.

Science.gov (United States)

Ray, F Andrew; Zimmerman, Erin; Robinson, Bruce; Cornforth, Michael N; Bedford, Joel S; Goodwin, Edwin H; Bailey, Susan M

2013-04-01

Chromosomal rearrangements are a source of structural variation within the genome that figure prominently in human disease, where the importance of translocations and deletions is well recognized. In principle, inversions-reversals in the orientation of DNA sequences within a chromosome-should have similar detrimental potential. However, the study of inversions has been hampered by traditional approaches used for their detection, which are not particularly robust. Even with significant advances in whole genome approaches, changes in the absolute orientation of DNA remain difficult to detect routinely. Consequently, our understanding of inversions is still surprisingly limited, as is our appreciation for their frequency and involvement in human disease. Here, we introduce the directional genomic hybridization methodology of chromatid painting-a whole new way of looking at structural features of the genome-that can be employed with high resolution on a cell-by-cell basis, and demonstrate its basic capabilities for genome-wide discovery and targeted detection of inversions. Bioinformatics enabled development of sequence- and strand-specific directional probe sets, which when coupled with single-stranded hybridization, greatly improved the resolution and ease of inversion detection. We highlight examples of the far-ranging applicability of this cytogenomics-based approach, which include confirmation of the alignment of the human genome database and evidence that individuals themselves share similar sequence directionality, as well as use in comparative and evolutionary studies for any species whose genome has been sequenced. In addition to applications related to basic mechanistic studies, the information obtainable with strand-specific hybridization strategies may ultimately enable novel gene discovery, thereby benefitting the diagnosis and treatment of a variety of human disease states and disorders including cancer, autism, and idiopathic infertility.
Evaluation of PCR and DNA hybridization protocols for detection of viable enterotoxigenic Clostridium perfringens in irradiated beef

International Nuclear Information System (INIS)

Baez, L.A.; Juneja, V.K.; Thayer, D.W.; Sackitey, S.

1997-01-01

The sensitivity of DNA hybridization and polymerase chain reaction (PCR), was evaluated in irradiated cooked and raw beef samples. A membrane-based colony hybridization assay and a PCR protocol, both with specificity for the enterotoxin A gene of Clostridium perfringens, were compared with viable plate counts. The results of the colony hybridization procedure were in agreement with viable plate counts for detection and enumeration of enterotoxigenic C. perfringens. The PCR procedure combined a 4 h enrichment followed by a nucleic acid extraction step and assessed the amplification of 183 and 750 base pair enterotoxin gene targets. Detection of C. perfringens by PCR did not show a reliable correlation with viable plate counts or the colony hybridization assay. C. perfringens killed by irradiation were not detected by the plate count or colony hybridization methods; however, killed cells were detected with the PCR technique. By relying on the growth of viable cells for detection and/or enumeration, the colony hybridization and plate count methods provided a direct correlation with the presence of viable bacteria
Accurate Detection of Dysmorphic Nuclei Using Dynamic Programming and Supervised Classification.

Science.gov (United States)

Verschuuren, Marlies; De Vylder, Jonas; Catrysse, Hannes; Robijns, Joke; Philips, Wilfried; De Vos, Winnok H

2017-01-01

A vast array of pathologies is typified by the presence of nuclei with an abnormal morphology. Dysmorphic nuclear phenotypes feature dramatic size changes or foldings, but also entail much subtler deviations such as nuclear protrusions called blebs. Due to their unpredictable size, shape and intensity, dysmorphic nuclei are often not accurately detected in standard image analysis routines. To enable accurate detection of dysmorphic nuclei in confocal and widefield fluorescence microscopy images, we have developed an automated segmentation algorithm, called Blebbed Nuclei Detector (BleND), which relies on two-pass thresholding for initial nuclear contour detection, and an optimal path finding algorithm, based on dynamic programming, for refining these contours. Using a robust error metric, we show that our method matches manual segmentation in terms of precision and outperforms state-of-the-art nuclear segmentation methods. Its high performance allowed for building and integrating a robust classifier that recognizes dysmorphic nuclei with an accuracy above 95%. The combined segmentation-classification routine is bound to facilitate nucleus-based diagnostics and enable real-time recognition of dysmorphic nuclei in intelligent microscopy workflows.
Accurate Detection of Dysmorphic Nuclei Using Dynamic Programming and Supervised Classification.

Directory of Open Access Journals (Sweden)

Marlies Verschuuren

Full Text Available A vast array of pathologies is typified by the presence of nuclei with an abnormal morphology. Dysmorphic nuclear phenotypes feature dramatic size changes or foldings, but also entail much subtler deviations such as nuclear protrusions called blebs. Due to their unpredictable size, shape and intensity, dysmorphic nuclei are often not accurately detected in standard image analysis routines. To enable accurate detection of dysmorphic nuclei in confocal and widefield fluorescence microscopy images, we have developed an automated segmentation algorithm, called Blebbed Nuclei Detector (BleND, which relies on two-pass thresholding for initial nuclear contour detection, and an optimal path finding algorithm, based on dynamic programming, for refining these contours. Using a robust error metric, we show that our method matches manual segmentation in terms of precision and outperforms state-of-the-art nuclear segmentation methods. Its high performance allowed for building and integrating a robust classifier that recognizes dysmorphic nuclei with an accuracy above 95%. The combined segmentation-classification routine is bound to facilitate nucleus-based diagnostics and enable real-time recognition of dysmorphic nuclei in intelligent microscopy workflows.
Entanglement detection in hybrid optomechanical systems

International Nuclear Information System (INIS)

De Chiara, Gabriele; Paternostro, Mauro; Palma, G. Massimo

2011-01-01

We study a device formed by a Bose-Einstein condensate (BEC) coupled to the field of a cavity with a moving end mirror and find a working point such that the mirror-light entanglement is reproduced by the BEC-light quantum correlations. This provides an experimentally viable tool for inferring mirror-light entanglement with only a limited set of assumptions. We prove the existence of tripartite entanglement in the hybrid device, persisting up to temperatures of a few milli-Kelvin, and discuss a scheme to detect it.
Hybrid Synthetic Receptors on MOSFET Devices for Detection of Prostate Specific Antigen in Human Plasma.

Science.gov (United States)

Tamboli, Vibha K; Bhalla, Nikhil; Jolly, Pawan; Bowen, Chris R; Taylor, John T; Bowen, Jenna L; Allender, Chris J; Estrela, Pedro

2016-12-06

The study reports the use of extended gate field-effect transistors (FET) for the label-free and sensitive detection of prostate cancer (PCa) biomarkers in human plasma. The approach integrates for the first time hybrid synthetic receptors comprising of highly selective aptamer-lined pockets (apta-MIP) with FETs for sensitive detection of prostate specific antigen (PSA) at clinically relevant concentrations. The hybrid synthetic receptors were constructed by immobilizing an aptamer-PSA complex on gold and subjecting it to 13 cycles of dopamine electropolymerization. The polymerization resulted in the creation of highly selective polymeric cavities that retained the ability to recognize PSA post removal of the protein. The hybrid synthetic receptors were subsequently used in an extended gate FET setup for electrochemical detection of PSA. The sensor was reported to have a limit of detection of 0.1 pg/mL with a linear detection range from 0.1 pg/mL to 1 ng/mL PSA. Detection of 1-10 pg/mL PSA was also achieved in diluted human plasma. The present apta-MIP sensor developed in conjunction with FET devices demonstrates the potential for clinical application of synthetic hybrid receptors for the detection of clinically relevant biomarkers in complex samples.

Techniques of DNA hybridization detect small numbers of mycobacteria with no cross-hybridization with non-mycobacterial respiratory organisms

International Nuclear Information System (INIS)

Shoemaker, S.A.; Fisher, J.H.; Scoggin, C.H.

1985-01-01

The traditional methods used in identifying mycobacteria, such as acid-fast bacillus stains and culture, are often time-consuming, insensitive, and nonspecific. As part of an ongoing program to improve diagnosis and characterization of mycobacteria, the authors have found that deoxyribonucleic acid (DNA) hybridization techniques using isotopically labeled, single-stranded, total DNA can be used to detect as little as 10(-4) micrograms of Mycobacterium tuberculosis (MTb) DNA. This amount of DNA represents approximately 2 X 10(4) genomes. They have also shown the MTb DNA is sufficiently different from the DNA of non-mycobacterial microorganisms such that cross-hybridization with MTb DNA does not occur under the hybridization conditions employed. The authors speculate that DNA hybridization techniques may allow the rapid, sensitive, and specific identification of mycobacteria
Femtomolar detection of single mismatches by discriminant analysis of DNA hybridization events using gold nanoparticles.

Science.gov (United States)

Ma, Xingyi; Sim, Sang Jun

2013-03-21

Even though DNA-based nanosensors have been demonstrated for quantitative detection of analytes and diseases, hybridization events have never been numerically investigated for further understanding of DNA mediated interactions. Here, we developed a nanoscale platform with well-designed capture and detection gold nanoprobes to precisely evaluate the hybridization events. The capture gold nanoprobes were mono-laid on glass and the detection probes were fabricated via a novel competitive conjugation method. The two kinds of probes combined in a suitable orientation following the hybridization with the target. We found that hybridization efficiency was markedly dependent on electrostatic interactions between DNA strands, which can be tailored by adjusting the salt concentration of the incubation solution. Due to the much lower stability of the double helix formed by mismatches, the hybridization efficiencies of single mismatched (MMT) and perfectly matched DNA (PMT) were different. Therefore, we obtained an optimized salt concentration that allowed for discrimination of MMT from PMT without stringent control of temperature or pH. The results indicated this to be an ultrasensitive and precise nanosensor for the diagnosis of genetic diseases.
Experts and Machines against Bullies: A Hybrid Approach to Detect Cyberbullies

OpenAIRE

Dadvar, M.; Trieschnigg, Rudolf Berend; de Jong, Franciska M.G.

2014-01-01

Cyberbullying is becoming a major concern in online environments with troubling consequences. However, most of the technical studies have focused on the detection of cyberbullying through identifying harassing comments rather than preventing the incidents by detecting the bullies. In this work we study the automatic detection of bully users on YouTube. We compare three types of automatic detection: an expert system, supervised machine learning models, and a hybrid type combining the two. All ...
SERS-active ZnO/Ag hybrid WGM microcavity for ultrasensitive dopamine detection

Science.gov (United States)

Lu, Junfeng; Xu, Chunxiang; Nan, Haiyan; Zhu, Qiuxiang; Qin, Feifei; Manohari, A. Gowri; Wei, Ming; Zhu, Zhu; Shi, Zengliang; Ni, Zhenhua

2016-08-01

Dopamine (DA) is a potential neuro modulator in the brain which influences a variety of motivated behaviors and plays a key role in life science. A hybrid ZnO/Ag microcavity based on Whispering Gallery Mode (WGM) effect has been developed for ultrasensitive detection of dopamine. Utilizing this effect of structural cavity mode, a Raman signal of R6G (5 × 10-3 M) detected by this designed surface-enhanced Raman spectroscopy (SERS)-active substrate was enhanced more than 10-fold compared with that of ZnO film/Ag substrate. Also, this hybrid microcavity substrate manifests high SERS sensitivity to rhodamine 6 G and detection limit as low as 10-12 M to DA. The Localized Surface Plasmons of Ag nanoparticles and WGM-enhanced light-matter interaction mainly contribute to the high SERS sensitivity and help to achieve a lower detection limit. This designed SERS-active substrate based on the WGM effect has the potential for detecting neurotransmitters in life science.
Quantum dots-hyperbranched polyether hybrid nanospheres towards delivery and real-time detection of nitric oxide

DEFF Research Database (Denmark)

Liu, Shuiping; Gu, Tianxun; Fu, Jiajia

2014-01-01

In this work, novel hybrid nanosphere vehicles were synthesized for nitric oxide (NO) donating and real-time detection. The hybrid nanosphere vehicles consist of cadmium selenide quantum dots (CdSe QDs) as NO fluorescent probes, and the modified hyperbranched polyether (mHP)-based diazeniumdiolates...... as NO donors, respectively. The nanospheres have spherical outline with dimension of ~ 127 nm. The data of systematic characterization demonstrated that the mHP-based hybrid nanosphere vehicles (QDs-mHP-NO) can release and real-time detect NO with the low limit of 25 nM, based on fluorescence quenching...
Hybrid carbon nanomaterials for electrochemical detection of biomolecules

International Nuclear Information System (INIS)

Laurila, Tomi

2015-01-01

Electrochemical detection of different biomolecules in vivo is a promising path towards in situ monitoring of human body and its functions. However, there are several major obstacles, such as sensitivity, selectivity and biocompatiblity, which must be tackled in order to achieve reliably and safely operating sensor devices. Here we show that by utilizing hybrid carbon materials as electrodes to detect two types of neurotransmitters, dopamine and glutamate, several advantages over commonly used electrode materials can be achieved. In particular, we will demonstrate here that it is possible to combine the properties of different carbon allotropes to obtain hybrid materials with greatly improved electrochemical performance. Three following examples of the approach are given: (i) diamond-like carbon (DLC) thin film electrodes with different layer thicknesses, (ii) multi-walled carbon nanotubes grown directly on top of DLC and (iii) carbon nanofibres synthesized on top of DLC thin films. Detailed structural and electrochemical characterization is carried out to rationalize the reasons behind the observed behvior. In addition, results from the atomistic simulations are utilized to obtain more information about the properties of the amorphous carbon thin films. (paper)
Comparison of methods for accurate end-point detection of potentiometric titrations

Science.gov (United States)

Villela, R. L. A.; Borges, P. P.; Vyskočil, L.

2015-01-01

Detection of the end point in potentiometric titrations has wide application on experiments that demand very low measurement uncertainties mainly for certifying reference materials. Simulations of experimental coulometric titration data and consequential error analysis of the end-point values were conducted using a programming code. These simulations revealed that the Levenberg-Marquardt method is in general more accurate than the traditional second derivative technique used currently as end-point detection for potentiometric titrations. Performance of the methods will be compared and presented in this paper.
Comparison of methods for accurate end-point detection of potentiometric titrations

International Nuclear Information System (INIS)

Villela, R L A; Borges, P P; Vyskočil, L

2015-01-01

Detection of the end point in potentiometric titrations has wide application on experiments that demand very low measurement uncertainties mainly for certifying reference materials. Simulations of experimental coulometric titration data and consequential error analysis of the end-point values were conducted using a programming code. These simulations revealed that the Levenberg-Marquardt method is in general more accurate than the traditional second derivative technique used currently as end-point detection for potentiometric titrations. Performance of the methods will be compared and presented in this paper
Direct RNA detection without nucleic acid purification and PCR: Combining sandwich hybridization with signal amplification based on branched hybridization chain reaction.

Science.gov (United States)

Xu, Yao; Zheng, Zhi

2016-05-15

We have developed a convenient, robust and low-cost RNA detection system suitable for high-throughput applications. This system uses a highly specific sandwich hybridization to capture target RNA directly onto solid support, followed by on-site signal amplification via 2-dimensional, branched hybridizing chain polymerization through toehold-mediated strand displacement reaction. The assay uses SYBR Green to detect targets at concentrations as low as 1 pM, without involving nucleic acid purification or any enzymatic reaction, using ordinary oligonucleotides without modification or labeling. The system was demonstrated in the detection of malaria RNA in blood and GAPDH gene expression in cell lysate. Copyright © 2015 Elsevier B.V. All rights reserved.
In situ hybridization for the detection of infectious laryngotracheitis virus in sections of trachea from experimentally infected chickens

DEFF Research Database (Denmark)

Nielsen, O.L.; Handberg, Kurt; Jørgensen, Poul Henrik

1998-01-01

An in situ hybridization procedure for the detection of infectious laryngotracheitis virus (ILTV) in experimentally infected chickens is described. Formalin-fixed, paraffin-embedded sections of trachea, taken from chickens on days 3-10 post-inoculation (p.i.) with ILTV were hybridized with a mixt......An in situ hybridization procedure for the detection of infectious laryngotracheitis virus (ILTV) in experimentally infected chickens is described. Formalin-fixed, paraffin-embedded sections of trachea, taken from chickens on days 3-10 post-inoculation (p.i.) with ILTV were hybridized...... on day 5 p.i. No hybridization was observed in 3 out of 3 chickens examined on day 10 p.i. ILTV nucleic acid was detected in nuclei of degenerated tracheal epithelial cells and in intranuclear inclusion bodies of syncytia....
Robust and Accurate Anomaly Detection in ECG Artifacts Using Time Series Motif Discovery

Science.gov (United States)

Sivaraks, Haemwaan

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. PMID:25688284
Detection of hepatitis A virus by hybridization with single-stranded RNA probes

International Nuclear Information System (INIS)

Xi, J.; Estes, M.K.; Metcalf, T.G.

1987-01-01

An improved method of dot-blot hybridization to detect hepatitis A virus (HAV) was developed with single-stranded RNA (ssRNA) probes. Radioactive and nonradioactive ssRNA probes were generated by in vitro transcription of HAV templates inserted into the plasmid pGEM-1. 32 P-labeled ssRNA probes were at least eightfold more sensitive than the 32 P-labeled double-stranded cDNA counterparts, whereas biotin-labeled ssRNA probes showed a sensitivity comparable with that of the 32 P-labeled double-stranded cDNA counterparts. Hybridization of HAV with the ssRNA probes at high stringency revealed specific reactions with a high signal-to-noise ratio. The differential hybridization reactions seen with probes of positive and negative sense (compared with HAV genomic RNA) were used to detect HAV in clinical and field samples. A positive/negative ratio was introduced as an indicator that permitted an semiquantitative expression of a positive HAV reaction. Good agreement of this indicator was observed with normal stool samples and with HAV-seeded samples. By using this system, HAV was detected in estuarine and freshwater samples collected from a sewage-polluted bayou in Houston and a saltwater tributary of Galveston Bay
A novel SERRS sandwich-hybridization assay to detect specific DNA target.

Directory of Open Access Journals (Sweden)

Cécile Feuillie

Full Text Available In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR. In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.
An optimized method for neurotransmitters and their metabolites analysis in mouse hypothalamus by high performance liquid chromatography-Q Exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry.

Science.gov (United States)

Yang, Zong-Lin; Li, Hui; Wang, Bing; Liu, Shu-Ying

2016-02-15

Neurotransmitters (NTs) and their metabolites are known to play an essential role in maintaining various physiological functions in nervous system. However, there are many difficulties in the detection of NTs together with their metabolites in biological samples. A new method for NTs and their metabolites detection by high performance liquid chromatography coupled with Q Exactive hybrid quadruple-orbitrap high-resolution accurate mass spectrometry (HPLC-HRMS) was established in this paper. This method was a great development of the applying of Q Exactive MS in the quantitative analysis. This method enabled a rapid quantification of ten compounds within 18min. Good linearity was obtained with a correlation coefficient above 0.99. The concentration range of the limit of detection (LOD) and the limit of quantitation (LOQ) level were 0.0008-0.05nmol/mL and 0.002-25.0nmol/mL respectively. Precisions (relative standard deviation, RSD) of this method were at 0.36-12.70%. Recovery ranges were between 81.83% and 118.04%. Concentrations of these compounds in mouse hypothalamus were detected by Q Exactive LC-MS technology with this method. Copyright © 2016 Elsevier B.V. All rights reserved.
A hybrid solution using computational prediction and measured data to accurately determine process corrections with reduced overlay sampling

Science.gov (United States)

Noyes, Ben F.; Mokaberi, Babak; Mandoy, Ram; Pate, Alex; Huijgen, Ralph; McBurney, Mike; Chen, Owen

2017-03-01

Reducing overlay error via an accurate APC feedback system is one of the main challenges in high volume production of the current and future nodes in the semiconductor industry. The overlay feedback system directly affects the number of dies meeting overlay specification and the number of layers requiring dedicated exposure tools through the fabrication flow. Increasing the former number and reducing the latter number is beneficial for the overall efficiency and yield of the fabrication process. An overlay feedback system requires accurate determination of the overlay error, or fingerprint, on exposed wafers in order to determine corrections to be automatically and dynamically applied to the exposure of future wafers. Since current and future nodes require correction per exposure (CPE), the resolution of the overlay fingerprint must be high enough to accommodate CPE in the overlay feedback system, or overlay control module (OCM). Determining a high resolution fingerprint from measured data requires extremely dense overlay sampling that takes a significant amount of measurement time. For static corrections this is acceptable, but in an automated dynamic correction system this method creates extreme bottlenecks for the throughput of said system as new lots have to wait until the previous lot is measured. One solution is using a less dense overlay sampling scheme and employing computationally up-sampled data to a dense fingerprint. That method uses a global fingerprint model over the entire wafer; measured localized overlay errors are therefore not always represented in its up-sampled output. This paper will discuss a hybrid system shown in Fig. 1 that combines a computationally up-sampled fingerprint with the measured data to more accurately capture the actual fingerprint, including local overlay errors. Such a hybrid system is shown to result in reduced modelled residuals while determining the fingerprint, and better on-product overlay performance.
Detecting Android Malwares with High-Efficient Hybrid Analyzing Methods

Directory of Open Access Journals (Sweden)

Yu Liu

2018-01-01

Full Text Available In order to tackle the security issues caused by malwares of Android OS, we proposed a high-efficient hybrid-detecting scheme for Android malwares. Our scheme employed different analyzing methods (static and dynamic methods to construct a flexible detecting scheme. In this paper, we proposed some detecting techniques such as Com+ feature based on traditional Permission and API call features to improve the performance of static detection. The collapsing issue of traditional function call graph-based malware detection was also avoided, as we adopted feature selection and clustering method to unify function call graph features of various dimensions into same dimension. In order to verify the performance of our scheme, we built an open-access malware dataset in our experiments. The experimental results showed that the suggested scheme achieved high malware-detecting accuracy, and the scheme could be used to establish Android malware-detecting cloud services, which can automatically adopt high-efficiency analyzing methods according to the properties of the Android applications.
Parente2: a fast and accurate method for detecting identity by descent

KAUST Repository

Rodriguez, Jesse M.; Bercovici, Sivan; Huang, Lin; Frostig, Roy; Batzoglou, Serafim

2014-01-01

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.
In-Channel-Grown Polypyrrole Nanowire for the Detection of DNA Hybridization in an Electrochemical Microfluidic Biosensor

Directory of Open Access Journals (Sweden)

Thi Luyen Tran

2015-01-01

Full Text Available A triple electrode setup with a Pt pseudo-reference electrode integrated in a polydimethylsiloxane- (PDMS- based microchamber was designed and fabricated. The integrated electrodes were deposited onto SiO2/Si substrate by sputtering. The PDMS microchamber was patterned using an SU-8 mold and sealed with electrodes in oxygen plasma. Polypyrrole nanowires (PPy NWs were electrochemically grown in situ at an accurate position of the working electrode in the sealed microchamber instead of in an open system. The DNA probe sequences were simply introduced into the channel to form bonds with the nanowires. A detection limit of 20 pM was achieved using a lock-in amplifier. The electrochemical characteristics produced by the hybridization of DNA strands in the microchamber showed a good signal/noise ratio and high sensitivity. Measurement of the DNA sensor in narrow space also required much less volume of the analytical sample compared with that in an open measuring cell. Results showed that this simple system can potentially fabricate nanostructures and detect bio/chemical molecules in a sealed system.
A Hybrid Semi-Supervised Anomaly Detection Model for High-Dimensional Data

Directory of Open Access Journals (Sweden)

Hongchao Song

2017-01-01

Full Text Available Anomaly detection, which aims to identify observations that deviate from a nominal sample, is a challenging task for high-dimensional data. Traditional distance-based anomaly detection methods compute the neighborhood distance between each observation and suffer from the curse of dimensionality in high-dimensional space; for example, the distances between any pair of samples are similar and each sample may perform like an outlier. In this paper, we propose a hybrid semi-supervised anomaly detection model for high-dimensional data that consists of two parts: a deep autoencoder (DAE and an ensemble k-nearest neighbor graphs- (K-NNG- based anomaly detector. Benefiting from the ability of nonlinear mapping, the DAE is first trained to learn the intrinsic features of a high-dimensional dataset to represent the high-dimensional data in a more compact subspace. Several nonparametric KNN-based anomaly detectors are then built from different subsets that are randomly sampled from the whole dataset. The final prediction is made by all the anomaly detectors. The performance of the proposed method is evaluated on several real-life datasets, and the results confirm that the proposed hybrid model improves the detection accuracy and reduces the computational complexity.
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.

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

Directory of Open Access Journals (Sweden)

Nobuyuki Kawai

Full Text Available 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.
High affinity γPNA sandwich hybridization assay for rapid detection of short nucleic acid targets with single mismatch discrimination.

Science.gov (United States)

Goldman, Johnathan M; Zhang, Li Ang; Manna, Arunava; Armitage, Bruce A; Ly, Danith H; Schneider, James W

2013-07-08

Hybridization analysis of short DNA and RNA targets presents many challenges for detection. The commonly employed sandwich hybridization approach cannot be implemented for these short targets due to insufficient probe-target binding strengths for unmodified DNA probes. Here, we present a method capable of rapid and stable sandwich hybridization detection for 22 nucleotide DNA and RNA targets. Stable hybridization is achieved using an n-alkylated, polyethylene glycol γ-carbon modified peptide nucleic acid (γPNA) amphiphile. The γPNA's exceptionally high affinity enables stable hybridization of a second DNA-based probe to the remaining bases of the short target. Upon hybridization of both probes, an electrophoretic mobility shift is measured via interaction of the n-alkane modification on the γPNA with capillary electrophoresis running buffer containing nonionic surfactant micelles. We find that sandwich hybridization of both probes is stable under multiple binding configurations and demonstrate single base mismatch discrimination. The binding strength of both probes is also stabilized via coaxial stacking on adjacent hybridization to targets. We conclude with a discussion on the implementation of the proposed sandwich hybridization assay as a high-throughput microRNA detection method.
Time series analysis of infrared satellite data for detecting thermal anomalies: a hybrid approach

Science.gov (United States)

Koeppen, W. C.; Pilger, E.; Wright, R.

2011-07-01

We developed and tested an automated algorithm that analyzes thermal infrared satellite time series data to detect and quantify the excess energy radiated from thermal anomalies such as active volcanoes. Our algorithm enhances the previously developed MODVOLC approach, a simple point operation, by adding a more complex time series component based on the methods of the Robust Satellite Techniques (RST) algorithm. Using test sites at Anatahan and Kīlauea volcanoes, the hybrid time series approach detected ~15% more thermal anomalies than MODVOLC with very few, if any, known false detections. We also tested gas flares in the Cantarell oil field in the Gulf of Mexico as an end-member scenario representing very persistent thermal anomalies. At Cantarell, the hybrid algorithm showed only a slight improvement, but it did identify flares that were undetected by MODVOLC. We estimate that at least 80 MODIS images for each calendar month are required to create good reference images necessary for the time series analysis of the hybrid algorithm. The improved performance of the new algorithm over MODVOLC will result in the detection of low temperature thermal anomalies that will be useful in improving our ability to document Earth's volcanic eruptions, as well as detecting low temperature thermal precursors to larger eruptions.
A Hybrid Swarm Intelligence Algorithm for Intrusion Detection Using Significant Features

Directory of Open Access Journals (Sweden)

P. Amudha

2015-01-01

Full Text Available Intrusion detection has become a main part of network security due to the huge number of attacks which affects the computers. This is due to the extensive growth of internet connectivity and accessibility to information systems worldwide. To deal with this problem, in this paper a hybrid algorithm is proposed to integrate Modified Artificial Bee Colony (MABC with Enhanced Particle Swarm Optimization (EPSO to predict the intrusion detection problem. The algorithms are combined together to find out better optimization results and the classification accuracies are obtained by 10-fold cross-validation method. The purpose of this paper is to select the most relevant features that can represent the pattern of the network traffic and test its effect on the success of the proposed hybrid classification algorithm. To investigate the performance of the proposed method, intrusion detection KDDCup’99 benchmark dataset from the UCI Machine Learning repository is used. The performance of the proposed method is compared with the other machine learning algorithms and found to be significantly different.
Chromogenic in situ hybridization (CISH) to detect HER2 gene amplification in breast and gastric cancer: comparison with immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH).

Science.gov (United States)

Kiyose, Shinichiro; Igarashi, Hisaki; Nagura, Kiyoko; Kamo, Takaharu; Kawane, Kazunori; Mori, Hiroki; Ozawa, Takachika; Maeda, Matsuyoshi; Konno, Keisuke; Hoshino, Hideaki; Konno, Hiroyuki; Ogura, Hiroyuki; Shinmura, Kazuya; Hattori, Naohiko; Sugimura, Haruhiko

2012-11-01

The chromogenic in situ hybridization (CISH) assay, designed to detect the amplification of the HER2 gene in formalin-fixed, paraffin-embedded (FFPE) breast cancer (BC) and gastric cancer (GC) tissue specimens, was evaluated in 125 FFPE BC cases and 198 FFPE GC cases for which the HER2 status had been predetermined using immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). In the 125 BC cases and the 198 gastric cases, we found a very good concordance (98.4% and 99.0%, respectively) between CISH and FISH. In particular, we evaluated the polysomy cases, as these cases often have ambiguous treatment options in clinical practice. The polysomy of chromosome 17 was defined as the presence of three or more CEP17 signals in at least 10% of the tumor cells. In the 50 BC cases and 54 GC cases displaying chromosome 17 polysomy, the concordance between FISH and CISH was 98.0% and 98.1%, respectively. These results indicate that CISH could provide an accurate and practical alternative to FISH for the clinical diagnosis of HER2 gene amplification in FFPE BC and FFPE GC samples. © 2012 The Authors. Pathology International © 2012 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.
A Hybrid Vision-Map Method for Urban Road Detection

Directory of Open Access Journals (Sweden)

Carlos Fernández

2017-01-01

Full Text Available A hybrid vision-map system is presented to solve the road detection problem in urban scenarios. The standardized use of machine learning techniques in classification problems has been merged with digital navigation map information to increase system robustness. The objective of this paper is to create a new environment perception method to detect the road in urban environments, fusing stereo vision with digital maps by detecting road appearance and road limits such as lane markings or curbs. Deep learning approaches make the system hard-coupled to the training set. Even though our approach is based on machine learning techniques, the features are calculated from different sources (GPS, map, curbs, etc., making our system less dependent on the training set.
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.
Lower hybrid wave cavities detected by the FREJA satellite

International Nuclear Information System (INIS)

Pecseli, H.L.; Iranpour, K.; Holter, Oe.; Lybekk, B.; Holtet J.; Truelsen, J.; Holback, B.

1994-12-01

Localized electrostatic wave packets in the frequency region of lower-hybrid waves have been detected by the instruments on the FREJA satellite. These waves are usually associated with local density depletions indicating that the structures can be interpreted as wave filled cavities. The basic features of the observations are discussed. Based on simple statistical arguments it is attempted to present some characteristics which have to be accommodated within an ultimate theory describing the observed wave phenomena. An explanation in terms of collapse of nonlinear lower-hybrid waves is discussed in particular. It is argued that such a model seems inapplicable, at least in its simplest form, by providing time and length scales which are not in agreement with observations. Alternatives to this model are presented. 24 refs., 8 figs
Appendix: a solution hybridization assay to detect radioactive globin messenger RNA nucleotide sequences

Energy Technology Data Exchange (ETDEWEB)

Ross, J

1976-09-15

In view of the sensitivity and specificity of the solution hybridization assay for unlabeled globin mRNA a similar technique has been devised to detect radioactive globin mRNA sequences with unlabeled globin cDNA. Several properties of the hybridization reaction are presented since RNA kinetic experiments reported recently depend on the validity of this assay. Data on hybridization analysis of (/sup 3/H)RNA from mouse fetal liver or erythroleukemia cell cytoplasm are presented. These data indicate that the excess cDNA solution assay for radioactive globin mRNA detection is specific for globin mRNA sequences. It can be performed rapidly and is highly reproducible from experiment. It is at least 500-fold less sensitive than the assay for unlabeled globin mRNA, due to the RNAase backgrounds of 0.05 to 0.15 %. However, this limitation has not affected kinetic experiments with non-dividing fetal liver erythroid cells, which synthesize relatively large quantities of globin mRNA.
A Pilot Study of Pedestrians with Visual Impairments Detecting Traffic Gaps and Surges Containing Hybrid Vehicles.

Science.gov (United States)

Emerson, Robert Wall; Naghshineh, Koorosh; Hapeman, Julie; Wiener, William

2011-03-01

The increasing number of hybrid and quiet internal combustion engine vehicles may impact the travel abilities of pedestrians who are blind. Pedestrians who rely on auditory cues for structuring their travel may face challenges in making crossing decisions in the presence of quiet vehicles. This article describes results of initial studies looking at the crossing decisions of pedestrians who are blind at an uncontrolled crossing (no traffic control) and a light controlled intersection. The presence of hybrid vehicles was a factor in each situation. At the uncontrolled crossing, Toyota hybrids were most difficult to detect but crossing decisions were made more often in small gaps ended by a Honda hybrid. These effects were seen only at speed under 20 mph. At the light controlled intersection, parallel surges of traffic were most difficult to detect when made up only of a Ford Escape hybrid. Results suggest that more controlled studies of vehicle characteristics impacting crossing decisions of pedestrians who are blind are warranted.
A Pilot Study of Pedestrians with Visual Impairments Detecting Traffic Gaps and Surges Containing Hybrid Vehicles

Science.gov (United States)

Emerson, Robert Wall; Naghshineh, Koorosh; Hapeman, Julie; Wiener, William

2010-01-01

The increasing number of hybrid and quiet internal combustion engine vehicles may impact the travel abilities of pedestrians who are blind. Pedestrians who rely on auditory cues for structuring their travel may face challenges in making crossing decisions in the presence of quiet vehicles. This article describes results of initial studies looking at the crossing decisions of pedestrians who are blind at an uncontrolled crossing (no traffic control) and a light controlled intersection. The presence of hybrid vehicles was a factor in each situation. At the uncontrolled crossing, Toyota hybrids were most difficult to detect but crossing decisions were made more often in small gaps ended by a Honda hybrid. These effects were seen only at speed under 20 mph. At the light controlled intersection, parallel surges of traffic were most difficult to detect when made up only of a Ford Escape hybrid. Results suggest that more controlled studies of vehicle characteristics impacting crossing decisions of pedestrians who are blind are warranted. PMID:21379367
Grid impedance estimation based hybrid islanding detection method for AC microgrids

DEFF Research Database (Denmark)

Ghzaiel, Walid; Jebali-Ben Ghorbal, Manel; Slama-Belkhodja, Ilhem

2017-01-01

This paper focuses on a hybrid islanding detection algorithm for parallel-inverters-based microgrids. The proposed algorithm is implemented on the unit ensuring the control of the intelligent bypass switch connecting or disconnecting the microgrid from the utility. This method employs a grid...... to avoid interactions with other units. The selected inverter will be the one closest to the controllable distributed generation system or to a healthy grid side in case of meshed microgrid with multiple-grid connections. The detection algorithm is applied to quickly detect the resonance phenomena, so...
Reliability of chromogenic in situ hybridization for epidermal growth factor receptor gene copy number detection in non-small-cell lung carcinomas: a comparison with fluorescence in situ hybridization study.

Science.gov (United States)

Yoo, Seol Bong; Lee, Hyun Ju; Park, Jung Ok; Choe, Gheeyoung; Chung, Doo Hyun; Seo, Jeong-Wook; Chung, Jin-Haeng

2010-03-01

Fluorescence in situ hybridization (FISH) has been known to be the most representative and standardized test for assessing gene amplification. However, FISH requires a fluorescence microscope, the signals are labile and rapidly fade over time. Recently, chromogenic in situ hybridization (CISH) has emerged as a potential alternative to FISH. The aim of this study is to test the reliability of CISH technique for the detection of epidermal growth factor receptor (EGFR) gene amplification in non-small-cell lung carcinomas (NSCLC), to compare CISH results with FISH. A total of 277 formalin-fixed and paraffin embedded NSCLC tissue samples were retrieved from the surgical pathology archives at Seoul National University Bundang Hospital. CISH and FISH examinations were performed to test EGFR gene amplification status. There was high concordance in the assessment of EGFR gene copy number between CISH and FISH tests (Kappa coefficient=0.83). Excellent concordance was shown between two observers on the interpretation of the CISH results (Kappa coefficient=0.90). In conclusion, CISH result is highly reproducible, accurate and practical method to determine EGFR gene amplification in NSCLC. In addition, CISH allows a concurrent analysis of histological features of the tumors and gene copy numbers.
Detection and quantitative analysis of actin mRNA by in situ hybridization with an oligodeoxynucleotide probe

International Nuclear Information System (INIS)

Taneja, K.; Singer, R.

1987-01-01

In situ hybridization is a useful method for localizing specific nucleic acid sequences intracellularly and for studying regulation of gene expression. Recently synthetic oligonucleotides have been successfully used as probes in this technique. Since they can be made easily to specific nucleic acid regions, they may be the best approach for analysis of a gene family of highly conserved sequences. They have analyzed these probes for the development of an in situ hybridization method. Oligonucleotides were made to different regions of chick beta-actin mRNA and used for detection of these sequences in a culture of chicken fibroblasts and myoblasts. They found that synthetic DNAs have different efficiencies of hybridization, indicating that not all target sequences are equivalent. They have investigated in detail a particular probe to the actin mRNA coding region and have optimized hybridization parameters. When hybridization was quantitated it was found that an oligonucleotide end labelled with 35 S or 32 P was capable of detecting several thousand messages per cell with a signal-to-noise ratio of 10:1. In situ hybridization confirmed the specificity of the hybridization as well as the background level. Increase in the number of oligonucleotides used should increase the signal-to-noise ratio-proportionately. Under particular circumstances the specificity of oligonucleotides make them an important reagent for in situ hybridization
Chromosomal imbalances detected in primary bone tumors by comparative genomic hybridization and interphase fluorescence in situ hybridization

Directory of Open Access Journals (Sweden)

Marcelo Razera Baruffi

2003-01-01

Full Text Available We applied a combination of comparative genomic hybridization (CGH and fluorescence in situ hybridization (FISH, to characterize the genetic aberrations in three osteosarcomas (OS and one Ewing's sarcoma. CGH identified recurrent chromosomal losses at 10p14-pter and gains at 8q22.3-24.1 in OS. Interphase FISH allowed to confirm 8q gain in two cases. A high amplification level of 11q12-qter was detected in one OS. The Ewing's sarcoma showed gain at 1p32-36.1 as the sole chromosome alteration. These studies demonstrate the value of molecular cytogenetic methods in the characterization of recurrent genomic alterations in bone tumor tissue.
Accurate detection of male subclinical genital tract infection via cervical culture and DNA hybridization assay of the female partner

NARCIS (Netherlands)

Trum, J. W.; Pannekoek, Y.; Spanjaard, L.; Bleker, O. P.; van der Veen, F.

2000-01-01

The accuracy of the PACE2 DNA hybridization assay of the cervix and cervical culture in female partners for the diagnosis of male subclinical genital tract infection were assessed in a male infertility population. A total of 184 men were screened for the presence of Chlamydia trachomatis, Ureaplasma
Parkinsonian rest tremor can be detected accurately based on neuronal oscillations recorded from the subthalamic nucleus.

Science.gov (United States)

Hirschmann, J; Schoffelen, J M; Schnitzler, A; van Gerven, M A J

2017-10-01

To investigate the possibility of tremor detection based on deep brain activity. We re-analyzed recordings of local field potentials (LFPs) from the subthalamic nucleus in 10 PD patients (12 body sides) with spontaneously fluctuating rest tremor. Power in several frequency bands was estimated and used as input to Hidden Markov Models (HMMs) which classified short data segments as either tremor-free rest or rest tremor. HMMs were compared to direct threshold application to individual power features. Applying a threshold directly to band-limited power was insufficient for tremor detection (mean area under the curve [AUC] of receiver operating characteristic: 0.64, STD: 0.19). Multi-feature HMMs, in contrast, allowed for accurate detection (mean AUC: 0.82, STD: 0.15), using four power features obtained from a single contact pair. Within-patient training yielded better accuracy than across-patient training (0.84vs. 0.78, p=0.03), yet tremor could often be detected accurately with either approach. High frequency oscillations (>200Hz) were the best performing individual feature. LFP-based markers of tremor are robust enough to allow for accurate tremor detection in short data segments, provided that appropriate statistical models are used. LFP-based markers of tremor could be useful control signals for closed-loop deep brain stimulation. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.
Evaporator modeling - A hybrid approach

International Nuclear Information System (INIS)

Ding Xudong; Cai Wenjian; Jia Lei; Wen Changyun

2009-01-01

In this paper, a hybrid modeling approach is proposed to model two-phase flow evaporators. The main procedures for hybrid modeling includes: (1) Based on the energy and material balance, and thermodynamic principles to formulate the process fundamental governing equations; (2) Select input/output (I/O) variables responsible to the system performance which can be measured and controlled; (3) Represent those variables existing in the original equations but are not measurable as simple functions of selected I/Os or constants; (4) Obtaining a single equation which can correlate system inputs and outputs; and (5) Identify unknown parameters by linear or nonlinear least-squares methods. The method takes advantages of both physical and empirical modeling approaches and can accurately predict performance in wide operating range and in real-time, which can significantly reduce the computational burden and increase the prediction accuracy. The model is verified with the experimental data taken from a testing system. The testing results show that the proposed model can predict accurately the performance of the real-time operating evaporator with the maximum error of ±8%. The developed models will have wide applications in operational optimization, performance assessment, fault detection and diagnosis
SpotCaliper: fast wavelet-based spot detection with accurate size estimation.

Science.gov (United States)

Püspöki, Zsuzsanna; Sage, Daniel; Ward, John Paul; Unser, Michael

2016-04-15

SpotCaliper is a novel wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size. It is implemented as an ImageJ plugin with a friendly user interface. The user is allowed to edit the results by modifying the measurements (in a semi-automated way), extract data for further analysis. The fine tuning of the detections includes the possibility of adjusting or removing the original detections, as well as adding further spots. The main advantage of the software is its ability to capture the size of spots in a fast and accurate way. http://bigwww.epfl.ch/algorithms/spotcaliper/ zsuzsanna.puspoki@epfl.ch Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Spin injection and detection in lateral spin valves with hybrid interfaces

Science.gov (United States)

Wang, Le; Liu, Wenyu; Ying, Hao; Chen, Luchen; Lu, Zhanjie; Han, Shuo; Chen, Shanshan; Zhao, Bing; Xu, Xiaoguang; Jiang, Yong

2018-06-01

Spin injection and detection in lateral spin valves with hybrid interfaces comprising a Co/Ag transparent contact and a Co/MgO/Ag junction (III) are investigated at room temperature in comparison with pure Co/Ag transparent contacts (I) and Co/MgO/Ag junctions (II). The measured spin-accumulation signals of a type III device are five times higher than those for type I. The extracted spin diffusion length in Ag is 180 nm for all three types of devices. The enhancement of the spin signal of the hybrid structure is mainly attributed to the increase of the interfacial spin polarization from the Co/MgO/Ag junction.

Detection of Defective Sensors in Phased Array Using Compressed Sensing and Hybrid Genetic Algorithm

Directory of Open Access Journals (Sweden)

Shafqat Ullah Khan

2016-01-01

Full Text Available A compressed sensing based array diagnosis technique has been presented. This technique starts from collecting the measurements of the far-field pattern. The system linking the difference between the field measured using the healthy reference array and the field radiated by the array under test is solved using a genetic algorithm (GA, parallel coordinate descent (PCD algorithm, and then a hybridized GA with PCD algorithm. These algorithms are applied for fully and partially defective antenna arrays. The simulation results indicate that the proposed hybrid algorithm outperforms in terms of localization of element failure with a small number of measurements. In the proposed algorithm, the slow and early convergence of GA has been avoided by combining it with PCD algorithm. It has been shown that the hybrid GA-PCD algorithm provides an accurate diagnosis of fully and partially defective sensors as compared to GA or PCD alone. Different simulations have been provided to validate the performance of the designed algorithms in diversified scenarios.
Fast and accurate spectral estimation for online detection of partial broken bar in induction motors

Science.gov (United States)

Samanta, Anik Kumar; Naha, Arunava; Routray, Aurobinda; Deb, Alok Kanti

2018-01-01

In this paper, an online and real-time system is presented for detecting partial broken rotor bar (BRB) of inverter-fed squirrel cage induction motors under light load condition. This system with minor modifications can detect any fault that affects the stator current. A fast and accurate spectral estimator based on the theory of Rayleigh quotient is proposed for detecting the spectral signature of BRB. The proposed spectral estimator can precisely determine the relative amplitude of fault sidebands and has low complexity compared to available high-resolution subspace-based spectral estimators. Detection of low-amplitude fault components has been improved by removing the high-amplitude fundamental frequency using an extended-Kalman based signal conditioner. Slip is estimated from the stator current spectrum for accurate localization of the fault component. Complexity and cost of sensors are minimal as only a single-phase stator current is required. The hardware implementation has been carried out on an Intel i7 based embedded target ported through the Simulink Real-Time. Evaluation of threshold and detectability of faults with different conditions of load and fault severity are carried out with empirical cumulative distribution function.
Accurate LC peak boundary detection for ¹⁶O/¹⁸O labeled LC-MS data.

Science.gov (United States)

Cui, Jian; Petritis, Konstantinos; Tegeler, Tony; Petritis, Brianne; Ma, Xuepo; Jin, Yufang; Gao, Shou-Jiang S J; Zhang, Jianqiu Michelle

2013-01-01

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.
Hybrid Modified K-Means with C4.5 for Intrusion Detection Systems in Multiagent Systems.

Science.gov (United States)

Laftah Al-Yaseen, Wathiq; Ali Othman, Zulaiha; Ahmad Nazri, Mohd Zakree

2015-01-01

Presently, the processing time and performance of intrusion detection systems are of great importance due to the increased speed of traffic data networks and a growing number of attacks on networks and computers. Several approaches have been proposed to address this issue, including hybridizing with several algorithms. However, this paper aims at proposing a hybrid of modified K-means with C4.5 intrusion detection system in a multiagent system (MAS-IDS). The MAS-IDS consists of three agents, namely, coordinator, analysis, and communication agent. The basic concept underpinning the utilized MAS is dividing the large captured network dataset into a number of subsets and distributing these to a number of agents depending on the data network size and core CPU availability. KDD Cup 1999 dataset is used for evaluation. The proposed hybrid modified K-means with C4.5 classification in MAS is developed in JADE platform. The results show that compared to the current methods, the MAS-IDS reduces the IDS processing time by up to 70%, while improving the detection accuracy.
[Optimization and assessment of a reverse hybridization system for the detection of HBV drug-resistant mutations].

Science.gov (United States)

Liu, Yan-chen; Huang, Ai-long; Hu, Yuan; Hu, Jie-li; Lai, Guo-qi; Zhang, Wen-lu

2011-12-01

To establish a detection method for HBV drug-resistant mutations related to lamivudine, adefovir and entecavir by optimization and assessment of reverse hybridization system. 26 degenerated probes covering 10 drug-resistant hotspots of 3 drugs were synthesized and immobilized on the same positively charged nylon membrane. PCR products labeled with digoxigenin were hybridized with corresponding probes. To improve the sensitivity and specificity, 4 reaction steps of reverse hybridization were optimized including the number of labeled digoxigenin, the energy intensity of UV cross-linking, hybridization and stringency wash conditions. To prove the feasibility, the specificity, sensitivity and accuracy of this system were assessed respectively. Sensitive and specific results are obtained by the optimization of the following 4 reaction steps: the primers labeled with 3 digoxigenin, energy intensity of UV cross-linking for 1500 x 0.1 mJ/cm², hybridization at 42 degrees C and stringency wash with 0.5 x SSC and 0.1% SDS solution at 44 degrees C for 30 min. In the assessment of system, the majority of probes have high specificity. The quantity of PCR product with a concentration of 10 ng/μl or above can be detected by this method. The concordant rate between reverse hybridization and direct sequencing is 93.9% in the clinical sample test. Though the specificity of several probes needs to be improved further, it is a simple, rapid and sensitive method which can detect HBV resistant mutations related to lamivudine, adefovir and entecavir simultaneously. Due to the short distance between 180 and 181, likewise 202 and 204, the sequence of the same probe covers two codon positions, and hybridization will be interfered by each other. To avoid such interference, the possible solution is that probes are designed by arranging and combining various forms of two near codons.
Evaluation of a reverse-hybridization StripAssay for the detection of genetic polymorphisms leading to acenocoumarol sensitivity.

Science.gov (United States)

Gialeraki, Argyri; Markatos, Christos; Grouzi, Elisabeth; Merkouri, Efrosyni; Travlou, Anthi; Politou, Marianna

2010-04-01

Acenocoumarol is mainly catabolized by CYP2C9 isoform of cytochrome P450 (CYP) liver complex and exerts its anticoagulant effect through the inhibition of Vitamin K Epoxide Reductase (VKOR). The most important genetic polymorphisms which lead to an impaired enzymatic activity and therefore predispose to acenocoumarol sensitivity, are considered to be CYP2C9*2 (Arg144Cys), CYP2C9*3 (Ile359Leu) and VKORC1-1639G>A, respectively. In this study we compared the results of the PGXThrombo StripAssay kit (ViennaLab Diagnostics,Vienna, Austria) with direct DNA sequencing and in house Restriction Fragment Length Polymorphisms (RFLP) for the detection of the aforementioned Single Nucleotide Polymorphisms (SNPs). The reverse hybridization StripAssay was found to be equally effective with RFLP and direct DNA sequencing for the detection of CYP2C9*2 and CYP2C9*3 polymorphisms, respectively. The comparison of the RFLP reference method with the reverse hybridization StripAssay for the detection of VKORC1-1639 G>A polymorphism showed that the reverse hybridization StripAsssay might misclassify some A/A homozygotes as heterozygotes. Optimization of the hybridization procedures may eliminate the extra low signal band observed in some samples at the reverse hybridization StripAssay and improve its diagnostic value.
A Viola-Jones based hybrid face detection framework

Science.gov (United States)

Murphy, Thomas M.; Broussard, Randy; Schultz, Robert; Rakvic, Ryan; Ngo, Hau

2013-12-01

Improvements in face detection performance would benefit many applications. The OpenCV library implements a standard solution, the Viola-Jones detector, with a statistically boosted rejection cascade of binary classifiers. Empirical evidence has shown that Viola-Jones underdetects in some instances. This research shows that a truncated cascade augmented by a neural network could recover these undetected faces. A hybrid framework is constructed, with a truncated Viola-Jones cascade followed by an artificial neural network, used to refine the face decision. Optimally, a truncation stage that captured all faces and allowed the neural network to remove the false alarms is selected. A feedforward backpropagation network with one hidden layer is trained to discriminate faces based upon the thresholding (detection) values of intermediate stages of the full rejection cascade. A clustering algorithm is used as a precursor to the neural network, to group significant overlappings. Evaluated on the CMU/VASC Image Database, comparison with an unmodified OpenCV approach shows: (1) a 37% increase in detection rates if constrained by the requirement of no increase in false alarms, (2) a 48% increase in detection rates if some additional false alarms are tolerated, and (3) an 82% reduction in false alarms with no reduction in detection rates. These results demonstrate improved face detection and could address the need for such improvement in various applications.
Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples

International Nuclear Information System (INIS)

Sayler, G.S.; Shields, M.S.; Tedford, E.T.; Breen, A.; Hooper, S.W.; Sirotkin, K.M.; Davis, J.W.

1985-01-01

The application of preexisting DNA hybridization techniques was investigated for potential in determining populations of specific gene sequences in environmental samples. Cross-hybridizations among two degradative plasmids, TOL and NAH, and two cloning vehicles, pLAFR1 and RSF1010, were determined. The detection limits for the TOL plasmid against a nonhomologous plasmid-bearing bacterial background was ascertained. The colony hybridization technique allowed detection of one colony containing TOL plasmid among 10(6) Escherichia coli colonies of nonhomologous DNA. Comparisons between population estimates derived from growth on selective substrates and from hybridizations were examined. Findings indicated that standard sole carbon source enumeration procedures for degradative populations lead to overestimations due to nonspecific growth of other bacteria on the microcontaminant carbon sources present in the media. Population estimates based on the selective growth of a microcosm population on two aromatic substrates (toluene and naphthalene) and estimates derived from DNA-DNA colony hybridizations, using the TOL or NAH plasmid as a probe, corresponded with estimates of substrate mineralization rates and past exposure to environmental contaminants. The applications of such techniques are hoped to eventually allow enumeration of any specific gene sequences in the environment, including both anabolic and catabolic genes. In addition, this procedure should prove useful in monitoring recombinant DNA clones released into environmental situations
Towards Effective Network Intrusion Detection: A Hybrid Model Integrating Gini Index and GBDT with PSO

Directory of Open Access Journals (Sweden)

Longjie Li

2018-01-01

Full Text Available In order to protect computing systems from malicious attacks, network intrusion detection systems have become an important part in the security infrastructure. Recently, hybrid models that integrating several machine learning techniques have captured more attention of researchers. In this paper, a novel hybrid model was proposed with the purpose of detecting network intrusion effectively. In the proposed model, Gini index is used to select the optimal subset of features, the gradient boosted decision tree (GBDT algorithm is adopted to detect network attacks, and the particle swarm optimization (PSO algorithm is utilized to optimize the parameters of GBDT. The performance of the proposed model is experimentally evaluated in terms of accuracy, detection rate, precision, F1-score, and false alarm rate using the NSL-KDD dataset. Experimental results show that the proposed model is superior to the compared methods.
Sensitive detection of nucleic acids by PNA hybridization directed co-localization of fluorescent beads

DEFF Research Database (Denmark)

Shiraishi, Takehiko; Deborggraeve, Stijn; Büscher, Philippe

2011-01-01

)avidin-coated fluorescent beads, differing in size and color [green beads (1 µm) and red beads (5.9 µm)], thereby allowing distinct detection of each PNA probe by conventional fluorescence microscopy. These two PNA beads showed easily detectable co-localization when simultaneously hybridizing to a target nucleic acid...
Development of a PCR/LDR/flow-through hybridization assay using a capillary tube, probe DNA-immobilized magnetic beads and chemiluminescence detection.

Science.gov (United States)

Hommatsu, Manami; Okahashi, Hisamitsu; Ohta, Keisuke; Tamai, Yusuke; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

2013-01-01

A polymerase chain reaction (PCR)/ligase detection reaction (LDR)/flow-through hybridization assay using chemiluminescence (CL) detection was developed for analyzing point mutations in gene fragments with high diagnostic value for colorectal cancers. A flow-through hybridization format using a capillary tube, in which probe DNA-immobilized magnetic beads were packed, provided accelerated hybridization kinetics of target DNA (i.e. LDR product) to the probe DNA. Simple fluid manipulations enabled both allele-specific hybridization and the removal of non-specifically bound DNA in the wash step. Furthermore, the use of CL detection greatly simplified the detection scheme, since CL does not require a light source for excitation of the fluorescent dye tags on the LDR products. Preliminary results demonstrated that this analytical system could detect both homozygous and heterozygous mutations, without the expensive instrumentation and cumbersome procedures required by conventional DNA microarray-based methods.
A Hybrid Change Detection Approach for Damage Detection and Recovery Monitoring

Science.gov (United States)

de Alwis Pitts, Dilkushi; Wieland, Marc; Wang, Shifeng; So, Emily; Pittore, Massimiliano

2014-05-01

Following a disaster, change detection via pre- and post-event very high resolution remote sensing images is an essential technique for damage assessment and recovery monitoring over large areas in complex urban environments. Most assessments to date focus on detection, destruction and recovery of man-made objects that facilitate shelter and accessibility, such as buildings, roads, bridges, etc., as indicators for assessment and better decision making. Moreover, many current change-detection mechanisms do not use all the data and knowledge which are often available for the pre-disaster state. Recognizing the continuous rather than dichotomous character of the data-rich/data-poor distinction permits the incorporation of ancillary data and existing knowledge into the processing flow. Such incorporation could improve the reliability of the results and thereby enhance the usability of robust methods for disaster management. This study proposes an application-specific and robust change detection method from multi-temporal very high resolution multi-spectral satellite images. This hybrid indicator-specific method uses readily available pre-disaster GIS data and integrates existing knowledge into the processing flow to optimize the change detection while offering the possibility to target specific types of changes to man-made objects. The indicator-specific information of the GIS objects is used as a series of masks to treat the GIS objects with similar characteristics similarly for better accuracy. The proposed approach is based on a fusion of a multi-index change detection method based on gradient, texture and edge similarity filters. The change detection index is flexible for disaster cases in which the pre-disaster and post-disaster images are not of the same resolution. The proposed automated method is evaluated with QuickBird and Ikonos datasets for abrupt changes soon after disaster. The method could also be extended in a semi-automated way for monitoring
Detection of ALK gene rearrangement in non-small cell lung cancer: a comparison of fluorescence in situ hybridization and chromogenic in situ hybridization with correlation of ALK protein expression.

Science.gov (United States)

Kim, Hyojin; Yoo, Seol-Bong; Choe, Ji-Young; Paik, Jin Ho; Xu, Xianhua; Nitta, Hiroaki; Zhang, Wenjun; Grogan, Thomas M; Lee, Choon-Taek; Jheon, Sanghoon; Chung, Jin-Haeng

2011-08-01

Accurate determination of ALK rearrangement is important in lung cancer patients, especially in determining their eligibility for crizotinib therapy. Fluorescence in situ hybridization (FISH) has been regarded as the gold standard method for detecting ALK rearrangement. However, FISH requires a fluorescence microscope, and the signals are labile and rapidly fade over time. This study evaluates the concordance between ALK gene rearrangement in non-small cell lung cancer assessed by ALK FISH and a newly developed ALK chromogenic in situ hybridization (CISH) and correlates the results with ALK protein expression assessed by immunohistochemistry. A total of 465 formalin-fixed, paraffin-embedded non-small cell lung cancer samples were analyzed by ALK FISH (PathVysion, Vysis, Abbott) and ALK CISH. For comparison, all specimens were stained by immunohistochemistry (clone 5A4, Novocastra) and interobserver reproducibility was assessed. We found that agreement between the pathologists on the CISH-determined ALK status was achieved in 449 patients (96.6%), and ALK rearrangement was identified in 18 patients (4.0%) in CISH method. Among these cases, 443 cases (95.3%) had results matching the corresponding FISH results: 17 rearranged, 425 wild types, and 1 discordant case. There was high concordance in the assessment of ALK gene rearrangement between FISH and CISH techniques (κ = 0.92) and between observers (κ = 0.97). In addition, there was high concordance in the ALK gene status and ALK protein expression between CISH and IHC tests (κ = 0.82). CISH is a highly reproducible and practical method to detect ALK gene rearrangement and correlated well with ALK protein expression. Here, we present a diagnostic algorithm (Chung's SNUBH ALK protocol) to detect lung cancer with ALK rearrangements using IHC, FISH and CISH. Because CISH allows a concurrent analysis of histological features of the tumors and gene rearrangement, it appears to be a useful method in determining ALK gene
Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm

Science.gov (United States)

Öhrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

2010-01-01

One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes. PMID:20864443
Evaluation of cancer detection efficiency by means of hybrid and inverse filter in chest radiography

International Nuclear Information System (INIS)

Kim, Youn Young; Kim, Tae Young; Kim, Hyun Ji; Kim, Jung Min; Park, Min Seock

2013-01-01

The purpose of this study is to evaluate usefulness of Hybrid image and Inverse image about detection of tumor shadow in chest radiography using ROC analysis. Original images of 60 cases are selected from Standards digital image date base issued by the Japanese Society of Radiological Technology. Through computer language of C, Inverse images of 60 cases and Hybrid image of 30 cases are made. The continues reading experiment was conducted. In the case of inverse image were observed by 5 radiographer and 2 radiologist. In the case of In case of Hybrid image were observed by 3 student radiographer and 2 experienced radiographer. ROC curve are constructed using ROCKIT Program made by Metz. In Inverse image, a Az of average ROC curve was increases from 0.742 of original image to 0.775 of inverse image. In normal cases, the effect of the detrimental is same to that of the beneficial, however In abnormal cases, the beneficial effect is greater than detrimental effect. However in Hybrid image, a Az of average ROC curve was decreases from 0.5253 of original image to 0.4868 of Hybrid image. In Normal cases, the effect of the detrimental is greater than that of the Beneficial, however In abnormal cases, the Beneficial effect is greater than detrimental effect. The inverse image can be more positively considered for the detecting of tumor than the hybrid image
Genomic alterations detected by comparative genomic hybridization in ovarian endometriomas

Directory of Open Access Journals (Sweden)

L.C. Veiga-Castelli

2010-08-01

Full Text Available Endometriosis is a complex and multifactorial disease. Chromosomal imbalance screening in endometriotic tissue can be used to detect hot-spot regions in the search for a possible genetic marker for endometriosis. The objective of the present study was to detect chromosomal imbalances by comparative genomic hybridization (CGH in ectopic tissue samples from ovarian endometriomas and eutopic tissue from the same patients. We evaluated 10 ovarian endometriotic tissues and 10 eutopic endometrial tissues by metaphase CGH. CGH was prepared with normal and test DNA enzymatically digested, ligated to adaptors and amplified by PCR. A second PCR was performed for DNA labeling. Equal amounts of both normal and test-labeled DNA were hybridized in human normal metaphases. The Isis FISH Imaging System V 5.0 software was used for chromosome analysis. In both eutopic and ectopic groups, 4/10 samples presented chromosomal alterations, mainly chromosomal gains. CGH identified 11q12.3-q13.1, 17p11.1-p12, 17q25.3-qter, and 19p as critical regions. Genomic imbalances in 11q, 17p, 17q, and 19p were detected in normal eutopic and/or ectopic endometrium from women with ovarian endometriosis. These regions contain genes such as POLR2G, MXRA7 and UBA52 involved in biological processes that may lead to the establishment and maintenance of endometriotic implants. This genomic imbalance may affect genes in which dysregulation impacts both eutopic and ectopic endometrium.
Detection of MYCN Gene Amplification in Neuroblastoma by Fluorescence In Situ Hybridization: A Pediatric Oncology Group Study

Directory of Open Access Journals (Sweden)

Prasad Mathew

2001-01-01

Full Text Available To assess the utility of fluorescence in situ hybridization (FISH for analysis of MYCN gene amplification in neuroblastoma, we compared this assay with Southern blot analysis using tumor specimens collected from 232 patients with presenting characteristics typical of this disease. The FISH technique identified MYCN amplification in 47 cases, compared with 39 by Southern blotting, thus increasing the total number of positive cases by 21%. The major cause of discordancy was a low fraction of tumor cells (≤30% replacement in clinical specimens, which prevented an accurate estimate of MYCN copy number by Southern blotting. With FISH, by contrast, it was possible to analyze multiple interphase nuclei of tumor cells, regardless of the proportion of normal peripheral blood, bone marrow, or stromal cells in clinical samples. Thus, FISH could be performed accurately with very small numbers of tumor cells from touch preparations of needle biopsies. Moreover, this procedure allowed us to discern the heterogeneous pattern of MYCN amplification that is characteristic of neuroblastoma. We conclude that FISH improves the detection of MYCN gene amplification in childhood neuroblastomas in a clinical setting, thus facilitating therapeutic decisions based on the presence or absence of this prognostically important biologic marker.
Dendrimer-based biosensor for chemiluminescent detection of DNA hybridization

International Nuclear Information System (INIS)

Liu, P.; Hun, X.; Qing, H.

2011-01-01

We report on a highly sensitive chemiluminescent (CL) biosensor for the sequence-specific detection of DNA using a novel bio barcode DNA probe modified with gold nanoparticles that were covered with a dendrimer. The modified probe is composed of gold nanoparticles, a dendrimer, the CL reagent, and the DNA. The capture probe DNA was immobilized on magnetic beads covered with gold. It first hybridizes with the target DNA and then with one terminal end of the signal DNA on the barcoded DNA probe. CL was generated by adding H 2 O 2 and Co(II) ions as the catalyst. The immobilization of dendrimer onto the gold nanoparticles can significantly enhance sensitivity and gives a detection limit of 6 fmol L -1 of target DNA. (author)
Colorimetric detection of Ehrlichia canis via nucleic acid hybridization in gold nano-colloids.

Science.gov (United States)

Muangchuen, Ajima; Chaumpluk, Piyasak; Suriyasomboon, Annop; Ekgasit, Sanong

2014-08-08

Canine monocytic ehrlichiosis (CME) is a major thick-bone disease of dog caused by Ehrlichia canis. Detection of this causal agent outside the laboratory using conventional methods is not effective enough. Thus an assay for E. canis detection based on the p30 outer membrane protein gene was developed. It was based on the p30 gene amplification using loop-mediated isothermal DNA amplification (LAMP). The primer set specific to six areas within the target gene were designed and tested for their sensitivity and specificity. Detection of DNA signals was based on modulation of gold nanoparticles' surface properties and performing DNA/DNA hybridization using an oligonucleotide probe. Presence of target DNA affected the gold colloid nanoparticles in terms of particle aggregation with a plasmonic color change of the gold colloids from ruby red to purple, visible by the naked eye. All the assay steps were completed within 90 min including DNA extraction without relying on standard laboratory facilities. This method was very specific to target bacteria. Its sensitivity with probe hybridization was sufficient to detect 50 copies of target DNA. This method should provide an alternative choice for point of care control and management of the disease.
Hybrid feature selection for supporting lightweight intrusion detection systems

Science.gov (United States)

Song, Jianglong; Zhao, Wentao; Liu, Qiang; Wang, Xin

2017-08-01

Redundant and irrelevant features not only cause high resource consumption but also degrade the performance of Intrusion Detection Systems (IDS), especially when coping with big data. These features slow down the process of training and testing in network traffic classification. Therefore, a hybrid feature selection approach in combination with wrapper and filter selection is designed in this paper to build a lightweight intrusion detection system. Two main phases are involved in this method. The first phase conducts a preliminary search for an optimal subset of features, in which the chi-square feature selection is utilized. The selected set of features from the previous phase is further refined in the second phase in a wrapper manner, in which the Random Forest(RF) is used to guide the selection process and retain an optimized set of features. After that, we build an RF-based detection model and make a fair comparison with other approaches. The experimental results on NSL-KDD datasets show that our approach results are in higher detection accuracy as well as faster training and testing processes.

Quantum dots-hyperbranched polyether hybrid nanospheres towards delivery and real-time detection of nitric oxide

Energy Technology Data Exchange (ETDEWEB)

Liu, Shuiping; Gu, Tianxun; Fu, Jiajia [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China); Li, Xiaoqiang, E-mail: leecaiwei@163.com [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China); Technical University of Denmark, DTU Food, Søltofts plads, B227, 2800 Kgs. Lyngby (Denmark); Chronakis, Ioannis S. [Technical University of Denmark, DTU Food, Søltofts plads, B227, 2800 Kgs. Lyngby (Denmark); Ge, Mingqiao [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China)

2014-12-01

In this work, novel hybrid nanosphere vehicles were synthesized for nitric oxide (NO) donating and real-time detection. The hybrid nanosphere vehicles consist of cadmium selenide quantum dots (CdSe QDs) as NO fluorescent probes, and the modified hyperbranched polyether (mHP)-based diazeniumdiolates as NO donors, respectively. The nanospheres have spherical outline with dimension of ∼ 127 nm. The data of systematic characterization demonstrated that the mHP-based hybrid nanosphere vehicles (QDs-mHP-NO) can release and real-time detect NO with the low limit of 25 nM, based on fluorescence quenching mechanism. The low cell-toxicity of QDs-mHP-NO nanospheres was verified by means of MTT assay on L929 cells viability. The QDs-mHP-NO nanospheres provide perspectives for designing a new class of biocompatible NO donating and imaging systems. - Highlights: • QDs-mHP-NO fluorescent probe was prepared. • The QDs-mHP-NO probe is capable of releasing NO. • The QDs-mHP-NO probe can quantitatively detecting the release of NO in real time. • The low cell-toxicity of QDs-mHP-NO nanospheres was verified.
Efficient Hybrid Detection of Node Replication Attacks in Mobile Sensor Networks

Directory of Open Access Journals (Sweden)

Ze Wang

2017-01-01

Full Text Available The node replication attack is one of the notorious attacks that can be easily launched by adversaries in wireless sensor networks. A lot of literatures have studied mitigating the node replication attack in static wireless sensor networks. However, it is more difficult to detect the replicas in mobile sensor networks because of their node mobility. Considering the limitations of centralized detection schemes for static wireless sensor networks, a few distributed solutions have been recently proposed. Some existing schemes identified replicated attacks by sensing mobile nodes with identical ID but different locations. To facilitate the discovery of contradictory conflicts, we propose a hybrid local and global detection method. The local detection is performed in a local area smaller than the whole deployed area to improve the meeting probability of contradictory nodes, while the distant replicated nodes in larger area can also be efficiently detected by the global detection. The complementary two levels of detection achieve quick discovery by searching of the replicas with reasonable overhead.
A hybrid polarization-selective atomic sensor for radio-frequency field detection with a passive resonant-cavity field amplifier

OpenAIRE

Anderson, David A.; Paradis, Eric G.; Raithel, Georg

2018-01-01

We present a hybrid atomic sensor that realizes radio-frequency electric field detection with intrinsic field amplification and polarization selectivity for robust high-sensitivity field measurement. The hybrid sensor incorporates a passive resonator element integrated with an atomic vapor cell that provides amplification and polarization selectivity for detection of incident radio-frequency fields. The amplified intra-cavity radio-frequency field is measured by atoms using a quantum-optical ...
Detecting Urban Transport Modes Using a Hybrid Knowledge Driven Framework from GPS Trajectory

Directory of Open Access Journals (Sweden)

Rahul Deb Das

2016-11-01

Full Text Available Transport mode information is essential for understanding people’s movement behavior and travel demand estimation. Current approaches extract travel information once the travel is complete. Such approaches are limited in terms of generating just-in-time information for a number of mobility based applications, e.g., real time mode specific patronage estimation. In order to detect the transport modalities from GPS trajectories, various machine learning approaches have already been explored. However, the majority of them produce only a single conclusion from a given set of evidences, ignoring the uncertainty of any mode classification. Also, the existing machine learning approaches fall short in explaining their reasoning scheme. In contrast, a fuzzy expert system can explain its reasoning scheme in a human readable format along with a provision of inferring different outcome possibilities, but lacks the adaptivity and learning ability of machine learning. In this paper, a novel hybrid knowledge driven framework is developed by integrating a fuzzy logic and a neural network to complement each other’s limitations. Thus the aim of this paper is to automate the tuning process in order to generate an intelligent hybrid model that can perform effectively in near-real time mode detection using GPS trajectory. Tests demonstrate that a hybrid knowledge driven model works better than a purely knowledge driven model and at per the machine learning models in the context of transport mode detection.
Affordable and accurate large-scale hybrid-functional calculations on GPU-accelerated supercomputers

Science.gov (United States)

Ratcliff, Laura E.; Degomme, A.; Flores-Livas, José A.; Goedecker, Stefan; Genovese, Luigi

2018-03-01

Performing high accuracy hybrid functional calculations for condensed matter systems containing a large number of atoms is at present computationally very demanding or even out of reach if high quality basis sets are used. We present a highly optimized multiple graphics processing unit implementation of the exact exchange operator which allows one to perform fast hybrid functional density-functional theory (DFT) calculations with systematic basis sets without additional approximations for up to a thousand atoms. With this method hybrid DFT calculations of high quality become accessible on state-of-the-art supercomputers within a time-to-solution that is of the same order of magnitude as traditional semilocal-GGA functionals. The method is implemented in a portable open-source library.
Hybrid Model-Based and Data-Driven Fault Detection and Diagnostics for Commercial Buildings: Preprint

Energy Technology Data Exchange (ETDEWEB)

Frank, Stephen; Heaney, Michael; Jin, Xin; Robertson, Joseph; Cheung, Howard; Elmore, Ryan; Henze, Gregor

2016-08-01

Commercial buildings often experience faults that produce undesirable behavior in building systems. Building faults waste energy, decrease occupants' comfort, and increase operating costs. Automated fault detection and diagnosis (FDD) tools for buildings help building owners discover and identify the root causes of faults in building systems, equipment, and controls. Proper implementation of FDD has the potential to simultaneously improve comfort, reduce energy use, and narrow the gap between actual and optimal building performance. However, conventional rule-based FDD requires expensive instrumentation and valuable engineering labor, which limit deployment opportunities. This paper presents a hybrid, automated FDD approach that combines building energy models and statistical learning tools to detect and diagnose faults noninvasively, using minimal sensors, with little customization. We compare and contrast the performance of several hybrid FDD algorithms for a small security building. Our results indicate that the algorithms can detect and diagnose several common faults, but more work is required to reduce false positive rates and improve diagnosis accuracy.
Hybrid Computational Simulation and Study of Terahertz Pulsed Photoconductive Antennas

Science.gov (United States)

Emadi, R.; Barani, N.; Safian, R.; Nezhad, A. Zeidaabadi

2016-11-01

A photoconductive antenna (PCA) has been numerically investigated in the terahertz (THz) frequency band based on a hybrid simulation method. This hybrid method utilizes an optoelectronic solver, Silvaco TCAD, and a full-wave electromagnetic solver, CST. The optoelectronic solver is used to find the accurate THz photocurrent by considering realistic material parameters. Performance of photoconductive antennas and temporal behavior of the excited photocurrent for various active region geometries such as bare-gap electrode, interdigitated electrodes, and tip-to-tip rectangular electrodes are investigated. Moreover, investigations have been done on the center of the laser illumination on the substrate, substrate carrier lifetime, and diffusion photocurrent associated with the carriers temperature, to achieve efficient and accurate photocurrent. Finally, using the full-wave electromagnetic solver and the calculated photocurrent obtained from the optoelectronic solver, electromagnetic radiation of the antenna and its associated detected THz signal are calculated and compared with a measurement reference for verification.
Detection of airborne Legionella while showering using liquid impingement and fluorescent in situ hybridization (FISH).

Science.gov (United States)

Deloge-Abarkan, Magali; Ha, Thi-Lan; Robine, Enric; Zmirou-Navier, Denis; Mathieu, Laurence

2007-01-01

Aerosols of water contaminated with Legionella bacteria constitute the only mode of exposure for humans. However, the prevention strategy against this pathogenic bacteria risk is managed through the survey of water contamination. No relationship linked the Legionella bacteria water concentration and their airborne abundance. Therefore, new approaches in the field of the metrological aspects of Legionella bioaerosols are required. This study was aimed at testing the main principles for bioaerosol collection (solid impaction, liquid impingement and filtration) and the in situ hybridization (FISH) method, both in laboratory and field assays, with the intention of applying such methodologies for airborne Legionella bacteria detection while showering. An aerosolization chamber was developed to generate controlled and reproducible L. pneumophila aerosols. This tool allowed the identification of the liquid impingement method as the most appropriate one for collecting airborne Legionella bacteria. The culturable fraction of airborne L. pneumophila recovered with the liquid impingement principle was 4 and 700 times higher compared to the impaction and filtration techniques, respectively. Moreover, the concentrations of airborne L. pneumophila in the impinger fluid were on average 7.0 x 10(5) FISH-cells m(-3) air with the fluorescent in situ hybridization (FISH) method versus 9.0 x 10(4) CFU m(-3) air with the culture method. These results, recorded under well-controlled conditions, were confirmed during the field experiments performed on aerosols generated by hot water showers in health institutions. This new approach may provide a more accurate characterization of aerobiocontamination by Legionella bacteria.
Lung ultrasound accurately detects pneumothorax in a preterm newborn lamb model.

Science.gov (United States)

Blank, Douglas A; Hooper, Stuart B; Binder-Heschl, Corinna; Kluckow, Martin; Gill, Andrew W; LaRosa, Domenic A; Inocencio, Ishmael M; Moxham, Alison; Rodgers, Karyn; Zahra, Valerie A; Davis, Peter G; Polglase, Graeme R

2016-06-01

Pneumothorax is a common emergency affecting extremely preterm. In adult studies, lung ultrasound has performed better than chest x-ray in the diagnosis of pneumothorax. The purpose of this study was to determine the efficacy of lung ultrasound (LUS) examination to detect pneumothorax using a preterm animal model. This was a prospective, observational study using newborn Border-Leicester lambs at gestational age = 126 days (equivalent to gestational age = 26 weeks in humans) receiving mechanical ventilation from birth to 2 h of life. At the conclusion of the experiment, LUS was performed, the lambs were then euthanised and a post-mortem exam was immediately performed. We used previously published ultrasound techniques to identify pneumothorax. Test characteristics of LUS to detect pneumothorax were calculated, using the post-mortem exam as the 'gold standard' test. Nine lambs (18 lungs) were examined. Four lambs had a unilateral pneumothorax, all of which were identified by LUS with no false positives. This was the first study to use post-mortem findings to test the efficacy of LUS to detect pneumothorax in a newborn animal model. Lung ultrasound accurately detected pneumothorax, verified by post-mortem exam, in premature, newborn lambs. © 2016 Paediatrics and Child Health Division (The Royal Australasian College of Physicians).
A hybrid approach for efficient anomaly detection using metaheuristic methods

Directory of Open Access Journals (Sweden)

Tamer F. Ghanem

2015-07-01

Full Text Available Network intrusion detection based on anomaly detection techniques has a significant role in protecting networks and systems against harmful activities. Different metaheuristic techniques have been used for anomaly detector generation. Yet, reported literature has not studied the use of the multi-start metaheuristic method for detector generation. This paper proposes a hybrid approach for anomaly detection in large scale datasets using detectors generated based on multi-start metaheuristic method and genetic algorithms. The proposed approach has taken some inspiration of negative selection-based detector generation. The evaluation of this approach is performed using NSL-KDD dataset which is a modified version of the widely used KDD CUP 99 dataset. The results show its effectiveness in generating a suitable number of detectors with an accuracy of 96.1% compared to other competitors of machine learning algorithms.
Accurate Fall Detection in a Top View Privacy Preserving Configuration.

Science.gov (United States)

Ricciuti, Manola; Spinsante, Susanna; Gambi, Ennio

2018-05-29

Fall detection is one of the most investigated themes in the research on assistive solutions for aged people. In particular, a false-alarm-free discrimination between falls and non-falls is indispensable, especially to assist elderly people living alone. Current technological solutions designed to monitor several types of activities in indoor environments can guarantee absolute privacy to the people that decide to rely on them. Devices integrating RGB and depth cameras, such as the Microsoft Kinect, can ensure privacy and anonymity, since the depth information is considered to extract only meaningful information from video streams. In this paper, we propose an accurate fall detection method investigating the depth frames of the human body using a single device in a top-view configuration, with the subjects located under the device inside a room. Features extracted from depth frames train a classifier based on a binary support vector machine learning algorithm. The dataset includes 32 falls and 8 activities considered for comparison, for a total of 800 sequences performed by 20 adults. The system showed an accuracy of 98.6% and only one false positive.
Detection of c-myc amplification in formalin-fixed paraffin-embedded tumor tissue by chromogenic in situ hybridization (CISH).

Science.gov (United States)

Todorović-Raković, Nataša

2013-01-01

In situ hybridization (ISH) allows evaluation of genetic abnormalities, such as changes in chromosome number, chromosome translocations or gene amplifications, by hybridization of tagged DNA (or RNA) probes with complementary DNA (or RNA) sequences in interphase nuclei of target tissue. However, chromogenic in situ hybridization (CISH) is also applicable to formalin-fixed, paraffin-embedded (FFPE) tissues, besides metaphase chromosome spreads. CISH is similar to fluorescent in situ hybridization (FISH) regarding pretreatments and hybridization protocols but differs in the way of visualization. Indeed, CISH signal detection is similar to that used in immunohistochemistry, making use of a peroxidase-based chromogenic reaction instead of fluorescent dyes. In particular, tagged DNA probes are indirectly detected using an enzyme-conjugated antibody targeting the tags. The enzymatic reaction of the chromogenic substrate leads to the formation of strong permanent brown signals that can be visualized by bright-field microscopy at 40 × magnification. The advantage of CISH is that it allows the simultaneous observation of gene amplification and tissue morphology and the slides can be stored for a long time.
Biomarkers for ALK and ROS1 in Lung Cancer: Immunohistochemistry and Fluorescent In Situ Hybridization.

Science.gov (United States)

Luk, Peter P; Selinger, Christina I; Mahar, Annabelle; Cooper, Wendy A

2018-06-14

- A small proportion of non-small cell lung cancers harbor rearrangements of ALK or ROS1 genes, and these tumors are sensitive to targeted tyrosine kinase inhibitors. It is crucial for pathologists to accurately identify tumors with these genetic alterations to enable patients to access optimal treatments and avoid unnecessary side effects of less effective agents. Although a number of different techniques can be used to identify ALK- and ROS1-rearranged lung cancers, immunohistochemistry and fluorescence in situ hybridization are the mainstays. - To review the role of immunohistochemistry in assessment of ALK and ROS1 rearrangements in lung cancer, focusing on practical issues in comparison with other modalities such as fluorescence in situ hybridization. - This manuscript reviews the current literature on ALK and ROS1 detection using immunohistochemistry and fluorescence in situ hybridization as well as current recommendations. - Although fluorescence in situ hybridization remains the gold standard for detecting ALK and ROS1 rearrangement in non-small cell lung cancer, immunohistochemistry plays an important role and can be an effective screening method for detection of these genetic alterations, or a diagnostic test in the setting of ALK.
Detection of DNA hybridization based on SnO2 nanomaterial enhanced fluorescence

International Nuclear Information System (INIS)

Gu Cuiping; Huang Jiarui; Ni Ning; Li Minqiang; Liu Jinhuai

2008-01-01

In this paper, enhanced fluorescence emissions were firstly investigated based on SnO 2 nanomaterial, and its application in the detection of DNA hybridization was also demonstrated. The microarray of SnO 2 nanomaterial was fabricated by the vapour phase transport method catalyzed by patterned Au nanoparticles on a silicon substrate. A probe DNA was immobilized on the substrate with patterned SnO 2 nanomaterial, respectively, by covalent and non-covalent linking schemes. When a fluorophore labelled target DNA was hybridized with a probe DNA on the substrate, fluorescence emissions were only observed on the surface of SnO 2 nanomaterial, which indicated the property of enhancing fluorescence signals from the SnO 2 nanomaterial. By comparing the different fluorescence images from covalent and non-covalent linking schemes, the covalent method was confirmed to be more effective for immobilizing a probe DNA. With the combined use of SnO 2 nanomaterial and the covalent linking scheme, the target DNA could be detected at a very low concentration of 10 fM. And the stability of SnO 2 nanomaterial under the experimental conditions was also compared with silicon nanowires. The findings strongly suggested that SnO 2 nanomaterial could be extensively applied in detections of biological samples with enhancing fluorescence property and high stability
An efficient enzyme-powered micromotor device fabricated by cyclic alternate hybridization assembly for DNA detection.

Science.gov (United States)

Fu, Shizhe; Zhang, Xueqing; Xie, Yuzhe; Wu, Jie; Ju, Huangxian

2017-07-06

An efficient enzyme-powered micromotor device was fabricated by assembling multiple layers of catalase on the inner surface of a poly(3,4-ethylenedioxythiophene and sodium 4-styrenesulfonate)/Au microtube (PEDOT-PSS/Au). The catalase assembly was achieved by programmed DNA hybridization, which was performed by immobilizing a designed sandwich DNA structure as the sensing unit on the PEDOT-PSS/Au, and then alternately hybridizing with two assisting DNA to bind the enzyme for efficient motor motion. The micromotor device showed unique features of good reproducibility, stability and motion performance. Under optimal conditions, it showed a speed of 420 μm s -1 in 2% H 2 O 2 and even 51 μm s -1 in 0.25% H 2 O 2 . In the presence of target DNA, the sensing unit hybridized with target DNA to release the multi-layer DNA as well as the multi-catalase, resulting in a decrease of the motion speed. By using the speed as a signal, the micromotor device could detect DNA from 10 nM to 1 μM. The proposed micromotor device along with the cyclic alternate DNA hybridization assembly technique provided a new path to fabricate efficient and versatile micromotors, which would be an exceptional tool for rapid and simple detection of biomolecules.
Hybrid light transport model based bioluminescence tomography reconstruction for early gastric cancer detection

Science.gov (United States)

Chen, Xueli; Liang, Jimin; Hu, Hao; Qu, Xiaochao; Yang, Defu; Chen, Duofang; Zhu, Shouping; Tian, Jie

2012-03-01

Gastric cancer is the second cause of cancer-related death in the world, and it remains difficult to cure because it has been in late-stage once that is found. Early gastric cancer detection becomes an effective approach to decrease the gastric cancer mortality. Bioluminescence tomography (BLT) has been applied to detect early liver cancer and prostate cancer metastasis. However, the gastric cancer commonly originates from the gastric mucosa and grows outwards. The bioluminescent light will pass through a non-scattering region constructed by gastric pouch when it transports in tissues. Thus, the current BLT reconstruction algorithms based on the approximation model of radiative transfer equation are not optimal to handle this problem. To address the gastric cancer specific problem, this paper presents a novel reconstruction algorithm that uses a hybrid light transport model to describe the bioluminescent light propagation in tissues. The radiosity theory integrated with the diffusion equation to form the hybrid light transport model is utilized to describe light propagation in the non-scattering region. After the finite element discretization, the hybrid light transport model is converted into a minimization problem which fuses an l1 norm based regularization term to reveal the sparsity of bioluminescent source distribution. The performance of the reconstruction algorithm is first demonstrated with a digital mouse based simulation with the reconstruction error less than 1mm. An in situ gastric cancer-bearing nude mouse based experiment is then conducted. The primary result reveals the ability of the novel BLT reconstruction algorithm in early gastric cancer detection.
Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

Science.gov (United States)

Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

2013-01-01

Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry. PMID:23435052
Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

Directory of Open Access Journals (Sweden)

Yuji Miyahara

2013-02-01

Full Text Available Peptide nucleic acid (PNA has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.
An accurate modelling of the two-diode model of PV module using a hybrid solution based on differential evolution

International Nuclear Information System (INIS)

Chin, Vun Jack; Salam, Zainal; Ishaque, Kashif

2016-01-01

Highlights: • An accurate computational method for the two-diode model of PV module is proposed. • The hybrid method employs analytical equations and Differential Evolution (DE). • I PV , I o1 , and R p are computed analytically, while a 1 , a 2 , I o2 and R s are optimized. • This allows the model parameters to be computed without using costly assumptions. - Abstract: This paper proposes an accurate computational technique for the two-diode model of PV module. Unlike previous methods, it does not rely on assumptions that cause the accuracy to be compromised. The key to this improvement is the implementation of a hybrid solution, i.e. by incorporating the analytical method with the differential evolution (DE) optimization technique. Three parameters, i.e. I PV , I o1 , and R p are computed analytically, while the remaining, a 1 , a 2 , I o2 and R s are optimized using the DE. To validate its accuracy, the proposed method is tested on three PV modules of different technologies: mono-crystalline, poly-crystalline and thin film. Furthermore, its performance is evaluated against two popular computational methods for the two-diode model. The proposed method is found to exhibit superior accuracy for the variation in irradiance and temperature for all module types. In particular, the improvement in accuracy is evident at low irradiance conditions; the root-mean-square error is one order of magnitude lower than that of the other methods. In addition, the values of the model parameters are consistent with the physics of PV cell. It is envisaged that the method can be very useful for PV simulation, in which accuracy of the model is of prime concern.
Resolution-improved in situ DNA hybridization detection based on microwave photonic interrogation.

Science.gov (United States)

Cao, Yuan; Guo, Tuan; Wang, Xudong; Sun, Dandan; Ran, Yang; Feng, Xinhuan; Guan, Bai-ou

2015-10-19

In situ bio-sensing system based on microwave photonics filter (MPF) interrogation method with improved resolution is proposed and experimentally demonstrated. A microfiber Bragg grating (mFBG) is used as sensing probe for DNA hybridization detection. Different from the traditional wavelength monitoring technique, we use the frequency interrogation scheme for resolution-improved bio-sensing detection. Experimental results show that the frequency shift of MPF notch presents a linear response to the surrounding refractive index (SRI) change over the range of 1.33 to 1.38, with a SRI resolution up to 2.6 × 10(-5) RIU, which has been increased for almost two orders of magnitude compared with the traditional fundamental mode monitoring technique (~3.6 × 10(-3) RIU). Due to the high Q value (about 27), the whole process of DNA hybridization can be in situ monitored. The proposed MPF-based bio-sensing system provides a new interrogation method over the frequency domain with improved sensing resolution and rapid interrogation rate for biochemical and environmental measurement.

Electrochemically fabricated polyaniline nanowire-modified electrode for voltammetric detection of DNA hybridization

International Nuclear Information System (INIS)

Zhu Ningning; Chang Zhu; He Pingang; Fang Yuzhi

2006-01-01

A novel and sensitive electrochemical DNA biosensor based on electrochemically fabricated polyaniline nanowire and methylene blue for DNA hybridization detection is presented. Nanowires of conducting polymers were directly synthesized through a three-step electrochemical deposition procedure in an aniline-containing electrolyte solution, by using the glassy carbon electrode (GCE) as the working electrode. The morphology of the polyaniline films was examined using a field emission scanning electron microscope (SEM). The diameters of the nanowires range from 80 to 100 nm. The polyaniline nanowires-coated electrode exhibited very good electrochemical conductivity. Oligonucleotides with phosphate groups at the 5' end were covalently linked onto the amino groups of polyaniline nanowires on the electrode. The hybridization events were monitored with differential pulse voltammetry (DPV) measurement using methylene blue (MB) as an indicator. The approach described here can effectively discriminate complementary from non-complementary DNA sequence, with a detection limit of 1.0 x 10 -12 mol l -1 of complementary target, suggesting that the polyaniline nanowires hold great promises for sensitive electrochemical biosensor applications
Hybrid functional pseudopotentials

Science.gov (United States)

Yang, Jing; Tan, Liang Z.; Rappe, Andrew M.

2018-02-01

The consistency between the exchange-correlation functional used in pseudopotential construction and in the actual density functional theory calculation is essential for the accurate prediction of fundamental properties of materials. However, routine hybrid density functional calculations at present still rely on generalized gradient approximation pseudopotentials due to the lack of hybrid functional pseudopotentials. Here, we present a scheme for generating hybrid functional pseudopotentials, and we analyze the importance of pseudopotential density functional consistency for hybrid functionals. For the PBE0 hybrid functional, we benchmark our pseudopotentials for structural parameters and fundamental electronic gaps of the Gaussian-2 (G2) molecular dataset and some simple solids. Our results show that using our PBE0 pseudopotentials in PBE0 calculations improves agreement with respect to all-electron calculations.
Detection of a variable number of ribosomal DNA loci by fluorescent in situ hybridization in Populus species.

Science.gov (United States)

Prado, E A; Faivre-Rampant, P; Schneider, C; Darmency, M A

1996-10-01

Fluorescent in situ hybridization (FISH) was applied to related Populus species (2n = 19) in order to detect rDNA loci. An interspecific variability in the number of hybridization sites was revealed using as probe an homologous 25S clone from Populus deltoides. The application of image analysis methods to measure fluorescence intensity of the hybridization signals has enabled us to characterize major and minor loci in the 18S-5.8S-25S rDNA. We identified one pair of such rDNA clusters in Populus alba; two pairs, one major and one minor, in both Populus nigra and P. deltoides; and three pairs in Populus balsamifera, (two major and one minor) and Populus euroamericana (one major and two minor). FISH results are in agreement with those based on RFLP analysis. The pBG13 probe containing 5S sequence from flax detected two separate clusters corresponding to the two size classes of units that coexist within 5S rDNA of most Populus species. Key words : Populus spp., fluorescent in situ hybridization, FISH, rDNA variability, image analysis.
Hybrid nanosensor for colorimetric and ultrasensitive detection of nuclease contaminations

Science.gov (United States)

Cecere, Paola; Valentini, Paola; Pompa, Pier Paolo

2016-04-01

Nucleases are ubiquitous enzymes that degrade DNA or RNA, thus they can prejudice the good outcome of molecular biology experiments involving nucleic acids. We propose a colorimetric test for the naked-eye detection of nuclease contaminations. The system uses an hybrid nanosensor, based on gold nanoparticles functionalized with DNA probes. Our assay is rapid, instrument-free, simple and low-cost. Moreover, it reaches sensitivity equal or better than those of commercial kits, and presents a lot of advantageous aspects. Therefore, it is very competitive, with a real market potential. This test will be relevant in routine process monitoring in scientific laboratories, and in quality control in clinical laboratories and industrial processes, allowing the simultaneous detection of nucleases with different substrate specificities and large-scale screening.
Detection of Methylobacterium radiotolerans IMBG290 in potato plants by in situ hybridization

OpenAIRE

Pirttila A. M.; Kozyrovska N. O.; Ovcharenko L. P.; Podolich O. V.

2009-01-01

A new bacterial strain of pink-pigmented facultative methylotroph (M. radiotolerans IMBG290) which was previously isolated from in vitro grown potato plantlets after their inoculation with Pseudomonas fluorescens IMBG163 was detected in tissues by in situ hybridization method (ISH/FISH). The presence of Methylobacterium rRNA was observed in leaves and stems of potato plantlets, whereas no signal was detected in potato roots. The signal was less abundant in the untreated plants than in the pla...
Amperometric glucose biosensor based on glucose oxidase dispersed in multiwalled carbon nanotubes/graphene oxide hybrid biocomposite.

Science.gov (United States)

Palanisamy, Selvakumar; Cheemalapati, Srikanth; Chen, Shen-Ming

2014-01-01

An amperometric glucose biosensor based on enhanced and fast direct electron transfer (DET) of glucose oxidase (GOx) at enzyme dispersed multiwalled carbon nanotubes/graphene oxide (MWCNT/GO) hybrid biocomposite was developed. The fabricated hybrid biocomposite was characterized by transmission electron microscopy (TEM), Raman and infrared spectroscopy (IR). The TEM image of hybrid biocomposite reveals that a thin layer of GOx was covered on the surface of MWCNT/GO hybrid composite. IR results validate that the hybrid biocomposite was formed through the electrostatic interactions between GOx and MWCNT/GO hybrid composite. Further, MWCNT/GO hybrid composite has also been characterized by TEM and UV-visible spectroscopy. A pair of well-defined redox peak was observed for GOx immobilized at the hybrid biocomposite electrode than that immobilized at the MWCNT modified electrode. The electron transfer rate constant (Ks) of GOx at the hybrid biocomposite was calculated to be 11.22s(-1). The higher Ks value revealed that fast DET of GOx occurred at the electrode surface. Moreover, fabricated biosensor showed a good sensitivity towards glucose oxidation over a linear range 0.05-23.2mM. The limit of detection (LOD) was estimated to be 28μM. The good features of the proposed biosensor could be used for the accurate detection of glucose in the biological samples. © 2013.
Application of Islanding Detection and Classification of Power Quality Disturbance in Hybrid Energy System

Science.gov (United States)

Sun, L. B.; Wu, Z. S.; Yang, K. K.

2018-04-01

Islanding and power quality (PQ) disturbances in hybrid energy system become more serious with the application of renewable energy sources. In this paper, a novel method based on wavelet transform (WT) and modified feed forward neural network (FNN) is proposed to detect islanding and classify PQ problems. First, the performance indices, i.e., the energy content and SD of the transformed signal are extracted from the negative sequence component of the voltage signal at PCC using WT. Afterward, WT indices are fed to train FNNs midfield by Particle Swarm Optimization (PSO) which is a novel heuristic optimization method. Then, the results of simulation based on WT-PSOFNN are discussed in MATLAB/SIMULINK. Simulations on the hybrid power system show that the accuracy can be significantly improved by the proposed method in detecting and classifying of different disturbances connected to multiple distributed generations.
Computational Intelligence based techniques for islanding detection of distributed generation in distribution network: A review

International Nuclear Information System (INIS)

Laghari, J.A.; Mokhlis, H.; Karimi, M.; Bakar, A.H.A.; Mohamad, Hasmaini

2014-01-01

Highlights: • Unintentional and intentional islanding, their causes, and solutions are presented. • Remote, passive, active and hybrid islanding detection techniques are discussed. • The limitation of these techniques in accurately detect islanding are discussed. • Computational intelligence techniques ability in detecting islanding is discussed. • Review of ANN, fuzzy logic control, ANFIS, Decision tree techniques is provided. - Abstract: Accurate and fast islanding detection of distributed generation is highly important for its successful operation in distribution networks. Up to now, various islanding detection technique based on communication, passive, active and hybrid methods have been proposed. However, each technique suffers from certain demerits that cause inaccuracies in islanding detection. Computational intelligence based techniques, due to their robustness and flexibility in dealing with complex nonlinear systems, is an option that might solve this problem. This paper aims to provide a comprehensive review of computational intelligence based techniques applied for islanding detection of distributed generation. Moreover, the paper compares the accuracies of computational intelligence based techniques over existing techniques to provide a handful of information for industries and utility researchers to determine the best method for their respective system
Radioactive and enzymatic cloned cDNA probes for bovine enteric coronavirus detection by molecular hybridization

International Nuclear Information System (INIS)

Collomb, J.; Finance, C.; Alabouch, S.; Laporte, J.

1992-01-01

Genomic RNA of F15 strain bovine enteric coronavirus (BECV) was cloned in E. coli. Three clones (174, 160, PG 78), selected in the cDNA library, including a large portion of the nucleocapsid (N), matrix (M) and peplomeric (S) protein genes , were used as probes for a slot blot hybridization assay. Two probe labelling techniques were compared, radiolabelling with 32 P and enzymatic labelling through covalent linkage to peroxidase and chemiluminescence detection. The radioactive probe 174 detected as little as 1 to 3 pg of viral RNA, while the less sensitive enzymatic probe could not reveal more than 100 pg of RNA. No significant detection amplification was achieved when a mixture of the three probes was used. Probe 174 allowed specific identification for BECV. No hybridization was noticed either with rotaviruses or even with other antigenically unrelated members of the family Coronaviridae such as transmissible gastroenteritis virus. The test proved valid for detection of BECV in the supernatant of infected HRT-18 cells: genomic RNA could be detected after direct spotting of samples, but prior nucleic acid extraction after proteinase K treatment improved virus detection. BECV diagnosis in faecal samples using enzymatic probe was compared with conventional diagnostic methods. (authors)
Radioactive and enzymatic cloned cDNA probes for bovine enteric coronavirus detection by molecular hybridization

Energy Technology Data Exchange (ETDEWEB)

Collomb, J; Finance, C; Alabouch, S [Lab. de Microbiologie Moleculaire, Faculte des Sciences Pharmaceutiques et Biologiques, Univ. de Nancy I, Nancy (France); Laporte, J [Station de Virologie et d' Immunologie Moleculaires, INRA, Jouy-en-Josas (France)

1992-01-01

Genomic RNA of F15 strain bovine enteric coronavirus (BECV) was cloned in E. coli. Three clones (174, 160, PG 78), selected in the cDNA library, including a large portion of the nucleocapsid (N), matrix (M) and peplomeric (S) protein genes , were used as probes for a slot blot hybridization assay. Two probe labelling techniques were compared, radiolabeled with [sup 32]P and enzymatic labeled through covalent linkage to peroxidase for chemiluminescence detection. The radioactive probe 174 detected as little as 1-3 pg of viral RNA, while the less sensitive enzymatic probe could not reveal more than 100 pg of RNA. No significant detection amplification was achieved when a mixture of the three probes was used. Probe 174 allowed specific identification for BECV. No hybridization was noticed either with rotaviruses or even with other antigenically unrelated members of the family Coronaviridae such as transmissible gastroenteritis virus. The test proved valid for detection of BECV in the supernatant of infected HRT-18 cells: genomic RNA could be detected after direct spotting of samples, but prior nucleic acid extraction after proteinase K treatment improved virus detection. BECV diagnosis in fecal samples using enzymatic probe was compared with conventional diagnostic methods. (authors).
Detection of dengue group viruses by fluorescence in situ hybridization

Directory of Open Access Journals (Sweden)

Raquin Vincent

2012-10-01

Full Text Available Abstract Background Dengue fever (DF and dengue hemorrhagic fever (DHF represent a global challenge in public health. It is estimated that 50 to 100 million infections occur each year causing approximately 20,000 deaths that are usually linked to severe cases like DHF and dengue shock syndrome. The causative agent of DF is dengue virus (genus Flavivirus that comprises four distinct serotypes (DENV-1 to DENV-4. Fluorescence in situ hybridization (FISH has been used successfully to detect pathogenic agents, but has not been implemented in detecting DENV. To improve our understanding of DENV infection and dissemination in host tissues, we designed specific probes to detect DENV in FISH assays. Methods Oligonucleotide probes were designed to hybridize with RNA from the broadest range of DENV isolates belonging to the four serotypes, but not to the closest Flavivirus genomes. Three probes that fit the criteria defined for FISH experiments were selected, targeting both coding and non-coding regions of the DENV genome. These probes were tested in FISH assays against the dengue vector Aedes albopictus (Diptera: Culicidae. The FISH experiments were led in vitro using the C6/36 cell line, and in vivo against dissected salivary glands, with epifluorescence and confocal microscopy. Results The three 60-nt oligonucleotides probes DENV-Probe A, B and C cover a broad range of DENV isolates from the four serotypes. When the three probes were used together, specific fluorescent signals were observed in C6/36 infected with each DENV serotypes. No signal was detected in either cells infected with close Flavivirus members West Nile virus or yellow fever virus. The same protocol was used on salivary glands of Ae. albopictus fed with a DENV-2 infectious blood-meal which showed positive signals in the lateral lobes of infected samples, with no significant signal in uninfected mosquitoes. Conclusion Based on the FISH technique, we propose a way to design and use
Detection of Helicobacter pylori in the Gastric Mucosa by Fluorescence In Vivo Hybridization

DEFF Research Database (Denmark)

Fontenete, Silvia; Leite, Marina; Figueiredo, Céu

2017-01-01

In this chapter, we describe a fluorescence in vivo hybridization (FIVH) protocol, using nucleic acid probes, for the detection of the bacterium Helicobacter pylori in the gastric mucosa of an infected C57BL/6 mouse model. This protocol should be easily extended to other microorganisms not only...
Proximity hybridization-mediated isothermal exponential amplification for ultrasensitive electrochemical protein detection

Directory of Open Access Journals (Sweden)

Yu Y

2017-08-01

Full Text Available Yanyan Yu, Gaoxing Su, Hongyan Zhu, Qing Zhu, Yong Chen, Bohui Xu, Yuqin Li, Wei Zhang School of Pharmacy, Nantong University, Nantong, People’s Republic of China Abstract: In this study, we fabricated a novel electrochemical biosensing platform on the basis of target-triggered proximity hybridization-mediated isothermal exponential amplification reaction (EXPAR for ultrasensitive protein analysis. Through rational design, the aptamers for protein recognition were integrated within two DNA probes. Via proximity hybridization principle, the affinity protein-binding event was converted into DNA assembly process. The recognition of protein by aptamers can trigger the strand displacement through the increase of the local concentrations of the involved probes. As a consequence, the output DNA was displaced, which can hybridize with the duplex probes immobilized on the electrode surface subsequently, leading to the initiation of the EXPAR as well as the cleavage of duplex probes. Each cleavage will release the gold nanoparticles (AuNPs binding sequence. With the modification of G-quadruplex sequence, electrochemical signals were yielded by the AuNPs through oxidizing 3,3',5,5'-tetramethylbenzidine in the presence of H2O2. The study we proposed exhibited high sensitivity toward platelet-derived growth factor BB (PDGF-BB with the detection limit of 52 fM. And, this method also showed great selectivity among the PDGF isoforms and performed well in spiked human serum samples. Keywords: electrochemical biosensor, proximity hybridization, PDGF-BB, isothermal exponential amplification, G-quadruplex
Fluorescence In Situ Hybridization for MicroRNA Detection in Archived Oral Cancer Tissues

Directory of Open Access Journals (Sweden)

Zonggao Shi

2012-01-01

Full Text Available The noncoding RNA designated as microRNA (miRNA is a large group of small single-stranded regulatory RNA and has generated wide-spread interest in human disease studies. To facilitate delineating the role of microRNAs in cancer pathology, we sought to explore the feasibility of detecting microRNA expression in formalin-fixed paraffin-embedded (FFPE tissues. Using FFPE materials, we have compared fluorescent in situ hybridization (FISH procedures to detect miR-146a with (a different synthetic probes: regular custom DNA oligonucleotides versus locked nucleic acid (LNA incorporated DNA oligonucleotides; (b different reporters for the probes: biotin versus digoxigenin (DIG; (c different visualization: traditional versus tyramide signal amplification (TSA system; (d different blocking reagents for endogenous peroxidase. Finally, we performed miR-146a FISH on a commercially available oral cancer tissue microarray, which contains 40 cases of oral squamous cell carcinoma (OSCC and 10 cases of normal epithelia from the human oral cavity. A sample FISH protocol for detecting miR-146a is provided. In summary, we have established reliable in situ hybridization procedures for detecting the expression of microRNA in FFPE oral cancer tissues. This method is an important tool for studies on the involvement of microRNA in oral cancer pathology and may have potential prognostic or diagnostic value.
Efficient in situ growth of enzyme-inorganic hybrids on paper strips for the visual detection of glucose.

Science.gov (United States)

Li, WanYun; Lu, ShiYu; Bao, ShuJuan; Shi, ZhuanZhuan; Lu, Zhisong; Li, ChangMing; Yu, Ling

2018-01-15

A visual colorimetric microfluidic paper-based analytical device (μPAD) was constructed following the direct synthesis of enzyme-inorganic hybrid nanomaterials on the paper matrix. An inorganic solution of MnSO 4 and KH 2 PO 4 containing a diluted enzyme (glucose oxidase, GOx) was subsequently pipetted onto cellulose paper for the in situ growth of GOx@Mn 3 (PO 4 ) 2 hybrid functional materials. The characterization of the morphology and chemical composition validated the presence of hybrid materials roots in the paper fiber, while the Mn 3 (PO 4 ) 2 of the hybrid provided both a surface for enzyme anchoring and a higher peroxidase-like catalytic activity as compared to the Mn 3 (PO 4 ) 2 crystal that was synthesized without enzyme modulation. This new approach for the in situ growth of an enzyme-inorganic hybrid on a paper matrix eliminates centrifugation and the dry process by casting the solution on paper. The sensing material loading was highly reproducible because of the accuracy and stability of pipetting, which eventually contributed to the reliability of the μPAD. The self-assembled natural and artificial enzyme hybrid on the μPADs specifically detected glucose from a group of interferences, which shows great specificity using this method. Moreover, the colorimetric signal exhibited detection limitation for glucose is 0.01mM, which lies in the physiological range of glucose in biological samples. Copyright © 2017 Elsevier B.V. All rights reserved.
Hybrid Bacterial Foraging and Particle Swarm Optimization for detecting Bundle Branch Block.

Science.gov (United States)

Kora, Padmavathi; Kalva, Sri Ramakrishna

2015-01-01

Abnormal cardiac beat identification is a key process in the detection of heart diseases. Our present study describes a procedure for the detection of left and right bundle branch block (LBBB and RBBB) Electrocardiogram (ECG) patterns. The electrical impulses that control the cardiac beat face difficulty in moving inside the heart. This problem is termed as bundle branch block (BBB). BBB makes it harder for the heart to pump blood effectively through the heart circulatory system. ECG feature extraction is a key process in detecting heart ailments. Our present study comes up with a hybrid method combining two heuristic optimization methods: Bacterial Forging Optimization (BFO) and Particle Swarm Optimization (PSO) for the feature selection of ECG signals. One of the major controlling forces of BFO algorithm is the chemotactic movement of a bacterium that models a test solution. The chemotaxis process of the BFO depends on random search directions which may lead to a delay in achieving the global optimum solution. The hybrid technique: Bacterial Forging-Particle Swarm Optimization (BFPSO) incorporates the concepts from BFO and PSO and it creates individuals in a new generation. This BFPSO method performs local search through the chemotactic movement of BFO and the global search over the entire search domain is accomplished by a PSO operator. The BFPSO feature values are given as the input for the Levenberg-Marquardt Neural Network classifier.
Preparation of Pd/Bacterial Cellulose Hybrid Nanofibers for Dopamine Detection

Directory of Open Access Journals (Sweden)

Dawei Li

2016-05-01

Full Text Available Palladium nanoparticle-bacterial cellulose (PdBC hybrid nanofibers were synthesized by in-situ chemical reduction method. The obtained PdBC nanofibers were characterized by a series of analytical techniques. The results revealed that Pd nanoparticles were evenly dispersed on the surfaces of BC nanofibers. Then, the as-prepared PdBC nanofibers were mixed with laccase (Lac and Nafion to obtain mixture suspension, which was further modified on electrode surface to construct novel biosensing platform. Finally, the prepared electrochemical biosensor was employed to detect dopamine. The analysis result was satisfactory, the sensor showed excellent electrocatalysis towards dopamine with high sensitivity (38.4 µA·mM−1, low detection limit (1.26 µM, and wide linear range (5–167 µM. Moreover, the biosensor also showed good repeatability, reproducibility, selectivity and stability and was successfully used in the detection of dopamine in human urine, thus providing a promising method for dopamine analysis in clinical application.
Unsupervised obstacle detection in driving environments using deep-learning-based stereovision

KAUST Repository

Dairi, Abdelkader; Harrou, Fouzi; Senouci, Mohamed; Sun, Ying

2017-01-01

A vision-based obstacle detection system is a key enabler for the development of autonomous robots and vehicles and intelligent transportation systems. This paper addresses the problem of urban scene monitoring and tracking of obstacles based on unsupervised, deep-learning approaches. Here, we design an innovative hybrid encoder that integrates deep Boltzmann machines (DBM) and auto-encoders (AE). This hybrid auto-encode (HAE) model combines the greedy learning features of DBM with the dimensionality reduction capacity of AE to accurately and reliably detect the presence of obstacles. We combine the proposed hybrid model with the one-class support vector machines (OCSVM) to visually monitor an urban scene. We also propose an efficient approach to estimating obstacles location and track their positions via scene densities. Specifically, we address obstacle detection as an anomaly detection problem. If an obstacle is detected by the OCSVM algorithm, then localization and tracking algorithm is executed. We validated the effectiveness of our approach by using experimental data from two publicly available dataset, the Malaga stereovision urban dataset (MSVUD) and the Daimler urban segmentation dataset (DUSD). Results show the capacity of the proposed approach to reliably detect obstacles.
Unsupervised obstacle detection in driving environments using deep-learning-based stereovision

KAUST Repository

Dairi, Abdelkader

2017-12-06

A vision-based obstacle detection system is a key enabler for the development of autonomous robots and vehicles and intelligent transportation systems. This paper addresses the problem of urban scene monitoring and tracking of obstacles based on unsupervised, deep-learning approaches. Here, we design an innovative hybrid encoder that integrates deep Boltzmann machines (DBM) and auto-encoders (AE). This hybrid auto-encode (HAE) model combines the greedy learning features of DBM with the dimensionality reduction capacity of AE to accurately and reliably detect the presence of obstacles. We combine the proposed hybrid model with the one-class support vector machines (OCSVM) to visually monitor an urban scene. We also propose an efficient approach to estimating obstacles location and track their positions via scene densities. Specifically, we address obstacle detection as an anomaly detection problem. If an obstacle is detected by the OCSVM algorithm, then localization and tracking algorithm is executed. We validated the effectiveness of our approach by using experimental data from two publicly available dataset, the Malaga stereovision urban dataset (MSVUD) and the Daimler urban segmentation dataset (DUSD). Results show the capacity of the proposed approach to reliably detect obstacles.
A Hybrid Heuristic Optimization Approach for Leak Detection in Pipe Networks Using Ordinal Optimization Approach and the Symbiotic Organism Search

Directory of Open Access Journals (Sweden)

Chao-Chih Lin

2017-10-01

Full Text Available A new transient-based hybrid heuristic approach is developed to optimize a transient generation process and to detect leaks in pipe networks. The approach couples the ordinal optimization approach (OOA and the symbiotic organism search (SOS to solve the optimization problem by means of iterations. A pipe network analysis model (PNSOS is first used to determine steady-state head distribution and pipe flow rates. The best transient generation point and its relevant valve operation parameters are optimized by maximizing the objective function of transient energy. The transient event is created at the chosen point, and the method of characteristics (MOC is used to analyze the transient flow. The OOA is applied to sift through the candidate pipes and the initial organisms with leak information. The SOS is employed to determine the leaks by minimizing the sum of differences between simulated and computed head at the observation points. Two synthetic leaking scenarios, a simple pipe network and a water distribution network (WDN, are chosen to test the performance of leak detection ordinal symbiotic organism search (LDOSOS. Leak information can be accurately identified by the proposed approach for both of the scenarios. The presented technique makes a remarkable contribution to the success of leak detection in the pipe networks.

A DDoS Attack Detection Method Based on Hybrid Heterogeneous Multiclassifier Ensemble Learning

Directory of Open Access Journals (Sweden)

Bin Jia

2017-01-01

Full Text Available The explosive growth of network traffic and its multitype on Internet have brought new and severe challenges to DDoS attack detection. To get the higher True Negative Rate (TNR, accuracy, and precision and to guarantee the robustness, stability, and universality of detection system, in this paper, we propose a DDoS attack detection method based on hybrid heterogeneous multiclassifier ensemble learning and design a heuristic detection algorithm based on Singular Value Decomposition (SVD to construct our detection system. Experimental results show that our detection method is excellent in TNR, accuracy, and precision. Therefore, our algorithm has good detective performance for DDoS attack. Through the comparisons with Random Forest, k-Nearest Neighbor (k-NN, and Bagging comprising the component classifiers when the three algorithms are used alone by SVD and by un-SVD, it is shown that our model is superior to the state-of-the-art attack detection techniques in system generalization ability, detection stability, and overall detection performance.
Nationwide Hybrid Change Detection of Buildings

Science.gov (United States)

Hron, V.; Halounova, L.

2016-06-01

The Fundamental Base of Geographic Data of the Czech Republic (hereinafter FBGD) is a national 2D geodatabase at a 1:10,000 scale with more than 100 geographic objects. This paper describes the design of the permanent updating mechanism of buildings in FBGD. The proposed procedure belongs to the category of hybrid change detection (HCD) techniques which combine pixel-based and object-based evaluation. The main sources of information for HCD are cadastral information and bi-temporal vertical digital aerial photographs. These photographs have great information potential because they contain multispectral, position and also elevation information. Elevation information represents a digital surface model (DSM) which can be obtained using the image matching technique. Pixel-based evaluation of bi-temporal DSMs enables fast localization of places with potential building changes. These coarse results are subsequently classified through the object-based image analysis (OBIA) using spectral, textural and contextual features and GIS tools. The advantage of the two-stage evaluation is the pre-selection of locations where image segmentation (a computationally demanding part of OBIA) is performed. It is not necessary to apply image segmentation to the entire scene, but only to the surroundings of detected changes, which contributes to significantly faster processing and lower hardware requirements. The created technology is based on open-source software solutions that allow easy portability on multiple computers and parallelization of processing. This leads to significant savings of financial resources which can be expended on the further development of FBGD.
Novel RNA hybridization method for the in situ detection of ETV1, ETV4, and ETV5 gene fusions in prostate cancer.

Science.gov (United States)

Kunju, Lakshmi P; Carskadon, Shannon; Siddiqui, Javed; Tomlins, Scott A; Chinnaiyan, Arul M; Palanisamy, Nallasivam

2014-09-01

The genetic basis of 50% to 60% of prostate cancer (PCa) is attributable to rearrangements in E26 transformation-specific (ETS) (ERG, ETV1, ETV4, and ETV5), BRAF, and RAF1 genes and overexpression of SPINK1. The development and validation of reliable detection methods are warranted to classify various molecular subtypes of PCa for diagnostic and prognostic purposes. ETS gene rearrangements are typically detected by fluorescence in situ hybridization and reverse-transcription polymerase chain reaction methods. Recently, monoclonal antibodies against ERG have been developed that detect the truncated ERG protein in immunohistochemical assays where staining levels are strongly correlated with ERG rearrangement status by fluorescence in situ hybridization. However, specific antibodies for ETV1, ETV4, and ETV5 are unavailable, challenging their clinical use. We developed a novel RNA in situ hybridization-based assay for the in situ detection of ETV1, ETV4, and ETV5 in formalin-fixed paraffin-embedded tissues from prostate needle biopsies, prostatectomy, and metastatic PCa specimens using RNA probes. Further, with combined RNA in situ hybridization and immunohistochemistry we identified a rare subset of PCa with dual ETS gene rearrangements in collisions of independent tumor foci. The high specificity and sensitivity of RNA in situ hybridization provides an alternate method enabling bright-field in situ detection of ETS gene aberrations in routine clinically available PCa specimens.
Triplex in-situ hybridization

Science.gov (United States)

Fresco, Jacques R.; Johnson, Marion D.

2002-01-01

Disclosed are methods for detecting in situ the presence of a target sequence in a substantially double-stranded nucleic acid segment, which comprises: a) contacting in situ under conditions suitable for hybridization a substantially double-stranded nucleic acid segment with a detectable third strand, said third strand being capable of hybridizing to at least a portion of the target sequence to form a triple-stranded structure, if said target sequence is present; and b) detecting whether hybridization between the third strand and the target sequence has occured.
Lack of detection of human papillomavirus infection by hybridization test in prostatic biopsies

International Nuclear Information System (INIS)

Gazzaz, Faten S; Mosli, Hisham A

2009-01-01

To explore the possibility of finding human papillomavirus (HPV) infection in the prostate tissue of a cohort of Saudi men presenting with benign prostatic hyperplasia (BPH) or prostate cancer. A cohort study on prospectively collected tissue samples was conducted at King Abdulaziz University Hospital (KAUH), Jeddah, Kingdom of Saudi Arabia from March 2007 to December 2008 on a total of 56 male patients, age range 50-93 years (average 68), diagnosed as having BPH or prostate cancer. The HPV DNA hybridization by hybrid capture 2 technology was performed on prostate biopsies of these patients to detect 18 types of HPV infection, and differentiate between 2 HPV DNA groups, the low-risk types, and the high/intermediate risk types.The tissues of all the prostatic biopsies were negative for HPV DNA. Our results, using the hybridization test, indicate that it is unlikely that HPV-16 or HPV-18, or the other tested subtypes, enhance the risk of prostate cancer. (author)
Detection of Protein Interactions in T3S Systems Using Yeast Two-Hybrid Analysis.

Science.gov (United States)

Nilles, Matthew L

2017-01-01

Two-hybrid systems, sometimes termed interaction traps, are genetic systems designed to find and analyze interactions between proteins. The most common systems are yeast based (commonly Saccharomyces cerevisae) and rely on the functional reconstitution of the GAL4 transcriptional activator. Reporter genes, such as the lacZ gene of Escherichia coli (encodes β-galactosidase), are placed under GAL4-dependent transcriptional control to provide quick and reliable detection of protein interactions. In this method the use of a yeast-based two-hybrid system is described to study protein interactions between components of type III secretion systems.
Detection of Methylobacterium radiotolerans IMBG290 in potato plants by in situ hybridization

Directory of Open Access Journals (Sweden)

Pirttila A. M.

2009-04-01

Full Text Available A new bacterial strain of pink-pigmented facultative methylotroph (M. radiotolerans IMBG290 which was previously isolated from in vitro grown potato plantlets after their inoculation with Pseudomonas fluorescens IMBG163 was detected in tissues by in situ hybridization method (ISH/FISH. The presence of Methylobacterium rRNA was observed in leaves and stems of potato plantlets, whereas no signal was detected in potato roots. The signal was less abundant in the untreated plants than in the plantlets infected with M. radiotolerans IMBG290.
Detection of TTV-DNA in PBMC using digoxigenin labelled probe by in situ hybridization

International Nuclear Information System (INIS)

Liu Yang; Qi Qige

2002-01-01

To determine TTV-DNA in PBMC in patients with viral hepatitis, a study of in situ hybridization using digoxigenin labelled probe by PCR method to the TTV ORF1 region was performed on PBMC. Results showed that the detection rate of TTV-DNA using double-stranded probe in TTV-DNA positive group in sera was 58.06 (18/31), and the detection rate of TTV-DNA using double-stranded probe in TTV-DNA negative group in sera was 27.59 (8/29). For TTV-DNA positive group detected by double- stranded probe, then we use negative- stranded probe to detect their replication. The detection rate was 22.2%(4/18). Conclusions: TTV can infect PBMC and replicate in PBMC
Tissue resonance interaction accurately detects colon lesions: A double-blind pilot study.

Science.gov (United States)

Dore, Maria P; Tufano, Marcello O; Pes, Giovanni M; Cuccu, Marianna; Farina, Valentina; Manca, Alessandra; Graham, David Y

2015-07-07

To investigated the performance of the tissue resonance interaction method (TRIM) for the non-invasive detection of colon lesions. We performed a prospective single-center blinded pilot study of consecutive adults undergoing colonoscopy at the University Hospital in Sassari, Italy. Before patients underwent colonoscopy, they were examined by the TRIMprobe which detects differences in electromagnetic properties between pathological and normal tissues. All patients had completed the polyethylene glycol-containing bowel prep for the colonoscopy procedure before being screened. During the procedure the subjects remained fully dressed. A hand-held probe was moved over the abdomen and variations in electromagnetic signals were recorded for 3 spectral lines (462-465 MHz, 930 MHz, and 1395 MHz). A single investigator, blind to any clinical information, performed the test using the TRIMprob system. Abnormal signals were identified and recorded as malignant or benign (adenoma or hyperplastic polyps). Findings were compared with those from colonoscopy with histologic confirmation. Statistical analysis was performed by χ(2) test. A total of 305 consecutive patients fulfilling the inclusion criteria were enrolled over a period of 12 months. The most frequent indication for colonoscopy was abdominal pain (33%). The TRIMprob was well accepted by all patients; none spontaneously complained about the procedure, and no adverse effects were observed. TRIM proved inaccurate for polyp detection in patients with inflammatory bowel disease (IBD) and they were excluded leaving 281 subjects (mean age 59 ± 13 years; 107 males). The TRIM detected and accurately characterized all 12 adenocarcinomas and 135/137 polyps (98.5%) including 64 adenomatous (100%) found. The method identified cancers and polyps with 98.7% sensitivity, 96.2% specificity, and 97.5% diagnostic accuracy, compared to colonoscopy and histology analyses. The positive predictive value was 96.7% and the negative predictive
Feasibility of using fluorescence in situ hybridization (FISH) to detect early gene changes in sputum cells from uranium miners

Energy Technology Data Exchange (ETDEWEB)

Neft, R.E.; Rogers, J.L.; Belinsky, S.A. [and others

1995-12-01

Epidemiological studies have shown that combined exposure to radon progeny and tobacco smoke produce a greater than additive or synergistic increase in lung cancer risk. Lung cancer results from multiple genetic changes over a long period of time. An early change that occurs in lung cancer is trisomy 7 which is found in 50% of non-small cell lung cancer and in the far margins of resected lung tumors. The 80% mortality associated with lung cancer is in part related to the high proportion of patients who present with an advanced, unresectable tumor. Therefore, early detection of patients at risk for tumor development is critical to improve treatment of this disease. Currently, it is difficult to detect lung cancer early while it is still amendable by surgery. Saccomanno, G. has shown that premalignant cytologic changes in sputum cells collected from uranium miners can be detected by a skilled, highly trained cytopathologist. A more objective alternative for identifying premalignant cells in sputum may be to determine whether an early genetic change such as trisomy 7 is present in these cells. Fluorescence in situ hybridization (FISH) can be used to identify cells with trisomy 7. The results of this investigation indicate that FISH may prove to be an accurate, efficient method to test at-risk individuals for genetic alterations in bronchial epithelial cells from sputum.
Feasibility of using fluorescence in situ hybridization (FISH) to detect early gene changes in sputum cells from uranium miners

International Nuclear Information System (INIS)

Neft, R.E.; Rogers, J.L.; Belinsky, S.A.

1995-01-01

Epidemiological studies have shown that combined exposure to radon progeny and tobacco smoke produce a greater than additive or synergistic increase in lung cancer risk. Lung cancer results from multiple genetic changes over a long period of time. An early change that occurs in lung cancer is trisomy 7 which is found in 50% of non-small cell lung cancer and in the far margins of resected lung tumors. The 80% mortality associated with lung cancer is in part related to the high proportion of patients who present with an advanced, unresectable tumor. Therefore, early detection of patients at risk for tumor development is critical to improve treatment of this disease. Currently, it is difficult to detect lung cancer early while it is still amendable by surgery. Saccomanno, G. has shown that premalignant cytologic changes in sputum cells collected from uranium miners can be detected by a skilled, highly trained cytopathologist. A more objective alternative for identifying premalignant cells in sputum may be to determine whether an early genetic change such as trisomy 7 is present in these cells. Fluorescence in situ hybridization (FISH) can be used to identify cells with trisomy 7. The results of this investigation indicate that FISH may prove to be an accurate, efficient method to test at-risk individuals for genetic alterations in bronchial epithelial cells from sputum
Accurate SERS detection of malachite green in aquatic products on basis of graphene wrapped flexible sensor.

Science.gov (United States)

Ouyang, Lei; Yao, Ling; Zhou, Taohong; Zhu, Lihua

2018-10-16

Malachite Green (MG) is a banned pesticide for aquaculture products. As a required inspection item, its fast and accurate determination before the products' accessing market is very important. Surface enhanced Raman scattering (SERS) is a promising tool for MG sensing, but it requires the overcoming of several problems such as fairly poor sensitivity and reproducibility, especially laser induced chemical conversion and photo-bleaching during SERS observation. By using a graphene wrapped Ag array based flexible membrane sensor, a modified SERS strategy was proposed for the sensitive and accurate detection of MG. The graphene layer functioned as an inert protector for impeding chemical transferring of the bioproduct Leucomalachite Green (LMG) to MG during the SERS detection, and as a heat transmitter for preventing laser induced photo-bleaching, which enables the separate detection of MG and LMG in fish extracts. The combination of the Ag array and the graphene cover also produced plentiful densely and uniformly distributed hot spots, leading to analytical enhancement factor up to 3.9 × 10 8 and excellent reproducibility (relative standard deviation low to 5.8% for 70 runs). The proposed method was easily used for MG detection with limit of detection (LOD) as low as 2.7 × 10 -11  mol L -1 . The flexibility of the sensor enable it have a merit for in-field fast detection of MG residues on the scale of a living fish through a surface extraction and paste transferring manner. The developed strategy was successfully applied in the analysis of real samples, showing good prospects for both the fast inspection and quantitative detection of MG. Copyright © 2018 Elsevier B.V. All rights reserved.
A PDMS/paper/glass hybrid microfluidic biochip integrated with aptamer-functionalized graphene oxide nano-biosensors for one-step multiplexed pathogen detection

OpenAIRE

Zuo, Peng; Li, XiuJun; Dominguez, Delfina C.; Ye, Bang-Ce

2013-01-01

Infectious pathogens often cause serious public health concerns throughout the world. There is an increasing demand for simple, rapid and sensitive approaches for multiplexed pathogen detection. In this paper we have developed a polydimethylsiloxane (PDMS)/paper/glass hybrid microfluidic system integrated with aptamer-functionalized graphene oxide (GO) nano-biosensors for simple, one-step, multiplexed pathogen detection. The paper substrate used in this hybrid microfluidic system facilitated ...
Hybrid Video Stabilization for Mobile Vehicle Detection on SURF in Aerial Surveillance

Directory of Open Access Journals (Sweden)

Gao Chunxian

2015-01-01

Full Text Available Detection of moving vehicles in aerial video sequences is of great importance with many promising applications in surveillance, intelligence transportation, or public service applications such as emergency evacuation and policy security. However, vehicle detection is a challenging task due to global camera motion, low resolution of vehicles, and low contrast between vehicles and background. In this paper, we present a hybrid method to efficiently detect moving vehicle in aerial videos. Firstly, local feature extraction and matching were performed to estimate the global motion. It was demonstrated that the Speeded Up Robust Feature (SURF key points were more suitable for the stabilization task. Then, a list of dynamic pixels was obtained and grouped for different moving vehicles by comparing the different optical flow normal. To enhance the precision of detection, some preprocessing methods were applied to the surveillance system, such as road extraction and other features. A quantitative evaluation on real video sequences indicated that the proposed method improved the detection performance significantly.
Hybrid online sensor error detection and functional redundancy for systems with time-varying parameters.

Science.gov (United States)

Feng, Jianyuan; Turksoy, Kamuran; Samadi, Sediqeh; Hajizadeh, Iman; Littlejohn, Elizabeth; Cinar, Ali

2017-12-01

Supervision and control systems rely on signals from sensors to receive information to monitor the operation of a system and adjust manipulated variables to achieve the control objective. However, sensor performance is often limited by their working conditions and sensors may also be subjected to interference by other devices. Many different types of sensor errors such as outliers, missing values, drifts and corruption with noise may occur during process operation. A hybrid online sensor error detection and functional redundancy system is developed to detect errors in online signals, and replace erroneous or missing values detected with model-based estimates. The proposed hybrid system relies on two techniques, an outlier-robust Kalman filter (ORKF) and a locally-weighted partial least squares (LW-PLS) regression model, which leverage the advantages of automatic measurement error elimination with ORKF and data-driven prediction with LW-PLS. The system includes a nominal angle analysis (NAA) method to distinguish between signal faults and large changes in sensor values caused by real dynamic changes in process operation. The performance of the system is illustrated with clinical data continuous glucose monitoring (CGM) sensors from people with type 1 diabetes. More than 50,000 CGM sensor errors were added to original CGM signals from 25 clinical experiments, then the performance of error detection and functional redundancy algorithms were analyzed. The results indicate that the proposed system can successfully detect most of the erroneous signals and substitute them with reasonable estimated values computed by functional redundancy system.
Applicability of major histocompatibility complex DRB1 alleles as markers to detect vertebrate hybridization: a case study from Iberian ibex × domestic goat in southern Spain

Directory of Open Access Journals (Sweden)

Alasaad Samer

2012-09-01

Full Text Available Abstract Background Hybridization between closely related wild and domestic species is of great concern because it can alter the evolutionary integrity of the affected populations. The high allelic variability of Major Histocompatibility Complex (MHC loci usually excludes them from being used in studies to detect hybridization events. However, if a the parental species don’t share alleles, and b one of the parental species possesses an exceptionally low number of alleles (to facilitate analysis, then even MHC loci have the potential to detect hybrids. Results By genotyping the exon2 of the MHC class II DRB1 locus, we were able to detect hybridization between domestic goats (Capra hircus and free-ranging Iberian ibex (Capra pyrenaica hispanica by molecular means. Conclusions This is the first documentation of a Capra pyrenaica × Capra hircus hybridization, which presented us the opportunity to test the applicability of MHC loci as new, simple, cost-effective, and time-saving approach to detect hybridization between wild species and their domesticated relatives, thus adding value to MHC genes role in animal conservation and management.
NATIONWIDE HYBRID CHANGE DETECTION OF BUILDINGS

Directory of Open Access Journals (Sweden)

V. Hron

2016-06-01

Full Text Available The Fundamental Base of Geographic Data of the Czech Republic (hereinafter FBGD is a national 2D geodatabase at a 1:10,000 scale with more than 100 geographic objects. This paper describes the design of the permanent updating mechanism of buildings in FBGD. The proposed procedure belongs to the category of hybrid change detection (HCD techniques which combine pixel-based and object-based evaluation. The main sources of information for HCD are cadastral information and bi-temporal vertical digital aerial photographs. These photographs have great information potential because they contain multispectral, position and also elevation information. Elevation information represents a digital surface model (DSM which can be obtained using the image matching technique. Pixel-based evaluation of bi-temporal DSMs enables fast localization of places with potential building changes. These coarse results are subsequently classified through the object-based image analysis (OBIA using spectral, textural and contextual features and GIS tools. The advantage of the two-stage evaluation is the pre-selection of locations where image segmentation (a computationally demanding part of OBIA is performed. It is not necessary to apply image segmentation to the entire scene, but only to the surroundings of detected changes, which contributes to significantly faster processing and lower hardware requirements. The created technology is based on open-source software solutions that allow easy portability on multiple computers and parallelization of processing. This leads to significant savings of financial resources which can be expended on the further development of FBGD.
Detection and quantification of Epstein-Barr virus EBER1 in EBV-infected cells by fluorescent in situ hybridization and flow cytometry

Science.gov (United States)

Stowe, R. P.; Cubbage, M. L.; Sams, C. F.; Pierson, D. L.; Barrett, A. D.

1998-01-01

A rapid and highly sensitive fluorescent in situ hybridization (FISH) assay was developed to detect Epstein Barr virus (EBV)-infected cells in peripheral blood. Multiple fluorescein-labeled antisense oligonucleotide probes were designed to hybridize to the EBER1 transcript, which is highly expressed in latently infected cells. After a rapid (30 min) hybridization, the cells were analyzed by flow cytometry. EBER1 was detected in several positive control cell lines that have variable numbers of EBV genome copies. No EBER1 was detected in two known EBV-negative cell lines. Northern blot analyses confirmed the presence and quantity of EBER1 transcripts in each cell line. This method was used to quantify the number of EBV-infected cells in peripheral blood from a patient with chronic mononucleosis. These results indicate that EBV-infected cells can be detected at the single cell level, and that this assay can be used to quantify the number of EBV-infected cells in clinical samples.
Hybrid simulation of scatter intensity in industrial cone-beam computed tomography

International Nuclear Information System (INIS)

Thierry, R.; Miceli, A.; Hofmann, J.; Flisch, A.; Sennhauser, U.

2009-01-01

A cone-beam computed tomography (CT) system using a 450 kV X-ray tube has been developed to challenge the three-dimensional imaging of parts of the automotive industry in short acquisition time. Because the probability of detecting scattered photons is high regarding the energy range and the area of detection, a scattering correction becomes mandatory for generating reliable images with enhanced contrast detectability. In this paper, we present a hybrid simulator for the fast and accurate calculation of the scattering intensity distribution. The full acquisition chain, from the generation of a polyenergetic photon beam, its interaction with the scanned object and the energy deposit in the detector is simulated. Object phantoms can be spatially described in form of voxels, mathematical primitives or CAD models. Uncollided radiation is treated with a ray-tracing method and scattered radiation is split into single and multiple scattering. The single scattering is calculated with a deterministic approach accelerated with a forced detection method. The residual noisy signal is subsequently deconvoluted with the iterative Richardson-Lucy method. Finally the multiple scattering is addressed with a coarse Monte Carlo (MC) simulation. The proposed hybrid method has been validated on aluminium phantoms with varying size and object-to-detector distance, and found in good agreement with the MC code Geant4. The acceleration achieved by the hybrid method over the standard MC on a single projection is approximately of three orders of magnitude.
Cardiac hybrid imaging

Energy Technology Data Exchange (ETDEWEB)

Gaemperli, Oliver [University Hospital Zurich, Cardiac Imaging, Zurich (Switzerland); University Hospital Zurich, Nuclear Cardiology, Cardiovascular Center, Zurich (Switzerland); Kaufmann, Philipp A. [University Hospital Zurich, Cardiac Imaging, Zurich (Switzerland); Alkadhi, Hatem [University Hospital Zurich, Institute of Diagnostic and Interventional Radiology, Zurich (Switzerland)

2014-05-15

Hybrid cardiac single photon emission computed tomography (SPECT)/CT imaging allows combined assessment of anatomical and functional aspects of cardiac disease. In coronary artery disease (CAD), hybrid SPECT/CT imaging allows detection of coronary artery stenosis and myocardial perfusion abnormalities. The clinical value of hybrid imaging has been documented in several subsets of patients. In selected groups of patients, hybrid imaging improves the diagnostic accuracy to detect CAD compared to the single imaging techniques. Additionally, this approach facilitates functional interrogation of coronary stenoses and guidance with regard to revascularization procedures. Moreover, the anatomical information obtained from CT coronary angiography or coronary artery calcium scores (CACS) adds prognostic information over perfusion data from SPECT. The use of cardiac hybrid imaging has been favoured by the dissemination of dedicated hybrid systems and the release of dedicated image fusion software, which allow simple patient throughput for hybrid SPECT/CT studies. Further technological improvements such as more efficient detector technology to allow for low-radiation protocols, ultra-fast image acquisition and improved low-noise image reconstruction algorithms will be instrumental to further promote hybrid SPECT/CT in research and clinical practice. (orig.)

Accurate Detection of Methicillin-Resistant Staphylococcus aureus in Mixtures by Use of Single-Bacterium Duplex Droplet Digital PCR.

Science.gov (United States)

Luo, Jun; Li, Junhua; Yang, Hang; Yu, Junping; Wei, Hongping

2017-10-01

Accurate and rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is needed to screen MRSA carriers and improve treatment. The current widely used duplex PCR methods are not able to differentiate MRSA from coexisting methicillin-susceptible S. aureus (MSSA) or other methicillin-resistant staphylococci. In this study, we aimed to develop a direct method for accurate and rapid detection of MRSA in clinical samples from open environments, such as nasal swabs. The new molecular assay is based on detecting the cooccurrence of nuc and mecA markers in a single bacterial cell by utilizing droplet digital PCR (ddPCR) with the chimeric lysin ClyH for cell lysis. The method consists of (i) dispersion of an intact single bacterium into nanoliter droplets, (ii) temperature-controlled release of genomic DNA (gDNA) by ClyH at 37°C, and (iii) amplification and detection of the markers ( nuc and mecA ) using standard TaqMan chemistries with ddPCR. Results were analyzed based on MRSA index ratios used for indicating the presence of the duplex-positive markers in droplets. The method was able to achieve an absolute limit of detection (LOD) of 2,900 CFU/ml for MRSA in nasal swabs spiked with excess amounts of Escherichia coli , MSSA, and other mecA -positive bacteria within 4 h. Initial testing of 104 nasal swabs showed that the method had 100% agreement with the standard culture method, while the normal duplex qPCR method had only about 87.5% agreement. The single-bacterium duplex ddPCR assay is rapid and powerful for more accurate detection of MRSA directly from clinical specimens. Copyright © 2017 American Society for Microbiology.
Utility of chromogenic in situ hybridization (CISH) for detection of EGFR amplification in glioblastoma: comparison with fluorescence in situ hybridization (FISH).

Science.gov (United States)

Fischer, Ingeborg; de la Cruz, Clarissa; Rivera, Andreana L; Aldape, Kenneth

2008-12-01

In this study, we test the reliability of chromogenic in situ hybridization (CISH) for the detection of epidermal growth factor receptor (EGFR) gene amplification in glioblastoma. Earlier reports have described EGFR CISH in glioblastoma multiforme, but a comparison of CISH with a "gold standard" testing method, such as fluorescence in situ hybridization (FISH), has not been described. Therapies targeting the EGFR-signaling pathway might increase the importance of assessment of EGFR-amplification status. CISH is a potential alternative to FISH as a testing method. To test its reliability, EGFR-amplification status by CISH was assessed in 89 cases of glioblastoma and compared with FISH results, and correlated with the protein expression using immunohistochemistry (IHC) for EGFR. FISH was scored as being EGFR-amplified in 47/89 tumors, CISH as being amplified in 43/89 tumors. The CISH and FISH results were in agreement in 83/89 cases (93%). Four glioblastomas were scored as being amplified by FISH, but not by CISH; whereas amplification was detected in 2 tumors by CISH that were not amplified using FISH. Forty-eight of the 89 cases were positive for EGFR expression by IHC. EGFR amplification was highly correlated with protein expression by IHC, as 40/48 (83%) EGFR IHC-positive cases were found to be EGFR-amplified. The high concordance of CISH and FISH for the assessment of EGFR gene-amplification status indicates that CISH is a viable alternative to FISH for the detection of EGFR gene amplification in glioblastoma. Detectable EGFR expression by IHC can occur in the absence of gene amplification, but is uncommon.
Study on sensitivity of southern blotting hybridization using a 32P-labeled probe of PCR products in detecting human cytomegalovirus

International Nuclear Information System (INIS)

Bu Hengfu; Chen Juan; Shen Rongsen; Ma Liren; Xu Yongqiang

1996-01-01

Southern blotting hybridization (SBH) using a 32 P-labeled probe is one of the most practical methods for genetic diagnosis of pathogen. On the basis of establishing PCR and nested PCR for detecting human cytomegalovirus (HCMV), a 32 P-labeled probe was prepared with the amplified products of 613 bp PCR outer primers and hybridized with 300 bp inner primer amplified product, resulting in increase in detecting sensitivity from 17 ng (in 1.2% agarose electrophoresis) before SBH to 500 pg (autoradiographed), in other words, increasing the sensitivity of detecting HCMV by 10 2 dilutions after using SBH. The method of PCR and SBH using a 32 P-labeled probe could detect less than 1 gene copy of HCMV, therefore, it is a rapid and reliable diagnosis method for detecting HCMV latent infection
Ultrahigh Responsivity and Detectivity Graphene-Perovskite Hybrid Phototransistors by Sequential Vapor Deposition

Science.gov (United States)

Chang, Po-Han; Liu, Shang-Yi; Lan, Yu-Bing; Tsai, Yi-Chen; You, Xue-Qian; Li, Chia-Shuo; Huang, Kuo-You; Chou, Ang-Sheng; Cheng, Tsung-Chin; Wang, Juen-Kai; Wu, Chih-I.

2017-04-01

In this work, graphene-methylammonium lead iodide (MAPbI3) perovskite hybrid phototransistors fabricated by sequential vapor deposition are demonstrated. Ultrahigh responsivity of 1.73 × 107 A W-1 and detectivity of 2 × 1015 Jones are achieved, with extremely high effective quantum efficiencies of about 108% in the visible range (450-700 nm). This excellent performance is attributed to the ultra-flat perovskite films grown by vapor deposition on the graphene sheets. The hybrid structure of graphene covered with uniform perovskite has high exciton separation ability under light exposure, and thus efficiently generates photocurrents. This paper presents photoluminescence (PL) images along with statistical analysis used to study the photo-induced exciton behavior. Both uniform and dramatic PL intensity quenching has been observed over entire measured regions, consistently demonstrating excellent exciton separation in the devices.
Development of real-time PCR and hybridization methods for detection and identification of thermophilic Campylobacter spp. in pig faecal samples

DEFF Research Database (Denmark)

Jensen, Annette Nygaard; Andersen, M. T.; Dalsgaard, Anders

2005-01-01

species-specific detection of Campylobacter spp. in naturally infected pig faecal samples after an enrichment step, whereas the hybridization approach enhanced the specific isolation of C. jejuni (present in minority to C. coli) from pigs. Conclusions: The rt-PCR was specific for Campylobacter jejuni, C...... by phenotypic methods and the developed rt-PCR provides an easy and fast method for such differentiation. Detection of C. jejuni by colony hybridization may increase the isolation rate of this species from pig faeces....
Double positive effect of adding hexaethyelene glycol when optimizing the hybridization efficiency of a microring DNA detection assay

Energy Technology Data Exchange (ETDEWEB)

Van Eeghem, Anabelle, E-mail: anabelle.vaneeghem@gmail.com [Polymer Chemistry and Biomaterials Research Group, Department of Organic and Macromolecular Chemistry, Ghent University (Belgium); Center for Nano- and Biophotonics, Ghent University (Belgium); Werquin, Sam [Center for Nano- and Biophotonics, Ghent University (Belgium); Photonics Research Group, Department of Information Technology, Ghent University – IMEC (Belgium); Hoste, Jan-Willem, E-mail: janwillem.hoste@ugent.be [Center for Nano- and Biophotonics, Ghent University (Belgium); Photonics Research Group, Department of Information Technology, Ghent University – IMEC (Belgium); Goes, Arne [Polymer Chemistry and Biomaterials Research Group, Department of Organic and Macromolecular Chemistry, Ghent University (Belgium); Agrosavfe NV, Technologiepark 4 (Bio-incubator), Zwijnaarde (Belgium); Vanderleyden, Els [Polymer Chemistry and Biomaterials Research Group, Department of Organic and Macromolecular Chemistry, Ghent University (Belgium); Center for Nano- and Biophotonics, Ghent University (Belgium); Bienstman, Peter [Center for Nano- and Biophotonics, Ghent University (Belgium); Photonics Research Group, Department of Information Technology, Ghent University – IMEC (Belgium); Dubruel, Peter [Polymer Chemistry and Biomaterials Research Group, Department of Organic and Macromolecular Chemistry, Ghent University (Belgium); Center for Nano- and Biophotonics, Ghent University (Belgium)

2017-05-31

Highlights: • The hybridization efficiency of a DNA assay was investigated based on SOI microring resonators. • A 4-fold increase in efficiency was obtained by using HEG as backfilling agent, as well as improving robustness. • The dual polarization microring technique shows that HEG reorients the DNA in an upright position. • Hybridizing at 35 °C and with a buffer containing 50 v/v% of formamide greatly improves the robustness. - Abstract: In this paper, a method for detection of DNA molecules using silicon-on-insulator (SOI) microring resonators is described. The influence of temperature and the use of formamide on the hybridization efficiency were studied. It was shown that 50 v/v% of formamide in the hybridization buffer can ensure hybridization when working close to physiological temperature. Furthermore, the use of hexaethylene glycol (HEG) as backfilling agent was studied in order to resolve issues of non-specific adsorption to the surface. The results indicated that not only non-specific binding was reduced significantly but also that HEG improves the orientation of the DNA probes on the surface. This led to a 4-fold increase in hybridization efficiency and thus in an equal decrease in the detection limit, compared to hybridization without the use of HEG. An improvement in robustness of the assay was also observed. This DNA reorientation hypothesis was confirmed by studying the thickness and density of the layers by using dual polarization microring sensing. Finally, the different steps in the sensing experiment were characterized in more detail by static contact angle (SCA) and X-ray photoelectron spectroscopy (XPS) analysis. The results showed quantitatively that the surface modifications were successful.
Amperometric glucose biosensor based on glucose oxidase dispersed in multiwalled carbon nanotubes/graphene oxide hybrid biocomposite

International Nuclear Information System (INIS)

Palanisamy, Selvakumar; Cheemalapati, Srikanth; Chen, Shen-Ming

2014-01-01

An amperometric glucose biosensor based on enhanced and fast direct electron transfer (DET) of glucose oxidase (GOx) at enzyme dispersed multiwalled carbon nanotubes/graphene oxide (MWCNT/GO) hybrid biocomposite was developed. The fabricated hybrid biocomposite was characterized by transmission electron microscopy (TEM), Raman and infrared spectroscopy (IR). The TEM image of hybrid biocomposite reveals that a thin layer of GOx was covered on the surface of MWCNT/GO hybrid composite. IR results validate that the hybrid biocomposite was formed through the electrostatic interactions between GOx and MWCNT/GO hybrid composite. Further, MWCNT/GO hybrid composite has also been characterized by TEM and UV–visible spectroscopy. A pair of well-defined redox peak was observed for GOx immobilized at the hybrid biocomposite electrode than that immobilized at the MWCNT modified electrode. The electron transfer rate constant (K s ) of GOx at the hybrid biocomposite was calculated to be 11.22 s −1 . The higher K s value revealed that fast DET of GOx occurred at the electrode surface. Moreover, fabricated biosensor showed a good sensitivity towards glucose oxidation over a linear range 0.05–23.2 mM. The limit of detection (LOD) was estimated to be 28 μM. The good features of the proposed biosensor could be used for the accurate detection of glucose in the biological samples. - Highlights: • An amperometric glucose biosensor has been developed at MWCNT/GO hybrid biocomposite. • Enhanced and fast direct electron transfer kinetics of glucose oxidase has been achieved at hybrid biocomposite. • Hybrid biocomposite has been characterized by TEM, IR and Raman spectroscopy. • Highly sensitive and selective for glucose determination
Amperometric glucose biosensor based on glucose oxidase dispersed in multiwalled carbon nanotubes/graphene oxide hybrid biocomposite

Energy Technology Data Exchange (ETDEWEB)

Palanisamy, Selvakumar; Cheemalapati, Srikanth; Chen, Shen-Ming, E-mail: smchen78@ms15.hinet.net

2014-01-01

An amperometric glucose biosensor based on enhanced and fast direct electron transfer (DET) of glucose oxidase (GOx) at enzyme dispersed multiwalled carbon nanotubes/graphene oxide (MWCNT/GO) hybrid biocomposite was developed. The fabricated hybrid biocomposite was characterized by transmission electron microscopy (TEM), Raman and infrared spectroscopy (IR). The TEM image of hybrid biocomposite reveals that a thin layer of GOx was covered on the surface of MWCNT/GO hybrid composite. IR results validate that the hybrid biocomposite was formed through the electrostatic interactions between GOx and MWCNT/GO hybrid composite. Further, MWCNT/GO hybrid composite has also been characterized by TEM and UV–visible spectroscopy. A pair of well-defined redox peak was observed for GOx immobilized at the hybrid biocomposite electrode than that immobilized at the MWCNT modified electrode. The electron transfer rate constant (K{sub s}) of GOx at the hybrid biocomposite was calculated to be 11.22 s{sup −1}. The higher K{sub s} value revealed that fast DET of GOx occurred at the electrode surface. Moreover, fabricated biosensor showed a good sensitivity towards glucose oxidation over a linear range 0.05–23.2 mM. The limit of detection (LOD) was estimated to be 28 μM. The good features of the proposed biosensor could be used for the accurate detection of glucose in the biological samples. - Highlights: • An amperometric glucose biosensor has been developed at MWCNT/GO hybrid biocomposite. • Enhanced and fast direct electron transfer kinetics of glucose oxidase has been achieved at hybrid biocomposite. • Hybrid biocomposite has been characterized by TEM, IR and Raman spectroscopy. • Highly sensitive and selective for glucose determination.
Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

Science.gov (United States)

Ramos, Enrique; Levinson, Benjamin T; Chasnoff, Sara; Hughes, Andrew; Young, Andrew L; Thornton, Katherine; Li, Allie; Vallania, Francesco L M; Province, Michael; Druley, Todd E

2012-12-06

reads against the entire genome using Novoalign followed by variant calling of non-indexed pools using SPLINTER or SAMtools for indexed samples. With these pipelines, we find sensitivity and specificity of 99.4% and 99.7% for pooled exome sequencing. Sensitivity, and to a lesser degree specificity, proved to be a function of coverage. For rare variants (≤2% minor allele frequency), we achieved sensitivity and specificity of ≥94.9% and ≥99.99% for custom capture of 2.5 Mb in multiplexed libraries of 22-48 individuals with only ≥5-fold coverage/chromosome, but these parameters improved to ≥98.7 and 100% with 20-fold coverage/chromosome. This highly scalable methodology enables accurate rare variant detection, with or without individual DNA sample indexing, while reducing the amount of required source DNA and total costs through less hybridization reagent consumption, multi-sample sonication in a standard PCR plate, multiplexed pre-enrichment pooling with a single hybridization and lesser sequencing coverage required to obtain high sensitivity.
Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing

Directory of Open Access Journals (Sweden)

Ramos Enrique

2012-12-01

. These results were obtained aligning raw reads against the entire genome using Novoalign followed by variant calling of non-indexed pools using SPLINTER or SAMtools for indexed samples. With these pipelines, we find sensitivity and specificity of 99.4% and 99.7% for pooled exome sequencing. Sensitivity, and to a lesser degree specificity, proved to be a function of coverage. For rare variants (≤2% minor allele frequency, we achieved sensitivity and specificity of ≥94.9% and ≥99.99% for custom capture of 2.5 Mb in multiplexed libraries of 22–48 individuals with only ≥5-fold coverage/chromosome, but these parameters improved to ≥98.7 and 100% with 20-fold coverage/chromosome. Conclusions This highly scalable methodology enables accurate rare variant detection, with or without individual DNA sample indexing, while reducing the amount of required source DNA and total costs through less hybridization reagent consumption, multi-sample sonication in a standard PCR plate, multiplexed pre-enrichment pooling with a single hybridization and lesser sequencing coverage required to obtain high sensitivity.
Fluorescence in situ hybridization on human metaphase chromosomes detected by near-field scanning optical microscopy

NARCIS (Netherlands)

Moers, M.H.P.; Moers, M.H.P.; Kalle, W.H.J.; Kalle, W.H.J.; Ruiter, A.G.T.; Wiegant, J.C.A.G.; Raap, A.K.; Greve, Jan; de Grooth, B.G.; van Hulst, N.F.

1996-01-01

Fluorescence in situ hybridization on human metaphase chromosomes is detected by near-field scanning optical microscopy. This combination of cytochemical and scanning probe techniques enables the localization and identification of several fluorescently labelled genomic DNA fragments on a single
A neural network detection system for lower-hybrid cavities in electron plasma density measured by the FREJA satellite

International Nuclear Information System (INIS)

Waldemark, J.; Karlsson, Jan

1995-03-01

This paper presents a lower-hybrid cavity detection system, CDS, for measurements of electron plasma density on the FREJA satellite wave experiment. The system can reduce the amount of data to be analysed by as much as 96% and still retain more than 85% of the desired information. The CDS is a combination of a hybrid neural network, HNN and expert rules. The HNN is a Self Organizing Map, SOM, combined with a feed forward back propagation neural net, BP. The CDS can be controlled by the user to operate with various degrees of sensitivity. Maximum detection capability is as high as 95% with data reduction lowered to 85%. 10 refs
Development of a Premature Stop Codon-detection method based on a bacterial two-hybrid system

Directory of Open Access Journals (Sweden)

Mayorga Luis S

2006-09-01

Full Text Available Abstract Background The detection of Premature Stop Codons (PSCs in human genes is very useful for the genetic diagnosis of different hereditary cancers, e.g. Familial Breast Cancer and Hereditary Non-Polyposis Colorectal Cancer (HNPCC. The products of these PSCs are truncated proteins, detectable in vitro by the Protein Truncation Test and in vivo by using the living translation machinery of yeast or bacteria. These living strategies are based on the construction of recombinant plasmids where the human sequence of interest is inserted upstream of a reporter gene. Although simple, these assays have their limitations. The yeast system requires extensive work to enhance its specificity, and the bacterial systems yield many false results due to translation re-initiation events occurring post PSCs. Our aim was to design a recombinant plasmid useful for detecting PSCs in human genes and resistant to bacterial translation re-initiation interferences. Results A functional recombinant plasmid (pREAL was designed based on a bacterial two-hybrid system. In our design, the in vivo translation of fused fragments of the Bordetella pertussis adenylate cyclase triggers the production of cAMP giving rise to a selectable bacterial phenotype. When a gene of interest is inserted between the two fragments, any PSC inhibits the enzymatic activity of the product, and translation re-initiation events post-PSC yield separated inactive fragments. We demonstrated that the system can accurately detect PSCs in human genes by inserting mutated fragments of the brca1 and msh2 gene. Western Blot assays revealed translation re-initiation events in all the tested colonies, implying that a simpler plasmid would not be resistant to this source of false negative results. The application of the system to a HNPCC family with a nonsense mutation in the msh2 gene correctly diagnosed wild type homozygous and heterozygous patients. Conclusion The developed pREAL is applicable to the
Carbon nanotube-polyamidoamine dendrimer hybrid-modified electrodes for highly sensitive electrochemical detection of microRNA24.

Science.gov (United States)

Li, Fengye; Peng, Jing; Zheng, Qiong; Guo, Xiang; Tang, Hao; Yao, Shouzhuo

2015-01-01

A simple and ultrasensitive microRNA (miRNA) electrochemical biosensor employing multiwalled carbon nanotube (MWCNT)-polyamidoamine (PAMAM) dendrimer and methylene blue (MB) redox indicator is reported in this work. The assay utilizes a glass carbon (GC) electrode modified with MWCNT-PAMAM, on which the oligonucleotide capture probes are immobilized. The electrochemical detection of miRNAs is completed by measuring the reduction signal change of MB before and after the probe hybridization with target miRNA (miRNA24 is used as a model case). The MWCNT-PAMAM/GC electrode shows greatly enhanced signal to MB reduction in contrast to bare GC electrode. The functionalization of MWCNT with PAMAM maintains the electrochemical property of MWCNT to MB reduction but minimizes the undesired adsorption of MB on the MWCNT surface. The effect of experimental variables on the miRNA detection is investigated and optimized. A detection limit of 0.5 fM and a linear peak current density-concentration relationship up to 100 nM are obtained following 60 min hybridization. The proposed assay is successfully used to detect miRNA24 in total RNA sample extracted from HeLa cells.
MOSFET-BJT hybrid mode of the gated lateral bipolar junction transistor for C-reactive protein detection.

Science.gov (United States)

Yuan, Heng; Kwon, Hyurk-Choon; Yeom, Se-Hyuk; Kwon, Dae-Hyuk; Kang, Shin-Won

2011-10-15

In this study, we propose a novel biosensor based on a gated lateral bipolar junction transistor (BJT) for biomaterial detection. The gated lateral BJT can function as both a BJT and a metal-oxide-semiconductor field-effect transistor (MOSFET) with both the emitter and source, and the collector and drain, coupled. C-reactive protein (CRP), which is an important disease marker in clinical examinations, can be detected using the proposed device. In the MOSFET-BJT hybrid mode, the sensitivity, selectivity, and reproducibility of the gated lateral BJT for biosensors were evaluated in this study. According to the results, in the MOSFET-BJT hybrid mode, the gated lateral BJT shows good selectivity and reproducibility. Changes in the emitter (source) current of the device for CRP antigen detection were approximately 0.65, 0.72, and 0.80 μA/decade at base currents of -50, -30, and -10 μA, respectively. The proposed device has significant application in the detection of certain biomaterials that require a dilution process using a common biosensor, such as a MOSFET-based biosensor. Copyright © 2011 Elsevier B.V. All rights reserved.
Evaluation of hybrids algorithms for mass detection in digitalized mammograms

International Nuclear Information System (INIS)

Cordero, Jose; Garzon Reyes, Johnson

2011-01-01

The breast cancer remains being a significant public health problem, the early detection of the lesions can increase the success possibilities of the medical treatments. The mammography is an image modality effective to early diagnosis of abnormalities, where the medical image is obtained of the mammary gland with X-rays of low radiation, this allows detect a tumor or circumscribed mass between two to three years before that it was clinically palpable, and is the only method that until now achieved reducing the mortality by breast cancer. In this paper three hybrids algorithms for circumscribed mass detection on digitalized mammograms are evaluated. In the first stage correspond to a review of the enhancement and segmentation techniques used in the processing of the mammographic images. After a shape filtering was applied to the resulting regions. By mean of a Bayesian filter the survivors regions were processed, where the characteristics vector for the classifier was constructed with few measurements. Later, the implemented algorithms were evaluated by ROC curves, where 40 images were taken for the test, 20 normal images and 20 images with circumscribed lesions. Finally, the advantages and disadvantages in the correct detection of a lesion of every algorithm are discussed.
Label-free DNA hybridization detection and single base-mismatch discrimination using CE-ICP-MS assay.

Science.gov (United States)

Li, Yan; Sun, Shao-kai; Yang, Jia-lin; Jiang, Yan

2011-12-07

Detecting a specific DNA sequence and discriminating single base-mismatch is critical to clinical diagnosis, paternity testing, forensic sciences, food and drug industry, pathology, genetics, environmental monitoring, and anti-bioterrorism. To this end, capillary electrophoresis (CE) coupled with the inductively coupled plasma mass spectrometry (ICP-MS) method is developed using the displacing interaction between the target ssDNA and the competitor Hg(2+) for the first time. The thymine-rich capture ssDNA 1 is interacted with the competitor Hg(2+), forming an assembled complex in a hairpin-structure between the thymine bases arrangement at both sides of the capture ssDNA 1. In the presence of a target ssDNA with stronger affinity than that of the competitor Hg(2+), the energetically favorable hybridization between capture ssDNA 1 and the target ssDNA destroys the hairpin-structure and releases the competitor as free Hg(2+), which was then read out and accurately quantified by CE-ICP-MS assay. Under the optimal CE separation conditions, free Hg(2+) ions and its capture ssDNA 1 adduct were baseline separated and detected on-line by ICP-MS; the increased peak intensity of free Hg(2+) against the concentration of perfectly complementary target ssDNA was linear over the concentration range of 30-600 nmol L(-1) with a limit of detection of 8 nmol L(-1) (3s, n = 11) in the pre-incubated mixture containing 1 μmol L(-1) Hg(2+) and 0.2 μmol L(-1) capture ssDNA 1. This new assay method is simple in design since any target ssDNA binding can in principle result in free Hg(2+) release by 6-fold Hg(2+) signal amplification, avoiding oligonucleotide labeling or assistance by excess signal transducer and signal reporter to read out the target. Due to element-specific detection of ICP-MS in our assay procedure, the interference from the autofluorescence of substrata was eliminated.
MicroRNA Detection by Whole-Mount In Situ Hybridization in C. elegans.

Science.gov (United States)

Andachi, Yoshiki; Kohara, Yuji

2018-01-01

MicroRNAs (miRNAs) loaded on argonaute proteins guide RNA-induced silencing complexes to target mRNAs. An excellent method to decipher the spatiotemporal expression patterns of miRNAs is whole-mount in situ hybridization (WISH), which has been successfully used in vertebrate embryos but still remains unavailable for many animal species. Here, we describe a WISH method for miRNA detection in Caenorhabditis elegans at both embryonic and post-embryonic stages. Strategies devised for detection include fixation of animals with carbodiimide at a high temperature and subsequent partial digestion of the fixed animals with an extremely high concentration of proteinase. WISH signals are visualized by staining with a chromogenic substrate or a fluorescent dye.
Application of fluorescence in situ hybridization technique in the diagnosis of acute promyelocytic leukemia with abnormal immunophenotype

International Nuclear Information System (INIS)

Chen Leilei; Sun Xuemei; Chen Junhao; Zhang Le

2005-01-01

To evaluate the utilization of fluorescence in situ hybridization (FISH) technique in the diagnosis of acute promyelocytic leukemia(APL) with abnormal immunophenotype, flow cytometry was used to detect the immunophenotype of mononuclear cells in APL patients and PML/RARα fusion gene was detected by FISH. The mononuclear cells of several APL patients showed abnormal immunophenotype: CD13 + , CD33 + , CD34 - , HLA-DR + and PML/RARα fusion gene was also detected, which was different from the regular result of APL: HLA- DR - , PML/RARα + . Therefore, the detection of immunophenotype in APL patients should not be regarded as the sole accurate target for diagnosing leukemia. FISH ,associated with traditional FAB classification, is a simple, rapid, accurate and direct method. It can be used to help confirm the diagnosis, to guide the formulation of a reasonable chemotherapy scheme and to supervise the efficacy of the treatment in patients with leukemia. (authors)
Label-free detection of DNA hybridization and single point mutations in a nano-gap biosensor

International Nuclear Information System (INIS)

Zaffino, R L; Mir, M; Samitier, J

2014-01-01

We describe a conductance-based biosensor that exploits DNA-mediated long-range electron transport for the label-free and direct electrical detection of DNA hybridization. This biosensor platform comprises an array of vertical nano-gap biosensors made of gold and fabricated through standard photolithography combined with focused ion beam lithography. The nano-gap walls are covalently modified with short, anti-symmetric thiolated DNA probes, which are terminated by 19 bases complementary to both the ends of a target DNA strand. The nano-gaps are separated by a distance of 50nm, which was adjusted to fit the length of the DNA target plus the DNA probes. The hybridization of the target DNA closes the gap circuit in a switch on/off fashion, in such a way that it is readily detected by an increase in the current after nano-gap closure. The nano-biosensor shows high specificity in the discrimination of base-pair mismatching and does not require signal indicators or enhancing molecules. The design of the biosensor platform is applicable for multiplexed detection in a straightforward manner. The platform is well-suited to mass production, point-of-care diagnostics, and wide-scale DNA analysis applications. (paper)

SNP data in the detection of hybridization levels between wild boar and domestic pig in Europe

DEFF Research Database (Denmark)

Iacolina, Laura; Bakan, Jana; Cubric-Curik, Vlatka

, a better understanding of hybridization patterns in Europe might have important implications for conservation and management of both wild populations and local breeds, as well as for the contingency of infectious diseases. Here we present the results for the analysis of 235 wild boars (WB; from 22 areas......, additionally, highlights the presence of several individuals, of both ancestries, with intermediate positions. This result was confirmed by Admixture analysis that detected the presence of hybrid individuals in both WB and local domestic pig breeds. The introgression level varies considerably among populations...
A hybrid Boundary Element Unstructured Transmission-line (BEUT) method for accurate 2D electromagnetic simulation

Energy Technology Data Exchange (ETDEWEB)

Simmons, Daniel, E-mail: daniel.simmons@nottingham.ac.uk; Cools, Kristof; Sewell, Phillip

2016-11-01

Time domain electromagnetic simulation tools have the ability to model transient, wide-band applications, and non-linear problems. The Boundary Element Method (BEM) and the Transmission Line Modeling (TLM) method are both well established numerical techniques for simulating time-varying electromagnetic fields. The former surface based method can accurately describe outwardly radiating fields from piecewise uniform objects and efficiently deals with large domains filled with homogeneous media. The latter volume based method can describe inhomogeneous and non-linear media and has been proven to be unconditionally stable. Furthermore, the Unstructured TLM (UTLM) enables modelling of geometrically complex objects by using triangular meshes which removes staircasing and unnecessary extensions of the simulation domain. The hybridization of BEM and UTLM which is described in this paper is named the Boundary Element Unstructured Transmission-line (BEUT) method. It incorporates the advantages of both methods. The theory and derivation of the 2D BEUT method is described in this paper, along with any relevant implementation details. The method is corroborated by studying its correctness and efficiency compared to the traditional UTLM method when applied to complex problems such as the transmission through a system of Luneburg lenses and the modelling of antenna radomes for use in wireless communications. - Graphical abstract:.
Detection of Mycobacterium tuberculosis in clinical samples by two-step polymerase chain reaction and nonisotopic hybridization methods.

OpenAIRE

Shawar, R M; el-Zaatari, F A; Nataraj, A; Clarridge, J E

1993-01-01

Detection of Mycobacterium tuberculosis in clinical specimens by the polymerase chain reaction (PCR) was compared with detection by culture. A 317-bp segment within the M. tuberculosis-specific insertion sequence IS6110 was amplified. The detection limit of the PCR assay for cultured mycobacteria was 50 cells per reaction by ethidium bromide-stained agarose gel electrophoresis and 5 cells per reaction by hybridization with an oligonucleotide probe conjugated with either digoxigenin or alkalin...
A simple and accurate onset detection method for a measured bell-shaped speed profile

Directory of Open Access Journals (Sweden)

Lior Botzer

2009-06-01

Full Text Available Motor control neuroscientists measure limb trajectories and extract the onset of the movement for a variety of purposes. Such trajectories are often aligned relative to the onset of individual movement before the features of that movement are extracted and their properties are inspected. Onset detection is performed either manually or automatically, typically by selecting a velocity threshold. Here, we present a simple onset detection algorithm that is more accurate than the conventional velocity threshold technique. The proposed method is based on a simple regression and follows the minimum acceleration with constraints model, in which the initial phase of the bell-shaped movement is modeled by a cubic power of the time. We demonstrate the performance of the suggested method and compare it to the velocity threshold technique and to manual onset detection by a group of motor control experts. The database for this comparison consists of simulated minimum jerk trajectories and recorded reaching movements.
Hybrid CMOS-Graphene Sensor Array for Subsecond Dopamine Detection.

Science.gov (United States)

Nasri, Bayan; Wu, Ting; Alharbi, Abdullah; You, Kae-Dyi; Gupta, Mayank; Sebastian, Sunit P; Kiani, Roozbeh; Shahrjerdi, Davood

2017-12-01

We introduce a hybrid CMOS-graphene sensor array for subsecond measurement of dopamine via fast-scan cyclic voltammetry (FSCV). The prototype chip has four independent CMOS readout channels, fabricated in a 65-nm process. Using planar multilayer graphene as biologically compatible sensing material enables integration of miniaturized sensing electrodes directly above the readout channels. Taking advantage of the chemical specificity of FSCV, we introduce a region of interest technique, which subtracts a large portion of the background current using a programmable low-noise constant current at about the redox potentials. We demonstrate the utility of this feature for enhancing the sensitivity by measuring the sensor response to a known dopamine concentration in vitro at three different scan rates. This strategy further allows us to significantly reduce the dynamic range requirements of the analog-to-digital converter (ADC) without compromising the measurement accuracy. We show that an integrating dual-slope ADC is adequate for digitizing the background-subtracted current. The ADC operates at a sampling frequency of 5-10 kHz and has an effective resolution of about 60 pA, which corresponds to a theoretical dopamine detection limit of about 6 nM. Our hybrid sensing platform offers an effective solution for implementing next-generation FSCV devices that can enable precise recording of dopamine signaling in vivo on a large scale.
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.
A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2.

Science.gov (United States)

Li, Jianli; Dai, Hongzheng; Feng, Yanming; Tang, Jia; Chen, Stella; Tian, Xia; Gorman, Elizabeth; Schmitt, Eric S; Hansen, Terah A A; Wang, Jing; Plon, Sharon E; Zhang, Victor Wei; Wong, Lee-Jun C

2015-09-01

Germline mutations in the DNA mismatch repair gene PMS2 underlie the cancer susceptibility syndrome, Lynch syndrome. However, accurate molecular testing of PMS2 is complicated by a large number of highly homologous sequences. To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2. Exonic deletions (E2 to E9, E5 to E9, E8, E10, E14, and E1 to E15), duplications (E11 to E12), and a nonsense mutation, p.S22*, were identified. Traditional multiplex ligation-dependent probe amplification and Sanger sequencing approaches cannot differentiate the origin of the exonic deletions in the 3' region when PMS2 and PMS2CL share identical sequences as a result of gene conversion. Our approach allows unambiguous identification of mutations in the active gene with a straightforward long-range-PCR/NGS method. Breakpoint analysis of multiple samples revealed that recurrent exon 14 deletions are mediated by homologous Alu sequences. Our comprehensive approach provides a reliable tool for accurate molecular analysis of genes containing multiple copies of highly homologous sequences and should improve PMS2 molecular analysis for patients with Lynch syndrome. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
Rapid detection of Cyprinid herpesvirus-3 (CyHV-3) using a gold nanoparticle-based hybridization assay.

Science.gov (United States)

Saleh, Mona; El-Matbouli, Mansour

2015-06-01

Cyprinid herpesvirus-3 (CyHV-3) is a highly infectious pathogen that causes fatal disease in common and koi carp Cyprinus carpio L. CyHV-3 detection is usually based on virus propagation or amplification of the viral DNA using the PCR or LAMP techniques. However, due to the limited susceptibility of cells used for propagation, it is not always possible to successfully isolate CyHV-3 even from tissue samples that have high virus titres. All previously described detection methods including PCR-based assays are time consuming, laborious and require specialized equipment. To overcome these limitations, gold nanoparticles (AuNPs) have been explored for direct and sensitive detection of DNA. In this study, a label-free colorimetric nanodiagnostic method for direct detection of unamplified CyHV-3 DNA using gold nanoparticles is introduced. Under appropriate conditions, DNA probes hybridize with their complementary target sequences in the sample DNA, which results in aggregation of the gold nanoparticles and a concomitant colour change from red to blue, whereas test samples with non complementary DNA sequences remain red. In this study, gold nanoparticles were used to develop and evaluate a specific and sensitive hybridization assay for direct and rapid detection of the highly infectious pathogen termed Cyprinid herpesvirus-3. Copyright © 2015 Elsevier B.V. All rights reserved.
The phase detection and calculation for low hybrid wave phase-feedback control system

International Nuclear Information System (INIS)

Liu Qiang; Liang Hao; Zhou Yongzhao; Shan Jiafang

2008-01-01

A method of phase detection and calculation for low hybrid wave phase-feedback control system and the implementing the algorithms on DSP cores embedded in FPGA is introduced. By taking the advantages of matlab-aided design and algorithms optimization to carry out parallel processing of multi-channel phase calculation in FPGA with rich resources, the purposed of fast phase-feedback control is achieved under the need of complicated mathematical operations. (authors)
Detection of a magnetic bead by hybrid nanodevices using scanning gate microscopy

Science.gov (United States)

Corte-León, H.; Krzysteczko, P.; Marchi, F.; Motte, J.-F.; Manzin, A.; Schumacher, H. W.; Antonov, V.; Kazakova, O.

2016-05-01

Hybrid ferromagnetic(Py)/non-magnetic metal(Au) junctions with a width of 400 nm are studied by magnetotransport measurements, magnetic scanning gate microscopy (SGM) with a magnetic bead (MB) attached to the probe, and micromagnetic simulations. In the transverse geometry, the devices demonstrate a characteristic magnetoresistive behavior that depends on the direction of the in plane magnetic field, with minimum/maximum variation when the field is applied parallel/perpendicular to the Py wire. The SGM is performed with a NdFeB bead of 1.6 μm diameter attached to the scanning probe. Our results demonstrate that the hybrid junction can be used to detect this type of MB. A rough approximation of the sensing volume of the junction has the shape of elliptical cylinder with the volume of ˜1.51 μm3. Micromagnetic simulations coupled to a magnetotransport model including anisotropic magnetoresistance and planar Hall effects are in good agreement with the experimental findings, enabling the interpretation of the SGM images.
Hyperbranched polyether hybrid nanospheres with CdSe quantum dots incorporated for selective detection of nitric oxide

DEFF Research Database (Denmark)

Liu, Shuiping; Jin, Lanming; Chronakis, Ioannis S.

2014-01-01

In this work, hybrid nanosphere vehicles consisting of cadmium selenide quantum dots (CdSe QDs) were synthesized for nitric oxide (NO) donating and real-time detecting. The nanospheres with QDs being encapsulation have spherical outline with dimension of ~127 nm. The fluorescence properties...
Simultaneous detection of P300 and steady-state visually evoked potentials for hybrid brain-computer interface.

Science.gov (United States)

Combaz, Adrien; Van Hulle, Marc M

2015-01-01

We study the feasibility of a hybrid Brain-Computer Interface (BCI) combining simultaneous visual oddball and Steady-State Visually Evoked Potential (SSVEP) paradigms, where both types of stimuli are superimposed on a computer screen. Potentially, such a combination could result in a system being able to operate faster than a purely P300-based BCI and encode more targets than a purely SSVEP-based BCI. We analyse the interactions between the brain responses of the two paradigms, and assess the possibility to detect simultaneously the brain activity evoked by both paradigms, in a series of 3 experiments where EEG data are analysed offline. Despite differences in the shape of the P300 response between pure oddball and hybrid condition, we observe that the classification accuracy of this P300 response is not affected by the SSVEP stimulation. We do not observe either any effect of the oddball stimulation on the power of the SSVEP response in the frequency of stimulation. Finally results from the last experiment show the possibility of detecting both types of brain responses simultaneously and suggest not only the feasibility of such hybrid BCI but also a gain over pure oddball- and pure SSVEP-based BCIs in terms of communication rate.
Sensitive detection of mercury and copper ions by fluorescent DNA/Ag nanoclusters in guanine-rich DNA hybridization.

Science.gov (United States)

Peng, Jun; Ling, Jian; Zhang, Xiu-Qing; Bai, Hui-Ping; Zheng, Liyan; Cao, Qiu-E; Ding, Zhong-Tao

2015-02-25

In this work, we designed a new fluorescent oligonucleotides-stabilized silver nanoclusters (DNA/AgNCs) probe for sensitive detection of mercury and copper ions. This probe contains two tailored DNA sequence. One is a signal probe contains a cytosine-rich sequence template for AgNCs synthesis and link sequence at both ends. The other is a guanine-rich sequence for signal enhancement and link sequence complementary to the link sequence of the signal probe. After hybridization, the fluorescence of hybridized double-strand DNA/AgNCs is 200-fold enhanced based on the fluorescence enhancement effect of DNA/AgNCs in proximity of guanine-rich DNA sequence. The double-strand DNA/AgNCs probe is brighter and stable than that of single-strand DNA/AgNCs, and more importantly, can be used as novel fluorescent probes for detecting mercury and copper ions. Mercury and copper ions in the range of 6.0-160.0 and 6-240 nM, can be linearly detected with the detection limits of 2.1 and 3.4 nM, respectively. Our results indicated that the analytical parameters of the method for mercury and copper ions detection are much better than which using a single-strand DNA/AgNCs. Copyright © 2014 Elsevier B.V. All rights reserved.
Accurate Identification of Cancerlectins through Hybrid Machine Learning Technology.

Science.gov (United States)

Zhang, Jieru; Ju, Ying; Lu, Huijuan; Xuan, Ping; Zou, Quan

2016-01-01

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.
Design of Passive Power Filter for Hybrid Series Active Power Filter using Estimation, Detection and Classification Method

Science.gov (United States)

Swain, Sushree Diptimayee; Ray, Pravat Kumar; Mohanty, K. B.

2016-06-01

This research paper discover the design of a shunt Passive Power Filter (PPF) in Hybrid Series Active Power Filter (HSAPF) that employs a novel analytic methodology which is superior than FFT analysis. This novel approach consists of the estimation, detection and classification of the signals. The proposed method is applied to estimate, detect and classify the power quality (PQ) disturbance such as harmonics. This proposed work deals with three methods: the harmonic detection through wavelet transform method, the harmonic estimation by Kalman Filter algorithm and harmonic classification by decision tree method. From different type of mother wavelets in wavelet transform method, the db8 is selected as suitable mother wavelet because of its potency on transient response and crouched oscillation at frequency domain. In harmonic compensation process, the detected harmonic is compensated through Hybrid Series Active Power Filter (HSAPF) based on Instantaneous Reactive Power Theory (IRPT). The efficacy of the proposed method is verified in MATLAB/SIMULINK domain and as well as with an experimental set up. The obtained results confirm the superiority of the proposed methodology than FFT analysis. This newly proposed PPF is used to make the conventional HSAPF more robust and stable.
Combined Hybrid DFE and CCK Remodulator for Medium-Range Single-Carrier Underwater Acoustic Communications

Directory of Open Access Journals (Sweden)

Xialin Jiang

2017-01-01

Full Text Available Advanced modulation and channel equalization techniques are essential for improving the performance of medium-range single-carrier underwater acoustic communications. In this paper, an enhanced detection scheme, hybrid time-frequency domain decision feedback equalizer (DFE combined with complementary code keying (CCK remodulator, is presented. CCK modulation technique provides strong tolerance to intersymbol interference caused by multipath propagation in underwater acoustic channels. The conventional hybrid DFE, using a frequency domain feedforward filter and a time domain feedback filter, provides good performance along with low computational complexity. The error propagation in the feedback filter, caused by feedbacking wrong decisions prior to CCK demodulation, may lead to great performance degradation. In our proposed scheme, with the help of CCK coding gain, more accurate remodulated CCK chips can be used as feedback. The proposed detection scheme is tested by the practical ocean experiments. The experimental results show that the proposed detection scheme ensures robust communications over 10-kilometre underwater acoustic channels with the data rate at 5 Kbits/s in 3 kHz of channel bandwidth.
Electrogenerated chemiluminescence detection for deoxyribonucleic acid hybridization based on gold nanoparticles carrying multiple probes

International Nuclear Information System (INIS)

Wang Hui; Zhang Chengxiao; Li Yan; Qi Honglan

2006-01-01

A novel sensitive electrogenerated chemiluminescence (ECL) method for the detection deoxyribonucleic acid (DNA) hybridization based on gold nanoparticles carrying multiple probes was developed. Ruthenium bis(2,2'-bipyridine)(2,2'-bipyridine-4,4'-dicarboxylic acid)-N-hydroxysuccinimide ester (Ru(bpy) 2 (dcbpy)NHS) was used as a ECL label and gold nanoparticle as a carrier. Probe single strand DNA (ss-DNA) was self-assembled at the 3'-terminal with a thiol group to the surface of gold nanoparticle and covalently labeled at the 5'-terminal of a phosphate group with Ru(bpy) 2 (dcbpy)NHS and the resulting conjugate (Ru(bpy) 2 (dcbpy)NHS)-ss-DNA-Au, was taken as a ECL probe. When target analyte ss-DNA was immobilized on a gold electrode by self-assembled monolayer technique and then hybridized with the ECL probe to form a double-stranded DNA (ds-DNA), a strong ECL response was electrochemically generated. The ECL intensity was linearly related to the concentration of the complementary sequence (target ss-DNA) in the range from 1.0 x 10 -11 to 1.0 x 10 -8 mol L -1 , and the linear regression equation was S = 57301 + 4579.6 lg C (unit of C is mol L -1 ). A detection limit of 5.0 x 10 -12 mol L -1 for target ss-DNA was achieved. The ECL signal generated from many reporters of ECL probe prepared is greatly amplified, compared to the convention scheme which is based on one reporter per hybridization event
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.
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.
Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.

Directory of Open Access Journals (Sweden)

Jie Zhu

Full Text Available DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.

Accurate Quantification of microRNA via Single Strand Displacement Reaction on DNA Origami Motif

Science.gov (United States)

Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

2013-01-01

DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs. PMID:23990889
Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.

Science.gov (United States)

Zhu, Jie; Feng, Xiaolu; Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

2013-01-01

DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.
Hybrid MWPC gamma ray detecting system for applications in nuclear medicine

Energy Technology Data Exchange (ETDEWEB)

Bateman, J E; Connolly, J F [Science Research Council, Chilton (UK). Rutherford Lab.

1978-10-15

Results are presented from prototype MWPC gas-solid hybrid imaging detectors designed for applications in nuclear medicine. Using a multi-section chamber with foil converter cathodes and a delay line readout technique, the authors have made a sup(99m)Tc imaging detector with a spatial resolution of 5 mm fwhm and a projected quantum efficiency of 15% for a full scale device. With lead foil cathodes the detector design yields similar spatial resolution and quantum efficiency when positron annihilation gammas are detected. Images of positron emitters (/sup 22/Na and /sup 68/Ga) are presented.
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
Reproducible Molecularly Imprinted Piezoelectric Sensor for Accurate and Sensitive Detection of Ractopamine in Swine and Feed Products

Directory of Open Access Journals (Sweden)

Mingfei Pan

2018-06-01

Full Text Available This paper describes the development of a reproducible molecularly imprinted piezoelectric sensor for the accurate and sensitive detection of ractopamine (RAC in swine and feed products. The synthesized molecularly imprinted polymer (MIP was directly immobilized on the surface of a quartz crystal microbalance (QCM Au chip as the recognition element. The experimental parameters in the fabrication, measurement and regeneration process were evaluated in detail to produce an MIP-based piezoelectric sensor with high sensing capability. The developed piezoelectric sensor was verified to perform favorably in the RAC analysis of swine and feed products, with acceptable accuracy (recovery: 75.9–93.3%, precision [relative standard deviation (n = 3: 2.3–6.4%], and sensitivity [limit of detection: 0.46 ng g−1 (swine and 0.38 ng g−1 (feed]. This portable MIP-based chip for the piezoelectric sensing of RAC could be reused for at least 30 cycles and easily stored for a long time. These results demonstrated that the developed MIP-based piezoelectric sensor presents an accurate, sensitive and cost-effective method for the quantitative detection of RAC in complex samples. This research offers a promising strategy for the development of novel effective devices used for use in food safety analysis.
Detection of Alien Oryza punctata Kotschy Chromosomes in Rice, Oryza sativa L., by Genomic in situ Hybridization

OpenAIRE

Yasui, Hideshi; Nonomura, Ken-ichi; Iwata, Nobuo; 安井, 秀; 野々村, 賢一; 岩田, 伸夫

1997-01-01

Genomic in situ hybridization (GIS H) using total Oryza punctata Kotschy genomic DNA as a probe was applied to detect alien chromosomes transferred from O. punctata (W1514: 2n=2x=24: BB) to O. sativa Japonica cultivar, Nipponbare (2n=2x=24: AA). Only 12 chromosomes in the interspecific hybrids (2n=3x=36: AAB) between autotetraploid of O. sativa cultivar Nipponbare and a diploid strain of O. punctata (W1514) showed intense staining by FITC in mitotic metaphase spreads. Only one homologous pair...
Facile synthesis of graphene hybrid tube-like structure for simultaneous detection of ascorbic acid, dopamine, uric acid and tryptophan

Energy Technology Data Exchange (ETDEWEB)

Zhang Wen [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Chai Yaqin, E-mail: yqchai@swu.edu.cn [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Yuan Ruo, E-mail: yuanruo@swu.edu.cn [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Chen Shihong; Han Jing; Yuan Dehua [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China)

2012-12-05

Graphical abstract: A tube-like structure of graphene hybrid (GS-PTCA) was synthesized via {pi}-{pi} stacking interaction, and was used as modifier to fabricate electrode for simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA) and tryptophan (Trp). SEM images of GS, PTCA and GS-PTCA were presented. Under the synergistic effects between GS and PTCA, the modified electrode displayed high catalytic activity and selectivity toward the oxidation of AA, DA, UA, and Trp. Highlights: Black-Right-Pointing-Pointer A simple strategy for simultaneous detection of AA, DA, UA and Trp has been constructed. Black-Right-Pointing-Pointer The tube-like structure of graphene hybrid (GS-PTCA) was synthesized. Black-Right-Pointing-Pointer The GS-PTCA provided a selective interface for discrimination of AA, DA, UA and Trp. - Abstract: In the present work, a tube-like structure of graphene hybrid as modifier to fabricate electrode for simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA) and tryptophan (Trp) was reported. The hybrid was synthesized by a simple method based on graphene sheets (GS) and 3,4,9,10-perylenetetracarboxylic acid (PTCA) via {pi}-{pi} stacking interaction under ultrasonic condition. The combination of GS and PTCA could effectively improve the dispersion of GS, owing to PTCA with the carboxylic-functionalized interface. Comparing with pure GS or PTCA modified electrode, GS-PTCA displayed high catalytic activity and selectivity toward the oxidation of AA, DA, UA, and Trp. Moreover, cyclic voltammetry, different pulse voltammetry and scanning electron microscopy were employed to characterize the sensors. The experiment results showed that the linear response range for simultaneous detection of AA, DA, UA, and Trp were 20-420 {mu}M, 0.40-374 {mu}M, 4-544 {mu}M and 0.40-138 {mu}M, respectively, and the detection limits were 5.60 {mu}M, 0.13 {mu}M, 0.92 {mu}M and 0.06 {mu}M (S/N = 3). Importantly, the proposed method offers
Hybrid islanding detection method by using grid impedance estimation in parallel-inverters-based microgrid

DEFF Research Database (Denmark)

Ghzaiel, Walid; Jebali-Ben Ghorbal, Manel; Slama-Belkhodja, Ilhem

2014-01-01

This paper presents a hybrid islanding detection algorithm integrated on the distributed generation unit more close to the point of common coupling of a Microgrid based on parallel inverters where one of them is responsible to control the system. The method is based on resonance excitation under...... parameters, both resistive and inductive parts, from the injected resonance frequency determination. Finally, the inverter will disconnect the microgrid from the faulty grid and reconnect the parallel inverter system to the controllable distributed system in order to ensure high power quality. This paper...... shows that grid impedance variation detection estimation can be an efficient method for islanding detection in microgrid systems. Theoretical analysis and simulation results are presented to validate the proposed method....
Endogenous field feedback promotes the detectability for exogenous electric signal in the hybrid coupled population

Energy Technology Data Exchange (ETDEWEB)

Wei, Xile; Zhang, Danhong; Wang, Jiang; Yu, Haitao, E-mail: htyu@tju.edu.cn [Tianjin Key Laboratory of Process Measurement and Control, School of Electrical Engineering and Automation, Tianjin University, Tianjin 300072 (China); Lu, Meili [School of Informational Technology and Engineering, Tianjin University of Technology and Education, Tianjin 300222 (China); Che, Yanqiu [School of Automation and Electrical Engineering, Tianjin University of Technology and Education, Tianjin 300222 (China)

2015-01-15

This paper presents the endogenous electric field in chemical or electrical synaptic coupled networks, aiming to study the role of endogenous field feedback in the signal propagation in neural systems. It shows that the feedback of endogenous fields to network activities can reduce the required energy of the noise and enhance the transmission of input signals in hybrid coupled populations. As a common and important nonsynaptic interactive method among neurons, particularly, the endogenous filed feedback can not only promote the detectability of exogenous weak signal in hybrid coupled neural population but also enhance the robustness of the detectability against noise. Furthermore, with the increasing of field coupling strengths, the endogenous field feedback is conductive to the stochastic resonance by facilitating the transition of cluster activities from the no spiking to spiking regions. Distinct from synaptic coupling, the endogenous field feedback can play a role as internal driving force to boost the population activities, which is similar to the noise. Thus, it can help to transmit exogenous weak signals within the network in the absence of noise drive via the stochastic-like resonance.
Endogenous field feedback promotes the detectability for exogenous electric signal in the hybrid coupled population.

Science.gov (United States)

Wei, Xile; Zhang, Danhong; Lu, Meili; Wang, Jiang; Yu, Haitao; Che, Yanqiu

2015-01-01

This paper presents the endogenous electric field in chemical or electrical synaptic coupled networks, aiming to study the role of endogenous field feedback in the signal propagation in neural systems. It shows that the feedback of endogenous fields to network activities can reduce the required energy of the noise and enhance the transmission of input signals in hybrid coupled populations. As a common and important nonsynaptic interactive method among neurons, particularly, the endogenous filed feedback can not only promote the detectability of exogenous weak signal in hybrid coupled neural population but also enhance the robustness of the detectability against noise. Furthermore, with the increasing of field coupling strengths, the endogenous field feedback is conductive to the stochastic resonance by facilitating the transition of cluster activities from the no spiking to spiking regions. Distinct from synaptic coupling, the endogenous field feedback can play a role as internal driving force to boost the population activities, which is similar to the noise. Thus, it can help to transmit exogenous weak signals within the network in the absence of noise drive via the stochastic-like resonance.
Endogenous field feedback promotes the detectability for exogenous electric signal in the hybrid coupled population

International Nuclear Information System (INIS)

Wei, Xile; Zhang, Danhong; Wang, Jiang; Yu, Haitao; Lu, Meili; Che, Yanqiu

2015-01-01

This paper presents the endogenous electric field in chemical or electrical synaptic coupled networks, aiming to study the role of endogenous field feedback in the signal propagation in neural systems. It shows that the feedback of endogenous fields to network activities can reduce the required energy of the noise and enhance the transmission of input signals in hybrid coupled populations. As a common and important nonsynaptic interactive method among neurons, particularly, the endogenous filed feedback can not only promote the detectability of exogenous weak signal in hybrid coupled neural population but also enhance the robustness of the detectability against noise. Furthermore, with the increasing of field coupling strengths, the endogenous field feedback is conductive to the stochastic resonance by facilitating the transition of cluster activities from the no spiking to spiking regions. Distinct from synaptic coupling, the endogenous field feedback can play a role as internal driving force to boost the population activities, which is similar to the noise. Thus, it can help to transmit exogenous weak signals within the network in the absence of noise drive via the stochastic-like resonance
Negative chemical ionization gas chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry and automated accurate mass data processing for determination of pesticides in fruit and vegetables.

Science.gov (United States)

Besil, Natalia; Uclés, Samanta; Mezcúa, Milagros; Heinzen, Horacio; Fernández-Alba, Amadeo R

2015-08-01

Gas chromatography coupled to high resolution hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS), operating in negative chemical ionization (NCI) mode and combining full scan with MSMS experiments using accurate mass analysis, has been explored for the automated determination of pesticide residues in fruit and vegetables. Seventy compounds were included in this approach where 50 % of them are not approved by the EU legislation. A global 76 % of the analytes could be identified at 1 μg kg(-1). Recovery studies were developed at three concentration levels (1, 5, and 10 μg kg(-1)). Seventy-seven percent of the detected pesticides at the lowest level yielded recoveries within the 70 %-120 % range, whereas 94 % could be quantified at 5 μg kg(-1), and the 100 % were determined at 10 μg kg(-1). Good repeatability, expressed as relative standard deviation (RSD home-made database was developed and applied to an automatic accurate mass data processing. Measured mass accuracies of the generated ions were mainly less than 5 ppm for at least one diagnostic ion. When only one ion was obtained in the single-stage NCI-MS, a representative product ion from MSMS experiments was used as identification criterion. A total of 30 real samples were analyzed and 67 % of the samples were positive for 12 different pesticides in the range 1.0-1321.3 μg kg(-1).
Multisensors Cooperative Detection Task Scheduling Algorithm Based on Hybrid Task Decomposition and MBPSO

Directory of Open Access Journals (Sweden)

Changyun Liu

2017-01-01

Full Text Available A multisensor scheduling algorithm based on the hybrid task decomposition and modified binary particle swarm optimization (MBPSO is proposed. Firstly, aiming at the complex relationship between sensor resources and tasks, a hybrid task decomposition method is presented, and the resource scheduling problem is decomposed into subtasks; then the sensor resource scheduling problem is changed into the match problem of sensors and subtasks. Secondly, the resource match optimization model based on the sensor resources and tasks is established, which considers several factors, such as the target priority, detecting benefit, handover times, and resource load. Finally, MBPSO algorithm is proposed to solve the match optimization model effectively, which is based on the improved updating means of particle’s velocity and position through the doubt factor and modified Sigmoid function. The experimental results show that the proposed algorithm is better in terms of convergence velocity, searching capability, solution accuracy, and efficiency.
Polymerase chain reaction-hybridization method using urease gene sequences for high-throughput Ureaplasma urealyticum and Ureaplasma parvum detection and differentiation.

Science.gov (United States)

Xu, Chen; Zhang, Nan; Huo, Qianyu; Chen, Minghui; Wang, Rengfeng; Liu, Zhili; Li, Xue; Liu, Yunde; Bao, Huijing

2016-04-15

In this article, we discuss the polymerase chain reaction (PCR)-hybridization assay that we developed for high-throughput simultaneous detection and differentiation of Ureaplasma urealyticum and Ureaplasma parvum using one set of primers and two specific DNA probes based on urease gene nucleotide sequence differences. First, U. urealyticum and U. parvum DNA samples were specifically amplified using one set of biotin-labeled primers. Furthermore, amine-modified DNA probes, which can specifically react with U. urealyticum or U. parvum DNA, were covalently immobilized to a DNA-BIND plate surface. The plate was then incubated with the PCR products to facilitate sequence-specific DNA binding. Horseradish peroxidase-streptavidin conjugation and a colorimetric assay were used. Based on the results, the PCR-hybridization assay we developed can specifically differentiate U. urealyticum and U. parvum with high sensitivity (95%) compared with cultivation (72.5%). Hence, this study demonstrates a new method for high-throughput simultaneous differentiation and detection of U. urealyticum and U. parvum with high sensitivity. Based on these observations, the PCR-hybridization assay developed in this study is ideal for detecting and discriminating U. urealyticum and U. parvum in clinical applications. Copyright © 2016 Elsevier Inc. All rights reserved.
Rapid and Simple Detection of Hot Spot Point Mutations of Epidermal Growth Factor Receptor, BRAF, and NRAS in Cancers Using the Loop-Hybrid Mobility Shift Assay

Science.gov (United States)

Matsukuma, Shoichi; Yoshihara, Mitsuyo; Kasai, Fumio; Kato, Akinori; Yoshida, Akira; Akaike, Makoto; Kobayashi, Osamu; Nakayama, Haruhiko; Sakuma, Yuji; Yoshida, Tsutomu; Kameda, Yoichi; Tsuchiya, Eiju; Miyagi, Yohei

2006-01-01

A simple and rapid method to detect the epidermal growth factor receptor hot spot mutation L858R in lung adenocarcinoma was developed based on principles similar to the universal heteroduplex generator technology. A single-stranded oligonucleotide with an internal deletion was used to generate heteroduplexes (loop-hybrids) bearing a loop in the complementary strand derived from the polymerase chain reaction product of the normal or mutant allele. By placing deletion in the oligonucleotide adjacent to the mutational site, difference in electrophoretic mobility between loop-hybrids with normal and mutated DNA was distinguishable in a native polyacrylamide gel. The method was also modified to detect in-frame deletion mutations of epidermal growth factor receptor in lung adenocarcinomas. In addition, the method was adapted to detect hot spot mutations in the B-type Raf kinase (BRAF) at V600 and in a Ras-oncogene (NRAS) at Q61, the mutations commonly found in thyroid carcinomas. Our mutation detection system, designated the loop-hybrid mobility shift assay was sensitive enough to detect mutant DNA comprising 7.5% of the total DNA. As a simple and straightforward mutation detection technique, loop-hybrid mobility shift assay may be useful for the molecular diagnosis of certain types of clinical cancers. Other applications are also discussed. PMID:16931592
Characteristic LDH isozyme electrophoretic patterns in six flatfish species in the Trondheimsfjord, Norway and their utility for the detection of natural species hybrids

KAUST Repository

He, Song

2014-11-19

Abstract: LDH isozyme electrophoretic patterns among 621 specimens of six different flatfish species collected in the Trondheimsfjord, Norway, were characterized by using the isoelectric focusing in polyacrylamide gel (IFPAG) technique. The LDH locus appears to be a reliable tool for species identification in the Trondheimsfjord flatfishes. Hence, these patterns were used to detect and identify potential hybrids, together with morphological traits. Among all the specimens collected during this study no hybrids were detected. From the actual numbers analysed, the natural hybridization rate between European plaice and European flounder in the Trondheimsfjord can be roughly estimated to be less than 1%. This is substantially lower than corresponding values reported from Baltic and Danish waters.
Characteristic LDH isozyme electrophoretic patterns in six flatfish species in the Trondheimsfjord, Norway and their utility for the detection of natural species hybrids

KAUST Repository

He, Song; Mork, Jarle

2014-01-01

Abstract: LDH isozyme electrophoretic patterns among 621 specimens of six different flatfish species collected in the Trondheimsfjord, Norway, were characterized by using the isoelectric focusing in polyacrylamide gel (IFPAG) technique. The LDH locus appears to be a reliable tool for species identification in the Trondheimsfjord flatfishes. Hence, these patterns were used to detect and identify potential hybrids, together with morphological traits. Among all the specimens collected during this study no hybrids were detected. From the actual numbers analysed, the natural hybridization rate between European plaice and European flounder in the Trondheimsfjord can be roughly estimated to be less than 1%. This is substantially lower than corresponding values reported from Baltic and Danish waters.
Development of an in situ hybridization assay for the detection of ostreid herpesvirus type 1 mRNAs in the Pacific oyster, Crassostrea gigas.

Science.gov (United States)

Corbeil, Serge; Faury, Nicole; Segarra, Amélie; Renault, Tristan

2015-01-01

An in situ hybridization protocol for detecting mRNAs of ostreid herpesvirus type 1 (OsHV-1) which infects Pacific oysters, Crassostrea gigas, was developed. Three RNA probes were synthesized by cloning three partial OsHV-1 genes into plasmids using three specific primer pairs, and performing a transcription in the presence of digoxigenin dUTP. The RNA probes were able to detect the virus mRNAs in paraffin sections of experimentally infected oysters 26 h post-injection. The in situ hybridization showed that the OsHV-1 mRNAs were mainly present in connective tissues in gills, mantle, adductor muscle, digestive gland and gonads. DNA detection by in situ hybridization using a DNA probe and viral DNA quantitation by real-time PCR were also performed and results were compared with those obtained using RNA probes. Copyright © 2014 Elsevier B.V. All rights reserved.
Detection of a magnetic bead by hybrid nanodevices using scanning gate microscopy

Directory of Open Access Journals (Sweden)

H. Corte-León

2016-05-01

Full Text Available Hybrid ferromagnetic(Py/non-magnetic metal(Au junctions with a width of 400 nm are studied by magnetotransport measurements, magnetic scanning gate microscopy (SGM with a magnetic bead (MB attached to the probe, and micromagnetic simulations. In the transverse geometry, the devices demonstrate a characteristic magnetoresistive behavior that depends on the direction of the in plane magnetic field, with minimum/maximum variation when the field is applied parallel/perpendicular to the Py wire. The SGM is performed with a NdFeB bead of 1.6 μm diameter attached to the scanning probe. Our results demonstrate that the hybrid junction can be used to detect this type of MB. A rough approximation of the sensing volume of the junction has the shape of elliptical cylinder with the volume of ∼1.51 μm3. Micromagnetic simulations coupled to a magnetotransport model including anisotropic magnetoresistance and planar Hall effects are in good agreement with the experimental findings, enabling the interpretation of the SGM images.
Electronic Detection of DNA Hybridization by Coupling Organic Field-Effect Transistor-Based Sensors and Hairpin-Shaped Probes

Directory of Open Access Journals (Sweden)

Corrado Napoli

2018-03-01

Full Text Available In this paper, the electronic transduction of DNA hybridization is presented by coupling organic charge-modulated field-effect transistors (OCMFETs and hairpin-shaped probes. These probes have shown interesting properties in terms of sensitivity and selectivity in other kinds of assays, in the form of molecular beacons (MBs. Their integration with organic-transistor based sensors, never explored before, paves the way to a new class of low-cost, easy-to-use, and portable genetic sensors with enhanced performances. Thanks to the peculiar characteristics of the employed sensor, measurements can be performed at relatively high ionic strengths, thus optimizing the probes’ functionality without affecting the detection ability of the device. A complete electrical characterization of the sensor is reported, including calibration with different target concentrations in the measurement environment and selectivity evaluation. In particular, DNA hybridization detection for target concentration as low as 100 pM is demonstrated.

From hybrid swarms to swarms of hybrids

Science.gov (United States)

Stohlgren, Thomas J.; Szalanski, Allen L; Gaskin, John F.; Young, Nicholas E.; West, Amanda; Jarnevich, Catherine S.; Tripodi, Amber

2014-01-01

Science has shown that the introgression or hybridization of modern humans (Homo sapiens) with Neanderthals up to 40,000 YBP may have led to the swarm of modern humans on earth. However, there is little doubt that modern trade and transportation in support of the humans has continued to introduce additional species, genotypes, and hybrids to every country on the globe. We assessed the utility of species distributions modeling of genotypes to assess the risk of current and future invaders. We evaluated 93 locations of the genus Tamarix for which genetic data were available. Maxent models of habitat suitability showed that the hybrid, T. ramosissima x T. chinensis, was slightly greater than the parent taxa (AUCs > 0.83). General linear models of Africanized honey bees, a hybrid cross of Tanzanian Apis mellifera scutellata and a variety of European honey bee including A. m. ligustica, showed that the Africanized bees (AUC = 0.81) may be displacing European honey bees (AUC > 0.76) over large areas of the southwestern U.S. More important, Maxent modeling of sub-populations (A1 and A26 mitotypes based on mDNA) could be accurately modeled (AUC > 0.9), and they responded differently to environmental drivers. This suggests that rapid evolutionary change may be underway in the Africanized bees, allowing the bees to spread into new areas and extending their total range. Protecting native species and ecosystems may benefit from risk maps of harmful invasive species, hybrids, and genotypes.
Fluorescence in situ hybridization detection of cytogenetic abnormalities and prognosis in multiple myeloma

Directory of Open Access Journals (Sweden)

Zhou Xu

2015-01-01

Full Text Available We evaluated the prognosis of patients with newly diagnosed multiple myeloma (MM and attempted to find a suitable treatment strategy for them. Interphase fluorescence in situ hybridization (FISH detection was performed on 57 patients with MM. The following probes: IgH, p53, 1q21, RB1, and D13S319 specific for the rearrangements of 14q32, 17p13, 1q21 and 13q14 were used. Fluorescent hybridization signals were observed using an Olympus BX60 epifluorescence microscope equipped with filters for detecting fluoroisothiocyanate (FITC, Texas red, and 4'-6-Diamidino-2-phenylindole (DAPI. Triple color clone-specific images were captured using a Quips XL genetic workstation. The mortalities in patients with moderate prognosis (66.7% and poor prognosis (50% were significantly higher compared with that in patients with good prognosis (15%, P<0.05. All the patients in good and moderate prognosis groups achieved complete remission (CR/very good partial remission (VGPR/partial remission (PR, whereas only half of the cases in the poor prognosis group reached this level. Patients 2 supported by autologous hematopoietic stem-cell transplantation presented CR/PR and long survival. For those with poor prognosis, a proper therapeutic regimen and timely transplantation, especially tandem transplantation, was necessary due to the rapid progression and complications.
Detection of Chrysanthemum stunt viroid (CSV) by nucleic acid spot hybridization

Energy Technology Data Exchange (ETDEWEB)

Bothma, G C

1985-01-01

Chrysanthemum stunt viroid (CSV) was extracted from Chrysanthemum stunt viroid-infected Chrysanthemum plants. The CSV was then purified to homogenicity from this extract by one cycle of non-denaturating vertical slab gel electrophoresis and was followed by one cycle of denaturating vertical slab gel electrophoresis. No pure circular CSV was obtained. The 3' terminal of purified ASBV was polyadenylated using poly (A) polymerase. The polyadenylated ASBV was used as a template to synthesise radioactively labelled single stranded ASBV cDNA using reverse transcriptase. The radioactively labelled recombinant DNA was hybridised to crude extracts from avocado leaves and chrysanthemum leaves. Autoradiography was employed to detect cDNA-RNA hybrids.
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; Noh, Yeonsik; Chong, Jo Woon; Cho, Chae Ho; McManus, Dave; Darling, Chad E; Mendelson, Yitzhak; Chon, Ki H

2017-09-01

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 nonusable part of the corrupted data. The term "nonusable" 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 dataset. 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 laboratory-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 laboratory-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
Sensitive electrochemiluminescence biosensor based on Au-ITO hybrid bipolar electrode amplification system for cell surface protein detection.

Science.gov (United States)

Wu, Mei-Sheng; Yuan, Da-Jing; Xu, Jing-Juan; Chen, Hong-Yuan

2013-12-17

Here we developed a novel hybrid bipolar electrode (BPE)-electrochemiluminescence (ECL) biosensor based on hybrid bipolar electrode (BPE) for the measurement of cancer cell surface protein using ferrocence (Fc) labeled aptamer as signal recognition and amplification probe. According to the electric neutrality of BPE, the cathode of U-shaped ITO BPE was electrochemically deposited by Au nanoparticles (NPs) to enhance its conductivity and surface area, decrease the overpotential of O2 reduction, which would correspondingly increase the oxidation current of Ru(bpy)3(2+)/tripropylamine (TPA) on the anode of BPE and resulting a ∼4-fold enhancement of ECL intensity. Then a signal amplification strategy was designed by introducing Fc modified aptamer on the anode surface of BPE through hybridization for detecting the amount of mucin-1 on MCF-7 cells. The presence of Fc could not only inhibit the oxidation of Ru(bpy)3(2+) because of its lower oxidation potential, its oxidation product Fc(+) could also quench the ECL of Ru(bpy)3(2+)/TPA by efficient energy-transfer from the excited-state Ru(bpy)3(2+)* to Fc(+), making the ECL intensity greatly quenched. On the basis of the cathodic Au NPs induced ECL enhancing coupled with anodic Fc induced signal quenching amplification, the approach allowed detection of mucin-1 aptamer at a concentration down to 0.5 fM and was capable of detecting a minimum of 20 MCF-7 cells. Besides, the amount of mucin-1 on MCF-7 cells was calculated to be 9041 ± 388 molecules/cell. This approach therefore shows great promise in bioanalysis.
Simple Objective Detection of Human Lyme Disease Infection Using Immuno-PCR and a Single Recombinant Hybrid Antigen

Science.gov (United States)

Halpern, Micah D.; Molins, Claudia R.; Schriefer, Martin

2014-01-01

A serology-based tiered approach has, to date, provided the most effective means of laboratory confirmation of clinically suspected cases of Lyme disease, but it lacks sensitivity in the early stages of disease and is often dependent on subjectively scored immunoblots. We recently demonstrated the use of immuno-PCR (iPCR) for detecting Borrelia burgdorferi antibodies in patient serum samples that were positive for Lyme disease. To better understand the performance of the Lyme disease iPCR assay, the repeatability and variability of the background of the assay across samples from a healthy population (n = 36) were analyzed. Both of these parameters were found to have coefficients of variation of Lyme disease patient serum samples (n = 12) demonstrated a strong correlation with that of 2-tier testing. Furthermore, a simplified iPCR approach using a single hybrid antigen and detecting only IgG antibodies confirmed the 2-tier diagnosis in the Lyme disease patient serum samples (n = 12). Validation of the hybrid antigen IgG iPCR assay using a blinded panel of Lyme disease and non-Lyme disease patient serum samples (n = 92) resulted in a sensitivity of 69% (95% confidence interval [CI], 50% to 84%), compared to that of the 2-tier analysis at 59% (95% CI, 41% to 76%), and a specificity of 98% (95% CI, 91% to 100%) compared to that of the 2-tier analysis at 97% (95% CI, 88% to 100%). A single-tier hybrid antigen iPCR assay has the potential to be an improved method for detecting host-generated antibodies against B. burgdorferi. PMID:24899074
A new nonlinear blind source separation method with chaos indicators for decoupling diagnosis of hybrid failures: A marine propulsion gearbox case with a large speed variation

International Nuclear Information System (INIS)

Li, Zhixiong; Peng, Z

2016-01-01

The normal operation of propulsion gearboxes ensures the ship safety. Chaos indicators could efficiently indicate the state change of the gearboxes. However, accurate detection of gearbox hybrid faults using Chaos indicators is a challenging task and the detection under speed variation conditions is attracting considerable attentions. Literature review suggests that the gearbox vibration is a kind of nonlinear mixture of variant vibration sources and the blind source separation (BSS) is reported to be a promising technique for fault vibration analysis, but very limited work has addressed the nonlinear BSS approach for hybrid faults decoupling diagnosis. Aiming to enhance the fault detection performance of Chaos indicators, this work presents a new nonlinear BSS algorithm for gearbox hybrid faults detection under a speed variation condition. This new method appropriately introduces the kernel spectral regression (KSR) framework into the morphological component analysis (MCA). The original vibration data are projected into the reproducing kernel Hilbert space (RKHS) where the instinct nonlinear structure in the original data can be linearized by KSR. Thus the MCA is able to deal with nonlinear BSS in the KSR space. Reliable hybrid faults decoupling is then achieved by this new nonlinear MCA (NMCA). Subsequently, by calculating the Chaos indicators of the decoupled fault components and comparing them with benchmarks, the hybrid faults can be precisely identified. Two specially designed case studies were implemented to evaluate the proposed NMCA-Chaos method on hybrid gear faults decoupling diagnosis. The performance of the NMCA-Chaos was compared with state of art techniques. The analysis results show high performance of the proposed method on hybrid faults detection in a marine propulsion gearbox with large speed variations.
Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

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Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

2018-04-01

One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community
Hybrid optical navigation by crater detection for lunar pin-point landing: trajectories from helicopter flight tests

Science.gov (United States)

Trigo, Guilherme F.; Maass, Bolko; Krüger, Hans; Theil, Stephan

2018-01-01

Accurate autonomous navigation capabilities are essential for future lunar robotic landing missions with a pin-point landing requirement, since in the absence of direct line of sight to ground control during critical approach and landing phases, or when facing long signal delays the herein before mentioned capability is needed to establish a guidance solution to reach the landing site reliably. This paper focuses on the processing and evaluation of data collected from flight tests that consisted of scaled descent scenarios where the unmanned helicopter of approximately 85 kg approached a landing site from altitudes of 50 m down to 1 m for a downrange distance of 200 m. Printed crater targets were distributed along the ground track and their detection provided earth-fixed measurements. The Crater Navigation (CNav) algorithm used to detect and match the crater targets is an unmodified method used for real lunar imagery. We analyze the absolute position and attitude solutions of CNav obtained and recorded during these flight tests, and investigate the attainable quality of vehicle pose estimation using both CNav and measurements from a tactical-grade inertial measurement unit. The navigation filter proposed for this end corrects and calibrates the high-rate inertial propagation with the less frequent crater navigation fixes through a closed-loop, loosely coupled hybrid setup. Finally, the attainable accuracy of the fused solution is evaluated by comparison with the on-board ground-truth solution of a dual-antenna high-grade GNSS receiver. It is shown that the CNav is an enabler for building autonomous navigation systems with high quality and suitability for exploration mission scenarios.
Label-free detection of DNA hybridization using transistors based on CVD grown graphene.

Science.gov (United States)

Chen, Tzu-Yin; Loan, Phan Thi Kim; Hsu, Chang-Lung; Lee, Yi-Hsien; Tse-Wei Wang, Jacob; Wei, Kung-Hwa; Lin, Cheng-Te; Li, Lain-Jong

2013-03-15

The high transconductance and low noise of graphene-based field-effect transistors based on large-area monolayer graphene produced by chemical vapor deposition are used for label-free electrical detection of DNA hybridization. The gate materials, buffer concentration and surface condition of graphene have been optimized to achieve the DNA detection sensitivity as low as 1 pM (10(-12) M), which is more sensitive than the existing report based on few-layer graphene. The graphene films obtained using conventional PMMA-assisted transfer technique exhibits PMMA residues, which degrade the sensing performance of graphene. We have demonstrated that the sensing performance of the graphene samples prepared by gold-transfer is largely enhanced (by 125%). Copyright © 2012 Elsevier B.V. All rights reserved.
Near infrared optical biosensor based on peptide functionalized single-walled carbon nanotubes hybrids for 2,4,6-trinitrotoluene (TNT) explosive detection.

Science.gov (United States)

Wang, Jin

2018-06-01

A near infrared (NIR) optical biosensor based on peptide functionalized single-walled carbon nanotubes (SWCNTs) hybrids for 2,4,6-trinitrotoluene (TNT) explosive detection was developed. The TNT binding peptide was directly anchored on the sidewall of the SWCNTs using the π-π interaction between the aromatic amino acids and SWCNTs, forming the peptide-SWCNTs hybrids for near infrared absorption spectra measurement. The evidence of the morphology of peptide-SWCNTs hybrids was obtained using atomic force microscopy (AFM). The results demonstrated that peptide-SWCNTs hybrids based NIR optical biosensor exhibited sensitive and highly selective for TNT explosive determination, addressing a promising optical biosensor for security application. Copyright © 2018. Published by Elsevier Inc.
Uncertainty characterization of particle depth measurement using digital in-line holography and the hybrid method.

Science.gov (United States)

Gao, Jian; Guildenbecher, Daniel R; Reu, Phillip L; Chen, Jun

2013-11-04

In the detection of particles using digital in-line holography, measurement accuracy is substantially influenced by the hologram processing method. In particular, a number of methods have been proposed to determine the out-of-plane particle depth (z location). However, due to the lack of consistent uncertainty characterization, it has been unclear which method is best suited to a given measurement problem. In this work, depth determination accuracies of seven particle detection methods, including a recently proposed hybrid method, are systematically investigated in terms of relative depth measurement errors and uncertainties. Both synthetic and experimental holograms of particle fields are considered at conditions relevant to particle sizing and tracking. While all methods display a range of particle conditions where they are most accurate, in general the hybrid method is shown to be the most robust with depth uncertainty less than twice the particle diameter over a wide range of particle field conditions.
Hybrid Models of Alternative Current Filter for Hvdc

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Ufa Ruslan A.

2017-01-01

Full Text Available Based on a hybrid simulation concept of HVDC, the developed hybrid AC filter models, providing the sufficiently full and adequate modeling of all single continuous spectrum of quasi-steady-state and transient processes in the filter, are presented. The obtained results suggest that usage of the hybrid simulation approach is carried out a methodically accurate with guaranteed instrumental error solution of differential equation systems of mathematical models of HVDC.
Hybrid quadrupole-orbitrap mass spectrometry analysis with accurate-mass database and parallel reaction monitoring for high-throughput screening and quantification of multi-xenobiotics in honey.

Science.gov (United States)

Li, Yi; Zhang, Jinzhen; Jin, Yue; Wang, Lin; Zhao, Wen; Zhang, Wenwen; Zhai, Lifei; Zhang, Yaping; Zhang, Yongxin; Zhou, Jinhui

2016-01-15

This study reports a rapid, automated screening and quantification method for the determination of multi-xenobiotic residues in honey using ultra-high performance liquid chromatography-hybrid quadrupole-Orbitrap mass spectrometry (UHPLC-Q-Orbitrap) with a user-built accurate-mass database plus parallel reaction monitoring (PRM). The database contains multi-xenobiotic information including formulas, adduct types, theoretical exact mass and retention time, characteristic fragment ions, ion ratios, and mass accuracies. A simple sample preparation method was developed to reduce xenobiotic loss in the honey samples. The screening method was validated based on retention time deviation, mass accuracy via full scan-data-dependent MS/MS (full scan-ddMS2), multi-isotope ratio, characteristic ion ratio, sensitivity, and positive/negative switching performance between the spiked sample and corresponding standard solution. The quantification method based on the PRM mode is a promising new quantitative tool which we validated in terms of selectivity, linearity, recovery (accuracy), repeatability (precision), decision limit (CCα), detection capability (CCβ), matrix effects, and carry-over. The optimized methods proposed in this study enable the automated screening and quantification of 157 compounds in less than 15 min in honey. The results of this study, as they represent a convenient protocol for large-scale screening and quantification, also provide a research approach for analysis of various contaminants in other matrices. Copyright © 2015 Elsevier B.V. All rights reserved.
Colorimetric microwell plate reverse-hybridization assay for Mycobacterium tuberculosis detection

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Candice Tosi Michelon

2011-03-01

Full Text Available Direct smear examination using Ziehl-Neelsen staining for pulmonary tuberculosis (PTB diagnosis is inexpensive and easy to use, but has the major limitation of low sensitivity. Rapid molecular methods are becoming more widely available in centralized laboratories, but they depend on timely reporting of results and strict quality assurance obtainable only from costly commercial kits available in high burden nations. This study describes a pre-commercial colorimetric method, Detect-TB, for detecting Mycobacterium tuberculosis DNA in which an oligonucleotide probe is fixed onto wells of microwell plates and hybridized with biotinylated polymerase chain reaction amplification products derived from clinical samples. The probe is capable of hybridising with the IS6110 insertion element and was used to specifically recognise the M. tuberculosis complex. When combined with an improved silica-based DNA extraction method, the sensitivity of the test was 50 colony-forming units of the M. tuberculosis reference strain H37Rv. The results that were in agreement with reference detection methods were observed in 95.2% (453/476 of samples included in the analysis. Sensitivity and specificity for 301 induced sputum samples and 175 spontaneous sputum samples were 85% and 98%, and 94% and 100%, respectively. This colorimetric method showed similar specificity to that described for commercially available kits and may provide an important contribution for PTB diagnosis.
Detection of KatG Gen Mutation on Mycobacterium Tuberculosis by Means of PCR-Dot Blot Hybridization with 32P Labeled Oligonucleotide Probe Methods

International Nuclear Information System (INIS)

Maria Lina R; Budiman Bela; Andi Yasmon

2009-01-01

Handling and controlling of tuberculosis, a disease caused by Mycobacterium tuberculosis (MTB), is now complicated since there are many MTBs that are resistant against anti-tuberculosis drugs such as isoniazid. The drug resistance could occurred due to the inadequate and un-regular drug utilization that cause gene mutation of the drug target such as katG gene for isoniazid. The molecular biology techniques such as the PCR- dot blot hybridization with radioisotope ( 32 P) labeled oligonucleotide probe, has been reported as a technique that is more sensitive and rapid for detection of gene mutations related with drug resistances. Hence, the aim of this study was to apply the PCR- dot blot hybridization technique using 32 P labeled oligonucleotide probe for detection of single mutation at codon 315 of katG gene of MTBs that rise the isoniazid resistance. In this study, we used 89 sputum specimens and a standard MTB (MTB H 37 RV) as a control. DNA extractions were performed by the BOOM method and the phenol chloroform for sputum samples and standard MTB, respectively. Primers used for PCR technique were Pt8 and Pt9 and RTB59 and RTB36 for detecting tuberculosis causing Mycobacterium and the existence of katG gene, respectively. Both of the primers are specific for IS6110 region and katG gene, respectively. PCR products were detected by an agarose gel electrophoresis technique. Dot blot hybridization with 32 P-oligonucleotide probe 315mu was performed to detect mutation at codon 315 of tested samples. Results of the PCR using primer Pt8 and Pt9 showed that all sputum specimens had positive results. Mutation detection by PCR- dot blot hybridization with 32 P-oligonucleotide probe 315mu, revealed that 11 of 89 tested samples had a mutation at their codon 315 of katG gene. Based upon these results, it is concluded that PCR-dot blot hybridization with 32 P-oligonucleotide probe is a technique that is rapid and highly specific and sensitive for detection of mutation at codon
Diagnostic performance of reduced-dose CT with a hybrid iterative reconstruction algorithm for the detection of hypervascular liver lesions: a phantom study

Energy Technology Data Exchange (ETDEWEB)

Nakamoto, Atsushi; Tanaka, Yoshikazu; Juri, Hiroshi; Nakai, Go; Narumi, Yoshifumi [Osaka Medical College, Department of Radiology, Takatsuki, Osaka (Japan); Yoshikawa, Shushi [Osaka Medical College Hospital, Central Radiology Department, Takatsuki, Osaka (Japan)

2017-07-15

To investigate the diagnostic performance of reduced-dose CT with a hybrid iterative reconstruction (IR) algorithm for the detection of hypervascular liver lesions. Thirty liver phantoms with or without simulated hypervascular lesions were scanned with a 320-slice CT scanner with control-dose (40 mAs) and reduced-dose (30 and 20 mAs) settings. Control-dose images were reconstructed with filtered back projection (FBP), and reduced-dose images were reconstructed with FBP and a hybrid IR algorithm. Objective image noise and the lesion to liver contrast-to-noise ratio (CNR) were evaluated quantitatively. Images were interpreted independently by 2 blinded radiologists, and jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Hybrid IR images with reduced-dose settings (both 30 and 20 mAs) yielded significantly lower objective image noise and higher CNR than control-dose FBP images (P <.05). However, hybrid IR images with reduced-dose settings had lower JAFROC1 figure of merit than control-dose FBP images, although only the difference between 20 mAs images and control-dose FBP images was significant for both readers (P <.01). An aggressive reduction of the radiation dose would impair the detectability of hypervascular liver lesions, although objective image noise and CNR would be preserved by a hybrid IR algorithm. (orig.)
A Smart DNA Tweezer for Detection of Human Telomerase Activity.

Science.gov (United States)

Xu, Xiaowen; Wang, Lei; Li, Kan; Huang, Qihong; Jiang, Wei

2018-03-06

Reliable and accurate detection of telomerase activity is crucial to better understand its role in cancer cells and to further explore its function in cancer diagnosis and treatment. Here, we construct a smart DNA tweezer (DT) for detection of telomerase activity. The DT is assembled by three specially designed single-stranded oligonucleotides: a central strand dually labeled with donor/acceptor fluorophores and two arm strands containing overhangs complementary to telomerase reaction products (TRPs). It can get closed through hybridization with TRPs and get reopen through strand displacement reaction by TRPs' complementary sequences. First, under the action of telomerase, telomerase binding substrates (TS) are elongated to generate TRPs ended with telomeric repeats (TTAGGG) n . TRPs hybridize with the two arm overhangs cooperatively and strain DT to closed state, inducing an increased fluorescence resonance energy transfer (FRET) efficiency, which is utilized for telomerase activity detection. Second, upon introduction of a removal strand (RS) complementary to TRPs, the closed DT is relaxed to open state via the toehold-mediated strand displacement, inducing a decreased FRET efficiency, which is utilized for determination of TRP length distribution. The detection limit of telomerase activity is equivalent to 141 cells/μL for HeLa cells, and telomerase-active cellular extracts can be differentiated from telomerase-inactive cellular extracts. Furthermore, TRPs owning 1, 2, 3, 4, and ≥5 telomeric repeats are identified to account for 25.6%, 20.5%, 15.7%, 12.5%, and 25.7%, respectively. The proposed strategy will offer a new approach for reliable, accurate detection of telomerase activity and product length distribution for deeper studying its role and function in cancer.
Hybrid Clustering And Boundary Value Refinement for Tumor Segmentation using Brain MRI

Science.gov (United States)

Gupta, Anjali; Pahuja, Gunjan

2017-08-01

The method of brain tumor segmentation is the separation of tumor area from Brain Magnetic Resonance (MR) images. There are number of methods already exist for segmentation of brain tumor efficiently. However it’s tedious task to identify the brain tumor from MR images. The segmentation process is extraction of different tumor tissues such as active, tumor, necrosis, and edema from the normal brain tissues such as gray matter (GM), white matter (WM), as well as cerebrospinal fluid (CSF). As per the survey study, most of time the brain tumors are detected easily from brain MR image using region based approach but required level of accuracy, abnormalities classification is not predictable. The segmentation of brain tumor consists of many stages. Manually segmenting the tumor from brain MR images is very time consuming hence there exist many challenges in manual segmentation. In this research paper, our main goal is to present the hybrid clustering which consists of Fuzzy C-Means Clustering (for accurate tumor detection) and level set method(for handling complex shapes) for the detection of exact shape of tumor in minimal computational time. using this approach we observe that for a certain set of images 0.9412 sec of time is taken to detect tumor which is very less in comparison to recent existing algorithm i.e. Hybrid clustering (Fuzzy C-Means and K Means clustering).
Clinical value of FDG hybrid-PET in staging and restaging of malignant lymphoma. Compared with conventional diagnostic methods

International Nuclear Information System (INIS)

Pichler, R.; Maschek, W.; Hatzl-Griesenhofer, M.; Huber, H.; Wimmer, G.; Wahl, G.; Fridrik, M.

2000-01-01

Aim of the present retrospective study was to validate the clinical value of F-18-FDG PET imaging in lymphoma patients with a dual head camera modified for coincidence detection. Staging before and after oncological treatment was compared with a conservative diagnostic approach. Methods: 48 patients (28 non-Hodgkin lymphoma, 20 Hodgkin's disease) received FDG-Hybrid-PET scans. Pretherapeutic staging was realized in 28 patients, 9 of them had control studies after they had completed therapy. Totally 29 persons were examined for posttherapeutic restaging. Computed tomography imaging and lymph node sonography was performed in all cases. Results were validated by clinical follow-up, in three cases a recidive was proven by biopsy. Results: CT and ultrasound detected 77 lesions in 28 patients compared with 100 visualized by PET, but this difference in pretherapeutic staging did not reach significance at p>0.05 by Fisher's t-test. Hybrid-PET obtained a sensitivity of 93%, a specifity of 79%, a positive of 82% and a negative predictive value of 92% for detection of residual disease. The values for CT+US were 87%, 64%, 72% and 88% respectively. Conclusion: FDG Hybrid-PET is as or even more accurate than standard morphologic diagnostic methods for prestaging in malignant lymphoma. Additionally, there is a substancial benefit for therapy monitoring of residual disease using coincidence detection PET with a 3/4-inch crystal gamma camera. (orig.) [de

Towards Fluorescence In Vivo Hybridization (FIVH) Detection of H. pylori in Gastric Mucosa Using Advanced LNA Probes

DEFF Research Database (Denmark)

Fontenete, Sílvia; Leite, Marina; Guimarães, Nuno

2015-01-01

acid (LNA)/ 2' O-methyl RNA (2'OMe) probe using standard phosphoramidite chemistry and FISH hybridization was then successfully performed both on adhered and suspended bacteria at 37°C. In this work we simplified, shortened and adapted FISH to work at gastric pH values, meaning that the hybridization...... step now takes only 30 minutes and, in addition to the buffer, uses only urea and probe at non-toxic concentrations. Importantly, the sensitivity and specificity of the FISH method was maintained in the range of conditions tested, even at low stringency conditions (e.g., low pH). In conclusion......In recent years, there have been several attempts to improve the diagnosis of infection caused by Helicobacter pylori. Fluorescence in situ hybridization (FISH) is a commonly used technique to detect H. pylori infection but it requires biopsies from the stomach. Thus, the development of an in vivo...
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. Copyright © 2014 Elsevier Ltd. All rights reserved.
High-Throughput Analysis of Plasma Hybrid Markers for Early Detection of Cancers

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Jung-hyun Rho

2014-01-01

Full Text Available Biomarkers for the early detection of cancer in the general population have to perform with high sensitivity and specificity in order to prevent the costs associated with over-diagnosis. There are only a few current tissue or blood markers that are recommended for generalized cancer screening. Despite the recognition that combinations of multiple biomarkers will likely improve their utility, biomarker panels are usually limited to a single class of molecules. Tissues and body fluids including plasma and serum contain not only proteins, DNA and microRNAs that are differentially expressed in cancers but further cancer specific information might be gleaned by comparing different classes of biomolecules. For example, the level of a certain microRNA might be related to the level of a particular protein in a cancer specific manner. Proteins might have cancer-specific post-translational modifications (e.g., phosphorylation or glycosylation or lead to the generation of autoantibodies. Most currently approved biomarkers are glycoproteins. Autoantibodies can be produced as a host’s early surveillance response to cancer-specific proteins in pre-symptomatic and pre-diagnostic stages of cancer. Thus, measurement of the level of a protein, the level of its glycosylation or phosphorylation and whether autoantibodies are produced to it can yield multi-dimensional information on each protein. We consider specific proteins that show consistent cancer-specific changes in two or three of these measurements to be “hybrid markers”. We hypothesize these markers will suffer less variation between different individuals since one component can act to “standardize” the other measurement. As a proof of principle, a 180 plasma sample set consisting of 120 cases (60 colon cancers and 60 adenomas and 60 controls were analyzed using our high-density antibody array for changes in their protein, IgG-complex and sialyl-Lewis A (SLeA modified proteins. At p < 0
Towards Fluorescence In Vivo Hybridization (FIVH) Detection of H. pylori in Gastric Mucosa Using Advanced LNA Probes

Science.gov (United States)

Fontenete, Sílvia; Leite, Marina; Guimarães, Nuno; Madureira, Pedro; Ferreira, Rui Manuel; Figueiredo, Céu; Wengel, Jesper; Azevedo, Nuno Filipe

2015-01-01

In recent years, there have been several attempts to improve the diagnosis of infection caused by Helicobacter pylori. Fluorescence in situ hybridization (FISH) is a commonly used technique to detect H. pylori infection but it requires biopsies from the stomach. Thus, the development of an in vivo FISH-based method (FIVH) that directly detects and allows the visualization of the bacterium within the human body would significantly reduce the time of analysis, allowing the diagnosis to be performed during endoscopy. In a previous study we designed and synthesized a phosphorothioate locked nucleic acid (LNA)/ 2’ O-methyl RNA (2’OMe) probe using standard phosphoramidite chemistry and FISH hybridization was then successfully performed both on adhered and suspended bacteria at 37°C. In this work we simplified, shortened and adapted FISH to work at gastric pH values, meaning that the hybridization step now takes only 30 minutes and, in addition to the buffer, uses only urea and probe at non-toxic concentrations. Importantly, the sensitivity and specificity of the FISH method was maintained in the range of conditions tested, even at low stringency conditions (e.g., low pH). In conclusion, this methodology is a promising approach that might be used in vivo in the future in combination with a confocal laser endomicroscope for H. pylori visualization. PMID:25915865
Towards Fluorescence In Vivo Hybridization (FIVH Detection of H. pylori in Gastric Mucosa Using Advanced LNA Probes.

Directory of Open Access Journals (Sweden)

Sílvia Fontenete

Full Text Available In recent years, there have been several attempts to improve the diagnosis of infection caused by Helicobacter pylori. Fluorescence in situ hybridization (FISH is a commonly used technique to detect H. pylori infection but it requires biopsies from the stomach. Thus, the development of an in vivo FISH-based method (FIVH that directly detects and allows the visualization of the bacterium within the human body would significantly reduce the time of analysis, allowing the diagnosis to be performed during endoscopy. In a previous study we designed and synthesized a phosphorothioate locked nucleic acid (LNA/ 2' O-methyl RNA (2'OMe probe using standard phosphoramidite chemistry and FISH hybridization was then successfully performed both on adhered and suspended bacteria at 37°C. In this work we simplified, shortened and adapted FISH to work at gastric pH values, meaning that the hybridization step now takes only 30 minutes and, in addition to the buffer, uses only urea and probe at non-toxic concentrations. Importantly, the sensitivity and specificity of the FISH method was maintained in the range of conditions tested, even at low stringency conditions (e.g., low pH. In conclusion, this methodology is a promising approach that might be used in vivo in the future in combination with a confocal laser endomicroscope for H. pylori visualization.
Detection of human papillomavirus by hybrid capture and real time PCR methods in patients with chronic cervicitis and cervical intraepithelial

Directory of Open Access Journals (Sweden)

Elisha Khandker

2016-07-01

Full Text Available Background and objectives:Cervical cancer due to Human papillomavirus (HPV is one of the leading causes of morbidity and mortality in women. Testing of HPV can identify women who are at risk of cervical cancer. Nowadays, molecular methods like real time polymerase chain reaction (PCR and hybrid capture technique are applied for detecting HPV in cervical specimens. The objective of the present study was to determine the rate of HPV infection in women with chronic cervicitis and cervical intraepithelial neoplasia (CIN by a commercial real time polymerase chain reaction test kit and by a hybrid capture HPV DNA test. Methods:Women aged between 20 to 55 years with chronic cervicitis and CIN were enrolled in the study after obtaining informed consent. Cervical specimen was collected by using cervical brush and stored in transport medium until used. HPV was detected by High Risk Screen Real-TM Quant 2x (Sacace, Biotechnologies SrI, Italy real time PCR kit (HR RT-PCR and by Hybrid Capture-2 High-Risk HPV DNA (Hc-2; Digene Corporation, USA test. Results: Total 72 women with chronic cervicitis and CIN of different grades were included in the study. Out of this, HPV infection detected by HR RT-PCR was 31 (43% and by Hc-2 was 14 (19.4%. Both the tests were able to detect HPV infection in all the CIN 3 cases and in most of the CIN 2 cases. However, HR RT-PCR detected higher number of HPV in chronic cervicitis and CIN1 cases. Conclusion:The study has shown that HR RT-PCR and Hc-2 tests are equally effective in detecting HPV infection in patients with CIN 2 and CIN 3 lesions. However, HR RT-PCR is more sensitive test for detecting HPV in chronic cervicitis and early CIN lesions and, therefore can be used in epidemiological study to detect presence of HPV in general population. IMC J Med Sci 2016; 10(2: 45-48
Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique.

Science.gov (United States)

Xiong, L Z; Xu, C G; Saghai Maroof, M A; Zhang, Q

1999-04-01

DNA methylation is known to play an important role in the regulation of gene expression in eukaryotes. In this study, we assessed the extent and pattern of cytosine methylation in the rice genome, using the technique of methylation-sensitive amplified polymorphism (MSAP), which is a modification of the amplified fragment length polymorphism (AFLP) method that makes use of the differential sensitivity of a pair of isoschizomers to cytosine methylation. The tissues assayed included seedlings and flag leaves of an elite rice hybrid, Shanyou 63, and the parental lines Zhenshan 97 and Minghui 63. In all, 1076 fragments, each representing a recognition site cleaved by either or both of the isoschizomers, were amplified using 16 pairs of selective primers. A total of 195 sites were found to be methylated at cytosines in one or both parents, and the two parents showed approximately the same overall degree of methylation (16.3%), as revealed by the incidence of differential digestion by the isoschizomers. Four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrid; increased methylation was detected in the hybrid compared to the parents at some of the recognition sites, while decreased methylation in the hybrid was detected at other sites. A small proportion of the sites was found to be differentially methylated in seedlings and flag leaves; DNA from young seedlings was methylated to a greater extent than that from flag leaves. Almost all of the methylation patterns detected by MSAP could be confirmed by Southern analysis using the isolated amplified fragments as probes. The results clearly demonstrate that the MSAP technique is highly efficient for large-scale detection of cytosine methylation in the rice genome. We believe that the technique can be adapted for use in other plant species.
DNA hybridization sensing for cytogenetic analysis

DEFF Research Database (Denmark)

Kwasny, Dorota; Dapra, Johannes; Brøgger, Anna Line

2013-01-01

are rearrangements between two chromosome arms that results in two derivative chromosomes having a mixed DNA sequence. The current detection method is a Fluorescent In situ Hybridization, which requires a use of expensive, fluorescently labeled probes that target the DNA sequences of two chromosomes involved...... in the translocation (Kwasny et al., 2012). We have developed a new double hybridization assay that allows for sorting of the DNA chromosomal fragments into separate compartment, moreover allowing for detection of the translocation. To detect the translocation it is necessary to determine that the two DNA sequences...... forming a derivative chromosome are connected, which is achieved by two subsequent hybridization steps. The first example of the translocation detection was presented on lab-on-a-disc using fluorescently labeled DNA fragments, representing the derivative chromosome (Brøgger et al., 2012). To allow...
Hybrid PAPR reduction scheme with Huffman coding and DFT-spread technique for direct-detection optical OFDM systems

Science.gov (United States)

Peng, Miao; Chen, Ming; Zhou, Hui; Wan, Qiuzhen; Jiang, LeYong; Yang, Lin; Zheng, Zhiwei; Chen, Lin

2018-01-01

High peak-to-average power ratio (PAPR) of the transmit signal is a major drawback in optical orthogonal frequency division multiplexing (OOFDM) system. In this paper, we propose and experimentally demonstrate a novel hybrid scheme, combined the Huffman coding and Discrete Fourier Transmission-Spread (DFT-spread), in order to reduce high PAPR in a 16-QAM short-reach intensity-modulated and direct-detection OOFDM (IMDD-OOFDM) system. The experimental results demonstrated that the hybrid scheme can reduce the PAPR by about 1.5, 2, 3 and 6 dB, and achieve 1.5, 1, 2.5 and 3 dB receiver sensitivity improvement compared to clipping, DFT-spread and Huffman coding and original OFDM signals, respectively, at an error vector magnitude (EVM) of -10 dB after transmission over 20 km standard single-mode fiber (SSMF). Furthermore, the throughput gain can be of the order of 30% by using the hybrid scheme compared with the cases of without applying the Huffman coding.
A whole-mount in situ hybridization method for microRNA detection in Caenorhabditis elegans.

Science.gov (United States)

Andachi, Yoshiki; Kohara, Yuji

2016-07-01

Whole-mount in situ hybridization (WISH) is an outstanding method to decipher the spatiotemporal expression patterns of microRNAs (miRNAs) and provides important clues for elucidating their functions. The first WISH method for miRNA detection was developed in zebrafish. Although this method was quickly adapted for other vertebrates and fruit flies, WISH analysis has not been successfully used to detect miRNAs in Caenorhabditis elegans Here, we show a novel WISH method for miRNA detection in C. elegans Using this method, mir-1 miRNA was detected in the body-wall muscle where the expression and roles of mir-1 miRNA have been previously elucidated. Application of the method to let-7 family miRNAs, let-7, mir-48, mir-84, and mir-241, revealed their distinct but partially overlapping expression patterns, indicating that miRNAs sharing a short common sequence were distinguishably detected. In pash-1 mutants that were depleted of mature miRNAs, signals of mir-48 miRNA were greatly reduced, suggesting that mature miRNAs were detected by the method. These results demonstrate the validity of WISH to detect mature miRNAs in C. elegans. © 2016 Andachi and Kohara; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Modification of ordinary-mode reflectometry system to detect lower-hybrid waves in Alcator C-Moda)

Science.gov (United States)

Baek, S. G.; Shiraiwa, S.; Parker, R. R.; Dominguez, A.; Kramer, G. J.; Marmar, E. S.

2012-10-01

Backscattering experiments to detect lower-hybrid (LH) waves have been performed in Alcator C-Mod, using the two modified channels (60 GHz and 75 GHz) of an ordinary-mode reflectometry system with newly developed spectral recorders that can continuously monitor spectral power at a target frequency. The change in the baseline of the spectral recorder during the LH wave injection is highly correlated to the strength of the X-mode non-thermal electron cyclotron emission. In high density plasmas where an anomalous drop in the lower hybrid current drive efficiency is observed, the observed backscattered signals are expected to be generated near the last closed flux surface, demonstrating the presence of LH waves within the plasma. This experimental technique can be useful in identifying spatially localized LH electric fields in the periphery of high-density plasmas.
Accurate treatment of solids with the HSE screened hybrid

Energy Technology Data Exchange (ETDEWEB)

Henderson, Thomas M.; Paier, Joachim; Scuseria, Gustavo E. [Department of Chemistry and Department of Physics and Astronomy, Rice University, Houston, TX 77005 (United States); Department of Physics and Astronomy, Rice University, Houston, TX 77005 (United States)

2011-04-15

Density functional theory (DFT) is the most widely used technique in the realm of first-principles electronic structure methods. Principally, this is because DFT in the Kohn-Sham (KS) formalism offers the appealing combination of relatively high accuracy and relatively low computational cost. Despite their great successes, traditional semilocal functionals fail to describe some important problems in solid state physics and materials science, the most conspicuous example being the notorious band gap problem. More sophisticated functionals providing greater accuracy without sacrificing computational efficiency are therefore needed. The Heyd-Scuseria-Ernzerhof (HSE) screened hybrid density functional [J. Heyd, G. E. Scuseria, and M. Ernzerhof, J. Chem. Phys. 118, 8207 (2003); J. Heyd and G. E. Scuseria, J. Chem. Phys. 121, 1187 (2004)] successfully addresses some of the chief problems which plague semilocal functionals by including only the important parts of exact nonlocal Hartree-Fock-type exchange. This work discusses some of the concepts underlying HSE and provides illustrative examples highlighting the successes of HSE in numerous solid state applications. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation

International Nuclear Information System (INIS)

Chen, Chung H.

2004-01-01

The objective of this program is to develop innovative DNA detection technologies to achieve fast microbial community assessment. The specific approaches are (1) to develop inexpensive and reliable sequence-proof hybridization DNA detection technology (2) to develop quantitative DNA hybridization technology for microbial community assessment and (3) to study the microbes which have demonstrated the potential to have nuclear waste bioremediation
The strategies of DNA immobilization and hybridization detection mechanism in the construction of electrochemical DNA sensor: A review

Directory of Open Access Journals (Sweden)

Jahwarhar Izuan Abdul Rashid

2017-11-01

Full Text Available In recent years, electrochemical deoxyribonucleic acid (DNA sensor has recently emerged as promising alternative clinical diagnostic devices especially for infectious disease by exploiting DNA recognition events and converting them into an electrochemical signal. This is because the existing DNA diagnostic method possesses certain drawbacks such as time-consuming, expensive, laborious, low selectivity and sensitivity. DNA immobilization strategies and mechanism of electrochemical detection are two the most important aspects that should be considered before developing highly selective and sensitive electrochemical DNA sensor. Here, we focus on some recent strategies for DNA probes immobilization on the surface of electrochemical transducer such as adsorption, covalent bonding and Avidin/Streptavidin-Biotin interaction on the electrode surface for specific interaction with its complementary DNA target. A numerous approach for DNA hybridization detection based electrochemical technique that frequently used including direct DNA electrochemical detection and label based electrochemical (redox-active indicator, enzyme label and nanoparticles were also discussed in aiming to provide general guide for the design of electrochemical DNA sensor. We also discussed the challenges and suggestions to improve the application of electrochemical DNA sensor at point-care setting. Keywords: Electrochemical DNA sensor, DNA immobilization, DNA hybridization, Electrochemical mechanism
Direct detection of lower hybrid wave using a reflectometer on Alcator C-Moda)

Science.gov (United States)

Shiraiwa, S.; Baek, S.; Dominguez, A.; Marmar, E.; Parker, R.; Kramer, G. J.

2010-10-01

The possibility of directly detecting a density perturbation produced by lower hybrid (LH) waves using a reflectometer is presented. We investigate the microwave scattering of reflectometer probe beams by a model density fluctuation produced by short wavelength LH waves in an Alcator C-Mod experimental condition. In the O-mode case, the maximum response of phase measurement is found to occur when the density perturbation is approximately centimeters in front of the antenna, where Bragg scattering condition is satisfied. In the X-mode case, the phase measurement is predicted to be more sensitive to the density fluctuation close to the cut-off layer. A feasibility test was carried out using a 50 GHz O-mode reflectometer on the Alcator C-Mod tokamak, and positive results including the detection of 4.6 GHz pump wave and parametric decay instabilities were obtained.
Detecting Cancer Quickly and Accurately

Science.gov (United States)

Gourley, Paul; McDonald, Anthony; Hendricks, Judy; Copeland, Guild; Hunter, John; Akhil, Ohmar; Capps, Heather; Curry, Marc; Skirboll, Steve

2000-03-01

We present a new technique for high throughput screening of tumor cells in a sensitive nanodevice that has the potential to quickly identify a cell population that has begun the rapid protein synthesis and mitosis characteristic of cancer cell proliferation. Currently, pathologists rely on microscopic examination of cell morphology using century-old staining methods that are labor-intensive, time-consuming and frequently in error. New micro-analytical methods for automated, real time screening without chemical modification are critically needed to advance pathology and improve diagnoses. We have teamed scientists with physicians to create a microlaser biochip (based upon our R&D award winning bio-laser concept)1 which evaluates tumor cells by quantifying their growth kinetics. The key new discovery was demonstrating that the lasing spectra are sensitive to the biomolecular mass in the cell, which changes the speed of light in the laser microcavity. Initial results with normal and cancerous human brain cells show that only a few hundred cells -- the equivalent of a billionth of a liter -- are required to detect abnormal growth. The ability to detect cancer in such a minute tissue sample is crucial for resecting a tumor margin or grading highly localized tumor malignancy. 1. P. L. Gourley, NanoLasers, Scientific American, March 1998, pp. 56-61. This work supported under DOE contract DE-AC04-94AL85000 and the Office of Basic Energy Sciences.
Electrochemical detection of avian influenza virus H5N1 gene sequence using a DNA aptamer immobilized onto a hybrid nanomaterial-modified electrode

International Nuclear Information System (INIS)

Liu Xianggang; Cheng Ziqiang; Fan Hai; Ai Shiyun; Han Ruixia

2011-01-01

Highlights: → A sensitive electrochemical biosensor for the detection of gene sequence was developed. → The biosensor was assembled by MWNT, polypyrrole nanowires and gold nanoparticles. → The hybrid nanomaterials could provide a porous structure with good properties. → The biosensor has highly selectivity and sensitivity. → The design strategy is expected to have extensive applications in other biosensors - Abstract: A sensitive electrochemical method for the detection of avian influenza virus (AIV) H5N1 gene sequence using a DNA aptamer immobilized onto a hybrid nanomaterial-modified electrode was developed. To enhance the selectivity and sensitivity, the modified electrode was assembled with multi-wall carbon nanotubes (MWNT), polypyrrole nanowires (PPNWs) and gold nanoparticles (GNPs). This electrode offered a porous structure with a large effective surface area, highly electrocatalytic activities and electronic conductivity. Therefore, the amount of DNA aptamer immobilized onto the electrode was increased while the accessibility of the detection target was maintained. The biosensor is based on the hybridization and preferred orientation of a DNA aptamer immobilized onto a modified electrode surface with its target (H5N1 specific sequence) present in solution. It is selective for the H5N1 specific sequence, and the signal of the indicator was approximately linear to log(concentration) of the H5N1 specific sequence from 5.0 x 10 -12 to 1.0 x 10 -9 M (R = 0.9863) with a detection limit of 4.3 x 10 -13 M. These studies showed that the new hybrid nanomaterial (MWNT/PPNWs/GNPs) and the DNA aptamer could be used to fabricate an electrochemical biosensor for gene sequence detection. Furthermore, this design strategy is expected to have extensive applications in other biosensors.
Electrochemical detection of avian influenza virus H5N1 gene sequence using a DNA aptamer immobilized onto a hybrid nanomaterial-modified electrode

Energy Technology Data Exchange (ETDEWEB)

Liu Xianggang [College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, Shandong (China); Cheng Ziqiang, E-mail: czqsd@126.com [College of Animal Science and Technology, Shandong Agricultural University, Taian 271018, Shandong (China); Fan Hai [College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, Shandong (China); Ai Shiyun, E-mail: ashy@sdau.edu.cn [College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, Shandong (China); Han Ruixia [College of Chemistry and Material Science, Shandong Agricultural University, Taian 271018, Shandong (China)

2011-07-15

Highlights: > A sensitive electrochemical biosensor for the detection of gene sequence was developed. > The biosensor was assembled by MWNT, polypyrrole nanowires and gold nanoparticles. > The hybrid nanomaterials could provide a porous structure with good properties. > The biosensor has highly selectivity and sensitivity. > The design strategy is expected to have extensive applications in other biosensors - Abstract: A sensitive electrochemical method for the detection of avian influenza virus (AIV) H5N1 gene sequence using a DNA aptamer immobilized onto a hybrid nanomaterial-modified electrode was developed. To enhance the selectivity and sensitivity, the modified electrode was assembled with multi-wall carbon nanotubes (MWNT), polypyrrole nanowires (PPNWs) and gold nanoparticles (GNPs). This electrode offered a porous structure with a large effective surface area, highly electrocatalytic activities and electronic conductivity. Therefore, the amount of DNA aptamer immobilized onto the electrode was increased while the accessibility of the detection target was maintained. The biosensor is based on the hybridization and preferred orientation of a DNA aptamer immobilized onto a modified electrode surface with its target (H5N1 specific sequence) present in solution. It is selective for the H5N1 specific sequence, and the signal of the indicator was approximately linear to log(concentration) of the H5N1 specific sequence from 5.0 x 10{sup -12} to 1.0 x 10{sup -9} M (R = 0.9863) with a detection limit of 4.3 x 10{sup -13} M. These studies showed that the new hybrid nanomaterial (MWNT/PPNWs/GNPs) and the DNA aptamer could be used to fabricate an electrochemical biosensor for gene sequence detection. Furthermore, this design strategy is expected to have extensive applications in other biosensors.
Application of Fluorescence In Situ Hybridization (FISH) Technique for the Detection of Genetic Aberration in Medical Science

Science.gov (United States)

Ratan, Zubair Ahmed; Zaman, Sojib Bin; Haidere, Mohammad Faisal; Runa, Nusrat Jahan; Akter, Nasrin

2017-01-01

Fluorescence in situ hybridization (FISH) is a macromolecule recognition technique, which is considered as a new advent in the field of cytology. Initially, it was developed as a physical mapping tool to delineate genes within chromosomes. The accuracy and versatility of FISH were subsequently capitalized upon in biological and medical research. This visually appealing technique provides an intermediate degree of resolution between DNA analysis and chromosomal investigations. FISH consists of a hybridizing DNA probe, which can be labeled directly or indirectly. In the case of direct labeling, fluorescent nucleotides are used, while indirect labeling is incorporated with reporter molecules that are subsequently detected by fluorescent antibodies or other affinity molecules. FISH is applied to detect genetic abnormalities that include different characteristic gene fusions or the presence of an abnormal number of chromosomes in a cell or loss of a chromosomal region or a whole chromosome. It is also applied in different research applications, such as gene mapping or the identification of novel oncogenes. This article reviews the concept of FISH, its application, and its advantages in medical science. PMID:28690958
Ratiometric fluorescence transduction by hybridization after isothermal amplification for determination of zeptomole quantities of oligonucleotide biomarkers with a paper-based platform and camera-based detection

Energy Technology Data Exchange (ETDEWEB)

Noor, M. Omair; Hrovat, David [Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada); Moazami-Goudarzi, Maryam [Department of Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada); Espie, George S. [Department of Cell and Systems Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada); Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada); Krull, Ulrich J., E-mail: ulrich.krull@utoronto.ca [Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6 (Canada)

2015-07-23

Highlights: • Solid-phase QD-FRET transduction of isothermal tHDA amplicons on paper substrates. • Ratiometric QD-FRET transduction improves assay precision and lowers the detection limit. • Zeptomole detection limit by an iPad camera after isothermal amplification. • Tunable assay sensitivity by immobilizing different amounts of QD–probe bioconjugates. - Abstract: Paper is a promising platform for the development of decentralized diagnostic assays owing to the low cost and ease of use of paper-based analytical devices (PADs). It can be challenging to detect on PADs very low concentrations of nucleic acid biomarkers of lengths as used in clinical assays. Herein we report the use of thermophilic helicase-dependent amplification (tHDA) in combination with a paper-based platform for fluorescence detection of probe-target hybridization. Paper substrates were patterned using wax printing. The cellulosic fibers were chemically derivatized with imidazole groups for the assembly of the transduction interface that consisted of immobilized quantum dot (QD)–probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as the acceptor dye in a fluorescence resonance energy transfer (FRET)-based transduction method. After probe-target hybridization, a further hybridization event with a reporter sequence brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs, triggering a FRET sensitized emission that served as an analytical signal. Ratiometric detection was evaluated using both an epifluorescence microscope and a low-cost iPad camera as detectors. Addition of the tHDA method for target amplification to produce sequences of ∼100 base length allowed for the detection of zmol quantities of nucleic acid targets using the two detection platforms. The ratiometric QD-FRET transduction method not only offered improved assay precision, but also lowered the limit of detection of the assay when compared with the non

Ratiometric fluorescence transduction by hybridization after isothermal amplification for determination of zeptomole quantities of oligonucleotide biomarkers with a paper-based platform and camera-based detection

International Nuclear Information System (INIS)

Noor, M. Omair; Hrovat, David; Moazami-Goudarzi, Maryam; Espie, George S.; Krull, Ulrich J.

2015-01-01

Highlights: • Solid-phase QD-FRET transduction of isothermal tHDA amplicons on paper substrates. • Ratiometric QD-FRET transduction improves assay precision and lowers the detection limit. • Zeptomole detection limit by an iPad camera after isothermal amplification. • Tunable assay sensitivity by immobilizing different amounts of QD–probe bioconjugates. - Abstract: Paper is a promising platform for the development of decentralized diagnostic assays owing to the low cost and ease of use of paper-based analytical devices (PADs). It can be challenging to detect on PADs very low concentrations of nucleic acid biomarkers of lengths as used in clinical assays. Herein we report the use of thermophilic helicase-dependent amplification (tHDA) in combination with a paper-based platform for fluorescence detection of probe-target hybridization. Paper substrates were patterned using wax printing. The cellulosic fibers were chemically derivatized with imidazole groups for the assembly of the transduction interface that consisted of immobilized quantum dot (QD)–probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as the acceptor dye in a fluorescence resonance energy transfer (FRET)-based transduction method. After probe-target hybridization, a further hybridization event with a reporter sequence brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs, triggering a FRET sensitized emission that served as an analytical signal. Ratiometric detection was evaluated using both an epifluorescence microscope and a low-cost iPad camera as detectors. Addition of the tHDA method for target amplification to produce sequences of ∼100 base length allowed for the detection of zmol quantities of nucleic acid targets using the two detection platforms. The ratiometric QD-FRET transduction method not only offered improved assay precision, but also lowered the limit of detection of the assay when compared with the non
Nucleic acid detection system and method for detecting influenza

Science.gov (United States)

Cai, Hong; Song, Jian

2015-03-17

The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.
A PDMS/paper/glass hybrid microfluidic biochip integrated with aptamer-functionalized graphene oxide nano-biosensors for one-step multiplexed pathogen detection.

Science.gov (United States)

Zuo, Peng; Li, XiuJun; Dominguez, Delfina C; Ye, Bang-Ce

2013-10-07

Infectious pathogens often cause serious public health concerns throughout the world. There is an increasing demand for simple, rapid and sensitive approaches for multiplexed pathogen detection. In this paper we have developed a polydimethylsiloxane (PDMS)/paper/glass hybrid microfluidic system integrated with aptamer-functionalized graphene oxide (GO) nano-biosensors for simple, one-step, multiplexed pathogen detection. The paper substrate used in this hybrid microfluidic system facilitated the integration of aptamer biosensors on the microfluidic biochip, and avoided complicated surface treatment and aptamer probe immobilization in a PDMS or glass-only microfluidic system. Lactobacillus acidophilus was used as a bacterium model to develop the microfluidic platform with a detection limit of 11.0 cfu mL(-1). We have also successfully extended this method to the simultaneous detection of two infectious pathogens - Staphylococcus aureus and Salmonella enterica. This method is simple and fast. The one-step 'turn on' pathogen assay in a ready-to-use microfluidic device only takes ~10 min to complete on the biochip. Furthermore, this microfluidic device has great potential in rapid detection of a wide variety of different other bacterial and viral pathogens.
How to perform RT-qPCR accurately in plant species? A case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population.

Science.gov (United States)

De Keyser, Ellen; Desmet, Laurence; Van Bockstaele, Erik; De Riek, Jan

2013-06-24

Flower colour variation is one of the most crucial selection criteria in the breeding of a flowering pot plant, as is also the case for azalea (Rhododendron simsii hybrids). Flavonoid biosynthesis was studied intensively in several species. In azalea, flower colour can be described by means of a 3-gene model. However, this model does not clarify pink-coloration. The last decade gene expression studies have been implemented widely for studying flower colour. However, the methods used were often only semi-quantitative or quantification was not done according to the MIQE-guidelines. We aimed to develop an accurate protocol for RT-qPCR and to validate the protocol to study flower colour in an azalea mapping population. An accurate RT-qPCR protocol had to be established. RNA quality was evaluated in a combined approach by means of different techniques e.g. SPUD-assay and Experion-analysis. We demonstrated the importance of testing noRT-samples for all genes under study to detect contaminating DNA. In spite of the limited sequence information available, we prepared a set of 11 reference genes which was validated in flower petals; a combination of three reference genes was most optimal. Finally we also used plasmids for the construction of standard curves. This allowed us to calculate gene-specific PCR efficiencies for every gene to assure an accurate quantification. The validity of the protocol was demonstrated by means of the study of six genes of the flavonoid biosynthesis pathway. No correlations were found between flower colour and the individual expression profiles. However, the combination of early pathway genes (CHS, F3H, F3'H and FLS) is clearly related to co-pigmentation with flavonols. The late pathway genes DFR and ANS are to a minor extent involved in differentiating between coloured and white flowers. Concerning pink coloration, we could demonstrate that the lower intensity in this type of flowers is correlated to the expression of F3'H. Currently in plant
Accurate Natural Trail Detection Using a Combination of a Deep Neural Network and Dynamic Programming.

Science.gov (United States)

Adhikari, Shyam Prasad; Yang, Changju; Slot, Krzysztof; Kim, Hyongsuk

2018-01-10

This paper presents a vision sensor-based solution to the challenging problem of detecting and following trails in highly unstructured natural environments like forests, rural areas and mountains, using a combination of a deep neural network and dynamic programming. The deep neural network (DNN) concept has recently emerged as a very effective tool for processing vision sensor signals. A patch-based DNN is trained with supervised data to classify fixed-size image patches into "trail" and "non-trail" categories, and reshaped to a fully convolutional architecture to produce trail segmentation map for arbitrary-sized input images. As trail and non-trail patches do not exhibit clearly defined shapes or forms, the patch-based classifier is prone to misclassification, and produces sub-optimal trail segmentation maps. Dynamic programming is introduced to find an optimal trail on the sub-optimal DNN output map. Experimental results showing accurate trail detection for real-world trail datasets captured with a head mounted vision system are presented.
Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.

Science.gov (United States)

Gillet-Markowska, Alexandre; Richard, Hugues; Fischer, Gilles; Lafontaine, Ingrid

2015-03-15

The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging. Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Photogrammetry: an accurate and reliable tool to detect thoracic musculoskeletal abnormalities in preterm infants.

Science.gov (United States)

Davidson, Josy; dos Santos, Amelia Miyashiro N; Garcia, Kessey Maria B; Yi, Liu C; João, Priscila C; Miyoshi, Milton H; Goulart, Ana Lucia

2012-09-01

To analyse the accuracy and reproducibility of photogrammetry in detecting thoracic abnormalities in infants born prematurely. Cross-sectional study. The Premature Clinic at the Federal University of São Paolo. Fifty-eight infants born prematurely in their first year of life. Measurement of the manubrium/acromion/trapezius angle (degrees) and the deepest thoracic retraction (cm). Digitised photographs were analysed by two blinded physiotherapists using a computer program (SAPO; http://SAPO.incubadora.fapesp.br) to detect shoulder elevation and thoracic retraction. Physical examinations performed independently by two physiotherapists were used to assess the accuracy of the new tool. Thoracic alterations were detected in 39 (67%) and in 40 (69%) infants by Physiotherapists 1 and 2, respectively (kappa coefficient=0.80). Using a receiver operating characteristic curve, measurement of the manubrium/acromion/trapezius angle and the deepest thoracic retraction indicated accuracy of 0.79 and 0.91, respectively. For measurement of the manubrium/acromion/trapezius angle, the Bland and Altman limits of agreement were -6.22 to 7.22° [mean difference (d)=0.5] for repeated measures by one physiotherapist, and -5.29 to 5.79° (d=0.75) between two physiotherapists. For thoracic retraction, the intra-rater limits of agreement were -0.14 to 0.18cm (d=0.02) and the inter-rater limits of agreement were -0.20 to -0.17cm (d=0.02). SAPO provided an accurate and reliable tool for the detection of thoracic abnormalities in preterm infants. Copyright © 2011 Chartered Society of Physiotherapy. Published by Elsevier Ltd. All rights reserved.
Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

Science.gov (United States)

Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

2016-05-13

Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content.
Electrochemiluminescence polymerase chain reaction detection of genetically modified organisms

International Nuclear Information System (INIS)

Liu Jinfeng; Xing Da; Shen Xingyan; Zhu Debin

2005-01-01

With the development of biotechnology, more and more genetically modified organisms (GMOs) have entered commercial market. Because of the safety concerns, detection and characterization of GMOs have attracted much attention recently. Electrochemiluminescence (ECL) method is a chemiluminescent (CL) reaction of species generated electrochemically on an electrode surface. It is a highly efficient and accurate detection method. In this paper, ECL polymerase chain reaction (PCR) combined with two types of nucleic acid probes hybridization was applied to detect GMOs for the first time. Whether the organisms contain GM components was discriminated by detecting the cauliflower mosaic virus 35S (CaMV35S) promoter and nopaline synthase (NOS) terminator. The experiment results show that the detection limit is 100 fmol of PCR products. The promoter and the terminator can be clearly detected in GMOs. The method may provide a new means for the detection of GMOs due to its simplicity and high efficiency
Accurate method for luminous transmittance and signal detection quotients measurements in sunglasses lenses

Science.gov (United States)

Loureiro, A. D.; Gomes, L. M.; Ventura, L.

2018-02-01

The international standard ISO 12312-1 proposes transmittance tests that quantify how dark sunglasses lenses are and whether or not they are suitable for driving. To perform these tests a spectrometer is required. In this study, we present and analyze theoretically an accurate alternative method for performing these measurements using simple components. Using three LEDs and a four-channel sensor we generated weighting functions similar to the standard ones for luminous and traffic lights transmittances. From 89 sunglasses lens spectroscopy data, we calculated luminous transmittance and signal detection quotients using our obtained weighting functions and the standard ones. Mean-difference Tukey plots were used to compare the results. All tested sunglasses lenses were classified in the right category and correctly as suitable or not for driving. The greatest absolute errors for luminous transmittance and red, yellow, green and blue signal detection quotients were 0.15%, 0.17, 0.06, 0.04 and 0.18, respectively. This method will be used in a device capable to perform transmittance tests (visible, traffic lights and ultraviolet (UV)) according to the standard. It is important to measure rightly luminous transmittance and relative visual attenuation quotients to report correctly whether or not sunglasses are suitable for driving. Moreover, standard UV requirements depend on luminous transmittance.
A Paper-Based Sandwich Format Hybridization Assay for Unlabeled Nucleic Acid Detection Using Upconversion Nanoparticles as Energy Donors in Luminescence Resonance Energy Transfer.

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Zhou, Feng; Noor, M Omair; Krull, Ulrich J

2015-09-24

Bioassays based on cellulose paper substrates are gaining increasing popularity for the development of field portable and low-cost diagnostic applications. Herein, we report a paper-based nucleic acid hybridization assay using immobilized upconversion nanoparticles (UCNPs) as donors in luminescence resonance energy transfer (LRET). UCNPs with intense green emission served as donors with Cy3 dye as the acceptor. The avidin functionalized UCNPs were immobilized on cellulose paper and subsequently bioconjugated to biotinylated oligonucleotide probes. Introduction of unlabeled oligonucleotide targets resulted in a formation of probe-target duplexes. A subsequent hybridization of Cy3 labeled reporter with the remaining single stranded portion of target brought the Cy3 dye in close proximity to the UCNPs to trigger a LRET-sensitized emission from the acceptor dye. The hybridization assays provided a limit of detection (LOD) of 146.0 fmol and exhibited selectivity for one base pair mismatch discrimination. The assay was functional even in undiluted serum samples. This work embodies important progress in developing DNA hybridization assays on paper. Detection of unlabeled targets is achieved using UCNPs as LRET donors, with minimization of background signal from paper substrates owing to the implementation of low energy near-infrared (NIR) excitation.
An Unscented Kalman-Particle Hybrid Filter for Space Object Tracking

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Raihan A. V, Dilshad; Chakravorty, Suman

2018-03-01

Optimal and consistent estimation of the state of space objects is pivotal to surveillance and tracking applications. However, probabilistic estimation of space objects is made difficult by the non-Gaussianity and nonlinearity associated with orbital mechanics. In this paper, we present an unscented Kalman-particle hybrid filtering framework for recursive Bayesian estimation of space objects. The hybrid filtering scheme is designed to provide accurate and consistent estimates when measurements are sparse without incurring a large computational cost. It employs an unscented Kalman filter (UKF) for estimation when measurements are available. When the target is outside the field of view (FOV) of the sensor, it updates the state probability density function (PDF) via a sequential Monte Carlo method. The hybrid filter addresses the problem of particle depletion through a suitably designed filter transition scheme. To assess the performance of the hybrid filtering approach, we consider two test cases of space objects that are assumed to undergo full three dimensional orbital motion under the effects of J 2 and atmospheric drag perturbations. It is demonstrated that the hybrid filters can furnish fast, accurate and consistent estimates outperforming standard UKF and particle filter (PF) implementations.
Hybrid optical-fibre/geopolymer sensors for structural health monitoring of concrete structures

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Perry, M.; Saafi, M.; Fusiek, G.; Niewczas, P.

2015-04-01

In this work, we demonstrate hybrid optical-fibre/geopolymer sensors for monitoring temperature, uniaxial strain and biaxial strain in concrete structures. The hybrid sensors detect these measurands via changes in geopolymer electrical impedance, and via optical wavelength measurements of embedded fibre Bragg gratings. Electrical and optical measurements were both facilitated by metal-coated optical fibres, which provided the hybrid sensors with a single, shared physical path for both voltage and wavelength signals. The embedded fibre sensors revealed that geopolymer specimens undergo 2.7 mɛ of shrinkage after one week of curing at 42 °C. After curing, an axial 2 mɛ compression of the uniaxial hybrid sensor led to impedance and wavelength shifts of 7 × 10-2 and -2 × 10-4 respectively. The typical strain resolution in the uniaxial sensor was 100 μ \\varepsilon . The biaxial sensor was applied to the side of a concrete cylinder, which was then placed under 0.6 mɛ of axial, compressive strain. Fractional shifts in impedance and wavelength, used to monitor axial and circumferential strain, were 3 × 10-2 and 4 × 10-5 respectively. The biaxial sensor’s strain resolution was approximately 10 μ \\varepsilon in both directions. Due to several design flaws, the uniaxial hybrid sensor was unable to accurately measure ambient temperature changes. The biaxial sensor, however, successfully monitored local temperature changes with 0.5 °C resolution.
Tamm-plasmon and surface-plasmon hybrid-mode based refractometry in photonic bandgap structures.

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Das, Ritwick; Srivastava, Triranjita; Jha, Rajan

2014-02-15

The transverse magnetic (TM) polarized hybrid modes formed as a consequence of coupling between Tamm plasmon polariton (TM-TPP) mode and surface plasmon polariton (SPP) mode exhibit interesting dispersive features for realizing a highly sensitive and accurate surface plasmon resonance (SPR) sensor. We found that the TM-TPP modes, formed at the interface of distributed Bragg reflector and metal, are strongly dispersive as compared to SPP modes at optical frequencies. This causes an appreciably narrow interaction bandwidth between TM-TPP and SPP modes, which leads to highly accurate sensing. In addition, appropriate tailoring of dispersion characteristics of TM-TPP as well as SPP modes could ensure high sensitivity of a novel SPR platform. By suitably designing the Au/TiO₂/SiO₂-based geometry, we propose a TM-TPP/SPP hybrid-mode sensor and achieve a sensitivity ≥900 nm/RIU with high detection accuracy (≥30 μm⁻¹) for analyte refractive indices varying between 1.330 and 1.345 in 600-700 nm wavelength range. The possibility to achieve desired dispersive behavior in any spectral band makes the sensing configuration an extremely attractive candidate to design sensors depending on the availability of optical sources.
In situ hybridization; principles and applications: review article

Directory of Open Access Journals (Sweden)

Zahra Nozhat

2015-06-01

Full Text Available In situ hybridization (ISH is a method that uses labeled complementary single strand DNA or RNA to localize specific DNA or RNA sequences in an intact cell or in a fixed tissue section. The main steps of ISH consist of: probe selection, tissue or sample preparation, pre-hybridization treatment, hybridization and washing, detection and control procedure. Probe selection is one of the important aspects of successful hybridization. ISH sensitivity and specificity can be influenced by: probe construct, efficiency of labeling, percentage of GC, probe length and signal detection systems. Different methods such as nick translation, random priming, end tailing and T4 DNA polymerase replacement are used for probe generation. Both radioactive and non-radioactive labels can be used in order to probe labeling. Nucleic acid maintenance in samples, prevention of morphological changes of samples and probe penetration into tissue section are the main aims of sample preparation step. Then, a small amount of solution containing probe, is added on slides containing tissue sections for hybridization process, then slides are incubated overnight. Next day, washes are carried out to remove the probes which are not bound to target DNA or RNA. Finally, in order to be sure that the observed labeling is specific to the target sequence, using several control procedures is very important. Various techniques based on ISH consist of: Fluorescence in situ hybridization (FISH, chromogenic in situ hybridization (CISH, genomic in situ hybridization (GISH, comparative genomic hybridization (CGH, spectral karyotyping (SKY and multiplex fluorescence in situ hybridization (MFISH. One of the most common techniques of ISH is fluorescence in situ hybridization. FISH can be used to: 1 detect small deletions and duplications that are not visible using microscope analysis, 2 detect how many chromosomes of a certain type are present in each cell and 3 confirm rearrangements that are
Maximized Inter-Class Weighted Mean for Fast and Accurate Mitosis Cells Detection in Breast Cancer Histopathology Images.

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Nateghi, Ramin; Danyali, Habibollah; Helfroush, Mohammad Sadegh

2017-08-14

Based on the Nottingham criteria, the number of mitosis cells in histopathological slides is an important factor in diagnosis and grading of breast cancer. For manual grading of mitosis cells, histopathology slides of the tissue are examined by pathologists at 40× magnification for each patient. This task is very difficult and time-consuming even for experts. In this paper, a fully automated method is presented for accurate detection of mitosis cells in histopathology slide images. First a method based on maximum-likelihood is employed for segmentation and extraction of mitosis cell. Then a novel Maximized Inter-class Weighted Mean (MIWM) method is proposed that aims at reducing the number of extracted non-mitosis candidates that results in reducing the false positive mitosis detection rate. Finally, segmented candidates are classified into mitosis and non-mitosis classes by using a support vector machine (SVM) classifier. Experimental results demonstrate a significant improvement in accuracy of mitosis cells detection in different grades of breast cancer histopathological images.
A hybrid symplectic principal component analysis and central tendency measure method for detection of determinism in noisy time series with application to mechanomyography.

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Xie, Hong-Bo; Dokos, Socrates

2013-06-01

We present a hybrid symplectic geometry and central tendency measure (CTM) method for detection of determinism in noisy time series. CTM is effective for detecting determinism in short time series and has been applied in many areas of nonlinear analysis. However, its performance significantly degrades in the presence of strong noise. In order to circumvent this difficulty, we propose to use symplectic principal component analysis (SPCA), a new chaotic signal de-noising method, as the first step to recover the system dynamics. CTM is then applied to determine whether the time series arises from a stochastic process or has a deterministic component. Results from numerical experiments, ranging from six benchmark deterministic models to 1/f noise, suggest that the hybrid method can significantly improve detection of determinism in noisy time series by about 20 dB when the data are contaminated by Gaussian noise. Furthermore, we apply our algorithm to study the mechanomyographic (MMG) signals arising from contraction of human skeletal muscle. Results obtained from the hybrid symplectic principal component analysis and central tendency measure demonstrate that the skeletal muscle motor unit dynamics can indeed be deterministic, in agreement with previous studies. However, the conventional CTM method was not able to definitely detect the underlying deterministic dynamics. This result on MMG signal analysis is helpful in understanding neuromuscular control mechanisms and developing MMG-based engineering control applications.
Marine Fish Hybridization

KAUST Repository

He, Song

2017-04-01

Natural hybridization is reproduction (without artificial influence) between two or more species/populations which are distinguishable from each other by heritable characters. Natural hybridizations among marine fishes were highly underappreciated due to limited research effort; it seems that this phenomenon occurs more often than is commonly recognized. As hybridization plays an important role in biodiversity processes in the marine environment, detecting hybridization events and investigating hybridization is important to understand and protect biodiversity. The first chapter sets the framework for this disseration study. The Cohesion Species Concept was selected as the working definition of a species for this study as it can handle marine fish hybridization events. The concept does not require restrictive species boundaries. A general history and background of natural hybridization in marine fishes is reviewed during in chapter as well. Four marine fish hybridization cases were examed and documented in Chapters 2 to 5. In each case study, at least one diagnostic nuclear marker, screened from among ~14 candidate markers, was found to discriminate the putative hybridizing parent species. To further investigate genetic evidence to support the hybrid status for each hybrid offspring in each case, haploweb analysis on diagnostic markers (nuclear and/or mitochondrial) and the DAPC/PCA analysis on microsatellite data were used. By combining the genetic evidences, morphological traits, and ecological observations together, the potential reasons that triggered each hybridization events and the potential genetic/ecology effects could be discussed. In the last chapter, sequences from 82 pairs of hybridizing parents species (for which COI barcoding sequences were available either on GenBank or in our lab) were collected. By comparing the COI fragment p-distance between each hybridizing parent species, some general questions about marine fish hybridization were discussed: Is
Electrochemical detection of C-reactive protein using Copper nanoparticles and hybridization chain reaction amplifying signal.

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Zhang, Junjun; Zhang, Wenjuan; Guo, Jinjin; Wang, Junchun; Zhang, Yuzhong

2017-12-15

In this study, a sandwich-type electrochemical immunosensor for the detection of C-reactive protein (CRP) is described. In design, Copper nanoparticles (Cu NPs) were used for signal tag and hybridization chain reaction (HCR)amplified output signal. The immunosensor fabrication involved three steps: (i) primary antibodies (Ab 1 ) were immobilized on the surface of gold nanoparticles (Au NPs); (ii) the sandwich-type structure formation contained "primary antibodies-antigen-secondary antibodies conjugated with primer (Ab 2 -S 0 )"; and (iii) long DNA concatemers intercalating amounts of Cu NPs was linked to the sandwich-type structure via hybridization reaction. Differential pulse voltammetry (DPV) was used to record the response signal of the immunosensor in phosphate-buffered saline (PBS). Under optimal conditions, the anodic peak currents of Cu NPs at the peak potential of about 0.08V(VS.SCE) were linear with the logarithm of CRP concentration in the range of 1.0 fg mL -1 to 100 ng mL -1 with a detection limit of 0.33 fg mL -1 (at signal/noise [S/N] = 3). In addition, the practical application of immunosensor was evaluated by analyzing CRP in real human serum samples, the recoveries obtained were within 95.3%-103.8%, indicating the immunosensor possessed potential application ability for practical disease diagnosis. Copyright © 2017 Elsevier Inc. All rights reserved.
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.

A method of layer-by-layer gold nanoparticle hybridization in a quartz crystal microbalance DNA sensing system used to detect dengue virus

International Nuclear Information System (INIS)

Chen, S-H; Chuang, Y-C; Lu, Y-C; Lin, H-C; Yang, Y-L; Lin, C-S

2009-01-01

Dengue virus (DENV) is nowadays the most important arthropod-spread virus affecting humans existing in more than 100 countries worldwide. A rapid and sensitive detection method for the early diagnosis of infectious dengue virus urgently needs to be developed. In the present study, a circulating-flow quartz crystal microbalance (QCM) biosensing method combining oligonucleotide-functionalized gold nanoparticles (i.e. AuNP probes) used to detect DENV has been established. In the DNA-QCM method, two kinds of specific AuNP probes were linked by the target sequences onto the QCM chip to amplify the detection signal, i.e. oscillatory frequency change (ΔF) of the QCM sensor. The target sequences amplified from the DENV genome act as a bridge for the layer-by-layer AuNP probes' hybridization in the method. Besides being amplifiers of the detection signal, the specific AuNP probes used in the DNA-QCM method also play the role of verifiers to specifically recognize their target sequences in the detection. The effect of four AuNP sizes on the layer-by-layer hybridization has been evaluated and it is found that 13 nm AuNPs collocated with 13 nm AuNPs showed the best hybridization efficiency. According to the nanoparticle application, the DNA-QCM biosensing method was able to detect dengue viral RNA in virus-contaminated serum as plaque titers being 2 PFU ml -1 and a linear correlation (R 2 = 0.987) of ΔF versus virus titration from 2 x 10 0 to 2 x 10 6 PFU ml -1 was found. The sensitivity and specificity of the present DNA-QCM method with nanoparticle technology showed it to be comparable to the fluorescent real-time PCR methods. Moreover, the method described herein was shown to not require expensive equipment, was label-free and highly sensitive.
A method of layer-by-layer gold nanoparticle hybridization in a quartz crystal microbalance DNA sensing system used to detect dengue virus

Energy Technology Data Exchange (ETDEWEB)

Chen, S-H; Chuang, Y-C; Lu, Y-C; Lin, H-C; Yang, Y-L; Lin, C-S [Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan (China)], E-mail: lincs@mail.nctu.edu.tw

2009-05-27

Dengue virus (DENV) is nowadays the most important arthropod-spread virus affecting humans existing in more than 100 countries worldwide. A rapid and sensitive detection method for the early diagnosis of infectious dengue virus urgently needs to be developed. In the present study, a circulating-flow quartz crystal microbalance (QCM) biosensing method combining oligonucleotide-functionalized gold nanoparticles (i.e. AuNP probes) used to detect DENV has been established. In the DNA-QCM method, two kinds of specific AuNP probes were linked by the target sequences onto the QCM chip to amplify the detection signal, i.e. oscillatory frequency change ({delta}F) of the QCM sensor. The target sequences amplified from the DENV genome act as a bridge for the layer-by-layer AuNP probes' hybridization in the method. Besides being amplifiers of the detection signal, the specific AuNP probes used in the DNA-QCM method also play the role of verifiers to specifically recognize their target sequences in the detection. The effect of four AuNP sizes on the layer-by-layer hybridization has been evaluated and it is found that 13 nm AuNPs collocated with 13 nm AuNPs showed the best hybridization efficiency. According to the nanoparticle application, the DNA-QCM biosensing method was able to detect dengue viral RNA in virus-contaminated serum as plaque titers being 2 PFU ml{sup -1} and a linear correlation (R{sup 2} = 0.987) of {delta}F versus virus titration from 2 x 10{sup 0} to 2 x 10{sup 6} PFU ml{sup -1} was found. The sensitivity and specificity of the present DNA-QCM method with nanoparticle technology showed it to be comparable to the fluorescent real-time PCR methods. Moreover, the method described herein was shown to not require expensive equipment, was label-free and highly sensitive.
A Ag synchronously deposited and doped TiO2 hybrid as an ultrasensitive SERS substrate: a multifunctional platform for SERS detection and photocatalytic degradation.

Science.gov (United States)

Yang, Libin; Sang, Qinqin; Du, Juan; Yang, Ming; Li, Xiuling; Shen, Yu; Han, Xiaoxia; Jiang, Xin; Zhao, Bing

2018-06-06

Ag simultaneously deposited and doped TiO2 (Ag-TiO2) hybrid nanoparticles (NPs) were prepared via a sol-hydrothermal method, as both a sensitive surface-enhanced Raman scattering (SERS) substrate and a superior photocatalyst for the first time. Ag-TiO2 hybrid NPs exhibit excellent SERS performance for several probe molecules and the enhancement factor is calculated to be 1.86 × 105. The detection limit of the 4-mercaptobenzoic acid (4-MBA) probe on the Ag-TiO2 substrate is 1 × 10-9 mol L-1, which is four orders of magnitude lower than that on pure TiO2 as a consequence of the synergistic effects of TiO2 and Ag. This is the highest SERS sensitivity among the reported semiconductor substrates and even comparable to noble metal substrates, and a SERS enhancement mechanism from the synergistic contribution of the semiconductor and noble metal was proposed. And importantly, the Ag-TiO2 hybrid shows excellent photocatalytic degradation activity for the detected species under UV light irradiation at lower concentration conditions, even for the hard to degrade 4-MBA molecule. This makes the Ag-TiO2 hybrid promising as a dual-function platform for both highly sensitive SERS detection and photocatalytic degradation of a pollutant system. Moreover, it also proves that the Ag-TiO2 hybrid can serve as a promising recyclable SERS-active substrate by virtue of its photocatalytic self-cleaning properties for some specific applications, for instance comparative studies of different species on the same SERS platform, in addition to the economic benefit.
Identification and Prediction of Large Pedestrian Flow in Urban Areas Based on a Hybrid Detection Approach

Directory of Open Access Journals (Sweden)

Kaisheng Zhang

2016-12-01

Full Text Available Recently, population density has grown quickly with the increasing acceleration of urbanization. At the same time, overcrowded situations are more likely to occur in populous urban areas, increasing the risk of accidents. This paper proposes a synthetic approach to recognize and identify the large pedestrian flow. In particular, a hybrid pedestrian flow detection model was constructed by analyzing real data from major mobile phone operators in China, including information from smartphones and base stations (BS. With the hybrid model, the Log Distance Path Loss (LDPL model was used to estimate the pedestrian density from raw network data, and retrieve information with the Gaussian Progress (GP through supervised learning. Temporal-spatial prediction of the pedestrian data was carried out with Machine Learning (ML approaches. Finally, a case study of a real Central Business District (CBD scenario in Shanghai, China using records of millions of cell phone users was conducted. The results showed that the new approach significantly increases the utility and capacity of the mobile network. A more reasonable overcrowding detection and alert system can be developed to improve safety in subway lines and other hotspot landmark areas, such as the Bundle, People’s Square or Disneyland, where a large passenger flow generally exists.
Hybrid graphene oxide/DAB-Am-16 dendrimer: Preparation, characterization chemical reactivity and their electrocatalytic detection of L-Dopamine

Science.gov (United States)

Do Carmo, Devaney Ribeiro; Fernandes, Daniela Silvestrini

2017-09-01

Graphene oxide (GO) was chemically modified with a poly(propylene)imine Generation 3.0 dendrimer (DAB-Am-16). The characterization, structure and properties of hybrid graphene oxide/DAB-Am-16 dendrimer was studied by Raman spectroscopy, Fourier-Transforming Infrared Spectroscopy (FT-IR), X-Ray Photoelectron Spectroscopic (XPS), X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Thermogravimetric analysis. After functionalized the hybrid material (GOD) can interact with copper and subsequently with hexacyanoferrate (III) ions (GODHCu). The GODHCu incorporated into a graphite paste electrode (20% w/w) was applied to an electrocatalytic detection of neurotransmitter L-dopamine using differential pulse voltammetry. The analytical curve showed a linear response in the concentration range from 1.0 × 10-7 to 1.0 × 10-5 mol L-1 with a corresponding equation Y(A) = 1.706 × 10-5 + 0.862 [L-dopamine] and a correlation coefficient r2 = 0.998. The detection limit was 6.36 × 10-7 mol L-1 with a relative standard deviation of ±4% (n = 3) and an amperometric sensitivity of 0.862 A/mol L-1.
A Hybrid Vehicle Detection Method Based on Viola-Jones and HOG + SVM from UAV Images

Science.gov (United States)

Xu, Yongzheng; Yu, Guizhen; Wang, Yunpeng; Wu, Xinkai; Ma, Yalong

2016-01-01

A new hybrid vehicle detection scheme which integrates the Viola-Jones (V-J) and linear SVM classifier with HOG feature (HOG + SVM) methods is proposed for vehicle detection from low-altitude unmanned aerial vehicle (UAV) images. As both V-J and HOG + SVM are sensitive to on-road vehicles’ in-plane rotation, the proposed scheme first adopts a roadway orientation adjustment method, which rotates each UAV image to align the roads with the horizontal direction so the original V-J or HOG + SVM method can be directly applied to achieve fast detection and high accuracy. To address the issue of descending detection speed for V-J and HOG + SVM, the proposed scheme further develops an adaptive switching strategy which sophistically integrates V-J and HOG + SVM methods based on their different descending trends of detection speed to improve detection efficiency. A comprehensive evaluation shows that the switching strategy, combined with the road orientation adjustment method, can significantly improve the efficiency and effectiveness of the vehicle detection from UAV images. The results also show that the proposed vehicle detection method is competitive compared with other existing vehicle detection methods. Furthermore, since the proposed vehicle detection method can be performed on videos captured from moving UAV platforms without the need of image registration or additional road database, it has great potentials of field applications. Future research will be focusing on expanding the current method for detecting other transportation modes such as buses, trucks, motors, bicycles, and pedestrians. PMID:27548179
A Hybrid Vehicle Detection Method Based on Viola-Jones and HOG + SVM from UAV Images.

Science.gov (United States)

Xu, Yongzheng; Yu, Guizhen; Wang, Yunpeng; Wu, Xinkai; Ma, Yalong

2016-08-19

A new hybrid vehicle detection scheme which integrates the Viola-Jones (V-J) and linear SVM classifier with HOG feature (HOG + SVM) methods is proposed for vehicle detection from low-altitude unmanned aerial vehicle (UAV) images. As both V-J and HOG + SVM are sensitive to on-road vehicles' in-plane rotation, the proposed scheme first adopts a roadway orientation adjustment method, which rotates each UAV image to align the roads with the horizontal direction so the original V-J or HOG + SVM method can be directly applied to achieve fast detection and high accuracy. To address the issue of descending detection speed for V-J and HOG + SVM, the proposed scheme further develops an adaptive switching strategy which sophistically integrates V-J and HOG + SVM methods based on their different descending trends of detection speed to improve detection efficiency. A comprehensive evaluation shows that the switching strategy, combined with the road orientation adjustment method, can significantly improve the efficiency and effectiveness of the vehicle detection from UAV images. The results also show that the proposed vehicle detection method is competitive compared with other existing vehicle detection methods. Furthermore, since the proposed vehicle detection method can be performed on videos captured from moving UAV platforms without the need of image registration or additional road database, it has great potentials of field applications. Future research will be focusing on expanding the current method for detecting other transportation modes such as buses, trucks, motors, bicycles, and pedestrians.
WRHT: A Hybrid Technique for Detection of Wormhole Attack in Wireless Sensor Networks

Directory of Open Access Journals (Sweden)

Rupinder Singh

2016-01-01

Full Text Available Wormhole attack is a challenging security threat to wireless sensor networks which results in disrupting most of the routing protocols as this attack can be triggered in different modes. In this paper, WRHT, a wormhole resistant hybrid technique, is proposed, which can detect the presence of wormhole attack in a more optimistic manner than earlier techniques. WRHT is based on the concept of watchdog and Delphi schemes and ensures that the wormhole will not be left untreated in the sensor network. WRHT makes use of the dual wormhole detection mechanism of calculating probability factor time delay probability and packet loss probability of the established path in order to find the value of wormhole presence probability. The nodes in the path are given different ranking and subsequently colors according to their behavior. The most striking feature of WRHT consists of its capacity to defend against almost all categories of wormhole attacks without depending on any required additional hardware such as global positioning system, timing information or synchronized clocks, and traditional cryptographic schemes demanding high computational needs. The experimental results clearly indicate that the proposed technique has significant improvement over the existing wormhole attack detection techniques.
DNA Immobilization and Hybridization Detection by the Intrinsic Molecular Charge Using Capacitive Field-Effect Sensors Modified with a Charged Weak Polyelectrolyte Layer.

Science.gov (United States)

Bronder, Thomas S; Poghossian, Arshak; Scheja, Sabrina; Wu, Chunsheng; Keusgen, Michael; Mewes, Dieter; Schöning, Michael J

2015-09-16

Miniaturized setup, compatibility with advanced micro- and nanotechnologies, and ability to detect biomolecules by their intrinsic molecular charge favor the semiconductor field-effect platform as one of the most attractive approaches for the development of label-free DNA chips. In this work, a capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensor covered with a layer-by-layer prepared, positively charged weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was used for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization. The negatively charged probe single-stranded DNA (ssDNA) molecules were electrostatically adsorbed onto the positively charged PAH layer, resulting in a preferentially flat orientation of the ssDNA molecules within the Debye length, thus yielding a reduced charge-screening effect and a higher sensor signal. Each sensor-surface modification step (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), reducing an unspecific adsorption by a blocking agent, incubation with noncomplementary DNA (ncDNA) solution) was monitored by means of capacitance-voltage and constant-capacitance measurements. In addition, the surface morphology of the PAH layer was studied by atomic force microscopy and contact-angle measurements. High hybridization signals of 34 and 43 mV were recorded in low-ionic strength solutions of 10 and 1 mM, respectively. In contrast, a small signal of 4 mV was recorded in the case of unspecific adsorption of fully mismatched ncDNA. The density of probe ssDNA and dsDNA molecules as well as the hybridization efficiency was estimated using the experimentally measured DNA immobilization and hybridization signals and a simplified double-layer capacitor model. The results of field-effect experiments were supported by fluorescence measurements, verifying the DNA-immobilization and hybridization event.
Application of Genomic In Situ Hybridization in Horticultural Science

Directory of Open Access Journals (Sweden)

Fahad Ramzan

2017-01-01

Full Text Available Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH techniques in horticultural plants.
Real-time PCR Detection of Brucella Abortus: A Comparative Study of SYBR Green I, 5'-exonuclease, and Hybridization Probe Assays

Energy Technology Data Exchange (ETDEWEB)

Newby, Deborah Trishelle; Hadfield, Ted; Roberto, Francisco Figueroa

2003-08-01

Real-time PCR provides a means of detecting and quantifying DNA targets by monitoring PCR product accumulation during cycling as indicated by increased fluorescence. A number of different approaches can be used to generate the fluorescence signal. Three approaches—SYBR Green I (a double-stranded DNA intercalating dye), 5'-exonuclease (enzymatically released fluors), and hybridization probes (fluorescence resonance energy transfer)—were evaluated for use in a real-time PCR assay to detect Brucella abortus. The three assays utilized the same amplification primers to produce an identical amplicon. This amplicon spans a region of the B. abortus genome that includes portions of the alkB gene and the IS711 insertion element. All three assays were of comparable sensitivity, providing a linear assay over 7 orders of magnitude (from 7.5 ng down to 7.5 fg). However, the greatest specificity was achieved with the hybridization probe assay.
Electrokinetically-controlled RNA-DNA hybridization assay for foodborne pathogens

International Nuclear Information System (INIS)

Weng, X.; Jiang, H.; Li, D.

2012-01-01

We have developed a microfluidic chip for use in an RNA-DNA hybridization assay for foodborne pathogens. Automatic sequential reagent dispensing and washing was realized with a programmable DC voltage sequencer. Signal detection was achieved with a miniaturized optical detection module. Salmonella and Listeria monocytogenes bacteria in different concentrations were quantitatively determined by this RNA-DNA hybridization assay in the microfluidic chip. The detection limit for the Salmonella and Listeria monocytogenes bacteria is 10 3 to 10 4 CFU mL -1 . The method excels by a significant reduction in the consumption of sample and reagent, and a short assay time. This automatic-operating microfluidic RNA-DNA hybridization assay is promising for on-site pathogen detection. (author)
Swelling behavior detection of irradiated U-10Zr alloy fuel using indirect neutron radiography

Energy Technology Data Exchange (ETDEWEB)

Sun, Yong; Huo, He-yong; Wu, Yang [Institute of Nuclear Physics and Chemistry, Chinese Academy of Engineering Physics, Mianyang (China); Key Laboratory of Neutron Physics, Chinese Academy of Engineering Physics, Mianyang (China); Li, Jiangbo [Institute of Nuclear Physics and Chemistry, Chinese Academy of Engineering Physics, Mianyang (China); Zhou, Wei; Guo, Hai-bing [Institute of Nuclear Physics and Chemistry, Chinese Academy of Engineering Physics, Mianyang (China); Key Laboratory of Neutron Physics, Chinese Academy of Engineering Physics, Mianyang (China); Li, Hang, E-mail: lihang32@gmail.com [Institute of Nuclear Physics and Chemistry, Chinese Academy of Engineering Physics, Mianyang (China); Key Laboratory of Neutron Physics, Chinese Academy of Engineering Physics, Mianyang (China); Cao, Chao; Yin, Wei; Wang, Sheng; Liu, Bin; Feng, Qi-jie; Tang, Bin [Institute of Nuclear Physics and Chemistry, Chinese Academy of Engineering Physics, Mianyang (China); Key Laboratory of Neutron Physics, Chinese Academy of Engineering Physics, Mianyang (China)

2016-11-21

It is hopeful that fusion-fission hybrid energy system will become an effective approach to achieve long-term sustainable development of fission energy. U-10Zr alloy (which means the mass ratio of Zr is 10%) fuel is the key material of subcritical blanket for fusion-fission hybrid energy system which the irradiation performance need to be considered. Indirect neutron radiography is used to detect the irradiated U-10Zr alloy because of the high residual dose in this paper. Different burnup samples (0.1%, 0.3%, 0.5% and 0.7%) have been tested with a special indirect neutron radiography device at CMRR (China Mianyang Research Reactor). The resolution of the device is better than 50 µm and the quantitative analysis of swelling behaviors was carried out. The results show that the swelling behaviors relate well to burnup character which can be detected accurately by indirect neutron radiography.
Enhanced electrocatalytic activity of graphene-gold nanoparticles hybrids for peroxynitrite electrochemical detection on hemin-based electrode.

Science.gov (United States)

Wang, Beibei; Ji, Xueping; Ren, Jujie; Ni, Ruixing; Wang, Lin

2017-12-01

A simple, ultrasensitive peroxynitrite anion (ONOO - ) electrochemical sensing platform was developed by immobilizing hemin on a density controllable electrochemically reduced graphene oxide-Au nanoparticles (ERGO-AuNPs) nanohybrids. The ERGO-AuNPs in situ nanohybrids were produced onto a glass carbon electrode (GCE) by one-step electrodeposition, the density of which could be easily controlled by electrodeposited time. The morphology of ERGO-AuNPs nanohybrids was characterized by a scanning electron microscope (SEM). The ERGO-AuNPs nanohybrids showed a high electrocatalytic activity for immobilized-hemin, because the nanostructures hybrids could effectively promote electron transfer rate between hemin and the electrode. Due to nanohybrids-enhanced catalytic effect for hemin, they were firstly selected for use as a highly sensitive electrochemical platform for ONOO - detection. The resulted sensor showed a high electrocatalytic activity toward ONOO - oxidation, being free from the electroactive interferents, including nitrite, nitrate, dopamine and uric acid at an applied potential of 0.7V. The sensor exhibited a high sensitivity of 123.1nAμM -1 and a lower detection limit of 0.1μM, and a wide linear range of 2.4×10 -6 to 5.5×10 -5 M, which could be attributed to the synergy between ERGO and AuNPs in hybrids. The nanohybrids in situ preparation and ONOO - detection methods would be beneficial to developing other sensing interface and have promising applications in biological molecules analysis and clinical diagnostic. Copyright © 2017 Elsevier B.V. All rights reserved.
Analytical solution to the hybrid diffusion-transport equation

International Nuclear Information System (INIS)

Nanneh, M.M.; Williams, M.M.R.

1986-01-01

A special integral equation was derived in previous work using a hybrid diffusion-transport theory method for calculating the flux distribution in slab lattices. In this paper an analytical solution of this equation has been carried out on a finite reactor lattice. The analytical results of disadvantage factors are shown to be accurate in comparison with the numerical results and accurate transport theory calculations. (author)
Extraordinary tunable dynamic range of electrochemical aptasensor for accurate detection of ochratoxin A in food samples

Directory of Open Access Journals (Sweden)

Lin Cheng

2017-06-01

Full Text Available We report the design of a sensitive, electrochemical aptasensor for detection of ochratoxin A (OTA with an extraordinary tunable dynamic sensing range. This electrochemical aptasensor is constructed based on the target induced aptamer-folding detection mechanism and the recognition between OTA and its aptamers results in the conformational change of the aptamer probe and thus signal changes for measurement. The dynamic sensing range of the electrochemical aptasensor is successfully tuned by introduction of free assistant aptamer probes in the sensing system. Our electrochemical aptasensor shows an extraordinary dynamic sensing range of 11-order magnitude of OTA concentration from 10−8 to 102 ng/g. Of great significance, the signal response in all OTA concentration ranges is at the same current scale, demonstrating that our sensing protocol in this research could be applied for accurate detections of OTA in a broad range without using any complicated treatment of signal amplification. Finally, OTA spiked red wine and maize samples in different dynamic sensing ranges are determined with the electrochemical aptasensor under optimized sensing conditions. This tuning strategy of dynamic sensing range may offer a promising platform for electrochemical aptasensor optimizations in practical applications.
A hybrid condenser model for real-time applications in performance monitoring, control and optimization

International Nuclear Information System (INIS)

Ding Xudong; Cai Wenjian; Jia Lei; Wen Changyun; Zhang Guiqing

2009-01-01

In this paper, a simple, yet accurate hybrid modeling technique for condensers is presented. The method starts with fundamental physical principles but captures only few key operational characteristic parameters to predict the system performances. The advantages of the methods lie that linear or non-linear least-squares methods can be directly used to determine no more than four key operational characteristic parameters in the model, which can significantly reduce the computational burden. The developed model is verified with the experimental data taken from a pilot system. The testing results confirm that the proposed model can predict accurately the performance of the real-time operating condenser with the maximum error of less than ±10%. The model technique proposed will have wide applications not only in condenser operating optimization, but also in performance assessment and fault detection and diagnosis.
StackInsights: Cognitive Learning for Hybrid Cloud Readiness

OpenAIRE

Qiao, Mu; Bathen, Luis; Génot, Simon-Pierre; Lee, Sunhwan; Routray, Ramani

2017-01-01

Hybrid cloud is an integrated cloud computing environment utilizing a mix of public cloud, private cloud, and on-premise traditional IT infrastructures. Workload awareness, defined as a detailed full range understanding of each individual workload, is essential in implementing the hybrid cloud. While it is critical to perform an accurate analysis to determine which workloads are appropriate for on-premise deployment versus which workloads can be migrated to a cloud off-premise, the assessment...
DNA hybridization sensor based on pentacene thin film transistor.

Science.gov (United States)

Kim, Jung-Min; Jha, Sandeep Kumar; Chand, Rohit; Lee, Dong-Hoon; Kim, Yong-Sang

2011-01-15

A DNA hybridization sensor using pentacene thin film transistors (TFTs) is an excellent candidate for disposable sensor applications due to their low-cost fabrication process and fast detection. We fabricated pentacene TFTs on glass substrate for the sensing of DNA hybridization. The ss-DNA (polyA/polyT) or ds-DNA (polyA/polyT hybrid) were immobilized directly on the surface of the pentacene, producing a dramatic change in the electrical properties of the devices. The electrical characteristics of devices were studied as a function of DNA immobilization, single-stranded vs. double-stranded DNA, DNA length and concentration. The TFT device was further tested for detection of λ-phage genomic DNA using probe hybridization. Based on these results, we propose that a "label-free" detection technique for DNA hybridization is possible through direct measurement of electrical properties of DNA-immobilized pentacene TFTs. Copyright Â© 2010 Elsevier B.V. All rights reserved.
Towards the accurate electronic structure descriptions of typical high-constant dielectrics

Science.gov (United States)

Jiang, Ting-Ting; Sun, Qing-Qing; Li, Ye; Guo, Jiao-Jiao; Zhou, Peng; Ding, Shi-Jin; Zhang, David Wei

2011-05-01

High-constant dielectrics have gained considerable attention due to their wide applications in advanced devices, such as gate oxides in metal-oxide-semiconductor devices and insulators in high-density metal-insulator-metal capacitors. However, the theoretical investigations of these materials cannot fulfil the requirement of experimental development, especially the requirement for the accurate description of band structures. We performed first-principles calculations based on the hybrid density functionals theory to investigate several typical high-k dielectrics such as Al2O3, HfO2, ZrSiO4, HfSiO4, La2O3 and ZrO2. The band structures of these materials are well described within the framework of hybrid density functionals theory. The band gaps of Al2O3, HfO2, ZrSiO4, HfSiO4, La2O3 and ZrO2are calculated to be 8.0 eV, 5.6 eV, 6.2 eV, 7.1 eV, 5.3 eV and 5.0 eV, respectively, which are very close to the experimental values and far more accurate than those obtained by the traditional generalized gradient approximation method.

Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA.

Science.gov (United States)

Majid, Farjana; Jahan, Munira; Lutful Moben, Ahmed; Tabassum, Shahina

2014-01-01

Both real-time-polymerase chain reaction (PCR) and hybrid capture 2 (HC2) assay can detect and quantify hepatitis B virus (HBV) DNA. However, real-time-PCR can detect a wide range of HBV DNA, while HC2 assay could not detect lower levels of viremia. The present study was designed to detect and quantify HBV DNA by real-time-PCR and HC2 assay and compare the quantitative data of these two assays. A cross-sectional study was conducted in between July 2010 and June 2011. A total of 66 serologically diagnosed chronic hepatitis B (CHB) patients were selected for the study. Real-time-PCR and HC2 assay was done to detect HBV DNA. Data were analyzed by statistical Package for the social sciences (SPSS). Among 66 serologically diagnosed chronic hepatitis B patients 40 (60.61%) patients had detectable and 26 (39.39%) had undetectable HBV DNA by HC2 assay. Concordant results were obtained for 40 (60.61%) out of these 66 patients by real-time-PCR and HC2 assay with mean viral load of 7.06 ± 1.13 log 10 copies/ml and 6.95 ± 1.08 log 10 copies/ml, respectively. In the remaining 26 patients, HBV DNA was detectable by real-time-PCR in 20 patients (mean HBV DNA level was 3.67 ± 0.72 log 10 copies/ml. However, HBV DNA could not be detectable in six cases by the both assays. The study showed strong correlation (r = 0.915) between real-time-PCR and HC2 assay for the detection and quantification of HBV DNA. HC2 assay may be used as an alternative to real-time-PCR for CHB patients. How to cite this article: Majid F, Jahan M, Moben AL, Tabassum S. Comparison of Hybrid Capture 2 Assay with Real-time-PCR for Detection and Quantitation of Hepatitis B Virus DNA. Euroasian J Hepato-Gastroenterol 2014;4(1):31-35.
2D Hybrid Nanomaterials for Selective Detection of NO2 and SO2 Using "Light On and Off" Strategy.

Science.gov (United States)

Chen, Aimin; Liu, Rui; Peng, Xiao; Chen, Qiaofen; Wu, Jianmin

2017-10-25

In order to distinguish NO 2 and SO 2 gas with one sensor, we designed a paper chip assembled with a 2D g-C 3 N 4 /rGO stacking hybrid fabricated via a layer-by-layer self-assembly approach. The g-C 3 N 4 /rGO hybrid exhibited a remarkable photoelectric property due to the construction of a van der Waals heterostructure. For the first time, we have been able to selectively detect NO 2 and SO 2 gas using a "light on and off" strategy. Under the "light off" condition, the g-C 3 N 4 /rGO sensor exhibited a p-type semiconducting behavior with a low detection limit of 100 ppb of NO 2 , but with no response toward SO 2 . In contrast, the sensor showed n-type semiconducting behavior which could detect SO 2 at concentration as low as 2 ppm under UV light irradiation. The effective electron transfer among the 2D structure of g-C 3 N 4 and rGO nanosheets as well as highly porous structures could play an important role in gas sensing. The different sensing mechanisms at "light on and off" circumstances were also investigated in detail.
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.
Borrelia burgdorferi genospecies detection by RLB hybridization in Ixodes cinus ticks from different sites of North-Eastern Poland

OpenAIRE

Justyna Dunaj; Joanna Maria Zajkowska; Maciej Kondrusik; Lise Gern; Oliver Rais; Anna Moniuszko; Sławomir Pancewicz; Renata Świerzbińska

2014-01-01

Introduction. RLB (Reverse Line Blot Hybridization) is a molecular biology technique that might be used for [i]Borrelia burgdorferi [/i]sensu lato (sl) DNA detection with genospecies specification. Among[i] B. burgdorferi[/i] sl genospecies at least 7 are regarded as pathogenic in Europe. objective. The aim of the study was to evaluate the frequency of different [i]Borrelia[/i] genospecies DNA detection in Ixodes ricinus ticks in the endemic area of North-Eastern Poland by using RLB. ...
Charging and discharging tests for obtaining an accurate dynamic electro-thermal model of high power lithium-ion pack system for hybrid and EV applications

DEFF Research Database (Denmark)

Mihet-Popa, Lucian; Camacho, Oscar Mauricio Forero; Nørgård, Per Bromand

2013-01-01

This paper presents a battery test platform including two Li-ion battery designed for hybrid and EV applications, and charging/discharging tests under different operating conditions carried out for developing an accurate dynamic electro-thermal model of a high power Li-ion battery pack system....... The aim of the tests has been to study the impact of the battery degradation and to find out the dynamic characteristics of the cells including nonlinear open circuit voltage, series resistance and parallel transient circuit at different charge/discharge currents and cell temperature. An equivalent...... circuit model, based on the runtime battery model and the Thevenin circuit model, with parameters obtained from the tests and depending on SOC, current and temperature has been implemented in MATLAB/Simulink and Power Factory. A good alignment between simulations and measurements has been found....
A Hybrid Islanding Detection Technique Using Average Rate of Voltage Change and Real Power Shift

DEFF Research Database (Denmark)

Mahat, Pukar; Chen, Zhe; Bak-Jensen, Birgitte

2009-01-01

The mainly used islanding detection techniques may be classified as active and passive techniques. Passive techniques don't perturb the system but they have larger nondetection znes, whereas active techniques have smaller nondetection zones but they perturb the system. In this paper, a new hybrid...... technique is proposed to solve this problem. An average rate of voltage change (passive technique) has been used to initiate a real power shift (active technique), which changes the eal power of distributed generation (DG), when the passive technique cannot have a clear discrimination between islanding...
Fast, accurate, and robust automatic marker detection for motion correction based on oblique kV or MV projection image pairs

International Nuclear Information System (INIS)

Slagmolen, Pieter; Hermans, Jeroen; Maes, Frederik; Budiharto, Tom; Haustermans, Karin; Heuvel, Frank van den

2010-01-01

Purpose: A robust and accurate method that allows the automatic detection of fiducial markers in MV and kV projection image pairs is proposed. The method allows to automatically correct for inter or intrafraction motion. Methods: Intratreatment MV projection images are acquired during each of five treatment beams of prostate cancer patients with four implanted fiducial markers. The projection images are first preprocessed using a series of marker enhancing filters. 2D candidate marker locations are generated for each of the filtered projection images and 3D candidate marker locations are reconstructed by pairing candidates in subsequent projection images. The correct marker positions are retrieved in 3D by the minimization of a cost function that combines 2D image intensity and 3D geometric or shape information for the entire marker configuration simultaneously. This optimization problem is solved using dynamic programming such that the globally optimal configuration for all markers is always found. Translational interfraction and intrafraction prostate motion and the required patient repositioning is assessed from the position of the centroid of the detected markers in different MV image pairs. The method was validated on a phantom using CT as ground-truth and on clinical data sets of 16 patients using manual marker annotations as ground-truth. Results: The entire setup was confirmed to be accurate to around 1 mm by the phantom measurements. The reproducibility of the manual marker selection was less than 3.5 pixels in the MV images. In patient images, markers were correctly identified in at least 99% of the cases for anterior projection images and 96% of the cases for oblique projection images. The average marker detection accuracy was 1.4±1.8 pixels in the projection images. The centroid of all four reconstructed marker positions in 3D was positioned within 2 mm of the ground-truth position in 99.73% of all cases. Detecting four markers in a pair of MV images
Accurate confidence aware clustering of array CGH tumor profiles.

NARCIS (Netherlands)

van Houte, B.P.P.; Heringa, J.

2010-01-01

Motivation: Chromosomal aberrations tend to be characteristic for given (sub)types of cancer. Such aberrations can be detected with array comparative genomic hybridization (aCGH). Clustering aCGH tumor profiles aids in identifying chromosomal regions of interest and provides useful diagnostic
Toward accurate tooth segmentation from computed tomography images using a hybrid level set model

Energy Technology Data Exchange (ETDEWEB)

Gan, Yangzhou; Zhao, Qunfei [Department of Automation, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240 (China); Xia, Zeyang, E-mail: zy.xia@siat.ac.cn, E-mail: jing.xiong@siat.ac.cn; Hu, Ying [Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, and The Chinese University of Hong Kong, Shenzhen 518055 (China); Xiong, Jing, E-mail: zy.xia@siat.ac.cn, E-mail: jing.xiong@siat.ac.cn [Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 510855 (China); Zhang, Jianwei [TAMS, Department of Informatics, University of Hamburg, Hamburg 22527 (Germany)

2015-01-15

Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm{sup 3}) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm{sup 3}, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm{sup 3}, 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0
Toward accurate tooth segmentation from computed tomography images using a hybrid level set model

International Nuclear Information System (INIS)

Gan, Yangzhou; Zhao, Qunfei; Xia, Zeyang; Hu, Ying; Xiong, Jing; Zhang, Jianwei

2015-01-01

Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm 3 ) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm 3 , 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm 3 , 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0.28 ± 0.03 mm
A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species.

Science.gov (United States)

Sinigaglia, Chiara; Thiel, Daniel; Hejnol, Andreas; Houliston, Evelyn; Leclère, Lucas

2018-02-01

In situ hybridization is a widely employed technique allowing spatial visualization of gene expression in fixed specimens. It has greatly advanced our understanding of biological processes, including developmental regulation. In situ protocols are today routinely followed in numerous laboratories, and although details might change, they all include a hybridization step, where specific antisense RNA or DNA probes anneal to the target nucleic acid sequence. This step is generally carried out at high temperatures and in a denaturing solution, called hybridization buffer, commonly containing 50% (v/v) formamide - a hazardous chemical. When applied to the soft-bodied hydrozoan medusa Clytia hemisphaerica, we found that this traditional hybridization approach was not fully satisfactory, causing extensive deterioration of morphology and tissue texture which compromised our observation and interpretation of results. We thus tested alternative solutions for in situ detection of gene expression and, inspired by optimized protocols for Northern and Southern blot analysis, we substituted the 50% formamide with an equal volume of 8M urea solution in the hybridization buffer. Our new protocol not only yielded better morphologies and tissue consistency, but also notably improved the resolution of the signal, allowing more precise localization of gene expression and reducing aspecific staining associated with problematic areas. Given the improved results and reduced manipulation risks, we tested the urea protocol on other metazoans, two brachiopod species (Novocrania anomala and Terebratalia transversa) and the priapulid worm Priapulus caudatus, obtaining a similar reduction of aspecific probe binding. Overall, substitution of formamide by urea during in situ hybridization offers a safer alternative, potentially of widespread use in research, medical and teaching contexts. We encourage other workers to test this approach on their study organisms, and hope that they will also
Accurate thermoelastic tensor and acoustic velocities of NaCl

Energy Technology Data Exchange (ETDEWEB)

Marcondes, Michel L., E-mail: michel@if.usp.br [Physics Institute, University of Sao Paulo, Sao Paulo, 05508-090 (Brazil); Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455 (United States); Shukla, Gaurav, E-mail: shukla@physics.umn.edu [School of Physics and Astronomy, University of Minnesota, Minneapolis, 55455 (United States); Minnesota supercomputer Institute, University of Minnesota, Minneapolis, 55455 (United States); Silveira, Pedro da [Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455 (United States); Wentzcovitch, Renata M., E-mail: wentz002@umn.edu [Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455 (United States); Minnesota supercomputer Institute, University of Minnesota, Minneapolis, 55455 (United States)

2015-12-15

Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor by using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.
Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation.

Science.gov (United States)

Clark, Alex M; Bunin, Barry A; Litterman, Nadia K; Schürer, Stephan C; Visser, Ubbo

2014-01-01

Bioinformatics and computer aided drug design rely on the curation of a large number of protocols for biological assays that measure the ability of potential drugs to achieve a therapeutic effect. These assay protocols are generally published by scientists in the form of plain text, which needs to be more precisely annotated in order to be useful to software methods. We have developed a pragmatic approach to describing assays according to the semantic definitions of the BioAssay Ontology (BAO) project, using a hybrid of machine learning based on natural language processing, and a simplified user interface designed to help scientists curate their data with minimum effort. We have carried out this work based on the premise that pure machine learning is insufficiently accurate, and that expecting scientists to find the time to annotate their protocols manually is unrealistic. By combining these approaches, we have created an effective prototype for which annotation of bioassay text within the domain of the training set can be accomplished very quickly. Well-trained annotations require single-click user approval, while annotations from outside the training set domain can be identified using the search feature of a well-designed user interface, and subsequently used to improve the underlying models. By drastically reducing the time required for scientists to annotate their assays, we can realistically advocate for semantic annotation to become a standard part of the publication process. Once even a small proportion of the public body of bioassay data is marked up, bioinformatics researchers can begin to construct sophisticated and useful searching and analysis algorithms that will provide a diverse and powerful set of tools for drug discovery researchers.
Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation

Directory of Open Access Journals (Sweden)

Alex M. Clark

2014-08-01

Full Text Available Bioinformatics and computer aided drug design rely on the curation of a large number of protocols for biological assays that measure the ability of potential drugs to achieve a therapeutic effect. These assay protocols are generally published by scientists in the form of plain text, which needs to be more precisely annotated in order to be useful to software methods. We have developed a pragmatic approach to describing assays according to the semantic definitions of the BioAssay Ontology (BAO project, using a hybrid of machine learning based on natural language processing, and a simplified user interface designed to help scientists curate their data with minimum effort. We have carried out this work based on the premise that pure machine learning is insufficiently accurate, and that expecting scientists to find the time to annotate their protocols manually is unrealistic. By combining these approaches, we have created an effective prototype for which annotation of bioassay text within the domain of the training set can be accomplished very quickly. Well-trained annotations require single-click user approval, while annotations from outside the training set domain can be identified using the search feature of a well-designed user interface, and subsequently used to improve the underlying models. By drastically reducing the time required for scientists to annotate their assays, we can realistically advocate for semantic annotation to become a standard part of the publication process. Once even a small proportion of the public body of bioassay data is marked up, bioinformatics researchers can begin to construct sophisticated and useful searching and analysis algorithms that will provide a diverse and powerful set of tools for drug discovery researchers.
Hybridization State Detection of DNA-Functionalized Gold Nanoparticles Using Hyperspectral Imaging

Directory of Open Access Journals (Sweden)

Richard C. Murdock

2017-01-01

Full Text Available Hyperspectral imaging has the unique ability of capturing spectral data for multiple wavelengths at each pixel in an image. This gives the ability to distinguish, with certainty, different nanomaterials and/or distinguish nanomaterials from biological materials. In this study, 4 nm and 13 nm gold nanoparticles (Au NPs were synthesized, functionalized with complimentary oligonucleotides, and hybridized to form large networks of NPs. Scattering spectra were collected from each sample (unfunctionalized, functionalized, and hybridized and evaluated. The spectra showed unique peaks for each size of Au NP sample and also exhibited narrowing and intensifying of the spectra as the NPs were functionalized and then subsequently hybridized. These spectra are different from normal aggregation effects where the LSPR and reflected spectrum broaden and are red-shifted. Rather, this appears to be dependent on the ability to control the interparticle distance through oligonucleotide length, which is also investigated through the incorporation of a poly-A spacer. Also, hybridized Au NPs were exposed to cells with no adverse effects and retained their unique spectral signatures. With the ability to distinguish between hybridization states at nearly individual NP levels, this could provide a new method of tracking the intracellular actions of nanomaterials as well as extracellular biosensing applications.
Hybrid Arrays for Chemical Sensing

Science.gov (United States)

Kramer, Kirsten E.; Rose-Pehrsson, Susan L.; Johnson, Kevin J.; Minor, Christian P.

In recent years, multisensory approaches to environment monitoring for chemical detection as well as other forms of situational awareness have become increasingly popular. A hybrid sensor is a multimodal system that incorporates several sensing elements and thus produces data that are multivariate in nature and may be significantly increased in complexity compared to data provided by single-sensor systems. Though a hybrid sensor is itself an array, hybrid sensors are often organized into more complex sensing systems through an assortment of network topologies. Part of the reason for the shift to hybrid sensors is due to advancements in sensor technology and computational power available for processing larger amounts of data. There is also ample evidence to support the claim that a multivariate analytical approach is generally superior to univariate measurements because it provides additional redundant and complementary information (Hall, D. L.; Linas, J., Eds., Handbook of Multisensor Data Fusion, CRC, Boca Raton, FL, 2001). However, the benefits of a multisensory approach are not automatically achieved. Interpretation of data from hybrid arrays of sensors requires the analyst to develop an application-specific methodology to optimally fuse the disparate sources of data generated by the hybrid array into useful information characterizing the sample or environment being observed. Consequently, multivariate data analysis techniques such as those employed in the field of chemometrics have become more important in analyzing sensor array data. Depending on the nature of the acquired data, a number of chemometric algorithms may prove useful in the analysis and interpretation of data from hybrid sensor arrays. It is important to note, however, that the challenges posed by the analysis of hybrid sensor array data are not unique to the field of chemical sensing. Applications in electrical and process engineering, remote sensing, medicine, and of course, artificial
Less accurate but more efficient family of search templates for detection of gravitational waves from inspiraling compact binaries

International Nuclear Information System (INIS)

Chronopoulos, Andreas E.; Apostolatos, Theocharis A.

2001-01-01

The network of interferometric detectors that is under construction at various locations on Earth is expected to start searching for gravitational waves in a few years. The number of search templates that is needed to be cross correlated with the noisy output of the detectors is a major issue since computing power capabilities are restricted. By choosing higher and higher post-Newtonian order expansions for the family of search templates we make sure that our filters are more accurate copies of the real waves that hit our detectors. However, this is not the only criterion for choosing a family of search templates. To make the process of detection as efficient as possible, one needs a family of templates with a relatively small number of members that manages to pick up any detectable signal with only a tiny reduction in signal-to-noise ratio. Evidently, one family is better than another if it accomplishes its goal with a smaller number of templates. Following the geometric language of Owen, we have studied the performance of the post 1.5 -Newtonian family of templates on detecting post 2 -Newtonian signals for binaries. Several technical issues arise from the fact that the two types of waveforms cannot be made to coincide by a suitable choice of parameters. In general, the parameter space of the signals is not identical with the parameter space of the templates, although in our case they are of the same dimension, and one has to take into account all such peculiarities before drawing any conclusion. An interesting result we have obtained is that the post 1.5 -Newtonian family of templates happens to be more economical for detecting post 2 -Newtonian signals than the perfectly accurate post 2 -Newtonian family of templates itself. The number of templates is reduced by 20-30%, depending on the acceptable level of reduction in signal-to-noise ratio due to discretization of the family of templates. This makes the post 1.5 -Newtonian family of templates more favorable
Analysis of Linear Hybrid Systems in CLP

DEFF Research Database (Denmark)

Banda, Gourinath; Gallagher, John Patrick

2009-01-01

In this paper we present a procedure for representing the semantics of linear hybrid automata (LHAs) as constraint logic programs (CLP); flexible and accurate analysis and verification of LHAs can then be performed using generic CLP analysis and transformation tools. LHAs provide an expressive...
Joint quantum state tomography of an entangled qubit–resonator hybrid

International Nuclear Information System (INIS)

LinPeng, X Y; Zhang, H Z; Xu, K; Li, C Y; Zhong, Y P; Wang, Z L; Wang, H; Xie, Q W

2013-01-01

The integration of superconducting qubits and resonators in one circuit offers a promising solution for quantum information processing (QIP), which also realizes the on-chip analogue of cavity quantum electrodynamics (QED), known as circuit QED. In most prototype circuit designs, qubits are active processing elements and resonators are peripherals. As resonators typically have better coherence performance and more accessible energy levels, it is proposed that the entangled qubit–resonator hybrid can be used as a processing element. To achieve such a goal, an accurate measurement of the hybrid is first necessary. Here we demonstrate a joint quantum state tomography (QST) technique to fully characterize an entangled qubit–resonator hybrid. We benchmarked our QST technique by generating and accurately characterizing multiple states, e.g. |gN〉 + |e(N − 1)〉 where (|g〉 and |e〉) are the ground and excited states of the qubit and (|0〉,…,|N〉) are Fock states of the resonator. We further provided a numerical method to improve the QST efficiency and measured the decoherence dynamics of the bipartite hybrid, witnessing dissipation coming from both the qubit and the N-photon Fock state. As such, the joint QST presents an important step toward actively using the qubit–resonator element for QIP in hybrid quantum devices and for studying circuit QED. (paper)
Battery control system for hybrid vehicle and method for controlling a hybrid vehicle battery

Science.gov (United States)

Bockelmann, Thomas R [Battle Creek, MI; Hope, Mark E [Marshall, MI; Zou, Zhanjiang [Battle Creek, MI; Kang, Xiaosong [Battle Creek, MI

2009-02-10

A battery control system for hybrid vehicle includes a hybrid powertrain battery, a vehicle accessory battery, and a prime mover driven generator adapted to charge the vehicle accessory battery. A detecting arrangement is configured to monitor the vehicle accessory battery's state of charge. A controller is configured to activate the prime mover to drive the generator and recharge the vehicle accessory battery in response to the vehicle accessory battery's state of charge falling below a first predetermined level, or transfer electrical power from the hybrid powertrain battery to the vehicle accessory battery in response to the vehicle accessory battery's state of charge falling below a second predetermined level. The invention further includes a method for controlling a hybrid vehicle powertrain system.

Nucleic Acid Sandwich Hybridization Assay with Quantum Dot-Induced Fluorescence Resonance Energy Transfer for Pathogen Detection

Science.gov (United States)

Chou, Cheng-Chung; Huang, Yi-Han

2012-01-01

This paper reports a nucleic acid sandwich hybridization assay with a quantum dot (QD)-induced fluorescence resonance energy transfer (FRET) reporter system. Two label-free hemagglutinin H5 sequences (60-mer DNA and 630-nt cDNA fragment) of avian influenza viruses were used as the targets in this work. Two oligonucleotides (16 mers and 18 mers) that specifically recognize two separate but neighboring regions of the H5 sequences were served as the capturing and reporter probes, respectively. The capturing probe was conjugated to QD655 (donor) in a molar ratio of 10:1 (probe-to-QD), and the reporter probe was labeled with Alexa Fluor 660 dye (acceptor) during synthesis. The sandwich hybridization assay was done in a 20 μL transparent, adhesive frame-confined microchamber on a disposable, temperature-adjustable indium tin oxide (ITO) glass slide. The FRET signal in response to the sandwich hybridization was monitored by a homemade optical sensor comprising a single 400 nm UV light-emitting diode (LED), optical fibers, and a miniature 16-bit spectrophotometer. The target with a concentration ranging from 0.5 nM to 1 μM was successfully correlated with both QD emission decrease at 653 nm and dye emission increase at 690 nm. To sum up, this work is beneficial for developing a portable QD-based nucleic acid sensor for on-site pathogen detection. PMID:23211753
Hybrid III-V/SOI Resonant Cavity Photodetector

DEFF Research Database (Denmark)

Learkthanakhachon, Supannee; Taghizadeh, Alireza; Park, Gyeong Cheol

2016-01-01

A hybrid III-V/SOI resonant cavity photo detector has been demonstrated, which comprises an InP grating reflectorand a Si grating reflector. It can selectively detects an incident light with 1.54-µm wavelength and TM polarization.......A hybrid III-V/SOI resonant cavity photo detector has been demonstrated, which comprises an InP grating reflectorand a Si grating reflector. It can selectively detects an incident light with 1.54-µm wavelength and TM polarization....
Chemical detection with nano/bio hybrid devices based on carbon nanotubes and graphene

Science.gov (United States)

Lerner, Mitchell Bryant

Carbon nanotube field-effect transistors (NT-FETs) and graphene field effect transistors (GFETs) provide a unique transduction platform for chemical and biomolecular detection. The work presented in this thesis describes the fabrication, characterization, and investigation of operational mechanisms of carbon-based biosensors. In the first set of experiments, we used carbon nanotubes as fast, all-electronic readout elements in novel vapor sensors, suitable for applications in environmental monitoring and medicine. Molecules bound to the hybrid alter the electrical properties of the NT-FET via several mechanisms, allowing direct detection as a change in the transistor conduction properties. Vapor sensors suitable for more complex system architectures characteristic of mammalian olfaction were demonstrated using NT-FETs functionalized with mouse olfactory receptor (mOR) proteins or single stranded DNA (ssDNA). Substitution of graphene as the channel material enabled production of hundreds of electronically similar devices with high yield. Etching large scale chemical vapor deposition (CVD)-grown graphene into small channels is itself a challenging problem, and we have developed novel fabrication methods to this end without sacrificing the inherent electrical quality that makes graphene such an attractive material. Large arrays of such devices have potential utility for understanding the physics of ligand-receptor interactions and contributing to the development of a new generation of devices for electronic olfaction. Tailored and specific detection was accomplished by chemically functionalizing the NT-FET or GFET with biomolecules, such as proteins or small molecules, to create a hybrid nanostructures. Targets for detection were widely varied, indicating the utility of these techniques, such as 1) live Salmonella cells in nutrient broth, 2) a biomarker protein indicative of prostate cancer, 3) antigen protein from the bacterium that causes Lyme disease, and 4) glucose
A new diagnostic tool for rapid and accurate detection of Mycobacterium tuberculosis

Directory of Open Access Journals (Sweden)

Ali Nour-Neamatollahi

2018-03-01

Full Text Available Mycobacterium tuberculosis, acid fast bacilli from the family of Mycobacteriaceae, is the causative agent of most cases of tuberculosis. Tuberculosis, as a communicable disease, remains a serious public health threat, killing more than one million people globally every year. Primary diagnosis of tuberculosis bacilli (TB relies mainly on microscopic detection of acid fast bacilli (AFB, but the method suffers from low sensitivity and the results largely depend on the technician’s skill. New diagnostic tools are necessary to be introduced for rapid and accurate detection of the bacilli in sputum samples. We, in collaboration with Anda Biologicals, have developed a new platform, named as “Patho-tb”, for rapid detection of AFB with high sensitivity and with low dependence on human skills. Evaluation of Patho-tb test performance was done in two settings: (1 primary field study conducted using 38 sputa from high TB prevalence area of Iran (Zabol city near to the Afghanistan border, and (2 main study conducted using 476 sputa from Tehran, capital of Iran. Patho-tb was applied for processed sputum samples in parallel with routine diagnostic methods (including AFB microscopy, culture and PCR. All test results were compared to final clinical diagnostic state of an individual and diagnostic sensitivity (DSe, specificity, positive predictive value, negative predictive value and accuracy of each test results were calculated using standard formulations. Analytical sensitivity and specificity of the Patho-tb test were also determined. Calculated values for five above mentioned parameters are as follows: for field study: AFB (DSe: 29.6, DSp: 81.8, PPV: 80, NPV: 23.1, AC: 44.7, Patho-tb (DSe: 63, DSp: 72.7, PPV: 85, NPV: 44.4, AC: 65.8, and for main study: AFB (DSe: 86.1, DSp: 99.4, PPV: 98.5, NPV: 93.9, AC: 95.2, Patho-tb (DSe: 97.4, DSp: 92.9, PPV: 86.5, NPV: 98.7, AC: 94.3. Reproducibility of Patho-tb test results were near to 100% (Cohen’s kappa value
Detection and Elimination of a Potential Fire in Engine and Battery Compartments of Hybrid Electric Vehicles

Directory of Open Access Journals (Sweden)

Macam S. Dattathreya

2012-01-01

Full Text Available This paper presents a novel fuzzy deterministic noncontroller type (FDNCT system and an FDNCT inference algorithm (FIA. The FDNCT uses fuzzy inputs and produces a deterministic non-fuzzy output. The FDNCT is an extension and alternative for the existing fuzzy singleton inference algorithm. The research described in this paper applies FDNCT to build an architecture for an intelligent system to detect and to eliminate potential fires in the engine and battery compartments of a hybrid electric vehicle. The fuzzy inputs consist of sensor data from the engine and battery compartments, namely, temperature, moisture, and voltage and current of the battery. The system synthesizes the data and detects potential fires, takes actions for eliminating the hazard, and notifies the passengers about the potential fire using an audible alarm. This paper also presents the computer simulation results of the comparison between the FIA and singleton inference algorithms for detecting potential fires and determining the actions for eliminating them.
A unique charge-coupled device/xenon arc lamp based imaging system for the accurate detection and quantitation of multicolour fluorescence.

Science.gov (United States)

Spibey, C A; Jackson, P; Herick, K

2001-03-01

In recent years the use of fluorescent dyes in biological applications has dramatically increased. The continual improvement in the capabilities of these fluorescent dyes demands increasingly sensitive detection systems that provide accurate quantitation over a wide linear dynamic range. In the field of proteomics, the detection, quantitation and identification of very low abundance proteins are of extreme importance in understanding cellular processes. Therefore, the instrumentation used to acquire an image of such samples, for spot picking and identification by mass spectrometry, must be sensitive enough to be able, not only, to maximise the sensitivity and dynamic range of the staining dyes but, as importantly, adapt to the ever changing portfolio of fluorescent dyes as they become available. Just as the available fluorescent probes are improving and evolving so are the users application requirements. Therefore, the instrumentation chosen must be flexible to address and adapt to those changing needs. As a result, a highly competitive market for the supply and production of such dyes and the instrumentation for their detection and quantitation have emerged. The instrumentation currently available is based on either laser/photomultiplier tube (PMT) scanning or lamp/charge-coupled device (CCD) based mechanisms. This review briefly discusses the advantages and disadvantages of both System types for fluorescence imaging, gives a technical overview of CCD technology and describes in detail a unique xenon/are lamp CCD based instrument, from PerkinElmer Life Sciences. The Wallac-1442 ARTHUR is unique in its ability to scan both large areas at high resolution and give accurate selectable excitation over the whole of the UV/visible range. It operates by filtering both the excitation and emission wavelengths, providing optimal and accurate measurement and quantitation of virtually any available dye and allows excellent spectral resolution between different fluorophores
Carbon nanotube TiO2 hybrid films for detecting traces of O2

Science.gov (United States)

Llobet, E.; Espinosa, E. H.; Sotter, E.; Ionescu, R.; Vilanova, X.; Torres, J.; Felten, A.; Pireaux, J. J.; Ke, X.; Van Tendeloo, G.; Renaux, F.; Paint, Y.; Hecq, M.; Bittencourt, C.

2008-09-01

Hybrid titania films have been prepared using an adapted sol-gel method for obtaining well-dispersed hydrogen plasma-treated multiwall carbon nanotubes in either pure titania or Nb-doped titania. The drop-coating method has been used to fabricate resistive oxygen sensors based on titania or on titania and carbon nanotube hybrids. Morphology and composition studies have revealed that the dispersion of low amounts of carbon nanotubes within the titania matrix does not significantly alter its crystallization behaviour. The gas sensitivity studies performed on the different samples have shown that the hybrid layers based on titania and carbon nanotubes possess an unprecedented responsiveness towards oxygen (i.e. more than four times higher than that shown by optimized Nb-doped TiO2 films). Furthermore, hybrid sensors containing carbon nanotubes respond at significantly lower operating temperatures than their non-hybrid counterparts. These new hybrid sensors show a strong potential for monitoring traces of oxygen (i.e. beverage industry.
Hybrid model for forecasting time series with trend, seasonal and salendar variation patterns

Science.gov (United States)

Suhartono; Rahayu, S. P.; Prastyo, D. D.; Wijayanti, D. G. P.; Juliyanto

2017-09-01

Most of the monthly time series data in economics and business in Indonesia and other Moslem countries not only contain trend and seasonal, but also affected by two types of calendar variation effects, i.e. the effect of the number of working days or trading and holiday effects. The purpose of this research is to develop a hybrid model or a combination of several forecasting models to predict time series that contain trend, seasonal and calendar variation patterns. This hybrid model is a combination of classical models (namely time series regression and ARIMA model) and/or modern methods (artificial intelligence method, i.e. Artificial Neural Networks). A simulation study was used to show that the proposed procedure for building the hybrid model could work well for forecasting time series with trend, seasonal and calendar variation patterns. Furthermore, the proposed hybrid model is applied for forecasting real data, i.e. monthly data about inflow and outflow of currency at Bank Indonesia. The results show that the hybrid model tend to provide more accurate forecasts than individual forecasting models. Moreover, this result is also in line with the third results of the M3 competition, i.e. the hybrid model on average provides a more accurate forecast than the individual model.
Accurate evaluation for the biofilm-activated sludge reactor using graphical techniques

Science.gov (United States)

Fouad, Moharram; Bhargava, Renu

2018-05-01

A complete graphical solution is obtained for the completely mixed biofilm-activated sludge reactor (hybrid reactor). The solution consists of a series of curves deduced from the principal equations of the hybrid system after converting them in dimensionless form. The curves estimate the basic parameters of the hybrid system such as suspended biomass concentration, sludge residence time, wasted mass of sludge, and food to biomass ratio. All of these parameters can be expressed as functions of hydraulic retention time, influent substrate concentration, substrate concentration in the bulk, stagnant liquid layer thickness, and the minimum substrate concentration which can maintain the biofilm growth in addition to the basic kinetics of the activated sludge process in which all these variables are expressed in a dimensionless form. Compared to other solutions of such system these curves are simple, easy to use, and provide an accurate tool for analyzing such system based on fundamental principles. Further, these curves may be used as a quick tool to get the effect of variables change on the other parameters and the whole system.
Simultaneous reconstruction of temperature distribution and radiative properties in participating media using a hybrid LSQR-PSO algorithm

Science.gov (United States)

Niu, Chun-Yang; Qi, Hong; Huang, Xing; Ruan, Li-Ming; Wang, Wei; Tan, He-Ping

2015-11-01

A hybrid least-square QR decomposition (LSQR)-particle swarm optimization (LSQR-PSO) algorithm was developed to estimate the three-dimensional (3D) temperature distributions and absorption coefficients simultaneously. The outgoing radiative intensities at the boundary surface of the absorbing media were simulated by the line-of-sight (LOS) method, which served as the input for the inverse analysis. The retrieval results showed that the 3D temperature distributions of the participating media with known radiative properties could be retrieved accurately using the LSQR algorithm, even with noisy data. For the participating media with unknown radiative properties, the 3D temperature distributions and absorption coefficients could be retrieved accurately using the LSQR-PSO algorithm even with measurement errors. It was also found that the temperature field could be estimated more accurately than the absorption coefficients. In order to gain insight into the effects on the accuracy of temperature distribution reconstruction, the selection of the detection direction and the angle between two detection directions was also analyzed. Project supported by the Major National Scientific Instruments and Equipment Development Special Foundation of China (Grant No. 51327803), the National Natural Science Foundation of China (Grant No. 51476043), and the Fund of Tianjin Key Laboratory of Civil Aircraft Airworthiness and Maintenance in Civil Aviation University of China.
Microcantilver-based DNA hybridization sensors for Salmonella identification

Directory of Open Access Journals (Sweden)

Carlo Ricciardi

2012-02-01

Full Text Available The detection of pathogenic microorganisms in foods remains a challenging since the safety of foodstuffs has to be ensured by the food producing companies. Conventional methods for the detection and identification of bacteria mainly rely on specific microbiological and biochemical identification. Biomolecular methods, are commonly used as a support for traditional techniques, thanks to their high sensitivity, specificity and not excessive costs. However, new methods like biosensors for example, can be an exciting alternative to the more traditional tecniques for the detection of pathogens in food. In this study we report Salmonella enterica serotype Enteritidis DNA detection through a novel class of label-free biosensors: microcantilevers (MCs. In general, MCs can operate as a microbalance and is used to detect the mass of the entities anchored to the cantilever surface using the decrease in the resonant frequency. We use DNA hybridization as model reaction system and for this reason, specific single stranded probe DNA of the pathogen and three different DNA targets (single-stranded complementary DNA, PCR product and serial dilutions of DNA extracted from S. Enteritidis strains were applied. Two protocols were reported in order to allow the probe immobilization on cantilever surface: i MC surface was functionalized with 3-aminopropyltriethoxysilane and glutaraldehyde and an amino-modified DNA probe was used; ii gold-coated sensors and thiolated DNA probes were used in order to generate a covalent bonding (Th-Au. For the first one, measures after hybridization with the PCR product showed related frequency shift 10 times higher than hybridization with complementary probe and detectable signals were obtained at the concentrations of 103 and 106 cfu/mL after hybridization with bacterial DNA. There are currently optimizations of the second protocol, where preliminary results have shown to be more uniform and therefore more precise within each of the
Identification of rice hybrids using microsatellite and RAPD markers

African Journals Online (AJOL)

STORAGESEVER

2009-05-18

May 18, 2009 ... presence of slower migrating heteroduplex DNA is, there- fore, useful for detection of heterozygous individuals. Maintenance of hybrid seeds conformity in high level is essential for exploitation of hybrid vigor. Therefore, test- ing the hybrid seed purity is necessarily required before its release into the market.
Sensitivity of Helicobacter pylori detection by Giemsa staining is poor in comparison with immunohistochemistry and fluorescent in situ hybridization and strongly depends on inflammatory activity.

Science.gov (United States)

Kocsmár, Éva; Szirtes, Ildikó; Kramer, Zsófia; Szijártó, Attila; Bene, László; Buzás, György Miklós; Kenessey, István; Bronsert, Peter; Csanadi, Agnes; Lutz, Lisa; Werner, Martin; Wellner, Ulrich Friedrich; Kiss, András; Schaff, Zsuzsa; Lotz, Gábor

2017-08-01

Conventional stainings (including H&E and special stains like Giemsa) are the most widely applied histopathologic detection methods of Helicobacter pylori (HP). We aimed to compare the diagnostic performance of Giemsa staining with immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) on a monocentric cohort of 2896 gastric biopsies and relate results to histologic alterations in order to find such histopathologic subgroups in which these methods underperform. All cases were categorized regarding presence or absence of chronic gastritis, inflammatory activity, and mucosal structural alterations. Giemsa revealed 687 cases (23.7%), IHC 795 cases (27.5%), and FISH 788 cases (27.2%) as being HP positive. Giemsa showed significantly lower overall sensitivity (83.3%) compared to IHC (98.8%) and FISH (98.0%). Moreover, the sensitivity of Giemsa dramatically dropped to 33.6% in the nonactive cases. We found that sensitivity of Giemsa strongly depends on HP density and, accordingly, on the presence of activity. Structural alterations (intestinal metaplasia, atrophy, etc.) had only no or weak effect on sensitivity of the three stainings. Both IHC and FISH proved to be equally reliable HP detecting techniques whose diagnostic performance is minimally influenced by mucosal inflammatory and structural alterations contrary to conventional stainings. We highly recommend immunohistochemistry for clinically susceptible, nonactive chronic gastritis cases, if the conventional stain-based HP detection is negative. Moreover, we recommend to use IHC more widely as basic HP stain. Helicobacter pylori FISH technique is primarily recommended to determine bacterial clarithromycin resistance. Furthermore, it is another accurate diagnostic tool for HP. © 2017 John Wiley & Sons Ltd.
Detection of DNA fingerprints of cultivated rice by hybridization with a human minisatellite DNA probe

International Nuclear Information System (INIS)

Dallas, J.F.

1988-01-01

A human minisatellite DNA probe detects several restriction fragment length polymorphisms in cultivars of Asian and African rice. Certain fragments appear to be inherited in a Mendelian fashion and may represent unlinked loci. The hybridization patterns appear to be cultivar-specific and largely unchanged after the regeneration of plants from tissue culture. The results suggest that these regions of the rice genome may be used to generate cultivar-specific DNA fingerprints. The demonstration of similarity between a human minisatellite sequence and polymorphic regions in the rice genome suggests that such regions also occur in the genomes of many other plant species
Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites.

Science.gov (United States)

Zhang, Yingjie; Liu, Qiqi; Zhou, Biao; Wang, Xiaobo; Chen, Suhong; Wang, Shengqi

2017-01-25

Mosquito-borne viruses (MBVs) and parasites (MBPs) are transmitted through hematophagous arthropods-mosquitoes to homoiothermous vertebrates. This study aims at developing a detection method to monitor the spread of mosquito-borne diseases to new areas and diagnose the infections caused by MBVs and MBPs. In this assay, an ultra-sensitive chemiluminescence (CL) detection method was developed and used to simultaneously detect 19 common MBVs and MBPs. In vitro transcript RNA, virus-like particles (VLPs), and plasmids were established as positive or limit of detection (LOD) reference materials. MBVs and MBPs could be genotyped with high sensitivity and specificity. The cut-off values of probes were calculated. The absolute LODs of this strategy to detect serially diluted in vitro transcribed RNAs of MBVs and serially diluted plasmids of MBPs were 10 2 -10 3 copies/μl and 10 1 -10 2 copies/μl, respectively. Further, the LOD of detecting a strain of pre-quantified JEV was 10 1.8 -10 0.8 PFU/ml, fitted well in a linear regression model (coefficient of determination = 0.9678). Ultra-sensitive CL imaging DNA hybridization was developed and could simultaneously detect various MBVs and MBPs. The method described here has the potential to provide considerable labor savings due to its ability to screen for 19 mosquito-borne pathogens simultaneously.
Double-staining chromogenic in situ hybridization as a useful alternative to split-signal fluorescence in situ hybridization in lymphoma diagnostics

DEFF Research Database (Denmark)

van Rijk, A.; Svenstroup-Poulsen, T.; Jones, M.

2010-01-01

within the reach of every pathology laboratory. Design and Methods Our study was initiated to determine the consistency between chromogenic in situ hybridization and fluorescence in situ hybridization, both using split-signal probes developed for the detection of chromosomal breaks. Five hundred...... and actual signal were compared to the original fluorescence hybridization results. In addition, hematoxylin background staining intensity and signal intensity of the double-staining chromogenic in situ hybridization procedure were analyzed. Results With respect to the presence or absence of chromosomal...
Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees.

Science.gov (United States)

Mirzaei, Sajad; Wu, Yufeng

2016-01-01

Hybridization networks represent plausible evolutionary histories of species that are affected by reticulate evolutionary processes. An established computational problem on hybridization networks is constructing the most parsimonious hybridization network such that each of the given phylogenetic trees (called gene trees) is "displayed" in the network. There have been several previous approaches, including an exact method and several heuristics, for this NP-hard problem. However, the exact method is only applicable to a limited range of data, and heuristic methods can be less accurate and also slow sometimes. In this paper, we develop a new algorithm for constructing near parsimonious networks for multiple binary gene trees. This method is more efficient for large numbers of gene trees than previous heuristics. This new method also produces more parsimonious results on many simulated datasets as well as a real biological dataset than a previous method. We also show that our method produces topologically more accurate networks for many datasets.
Detection of secondary electrons with pixelated hybrid semiconductor detectors

International Nuclear Information System (INIS)

Gebert, Ulrike Sonja

2011-01-01

Within the scope of this thesis, secondary electrons were detected with a pixelated semiconductor detector named Timepix. The Timepix detector consists of electronics and a sensor made from a semiconductor material. The connection of sensor and electronics is done for each pixel individually using bump bonds. Electrons with energies above 3 keV can be detected with the sensor. One electron produces a certain amount of electron-hole pairs according to its energy. The charge then drifts along an electric field to the pixel electronics, where it induces an electric signal. Even without a sensor it is possible to detect an electric signal from approximately 1000 electrons directly in the pixel electronics. Two different detector systems to detect secondary electrons using the Timepix detector were investigated during this thesis. First of all, a hybrid photon detector (HPD) was used to detect single photoelectrons. The HPD consists of a vacuum vessel with an entrance window and a cesium iodine photocathode at the inner surface of the window. Photoelectrons are released from the photocathode by incident light and are accelerated in an electric field towards the Timepix detector, where the point of interaction and the arrival time of the electron is determined. With a proximity focusing setup, a time resolution of 12 ns (with an acceleration voltage of 20 kV between photocathode and Timepix detector) was obtained. The HPD examined in this thesis showed a strong dependence of the dark rate form the acceleration voltage and the pressure in the vacuum vessel. At a pressure of few 10 -5 mbar and an acceleration voltage of 20 kV, the dark rate was about 800 Hz per mm 2 area of the read out photocathode. One possibility to reduce the dark rate is to identify ion feedback events. With a slightly modified setup it was possible to reduce the dark rate to 0.5 Hz/mm 2 . To achieve this, a new photocathode was mounted in a shorter distance to the detector. The measurements where
Carbon nanotube-TiO(2) hybrid films for detecting traces of O(2).

Science.gov (United States)

Llobet, E; Espinosa, E H; Sotter, E; Ionescu, R; Vilanova, X; Torres, J; Felten, A; Pireaux, J J; Ke, X; Van Tendeloo, G; Renaux, F; Paint, Y; Hecq, M; Bittencourt, C

2008-09-17

Hybrid titania films have been prepared using an adapted sol-gel method for obtaining well-dispersed hydrogen plasma-treated multiwall carbon nanotubes in either pure titania or Nb-doped titania. The drop-coating method has been used to fabricate resistive oxygen sensors based on titania or on titania and carbon nanotube hybrids. Morphology and composition studies have revealed that the dispersion of low amounts of carbon nanotubes within the titania matrix does not significantly alter its crystallization behaviour. The gas sensitivity studies performed on the different samples have shown that the hybrid layers based on titania and carbon nanotubes possess an unprecedented responsiveness towards oxygen (i.e. more than four times higher than that shown by optimized Nb-doped TiO(2) films). Furthermore, hybrid sensors containing carbon nanotubes respond at significantly lower operating temperatures than their non-hybrid counterparts. These new hybrid sensors show a strong potential for monitoring traces of oxygen (i.e. ≤10 ppm) in a flow of CO(2), which is of interest for the beverage industry.
Carbon nanotube-TiO2 hybrid films for detecting traces of O2

International Nuclear Information System (INIS)

Llobet, E; Espinosa, E H; Sotter, E; Ionescu, R; Vilanova, X; Torres, J; Felten, A; Pireaux, J J; Ke, X; Tendeloo, G Van; Renaux, F; Paint, Y; Hecq, M; Bittencourt, C

2008-01-01

Hybrid titania films have been prepared using an adapted sol-gel method for obtaining well-dispersed hydrogen plasma-treated multiwall carbon nanotubes in either pure titania or Nb-doped titania. The drop-coating method has been used to fabricate resistive oxygen sensors based on titania or on titania and carbon nanotube hybrids. Morphology and composition studies have revealed that the dispersion of low amounts of carbon nanotubes within the titania matrix does not significantly alter its crystallization behaviour. The gas sensitivity studies performed on the different samples have shown that the hybrid layers based on titania and carbon nanotubes possess an unprecedented responsiveness towards oxygen (i.e. more than four times higher than that shown by optimized Nb-doped TiO 2 films). Furthermore, hybrid sensors containing carbon nanotubes respond at significantly lower operating temperatures than their non-hybrid counterparts. These new hybrid sensors show a strong potential for monitoring traces of oxygen (i.e. ≤10 ppm) in a flow of CO 2 , which is of interest for the beverage industry

Compact and Hybrid Feature Description for Building Extraction

Science.gov (United States)

Li, Z.; Liu, Y.; Hu, Y.; Li, P.; Ding, Y.

2017-05-01

Building extraction in aerial orthophotos is crucial for various applications. Currently, deep learning has been shown to be successful in addressing building extraction with high accuracy and high robustness. However, quite a large number of samples is required in training a classifier when using deep learning model. In order to realize accurate and semi-interactive labelling, the performance of feature description is crucial, as it has significant effect on the accuracy of classification. In this paper, we bring forward a compact and hybrid feature description method, in order to guarantees desirable classification accuracy of the corners on the building roof contours. The proposed descriptor is a hybrid description of an image patch constructed from 4 sets of binary intensity tests. Experiments show that benefiting from binary description and making full use of color channels, this descriptor is not only computationally frugal, but also accurate than SURF for building extraction.
Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.

Science.gov (United States)

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

2016-07-15

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

International Nuclear Information System (INIS)

Lv Wei; Jin Fengmin; Guo Quangui; Yang Quanhong; Kang Feiyu

2012-01-01

Highlights: ► We investigated the potential of GNS/NiO/DNA hybrid used as a nonenzymatic sensor. ► DNA is a highly efficient disperse agent for GNS/NiO hybrid than ionic surfactants. ► GNS/NiO/DNA hybrid shows fast electron transfer in the electrochemical reaction. ► GNS/NiO/DNA hybrid shows good detection performance towards glucose. - Abstract: We demonstrate graphene nanosheet/NiO hybrids (GNS/NiO) as the active material for high-performance non-enzymatic glucose sensors. Such sensors are fabricated by DNA-dispersed GNS/NiO suspension deposited on glassy carbon electrodes. ss-DNA shows strong dispersing ability for the GNS/NiO hybrid materials resulting in stable water-dispersible GNS/NiO/DNA hybrids with fully separated layers. The GNS/NiO/DNA hybrids show enhanced electron transfer in the electrocatalytic reaction process, and accordingly, such hybrids modified electrodes show good sensing performance towards glucose and are characterized by large detection ranges, short response periods, low detection limit and high sensitivity and stability.
On the complexity of the Saccharomyces bayanus taxon: hybridization and potential hybrid speciation.

Directory of Open Access Journals (Sweden)

Laura Pérez-Través

Full Text Available Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum, which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99-100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I and heterozygous hybrids (type II, indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains.
First-in-human evaluation of a hybrid modality that allows combined radio- and (near-infrared) fluorescence tracing during surgery

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Berg, Nynke S. van den [Leiden University Medical Center, Interventional Molecular Imaging Laboratory, Department of Radiology (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Urology, Amsterdam (Netherlands); Simon, Herve [Eurorad S.A., Eckbolsheim (France); Kleinjan, Gijs H. [Leiden University Medical Center, Interventional Molecular Imaging Laboratory, Department of Radiology (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Nuclear Medicine, Amsterdam (Netherlands); Engelen, Thijs [Leiden University Medical Center, Interventional Molecular Imaging Laboratory, Department of Radiology (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Head and Neck Surgery and Oncology, Amsterdam (Netherlands); Bunschoten, Anton; Welling, Mick M. [Leiden University Medical Center, Interventional Molecular Imaging Laboratory, Department of Radiology (Netherlands); Tijink, Bernard M. [The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Head and Neck Surgery and Oncology, Amsterdam (Netherlands); Horenblas, Simon [The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Urology, Amsterdam (Netherlands); Chambron, Jacques [The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Nuclear Medicine, Amsterdam (Netherlands); Leeuwen, Fijs W.B. van [Leiden University Medical Center, Interventional Molecular Imaging Laboratory, Department of Radiology (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Urology, Amsterdam (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Head and Neck Surgery and Oncology, Amsterdam (Netherlands)

2015-10-15

The clinical introduction of the hybrid tracer indocyanine green (ICG)-{sup 99m}Tc-nanocolloid, composed of a radioactive and a near-infrared (NIR) fluorescence component, has created the need for surgical (imaging) modalities that allow for simultaneous detection of both signals. This study describes the first-in-human use of a prototype opto-nuclear probe during sentinel node (SN) biopsy using ICG-{sup 99m}Tc-nanocolloid. To allow for fluorescence tracing, a derivative of the conventional gamma probe technology was generated in which two optical fibers were integrated to allow for excitation (785 nm) and emission signal collection (> 810 nm). The ability of this opto-nuclear probe to detect the fluorescence signal of the hybrid tracer ICG-{sup 99m}Tc-nanocolloid was firstly determined ex vivo in (non)SNs samples obtained from 41 patients who underwent hybrid tracer-based SN biopsy in the head and neck or urogenital area. In an in vivo proof-of-concept study in nine of these 41 patients, SNs were localized using combined gamma and fluorescence tracing with the opto-nuclear probe. Fluorescence tracing was performed in a similar manner as gamma tracing and under ambient light conditions. Ex vivo, the gamma tracing option of the opto-nuclear probe correctly identified the SN in all 150 evaluated (non)SN samples. Ex vivo fluorescence tracing in the low-sensitivity mode correctly identified 71.7 % of the samples. This increased to 98.9 % when fluorescence tracing was performed in the high-sensitivity mode. In vivo fluorescence tracing (high-sensitivity mode) accurately identified the SNs in all nine patients (20 SNs evaluated; 100 %). This study demonstrates the first-in-human evaluation of a hybrid modality capable of detecting both gamma and fluorescence signals during a surgical procedure. Fluorescence tracing could be performed in ambient light. (orig.)
First Evidence of a Hybrid of Leishmania (Viannia) braziliensis/L. (V.) peruviana DNA Detected from the Phlebotomine Sand Fly Lutzomyia tejadai in Peru

Science.gov (United States)

Hashiguchi, Yoshihisa

2016-01-01

The natural infection of sand flies by Leishmania was examined in the Department of Huanuco of Peru, where cutaneous leishmaniasis caused by a hybrid of Leishmania (Viannia) braziliensis/L. (V.) peruviana is endemic. A total of 2,997 female sand flies were captured by CDC light traps and Shannon traps, of which 2,931 and 66 flies were identified as Lutzomyia tejadai and Lu fischeri, respectively. Using crude DNA extracted from individual sand flies as a template, Leishmania DNA was detected from one Lu. tejadai. The parasite species was identified as a hybrid of L. (V.) braziliensis/L. (V.) peruviana on the basis of cytochrome b and mannose phosphate isomerase gene analyses. The result suggested that Lu. tejadai is responsible for the transmission of the hybrid Leishmania circulating in this area. PMID:26735142
Simultaneous detection of six stone fruit viruses by non-isotopic molecular hybridization using a unique riboprobe or 'polyprobe'.

Science.gov (United States)

Herranz, M Carmen; Sanchez-Navarro, Jesus A; Aparicio, Frederic; Pallás, Vicente

2005-03-01

A new strategy for the simultaneous detection of plant viruses by molecular hybridization has been developed. Two, four or six viral sequences were fused in tandem and transcribed to render unique riboprobes and designated as 'polyprobes'. The 'polyprobe four' (poly 4) covered the four ilarviruses affecting stone fruit trees including apple mosaic virus (ApMV), prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), and American plum line pattern virus (APLPV) whereas the 'polyprobe two' (poly 2) was designed to detect simultaneously, plum pox virus (PPV) and apple chlorotic leaf spot virus (ACLSV), the two more important viruses affecting these trees. Finally, a 'polyprobe six' (poly 6) was generated to detect any of the six viruses. The three polyprobes were comparable to the individual riboprobes in terms of end-point dilution limit and specificity. The validation of the new simultaneous detection strategy was confirmed by the analysis of 46 field samples from up to seven different hosts collected from 10 different geographical areas.
Chromogenic in situ hybridization is a reliable assay for detection of ALK rearrangements in adenocarcinomas of the lung.

Science.gov (United States)

Schildhaus, Hans-Ulrich; Deml, Karl-Friedrich; Schmitz, Katja; Meiboom, Maren; Binot, Elke; Hauke, Sven; Merkelbach-Bruse, Sabine; Büttner, Reinhard

2013-11-01

Reliable detection of anaplastic lymphoma kinase (ALK) rearrangements is a prerequisite for personalized treatment of lung cancer patients, as ALK rearrangements represent a predictive biomarker for the therapy with specific tyrosine kinase inhibitors. Currently, fluorescent in situ hybridization (FISH) is considered to be the standard method for assessing formalin-fixed and paraffin-embedded tissue for ALK inversions and translocations. However, FISH requires a specialized equipment, the signals fade rapidly and it is difficult to detect overall morphology and tumor heterogeneity. Chromogenic in situ hybridization (CISH) has been successfully introduced as an alternative test for the detection of several genetic aberrations. This study validates a newly developed ALK CISH assay by comparing FISH and CISH signal patterns in lung cancer samples with and without ALK rearrangements. One hundred adenocarcinomas of the lung were included in this study, among them 17 with known ALK rearrangement. FISH and CISH were carried out and evaluated according to the manufacturers' recommendations. For both assays, tumors were considered positive if ≥15% of tumor cells showed either isolated 3' signals or break-apart patterns or a combination of both. A subset of tumors was exemplarily examined by using a novel EML4 (echinoderm microtubule-associated protein-like 4) CISH probe. Red, green and fusion CISH signals were clearcut and different signal patterns were easily recognized. The percentage of aberrant tumor cells was statistically highly correlated (PCISH. On the basis of 86 samples that were evaluable by ALK CISH, we found a 100% sensitivity and 100% specificity of this assay. Furthermore, EML4 rearrangements could be recognized by CISH. CISH is a highly reliable, sensitive and specific method for the detection of ALK gene rearrangements in pulmonary adenocarcinomas. Our results suggest that CISH might serve as a suitable alternative to FISH, which is the current gold
Ultrasensitive electrochemical detection of microRNA-21 combining layered nanostructure of oxidized single-walled carbon nanotubes and nanodiamonds by hybridization chain reaction.

Science.gov (United States)

Liu, Lingzhi; Song, Chao; Zhang, Zhang; Yang, Juan; Zhou, Lili; Zhang, Xing; Xie, Guoming

2015-08-15

Measurement of microRNA (miRNA) levels in body fluids is a crucial tool for the early diagnosis and prognosis of cancers. In this study, we developed an electrochemical assay to detect miRNA-21 by fabricating the electrode with layer-by-layer assembly of oxidized single-walled carbon nanotubes and nanodiamonds. Tetrahedron-structured probes with free-standing probe on the top served as receptors to hybridize with target miRNA directly. The probes were immobilized on the deposited gold nanoparticles through a well-established strong Au-S bond. The electrochemical signal was mainly derived from an ultrasensitive pattern by combining hybridization chain reaction with DNA-functionalized AuNPs, which provided DNAzyme to catalyze H2O2 reduction. Differential pulse voltammetry was applied to record the electrochemical signals, which was increased linearly with the target miRNA-21, and the linear detection range was 10 fM to 1.0 nM. The limit of detection reached 1.95 fM (S/N=3), and the proposed biosensor exhibited good reproducibility and stability, as well as high sensitivity. Hence, this biosensor has a promising potential in clinical application. Copyright © 2015 Elsevier B.V. All rights reserved.
A highly stable electrochemiluminescence sensing system of cadmium sulfide nanowires/graphene hybrid for supersensitive detection of pentachlorophenol

Science.gov (United States)

Deng, Yanan; Chang, Quanying; Yin, Kai; Liu, Chengbin; Wang, Ying

2017-10-01

A highly stable and effective electrochemiluminescence (ECL) sensing system of cadmium sulfide nanowires/reduced graphene oxide (CdS NWS/rGO) hybrid is presented for supersensitive detection of pentachlorophenol (PCP). CdS nanowire is for the first time exploited in ECL sensing. The rGO served as both ECL signal amplifier and immobilization platform, can perfectly enhance the ECL intensity and stability of the sensing system. With S2O82- as coreactant, the ECL signal can be significantly quenched by the addition of PCP. The established ECL sensing system presents a wider linear range from 1.0 × 10-14 to 1.0 × 10-8 M and a much low detection limit of 2 × 10-15 M under the optimum test conditions (e.g., pH 7.0 and 100 mM S2O82-). Furthermore, the ECL sensing system displays a good selectivity for PCP detection. The practicability of the ECL sensing system in real water sample shows that this system could be promisingly applied in the analytical detection of PCP in real water environments.
Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

Science.gov (United States)

Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

2013-01-01

Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179
Detection of biomarkers for Hepatocellular Carcinoma using a hybrid univariate gene selection methods

Directory of Open Access Journals (Sweden)

Abdel Samee Nagwan M

2012-08-01

Full Text Available Abstract Background Discovering new biomarkers has a great role in improving early diagnosis of Hepatocellular carcinoma (HCC. The experimental determination of biomarkers needs a lot of time and money. This motivates this work to use in-silico prediction of biomarkers to reduce the number of experiments required for detecting new ones. This is achieved by extracting the most representative genes in microarrays of HCC. Results In this work, we provide a method for extracting the differential expressed genes, up regulated ones, that can be considered candidate biomarkers in high throughput microarrays of HCC. We examine the power of several gene selection methods (such as Pearson’s correlation coefficient, Cosine coefficient, Euclidean distance, Mutual information and Entropy with different estimators in selecting informative genes. A biological interpretation of the highly ranked genes is done using KEGG (Kyoto Encyclopedia of Genes and Genomes pathways, ENTREZ and DAVID (Database for Annotation, Visualization, and Integrated Discovery databases. The top ten genes selected using Pearson’s correlation coefficient and Cosine coefficient contained six genes that have been implicated in cancer (often multiple cancers genesis in previous studies. A fewer number of genes were obtained by the other methods (4 genes using Mutual information, 3genes using Euclidean distance and only one gene using Entropy. A better result was obtained by the utilization of a hybrid approach based on intersecting the highly ranked genes in the output of all investigated methods. This hybrid combination yielded seven genes (2 genes for HCC and 5 genes in different types of cancer in the top ten genes of the list of intersected genes. Conclusions To strengthen the effectiveness of the univariate selection methods, we propose a hybrid approach by intersecting several of these methods in a cascaded manner. This approach surpasses all of univariate selection methods when
Hybrid soft computing approaches research and applications

CERN Document Server

Dutta, Paramartha; Chakraborty, Susanta

2016-01-01

The book provides a platform for dealing with the flaws and failings of the soft computing paradigm through different manifestations. The different chapters highlight the necessity of the hybrid soft computing methodology in general with emphasis on several application perspectives in particular. Typical examples include (a) Study of Economic Load Dispatch by Various Hybrid Optimization Techniques, (b) An Application of Color Magnetic Resonance Brain Image Segmentation by ParaOptiMUSIG activation Function, (c) Hybrid Rough-PSO Approach in Remote Sensing Imagery Analysis, (d) A Study and Analysis of Hybrid Intelligent Techniques for Breast Cancer Detection using Breast Thermograms, and (e) Hybridization of 2D-3D Images for Human Face Recognition. The elaborate findings of the chapters enhance the exhibition of the hybrid soft computing paradigm in the field of intelligent computing.
Impact of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization method.

Science.gov (United States)

do Nascimento, Cássio; dos Santos, Janine Navarro; Pedrazzi, Vinícius; Pita, Murillo Sucena; Monesi, Nadia; Ribeiro, Ricardo Faria; de Albuquerque, Rubens Ferreira

2014-01-01

Molecular diagnosis methods have been largely used in epidemiological or clinical studies to detect and quantify microbial species that may colonize the oral cavity in healthy or disease. The preservation of genetic material from samples remains the major challenge to ensure the feasibility of these methodologies. Long-term storage may compromise the final result. The aim of this study was to evaluate the effect of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization. Saliva and supragingival biofilm were taken from 10 healthy subjects, aliquoted (n=364) and processed according to proposed protocols: immediate processing and processed after 2 or 4 weeks, and 6 or 12 months of storage at 4°C, -20°C and -80°C. Either total or individual microbial counts were recorded in lower values for samples processed after 12 months of storage, irrespective of temperatures tested. Samples stored up to 6 months at cold temperatures showed similar counts to those immediately processed. The microbial incidence was also significantly reduced in samples stored during 12 months in all temperatures. Temperature and time of oral samples storage have relevant impact in the detection and quantification of bacterial and fungal species by Checkerboard DNA-DNA hybridization method. Samples should be processed immediately after collection or up to 6 months if conserved at cold temperatures to avoid false-negative results. Copyright © 2013 Elsevier Ltd. All rights reserved.
Seven-hour fluorescence in situ hybridization technique for enumeration of Enterobacteriaceae in food and environmental water sample.

Science.gov (United States)

Ootsubo, M; Shimizu, T; Tanaka, R; Sawabe, T; Tajima, K; Ezura, Y

2003-01-01

A fluorescent in situ hybridization (FISH) technique using an Enterobacteriaceae-specific probe (probe D) to target 16S rRNA was improved in order to enumerate, within a single working day, Enterobacteriaceae present in food and environmental water samples. In order to minimize the time required for the FISH procedure, each step of FISH with probe D was re-evaluated using cultured Escherichia coli. Five minutes of ethanol treatment for cell fixation and hybridization were sufficient to visualize cultured E. coli, and FISH could be performed within 1 h. Because of the difficulties in detecting low levels of bacterial cells by FISH without cultivation, a FISH technique for detecting microcolonies on membrane filters was investigated to improve the bacterial detection limit. FISH with probe D following 6 h of cultivation to grow microcolonies on a 13 mm diameter membrane filter was performed, and whole Enterobacteriaceae microcolonies on the filter were then detected and enumerated by manual epifluorescence microscopic scanning at magnification of x100 in ca 5 min. The total time for FISH with probe D following cultivation (FISHFC) was reduced to within 7 h. FISHFC can be applied to enumerate cultivable Enterobacteriaceae in food (above 100 cells g-1) and environmental water samples (above 1 cell ml-1). Cultivable Enterobacteriaceae in food and water samples were enumerated accurately within 7 h using the FISHFC method. A FISHFC method capable of evaluating Enterobacteriaceae contamination in food and environmental water within a single working day was developed.
Branched-DNA signal amplification combined with paper chromatography hybridization assay and used in hepatitis B virus DNA detection

International Nuclear Information System (INIS)

Fu, F.Z.; Liu, L.X.; Wang, W.Q.; Sun, S. H.; Liu, L.B.

2002-01-01

Nucleic acids detection method is vital to the clinical pathogen diagnosis. The established method can be classified into target direct amplification and signal amplification format according to the target DNA or RNA being directly amplified or not. Those methods have advantages and disadvantages respectively in the clinical application. In the United States of American, branched-DNA as a strong signal amplifier is broadly used in the quantification of the nucleic acids. To gain satisfied sensitivity, some expensive label molecular and instruments should be adopted. Personnel should be special trained to perform. Hence, those can't be widely carried out in the Third World. To avoid those disadvantages, we used the branched-DNA amplifier in the paper chromatography hybridization assay. Methods: Branched DNA signal amplifier and series of probes complementary to the nucleic acid sequence of hepatitis B virus (HBV) have been synthesized. HBV-DNA or it's capture probe were immobilized on the high flow nitrocellulose strip. Having loaded at one end of the strip in turn, probes or HBV-DNA in the hybridization solution migrate to the opposite end of the strip by capillary forces and hybridizes to the immobilized DNA. The branched-DNA signal amplifier and probe labeled with biotin or 32P were then loaded. Through streptavidin-alkaline phosphatase (SA-AP) conjugate and NBT/BCIP ( the specific chromogenic substrate of AP) or autoradiography, the result can be visualized by color reaction or image production on the X-ray film. Results: The sensitivity of this HBV-DNA detection method used probe labeled with biotin and 32P are 1ng and 10pg. The method using the probe labeled with biotin is simple and rapid (2h) without depending on special instruments, it also avoids the pollution of EtBr which can lead to tumor. And the method using the probe labeled with 32P is simple and sensitive, with the exception of long time autoradiography and the inconvenient isotopic disposal
Mobile, hybrid Compton/coded aperture imaging for detection, identification and localization of gamma-ray sources at stand-off distances

Science.gov (United States)

Tornga, Shawn R.

The Stand-off Radiation Detection System (SORDS) program is an Advanced Technology Demonstration (ATD) project through the Department of Homeland Security's Domestic Nuclear Detection Office (DNDO) with the goal of detection, identification and localization of weak radiological sources in the presence of large dynamic backgrounds. The Raytheon-SORDS Tri-Modal Imager (TMI) is a mobile truck-based, hybrid gamma-ray imaging system able to quickly detect, identify and localize, radiation sources at standoff distances through improved sensitivity while minimizing the false alarm rate. Reconstruction of gamma-ray sources is performed using a combination of two imaging modalities; coded aperture and Compton scatter imaging. The TMI consists of 35 sodium iodide (NaI) crystals 5x5x2 in3 each, arranged in a random coded aperture mask array (CA), followed by 30 position sensitive NaI bars each 24x2.5x3 in3 called the detection array (DA). The CA array acts as both a coded aperture mask and scattering detector for Compton events. The large-area DA array acts as a collection detector for both Compton scattered events and coded aperture events. In this thesis, developed coded aperture, Compton and hybrid imaging algorithms will be described along with their performance. It will be shown that multiple imaging modalities can be fused to improve detection sensitivity over a broader energy range than either alone. Since the TMI is a moving system, peripheral data, such as a Global Positioning System (GPS) and Inertial Navigation System (INS) must also be incorporated. A method of adapting static imaging algorithms to a moving platform has been developed. Also, algorithms were developed in parallel with detector hardware, through the use of extensive simulations performed with the Geometry and Tracking Toolkit v4 (GEANT4). Simulations have been well validated against measured data. Results of image reconstruction algorithms at various speeds and distances will be presented as well as
The Hybrid II assay: a sensitive and specific real-time hybridization assay for the diagnosis of Theileria parva infection in Cape buffalo (Syncerus caffer) and cattle.

Science.gov (United States)

Pienaar, Ronel; Potgieter, Fred T; Latif, Abdalla A; Thekisoe, Oriel M M; Mans, Ben J

2011-12-01

Corridor disease is an acute, fatal disease of cattle caused by buffalo-adapted Theileria parva. This is a nationally controlled disease in South Africa and strict control measures apply for the movement of buffalo, which includes mandatory testing for the presence of T. parva and other controlled diseases. Accurate diagnosis of the T. parva carrier state in buffalo using the official real-time hybridization PCR assay (Sibeko et al. 2008), has been shown to be affected by concurrent infection with T. sp. (buffalo)-like parasites. We describe the Hybrid II assay, a real-time hybridization PCR method, which compares well with the official hybridization assay in terms of specificity and sensitivity. It is, however, not influenced by mixed infections of T. sp. (buffalo)-like parasites and is as such a significant improvement on the current hybridization assay.
Rapid and sensitive suspension array for multiplex detection of organophosphorus pesticides and carbamate pesticides based on silica–hydrogel hybrid microbeads

International Nuclear Information System (INIS)

Wang, Xuan; Mu, Zhongde; Shangguan, Fengqi; Liu, Ran; Pu, Yuepu; Yin, Lihong

2014-01-01

Highlights: • Silica–hydrogel hybrid microbeads were used to develop suspension array. • The results in detecting pesticides agree well with those from LC–MS/MS. • The method showed the good capability for multiplex analysis of pesticides residues. - Abstract: A technique for multiplex detection of organophosphorus pesticides and carbamate pesticides has been developed using a suspension array based on silica–hydrogel hybrid microbeads (SHHMs). The main advantage of SHHMs, which consist of both silica and hydrogel materials, is that they not only could be distinguished by their characteristic reflection peak originating from the stop-band of the photonic crystal but also have low non-specific adsorption of proteins. Using fluorescent immunoassay, the LODs for fenitrothion, chlorpyrifos-methyl, fenthion, carbaryl and metolcarb were measured to be 0.02 ng/mL, 0.012 ng/mL, 0.04 ng/mL, 0.05 ng/mL and 0.1 ng/mL, respectively, all of which are much lower than the maximum residue limits, as reported in the European Union pesticides database. All the determination coefficients for these five pesticides were greater than 0.99, demonstrating excellent correlations. The suspension array was specific and had no significant cross-reactivity with other chemicals. The results for the detection of pesticide residues collected from agricultural samples using this method agree well with those from liquid chromatography–tandem mass spectrometry. Our results showed that this simple method is suitable for simultaneous detection of these five pesticides residues in fruits and vegetables
Rapid and sensitive suspension array for multiplex detection of organophosphorus pesticides and carbamate pesticides based on silica–hydrogel hybrid microbeads

Energy Technology Data Exchange (ETDEWEB)

Wang, Xuan [Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu (China); Mu, Zhongde; Shangguan, Fengqi [State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu (China); Liu, Ran; Pu, Yuepu [Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu (China); Yin, Lihong, E-mail: lhyin@seu.edu.cn [Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu (China)

2014-05-01

Highlights: • Silica–hydrogel hybrid microbeads were used to develop suspension array. • The results in detecting pesticides agree well with those from LC–MS/MS. • The method showed the good capability for multiplex analysis of pesticides residues. - Abstract: A technique for multiplex detection of organophosphorus pesticides and carbamate pesticides has been developed using a suspension array based on silica–hydrogel hybrid microbeads (SHHMs). The main advantage of SHHMs, which consist of both silica and hydrogel materials, is that they not only could be distinguished by their characteristic reflection peak originating from the stop-band of the photonic crystal but also have low non-specific adsorption of proteins. Using fluorescent immunoassay, the LODs for fenitrothion, chlorpyrifos-methyl, fenthion, carbaryl and metolcarb were measured to be 0.02 ng/mL, 0.012 ng/mL, 0.04 ng/mL, 0.05 ng/mL and 0.1 ng/mL, respectively, all of which are much lower than the maximum residue limits, as reported in the European Union pesticides database. All the determination coefficients for these five pesticides were greater than 0.99, demonstrating excellent correlations. The suspension array was specific and had no significant cross-reactivity with other chemicals. The results for the detection of pesticide residues collected from agricultural samples using this method agree well with those from liquid chromatography–tandem mass spectrometry. Our results showed that this simple method is suitable for simultaneous detection of these five pesticides residues in fruits and vegetables.

Fast and accurate implementation of Fourier spectral approximations of nonlocal diffusion operators and its applications

International Nuclear Information System (INIS)

Du, Qiang; Yang, Jiang

2017-01-01

This work is concerned with the Fourier spectral approximation of various integral differential equations associated with some linear nonlocal diffusion and peridynamic operators under periodic boundary conditions. For radially symmetric kernels, the nonlocal operators under consideration are diagonalizable in the Fourier space so that the main computational challenge is on the accurate and fast evaluation of their eigenvalues or Fourier symbols consisting of possibly singular and highly oscillatory integrals. For a large class of fractional power-like kernels, we propose a new approach based on reformulating the Fourier symbols both as coefficients of a series expansion and solutions of some simple ODE models. We then propose a hybrid algorithm that utilizes both truncated series expansions and high order Runge–Kutta ODE solvers to provide fast evaluation of Fourier symbols in both one and higher dimensional spaces. It is shown that this hybrid algorithm is robust, efficient and accurate. As applications, we combine this hybrid spectral discretization in the spatial variables and the fourth-order exponential time differencing Runge–Kutta for temporal discretization to offer high order approximations of some nonlocal gradient dynamics including nonlocal Allen–Cahn equations, nonlocal Cahn–Hilliard equations, and nonlocal phase-field crystal models. Numerical results show the accuracy and effectiveness of the fully discrete scheme and illustrate some interesting phenomena associated with the nonlocal models.
Dynamic Modeling and Simulation of a Switched Reluctance Motor in a Series Hybrid Electric Vehicle

OpenAIRE

Siavash Sadeghi; Mojtaba Mirsalim; Arash Hassanpour Isfahani

2010-01-01

Dynamic behavior analysis of electric motors is required in order to accuratelyevaluate the performance, energy consumption and pollution level of hybrid electricvehicles. Simulation tools for hybrid electric vehicles are divided into steady state anddynamic models. Tools with steady-state models are useful for system-level analysiswhereas tools that utilize dynamic models give in-depth information about the behavior ofsublevel components. For the accurate prediction of hybrid electric vehicl...
Accurate Point-of-Care Detection of Ruptured Fetal Membranes: Improved Diagnostic Performance Characteristics with a Monoclonal/Polyclonal Immunoassay

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Linda C. Rogers

2016-01-01

Full Text Available Objective Accurate and timely diagnosis of rupture of membranes (ROM is imperative to allow for gestational age-specific interventions. This study compared the diagnostic performance characteristics between two methods used for the detection of ROM as measured in the same patient. Methods Vaginal secretions were evaluated using the conventional fern test as well as a point-of-care monoclonal/polyclonal immunoassay test (ROM Plus® in 75 pregnant patients who presented to labor and delivery with complaints of leaking amniotic fluid. Both tests were compared to analytical confirmation of ROM using three external laboratory tests. Diagnostic performance characteristics were calculated including sensitivity, specificity, positive predictive value (PPV, negative predictive value (NPV, and accuracy. Results Diagnostic performance characteristics uniformly favored ROM detection using the immunoassay test compared to the fern test: sensitivity (100% vs. 77.8%, specificity (94.8% vs. 79.3%, PPV (75% vs. 36.8%, NPV (100% vs. 95.8%, and accuracy (95.5% vs. 79.1%. Conclusions The point-of-care immunoassay test provides improved diagnostic accuracy for the detection of ROM compared to fern testing. It has the potential of improving patient management decisions, thereby minimizing serious complications and perinatal morbidity.
Increasing the productivity of glycopeptides analysis by using higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation.

Science.gov (United States)

Saba, Julian; Dutta, Sucharita; Hemenway, Eric; Viner, Rosa

2012-01-01

Currently, glycans are attracting attention from the scientific community as potential biomarkers or as posttranslational modifications (PTMs) of therapeutic proteins. However, structural characterization of glycoproteins and glycopeptides remains analytically challenging. Here, we report on the implementation of a novel acquisition strategy termed higher-energy collision dissociation-accurate mass-product-dependent electron transfer dissociation (HCD-PD-ETD) on a hybrid linear ion trap-orbitrap mass spectrometer. This acquisition strategy uses the complementary fragmentations of ETD and HCD for glycopeptides analysis in an intelligent fashion. Furthermore, the approach minimizes user input for optimizing instrumental parameters and enables straightforward detection of glycopeptides. ETD spectra are only acquired when glycan oxonium ions from MS/MS HCD are detected. The advantage of this approach is that it streamlines data analysis and improves dynamic range and duty cycle. Here, we present the benefits of HCD-PD-ETD relative to the traditional alternating HCD/ETD for a trainer set containing twelve-protein mixture with two glycoproteins: human serotransferrin, ovalbumin and contaminations of two other: bovine alpha 1 acid glycoprotein (bAGP) and bovine fetuin.
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.
Hybrid nanostructures: synthesis, morphology and functional properties

International Nuclear Information System (INIS)

Povolotskaya, A V; Povolotskiy, A V; Manshina, A A

2015-01-01

Hybrid nanostructures representing combinations of different materials and possessing properties that are absent in separate components forming the hybrid are discussed. Particular attention is given to hybrid structures containing plasmonic and magnetic nanoparticles, methods of their synthesis and the relationship between the composition, structure and properties. The functional features of the hybrid nanomaterials of various morphology (with core–shell structures, with encapsulated metal nanoparticles and with metal nanoparticles on the surface) are considered. The unique properties of these hybrid materials are demonstrated, which are of interest for solving problems of catalysis and photocatalysis, detecting impurities in various media, in vivo visualization, bioanalysis, as well as for the design of optical labels and multifunctional diagnostic nanoplatforms. The bibliography includes 182 references
Hybrid methods for cybersecurity analysis :

Energy Technology Data Exchange (ETDEWEB)

Davis, Warren Leon,; Dunlavy, Daniel M.

2014-01-01

Early 2010 saw a signi cant change in adversarial techniques aimed at network intrusion: a shift from malware delivered via email attachments toward the use of hidden, embedded hyperlinks to initiate sequences of downloads and interactions with web sites and network servers containing malicious software. Enterprise security groups were well poised and experienced in defending the former attacks, but the new types of attacks were larger in number, more challenging to detect, dynamic in nature, and required the development of new technologies and analytic capabilities. The Hybrid LDRD project was aimed at delivering new capabilities in large-scale data modeling and analysis to enterprise security operators and analysts and understanding the challenges of detection and prevention of emerging cybersecurity threats. Leveraging previous LDRD research e orts and capabilities in large-scale relational data analysis, large-scale discrete data analysis and visualization, and streaming data analysis, new modeling and analysis capabilities were quickly brought to bear on the problems in email phishing and spear phishing attacks in the Sandia enterprise security operational groups at the onset of the Hybrid project. As part of this project, a software development and deployment framework was created within the security analyst work ow tool sets to facilitate the delivery and testing of new capabilities as they became available, and machine learning algorithms were developed to address the challenge of dynamic threats. Furthermore, researchers from the Hybrid project were embedded in the security analyst groups for almost a full year, engaged in daily operational activities and routines, creating an atmosphere of trust and collaboration between the researchers and security personnel. The Hybrid project has altered the way that research ideas can be incorporated into the production environments of Sandias enterprise security groups, reducing time to deployment from months and
Optical orientation in ferromagnet/semiconductor hybrids

International Nuclear Information System (INIS)

Korenev, V L

2008-01-01

The physics of optical pumping of semiconductor electrons in ferromagnet/semiconductor hybrids is discussed. Optically oriented semiconductor electrons detect the magnetic state of a ferromagnetic film. In turn, the ferromagnetism of the hybrid can be controlled optically with the help of a semiconductor. Spin–spin interactions near the ferromagnet/semiconductor interface play a crucial role in the optical readout and the manipulation of ferromagnetism
Optical orientation in ferromagnet/semiconductor hybrids

Science.gov (United States)

Korenev, V. L.

2008-11-01

The physics of optical pumping of semiconductor electrons in ferromagnet/semiconductor hybrids is discussed. Optically oriented semiconductor electrons detect the magnetic state of a ferromagnetic film. In turn, the ferromagnetism of the hybrid can be controlled optically with the help of a semiconductor. Spin-spin interactions near the ferromagnet/semiconductor interface play a crucial role in the optical readout and the manipulation of ferromagnetism.
Optical Orientation in Ferromagnet/Semiconductor Hybrids

OpenAIRE

Korenev, V. L.

2008-01-01

The physics of optical pumping of semiconductor electrons in the ferromagnet/semiconductor hybrids is discussed. Optically oriented semiconductor electrons detect the magnetic state of the ferromagnetic film. In turn, the ferromagnetism of the hybrid can be controlled optically with the help of the semiconductor. Spin-spin interactions near the interface ferromagnet/semiconductor play crucial role in the optical readout and the manipulation of ferromagnetism.
An Accurate Estimate of the Free Energy and Phase Diagram of All-DNA Bulk Fluids

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Emanuele Locatelli

2018-04-01

Full Text Available We present a numerical study in which large-scale bulk simulations of self-assembled DNA constructs have been carried out with a realistic coarse-grained model. The investigation aims at obtaining a precise, albeit numerically demanding, estimate of the free energy for such systems. We then, in turn, use these accurate results to validate a recently proposed theoretical approach that builds on a liquid-state theory, the Wertheim theory, to compute the phase diagram of all-DNA fluids. This hybrid theoretical/numerical approach, based on the lowest-order virial expansion and on a nearest-neighbor DNA model, can provide, in an undemanding way, a parameter-free thermodynamic description of DNA associating fluids that is in semi-quantitative agreement with experiments. We show that the predictions of the scheme are as accurate as those obtained with more sophisticated methods. We also demonstrate the flexibility of the approach by incorporating non-trivial additional contributions that go beyond the nearest-neighbor model to compute the DNA hybridization free energy.
Investigation of the binary fraction among candidate A-F type hybrid stars detected by Kepler

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Lampens P.

2015-01-01

Full Text Available We are currently monitoring up to 40 Kepler candidate δ Scuti-γ Doradus (resp. γ Doradus-δ Scuti hybrid stars in radial velocity in order to identify the physical cause behind the low frequencies observed in the periodograms based on the ultra-high accuracy Kepler space photometry. The presence of low frequency variability in unevolved or slightly evolved oscillating A/F-type stars can generally be explained in three ways: either 1 the star is an (undetected binary or multiple system, or 2 the star is a g-mode pulsator (i.e. a genuine hybrid, or 3 the star’s atmosphere displays an asymmetric intensity distribution (caused by spots, i.e. chemical anomalies, or by (very high rotation, which is detected through rotational modulation. Our targets were selected from the globally characterized variable A/F-type stars of the Kepler mission [7]. We observe each star at least 4 times unevenly spread over a time lapse up to 2 months with the HERMES spectrograph [6]. In the case of composite, multiple-lined spectra, these observations also provide the atmospheric properties of each component. Our principal goal is to estimate the fraction of short-period, spectroscopic systems in the sample.
Europium(III) complex-functionalized magnetic nanoparticle as a chemosensor for ultrasensitive detection and removal of copper(II) from aqueous solution.

Science.gov (United States)

Liu, Jing; Zuo, Wei; Zhang, Wei; Liu, Jian; Wang, Zhiyi; Yang, Zhengyin; Wang, Baodui

2014-10-07

Ultrasensitive, accurate detection and separation of heavy metal ions is very important in environmental monitoring and biological detection. In this paper, a highly sensitive and specific detection method for Cu(2+) based on the fluorescence quenching of a europium(III) hybrid magnetic nanoprobe is presented. This nanoprobe can detect Cu(2+) over a wide pH range (5.0-10.0) with a detection limit as low as 0.1 nM and it can be used for detecting Cu(2+) in living cells. After the magnetic separation, the Cu(2+) concentration decreased to 1.18 ppm, which is less than the US EPA drinking water standard (1.3 ppm), and more than 70% Cu(2+) could be removed when the amount of nanocomposite 1 reached 1 mg.
Ion cyclotron and lower hybrid arrays applicable to current drive in fusion reactors

Energy Technology Data Exchange (ETDEWEB)

Bosia, G.; Ragona, R. [Department of Physics, Università di Torino (Italy); Helou, W.; Goniche, M.; Hillaret, J. [CEA/DSM/IRFM F-13 108 St Paul Les Durance (France)

2014-02-12

This paper presents concepts for Ion Cyclotron and Lower Hybrid Current Drive arrays applicable to fusion reactors and based on periodically loaded line power division. It is shown that, in large arrays, such as the ones proposed for fusion reactor applications, these schemes can offer, in principle, a number of practical advantages, compared with currently adopted ones, such as in-blanket operation at significantly reduced power density, lay out suitable for water cooling, single ended or balanced power feed, simple and load independent impedance matching In addition, a remote and accurate real time measurement of the complex impedance of all array elements as well as detection, location, and measurement of the complex admittance of a single arc occurring anywhere in the structure is possible.
Highly accurate determination of relative gamma-ray detection efficiency for Ge detector and its application

International Nuclear Information System (INIS)

Miyahara, H.; Mori, C.; Fleming, R.F.; Dewaraja, Y.K.

1997-01-01

When quantitative measurements of γ-rays using High-Purity Ge (HPGe) detectors are made for a variety of applications, accurate knowledge of oy-ray detection efficiency is required. The emission rates of γ-rays from sources can be determined quickly in the case that the absolute peak efficiency is calibrated. On the other hand, the relative peak efficiencies can be used for determination of intensity ratios for plural samples and for comparison to the standard source. Thus, both absolute and relative detection efficiencies are important in use of γ-ray detector. The objective of this work is to determine the relative gamma-ray peak detection efficiency for an HPGe detector with the uncertainty approaching 0.1% . We used some nuclides which emit at least two gamma-rays with energies from 700 to 2400 keV for which the relative emission probabilities are known with uncertainties much smaller than 0.1%. The relative peak detection efficiencies were calculated from the measurements of the nuclides, 46 Sc, 48 Sc, 60 Co and 94 Nb, emitting two γ- rays with the emission probabilities of almost unity. It is important that various corrections for the emission probabilities, the cascade summing effect, and the self-absorption are small. A third order polynomial function on both logarithmic scales of energy and efficiency was fitted to the data, and the peak efficiency predicted at certain energy from covariance matrix showed the uncertainty less than 0.5% except for near 700 keV. As an application, the emission probabilities of the 1037.5 and 1212.9 keV γ-rays for 48 Sc were determined using the function of the highly precise relative peak efficiency. Those were 0.9777+0,.00079 and 0.02345+0.00017 for the 1037.5 and 1212.9 keV γ-rays, respectively. The sum of these probabilities is close to unity within the uncertainty which means that the certainties of the results are high and the accuracy has been improved considerably
Simultaneous detection of Acidovorax avenae subsp. citrulli and Didymella bryoniae in cucurbit seedlots using magnetic capture hybridization and real-time polymerase chain reaction.

Science.gov (United States)

Ha, Y; Fessehaie, A; Ling, K S; Wechter, W P; Keinath, A P; Walcott, R R

2009-06-01

To improve the simultaneous detection of two pathogens in cucurbit seed, a combination of magnetic capture hybridization (MCH) and multiplex real-time polymerase chain reaction (PCR) was developed. Single-stranded DNA hybridization capture probes targeting DNA of Acidovorax avenae subsp. citrulli, causal agent of bacterial fruit blotch, and Didymella bryoniae, causal agent of gummy stem blight, were covalently attached to magnetic particles and used to selectively concentrate template DNA from cucurbit seed samples. Sequestered template DNAs were subsequently amplified by multiplex real-time PCR using pathogen-specific TaqMan PCR assays. The MCH multiplex real-time PCR assay displayed a detection threshold of A. avenae subsp. citrulli at 10 CFU/ml and D. bryoniae at 10(5) conidia/ml in mixtures of pure cultures of the two pathogens, which was 10-fold more sensitive than the direct real-time PCR assays for the two pathogens separately. Although the direct real-time PCR assay displayed a detection threshold for A. avenae subsp. citrulli DNA of 100 fg/microl in 25% (1/4 samples) of the samples assayed, MCH real-time PCR demonstrated 100% detection frequency (4/4 samples) at the same DNA concentration. MCH did not improve detection sensitivity for D. bryoniae relative to direct real-time PCR using conidial suspensions or seed washes from D. bryoniae-infested cucurbit seed. However, MCH real-time PCR facilitated detection of both target pathogens in watermelon and melon seed samples (n = 5,000 seeds/sample) in which 0.02% of the seed were infested with A. avenae subsp. citrulli and 0.02% were infested with D. bryoniae.
Detection and genotyping of Entamoeba histolytica, Entamoeba dispar, Giardia lamblia, and Cryptosporidium parvum by oligonucleotide microarray.

Science.gov (United States)

Wang, Zheng; Vora, Gary J; Stenger, David A

2004-07-01

Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum are the most frequently identified protozoan parasites causing waterborne disease outbreaks. The morbidity and mortality associated with these intestinal parasitic infections warrant the development of rapid and accurate detection and genotyping methods to aid public health efforts aimed at preventing and controlling outbreaks. In this study, we describe the development of an oligonucleotide microarray capable of detecting and discriminating between E. histolytica, Entamoeba dispar, G. lamblia assemblages A and B, and C. parvum types 1 and 2 in a single assay. Unique hybridization patterns for each selected protozoan were generated by amplifying six to eight diagnostic sequences/organism by multiplex PCR; fluorescent labeling of the amplicons via primer extension; and subsequent hybridization to a set of genus-, species-, and subtype-specific covalently immobilized oligonucleotide probes. The profile-based specificity of this methodology not only permitted for the unequivocal identification of the six targeted species and subtypes, but also demonstrated its potential in identifying related species such as Cryptosporidium meleagridis and Cryptosporidium muris. In addition, sensitivity assays demonstrated lower detection limits of five trophozoites of G. lamblia. Taken together, the specificity and sensitivity of the microarray-based approach suggest that this methodology may provide a promising tool to detect and genotype protozoa from clinical and environmental samples.
An HMM-based comparative genomic framework for detecting introgression in eukaryotes.

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Kevin J Liu

2014-06-01

Full Text Available One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM-a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs to simultaneously capture the (potentially reticulate evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes. Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.
Real-time hybrid simulation using the convolution integral method

International Nuclear Information System (INIS)

Kim, Sung Jig; Christenson, Richard E; Wojtkiewicz, Steven F; Johnson, Erik A

2011-01-01

This paper proposes a real-time hybrid simulation method that will allow complex systems to be tested within the hybrid test framework by employing the convolution integral (CI) method. The proposed CI method is potentially transformative for real-time hybrid simulation. The CI method can allow real-time hybrid simulation to be conducted regardless of the size and complexity of the numerical model and for numerical stability to be ensured in the presence of high frequency responses in the simulation. This paper presents the general theory behind the proposed CI method and provides experimental verification of the proposed method by comparing the CI method to the current integration time-stepping (ITS) method. Real-time hybrid simulation is conducted in the Advanced Hazard Mitigation Laboratory at the University of Connecticut. A seismically excited two-story shear frame building with a magneto-rheological (MR) fluid damper is selected as the test structure to experimentally validate the proposed method. The building structure is numerically modeled and simulated, while the MR damper is physically tested. Real-time hybrid simulation using the proposed CI method is shown to provide accurate results
Dramatically improved RNA in situ hybridization signals using LNA-modified probes

DEFF Research Database (Denmark)

Thomsen, Rune; Nielsen, Peter Stein; Jensen, Torben Heick

2005-01-01

. This increases the thermal stability of hybrids formed with RNA. The LNA-based probes detect specific RNAs in fixed yeast cells with an efficiency far better than conventional DNA oligonucleotide probes of the same sequence. Using this probe design, we were also able to detect poly(A)+ RNA accumulation within......In situ detection of RNA by hybridization with complementary probes is a powerful technique. Probe design is a critical parameter in successful target detection. We have evaluated the efficiency of fluorescent DNA oligonucleotides modified to contain locked nucleic acid (LNA) residues...

Detection of Bacteria by Fluorescence in Situ Hybridization in Culture-Negative Soft Tissue Filler Lesions

DEFF Research Database (Denmark)

Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

2009-01-01

BACKGROUND Adverse reactions to polyacrylamide gel occur as swellings or nodules, and controversy exists whether these are due to bacterial infection or an autoimmune reaction to the filler. OBJECTIVES Biopsies from culture-negative long-lasting nodules after injection with different types...... of polyacrylamide gel were examined with a combination of Gram stain and fluorescence in situ hybridization. RESULTS Bacteria were detected in biopsies from seven of eight patients. They inhabited gel and intervening tissue and tended to lie in aggregates. CONCLUSION This study supports the assumption...... that infection with bacteria in aggregates causes culture-negative late adverse reactions to polyacrylamide gel, suggesting a biofilm environment. The authors have indicated no significant interest with commercial supporters....
Electochemical detection of chromosome translocation

DEFF Research Database (Denmark)

Kwasny, Dorota; Dimaki, Maria; Silahtaroglu, Asli

2014-01-01

Cytogenetics is a study of the cell structure with a main focus on chromosomes content and their structure. Chromosome abnormalities, such as translocations may cause various genetic disorders and heametological malignancies. Chromosome translocations are structural rearrangements of two...... chromosomes that results in formation of derivative chromosomes with a mixed DNA sequence. The method currently used for their detection is Fluorescent In Situ Hybridization, which requires a use of expensive, fluorescently labeled probes that target the derivative chromosomes. We present here a double...... hybridization approach developed for label-free detection of the chromosome translocations. For specific translocation detection it is necessary to determine that the two DNA sequences forming a derivative chromosome are connected, which is achieved by two subsequent hybridization steps. The electrochemical...
The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

Science.gov (United States)

Xu, Xin; Goddard, William A.

2004-01-01

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee–Yang–Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee–Yang–Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA. PMID:14981235
A Hybrid Estimator for Active/Reactive Power Control of Single-Phase Distributed Generation Systems with Energy Storage

DEFF Research Database (Denmark)

Pahlevani, Majid; Eren, Suzan; Guerrero, Josep M.

2016-01-01

This paper presents a new active/reactive power closed-loop control system for a hybrid renewable energy generation system used for single-phase residential/commercial applications. The proposed active/reactive control method includes a hybrid estimator, which is able to quickly and accurately es...
Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast

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Simon M. Dittami

2017-11-01

Full Text Available Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast.
Numerical and structural genomic aberrations are reliably detectable in tissue microarrays of formalin-fixed paraffin-embedded tumor samples by fluorescence in-situ hybridization.

Directory of Open Access Journals (Sweden)

Heike Horn

Full Text Available Few data are available regarding the reliability of fluorescence in-situ hybridization (FISH, especially for chromosomal deletions, in high-throughput settings using tissue microarrays (TMAs. We performed a comprehensive FISH study for the detection of chromosomal translocations and deletions in formalin-fixed and paraffin-embedded (FFPE tumor specimens arranged in TMA format. We analyzed 46 B-cell lymphoma (B-NHL specimens with known karyotypes for translocations of IGH-, BCL2-, BCL6- and MYC-genes. Locus-specific DNA probes were used for the detection of deletions in chromosome bands 6q21 and 9p21 in 62 follicular lymphomas (FL and six malignant mesothelioma (MM samples, respectively. To test for aberrant signals generated by truncation of nuclei following sectioning of FFPE tissue samples, cell line dilutions with 9p21-deletions were embedded into paraffin blocks. The overall TMA hybridization efficiency was 94%. FISH results regarding translocations matched karyotyping data in 93%. As for chromosomal deletions, sectioning artefacts occurred in 17% to 25% of cells, suggesting that the proportion of cells showing deletions should exceed 25% to be reliably detectable. In conclusion, FISH represents a robust tool for the detection of structural as well as numerical aberrations in FFPE tissue samples in a TMA-based high-throughput setting, when rigorous cut-off values and appropriate controls are maintained, and, of note, was superior to quantitative PCR approaches.
An exonuclease-assisted amplification electrochemical aptasensor for Hg(2+) detection based on hybridization chain reaction.

Science.gov (United States)

Bao, Ting; Wen, Wei; Zhang, Xiuhua; Xia, Qinghua; Wang, Shengfu

2015-08-15

In this work, a novel electrochemical aptasensor was developed for Hg(2+) detection based on exonuclease-assisted target recycling and hybridization chain reaction (HCR) dual signal amplification strategy. The presence of Hg(2+) induced the T-rich DNA partly folded into duplex-like structure via the Hg(2+) mediated T-Hg(2+)-T base pairs, which triggered the activity of exonuclease III (Exo III). Exo III selectively digested the double-strand DNA containing multiple T-Hg(2+)-T base pairs from its 3'-end, the released Hg(2+) participated analyte recycle. With each digestion cycle, a digestion product named as help DNA was obtained, which acted as a linkage between the capture DNA and auxiliary DNA. The presence of help DNA and two auxiliary DNA collectively facilitated successful HCR process and formed long double-stranded DNA. [Ru(NH3)6](3+) was used as redox indicator, which electrostatically bound to the double strands and produced an electrochemical signal. Exo III-assisted target recycling and HCR dual amplification significantly improved the sensitivity for Hg(2+) with a detection limit of 0.12 pM (S/N=3). Furthermore, the proposed aptasensor had a promising potential for the application of Hg(2+) detection in real aquatic sample analysis. Copyright © 2015 Elsevier B.V. All rights reserved.
An electrochemical impedance biosensor for Hg2+ detection based on DNA hydrogel by coupling with DNAzyme-assisted target recycling and hybridization chain reaction.

Science.gov (United States)

Cai, Wei; Xie, Shunbi; Zhang, Jin; Tang, Dianyong; Tang, Ying

2017-12-15

In this work, an electrochemical impedance biosensor for high sensitive detection of Hg 2+ was presented by coupling with Hg 2+ -induced activation of Mg 2+ -specific DNAzyme (Mg 2+ -DNAzyme) for target cycling and hybridization chain reaction (HCR) assembled DNA hydrogel for signal amplification. Firstly, we synthesized two different copolymer chains P1 and P2 by modifying hairpin DNA H3 and H4 with acrylamide polymer, respectively. Subsequently, Hg 2+ was served as trigger to activate the Mg 2+ -DNAzyme for selectively cleavage ribonucleobase-modified substrate in the presence of Mg 2+ . The partial substrate strand could dissociate from DNAzyme structure, and hybridize with capture probe H1 to expose its concealed sequence for further hybridization. With the help of the exposed sequence, the HCR between hairpin DNA H3 and H4 in P1 and P2 was initiated, and assembled a layer of DNA cross-linked hydrogel on the electrode surface. The formed non-conductive DNA hydrogel film could greatly hinder the interfacial electronic transfer which provided a possibility for us to construct a high sensitive impedance biosensor for Hg 2+ detection. Under the optimal conditions, the impedance biosensor showed an excellent sensitivity and selectivity toward Hg 2+ in a concentration range of 0.1pM - 10nM with a detection limit of 0.042pM Moreover, the real sample analysis reveal that the proposed biosensor is capable of discriminating Hg 2+ ions in reliable and quantitative manners, indicating this method has a promising potential for preliminary application in routine tests. Copyright © 2017 Elsevier B.V. All rights reserved.
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.
Accurately bearing measurement in non-cooperative passive location system

International Nuclear Information System (INIS)

Liu Zhiqiang; Ma Hongguang; Yang Lifeng

2007-01-01

The system of non-cooperative passive location based on array is proposed. In the system, target is detected by beamforming and Doppler matched filtering; and bearing is measured by a long-base-ling interferometer which is composed of long distance sub-arrays. For the interferometer with long-base-line, the bearing is measured accurately but ambiguously. To realize unambiguous accurately bearing measurement, beam width and multiple constraint adoptive beamforming technique is used to resolve azimuth ambiguous. Theory and simulation result shows this method is effective to realize accurately bearing measurement in no-cooperate passive location system. (authors)
Generation of Localized Surface Plasmon Resonance Using Hybrid Au–Ag Nanoparticle Arrays as a Sensor of Polychlorinated Biphenyls Detection

Directory of Open Access Journals (Sweden)

Jing Liu

2016-08-01

Full Text Available In this study, the hybrid Au–Ag hexagonal lattice of triangular and square lattice of quadrate periodic nanoparticle arrays (PNAs were designed to investigate their extinction spectra of the localized surface plasmon resonances (LSPRs. First, their simulating extinction spectra were calculated by discrete dipole approximation (DDA numerical method by changing the media refractive index. Simulation results showed that as the media refractive index was changed from 1.0 to 1.2, the maximum peak intensity of LSPRs spectra had no apparent change and the wavelength to reveal the maximum peak intensity of LSPRs spectra was shifted lower value. Polystyrene (PS nanospheres with two differently arranged structures were used as the templates to deposit the hybrid Au–Ag hexagonal lattice of triangular and square lattice of quadrate periodic PNAs by evaporation method. The hybrid Au–Ag hexagonal lattice of triangular and square lattice of quadrate PNAs were grown on single crystal silicon (c-Si substrates, and their measured extinction spectra were compared with the calculated results. Finally, the fabricated hexagonal lattices of triangular PNAs were investigated as a sensor of polychlorinated biphenyl solution (PCB-77 by observing the wavelength to reveal the maximum extinction efficiency (λmax. We show that the adhesion of β-cyclodextrins (SH-β-CD on the hybrid Au–Ag hexagonal lattice of triangular PNAs could be used to increase the variation of λmax. We also demonstrate that the adhesion of SH-β-CD increases the sensitivity and detection effect of PCB-77 in hexagonal lattice of triangular PNAs.
Performance of PCR-reverse blot hybridization assay for detection of rifampicin-resistant Mycobacterium leprae.

Science.gov (United States)

Wang, Hye-young; Kim, Hyunjung; Kim, Yeun; Bang, Hyeeun; Kim, Jong-Pill; Hwang, Joo Hwan; Cho, Sang-Nae; Kim, Tae Ue; Lee, Hyeyoung

2015-10-01

Drug resistance in Mycobacterium leprae is a significant problem in countries where leprosy is endemic. A sensitive, specific, and high-throughput reverse blot hybridization assay (REBA) for the detection of genotypic resistance to rifampicin (RIF) was designed and evaluated. It has been shown that resistance to RIF in M. leprae involves mutations in the rpoB gene encoding the -subunit of the RNA polymerase. The PCR-REBA simultaneously detects both 6 wild-type regions and 5 different mutations (507 AGC, 513 GTG, 516 TAT, 531 ATG, and 531 TTC) including the most prevalent mutations at positions 507 and 531. Thirty-one clinical isolates provided by Korea Institute of Hansen-s Disease were analyzed by PCR-REBA with RIF resistance of rpoB gene. As a result, missense mutations at codons 507 AGC and 531 ATG with 2-nucleotide substitutions were found in one sample, and a missense mutation at codon 516 TAT and ΔWT6 (deletion of 530-534) was found in another sample. These cases were confirmed by DNA sequence analysis. This rapid, simple, and highly sensitive assay provides a practical alternative to sequencing for genotypic evaluation of RIF resistance in M. leprae.
A rapid method of accurate detection and differentiation of Newcastle disease virus pathotypes by demonstrating multiple bands in degenerate primer based nested RT-PCR.

Science.gov (United States)

Desingu, P A; Singh, S D; Dhama, K; Kumar, O R Vinodh; Singh, R; Singh, R K

2015-02-01

A rapid and accurate method of detection and differentiation of virulent and avirulent Newcastle disease virus (NDV) pathotypes was developed. The NDV detection was carried out for different domestic avian field isolates and pigeon paramyxo virus-1 (25 field isolates and 9 vaccine strains) by using APMV-I "fusion" (F) gene Class II specific external primer A and B (535bp), internal primer C and D (238bp) based reverses transcriptase PCR (RT-PCR). The internal degenerative reverse primer D is specific for F gene cleavage position of virulent strain of NDV. The nested RT-PCR products of avirulent strains showed two bands (535bp and 424bp) while virulent strains showed four bands (535bp, 424bp, 349bp and 238bp) on agar gel electrophoresis. This is the first report regarding development and use of degenerate primer based nested RT-PCR for accurate detection and differentiation of NDV pathotypes by demonstrating multiple PCR band patterns. Being a rapid, simple, and economical test, the developed method could serve as a valuable alternate diagnostic tool for characterizing NDV isolates and carrying out molecular epidemiological surveillance studies for this important pathogen of poultry. Copyright © 2014 Elsevier B.V. All rights reserved.
Determination of HER2 gene amplification by chromogenic in situ hybridization (CISH) in archival breast carcinoma.

Science.gov (United States)

Zhao, Jianxin; Wu, Rina; Au, Alfred; Marquez, Abbey; Yu, Yibing; Shi, Zuorong

2002-06-01

To compare the efficacy of chromogenic in situ hybridization (CISH(TM)) with fluorescence in situ (FISH) hybridization and immunohistochemistry (IHC) in determination of the HER2 status in human breast cancer. HER2 gene amplification was determined on formalin-fixed paraffin-embedded (FFPE) sections of 62 invasive breast cancers by FISH and followed by CISH using a digoxigenin (DIG)-labeled HER2 DNA probe generated by Subtraction Probe Technology (SPT(TM)), and a biotin-labeled chromosome 17 centromeric (chr.17cen) probe. The sections were heat treated and enzyme digested. After in situ hybridization, the HER2 probe was detected with fluorescein (FITC)-anti-DIG for FISH, followed by peroxidase-anti-FITC and diaminobenzidine (DAB) for CISH. The chr.17cen probe was detected with peroxidase-streptavidin and DAB. For CISH application, HER2 gene copies or chromosome 17 centromeres and morphology of cells were easily visualized simultaneously with a 40x objective under bright-field microscope in hematoxylin-counterstained sections. IHC study of HER2 overexpression was performed on adjacent sections using a panel of three HER2 antibodies (TAB 250, CB11, A0485), and staining was scored according to the criteria specified in the HercepTest. HER2 gene amplification detected by CISH was visualized typically as large DAB-stained clusters or by many dots in the nucleus. FISH and CISH identified HER2 gene amplification in 19% of the tumors. Chromosome 17 polysomy was detected in 31% of the tumors. HER2 overexpression was demonstrated in 19% (TAB 250), 23% (CB11), and 36% (A0485) of the tumors. Complete concordance between the results of CISH with FISH, TAB 250, CB11, and A0485 was seen in 100%, 97%, 94%, and 84% of the cases, respectively. By permitting observation of morphology using a bright-field microscope, CISH is an accurate, practical, and economical approach to screen HER2 status in breast cancers. It is a useful methodology for confirming ambiguous IHC results.
Detection of human papillomavirus in pterygium and conjunctival papilloma by hybrid capture II and PCR assays.

Science.gov (United States)

Takamura, Y; Kubo, E; Tsuzuki, S; Akagi, Y

2008-11-01

To elucidate the putative role of human papillomavirus (HPV) infection in pterygium and conjunctival papilloma. Hybrid capture II (HC-II) and polymerase chain reaction (PCR) assays were performed to detect HPV in pterygium (42 samples obtained from 40 patients) and conjunctival papilloma (8 samples from 6 patients). The amount of HPV DNA was evaluated by measurement of relative light units (RLUs) on a luminometer. All papilloma samples were positive for HPV DNA by PCR and HC-II. The RLU values for specimens of recurrent and re-recurrent papilloma were markedly higher than those for specimens of primary lesions. HPV was detected by PCR in 2 of 42 (4.8%) beta-globin-positive pterygium specimens, whereas HC-II showed that HPV was negative in all pterygium samples. Our results support the hypothesis that HPV DNA is associated with the pathogenesis of conjunctival papilloma, but not pterygium. RLU measurement by HC-II may serve as a marker for evaluating the activity of HPV in conjunctival tumours.
A Hybrid Wavelet-Based Method for the Peak Detection of Photoplethysmography Signals

Directory of Open Access Journals (Sweden)

Suyi Li

2017-01-01

Full Text Available The noninvasive peripheral oxygen saturation (SpO2 and the pulse rate can be extracted from photoplethysmography (PPG signals. However, the accuracy of the extraction is directly affected by the quality of the signal obtained and the peak of the signal identified; therefore, a hybrid wavelet-based method is proposed in this study. Firstly, we suppressed the partial motion artifacts and corrected the baseline drift by using a wavelet method based on the principle of wavelet multiresolution. And then, we designed a quadratic spline wavelet modulus maximum algorithm to identify the PPG peaks automatically. To evaluate this hybrid method, a reflective pulse oximeter was used to acquire ten subjects’ PPG signals under sitting, raising hand, and gently walking postures, and the peak recognition results on the raw signal and on the corrected signal were compared, respectively. The results showed that the hybrid method not only corrected the morphologies of the signal well but also optimized the peaks identification quality, subsequently elevating the measurement accuracy of SpO2 and the pulse rate. As a result, our hybrid wavelet-based method profoundly optimized the evaluation of respiratory function and heart rate variability analysis.
A Hybrid Wavelet-Based Method for the Peak Detection of Photoplethysmography Signals.

Science.gov (United States)

Li, Suyi; Jiang, Shanqing; Jiang, Shan; Wu, Jiang; Xiong, Wenji; Diao, Shu

2017-01-01

The noninvasive peripheral oxygen saturation (SpO 2 ) and the pulse rate can be extracted from photoplethysmography (PPG) signals. However, the accuracy of the extraction is directly affected by the quality of the signal obtained and the peak of the signal identified; therefore, a hybrid wavelet-based method is proposed in this study. Firstly, we suppressed the partial motion artifacts and corrected the baseline drift by using a wavelet method based on the principle of wavelet multiresolution. And then, we designed a quadratic spline wavelet modulus maximum algorithm to identify the PPG peaks automatically. To evaluate this hybrid method, a reflective pulse oximeter was used to acquire ten subjects' PPG signals under sitting, raising hand, and gently walking postures, and the peak recognition results on the raw signal and on the corrected signal were compared, respectively. The results showed that the hybrid method not only corrected the morphologies of the signal well but also optimized the peaks identification quality, subsequently elevating the measurement accuracy of SpO 2 and the pulse rate. As a result, our hybrid wavelet-based method profoundly optimized the evaluation of respiratory function and heart rate variability analysis.
A Hybrid Wavelet-Based Method for the Peak Detection of Photoplethysmography Signals

Science.gov (United States)

Jiang, Shanqing; Jiang, Shan; Wu, Jiang; Xiong, Wenji

2017-01-01

The noninvasive peripheral oxygen saturation (SpO2) and the pulse rate can be extracted from photoplethysmography (PPG) signals. However, the accuracy of the extraction is directly affected by the quality of the signal obtained and the peak of the signal identified; therefore, a hybrid wavelet-based method is proposed in this study. Firstly, we suppressed the partial motion artifacts and corrected the baseline drift by using a wavelet method based on the principle of wavelet multiresolution. And then, we designed a quadratic spline wavelet modulus maximum algorithm to identify the PPG peaks automatically. To evaluate this hybrid method, a reflective pulse oximeter was used to acquire ten subjects' PPG signals under sitting, raising hand, and gently walking postures, and the peak recognition results on the raw signal and on the corrected signal were compared, respectively. The results showed that the hybrid method not only corrected the morphologies of the signal well but also optimized the peaks identification quality, subsequently elevating the measurement accuracy of SpO2 and the pulse rate. As a result, our hybrid wavelet-based method profoundly optimized the evaluation of respiratory function and heart rate variability analysis. PMID:29250135
Ultrasensitive and simultaneous detection of heavy metal ions based on three-dimensional graphene-carbon nanotubes hybrid electrode materials

International Nuclear Information System (INIS)

Huang, Hui; Chen, Ting; Liu, Xiuyu; Ma, Houyi

2014-01-01

Highlights: • Three-dimensional graphene-MWCNTs nanocomposites were prepared. • Graphene-MWCNTs based electrochemical sensor was used to detect heavy metal ions for the first time. • The proposed sensor was certified capable for real sample with satisfactory results. - Abstract: A green and facile method was developed to prepare a novel hybrid nanocomposite that consisted of one-dimensional multi-walled carbon nanotubes (MWCNTs) and two-dimensional graphene oxide (GO) sheets. The as-prepared three-dimensional GO–MWCNTs hybrid nanocomposites exhibit excellent water-solubility owing to the high hydrophilicity of GO components; meanwhile, a certain amount of MWCNTs loaded on the surface of GO sheets through π–π interaction seem to be “dissolved” in water. Moreover, the graphene(G)-MWCNTs nanocomposites with excellent conductivity were obtained conveniently by the direct electrochemical reduction of GO–MWCNTs nanocomposites. Seeing that there is a good synergistic effect between MWCNTs and graphene components in enhancing preconcentration efficiency of metal ions and accelerating electron transfer rate at G-MWCNTs/electrolyte interface, the G-MWCNTs nanocomposites possess fast, simultaneous and sensitive detection performance for trace amounts of heavy metal ions. The electrochemical results demonstrate that the G-MWCNTs nanocomposites can act as a kind of practical sensing material to simultaneously determine Pb 2+ and Cd 2+ ions in terms of anodic stripping voltammetry (ASV). The linear calibration plots for Pb 2+ and Cd 2+ ranged from 0.5 μg L −1 to 30 μg L −1 . The detection limits were determined to be 0.2 μg L −1 (S/N = 3) for Pb 2+ and 0.1 μg L −1 (S/N = 3) for Cd 2+ in the case of a deposition time of 180 s. It is worth mentioning that the G-MWCNTs modified electrodes were successfully applied to the simultaneous detection of Cd 2+ and Pb 2+ ions in real electroplating effluent samples containing lots of surface active impurities
Towards accurate detection of obfuscated web tracking

OpenAIRE

Le, Hoan; Fallace, Federico; Barlet Ros, Pere

2017-01-01

Web tracking is currently recognized as one of the most important privacy threats on the Internet. Over the last years, many methodologies have been developed to uncover web trackers. Most of them are based on static code analysis and the use of predefined blacklists. However, our main hypothesis is that web tracking has started to use obfuscated programming, a transformation of code that renders previous detection methodologies ineffective and easy to evade. In this paper, we propose a new m...

A Hybrid Approach on Tourism Demand Forecasting

Science.gov (United States)

Nor, M. E.; Nurul, A. I. M.; Rusiman, M. S.

2018-04-01

Tourism has become one of the important industries that contributes to the country’s economy. Tourism demand forecasting gives valuable information to policy makers, decision makers and organizations related to tourism industry in order to make crucial decision and planning. However, it is challenging to produce an accurate forecast since economic data such as the tourism data is affected by social, economic and environmental factors. In this study, an equally-weighted hybrid method, which is a combination of Box-Jenkins and Artificial Neural Networks, was applied to forecast Malaysia’s tourism demand. The forecasting performance was assessed by taking the each individual method as a benchmark. The results showed that this hybrid approach outperformed the other two models
A general range-separated double-hybrid density-functional theory.

Science.gov (United States)

Kalai, Cairedine; Toulouse, Julien

2018-04-28

A range-separated double-hybrid (RSDH) scheme which generalizes the usual range-separated hybrids and double hybrids is developed. This scheme consistently uses a two-parameter Coulomb-attenuating-method (CAM)-like decomposition of the electron-electron interaction for both exchange and correlation in order to combine Hartree-Fock exchange and second-order Møller-Plesset (MP2) correlation with a density functional. The RSDH scheme relies on an exact theory which is presented in some detail. Several semi-local approximations are developed for the short-range exchange-correlation density functional involved in this scheme. After finding optimal values for the two parameters of the CAM-like decomposition, the RSDH scheme is shown to have a relatively small basis dependence and to provide atomization energies, reaction barrier heights, and weak intermolecular interactions globally more accurate or comparable to range-separated MP2 or standard MP2. The RSDH scheme represents a new family of double hybrids with minimal empiricism which could be useful for general chemical applications.
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.
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

International Nuclear Information System (INIS)

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

2013-01-01

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
Hybrid chemical and nondestructive-analysis technique

International Nuclear Information System (INIS)

Hsue, S.T.; Marsh, S.F.; Marks, T.

1982-01-01

A hybrid chemical/NDA technique has been applied at the Los Alamos National Laboratory to the assay of plutonium in ion-exchange effluents. Typical effluent solutions contain low concentrations of plutonium and high concentrations of americium. A simple trioctylphosphine oxide (TOPO) separation can remove 99.9% of the americium. The organic phase that contains the separated plutonium can be accurately assayed by monitoring the uranium L x-ray intensities
An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test

KAUST Repository

Rodriguez, Jesse M.; Batzoglou, Serafim; Bercovici, Sivan

2013-01-01

, accurate and efficient detection of hidden relatedness becomes a challenge. To enable disease-mapping studies of increasingly large cohorts, a fast and accurate method to detect IBD segments is required. We present PARENTE, a novel method for detecting
A Novel Method for Rapid Hybridization of DNA to a Solid Support

Science.gov (United States)

Pettersson, Erik; Ahmadian, Afshin; Ståhl, Patrik L.

2013-01-01

Here we present a novel approach entitled Magnetic Forced Hybridization (MFH) that provides the means for efficient and direct hybridization of target nucleic acids to complementary probes immobilized on a glass surface in less than 15 seconds at ambient temperature. In addition, detection is carried out instantly since the beads become visible on the surface. The concept of MFH was tested for quality control of array manufacturing, and was combined with a multiplex competitive hybridization (MUCH) approach for typing of Human Papilloma Virus (HPV). Magnetic Forced Hybridization of bead-DNA constructs to a surface achieves a significant reduction in diagnostic testing time. In addition, readout of results by visual inspection of the unassisted eye eliminates the need for additional expensive instrumentation. The method uses the same set of beads throughout the whole process of manipulating and washing DNA constructs prior to detection, as in the actual detection step itself. PMID:23950946
Optimal pcr primers for rapid and accurate detection of Aspergillus flavus isolates.

Science.gov (United States)

Al-Shuhaib, Mohammed Baqur S; Albakri, Ali H; Alwan, Sabah H; Almandil, Noor B; AbdulAzeez, Sayed; Borgio, J Francis

2018-03-01

Aspergillus flavus is among the most devastating opportunistic pathogens of several food crops including rice, due to its high production of carcinogenic aflatoxins. The presence of these organisms in economically important rice strip farming is a serious food safety concern. Several polymerase chain reaction (PCR) primers have been designed to detect this species; however, a comparative assessment of their accuracy has not been conducted. This study aims to identify the optimal diagnostic PCR primers for the identification of A. flavus, among widely available primers. We isolated 122 A. flavus native isolates from randomly collected rice strips (N = 300). We identified 109 isolates to the genus level using universal fungal PCR primer pairs. Nine pairs of primers were examined for their PCR diagnostic specificity on the 109 isolates. FLA PCR was found to be the optimal PCR primer pair for specific identification of the native isolates, over aflP(1), aflM, aflA, aflD, aflP(3), aflP(2), and aflR. The PEP primer pair was found to be the most unsuitable for A. flavus identification. In conclusion, the present study indicates the powerful specificity of the FLA PCR primer over other commonly available diagnostic primers for accurate, rapid, and large-scale identification of A. flavus native isolates. This study provides the first simple, practical comparative guide to PCR-based screening of A. flavus infection in rice strips. Copyright © 2018 Elsevier Ltd. All rights reserved.
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
Modelling dependable systems using hybrid Bayesian networks

International Nuclear Information System (INIS)

Neil, Martin; Tailor, Manesh; Marquez, David; Fenton, Norman; Hearty, Peter

2008-01-01

A hybrid Bayesian network (BN) is one that incorporates both discrete and continuous nodes. In our extensive applications of BNs for system dependability assessment, the models are invariably hybrid and the need for efficient and accurate computation is paramount. We apply a new iterative algorithm that efficiently combines dynamic discretisation with robust propagation algorithms on junction tree structures to perform inference in hybrid BNs. We illustrate its use in the field of dependability with two example of reliability estimation. Firstly we estimate the reliability of a simple single system and next we implement a hierarchical Bayesian model. In the hierarchical model we compute the reliability of two unknown subsystems from data collected on historically similar subsystems and then input the result into a reliability block model to compute system level reliability. We conclude that dynamic discretisation can be used as an alternative to analytical or Monte Carlo methods with high precision and can be applied to a wide range of dependability problems
Fluorescent In Situ Hybridization to Detect Transgene Integration into Plant Genomes

Science.gov (United States)

Schwarzacher, Trude

Fluorescent chromosome analysis technologies have advanced our understanding of genome organization during the last 30 years and have enabled the investigation of DNA organization and structure as well as the evolution of chromosomes. Fluorescent chromosome staining allows even small chromosomes to be visualized, characterized by their composition and morphology, and counted. Aneuploidies and polyploidies can be established for species, breeding lines, and individuals, including changes occurring during hybridization or tissue culture and transformation protocols. Fluorescent in situ hybridization correlates molecular information of a DNA sequence with its physical location on chromosomes and genomes. It thus allows determination of the physical position of sequences and often is the only means to determine the abundance and distribution of DNA sequences that are difficult to map with any other molecular method or would require segregation analysis, in particular multicopy or repetitive DNA. Equally, it is often the best way to establish the incorporation of transgenes, their numbers, and physical organization along chromosomes. This chapter presents protocols for probe and chromosome preparation, fluorescent in situ hybridization, chromosome staining, and the analysis of results.
Detection of human papilloma virus 16 and 18 DNA sequences by southern blot hybridization in oral leukoplakia and squamous cell carcinoma.

Science.gov (United States)

Khanna, Rahul; Rao, G R K; Tiwary, S K; Rai, Ashish; Khanna, Seema; Khanna, A K

2009-04-01

The etiopathological role of human papilloma virus (HPV) in the causation of oral cancer is till a subject of speculation. We used the technique of Southern blot hybridization to detect the presence of HPV types 16 & 18 in biopsy specimens from oral cancer and leukoplakia patients as well as normal oral mucosal biopsies. The prevalence of either HPV type 16 or 18 was found in 64.5% (29/45) of oral cancer, 40%(12/30) of leukoplakia and 20%(9/45) of normal oral mucosal biopsies. No association could be demonstrated between tobacco usage habits or a history of genital warts with HPV prevalence. A significant finding was that none of the oral cancer patients were negative for both: a history of tobacco usage as well as presence of HPV infection, on Southern blot hybridization.
Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2016-01-06

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.
Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2015-01-07

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.
Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2014-01-06

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks among many others. In this work we present a novel hybrid algorithm for simulating individual trajectories which adaptively switches between the SSA and the Chernoff tauleap methods. This allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.
Accurate measurement of transgene copy number in crop plants using droplet digital PCR.

Science.gov (United States)

Collier, Ray; Dasgupta, Kasturi; Xing, Yan-Ping; Hernandez, Bryan Tarape; Shao, Min; Rohozinski, Dominica; Kovak, Emma; Lin, Jeanie; de Oliveira, Maria Luiza P; Stover, Ed; McCue, Kent F; Harmon, Frank G; Blechl, Ann; Thomson, James G; Thilmony, Roger

2017-06-01

Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. Alternatively, qPCR requires less DNA and is potentially simpler to perform, but its results can lack the accuracy and precision needed to confidently distinguish between one- and two-copy events in transgenic plants with large genomes. To address this need, we developed a droplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citrus, potato, maize, tomato and wheat. The method utilizes specific primers to amplify target transgenes, and endogenous reference genes in a single duplexed reaction containing thousands of droplets. Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. The results demonstrate that this approach can generate confident copy number measurements in independent transgenic lines in these crop species. This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.
Optofluidic analysis system for amplification-free, direct detection of Ebola infection

Science.gov (United States)

Cai, H.; Parks, J. W.; Wall, T. A.; Stott, M. A.; Stambaugh, A.; Alfson, K.; Griffiths, A.; Mathies, R. A.; Carrion, R.; Patterson, J. L.; Hawkins, A. R.; Schmidt, H.

2015-09-01

The massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately, and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.
Surface-enhanced Raman scattering based nonfluorescent probe for multiplex DNA detection.

Science.gov (United States)

Sun, Lan; Yu, Chenxu; Irudayaraj, Joseph

2007-06-01

To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive, and multiplex format, an alternative surface-enhanced Raman scattering based probe was designed and fabricated to covalently attach both DNA probing sequence and nonfluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the nonfluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). Excellent multiplexing capability of the DNA-AuP-RTag scheme was demonstrated by simultaneous identification of up to eight probes in a mixture. Detection of hybridization of single-stranded DNA to its complementary targets was successfully accomplished with a long-term goal to use nonfluorescent RTags in a Raman-based DNA microarray platform.
FERMENTATION PROCESS CHARACTERISTICS OF DIFFERENT MAIZE SILAGE HYBRIDS

Directory of Open Access Journals (Sweden)

Daniel Bíro

2009-03-01

Full Text Available The aim of this study was to detect the fermentation process differences in different hybrid maize silage. We conserved in laboratory conditions hybrids of whole maize plants with different length of the vegetative period (FAO number. Maize hybrids for silage were harvested in the vegetation stage of the milk-wax maturity of corn and the content of dry matter was from 377.7 to 422.8 g.kg-1. The highest content of dry matter was typical for silages made from the hybrids with FAO number 310 (400.0 g.kg-1 and FAO 300a (400.4 g.kg-1. The content of desirable lactic acid ranged from 23.7 g.kg-1 of dry matter (FAO 350 to 58.9 g.kg-1 of dry matter (FAO 420. We detected the occurrence of undesirable butyric acid in silages from hybrids FAO 250, 300b, 310 and 380. The highest content of total alcohols we found in silages made from hybrid with FAO number 240 (25.2 g.kg-1 of dry matter. Ammonia contents were in tested silages from 0.153 (FAO 270 to 0.223 g.kg-1 of dry matter (FAO 240. The lowest value of silage titration acidity we analyzed in silage made from hybrid FAO 420 (3.66. We observed in maize silages with different length of plant maturity tested in the experiment differences in content of lactic acid, total alcohols, titration acidity, pH and content of fermentation products.
Identification of novel CYP2D7-2D6 hybrids: non-functional and functional variants

Directory of Open Access Journals (Sweden)

Andrea Gaedigk

2010-10-01

Full Text Available Polymorphic expression of CYP2D6 contributes to the wide range of activity observed for this clinically important drug metabolizing enzyme. In this report we describe novel CYP2D7/2D6 hybrid genes encoding non-functional and functional CYP2D6 protein and a CYP2D7 variant that mimics a CYP2D7/2D6 hybrid gene. Five kb long PCR products encompassing the novel genes were entirely sequenced. A quantitative assay probing in different gene regions was employed to determine CYP2D6 and 2D7 copy number variations and the relative position of the hybrid genes within the locus was assessed by long-range PCR. In addition to the previously known CYP2D6*13 and *66 hybrids, we describe three novel non-functional CYP2D7-2D6 hybrids with gene switching in exon 2 (CYP2D6*79, intron 2 (CYP2D6*80 and intron 5 (CYP2D6*67. A CYP2D7-specific T-ins in exon 1 causes a detrimental frame shift. One subject revealed a CYP2D7 conversion in the 5’-flanking region of a CYP2D6*35 allele, was otherwise unaffected (designated CYP2D6*35B. Finally, three DNAs revealed a CYP2D7 gene with a CYP2D6-like region downstream of exon 9 (designated CYP2D7[REP6]. Quantitative copy number determination, sequence analyses and long-range PCR mapping were in agreement and excluded the presence of additional gene units. Undetected hybrid genes may cause over-estimation of CYP2D6 activity (CYP2D6*1/*1 vs *1/hybrid, etc, but may also cause results that may interfere with the genotype determination. Detection of hybrid events, ‘single’ and tandem, will contribute to more accurate phenotype prediction from genotype data.

Sensorless Suitability Analysis of Hybrid PM Machines for Electric Vehicles

DEFF Research Database (Denmark)

Matzen, Torben Nørregaard; Rasmussen, Peter Omand

2009-01-01

Electrical machines for traction in electric vehicles are an essential component which attract attention with respect to machine design and control as a part of the emerging renewable industry. For the hybrid electric machine to replace the familiar behaviour of the combustion engine torque......, control seems necessary to implement. For hybrid permanent magnet (PM) machines torque control in an indirect fashion using dq-current control is frequently done. This approach requires knowledge about the machine shaft position which may be obtained sensorless. In this article a method based on accurate...
A Semiactive and Adaptive Hybrid Control System for a Tracked Vehicle Hydropneumatic Suspension Based on Disturbance Identification

Directory of Open Access Journals (Sweden)

Shousong Han

2017-01-01

Full Text Available The riding conditions for a high-speed tracked vehicle are quite complex. To enhance the adaptability of suspension systems to different riding conditions, a semiactive and self-adaptive hybrid control strategy based on disturbance velocity and frequency identification was proposed. A mathematical model of the semiactive, self-adaptive hybrid suspension control system, along with a performance evaluation function, was established. Based on a two-degree-of-freedom (DOF suspension system, the kinematic relations and frequency zero-crossing detection method were defined, and expressions for the disturbance velocity and disturbance frequency of the road were obtained. Optimal scheduling of the semiactive hybrid damping control gain (csky, cground, chybrid and self-adaptive control gain (cv under different disturbances were realized by exploiting the particle swarm multiobjective optimization algorithm. An experimental study using a carefully designed test rig was performed under a number of typical riding conditions of tracked vehicles, and the results showed that the proposed control strategy is capable of accurately recognizing different disturbances, shifting between control modes (semiactive/self-adaptive, and scheduling the damping control gain according to the disturbance identification outcomes; hence, the proposed strategy could achieve a good trade-off between ride comfort and ride safety and efficiently increase the overall performance of the suspension under various riding conditions.
Monte Carlo simulation of simultaneous radiation detection in the hybrid tomography system ClearPET-XPAD3/CT

Energy Technology Data Exchange (ETDEWEB)

Dávila, H. Olaya, E-mail: hernan.olaya@uptc.edu.co; Martínez, S. A. [Physics Department, Universidad Pedagógica y Tecnológica de Colombia, Tunja-Colombia (Colombia); Sevilla, A. C., E-mail: acsevillam@unal.edu.co; Castro, H. F. [Physics Department, Universidad Nacional de Colombia, Bogotá D.C - Colombia (Colombia)

2016-07-07

Using the Geant4 based simulation framework SciFW1, a detailed simulation was performed for a detector array in the hybrid tomography prototype for small animals called ClearPET / XPAD, which was built in the Centre de Physique des Particules de Marseille. The detector system consists of an array of phoswich scintillation detectors: LSO (Lutetium Oxy-ortosilicate doped with cerium Lu{sub 2}SiO{sub 5}:Ce) and LuYAP (Lutetium Ortoaluminate of Yttrium doped with cerium Lu{sub 0.7}Y{sub 0.3}AlO{sub 3}:Ce) for Positron Emission Tomography (PET) and hybrid pixel detector XPAD for Computed Tomography (CT). Simultaneous acquisition of deposited energy and the corresponding time - position for each recorded event were analyzed, independently, for both detectors. interference between detection modules for PET and CT. Information about amount of radiation reaching each phoswich crystal and XPAD detector using a phantom in order to study the effectiveness by radiation attenuation and influence the positioning of the radioactive source {sup 22}Na was obtained. The simulation proposed will improve distribution of detectors rings and interference values will be taken into account in the new versions of detectors.
Monte Carlo simulation of simultaneous radiation detection in the hybrid tomography system ClearPET-XPAD3/CT

Science.gov (United States)

Dávila, H. Olaya; Sevilla, A. C.; Castro, H. F.; Martínez, S. A.

2016-07-01

Using the Geant4 based simulation framework SciFW1, a detailed simulation was performed for a detector array in the hybrid tomography prototype for small animals called ClearPET / XPAD, which was built in the Centre de Physique des Particules de Marseille. The detector system consists of an array of phoswich scintillation detectors: LSO (Lutetium Oxy-ortosilicate doped with cerium Lu2SiO5:Ce) and LuYAP (Lutetium Ortoaluminate of Yttrium doped with cerium Lu0.7Y0.3AlO3:Ce) for Positron Emission Tomography (PET) and hybrid pixel detector XPAD for Computed Tomography (CT). Simultaneous acquisition of deposited energy and the corresponding time - position for each recorded event were analyzed, independently, for both detectors. interference between detection modules for PET and CT. Information about amount of radiation reaching each phoswich crystal and XPAD detector using a phantom in order to study the effectiveness by radiation attenuation and influence the positioning of the radioactive source 22Na was obtained. The simulation proposed will improve distribution of detectors rings and interference values will be taken into account in the new versions of detectors.
A very accurate method for sentinel lymph node investigation: Gamma detecting probe associated with SPECT examination for depth

International Nuclear Information System (INIS)

Ascoli, G.; Cinti, P.; Nonni, M.; Rossi, B.

2002-01-01

Aim: aim of this study is to magnify the lymphoscintigraphy examination by gamma probe with SPECT acquisition for very accurate detection of depth of axilla node in patients affected by melanoma. Methods: according to physiological peculiarities the lymphatic system plays a very important role and represents the most important barrier to neoplastic cells spreading. The 'sentinel node' is the first lymph node draining the affected area. The tendency for surgery is a 'preventive' axillary dissection, even in presence of a clinically negative examination. In fact a high percentage of clinically negative lymph node shows a positive histology (presence of metastatic cells). The nuclear medicine method for researching 'sentinel node' is represented by a regional lymphoscintigraphy with normal gamma camera with a large field of view followed by examination with gamma detecting probe and, in following day, controlled in operating room to confirm the presence of the node early identified. We have completed this protocol with SPECT examination of affected axilla by use of injected laboratory capillary around axilla to perform an exact investigation of node depth. Discussion: Our experience in 150 cases in 18 months shows 100% of axilla 'sentinel node' detection, 25 cases with positive histologic examination and subsequently axillary dissection. Conclusions: In conclusion the scintigraphic examination with lymphoscintigraphy represents a good tool for management of patient with melanoma and the use of ''targeting' with collimated SPECT represent a very aid for the surgeon in reduction time for detection and dissection of lymph node, with high reduction of anesthesia duration
Carbon nanotube-TiO{sub 2} hybrid films for detecting traces of O{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Llobet, E; Espinosa, E H; Sotter, E; Ionescu, R; Vilanova, X [MINOS, EMaS, Universitat Rovira i Virgili, 43007 Tarragona (Spain); Torres, J [Research Department, Carburos Metalicos, MATGAS, Campus UAB, 08193 Cerdanyola del Valles (Spain); Felten, A; Pireaux, J J [LISE, University of Namur, B-5000 Namur (Belgium); Ke, X; Tendeloo, G Van [EMAT, University of Antwerp, B-2020 Antwerp (Belgium); Renaux, F; Paint, Y; Hecq, M; Bittencourt, C [LCIA, University of Mons-Hainaut, B-7000, Mons (Belgium)

2008-09-17

Hybrid titania films have been prepared using an adapted sol-gel method for obtaining well-dispersed hydrogen plasma-treated multiwall carbon nanotubes in either pure titania or Nb-doped titania. The drop-coating method has been used to fabricate resistive oxygen sensors based on titania or on titania and carbon nanotube hybrids. Morphology and composition studies have revealed that the dispersion of low amounts of carbon nanotubes within the titania matrix does not significantly alter its crystallization behaviour. The gas sensitivity studies performed on the different samples have shown that the hybrid layers based on titania and carbon nanotubes possess an unprecedented responsiveness towards oxygen (i.e. more than four times higher than that shown by optimized Nb-doped TiO{sub 2} films). Furthermore, hybrid sensors containing carbon nanotubes respond at significantly lower operating temperatures than their non-hybrid counterparts. These new hybrid sensors show a strong potential for monitoring traces of oxygen (i.e. {<=}10 ppm) in a flow of CO{sub 2}, which is of interest for the beverage industry.
5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH

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Jaime Gosálvez

2013-02-01

Full Text Available We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH. A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL, 10 with high-grade SIL (HG-SIL, and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.
5-bp Classical Satellite DNA Loci from Chromosome-1 Instability in Cervical Neoplasia Detected by DNA Breakage Detection/Fluorescence in Situ Hybridization (DBD-FISH).

Science.gov (United States)

Cortés-Gutiérrez, Elva I; Ortíz-Hernández, Brenda L; Dávila-Rodríguez, Martha I; Cerda-Flores, Ricardo M; Fernández, José Luis; López-Fernández, Carmen; Gosálvez, Jaime

2013-02-19

We aimed to evaluate the association between the progressive stages of cervical neoplasia and DNA damage in 5-bp classical satellite DNA sequences from chromosome-1 in cervical epithelium and in peripheral blood lymphocytes using DNA breakage detection/fluorescence in situ hybridization (DBD-FISH). A hospital-based unmatched case-control study was conducted in 2011 with a sample of 30 women grouped according to disease stage and selected according to histological diagnosis; 10 with low-grade squamous intraepithelial lesions (LG-SIL), 10 with high-grade SIL (HG-SIL), and 10 with no cervical lesions, from the Unidad Medica de Alta Especialidad of The Mexican Social Security Institute, IMSS, Mexico. Specific chromosome damage levels in 5-bp classical satellite DNA sequences from chromosome-1 were evaluated in cervical epithelium and peripheral blood lymphocytes using the DBD-FISH technique. Whole-genome DNA hybridization was used as a reference for the level of damage. Results of Kruskal-Wallis test showed a significant increase according to neoplastic development in both tissues. The instability of 5-bp classical satellite DNA sequences from chromosome-1 was evidenced using chromosome-orientation FISH. In conclusion, we suggest that the progression to malignant transformation involves an increase in the instability of 5-bp classical satellite DNA sequences from chromosome-1.
Ternary Surface Monolayers for Ultrasensitive (Zeptomole) Amperometric Detection of Nucleic-Acid Hybridization without Signal Amplification

Science.gov (United States)

Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A.; Wang, Joseph

2010-01-01

A ternary surface monolayer, consisting of co-assembled thiolated capture probe (SHCP) mercaptohexanol (MCH) and dithiothreitol (DTT), is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers (SAMs). Remarkably low detection limits down to 40 zmole (in 4 μL samples) as well as only 1 CFU E. coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3′,5,5′-tetramethylbenzidine (HRP/TMB) system. Such dramatic improvements in the detection limits (compared to common binary alkanethiol interfaces and to most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to non-specific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration ‘backfillers’ that leads to a remarkably low background noise even in the presence of complex sample matrices. A wide range of surface compositions have been investigated and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety and forensic analysis. PMID:20883023
Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification.

Science.gov (United States)

Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A; Wang, Joseph

2010-11-01

A ternary surface monolayer, consisting of coassembled thiolated capture probe, mercaptohexanol and dithiothreitol, is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers. Remarkably low detection limits down to 40 zmol (in 4 μL samples) as well as only 1 CFU Escherichia coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3',5,5'-tetramethylbenzidine system. Such dramatic improvements in the detection limits (compared to those of common binary alkanethiol interfaces and to those of most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to nonspecific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration "backfillers" that leads to a remarkably low background noise even in the presence of complex sample matrixes. A wide range of surface compositions have been investigated, and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety, and forensic analysis.
Quantitative 16S rDNA-targeted polymerase chain reaction and oligonucleotide hybridization for the detection of Paenibacillus azotofixans in soil and the wheat rhizosphere

NARCIS (Netherlands)

Rosado, A.S.; Seldin, L.; Wolters, A.; Elsas, van J.D.

1996-01-01

A molecular method for the detection of Paenibacillus azotofixans in soil and the wheat rhizosphere was developed. The system consisted of polymerase chain reaction (PCR) amplification of part of the variable V1 to V4 regions of the 16S ribosomal RNA gene, followed by hybridization with a specific
Hybrid III-V/SOI resonant cavity enhanced photodetector

DEFF Research Database (Denmark)

Learkthanakhachon, Supannee; Taghizadeh, Alireza; Park, Gyeong Cheol

2016-01-01

A hybrid III–V/SOI resonant-cavity-enhanced photodetector (RCE-PD) structure comprising a high-contrast grating (HCG) reflector, a hybrid grating (HG) reflector, and an air cavity between them, has been proposed and investigated. In the proposed structure, a light absorbing material is integrated...... as part of the HG reflector, enabling a very compact vertical cavity. Numerical investigations show that a quantum efficiency close to 100 % and a detection linewidth of about 1 nm can be achieved, which are desirable for wavelength division multiplexing applications. Based on these results, a hybrid RCE...
Measurement of the Photoelectron Detection Efficiency of the HPD Anode

CERN Document Server

Carson, L; Soler, P

2009-01-01

This paper reports on measurements carried out on the Hybrid Photon Detectors (HPDs) of the LHCb RICH detectors. The purpose of these tests is to determine the photoelectron detection efficiency $\\eta$ of the HPD anode. Knowledge of $\\eta$ is required for an accurate simulation of the RICH detectors. It is found that this efficiency is $(93.3\\pm0.7)\\%$ for a 50 ns digital readout window, and $(87.9\\pm1.4)\\%$ for a 25 ns digital readout window. The 25 ns result exceeds the LHCb-RICH requirement of 85\\%, and is in agreement both with direct $\\eta$ measurements using preseries HPDs, and with indirect measurements from testbeams using preseries and production HPDs.
Fluorescence In Vivo Hybridization (FIVH) for Detection of Helicobacter pylori Infection in a C57BL/6 Mouse Model

DEFF Research Database (Denmark)

Fontenete, Sílvia; Leite, Marina; Cappoen, Davie

2016-01-01

). Finally, the efficiency of FIVH to detect H. pylori SS1 strain in C57BL/6 infected mice was evaluated ex vivo in mucus samples, in cryosections and paraffin-embedded sections by epifluorescence and confocal microscopy. RESULTS: H. pylori SS1 strain infecting C57BL/6 mice was successfully detected...... by the Cy3_HP_LNA/2OMe_PS probe in the mucus, attached to gastric epithelial cells and colonizing the gastric pits. The specificity of the probe for H. pylori was confirmed by microscopy. CONCLUSIONS: In the future this methodology can be used in combination with a confocal laser endomicroscope for in vivo......INTRODUCTION: In this study, we applied fluorescence in vivo hybridization (FIVH) using locked nucleic acid (LNA) probes targeting the bacterial rRNA gene for in vivo detection of H. pylori infecting the C57BL/6 mouse model. A previously designed Cy3_HP_LNA/2OMe_PS probe, complementary...
Advancing surgical guidance : from (hybrid) molecule to man and beyond

NARCIS (Netherlands)

Berg, van den N.S.

2016-01-01

The work described in this thesis shows how intraoperative lesion identification can be improved via the introduction of (hybrid) tracers and optimised (hybrid) imaging modalities capable of detecting this tracers. In part one, the reader is introduced to the concept of fluorescence image-guided
Development and use of fluorescent 16S rRNA-targeted probes for the specific detection of Methylophaga species by in situ hybridization in marine sediments.

Science.gov (United States)

Janvier, Monique; Regnault, Béatrice; Grimont, Patrick

2003-09-01

Methylotrophic bacteria are widespread in nature. They may play an important role in the cycling of carbon and in the metabolism of dimethylsulfide in a marine environment. Bacteria belonging to the genus Methylophaga are a unique group of aerobic, halophilic, non-methane-utilizing methylotrophs. Two 16S rRNA-targeted oligonucleotide probes were developed for the specific detection of Methylophaga species, marine methylobacteria, by fluorescence in situ hybridization. Probe MPH-730 was highly specific for all members of the genus Methylophaga while probe MPHm-994 targeted exclusively M. marina. The application of these probes were demonstrated by the detection of Methylophaga species in enrichment cultures from various marine sediments. All isolates recovered were visualized by using the genus specific probe MPH-730. The results were confirmed by 16S rDNA sequencing which demonstrated that all selected isolates belong to Methylophaga. Five isolates could be detected by the M. marina-specific probe MPHm-994 and were confirmed by rRNA gene restriction pattern (ribotyping). With the development of these specific probes, fluorescence in situ hybridization shows that the genus Methylophaga is widespread in marine samples.
One-pot synthesis of Fe3O4@Chitosan-pSDCalix hybrid nanomaterial for the detection and removal of Hg2+ ion from aqueous media

Science.gov (United States)

Bhatti, Asif Ali; Oguz, Mehmet; Yilmaz, Mustafa

2018-03-01

New one pot mesoporous hybrid material containing iron nanoparticles fabricated with chitosan and p-sulfonato dansyl calix[4]arene composite (Fe3O4@Chitosan-pSDCalix) has been susccessfully synthesized. These mesoporous fluorescence iron nanoparticles were applied for the detection and removal of environmentally toxic Hg2+ ion from aqueous media. Different techniques were applied to confirm the preparation of Fe3O4@Chitosan-pSDCalix such as HRTEM, TGA/DTA, FTIR and XRD. Synthesized nanoparticles have average size of 17 nm with pore size of 0.19 nm as revealed from HRTEM images. Fluorescence study follow the photoinduced electron transfer process after addition of Hg2+ in the solution with decrease in intensity. Confocal microscope images were also acquired to confirm the presence of Hg2+ on nanoparticles. Adsorption study suggests that the removal of Hg2+ from aqueous media follows Langmuir adsorption isotherm. These studies suggest the synthesized Fe3O4@Chitosan-pSDCalix is an efficient hybrid material for the detection and removal of Hg2+ ion from aqueous media, and that it can also be used in biomolecules for the detection of toxic metal ions.
Hybrid piezoresistive-optical tactile sensor for simultaneous measurement of tissue stiffness and detection of tissue discontinuity in robot-assisted minimally invasive surgery

Science.gov (United States)

Bandari, Naghmeh M.; Ahmadi, Roozbeh; Hooshiar, Amir; Dargahi, Javad; Packirisamy, Muthukumaran

2017-07-01

To compensate for the lack of touch during minimally invasive and robotic surgeries, tactile sensors are integrated with surgical instruments. Surgical tools with tactile sensors have been used mainly for distinguishing among different tissues and detecting malignant tissues or tumors. Studies have revealed that malignant tissue is most likely stiffer than normal. This would lead to the formation of a sharp discontinuity in tissue mechanical properties. A hybrid piezoresistive-optical-fiber sensor is proposed. This sensor is investigated for its capabilities in tissue distinction and detection of a sharp discontinuity. The dynamic interaction of the sensor and tissue is studied using finite element method. The tissue is modeled as a two-term Mooney-Rivlin hyperelastic material. For experimental verification, the sensor was microfabricated and tested under the same conditions as of the simulations. The simulation and experimental results are in a fair agreement. The sensor exhibits an acceptable linearity, repeatability, and sensitivity in characterizing the stiffness of different tissue phantoms. Also, it is capable of locating the position of a sharp discontinuity in the tissue. Due to the simplicity of its sensing principle, the proposed hybrid sensor could also be used for industrial applications.
Strongly Iridescent Hybrid Photonic Sensors Based on Self-Assembled Nanoparticles for Hazardous Solvent Detection

Directory of Open Access Journals (Sweden)

Ayaka Sato

2018-03-01

Full Text Available Facile detection and the identification of hazardous organic solvents are essential for ensuring global safety and avoiding harm to the environment caused by industrial wastes. Here, we present a simple method for the fabrication of silver-coated monodisperse polystyrene nanoparticle photonic structures that are embedded into a polydimethylsiloxane (PDMS matrix. These hybrid materials exhibit a strong green iridescence with a reflectance peak at 550 nm that originates from the close-packed arrangement of the nanoparticles. This reflectance peak measured under Wulff-Bragg conditions displays a 20 to 50 nm red shift when the photonic sensors are exposed to five commonly employed and highly hazardous organic solvents. These red-shifts correlate well with PDMS swelling ratios using the various solvents, which suggests that the observable color variations result from an increase in the photonic crystal lattice parameter with a similar mechanism to the color modulation of the chameleon skin. Dynamic reflectance measurements enable the possibility of clearly identifying each of the tested solvents. Furthermore, as small amounts of hazardous solvents such as tetrahydrofuran can be detected even when mixed with water, the nanostructured solvent sensors we introduce here could have a major impact on global safety measures as innovative photonic technology for easily visualizing and identifying the presence of contaminants in water.
From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties

Science.gov (United States)

Xu, Xin; Goddard, William A., III

2004-03-01

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA.

Electrocatalytic behaviour of hybrid cobalt–manganese hexacyanoferrate film on glassy carbon electrode

International Nuclear Information System (INIS)

Vinu Mohan, A.M.; Rambabu, Gutru; Aswini, K.K.; Biju, V.M.

2014-01-01

A thin film of hybrid cobalt–manganese hexacyanoferrate (CoMnHCF), a redox mediator was electrodeposited on a glassy carbon (GC) electrode and was employed as an amperometric sensor towards L-Tryptophan (L-Trp). The hybrid film was characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction technique (XRD), scanning electron microscope–energy dispersive X-ray spectroscopy (SEM–EDAX), and electrochemical techniques. The atomic absorption spectroscopic analysis provided the stoichiometry of the hybrid film to be K 1.74-y Co y Mn 0.78 [Fe(CN) 6 ], y ≤ 0.68. The electrochemical impedance study revealed the excellent charge transfer properties of GC/CoMnHCF electrode. The voltammetric investigations demonstrated exceptional electrocatalytic properties of the hybrid film modified electrode when compared to that of bare GC, GC/CoHCF and GC/MnHCF electrodes, towards the L-Trp oxidation. The kinetic parameters such as electron transfer coefficient, the electron transfer rate constant, the diffusion coefficient and the catalytic rate constant for the electrooxidation process of L-Trp were investigated. The amperometric detection of L-Trp employing GC/CoMnHCF electrode possessed a good sensitivity of 10 × 10 −2 A M −1 cm −2 in a wide range of detection (2–200 μM) at a reduced overpotential of 680 mV. In addition, the proposed amperometric method was applied to the detection of L-Trp in commercial milk samples with reproducible results. - Highlights: • A hybrid cobalt–manganese hexacyanoferrate film was prepared. • The hybrid film possesses excellent charge transfer properties. • The hybrid film exhibits excellent electrocatalytic properties towards Tryptophan. • Tryptophan detection is possible from commercial milk samples
Hybrid Photonic Cavity with Metal-Organic Framework Coatings for the Ultra-Sensitive Detection of Volatile Organic Compounds with High Immunity to Humidity

Science.gov (United States)

Tao, Jifang; Wang, Xuerui; Sun, Tao; Cai, Hong; Wang, Yuxiang; Lin, Tong; Fu, Dongliang; Ting, Lennon Lee Yao; Gu, Yuandong; Zhao, Dan

2017-01-01

Detection of volatile organic compounds (VOCs) at parts-per-billion (ppb) level is one of the most challenging tasks for miniature gas sensors because of the high requirement on sensitivity and the possible interference from moisture. Herein, for the first time, we present a novel platform based on a hybrid photonic cavity with metal-organic framework (MOF) coatings for VOCs detection. We have fabricated a compact gas sensor with detection limitation ranging from 29 to 99 ppb for various VOCs including styrene, toluene, benzene, propylene and methanol. Compared to the photonic cavity without coating, the MOF-coated solution exhibits a sensitivity enhancement factor up to 1000. The present results have demonstrated great potential of MOF-coated photonic resonators in miniaturized gas sensing applications.
FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography.

Science.gov (United States)

Ale, Angelique; Ermolayev, Vladimir; Herzog, Eva; Cohrs, Christian; de Angelis, Martin Hrabé; Ntziachristos, Vasilis

2012-06-01

The development of hybrid optical tomography methods to improve imaging performance has been suggested over a decade ago and has been experimentally demonstrated in animals and humans. Here we examined in vivo performance of a camera-based hybrid fluorescence molecular tomography (FMT) system for 360° imaging combined with X-ray computed tomography (XCT). Offering an accurately co-registered, information-rich hybrid data set, FMT-XCT has new imaging possibilities compared to stand-alone FMT and XCT. We applied FMT-XCT to a subcutaneous 4T1 tumor mouse model, an Aga2 osteogenesis imperfecta model and a Kras lung cancer mouse model, using XCT information during FMT inversion. We validated in vivo imaging results against post-mortem planar fluorescence images of cryoslices and histology data. Besides offering concurrent anatomical and functional information, FMT-XCT resulted in the most accurate FMT performance to date. These findings indicate that addition of FMT optics into the XCT gantry may be a potent upgrade for small-animal XCT systems.
Label-free and direct detection of C-reactive protein using reduced graphene oxide-nanoparticle hybrid impedimetric sensor.

Science.gov (United States)

Yagati, Ajay Kumar; Pyun, Jae-Chul; Min, Junhong; Cho, Sungbo

2016-02-01

For label-free and direct detection of C-reactive protein (CRP), an impedimetric sensor based on an indium tin oxide (ITO) electrode array functionalized with reduced graphene oxide-nanoparticle (rGO-NP) hybrid was fabricated and evaluated. Analytical measurements were performed to examine the properties of rGO-NP-modified ITO microelectrodes and to determine the influence upon sensory performance of using nanostructures modified for antibody immobilization and for recognition of CRP binding events. Impedimetric measurements in the presence of the redox couple [Fe(CN)6](3-/4-) showed significant changes in charge transfer resistance upon binding of CRP. The impedance measurements were highly target specific, linear with logarithmic CRP concentrations in PBS and human serum across a 1 ng mL(-1) and 1000 ng mL(-1) range and associated with a detection limits of 0.06 and 0.08 ng mL(-1) respectively. Copyright © 2015 Elsevier B.V. All rights reserved.
Ultrasensitive electrochemical detection of DNA based on Zn²⁺ assistant DNA recycling followed with hybridization chain reaction dual amplification.

Science.gov (United States)

Qian, Yong; Wang, Chunyan; Gao, Fenglei

2015-01-15

A new strategy to combine Zn(2+) assistant DNA recycling followed with hybridization chain reaction dual amplification was designed for highly sensitive electrochemical detection of target DNA. A gold electrode was used to immobilize molecular beacon (MB) as the recognition probe and perform the amplification procedure. In the presence of the target DNA, the hairpin probe 1 was opened, and the DNAzyme was liberated from the caged structure. The activated DNAzyme hybridized with the MB and catalyzed its cleavage in the presence of Zn(2+) cofactor and resulting in a free DNAzyme strand. Finally, each target-induced activated DNAzyme underwent many cycles triggering the cleavage of MB, thus forming numerous MB fragments. The MB fragments triggered the HCR and formed a long double-helix DNA structure. Because both H1 and H2 were labeled by biotin, a lot of SA-ALP was captured on the electrode surface, thus catalyzing a silver deposition process for electrochemical stripping analysis. This novel cascade signal amplification strategy can detect target DNA down to the attomolar level with a dynamic range spanning 6 orders of magnitude. This highly sensitive and specific assay has a great potential to become a promising DNA quantification method in biomedical research and clinical diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.
Accurate, Fast and Cost-Effective Diagnostic Test for Monosomy 1p36 Using Real-Time Quantitative PCR

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Pricila da Silva Cunha

2014-01-01

Full Text Available Monosomy 1p36 is considered the most common subtelomeric deletion syndrome in humans and it accounts for 0.5–0.7% of all the cases of idiopathic intellectual disability. The molecular diagnosis is often made by microarray-based comparative genomic hybridization (aCGH, which has the drawback of being a high-cost technique. However, patients with classic monosomy 1p36 share some typical clinical characteristics that, together with its common prevalence, justify the development of a less expensive, targeted diagnostic method. In this study, we developed a simple, rapid, and inexpensive real-time quantitative PCR (qPCR assay for targeted diagnosis of monosomy 1p36, easily accessible for low-budget laboratories in developing countries. For this, we have chosen two target genes which are deleted in the majority of patients with monosomy 1p36: PRKCZ and SKI. In total, 39 patients previously diagnosed with monosomy 1p36 by aCGH, fluorescent in situ hybridization (FISH, and/or multiplex ligation-dependent probe amplification (MLPA all tested positive on our qPCR assay. By simultaneously using these two genes we have been able to detect 1p36 deletions with 100% sensitivity and 100% specificity. We conclude that qPCR of PRKCZ and SKI is a fast and accurate diagnostic test for monosomy 1p36, costing less than 10 US dollars in reagent costs.
Towards Accurate Node-Based Detection of P2P Botnets

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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.
Solution of the generalized Emden-Fowler equations by the hybrid functions method

International Nuclear Information System (INIS)

Tabrizidooz, H R; Marzban, H R; Razzaghi, M

2009-01-01

In this paper, we present a numerical algorithm for solving the generalized Emden-Fowler equations, which have many applications in mathematical physics and astrophysics. The method is based on hybrid functions approximations. The properties of hybrid functions, which consist of block-pulse functions and Lagrange interpolating polynomials, are presented. These properties are then utilized to reduce the computation of the generalized Emden-Fowler equations to a system of nonlinear equations. The method is easy to implement and yields very accurate results.
Quasi-closed phase forward-backward linear prediction analysis of speech for accurate formant detection and estimation.

Science.gov (United States)

Gowda, Dhananjaya; Airaksinen, Manu; Alku, Paavo

2017-09-01

Recently, a quasi-closed phase (QCP) analysis of speech signals for accurate glottal inverse filtering was proposed. However, the QCP analysis which belongs to the family of temporally weighted linear prediction (WLP) methods uses the conventional forward type of sample prediction. This may not be the best choice especially in computing WLP models with a hard-limiting weighting function. A sample selective minimization of the prediction error in WLP reduces the effective number of samples available within a given window frame. To counter this problem, a modified quasi-closed phase forward-backward (QCP-FB) analysis is proposed, wherein each sample is predicted based on its past as well as future samples thereby utilizing the available number of samples more effectively. Formant detection and estimation experiments on synthetic vowels generated using a physical modeling approach as well as natural speech utterances show that the proposed QCP-FB method yields statistically significant improvements over the conventional linear prediction and QCP methods.
Hybrid mesons with auxiliary fields

International Nuclear Information System (INIS)

Buisseret, F.; Mathieu, V.

2006-01-01

Hybrid mesons are exotic mesons in which the color field is not in the ground state. Their understanding deserves interest from a theoretical point of view, because it is intimately related to nonperturbative aspects of QCD. Moreover, it seems that some recently detected particles, such as the π 1 (1600) and the Y(4260), are serious hybrid candidates. In this work, we investigate the description of such exotic hadrons by applying the auxiliary fields technique (also known as the einbein field method) to the widely used spinless Salpeter Hamiltonian with appropriate linear confinement. Instead of the usual numerical resolution, this technique allows to find simplified analytical mass spectra and wave functions of the Hamiltonian, which still lead to reliable qualitative predictions. We analyse and compare two different descriptions of hybrid mesons, namely a two-body q system with an excited flux tube, or a three-body qg system. We also compute the masses of the 1 -+ hybrids. Our results are shown to be in satisfactory agreement with lattice QCD and other effective models. (orig.)
Improved detection of genetic markers of antimicrobial resistance by hybridization probe-based melting curve analysis using primers to mask proximal mutations: examples include the influenza H275Y substitution.

Science.gov (United States)

Whiley, David M; Jacob, Kevin; Nakos, Jennifer; Bletchly, Cheryl; Nimmo, Graeme R; Nissen, Michael D; Sloots, Theo P

2012-06-01

Numerous real-time PCR assays have been described for detection of the influenza A H275Y alteration. However, the performance of these methods can be undermined by sequence variation in the regions flanking the codon of interest. This is a problem encountered more broadly in microbial diagnostics. In this study, we developed a modification of hybridization probe-based melting curve analysis, whereby primers are used to mask proximal mutations in the sequence targets of hybridization probes, so as to limit the potential for sequence variation to interfere with typing. The approach was applied to the H275Y alteration of the influenza A (H1N1) 2009 strain, as well as a Neisseria gonorrhoeae mutation associated with antimicrobial resistance. Assay performances were assessed using influenza A and N. gonorrhoeae strains characterized by DNA sequencing. The modified hybridization probe-based approach proved successful in limiting the effects of proximal mutations, with the results of melting curve analyses being 100% consistent with the results of DNA sequencing for all influenza A and N. gonorrhoeae strains tested. Notably, these included influenza A and N. gonorrhoeae strains exhibiting additional mutations in hybridization probe targets. Of particular interest was that the H275Y assay correctly typed influenza A strains harbouring a T822C nucleotide substitution, previously shown to interfere with H275Y typing methods. Overall our modified hybridization probe-based approach provides a simple means of circumventing problems caused by sequence variation, and offers improved detection of the influenza A H275Y alteration and potentially other resistance mechanisms.
Hybrid vigour and gene action for two quantitative traits of castor ...

African Journals Online (AJOL)

Five homozygous lines of castor plant, namely RS1-Om, RN1-Om, RTl-2m, RSl- Owm, and RNl- Omb, were crossed to raise F1, F2, BC1, and BC2 generations. The hybrids were tested for hybrid vigour for two metric traits, viz; number of pods per plant and seed yield per plant. Highly significant hybrid vigour was detected ...
Ultrasensitive and simultaneous detection of heavy metal ions based on three-dimensional graphene-carbon nanotubes hybrid electrode materials

Energy Technology Data Exchange (ETDEWEB)

Huang, Hui; Chen, Ting [Key Laboratory for Colloid and Interface Chemistry of State Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China); Liu, Xiuyu [Shandong Academy of Sciences, Jinan 250114 (China); Ma, Houyi, E-mail: hyma@sdu.edu.cn [Key Laboratory for Colloid and Interface Chemistry of State Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100 (China)

2014-12-10

Highlights: • Three-dimensional graphene-MWCNTs nanocomposites were prepared. • Graphene-MWCNTs based electrochemical sensor was used to detect heavy metal ions for the first time. • The proposed sensor was certified capable for real sample with satisfactory results. - Abstract: A green and facile method was developed to prepare a novel hybrid nanocomposite that consisted of one-dimensional multi-walled carbon nanotubes (MWCNTs) and two-dimensional graphene oxide (GO) sheets. The as-prepared three-dimensional GO–MWCNTs hybrid nanocomposites exhibit excellent water-solubility owing to the high hydrophilicity of GO components; meanwhile, a certain amount of MWCNTs loaded on the surface of GO sheets through π–π interaction seem to be “dissolved” in water. Moreover, the graphene(G)-MWCNTs nanocomposites with excellent conductivity were obtained conveniently by the direct electrochemical reduction of GO–MWCNTs nanocomposites. Seeing that there is a good synergistic effect between MWCNTs and graphene components in enhancing preconcentration efficiency of metal ions and accelerating electron transfer rate at G-MWCNTs/electrolyte interface, the G-MWCNTs nanocomposites possess fast, simultaneous and sensitive detection performance for trace amounts of heavy metal ions. The electrochemical results demonstrate that the G-MWCNTs nanocomposites can act as a kind of practical sensing material to simultaneously determine Pb{sup 2+} and Cd{sup 2+} ions in terms of anodic stripping voltammetry (ASV). The linear calibration plots for Pb{sup 2+} and Cd{sup 2+} ranged from 0.5 μg L{sup −1} to 30 μg L{sup −1}. The detection limits were determined to be 0.2 μg L{sup −1} (S/N = 3) for Pb{sup 2+} and 0.1 μg L{sup −1} (S/N = 3) for Cd{sup 2+} in the case of a deposition time of 180 s. It is worth mentioning that the G-MWCNTs modified electrodes were successfully applied to the simultaneous detection of Cd{sup 2+} and Pb{sup 2+} ions in real electroplating
Short-Term Wind Power Forecasting Using the Enhanced Particle Swarm Optimization Based Hybrid Method

Directory of Open Access Journals (Sweden)

Wen-Yeau Chang

2013-09-01

Full Text Available High penetration of wind power in the electricity system provides many challenges to power system operators, mainly due to the unpredictability and variability of wind power generation. Although wind energy may not be dispatched, an accurate forecasting method of wind speed and power generation can help power system operators reduce the risk of an unreliable electricity supply. This paper proposes an enhanced particle swarm optimization (EPSO based hybrid forecasting method for short-term wind power forecasting. The hybrid forecasting method combines the persistence method, the back propagation neural network, and the radial basis function (RBF neural network. The EPSO algorithm is employed to optimize the weight coefficients in the hybrid forecasting method. To demonstrate the effectiveness of the proposed method, the method is tested on the practical information of wind power generation of a wind energy conversion system (WECS installed on the Taichung coast of Taiwan. Comparisons of forecasting performance are made with the individual forecasting methods. Good agreements between the realistic values and forecasting values are obtained; the test results show the proposed forecasting method is accurate and reliable.
Polymer Combustion as a Basis for Hybrid Propulsion: A Comprehensive Review and New Numerical Approaches

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Vasily Novozhilov

2011-10-01

Full Text Available Hybrid Propulsion is an attractive alternative to conventional liquid and solid rocket motors. This is an active area of research and technological developments. Potential wide application of Hybrid Engines opens the possibility for safer and more flexible space vehicle launching and manoeuvring. The present paper discusses fundamental combustion issues related to further development of Hybrid Rockets. The emphasis is made on the two aspects: (1 properties of potential polymeric fuels, and their modification, and (2 implementation of comprehensive CFD models for combustion in Hybrid Engines. Fundamentals of polymeric fuel combustion are discussed. Further, steps necessary to accurately describe their burning behaviour by means of CFD models are investigated. Final part of the paper presents results of preliminary CFD simulations of fuel burning process in Hybrid Engine using a simplified set-up.
BLESS 2: accurate, memory-efficient and fast error correction method.

Science.gov (United States)

Heo, Yun; Ramachandran, Anand; Hwu, Wen-Mei; Ma, Jian; Chen, Deming

2016-08-01

The most important features of error correction tools for sequencing data are accuracy, memory efficiency and fast runtime. The previous version of BLESS was highly memory-efficient and accurate, but it was too slow to handle reads from large genomes. We have developed a new version of BLESS to improve runtime and accuracy while maintaining a small memory usage. The new version, called BLESS 2, has an error correction algorithm that is more accurate than BLESS, and the algorithm has been parallelized using hybrid MPI and OpenMP programming. BLESS 2 was compared with five top-performing tools, and it was found to be the fastest when it was executed on two computing nodes using MPI, with each node containing twelve cores. Also, BLESS 2 showed at least 11% higher gain while retaining the memory efficiency of the previous version for large genomes. Freely available at https://sourceforge.net/projects/bless-ec dchen@illinois.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Role of dispersion corrected hybrid GGA class in accurately calculating the bond dissociation energy of carbon halogen bond: A benchmark study

Science.gov (United States)

Kosar, Naveen; Mahmood, Tariq; Ayub, Khurshid

2017-12-01

Benchmark study has been carried out to find a cost effective and accurate method for bond dissociation energy (BDE) of carbon halogen (Csbnd X) bond. BDE of C-X bond plays a vital role in chemical reactions, particularly for kinetic barrier and thermochemistry etc. The compounds (1-16, Fig. 1) with Csbnd X bond used for current benchmark study are important reactants in organic, inorganic and bioorganic chemistry. Experimental data of Csbnd X bond dissociation energy is compared with theoretical results. The statistical analysis tools such as root mean square deviation (RMSD), standard deviation (SD), Pearson's correlation (R) and mean absolute error (MAE) are used for comparison. Overall, thirty-one density functionals from eight different classes of density functional theory (DFT) along with Pople and Dunning basis sets are evaluated. Among different classes of DFT, the dispersion corrected range separated hybrid GGA class along with 6-31G(d), 6-311G(d), aug-cc-pVDZ and aug-cc-pVTZ basis sets performed best for bond dissociation energy calculation of C-X bond. ωB97XD show the best performance with less deviations (RMSD, SD), mean absolute error (MAE) and a significant Pearson's correlation (R) when compared to experimental data. ωB97XD along with Pople basis set 6-311g(d) has RMSD, SD, R and MAE of 3.14 kcal mol-1, 3.05 kcal mol-1, 0.97 and -1.07 kcal mol-1, respectively.
Multilevel Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2016-01-06

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks, among many others. In this work [6] we present a novel multilevel algorithm for the Chernoff-based hybrid tauleap algorithm. This variance reduction technique allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.
Multilevel Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2015-01-07

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks, among many others. In this work [6] we present a novel multilevel algorithm for the Chernoff-based hybrid tauleap algorithm. This variance reduction technique allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.
Multilevel Hybrid Chernoff Tau-Leap

KAUST Repository

Moraes, Alvaro

2014-01-06

Markovian pure jump processes can model many phenomena, e.g. chemical reactions at molecular level, protein transcription and translation, spread of epidemics diseases in small populations and in wireless communication networks, among many others. In this work [6] we present a novel multilevel algorithm for the Chernoff-based hybrid tauleap algorithm. This variance reduction technique allows us to: (a) control the global exit probability of any simulated trajectory, (b) obtain accurate and computable estimates for the expected value of any smooth observable of the process with minimal computational work.

Asymmetric hybridization and introgression between pink salmon and chinook salmon in the Laurentian Great Lakes

Science.gov (United States)

Rosenfield, Jonathan A.; Todd, Thomas; Greil, Roger

2000-01-01

Among Pacific salmon collected in the St. Marys River, five natural hybrids of pink salmon Oncorhynchus gorbuscha and chinook salmon Oncorhynchus tshawytscha and one suspected backcross have been detected using morphologic, meristic, and color evidence. One allozyme (LDH, l-lactate dehydrogenase from muscle) and one nuclear DNA locus (growth hormone) for which species-specific fixed differences exist were analyzed to detect additional hybrids and to determine if introgression had occurred. Restriction fragment length polymorphism of mitochondrial DNA (mtDNA) was used to identify the maternal parent of each hybrid. Evidence of introgression was found among the five previously identified hybrids. All hybrid specimens had chinook salmon mtDNA, indicating that hybridization between chinook salmon and pink salmon in the St. Marys River is asymmetric and perhaps unidirectional. Ecological, physiological, and sexual selection forces may contribute to this asymmetric hybridization. Introgression between these highly differentiated species has implications for management, systematics, and conservation of Pacific salmon.
MIDAS robust trend estimator for accurate GPS station velocities without step detection

Science.gov (United States)

Blewitt, Geoffrey; Kreemer, Corné; Hammond, William C.; Gazeaux, Julien

2016-03-01

Automatic estimation of velocities from GPS coordinate time series is becoming required to cope with the exponentially increasing flood of available data, but problems detectable to the human eye are often overlooked. This motivates us to find an automatic and accurate estimator of trend that is resistant to common problems such as step discontinuities, outliers, seasonality, skewness, and heteroscedasticity. Developed here, Median Interannual Difference Adjusted for Skewness (MIDAS) is a variant of the Theil-Sen median trend estimator, for which the ordinary version is the median of slopes vij = (xj-xi)/(tj-ti) computed between all data pairs i > j. For normally distributed data, Theil-Sen and least squares trend estimates are statistically identical, but unlike least squares, Theil-Sen is resistant to undetected data problems. To mitigate both seasonality and step discontinuities, MIDAS selects data pairs separated by 1 year. This condition is relaxed for time series with gaps so that all data are used. Slopes from data pairs spanning a step function produce one-sided outliers that can bias the median. To reduce bias, MIDAS removes outliers and recomputes the median. MIDAS also computes a robust and realistic estimate of trend uncertainty. Statistical tests using GPS data in the rigid North American plate interior show ±0.23 mm/yr root-mean-square (RMS) accuracy in horizontal velocity. In blind tests using synthetic data, MIDAS velocities have an RMS accuracy of ±0.33 mm/yr horizontal, ±1.1 mm/yr up, with a 5th percentile range smaller than all 20 automatic estimators tested. Considering its general nature, MIDAS has the potential for broader application in the geosciences.
The role of hybrid SPECT-CT in oncology: current and emerging clinical applications

International Nuclear Information System (INIS)

Chowdhury, F.U.; Scarsbrook, A.F.

2008-01-01

Single photon emission computed tomography - computed tomography (SPECT-CT) is an emerging dual-modality imaging technique with many established and potential clinical applications in the field of oncology. To date, there has been a considerable emphasis on the benefits of integrated positron emission tomography - computed tomography (PET-CT) in oncology, but relatively little focus on the clinical utility of SPECT-CT. As with PET-CT, accurate co-registration of anatomical and functional data from a combined SPECT-CT camera often provides complementary diagnostic information. Both sensitivity (superior disease localization) and specificity (exclusion of false-positives due to physiological tracer uptake) are improved, and the functional significance of indeterminate lesions detected on cross-sectional imaging can be defined. This article will review the scope of hybrid SPECT-CT in oncology and illustrate both current and emerging clinical applications
A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays

Directory of Open Access Journals (Sweden)

Fujisawa Hironori

2010-05-01

Full Text Available Abstract Background High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: Results We compared the single feature polymorphism (SFP detection performance of whole-genome and transcript hybridizations using the Affymetrix GeneChip® Rice Genome Array, using the rice cultivars with full genome sequence, japonica cultivar Nipponbare and indica cultivar 93-11. Both genomes were surveyed for all probe target sequences. Only completely matched 25-mer single copy probes of the Nipponbare genome were extracted, and SFPs between them and 93-11 sequences were predicted. We investigated optimum conditions for SFP detection in both whole genome and transcript hybridization using differences between perfect match and mismatch probe intensities of non-polymorphic targets, assuming that these differences are representative of those between mismatch and perfect targets. Several statistical methods of SFP detection by whole-genome hybridization were compared under the optimized conditions. Causes of false positives and negatives in SFP detection in both types of hybridization were investigated. Conclusions The optimizations allowed a more than 20% increase in true SFP detection in whole-genome hybridization and a large improvement of SFP detection performance in transcript hybridization. Significance analysis of the microarray for log-transformed raw intensities of PM probes gave the best performance in whole genome hybridization, and 22,936 true SFPs were detected with 23.58% false positives by whole genome hybridization. For transcript hybridization, stable SFP detection was achieved for highly expressed genes, and about 3,500 SFPs were detected at a high sensitivity (> 50% in both shoot and young panicle transcripts. High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of Oryza sativa can be
Detecting slow introgression of invasive alleles in an extensively restocked game bird

Directory of Open Access Journals (Sweden)

Ines eSanchez-Donoso

2014-04-01

Full Text Available Interbreeding of two species in the wild implies introgression of alleles from one species into the other only when admixed individuals survive and successfully backcross with the parental species. Consequently, estimating the proportion of first generation hybrids in a population may not inform about the evolutionary impact of hybridization. Samples obtained over a long time span may offer a more accurate view of the spreading of introgressed alleles in a species’ gene pool. Common quail (Coturnix coturnix populations in Europe have been restocked extensively with farm quails of hybrid origin (crosses with Japanese quails, C. japonica. We genetically monitored a common quail population over 15 years to investigate whether genetic introgression is occurring and used simulations to investigate our power to detect it. Our results revealed that some introgression has occurred, but we did not observe a significant increase over time in the proportion of admixed individuals. However, simulations showed that the degree of admixture may be larger than anticipated due to the limited power of analyses over a short time span, and that observed data was compatible with a low rate of introgression, probably resulting from reduced fitness of admixed individuals. Simulations predicted this could result in extensive admixture in the near future.
Travelling Waves in Hybrid Chemotaxis Models

KAUST Repository

Franz, Benjamin

2013-12-18

Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are investigated. Bacteria are modelled using an agent-based (individual-based) approach with internal dynamics describing signal transduction. In addition to the chemotactic behaviour of the bacteria, the individual-based model also includes cell proliferation and death. Cells consume the extracellular nutrient field (chemoattractant), which is modelled using a partial differential equation. Mesoscopic and macroscopic equations representing the behaviour of the hybrid model are derived and the existence of travelling wave solutions for these models is established. It is shown that cell proliferation is necessary for the existence of non-transient (stationary) travelling waves in hybrid models. Additionally, a numerical comparison between the wave speeds of the continuum models and the hybrid models shows good agreement in the case of weak chemotaxis and qualitative agreement for the strong chemotaxis case. In the case of slow cell adaptation, we detect oscillating behaviour of the wave, which cannot be explained by mean-field approximations. © 2013 Society for Mathematical Biology.
Multilevel Thresholding Method Based on Electromagnetism for Accurate Brain MRI Segmentation to Detect White Matter, Gray Matter, and CSF

Directory of Open Access Journals (Sweden)

G. Sandhya

2017-01-01

Full Text Available This work explains an advanced and accurate brain MRI segmentation method. MR brain image segmentation is to know the anatomical structure, to identify the abnormalities, and to detect various tissues which help in treatment planning prior to radiation therapy. This proposed technique is a Multilevel Thresholding (MT method based on the phenomenon of Electromagnetism and it segments the image into three tissues such as White Matter (WM, Gray Matter (GM, and CSF. The approach incorporates skull stripping and filtering using anisotropic diffusion filter in the preprocessing stage. This thresholding method uses the force of attraction-repulsion between the charged particles to increase the population. It is the combination of Electromagnetism-Like optimization algorithm with the Otsu and Kapur objective functions. The results obtained by using the proposed method are compared with the ground-truth images and have given best values for the measures sensitivity, specificity, and segmentation accuracy. The results using 10 MR brain images proved that the proposed method has accurately segmented the three brain tissues compared to the existing segmentation methods such as K-means, fuzzy C-means, OTSU MT, Particle Swarm Optimization (PSO, Bacterial Foraging Algorithm (BFA, Genetic Algorithm (GA, and Fuzzy Local Gaussian Mixture Model (FLGMM.
Diagnosis, prognosis and disease management using in situ hybridization

International Nuclear Information System (INIS)

Kucheria, K.; Talwar, R.

2002-01-01

The year 2001 saw unveiling of anatomy of the human genome with sequencing of 90% of the euchromatic region. But the ultimate goal of the Human Genome Project to delineate the positions of all genes is yet to be achieved. In Situ Hybridization (ISH) is one of the methods that help in localizing genes on chromosomes. The present study aimed to use radioactive- and fluorescent-labeled probes for screening various congenital anomalies (sex chromosomal and autosomal), for prenatal diagnosis and cancer genetics. Standard techniques were used for hybridization with radioactively and fluorescent labeled probes. Sex chromosome aneuploidies (XXY, XO, XXX, XYY etc.) were analyzed using centromeric probes for chromosomes X and Y. The cases with ambiguous genitalia were further analyzed using probe specific for the sex-determining region (SRY) on the Y chromosome. Suspected cases of Down syndrome were analyzed using probe specific for centromeric region of chromosome 21 to confirm trisomy 21. Prenatal diagnosis included screening aneuploidies of chromosomes 13, 18, 21, X and Y on uncultured cells and metaphases obtained from amniotic fluid and chorionic villi samplings. Gene alterations were also studied in Retinoblastoma patients, Chronic Myeloid Leukemia (CML) and Acute Promyelocytic Leukemia (APML) using probes specific for Rb1, bcr/abl and PML/RARα genes respectively. Response to therapy was assessed by evaluating minimal residual disease (MRD) in leukemia patients. Attempts were also made to analyze cells obtained from buccal mucosa and bladder epithelium that could facilitate rapid screening of sex chromosome anomalies and bladder cancer without painful invasive techniques. Prenatal diagnosis using ISH on uncultured cells could provide an accurate and rapid result. These results of prenatal diagnosis were in conformation with results of conventional cytogenetics obtained after long-term cultures. Molecular rearrangements that could not be detected with conventional
A hybrid hydrostatic and non-hydrostatic numerical model for shallow flow simulations

Science.gov (United States)

Zhang, Jingxin; Liang, Dongfang; Liu, Hua

2018-05-01

Hydrodynamics of geophysical flows in oceanic shelves, estuaries, and rivers, are often studied by solving shallow water model equations. Although hydrostatic models are accurate and cost efficient for many natural flows, there are situations where the hydrostatic assumption is invalid, whereby a fully hydrodynamic model is necessary to increase simulation accuracy. There is a growing concern about the decrease of the computational cost of non-hydrostatic pressure models to improve the range of their applications in large-scale flows with complex geometries. This study describes a hybrid hydrostatic and non-hydrostatic model to increase the efficiency of simulating shallow water flows. The basic numerical model is a three-dimensional hydrostatic model solved by the finite volume method (FVM) applied to unstructured grids. Herein, a second-order total variation diminishing (TVD) scheme is adopted. Using a predictor-corrector method to calculate the non-hydrostatic pressure, we extended the hydrostatic model to a fully hydrodynamic model. By localising the computational domain in the corrector step for non-hydrostatic pressure calculations, a hybrid model was developed. There was no prior special treatment on mode switching, and the developed numerical codes were highly efficient and robust. The hybrid model is applicable to the simulation of shallow flows when non-hydrostatic pressure is predominant only in the local domain. Beyond the non-hydrostatic domain, the hydrostatic model is still accurate. The applicability of the hybrid method was validated using several study cases.
Detection of Early Morning Daily Activities with Static Home and Wearable Wireless Sensors

Directory of Open Access Journals (Sweden)

David Vanderpool

2007-10-01

Full Text Available This paper describes a flexible, cost-effective, wireless in-home activity monitoring system for assisting patients with cognitive impairments due to traumatic brain injury (TBI. The system locates the subject with fixed home sensors and classifies early morning bathroom activities of daily living with a wearable wireless accelerometer. The system extracts time- and frequency-domain features from the accelerometer data and classifies these features with a hybrid classifier that combines Gaussian mixture models and a finite state machine. In particular, the paper establishes that despite similarities between early morning bathroom activities of daily living, it is possible to detect and classify these activities with high accuracy. It also discusses system training and provides data to show that with proper feature selection, accurate detection and classification are possible for any subject with no subject specific training.
Ultra fast, accurate PET image reconstruction for the Siemens hybrid MR/BrainPET scanner using raw LOR data

International Nuclear Information System (INIS)

Scheins, Juergen; Lerche, Christoph; Shah, Jon

2015-01-01

Fast PET image reconstruction algorithms usually use a Line-of-Response (LOR) preprocessing step where the detected raw LOR data are interpolated either to evenly spaced sinogram projection bins or alternatively to a generic projection space as for example proposed by the PET Reconstruction Software Toolkit (PRESTO) [1]. In this way, speed-optimised, versatile geometrical projectors can be implemented for iterative image reconstruction independent of the underlying scanner geometry. However, all strategies of projection data interpolation unavoidably lead to a loss of original information and result in some degradation of image quality. Here, direct LOR reconstructions overcome this evident drawback at cost of a massively enhanced computational burden. Therefore, computational optimisation techniques are essential to make such demanding approaches attractive and economical for widespread usage in the clinical environment. In this paper, we demonstrate for the Siemens Hybrid MR/BrainPET with 240 million physical LORs that a very fast quantitative direct LOR reconstruction can be realized using a modified version of PRESTO. Now, PRESTO is also capable to directly use sets of symmetric physical LORs instead of interpolating LORs to a generic projection space. Exploiting basic scanner symmetries together with the technique of Single Instruction Multipe Data (SIMD) and Simultaneous Multi-Threading (SMT) results in an overall calculation time of 2-3 minutes per frame on a single multi-core machine, i.e. neither requiring a cluster of mutliple machines nor Graphics Processing Units (GPUs).
Ultra fast, accurate PET image reconstruction for the Siemens hybrid MR/BrainPET scanner using raw LOR data

Energy Technology Data Exchange (ETDEWEB)

Scheins, Juergen; Lerche, Christoph; Shah, Jon [Forschungszentrum Jülich GmbH, Jülich (Germany)

2015-05-18

Fast PET image reconstruction algorithms usually use a Line-of-Response (LOR) preprocessing step where the detected raw LOR data are interpolated either to evenly spaced sinogram projection bins or alternatively to a generic projection space as for example proposed by the PET Reconstruction Software Toolkit (PRESTO) [1]. In this way, speed-optimised, versatile geometrical projectors can be implemented for iterative image reconstruction independent of the underlying scanner geometry. However, all strategies of projection data interpolation unavoidably lead to a loss of original information and result in some degradation of image quality. Here, direct LOR reconstructions overcome this evident drawback at cost of a massively enhanced computational burden. Therefore, computational optimisation techniques are essential to make such demanding approaches attractive and economical for widespread usage in the clinical environment. In this paper, we demonstrate for the Siemens Hybrid MR/BrainPET with 240 million physical LORs that a very fast quantitative direct LOR reconstruction can be realized using a modified version of PRESTO. Now, PRESTO is also capable to directly use sets of symmetric physical LORs instead of interpolating LORs to a generic projection space. Exploiting basic scanner symmetries together with the technique of Single Instruction Multipe Data (SIMD) and Simultaneous Multi-Threading (SMT) results in an overall calculation time of 2-3 minutes per frame on a single multi-core machine, i.e. neither requiring a cluster of mutliple machines nor Graphics Processing Units (GPUs).
Prediction of the optimum hybridization conditions of dot-blot-SNP analysis using estimated melting temperature of oligonucleotide probes.

Science.gov (United States)

Shiokai, Sachiko; Kitashiba, Hiroyasu; Nishio, Takeshi

2010-08-01

Although the dot-blot-SNP technique is a simple cost-saving technique suitable for genotyping of many plant individuals, optimization of hybridization and washing conditions for each SNP marker requires much time and labor. For prediction of the optimum hybridization conditions for each probe, we compared T (m) values estimated from nucleotide sequences using the DINAMelt web server, measured T (m) values, and hybridization conditions yielding allele-specific signals. The estimated T (m) values were comparable to the measured T (m) values with small differences of less than 3 degrees C for most of the probes. There were differences of approximately 14 degrees C between the specific signal detection conditions and estimated T (m) values. Change of one level of SSC concentrations of 0.1, 0.2, 0.5, and 1.0x SSC corresponded to a difference of approximately 5 degrees C in optimum signal detection temperature. Increasing the sensitivity of signal detection by shortening the exposure time to X-ray film changed the optimum hybridization condition for specific signal detection. Addition of competitive oligonucleotides to the hybridization mixture increased the suitable hybridization conditions by 1.8. Based on these results, optimum hybridization conditions for newly produced dot-blot-SNP markers will become predictable.
A hybrid sequential approach for data clustering using K-Means and ...

African Journals Online (AJOL)

Experiments on four kinds of data sets have been conducted. The obtained results are compared with K-Means, PSO, Hybrid, K-Means+Genetic Algorithm and it has been found that the proposed algorithm generates more accurate, robust and better clustering results. International Journal of Engineering, Science and ...
Hybrid Long-Distance Entanglement Distribution Protocol

DEFF Research Database (Denmark)

Brask, J.B.; Rigas, I.; Polzik, E.S.

2010-01-01

We propose a hybrid (continuous-discrete variable) quantum repeater protocol for long-distance entanglement distribution. Starting from states created by single-photon detection, we show how entangled coherent state superpositions can be generated by means of homodyne detection. We show that near......-deterministic entanglement swapping with such states is possible using only linear optics and homodyne detectors, and we evaluate the performance of our protocol combining these elements....
Non-enzymatic detection of glucose in fruits using TiO2-Mn3O4 hybrid nano interface

Science.gov (United States)

Jayanth Babu, K.; Sasya, Madhurantakam; Nesakumar, Noel; Shankar, Prabakaran; Gumpu, Manju Bhargavi; Ramachandra, Bhat Lakshmishri; Kulandaisamy, Arockia Jayalatha; Rayappan, John Bosco Balaguru

2017-08-01

Consumption of fruits leads to increase in glucose level in blood for diabetic patients, which in turn leads to peripheral, vascular, ocular complications and cardiac diseases. In this context, a non-enzymatic hybrid glucose biosensor was fabricated for the first time to detect glucose by immobilizing titanium oxide-manganese oxide (TiO2-Mn3O4) nanocomposite and chitosan membrane on to the surface of Pt working electrode (Pt/TiO2-Mn3O4/chitosan). TiO2-Mn3O4 nanocomposite catalyzed the oxidation of glucose to gluconolactone in the absence of glucose oxidase enzyme with high electron transfer rate, good biocompatibility and large surface coverage. Electrochemical measurements revealed the excellent sensing response of the developed biosensor towards glucose with a high sensitivity of 7.073 µA mM-1, linearity of 0.01-0.1 mM, low detection limit of 0.01 µM, reproducibility of 1.5% and stability of 98.8%. The electrochemical parameters estimated from the anodic process were subjected to linear regression models for the detection of unknown concentration of glucose in different fruit samples.
Enhancing Hybrid Perovskite Detectability in the Deep Ultraviolet Region with Down-Conversion Dual-Phase (CsPbBr3-Cs4PbBr6) Films.

Science.gov (United States)

Tong, Guoqing; Li, Huan; Zhu, Zhifeng; Zhang, Yan; Yu, Linwei; Xu, Jun; Jiang, Yang

2018-04-05

Hybrid perovskite photodetectors (PDs) exhibit outstanding performance in the ultraviolet-visible (UV-vis) spectrum but have poor detectability in the deep ultraviolet (DUV) region (200-350 nm). In this work, a novel inorganic-hybrid architecture that incorporates a dual-phase (CsPbBr 3 -Cs 4 PbBr 6 ) inorganic perovskite material as a down-conversion window layer and a hybrid perovskite as a light capture layer was prepared to achieve faster, highly sensitive photodetection in the DUV spectrum. A dual-phase inorganic perovskite film coated on the back surface of the photodetector enables strong light absorption and tunes the incident energy into emission bands that are optimized for the perovskite photodetector. The presence of Cs 4 PbBr 6 enhances the capture and down-conversion of the incident DUV light. Due to the down-conversion and transport of the DUV photons, a self-driven perovskite photodetector with this composite structure exhibits a fast response time of 7.8/33.6 μs and a high responsivity of 49.4 mA W -1 at 254 nm without extra power supply.
Probability of detecting marine predator-prey and species interactions using novel hybrid acoustic transmitter-receiver tags.

Directory of Open Access Journals (Sweden)

Laurie L Baker

Full Text Available Understanding the nature of inter-specific and conspecific interactions in the ocean is challenging because direct observation is usually impossible. The development of dual transmitter/receivers, Vemco Mobile Transceivers (VMT, and satellite-linked (e.g. GPS tags provides a unique opportunity to better understand between and within species interactions in space and time. Quantifying the uncertainty associated with detecting a tagged animal, particularly under varying field conditions, is vital for making accurate biological inferences when using VMTs. We evaluated the detection efficiency of VMTs deployed on grey seals, Halichoerus grypus, off Sable Island (NS, Canada in relation to environmental characteristics and seal behaviour using generalized linear models (GLM to explore both post-processed detection data and summarized raw VMT data. When considering only post-processed detection data, only about half of expected detections were recorded at best even when two VMT-tagged seals were estimated to be within 50-200 m of one another. At a separation of 400 m, only about 15% of expected detections were recorded. In contrast, when incomplete transmissions from the summarized raw data were also considered, the ratio of complete transmission to complete and incomplete transmissions was about 70% for distances ranging from 50-1000 m, with a minimum of around 40% at 600 m and a maximum of about 85% at 50 m. Distance between seals, wind stress, and depth were the most important predictors of detection efficiency. Access to the raw VMT data allowed us to focus on the physical and environmental factors that limit a transceiver's ability to resolve a transmitter's identity.
Fluorescence in situ hybridization of TP53 for the detection of chromosome 17 abnormalities in myelodysplastic syndromes.

Science.gov (United States)

Sánchez-Castro, Judit; Marco-Betés, Víctor; Gómez-Arbonés, Xavier; García-Cerecedo, Tomás; López, Ricard; Talavera, Elisabeth; Fernández-Ruiz, Sara; Ademà, Vera; Marugan, Isabel; Luño, Elisa; Sanzo, Carmen; Vallespí, Teresa; Arenillas, Leonor; Marco Buades, Josefa; Batlle, Ana; Buño, Ismael; Martín Ramos, María Luisa; Blázquez Rios, Beatriz; Collado Nieto, Rosa; Vargas, Ma Teresa; González Martínez, Teresa; Sanz, Guillermo; Solé, Francesc

2015-01-01

Conventional G-banding cytogenetics (CC) detects chromosome 17 (chr17) abnormalities in 2% of patients with de novo myelodysplastic syndromes (MDS). We used CC and fluorescence in situ hybridization (FISH) (LSI p53/17p13.1) to assess deletion of 17p in 531 patients with de novo MDS from the Spanish Group of Hematological Cytogenetics. FISH detected - 17 or 17p abnormalities in 13 cases (2.6%) in whom no 17p abnormalities were revealed by CC: 0.9% of patients with a normal karyotype, 0% in non-informative cytogenetics, 50% of patients with a chr17 abnormality without loss of 17p and 4.7% of cases with an abnormal karyotype not involving chr17. Our results suggest that applying FISH of 17p13 to identify the number of copies of the TP53 gene could be beneficial in patients with a complex karyotype. We recommend using FISH of 17p13 in young patients with a normal karyotype or non-informative cytogenetics, and always in isolated del(17p).
MMP activity in the hybrid layer detected with in situ zymography.

Science.gov (United States)

Mazzoni, A; Nascimento, F D; Carrilho, M; Tersariol, I; Papa, V; Tjäderhane, L; Di Lenarda, R; Tay, F R; Pashley, D H; Breschi, L

2012-05-01

Dentinal proteases are believed to play an important role in the degradation of hybrid layers (HL). This study investigated the HL gelatinolytic activity by in situ zymography and functional enzyme activity assay. The hypotheses were that HLs created by an etch-and-rinse adhesive exhibit active gelatinolytic activity, and MMP-2 and -9 activities in dentin increase during adhesive procedures. Etched-dentin specimens were bonded with Adper Scotchbond 1XT and restored with composite. Adhesive/dentin interface slices were placed on microscope slides, covered with fluorescein-conjugated gelatin, and observed with a multi-photon confocal microscope after 24 hrs. Human dentin powder aliquots were prepared and assigned to the following treatments: A, untreated; B, etched with 10% phosphoric acid; or C, etched with 10% phosphoric acid and mixed with Scotchbond 1XT. The MMP-2 and -9 activities of extracts of dentin powder were measured with functional enzyme assays. Intense and continuous enzyme activity was detected at the bottom of the HL, while that activity was more irregular in the upper HL. Both acid-etching and subsequent adhesive application significantly increased MMP-2 and -9 activities (p < 0.05). The results demonstrate, for the first time, intrinsic MMP activity in the HL, and intense activation of matrix-bound MMP activity with both etching and adhesive application.

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