Comparative Validation of the Determination of Sofosbuvir in Pharmaceuticals by Several Inexpensive Ecofriendly Chromatographic, Electrophoretic, and Spectrophotometric Methods.

PubMed

El-Yazbi, Amira F

2017-07-01

Sofosbuvir (SOFO) was approved by the U.S. Food and Drug Administration in 2013 for the treatment of hepatitis C virus infection with enhanced antiviral potency compared with earlier analogs. Notwithstanding, all current editions of the pharmacopeias still do not present any analytical methods for the quantification of SOFO. Thus, rapid, simple, and ecofriendly methods for the routine analysis of commercial formulations of SOFO are desirable. In this study, five accurate methods for the determination of SOFO in pharmaceutical tablets were developed and validated. These methods include HPLC, capillary zone electrophoresis, HPTLC, and UV spectrophotometric and derivative spectrometry methods. The proposed methods proved to be rapid, simple, sensitive, selective, and accurate analytical procedures that were suitable for the reliable determination of SOFO in pharmaceutical tablets. An analysis of variance test with P-value > 0.05 confirmed that there were no significant differences between the proposed assays. Thus, any of these methods can be used for the routine analysis of SOFO in commercial tablets.

A rapid method of accurate detection and differentiation of Newcastle disease virus pathotypes by demonstrating multiple bands in degenerate primer based nested RT-PCR.

PubMed

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.

A low-cost rapid upper limb assessment method in manual assembly line based on somatosensory interaction technology

NASA Astrophysics Data System (ADS)

Jiang, Shengqian; Liu, Peng; Fu, Danni; Xue, Yiming; Luo, Wentao; Wang, Mingjie

2017-04-01

As an effective survey method of upper limb disorder, rapid upper limb assessment (RULA) has a wide application in industry period. However, it is very difficult to rapidly evaluate operator's postures in real complex work place. In this paper, a real-time RULA method is proposed to accurately assess the potential risk of operator's postures based on the somatosensory data collected from Kinect sensor, which is a line of motion sensing input devices by Microsoft. First, the static position information of each bone point is collected to obtain the effective angles of body parts based on the calculating methods based on joints angles. Second, a whole RULA score of body is obtained to assess the risk level of current posture in real time. Third, those RULA scores are compared with the results provided by a group of ergonomic practitionerswho were asked to observe the same static postures. All the experiments were carried out in an ergonomic lab. The results show that the proposed method can detect operator's postures more accurately. What's more, this method is applied in a real-time condition which can improve the evaluating efficiency.

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

Hoke, Anderson; Shirazi, Mariko; Chakraborty, Sudipta

As deployment of power electronic coupled generation such as photovoltaic (PV) systems increases, grid operators have shown increasing interest in calling on inverter-coupled generation to help mitigate frequency contingency events by rapidly surging active power into the grid. When responding to contingency events, the faster the active power is provided, the more effective it may be for arresting the frequency event. This paper proposes a predictive PV inverter control method for very fast and accurate control of active power. This rapid active power control method will increase the effectiveness of various higher-level controls designed to mitigate grid frequency contingency events,more » including fast power-frequency droop, inertia emulation, and fast frequency response, without the need for energy storage. The rapid active power control method, coupled with a maximum power point estimation method, is implemented in a prototype PV inverter connected to a PV array. The prototype inverter's response to various frequency events is experimentally confirmed to be fast (beginning within 2 line cycles and completing within 4.5 line cycles of a severe test event) and accurate (below 2% steady-state error).« less

[Application of rapid PCR to authenticate medicinal snakes].

PubMed

Chen, Kang; Jiang, Chao; Yuan, Yuan; Huang, Lu-Qi; Li, Man

2014-10-01

To obtained an accurate, rapid and efficient method for authenticate medicinal snakes listed in Chinese Pharmacopoeia (Zaocysd humnades, Bungarus multicinctus, Agkistrodon acutus), a rapid PCR method for authenticate snakes and its adulterants was established based on the classic molecular authentication methods. DNA was extracted by alkaline lysis and the specific primers were amplified by two-steps PCR amplification method. The denatured and annealing temperature and cycle numbers were optimized. When 100 x SYBR Green I was added in the PCR product, strong green fluorescence was visualized under 365 nm UV whereas adulterants without. The whole process can complete in 30-45 minutes. The established method provides the technical support for authentication of the snakes on field.

Relationship between the Prediction Accuracy of Tsunami Inundation and Relative Distribution of Tsunami Source and Observation Arrays: A Case Study in Tokyo Bay

NASA Astrophysics Data System (ADS)

Takagawa, T.

2017-12-01

A rapid and precise tsunami forecast based on offshore monitoring is getting attention to reduce human losses due to devastating tsunami inundation. We developed a forecast method based on the combination of hierarchical Bayesian inversion with pre-computed database and rapid post-computing of tsunami inundation. The method was applied to Tokyo bay to evaluate the efficiency of observation arrays against three tsunamigenic earthquakes. One is a scenario earthquake at Nankai trough and the other two are historic ones of Genroku in 1703 and Enpo in 1677. In general, rich observation array near the tsunami source has an advantage in both accuracy and rapidness of tsunami forecast. To examine the effect of observation time length we used four types of data with the lengths of 5, 10, 20 and 45 minutes after the earthquake occurrences. Prediction accuracy of tsunami inundation was evaluated by the simulated tsunami inundation areas around Tokyo bay due to target earthquakes. The shortest time length of accurate prediction varied with target earthquakes. Here, accurate prediction means the simulated values fall within the 95% credible intervals of prediction. In Enpo earthquake case, 5-minutes observation is enough for accurate prediction for Tokyo bay, but 10-minutes and 45-minutes are needed in the case of Nankai trough and Genroku, respectively. The difference of the shortest time length for accurate prediction shows the strong relationship with the relative distance from the tsunami source and observation arrays. In the Enpo case, offshore tsunami observation points are densely distributed even in the source region. So, accurate prediction can be rapidly achieved within 5 minutes. This precise prediction is useful for early warnings. Even in the worst case of Genroku, where less observation points are available near the source, accurate prediction can be obtained within 45 minutes. This information can be useful to figure out the outline of the hazard in an early stage of reaction.

A Direct and Rapid Method to Determine Cyanide in Urine by Capillary Electrophoresis

PubMed Central

Zhang, Qiyang; Maddukuri, Naveen; Gong, Maojun

2015-01-01

Cyanides are poisonous chemicals that widely exist in nature and industrial processes as well as accidental fires. Rapid and accurate determination of cyanide exposure would facilitate forensic investigation, medical diagnosis, and chronic cyanide monitoring. Here, a rapid and direct method was developed for the determination of cyanide ions in urinary samples. This technique was based on an integrated capillary electrophoresis system coupled with laser-induced fluorescence (LIF) detection. Cyanide ions were derivatized with naphthalene-2,3-dicarboxaldehyde (NDA) and a primary amine (glycine) for LIF detection. Three separate reagents, NDA, glycine, and cyanide sample, were mixed online, which secured uniform conditions between samples for cyanide derivatization and reduced the risk of precipitation formation of mixtures. Conditions were optimized; the derivatization was completed in 2-4 minutes, and the separation was observed in 25 s. The limit of detection (LOD) was 4.0 nM at 3-fold signal-to-noise ratio for standard cyanide in buffer. The cyanide levels in urine samples from smokers and non-smokers were determined by using the method of standard addition, which demonstrated significant difference of cyanide levels in urinary samples from the two groups of people. The developed method was rapid and accurate, and is anticipated to be applicable to cyanide detection in waste water with appropriate modification. PMID:26342870

Rapid extraction from and direct identification in clinical samples of methicillin-resistant staphylococci using the PCR.

PubMed

Jaffe, R I; Lane, J D; Albury, S V; Niemeyer, D M

2000-09-01

Methicillin-resistant staphylococci (MRS) are one of the most common causes of nosocomial infections and bacteremia. Standard bacterial identification and susceptibility testing frequently require as long as 72 h to report results, and there may be difficulty in rapidly and accurately identifying methicillin resistance. The use of the PCR is a rapid and simple process for the amplification of target DNA sequences, which can be used to identify and test bacteria for antimicrobial resistance. However, many sample preparation methods are unsuitable for PCR utilization in the clinical laboratory because they either are not cost-effective, take too long to perform, or do not provide a satisfactory DNA template for PCR. Our goal was to provide same-day results to facilitate rapid diagnosis and therapy. In this report, we describe a rapid method for extraction of bacterial DNA directly from blood culture bottles that gave quality DNA for PCR in as little as 20 min. We compared this extraction method to the standard QIAGEN method for turnaround time (TAT), cost, purity, and use of template in PCR. Specific identification of MRS was determined using intragenic primer sets for bacterial and Staphylococcus 16S rRNA and mecA gene sequences. The PCR primer sets were validated with 416 isolates of staphylococci, including methicillin-resistant Staphylococcus aureus (n = 106), methicillin-sensitive S. aureus (n = 134), and coagulase-negative Staphylococcus (n = 176). The total supply cost of our extraction method and PCR was $2.15 per sample with a result TAT of less than 4 h. The methods described herein represent a rapid and accurate DNA extraction and PCR-based identification system, which makes the system an ideal candidate for use under austere field conditions and one that may have utility in the clinical laboratory.

Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers

PubMed Central

Han, Buhm; Kang, Hyun Min; Eskin, Eleazar

2009-01-01

With the development of high-throughput sequencing and genotyping technologies, the number of markers collected in genetic association studies is growing rapidly, increasing the importance of methods for correcting for multiple hypothesis testing. The permutation test is widely considered the gold standard for accurate multiple testing correction, but it is often computationally impractical for these large datasets. Recently, several studies proposed efficient alternative approaches to the permutation test based on the multivariate normal distribution (MVN). However, they cannot accurately correct for multiple testing in genome-wide association studies for two reasons. First, these methods require partitioning of the genome into many disjoint blocks and ignore all correlations between markers from different blocks. Second, the true null distribution of the test statistic often fails to follow the asymptotic distribution at the tails of the distribution. We propose an accurate and efficient method for multiple testing correction in genome-wide association studies—SLIDE. Our method accounts for all correlation within a sliding window and corrects for the departure of the true null distribution of the statistic from the asymptotic distribution. In simulations using the Wellcome Trust Case Control Consortium data, the error rate of SLIDE's corrected p-values is more than 20 times smaller than the error rate of the previous MVN-based methods' corrected p-values, while SLIDE is orders of magnitude faster than the permutation test and other competing methods. We also extend the MVN framework to the problem of estimating the statistical power of an association study with correlated markers and propose an efficient and accurate power estimation method SLIP. SLIP and SLIDE are available at http://slide.cs.ucla.edu. PMID:19381255

A close-range photogrammetric technique for mapping neotectonic features in trenches

USGS Publications Warehouse

Fairer, G.M.; Whitney, J.W.; Coe, J.A.

1989-01-01

Close-range photogrammetric techniques and newly available computerized plotting equipment were used to map exploratory trench walls that expose Quaternary faults in the vicinity of Yucca Mountain, Nevada. Small-scale structural, lithologic, and stratigraphic features can be rapidly mapped by the photogrammetric method. This method is more accurate and significantly more rapid than conventional trench-mapping methods, and the analytical plotter is capable of producing cartographic definition of high resolution when detailed trench maps are necessary. -from Authors

Rapid Methods for the Detection of General Fecal Indicators

EPA Science Inventory

Specified that EPA should develop: appropriate and effective indicators for improving detection in a timely manner of pathogens in coastal waters appropriate, accurate, expeditious and cost-effective methods for the timely detection of pathogens in coastal waters

Development and validation of a rapid method for microcystins in fish and comparing LC-MS/MS results with ELISA

USDA-ARS?s Scientific Manuscript database

Microcystins (MCs) are the most common cyanotoxins found world-wide in freshwater, brackish and marine environments. The rapid and accurate analysis of microcystins and nodularin in fish tissue is important for determining occurrence, monitoring trends, and exposure monitoring for risk assessment a...

Coincidental match of numerical simulation and physics

NASA Astrophysics Data System (ADS)

Pierre, B.; Gudmundsson, J. S.

2010-08-01

Consequences of rapid pressure transients in pipelines range from increased fatigue to leakages and to complete ruptures of pipeline. Therefore, accurate predictions of rapid pressure transients in pipelines using numerical simulations are critical. State of the art modelling of pressure transient in general, and water hammer in particular include unsteady friction in addition to the steady frictional pressure drop, and numerical simulations rely on the method of characteristics. Comparison of rapid pressure transient calculations by the method of characteristics and a selected high resolution finite volume method highlights issues related to modelling of pressure waves and illustrates that matches between numerical simulations and physics are purely coincidental.

Comparison of Nested PCR and RFLP for Identification and Classification of Malassezia Yeasts from Healthy Human Skin

PubMed Central

Oh, Byung Ho; Song, Young Chan; Choe, Yong Beom; Ahn, Kyu Joong

2009-01-01

Background Malassezia yeasts are normal flora of the skin found in 75~98% of healthy subjects. The accurate identification of the Malassezia species is important for determining the pathogenesis of the Malassezia yeasts with regard to various skin diseases such as Malassezia folliculitis, seborrheic dermatitis, and atopic dermatitis. Objective This research was conducted to determine a more accurate and rapid molecular test for the identification and classification of Malassezia yeasts. Methods We compared the accuracy and efficacy of restriction fragment length polymorphism (RFLP) and the nested polymerase chain reaction (PCR) for the identification of Malassezia yeasts. Results Although both methods demonstrated rapid and reliable results with regard to identification, the nested PCR method was faster. However, 7 different Malassezia species (1.2%) were identified by the nested PCR compared to the RFLP method. Conclusion Our results show that RFLP method was relatively more accurate and reliable for the detection of various Malassezia species compared to the nested PCR. But, in the aspect of simplicity and time saving, the latter method has its own advantages. In addition, the 26S rDNA, which was targeted in this study, contains highly conserved base sequences and enough sequence variation for inter-species identification of Malassezia yeasts. PMID:20523823

A rapid analytical method for predicting the oxygen demand of wastewater.

PubMed

Fogelman, Shoshana; Zhao, Huijun; Blumenstein, Michael

2006-11-01

In this study, an investigation was undertaken to determine whether the predictive accuracy of an indirect, multiwavelength spectroscopic technique for rapidly determining oxygen demand (OD) values is affected by the use of unfiltered and turbid samples, as well as by the use of absorbance values measured below 200 nm. The rapid OD technique was developed that uses UV-Vis spectroscopy and artificial neural networks (ANNs) to indirectly determine chemical oxygen demand (COD) levels. It was found that the most accurate results were obtained when a spectral range of 190-350 nm was provided as data input to the ANN, and when using unfiltered samples below a turbidity range of 150 NTU. This is because high correlations of above 0.90 were obtained with the data using the standard COD method. This indicates that samples can be measured directly without the additional need for preprocessing by filtering. Samples with turbidity values higher than 150 NTU were found to produce poor correlations with the standard COD method, which made them unsuitable for accurate, real-time, on-line monitoring of OD levels.

Proximate Composition Analysis.

PubMed

2016-01-01

The proximate composition of foods includes moisture, ash, lipid, protein and carbohydrate contents. These food components may be of interest in the food industry for product development, quality control (QC) or regulatory purposes. Analyses used may be rapid methods for QC or more accurate but time-consuming official methods. Sample collection and preparation must be considered carefully to ensure analysis of a homogeneous and representative sample, and to obtain accurate results. Estimation methods of moisture content, ash value, crude lipid, total carbohydrates, starch, total free amino acids and total proteins are put together in a lucid manner.

Application of Pyrosequencing® in Food Biodefense.

PubMed

Amoako, Kingsley Kwaku

2015-01-01

The perpetration of a bioterrorism attack poses a significant risk for public health with potential socioeconomic consequences. It is imperative that we possess reliable assays for the rapid and accurate identification of biothreat agents to make rapid risk-informed decisions on emergency response. The development of advanced methodologies for the detection of biothreat agents has been evolving rapidly since the release of the anthrax spores in the mail in 2001, and recent advances in detection and identification techniques could prove to be an essential component in the defense against biological attacks. Sequence-based approaches such as Pyrosequencing(®), which has the capability to determine short DNA stretches in real time using biotinylated PCR amplicons, have potential biodefense applications. Using markers from the virulence plasmids and chromosomal regions, my laboratory has demonstrated the power of this technology in the rapid, specific, and sensitive detection of B. anthracis spores and Yersinia pestis in food. These are the first applications for the detection of the two organisms in food. Furthermore, my lab has developed a rapid assay to characterize the antimicrobial resistance (AMR) gene profiles for Y. pestis using Pyrosequencing. Pyrosequencing is completed in about 60 min (following PCR amplification) and yields accurate and reliable results with an added layer of confidence, thus enabling rapid risk-informed decisions to be made. A typical run yields 40-84 bp reads with 94-100 % identity to the expected sequence. It also provides a rapid method for determining the AMR profile as compared to the conventional plate method which takes several days. The method described is proposed as a novel detection system for potential application in food biodefense.

Comparative Validation of the Determination of Sofosbuvir in Pharmaceuticals by Several Inexpensive Ecofriendly Chromatographic, Electrophoretic, and Spectrophotometric Methods.

PubMed

El-Yazbi, Amira F

2017-01-20

Sofosbuvir (SOFO) was approved by the U.S. Food and Drug Administration in 2013 for the treatment of hepatitis C virusinfection with enhanced antiviral potency compared with earlier analogs. Notwithstanding, all current editions of the pharmacopeias still do not present any analytical methods for the quantification of SOFO. Thus, rapid, simple, and ecofriendly methods for the routine analysis of commercial formulations of SOFO are desirable. In this study, five accurate methods for the determination of SOFO in pharmaceutical tablets were developed and validated. These methods include HPLC, capillary zone electrophoresis, HPTLC, and UV spectrophotometric and derivative spectrometry methods. The proposed methods proved to be rapid, simple, sensitive, selective, and accurate analytical procedures that were suitable for the reliable determination of SOFO in pharmaceutical tablets. An analysis of variance test with <em>P</em>-value &#x003E; 0.05 confirmed that there were no significant differences between the proposed assays. Thus, any of these methods can be used for the routine analysis of SOFO in commercial tablets.

NEW TARGET AND CONTROL ASSAYS FOR QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) ANALYSIS OF ENTEROCOCCI IN WATER

EPA Science Inventory

Enterococci are frequently monitored in water samples as indicators of fecal pollution. Attention is now shifting from culture based methods for enumerating these organisms to more rapid molecular methods such as QPCR. Accurate quantitative analyses by this method requires highly...

Evaluation of High-Resolution Melting Curve Analysis of Ligation-Mediated Real-Time PCR, a Rapid Method for Epidemiological Typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) Pathogens

PubMed Central

Ryberg, Anna; Billström, Hanna; Hällgren, Anita; Nilsson, Lennart E.; Marklund, Britt-Inger; Olsson-Liljequist, Barbro; Schön, Thomas

2014-01-01

A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97% agreement (60/62 isolates) was achieved in comparison to pulsed-field gel electrophoresis (PFGE) results, which indicates that LMqPCR HRMA is a rapid and accurate screening tool for monitoring nosocomial outbreaks. PMID:25232168

Mining Available Data from the United States Environmental Protection Agency to Support Rapid Life Cycle Inventory Modeling of Chemical Manufacturing

EPA Science Inventory

Demands for quick and accurate life cycle assessments create a need for methods to rapidly generate reliable life cycle inventories (LCI). Data mining is a suitable tool for this purpose, especially given the large amount of available governmental data. These data are typically a...

A direct and rapid method to determine cyanide in urine by capillary electrophoresis.

PubMed

Zhang, Qiyang; Maddukuri, Naveen; Gong, Maojun

2015-10-02

Cyanides are poisonous chemicals that widely exist in nature and industrial processes as well as accidental fires. Rapid and accurate determination of cyanide exposure would facilitate forensic investigation, medical diagnosis, and chronic cyanide monitoring. Here, a rapid and direct method was developed for the determination of cyanide ions in urinary samples. This technique was based on an integrated capillary electrophoresis system coupled with laser-induced fluorescence (LIF) detection. Cyanide ions were derivatized with naphthalene-2,3-dicarboxaldehyde (NDA) and a primary amine (glycine) for LIF detection. Three separate reagents, NDA, glycine, and cyanide sample, were mixed online, which secured uniform conditions between samples for cyanide derivatization and reduced the risk of precipitation formation of mixtures. Conditions were optimized; the derivatization was completed in 2-4min, and the separation was observed in 25s. The limit of detection (LOD) was 4.0nM at 3-fold signal-to-noise ratio for standard cyanide in buffer. The cyanide levels in urine samples from smokers and non-smokers were determined by using the method of standard addition, which demonstrated significant difference of cyanide levels in urinary samples from the two groups of people. The developed method was rapid and accurate, and is anticipated to be applicable to cyanide detection in waste water with appropriate modification. Published by Elsevier B.V.

Ball tonometry: a rapid, nondestructive method for measuring cell turgor pressure in thin-walled plant cells

NASA Technical Reports Server (NTRS)

Lintilhac, P. M.; Wei, C.; Tanguay, J. J.; Outwater, J. O.

2000-01-01

In this article we describe a new method for the determination of turgor pressures in living plant cells. Based on the treatment of growing plant cells as thin-walled pressure vessels, we find that pressures can be accurately determined by observing and measuring the area of the contact patch formed when a spherical glass probe is lowered onto the cell surface with a known force. Within the limits we have described, we can show that the load (determined by precalibration of the device) divided by the projected area of the contact patch (determined by video microscopy) provides a direct, rapid, and accurate measure of the internal turgor pressure of the cell. We demonstrate, by parallel measurements with the pressure probe, that our method yields pressure data that are consistent with those from the pressure probe. Also, by incubating target tissues in stepped concentrations of mannitol to incrementally reduce the turgor pressure, we show that the pressures measured by tonometry accurately reflect the predicted changes from the osmotic potential of the bathing medium. The advantages of this new method over the pressure probe are considerable, however, in that we can move rapidly from cell to cell, taking measurements every 20 s. In addition, the nondestructive nature of the method means that we can return to the same cell repeatedly for periodic pressure measurements. The limitations of the method lie in the fact that it is suitable only for superficial cells that are directly accessible to the probe and to cells that are relatively thin walled and not heavily decorated with surface features. It is also not suitable for measuring pressures in flaccid cells.

Accurate quantification of magnetic particle properties by intra-pair magnetophoresis for nanobiotechnology

NASA Astrophysics Data System (ADS)

van Reenen, Alexander; Gao, Yang; Bos, Arjen H.; de Jong, Arthur M.; Hulsen, Martien A.; den Toonder, Jaap M. J.; Prins, Menno W. J.

2013-07-01

The application of magnetic particles in biomedical research and in-vitro diagnostics requires accurate characterization of their magnetic properties, with single-particle resolution and good statistics. Here, we report intra-pair magnetophoresis as a method to accurately quantify the field-dependent magnetic moments of magnetic particles and to rapidly generate histograms of the magnetic moments with good statistics. We demonstrate our method with particles of different sizes and from different sources, with a measurement precision of a few percent. We expect that intra-pair magnetophoresis will be a powerful tool for the characterization and improvement of particles for the upcoming field of particle-based nanobiotechnology.

A fluorescence anisotropy method for measuring protein concentration in complex cell culture media.

PubMed

Groza, Radu Constantin; Calvet, Amandine; Ryder, Alan G

2014-04-22

The rapid, quantitative analysis of the complex cell culture media used in biopharmaceutical manufacturing is of critical importance. Requirements for cell culture media composition profiling, or changes in specific analyte concentrations (e.g. amino acids in the media or product protein in the bioprocess broth) often necessitate the use of complicated analytical methods and extensive sample handling. Rapid spectroscopic methods like multi-dimensional fluorescence (MDF) spectroscopy have been successfully applied for the routine determination of compositional changes in cell culture media and bioprocess broths. Quantifying macromolecules in cell culture media is a specific challenge as there is a need to implement measurements rapidly on the prepared media. However, the use of standard fluorescence spectroscopy is complicated by the emission overlap from many media components. Here, we demonstrate how combining anisotropy measurements with standard total synchronous fluorescence spectroscopy (TSFS) provides a rapid, accurate quantitation method for cell culture media. Anisotropy provides emission resolution between large and small fluorophores while TSFS provides a robust measurement space. Model cell culture media was prepared using yeastolate (2.5 mg mL(-1)) spiked with bovine serum albumin (0 to 5 mg mL(-1)). Using this method, protein emission is clearly discriminated from background yeastolate emission, allowing for accurate bovine serum albumin (BSA) quantification over a 0.1 to 4.0 mg mL(-1) range with a limit of detection (LOD) of 13.8 μg mL(-1). Copyright © 2014. Published by Elsevier B.V.

A Novel Method for Moisture Determination in Peanuts

USDA-ARS?s Scientific Manuscript database

Accurate determination of moisture content of the peanuts is an important factor for preserving the quality and prevention of spoilage in peanuts. Hence, it is very important to devise rapid methods for determining moisture during harvesting, storage, marketing, and processing of peanuts. This paper...

Identification and determination of the saikosaponins in Radix bupleuri by accelerated solvent extraction combined with rapid-resolution LC-MS.

PubMed

Yang, Yun-Yun; Tang, You-Zhi; Fan, Chun-Lin; Luo, Hui-Tai; Guo, Peng-Ran; Chen, Jian-Xin

2010-07-01

A method based on accelerated solvent extraction combined with rapid-resolution LC-MS for efficient extraction, rapid separation, online identification and accurate determination of the saikosaponins (SSs) in Radix bupleuri (RB) was developed. The RB samples were extracted by accelerated solvent extraction using 70% aqueous ethanol v/v as solvent, at a temperature of 120 degrees C and pressure of 100 bar, with 10 min of static extraction time and three extraction cycles. Rapid-resolution LC separation was performed by using a C(18) column at gradient elution of water (containing 0.5% formic acid) and acetonitrile, and the major constituents were well separated within 20 min. A TOF-MS and an IT-MS were used for online identification of the major constituents, and 27 SSs were identified or tentatively identified. Five major bioactive SSs (SSa, SSc, SSd, 6''-O-acetyl-SSa and 6''-O-acetyl-SSd) with obvious peak areas and good resolution were chosen as benchmark substances, and a triple quadrupole MS operating in multiple-reaction monitoring mode was used for their quantitative analysis. A total of 16 RB samples from different regions of China were analyzed. The results indicated that the method was rapid, efficient, accurate and suitable for use in the quality control of RB.

Rapid wide-field Mueller matrix polarimetry imaging based on four photoelastic modulators with no moving parts.

PubMed

Alali, Sanaz; Gribble, Adam; Vitkin, I Alex

2016-03-01

A new polarimetry method is demonstrated to image the entire Mueller matrix of a turbid sample using four photoelastic modulators (PEMs) and a charge coupled device (CCD) camera, with no moving parts. Accurate wide-field imaging is enabled with a field-programmable gate array (FPGA) optical gating technique and an evolutionary algorithm (EA) that optimizes imaging times. This technique accurately and rapidly measured the Mueller matrices of air, polarization elements, and turbid phantoms. The system should prove advantageous for Mueller matrix analysis of turbid samples (e.g., biological tissues) over large fields of view, in less than a second.

Angiotensin-converting enzyme insertion/deletion polymorphism genotyping error: the cause and a possible solution to the problem.

PubMed

Saracevic, Andrea; Simundic, Ana-Maria; Celap, Ivana; Luzanic, Valentina

2013-07-01

Rigat and colleagues were the first ones to develop a rapid PCR-based assay for identifying the angiotensin converting enzyme insertion/deletion (I/D) polymorphism. Due to a big difference between the length of the wild-type and mute alleles the PCR method is prone to mistyping because of preferential amplification of the D allele causing depicting I/D heterozygotes as D/D homozygotes. The aim of this study was to investigate whether this preferential amplification can be repressed by amplifying a longer DNA fragment in a so called Long PCR protocol. We also aimed to compare the results of genotyping using five different PCR protocols and to estimate the mistyping rate. The study included 200 samples which were genotyped using standard method used in our laboratory, a stepdown PCR, PCR protocol with the inclusion of 4 % DMSO, PCR with the use of insertion specific primers and new Long PCR method. The results of this study have shown that accurate ACE I/D polymorphism genotyping can be accomplished with the standard and the Long PCR method. Also, as of our results, accurate ACE I/D polymorphism genotyping can be accomplished regardless of the method used. Therefore, if the standard method is optimized more cautiously, accurate results can be obtained by this simple, inexpensive and rapid PCR protocol.

Rapid Determination of Thiabendazole Pesticides in Rape by Surface Enhanced Raman Spectroscopy

PubMed Central

Lin, Lei; Nie, Pengcheng; Qu, Fangfang; Chu, Bingquan; Xiao, Shupei

2018-01-01

Thiabendazole is widely used in sclerotium blight, downy mildew and black rot prevention and treatment in rape. Accurate monitoring of thiabendazole pesticides in plants will prevent potential adverse effects to the Environment and human health. Surface Enhanced Raman Spectroscopy (SERS) is a highly sensitive fingerprint with the advantages of simple operation, convenient portability and high detection efficiency. In this paper, a rapid determination method of thiabendazole pesticides in rape was conducted combining SERS with chemometric methods. The original SERS were pretreated and the partial least squares (PLS) was applied to establish the prediction model between SERS and thiabendazole pesticides in rape. As a result, the SERS enhancing effect based on silver Nano-substrate was better than that of gold Nano-substrate, where the detection limit of thiabendazole pesticides in rape could reach 0.1 mg/L. Moreover, 782, 1007 and 1576 cm−1 could be determined as thiabendazole pesticides Raman characteristic peaks in rape. The prediction effect of thiabendazole pesticides in rape was the best (Rp2 = 0.94, RMSEP = 3.17 mg/L) after the original spectra preprocessed with 1st-Derivative, and the linear relevance between thiabendazole pesticides concentration and Raman peak intensity at 782 cm−1 was the highest (R2 = 0.91). Furthermore, five rape samples with unknown thiabendazole pesticides concentration were used to verify the accuracy and reliability of this method. It was showed that prediction relative standard deviation was 0.70–9.85%, recovery rate was 94.71–118.92% and t value was −1.489. In conclusion, the thiabendazole pesticides in rape could be rapidly and accurately detected by SERS, which was beneficial to provide a rapid, accurate and reliable scheme for the detection of pesticides residues in agriculture products. PMID:29617288

Rapid Determination of Thiabendazole Pesticides in Rape by Surface Enhanced Raman Spectroscopy.

PubMed

Lin, Lei; Dong, Tao; Nie, Pengcheng; Qu, Fangfang; He, Yong; Chu, Bingquan; Xiao, Shupei

2018-04-04

Thiabendazole is widely used in sclerotium blight, downy mildew and black rot prevention and treatment in rape. Accurate monitoring of thiabendazole pesticides in plants will prevent potential adverse effects to the Environment and human health. Surface Enhanced Raman Spectroscopy (SERS) is a highly sensitive fingerprint with the advantages of simple operation, convenient portability and high detection efficiency. In this paper, a rapid determination method of thiabendazole pesticides in rape was conducted combining SERS with chemometric methods. The original SERS were pretreated and the partial least squares (PLS) was applied to establish the prediction model between SERS and thiabendazole pesticides in rape. As a result, the SERS enhancing effect based on silver Nano-substrate was better than that of gold Nano-substrate, where the detection limit of thiabendazole pesticides in rape could reach 0.1 mg/L. Moreover, 782, 1007 and 1576 cm −1 could be determined as thiabendazole pesticides Raman characteristic peaks in rape. The prediction effect of thiabendazole pesticides in rape was the best ( R p 2 = 0.94, RMSEP = 3.17 mg/L) after the original spectra preprocessed with 1st-Derivative, and the linear relevance between thiabendazole pesticides concentration and Raman peak intensity at 782 cm −1 was the highest ( R² = 0.91). Furthermore, five rape samples with unknown thiabendazole pesticides concentration were used to verify the accuracy and reliability of this method. It was showed that prediction relative standard deviation was 0.70–9.85%, recovery rate was 94.71–118.92% and t value was −1.489. In conclusion, the thiabendazole pesticides in rape could be rapidly and accurately detected by SERS, which was beneficial to provide a rapid, accurate and reliable scheme for the detection of pesticides residues in agriculture products.

A two-step method for rapid characterization of electroosmotic flows in capillary electrophoresis.

PubMed

Zhang, Wenjing; He, Muyi; Yuan, Tao; Xu, Wei

2017-12-01

The measurement of electroosmotic flow (EOF) is important in a capillary electrophoresis (CE) experiment in terms of performance optimization and stability improvement. Although several methods exist, there are demanding needs to accurately characterize ultra-low electroosmotic flow rates (EOF rates), such as in coated capillaries used in protein separations. In this work, a new method, called the two-step method, was developed to accurately and rapidly measure EOF rates in a capillary, especially for measuring the ultra-low EOF rates in coated capillaries. In this two-step method, the EOF rates were calculated by measuring the migration time difference of a neutral marker in two consecutive experiments, in which a pressure driven was introduced to accelerate the migration and the DC voltage was reversed to switch the EOF direction. Uncoated capillaries were first characterized by both this two-step method and a conventional method to confirm the validity of this new method. Then this new method was applied in the study of coated capillaries. Results show that this new method is not only fast in speed, but also better in accuracy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A novel endoscopic fluorescent band ligation method for tumor localization.

PubMed

Hyun, Jong Hee; Kim, Seok-Ki; Kim, Kwang Gi; Kim, Hong Rae; Lee, Hyun Min; Park, Sunup; Kim, Sung Chun; Choi, Yongdoo; Sohn, Dae Kyung

2016-10-01

Accurate tumor localization is essential for minimally invasive surgery. This study describes the development of a novel endoscopic fluorescent band ligation method for the rapid and accurate identification of tumor sites during surgery. The method utilized a fluorescent rubber band, made of indocyanine green (ICG) and a liquid rubber solution mixture, as well as a near-infrared fluorescence laparoscopic system with a dual light source using a high-powered light-emitting diode (LED) and a 785-nm laser diode. The fluorescent rubber bands were endoscopically placed on the mucosae of porcine stomachs and colons. During subsequent conventional laparoscopic stomach and colon surgery, the fluorescent bands were assayed using the near-infrared fluorescence laparoscopy system. The locations of the fluorescent clips were clearly identified on the fluorescence images in real time. The system was able to distinguish the two or three bands marked on the mucosal surfaces of the stomach and colon. Resection margins around the fluorescent bands were sufficient in the resected specimens obtained during stomach and colon surgery. These novel endoscopic fluorescent bands could be rapidly and accurately localized during stomach and colon surgery. Use of these bands may make possible the excision of exact target sites during minimally invasive gastrointestinal surgery.

The Use of Rapid Review Methods for the U.S. Preventive Services Task Force.

PubMed

Patnode, Carrie D; Eder, Michelle L; Walsh, Emily S; Viswanathan, Meera; Lin, Jennifer S

2018-01-01

Rapid review products are intended to synthesize available evidence in a timely fashion while still meeting the needs of healthcare decision makers. Various methods and products have been applied for rapid evidence syntheses, but no single approach has been uniformly adopted. Methods to gain efficiency and compress the review time period include focusing on a narrow clinical topic and key questions; limiting the literature search; performing single (versus dual) screening of abstracts and full-text articles for relevance; and limiting the analysis and synthesis. In order to maintain the scientific integrity, including transparency, of rapid evidence syntheses, it is imperative that procedures used to streamline standard systematic review methods are prespecified, based on sound review principles and empiric evidence when possible, and provide the end user with an accurate and comprehensive synthesis. The collection of clinical preventive service recommendations maintained by the U.S. Preventive Services Task Force, along with its commitment to rigorous methods development, provide a unique opportunity to refine, implement, and evaluate rapid evidence synthesis methods and add to an emerging evidence base on rapid review methods. This paper summarizes the U.S. Preventive Services Task Force's use of rapid review methodology, its criteria for selecting topics for rapid evidence syntheses, and proposed methods to streamline the review process. Copyright © 2018 American Journal of Preventive Medicine. All rights reserved.

Accurate mass measurement by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. II. Measurement of negative radical ions using porphyrin and fullerene standard reference materials.

PubMed

Shao, Zhecheng; Wyatt, Mark F; Stein, Bridget K; Brenton, A Gareth

2010-10-30

A method for the accurate mass measurement of negative radical ions by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) is described. This is an extension to our previously described method for the accurate mass measurement of positive radical ions (Griffiths NW, Wyatt MF, Kean SD, Graham AE, Stein BK, Brenton AG. Rapid Commun. Mass Spectrom. 2010; 24: 1629). The porphyrin standard reference materials (SRMs) developed for positive mode measurements cannot be observed in negative ion mode, so fullerene and fluorinated porphyrin compounds were identified as effective SRMs. The method is of immediate practical use for the accurate mass measurement of functionalised fullerenes, for which negative ion MALDI-TOFMS is the principal mass spectrometry characterisation technique. This was demonstrated by the accurate mass measurement of six functionalised C(60) compounds. Copyright © 2010 John Wiley & Sons, Ltd.

Reduction of astrometric plates

NASA Technical Reports Server (NTRS)

Stock, J.

1984-01-01

A rapid and accurate method for the reduction of comet or asteroid plates is described. Projection equations, scale length correction, rotation of coordinates, linearization, the search for additional reference stars, and the final solution are examined.

Rapid identification of ascomycetous yeasts from clinical specimens by a molecular method based on flow cytometry and comparison with identifications from phenotypic assays.

PubMed

Page, Brent T; Shields, Christine E; Merz, William G; Kurtzman, Cletus P

2006-09-01

This study was designed to compare the identification of ascomycetous yeasts recovered from clinical specimens by using phenotypic assays (PA) and a molecular flow cytometric (FC) method. Large-subunit rRNA domains 1 and 2 (D1/D2) gene sequence analysis was also performed and served as the reference for correct strain identification. A panel of 88 clinical isolates was tested that included representatives of nine commonly encountered species and six infrequently encountered species. The PA included germ tube production, fermentation of seven carbohydrates, morphology on corn meal agar, urease and phenoloxidase activities, and carbohydrate assimilation tests when needed. The FC method (Luminex) employed species-specific oligonucleotides attached to polystyrene beads, which were hybridized with D1/D2 amplicons from the unidentified isolates. The PA identified 81 of 88 strains correctly but misidentified 4 of Candida dubliniensis, 1 of C. bovina, 1 of C. palmioleophila, and 1 of C. bracarensis. The FC method correctly identified 79 of 88 strains and did not misidentify any isolate but did not identify nine isolates because oligonucleotide probes were not available in the current library. The FC assay takes approximately 5 h, whereas the PA takes from 2 h to 5 days for identification. In conclusion, PA did well with the commonly encountered species, was not accurate for uncommon species, and takes significantly longer than the FC method. These data strongly support the potential of FC technology for rapid and accurate identification of medically important yeasts. With the introduction of new antifungals, rapid, accurate identification of pathogenic yeasts is more important than ever for guiding antifungal chemotherapy.

Evaluation of high-resolution melting curve analysis of ligation-mediated real-time PCR, a rapid method for epidemiological typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) pathogens.

PubMed

Woksepp, Hanna; Ryberg, Anna; Billström, Hanna; Hällgren, Anita; Nilsson, Lennart E; Marklund, Britt-Inger; Olsson-Liljequist, Barbro; Schön, Thomas

2014-12-01

A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97% agreement (60/62 isolates) was achieved in comparison to pulsed-field gel electrophoresis (PFGE) results, which indicates that LMqPCR HRMA is a rapid and accurate screening tool for monitoring nosocomial outbreaks. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Rapid Magnetic Nanobiosensor for the detection of Serratia marcescen

NASA Astrophysics Data System (ADS)

Aljabali, Alaa A. A.; Hussein, Emad; Aljumaili, Omar; Zoubi, Mazhar Al; Altrad, Bahaa; Albatayneh, Khaled; Al-razaq, Mutaz A. Abd

2018-02-01

The development of rapid, sensitive, accurate and reliable bacterial detection methods are of keen interest to ensure food safety and hospital security. Therefore, the development of a fast, specific, low-cost and trusted methods is in high demand. Magnetic nanoparticles with their unique material properties have been utilized as a tool for pathogen detection. Here, we present a novel iron oxide nanoparticles labeled with specific targeting antibodies to improve specificity and extend the use of nanoparticles as nanosensors. The results indicated that antibody labeled iron oxide platform that binds specifically to Serriata marcescenst in a straightforward method is very specific and sensitive. The system is capable of rapid and specific detection of various clinically relevant bacterial species, with sensitivity down to single bacteria. The generic platform could be used to identify pathogens for a variety of applications rapidly.

Rapid Identification of Bacteria in Positive Blood Culture Broths by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry▿

PubMed Central

Stevenson, Lindsay G.; Drake, Steven K.; Murray, Patrick R.

2010-01-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid, accurate method for identifying bacteria and fungi recovered on agar culture media. We report herein a method for the direct identification of bacteria in positive blood culture broths by MALDI-TOF mass spectrometry. A total of 212 positive cultures were examined, representing 32 genera and 60 species or groups. The identification of bacterial isolates by MALDI-TOF mass spectrometry was compared with biochemical testing, and discrepancies were resolved by gene sequencing. No identification (spectral score of <1.7) was obtained for 42 (19.8%) of the isolates, due most commonly to insufficient numbers of bacteria in the blood culture broth. Of the bacteria with a spectral score of ≥1.7, 162 (95.3%) of 170 isolates were correctly identified. All 8 isolates of Streptococcus mitis were misidentified as being Streptococcus pneumoniae isolates. This method provides a rapid, accurate, definitive identification of bacteria within 1 h of detection in positive blood cultures with the caveat that the identification of S. pneumoniae would have to be confirmed by an alternative test. PMID:19955282

Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Stevenson, Lindsay G; Drake, Steven K; Murray, Patrick R

2010-02-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid, accurate method for identifying bacteria and fungi recovered on agar culture media. We report herein a method for the direct identification of bacteria in positive blood culture broths by MALDI-TOF mass spectrometry. A total of 212 positive cultures were examined, representing 32 genera and 60 species or groups. The identification of bacterial isolates by MALDI-TOF mass spectrometry was compared with biochemical testing, and discrepancies were resolved by gene sequencing. No identification (spectral score of < 1.7) was obtained for 42 (19.8%) of the isolates, due most commonly to insufficient numbers of bacteria in the blood culture broth. Of the bacteria with a spectral score of > or = 1.7, 162 (95.3%) of 170 isolates were correctly identified. All 8 isolates of Streptococcus mitis were misidentified as being Streptococcus pneumoniae isolates. This method provides a rapid, accurate, definitive identification of bacteria within 1 h of detection in positive blood cultures with the caveat that the identification of S. pneumoniae would have to be confirmed by an alternative test.

Rapid and Accurate Evaluation of the Quality of Commercial Organic Fertilizers Using Near Infrared Spectroscopy

PubMed Central

Wang, Chang; Huang, Chichao; Qian, Jian; Xiao, Jian; Li, Huan; Wen, Yongli; He, Xinhua; Ran, Wei; Shen, Qirong; Yu, Guanghui

2014-01-01

The composting industry has been growing rapidly in China because of a boom in the animal industry. Therefore, a rapid and accurate assessment of the quality of commercial organic fertilizers is of the utmost importance. In this study, a novel technique that combines near infrared (NIR) spectroscopy with partial least squares (PLS) analysis is developed for rapidly and accurately assessing commercial organic fertilizers quality. A total of 104 commercial organic fertilizers were collected from full-scale compost factories in Jiangsu Province, east China. In general, the NIR-PLS technique showed accurate predictions of the total organic matter, water soluble organic nitrogen, pH, and germination index; less accurate results of the moisture, total nitrogen, and electrical conductivity; and the least accurate results for water soluble organic carbon. Our results suggested the combined NIR-PLS technique could be applied as a valuable tool to rapidly and accurately assess the quality of commercial organic fertilizers. PMID:24586313

Rapid and accurate evaluation of the quality of commercial organic fertilizers using near infrared spectroscopy.

PubMed

Wang, Chang; Huang, Chichao; Qian, Jian; Xiao, Jian; Li, Huan; Wen, Yongli; He, Xinhua; Ran, Wei; Shen, Qirong; Yu, Guanghui

2014-01-01

The composting industry has been growing rapidly in China because of a boom in the animal industry. Therefore, a rapid and accurate assessment of the quality of commercial organic fertilizers is of the utmost importance. In this study, a novel technique that combines near infrared (NIR) spectroscopy with partial least squares (PLS) analysis is developed for rapidly and accurately assessing commercial organic fertilizers quality. A total of 104 commercial organic fertilizers were collected from full-scale compost factories in Jiangsu Province, east China. In general, the NIR-PLS technique showed accurate predictions of the total organic matter, water soluble organic nitrogen, pH, and germination index; less accurate results of the moisture, total nitrogen, and electrical conductivity; and the least accurate results for water soluble organic carbon. Our results suggested the combined NIR-PLS technique could be applied as a valuable tool to rapidly and accurately assess the quality of commercial organic fertilizers.

Rapid fusion method for the determination of refractory thorium and uranium isotopes in soil samples

DOE PAGES

Maxwell, Sherrod L.; Hutchison, Jay B.; McAlister, Daniel R.

2015-02-14

Recently, approximately 80% of participating laboratories failed to accurately determine uranium isotopes in soil samples in the U.S Department of Energy Mixed Analyte Performance Evaluation Program (MAPEP) Session 30, due to incomplete dissolution of refractory particles in the samples. Failing laboratories employed acid dissolution methods, including hydrofluoric acid, to recover uranium from the soil matrix. The failures illustrate the importance of rugged soil dissolution methods for the accurate measurement of analytes in the sample matrix. A new rapid fusion method has been developed by the Savannah River National Laboratory (SRNL) to prepare 1-2 g soil sample aliquots very quickly, withmore » total dissolution of refractory particles. Soil samples are fused with sodium hydroxide at 600 ºC in zirconium crucibles to enable complete dissolution of the sample. Uranium and thorium are separated on stacked TEVA and TRU extraction chromatographic resin cartridges, prior to isotopic measurements by alpha spectrometry on cerium fluoride microprecipitation sources. Plutonium can also be separated and measured using this method. Batches of 12 samples can be prepared for measurement in <5 hours.« less

Calculating the Financial Impact of Population Growth on Education.

ERIC Educational Resources Information Center

Cline, Daniel H.

It is particularly difficult to make accurate enrollment projections for areas that are experiencing a rapid expansion in their population. The traditional method of calculating cohort survival ratios must be modified and supplemented with additional information to ensure accuracy; cost projection methods require detailed analyses of current costs…

A rapid enzymatic assay for high-throughput screening of adenosine-producing strains

PubMed Central

Dong, Huina; Zu, Xin; Zheng, Ping; Zhang, Dawei

2015-01-01

Adenosine is a major local regulator of tissue function and industrially useful as precursor for the production of medicinal nucleoside substances. High-throughput screening of adenosine overproducers is important for industrial microorganism breeding. An enzymatic assay of adenosine was developed by combined adenosine deaminase (ADA) with indophenol method. The ADA catalyzes the cleavage of adenosine to inosine and NH3, the latter can be accurately determined by indophenol method. The assay system was optimized to deliver a good performance and could tolerate the addition of inorganic salts and many nutrition components to the assay mixtures. Adenosine could be accurately determined by this assay using 96-well microplates. Spike and recovery tests showed that this assay can accurately and reproducibly determine increases in adenosine in fermentation broth without any pretreatment to remove proteins and potentially interfering low-molecular-weight molecules. This assay was also applied to high-throughput screening for high adenosine-producing strains. The high selectivity and accuracy of the ADA assay provides rapid and high-throughput analysis of adenosine in large numbers of samples. PMID:25580842

A novel sample preparation method using rapid nonheated saponification method for the determination of cholesterol in emulsified foods.

PubMed

Jeong, In-Seek; Kwak, Byung-Man; Ahn, Jang-Hyuk; Leem, Donggil; Yoon, Taehyung; Yoon, Changyong; Jeong, Jayoung; Park, Jung-Min; Kim, Jin-Man

2012-10-01

In this study, nonheated saponification was employed as a novel, rapid, and easy sample preparation method for the determination of cholesterol in emulsified foods. Cholesterol content was analyzed using gas chromatography with a flame ionization detector (GC-FID). The cholesterol extraction method was optimized for maximum recovery from baby food and infant formula. Under these conditions, the optimum extraction solvent was 10 mL ethyl ether per 1 to 2 g sample, and the saponification solution was 0.2 mL KOH in methanol. The cholesterol content in the products was determined to be within the certified range of certified reference materials (CRMs), NIST SRM 1544 and SRM 1849. The results of the recovery test performed using spiked materials were in the range of 98.24% to 99.45% with an relative standard devitation (RSD) between 0.83% and 1.61%. This method could be used to reduce sample pretreatment time and is expected to provide an accurate determination of cholesterol in emulsified food matrices such as infant formula and baby food. A novel, rapid, and easy sample preparation method using nonheated saponification was developed for cholesterol detection in emulsified foods. Recovery tests of CRMs were satisfactory, and the recoveries of spiked materials were accurate and precise. This method was effective and decreased the time required for analysis by 5-fold compared to the official method. © 2012 Institute of Food Technologists®

Design synthesis and optimization of permanent magnet synchronous machines based on computationally-efficient finite element analysis

NASA Astrophysics Data System (ADS)

Sizov, Gennadi Y.

In this dissertation, a model-based multi-objective optimal design of permanent magnet ac machines, supplied by sine-wave current regulated drives, is developed and implemented. The design procedure uses an efficient electromagnetic finite element-based solver to accurately model nonlinear material properties and complex geometric shapes associated with magnetic circuit design. Application of an electromagnetic finite element-based solver allows for accurate computation of intricate performance parameters and characteristics. The first contribution of this dissertation is the development of a rapid computational method that allows accurate and efficient exploration of large multi-dimensional design spaces in search of optimum design(s). The computationally efficient finite element-based approach developed in this work provides a framework of tools that allow rapid analysis of synchronous electric machines operating under steady-state conditions. In the developed modeling approach, major steady-state performance parameters such as, winding flux linkages and voltages, average, cogging and ripple torques, stator core flux densities, core losses, efficiencies and saturated machine winding inductances, are calculated with minimum computational effort. In addition, the method includes means for rapid estimation of distributed stator forces and three-dimensional effects of stator and/or rotor skew on the performance of the machine. The second contribution of this dissertation is the development of the design synthesis and optimization method based on a differential evolution algorithm. The approach relies on the developed finite element-based modeling method for electromagnetic analysis and is able to tackle large-scale multi-objective design problems using modest computational resources. Overall, computational time savings of up to two orders of magnitude are achievable, when compared to current and prevalent state-of-the-art methods. These computational savings allow one to expand the optimization problem to achieve more complex and comprehensive design objectives. The method is used in the design process of several interior permanent magnet industrial motors. The presented case studies demonstrate that the developed finite element-based approach practically eliminates the need for using less accurate analytical and lumped parameter equivalent circuit models for electric machine design optimization. The design process and experimental validation of the case-study machines are detailed in the dissertation.

Statistical methods for analysing responses of wildlife to human disturbance.

Treesearch

Haiganoush K. Preisler; Alan A. Ager; Michael J. Wisdom

2006-01-01

1. Off-road recreation is increasing rapidly in many areas of the world, and effects on wildlife can be highly detrimental. Consequently, we have developed methods for studying wildlife responses to off-road recreation with the use of new technologies that allow frequent and accurate monitoring of human-wildlife interactions. To illustrate these methods, we studied the...

Obtaining the Iodine Value of Various Oils via Bromination with Pyridinium Tribromide

ERIC Educational Resources Information Center

Simurdiak, Michael; Olukoga, Olushola; Hedberg, Kirk

2016-01-01

A laboratory exercise was devised that allows students to rapidly and fairly accurately determine the iodine value of oleic acid. This method utilizes the addition of elemental bromine to the unsaturated bonds in oleic acid, due to bromine's relatively fast reaction rate compared to that of the traditional Wijs solution method. This method also…

Rapid, cost-effective and accurate quantification of Yucca schidigera Roezl. steroidal saponins using HPLC-ELSD method.

PubMed

Tenon, Mathieu; Feuillère, Nicolas; Roller, Marc; Birtić, Simona

2017-04-15

Yucca GRAS-labelled saponins have been and are increasingly used in food/feed, pharmaceutical or cosmetic industries. Existing techniques presently used for Yucca steroidal saponin quantification remain either inaccurate and misleading or accurate but time consuming and cost prohibitive. The method reported here addresses all of the above challenges. HPLC/ELSD technique is an accurate and reliable method that yields results of appropriate repeatability and reproducibility. This method does not over- or under-estimate levels of steroidal saponins. HPLC/ELSD method does not require each and every pure standard of saponins, to quantify the group of steroidal saponins. The method is a time- and cost-effective technique that is suitable for routine industrial analyses. HPLC/ELSD methods yield a saponin fingerprints specific to the plant species. As the method is capable of distinguishing saponin profiles from taxonomically distant species, it can unravel plant adulteration issues. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations.

PubMed

Tian, Kai; Chen, Xiaowei; Luan, Binquan; Singh, Prashant; Yang, Zhiyu; Gates, Kent S; Lin, Mengshi; Mustapha, Azlin; Gu, Li-Qun

2018-05-22

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing Escherichia coli (STEC) serotype O157:H7, and cancer-derived EGFR L858R and KRAS G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations.

Validation of an antibody-based biosensor for rapid quantification of 2,4,6-trinitrotoluene (TNT) contamination in ground water and river water.

PubMed

Bromage, Erin S; Vadas, George G; Harvey, Ellen; Unger, Michael A; Kaattari, Stephen L

2007-10-15

Nitroaromatics are common pollutants of soil and groundwater at military installations because of their manufacture, storage, and use at these sites. Long-term monitoring of these pollutants comprise a significant percentage of restoration costs. Further, remediation activities often have to be delayed, while the samples are processed via traditional chemical assessment protocols. Here we describe a rapid (<5 min), cost-effective, accurate method using a KinExA Inline Biosensor for monitoring of 2,4,6-trinitrotoluene (TNT) in field water samples. The biosensor, which is based on KinExA technology, accurately estimated the concentration of TNT in double-blind comparisons with similar accuracy to traditional high-performance liquid chromatography(HPLC). In the assessment of field samples, the biosensor accurately predicted the concentration of TNT over the range of 1-30,000 microg/L when compared to either HPLC or quantitative gas chromatography-mass spectrometry (GC-MS). Various pre-assessment techniques were explored to examine whether field samples could be assessed untreated, without the removal of particulates or the use of solvents. In most cases, the KinExA Inline Biosensor gave a uniform assessment of TNT concentration independent of pretreatment method. This indicates that this sensor possesses significant promise for rapid, on-site assessment of TNT pollution in environmental water samples.

Accurate high-throughput structure mapping and prediction with transition metal ion FRET

PubMed Central

Yu, Xiaozhen; Wu, Xiongwu; Bermejo, Guillermo A.; Brooks, Bernard R.; Taraska, Justin W.

2013-01-01

Mapping the landscape of a protein’s conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein Maltose Binding Protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells. PMID:23273426

Easy Leaf Area: Automated digital image analysis for rapid and accurate measurement of leaf area.

PubMed

Easlon, Hsien Ming; Bloom, Arnold J

2014-07-01

Measurement of leaf areas from digital photographs has traditionally required significant user input unless backgrounds are carefully masked. Easy Leaf Area was developed to batch process hundreds of Arabidopsis rosette images in minutes, removing background artifacts and saving results to a spreadsheet-ready CSV file. • Easy Leaf Area uses the color ratios of each pixel to distinguish leaves and calibration areas from their background and compares leaf pixel counts to a red calibration area to eliminate the need for camera distance calculations or manual ruler scale measurement that other software methods typically require. Leaf areas estimated by this software from images taken with a camera phone were more accurate than ImageJ estimates from flatbed scanner images. • Easy Leaf Area provides an easy-to-use method for rapid measurement of leaf area and nondestructive estimation of canopy area from digital images.

TSaT-MUSIC: a novel algorithm for rapid and accurate ultrasonic 3D localization

NASA Astrophysics Data System (ADS)

Mizutani, Kyohei; Ito, Toshio; Sugimoto, Masanori; Hashizume, Hiromichi

2011-12-01

We describe a fast and accurate indoor localization technique using the multiple signal classification (MUSIC) algorithm. The MUSIC algorithm is known as a high-resolution method for estimating directions of arrival (DOAs) or propagation delays. A critical problem in using the MUSIC algorithm for localization is its computational complexity. Therefore, we devised a novel algorithm called Time Space additional Temporal-MUSIC, which can rapidly and simultaneously identify DOAs and delays of mul-ticarrier ultrasonic waves from transmitters. Computer simulations have proved that the computation time of the proposed algorithm is almost constant in spite of increasing numbers of incoming waves and is faster than that of existing methods based on the MUSIC algorithm. The robustness of the proposed algorithm is discussed through simulations. Experiments in real environments showed that the standard deviation of position estimations in 3D space is less than 10 mm, which is satisfactory for indoor localization.

Euthanasia Method for Mice in Rapid Time-Course Pulmonary Pharmacokinetic Studies

PubMed Central

Schoell, Adam R; Heyde, Bruce R; Weir, Dana E; Chiang, Po-Chang; Hu, Yiding; Tung, David K

2009-01-01

To develop a means of euthanasia to support rapid time-course pharmacokinetic studies in mice, we compared retroorbital and intravenous lateral tail vein injection of ketamine–xylazine with regard to preparation time, utility, tissue distribution, and time to onset of euthanasia. Tissue distribution and time to onset of euthanasia did not differ between administration methods. However, retroorbital injection could be performed more rapidly than intravenous injection and was considered to be a technically simple and superior alternative for mouse euthanasia. Retroorbital ketamine–xylazine, CO2 gas, and intraperitoneal pentobarbital then were compared as euthanasia agents in a rapid time-point pharmacokinetic study. Retroorbital ketamine–xylazine was the most efficient and consistent of the 3 methods, with an average time to death of approximately 5 s after injection. In addition, euthanasia by retroorbital ketamine–xylazine enabled accurate sample collection at closely spaced time points and satisfied established criteria for acceptable euthanasia technique. PMID:19807971

Euthanasia method for mice in rapid time-course pulmonary pharmacokinetic studies.

PubMed

Schoell, Adam R; Heyde, Bruce R; Weir, Dana E; Chiang, Po-Chang; Hu, Yiding; Tung, David K

2009-09-01

To develop a means of euthanasia to support rapid time-course pharmacokinetic studies in mice, we compared retroorbital and intravenous lateral tail vein injection of ketamine-xylazine with regard to preparation time, utility, tissue distribution, and time to onset of euthanasia. Tissue distribution and time to onset of euthanasia did not differ between administration methods. However, retroorbital injection could be performed more rapidly than intravenous injection and was considered to be a technically simple and superior alternative for mouse euthanasia. Retroorbital ketamine-xylazine, CO(2) gas, and intraperitoneal pentobarbital then were compared as euthanasia agents in a rapid time-point pharmacokinetic study. Retroorbital ketamine-xylazine was the most efficient and consistent of the 3 methods, with an average time to death of approximately 5 s after injection. In addition, euthanasia by retroorbital ketamine-xylazine enabled accurate sample collection at closely spaced time points and satisfied established criteria for acceptable euthanasia technique.

Differentiation of live and dead salmonella cells using fourier transform infrared (FTIR) spectroscopy and principle component analysis (PCA) technique

USDA-ARS?s Scientific Manuscript database

Various technologies have been developed for pathogen detection using optical, electrochemical, biochemical and physical properties. Conventional microbiological methods need time from days to week to get the result. Though this method is very sensitive and accurate, a rapid detection of pathogens i...

Evaluation of fecal indicator and pathogenic bacteria originating from swine manure applied to agricultural lands using culture-based and quantitative real-time PCR methods.

EPA Science Inventory

Fecal bacteria, including those originating from concentrated animal feeding operations, are a leading contributor to water quality impairments in agricultural areas. Rapid and reliable methods are needed that can accurately characterize fecal pollution in agricultural settings....

Evaluation of Fecal Indicator and Pathogenic Bacteria Originating from Swine Manure Applied to Agricultural Lands Using Culture-Based and Quantitative Real-Time PCR Methods

EPA Science Inventory

Fecal bacteria, including those originating from concentrated animal feeding operations, are a leading contributor to water quality impairments in agricultural areas. Rapid and reliable methods are needed that can accurately characterize fecal pollution in agricultural settings....

Statistical methods for analysing responses of wildlife to human disturbance

Treesearch

Haiganoush K. Preisler; Alan A. Ager; Michael J. Wisdom

2006-01-01

Off-road recreation is increasing rapidly in many areas of the world, and effects on wildlife can be highly detrimental. Consequently, we have developed methods for studying wildlife responses to off-road recreation with the use of new technologies that allow frequent and accurate monitoring of human-wildlife interactions. To...

Fast determination of the spatially distributed photon fluence for light dose evaluation of PDT

NASA Astrophysics Data System (ADS)

Zhao, Kuanxin; Chen, Weiting; Li, Tongxin; Yan, Panpan; Qin, Zhuanping; Zhao, Huijuan

2018-02-01

Photodynamic therapy (PDT) has shown superiorities of noninvasiveness and high-efficiency in the treatment of early-stage skin cancer. Rapid and accurate determination of spatially distributed photon fluence in turbid tissue is essential for the dosimetry evaluation of PDT. It is generally known that photon fluence can be accurately obtained by Monte Carlo (MC) methods, while too much time would be consumed especially for complex light source mode or online real-time dosimetry evaluation of PDT. In this work, a method to rapidly calculate spatially distributed photon fluence in turbid medium is proposed implementing a classical perturbation and iteration theory on mesh Monte Carlo (MMC). In the proposed method, photon fluence can be obtained by superposing a perturbed and iterative solution caused by the defects in turbid medium to an unperturbed solution for the background medium and therefore repetitive MMC simulations can be avoided. To validate the method, a non-melanoma skin cancer model is carried out. The simulation results show the solution of photon fluence can be obtained quickly and correctly by perturbation algorithm.

Rapid Identification and Classification of Listeria spp. and Serotype Assignment of Listeria monocytogenes Using Fourier Transform-Infrared Spectroscopy and Artificial Neural Network Analysis

PubMed Central

Romanolo, K. F.; Gorski, L.; Wang, S.; Lauzon, C. R.

2015-01-01

The use of Fourier Transform-Infrared Spectroscopy (FT-IR) in conjunction with Artificial Neural Network software NeuroDeveloper™ was examined for the rapid identification and classification of Listeria species and serotyping of Listeria monocytogenes. A spectral library was created for 245 strains of Listeria spp. to give a biochemical fingerprint from which identification of unknown samples were made. This technology was able to accurately distinguish the Listeria species with 99.03% accuracy. Eleven serotypes of Listeria monocytogenes including 1/2a, 1/2b, and 4b were identified with 96.58% accuracy. In addition, motile and non-motile forms of Listeria were used to create a more robust model for identification. FT-IR coupled with NeuroDeveloper™ appear to be a more accurate and economic choice for rapid identification of pathogenic Listeria spp. than current methods. PMID:26600423

Rapid Identification of Pathogens from Positive Blood Cultures by Multiplex PCR using the FilmArray System

PubMed Central

Blaschke, Anne J.; Heyrend, Caroline; Byington, Carrie L.; Fisher, Mark A.; Barker, Elizabeth; Garrone, Nicholas F.; Thatcher, Stephanie A.; Pavia, Andrew T.; Barney, Trenda; Alger, Garrison D.; Daly, Judy A.; Ririe, Kirk M.; Ota, Irene; Poritz, Mark A.

2012-01-01

Sepsis is a leading cause of death. Rapid and accurate identification of pathogens and antimicrobial resistance directly from blood culture could improve patient outcomes. The FilmArray® (FA; Idaho Technology, Inc., Salt Lake City, UT) Blood Culture (BC) panel can identify > 25 pathogens and 4 antibiotic resistance genes from positive blood cultures in 1 hour. We compared a development version of the panel to conventional culture and susceptibility testing on 102 archived blood cultures from adults and children with bacteremia. Of 109 pathogens identified by culture, 95% were identified by FA. Among 111 prospectively collected blood cultures, the FA identified 84 of 92 pathogens (91%) covered by the panel. Among 25 Staphylococcus aureus and 21 Enterococcus species detected, FA identified all culture-proven MRSA and VRE. The FA BC panel is an accurate method for the rapid identification of pathogens and resistance genes from blood culture. PMID:22999332

Rapid Antibiotic Susceptibility Testing of Uropathogenic E. coli by Tracking Submicron Scale Motion of Single Bacterial Cells.

PubMed

Syal, Karan; Shen, Simon; Yang, Yunze; Wang, Shaopeng; Haydel, Shelley E; Tao, Nongjian

2017-08-25

To combat antibiotic resistance, a rapid antibiotic susceptibility testing (AST) technology that can identify resistant infections at disease onset is required. Current clinical AST technologies take 1-3 days, which is often too slow for accurate treatment. Here we demonstrate a rapid AST method by tracking sub-μm scale bacterial motion with an optical imaging and tracking technique. We apply the method to clinically relevant bacterial pathogens, Escherichia coli O157: H7 and uropathogenic E. coli (UPEC) loosely tethered to a glass surface. By analyzing dose-dependent sub-μm motion changes in a population of bacterial cells, we obtain the minimum bactericidal concentration within 2 h using human urine samples spiked with UPEC. We validate the AST method using the standard culture-based AST methods. In addition to population studies, the method allows single cell analysis, which can identify subpopulations of resistance strains within a sample.

Novel Accurate Bacterial Discrimination by MALDI-Time-of-Flight MS Based on Ribosomal Proteins Coding in S10-spc-alpha Operon at Strain Level S10-GERMS

NASA Astrophysics Data System (ADS)

Tamura, Hiroto; Hotta, Yudai; Sato, Hiroaki

2013-08-01

Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most widely used mass-based approaches for bacterial identification and classification because of the simple sample preparation and extremely rapid analysis within a few minutes. To establish the accurate MALDI-TOF MS bacterial discrimination method at strain level, the ribosomal subunit proteins coded in the S 10-spc-alpha operon, which encodes half of the ribosomal subunit protein and is highly conserved in eubacterial genomes, were selected as reliable biomarkers. This method, named the S10-GERMS method, revealed that the strains of genus Pseudomonas were successfully identified and discriminated at species and strain levels, respectively; therefore, the S10-GERMS method was further applied to discriminate the pathovar of P. syringae. The eight selected biomarkers (L24, L30, S10, S12, S14, S16, S17, and S19) suggested the rapid discrimination of P. syringae at the strain (pathovar) level. The S10-GERMS method appears to be a powerful tool for rapid and reliable bacterial discrimination and successful phylogenetic characterization. In this article, an overview of the utilization of results from the S10-GERMS method is presented, highlighting the characterization of the Lactobacillus casei group and discrimination of the bacteria of genera Bacillus and Sphingopyxis despite only two and one base difference in the 16S rRNA gene sequence, respectively.

Therapeutic Drug Monitoring of Phenytoin by Simple, Rapid, Accurate, Highly Sensitive and Novel Method and Its Clinical Applications.

PubMed

Shaikh, Abdul S; Guo, Ruichen

2017-01-01

Phenytoin has very challenging pharmacokinetic properties. To prevent its toxicity and ensure efficacy, continuous therapeutic monitoring is required. It is hard to get a simple, accurate, rapid, easily available, economical and highly sensitive assay in one method for therapeutic monitoring of phenytoin. The present study is directed towards establishing and validating a simpler, rapid, an accurate, highly sensitive, novel and environment friendly liquid chromatography/mass spectrometry (LC/MS) method for offering rapid and reliable TDM results of phenytoin in epileptic patients to physicians and clinicians for making immediate and rational decision. 27 epileptics patients with uncontrolled seizures or suspected of non-compliance or toxicity of phenytoin were selected and advised for TDM of phenytoin by neurologists of Qilu Hospital Jinan, China. The LC/MS assay was used for performing of therapeutic monitoring of phenytoin. The Agilent 1100 LC/MS system was used for TDM. The mixture of Ammonium acetate 5mM: Methanol at (35: 65 v/v) was used for the composition of mobile phase. The Diamonsil C18 (150mm×4.6mm, 5μm) column was used for the extraction of analytes in plasma. The samples were prepared with one step simple protein precipitation method. The technique was validated with the guidelines of International Conference on Harmonisation (ICH). The calibration curve demonstrated decent linearity within (0.2-20 µg/mL) concentration range with linearity equation, y= 0.0667855 x +0.00241785 and correlation coefficient (R2) of 0.99928. The specificity, recovery, linearity, accuracy, precision and stability results were within the accepted limits. The concentration of 0.2 µg/mL was observed as lower limit of quantitation (LLOQ), which is 12.5 times lower than the currently available enzyme-multiplied immunoassay technique (EMIT) for measurement of phenytoin in epilepsy patients. A rapid, simple, economical, precise, highly sensitive and novel LC/MS assay has been established, validated and applied successfully in TDM of 27 epileptics patients. It was alarmingly found that TDM results of all these patients were out of safe range except two patients. However, it needs further evaluation. Besides TDM, the stated method can also be applied in bioequivalence, pharmacokinetics, toxicokinetics and pharmacovigilance studies. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Rapid and sensitive detection of mink circovirus by recombinase polymerase amplification.

PubMed

Ge, Junwei; Shi, Yunjia; Cui, Xingyang; Gu, Shanshan; Zhao, Lili; Chen, Hongyan

2018-06-01

To date, the pathogenic role of mink circovirus (MiCV) remains unclear, and its prevalence and economic importance are unknown. Therefore, a rapid and sensitive molecular diagnosis is necessary for disease management and epidemiological surveillance. However, only PCR methods can identify MiCV infection at present. In this study, we developed a nested PCR and established a novel recombinase polymerase amplification (RPA) assay for MiCV detection. Sensitivity analysis showed that the detection limit of nested PCR and RPA assay was 10 1 copies/reaction, and these methods were more sensitive than conventional PCR, which has a detection limit of 10 5 copies/reaction. The RPA assay had no cross-reactivity with other related viral pathogens, and amplification was completed in less than 20 min with a simple device. Further assessment of clinical samples showed that the two assays were accurate in identifying positive and negative conventional PCR samples. The detection rate of MiCV by the RPA assay in clinical samples was 38.09%, which was 97% consistent with that by the nested PCR. The developed nested PCR is a highly sensitive tool for practical use, and the RPA assay is a simple, sensitive, and potential alternative method for rapid and accurate MiCV diagnosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Study of wave form compensation at CSNS/RCS magnets

NASA Astrophysics Data System (ADS)

Xu, S. Y.; Fu, S. N.; Wang, S.; Kang, W.; Qi, X.; Li, L.; Deng, C. D.; Zhou, J. X.

2018-07-01

A method of wave form compensation for magnets of the Rapid Cycling Synchrotron (RCS), which is based on transfer function between magnetic field and exciting current, was investigated on the magnets of RCS of Chinese Spallation Neutron Source (CSNS). By performing wave form compensation, the magnetic field ramping function for RCS magnets can be accurately controlled to the given wave form, which is not limited to sine function. The method of wave form compensation introduced in this paper can be used to reduce the magnetic field tracking errors, and can also be used to accurately control the betatron tune for RCS.

Rapid Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) by the Vitek MS Saramis system.

PubMed

Shan, Weiguang; Li, Jiaping; Fang, Ying; Wang, Xuan; Gu, Danxia; Zhang, Rong

2016-01-01

A rapid, sensitive, and accurate Vitek MS assay was developed to distinguish clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) from clinical isolates of methicillin-sensitive Staphylococcus aureus (MSSA) by developing an in-house knowledgebase of SuperSpectra. Three unique peaks, including peaks at 2305.6 and 3007.3 Da specific to MRSA, and 6816.7 Da specific to MSSA, were selected for differentiating MRSA and MSSA. This assay accurately identified 84 and 91% of clinical MRSA and MSSA strains out of the total 142 clinically acquired S. aureus strains that were tested. This method will greatly improve the efficiency of single clinical sample identification of MRSA, thereby facilitating a reduction in the transmission of MRSA in clinical settings.

[Research on the temperature field detection method of hot forging based on long-wavelength infrared spectrum].

PubMed

Zhang, Yu-Cun; Wei, Bin; Fu, Xian-Bin

2014-02-01

A temperature field detection method based on long-wavelength infrared spectrum for hot forging is proposed in the present paper. This method combines primary spectrum pyrometry and three-stage FP-cavity LCTF. By optimizing the solutions of three group nonlinear equations in the mathematical model of temperature detection, the errors are reduced, thus measuring results will be more objective and accurate. Then the system of three-stage FP-cavity LCTF was designed on the principle of crystal birefringence. The system realized rapid selection of any wavelength in a certain wavelength range. It makes the response of the temperature measuring system rapid and accurate. As a result, without the emissivity of hot forging, the method can acquire exact information of temperature field and effectively suppress the background light radiation around the hot forging and ambient light that impact the temperature detection accuracy. Finally, the results of MATLAB showed that the infrared spectroscopy through the three-stage FP-cavity LCTF could meet the requirements of design. And experiments verified the feasibility of temperature measuring method. Compared with traditional single-band thermal infrared imager, the accuracy of measuring result was improved.

An accurate and rapid radiographic method of determining total lung capacity

PubMed Central

Reger, R. B.; Young, A.; Morgan, W. K. C.

1972-01-01

The accuracy and reliability of Barnhard's radiographic method of determining total lung capacity have been confirmed by several groups of investigators. Despite its simplicity and general reliability, it has several shortcomings, especially when used in large-scale epidemiological surveys. Of these, the most serious is related to film technique; thus, when the cardiac and diaphragmatic shadows are poorly defined, the appropriate measurements cannot be made accurately. A further drawback involves the time needed to measure the segments and to perform the necessary calculations. We therefore set out to develop an abbreviated and simpler radiographic method for determining total lung capacity. This uses a step-wise multiple regression model which allows total lung capacity to be derived as follows: posteroanterior and lateral films are divided into the standard sections as described in the text, the width, depth, and height of sections 1 and 4 are measured in centimetres, finally the necessary derivations and substitutions are made and applied to the formula Ŷ = −1·41148 + (0·00479 X1) + (0·00097 X4), where Ŷ is the total lung capacity. In our hands this method has provided a simple, rapid, and acceptable method of determining total lung capacity. PMID:5034594

Apparatus for continuous, fast, and precise measurements of position and velocity of a small spherical particle

NASA Technical Reports Server (NTRS)

Venkataraman, T. S.; Eidson, W. W.; Cohen, L. D.; Farina, J. D.; Acquista, C.

1983-01-01

The position and velocity of optically levitated glass spheres (radii 10-20 microns) movng in a gas are measured accurately, rapidly, and continuously using a high-speed rotating polygon mirror. The experimental technique developed here has repeatable position accuracies better than 20 microns. Each measurement takes less than 1 microsec and can be repeated every 100 microsec. The position of the levitated glass spheres can be manipulated accurately by modulating the laser power with an acoustic optic modulator. The technique provides a fast and accurate method to study general particle dynamics in a fluid.

Justification of Estimates for Fiscal Year 1984 Submitted to Congress.

DTIC Science & Technology

1983-01-01

sponsoring different aspects related to unique manufacturing methods than those pursued by DARPA, and duplication of effort is prevented by direct...weapons systems. Rapid and economical methods of satisfying these requirements must significantly precede weapons systems developments to prevent... methods for obtaining accurate and efficient geodetic measurements. Also, a major advanced sensor/G&G data collection capability is being urdertaken by DNA

Zinc Biosorption by Seaweed Illustrated by the Zincon Colorimetric Method and the Langmuir Isotherm

ERIC Educational Resources Information Center

Areco, Maria Mar; dos Santos Afonso, Maria; Valdman, Erika

2007-01-01

An experiment is conducted to promote biotechnology knowledge that is an emerging technology on cleaning treatment, showing the potential of seaweed to remove heavy-metal ions from solution. The rapid and accurate determination of zinc in aqueous solution by the zincon colorimetric method gives an interesting and simple experiment for any…

Probe molecules (PrM) approach in adverse outcome pathway (AOP) based high throughput screening (HTS): in vivo discovery for developing in vitro target methods

EPA Science Inventory

Efficient and accurate adverse outcome pathway (AOP) based high-throughput screening (HTS) methods use a systems biology based approach to computationally model in vitro cellular and molecular data for rapid chemical prioritization; however, not all HTS assays are grounded by rel...

Rapid and reliable identification of Gram-negative bacteria and Gram-positive cocci by deposition of bacteria harvested from blood cultures onto the MALDI-TOF plate.

PubMed

Barnini, Simona; Ghelardi, Emilia; Brucculeri, Veronica; Morici, Paola; Lupetti, Antonella

2015-06-18

Rapid identification of the causative agent(s) of bloodstream infections using the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) methodology can lead to increased empirical antimicrobial therapy appropriateness. Herein, we aimed at establishing an easier and simpler method, further referred to as the direct method, using bacteria harvested by serum separator tubes from positive blood cultures and placed onto the polished steel target plate for rapid identification by MALDI-TOF. The results by the direct method were compared with those obtained by MALDI-TOF on bacteria isolated on solid media. Identification of Gram-negative bacilli was 100 % concordant using the direct method or MALDI-TOF on isolated bacteria (96 % with score > 2.0). These two methods were 90 % concordant on Gram-positive cocci (32 % with score > 2.0). Identification by the SepsiTyper method of Gram-positive cocci gave concordant results with MALDI-TOF on isolated bacteria in 87 % of cases (37 % with score > 2.0). The direct method herein developed allows rapid identification (within 30 min) of Gram-negative bacteria and Gram-positive cocci from positive blood cultures and can be used to rapidly report reliable and accurate results, without requiring skilled personnel or the use of expensive kits.

Rapid direct methods for enumeration of specific, active bacteria in water and biofilms

NASA Technical Reports Server (NTRS)

McFeters, G. A.; Pyle, B. H.; Lisle, J. T.; Broadaway, S. C.

1999-01-01

Conventional methods for detecting indicator and pathogenic bacteria in water may underestimate the actual population due to sublethal environmental injury, inability of the target bacteria to take up nutrients and other physiological factors which reduce bacterial culturability. Rapid and direct methods are needed to more accurately detect and enumerate active bacteria. Such a methodological advance would provide greater sensitivity in assessing the microbiological safety of water and food. The principle goal of this presentation is to describe novel approaches we have formulated for the rapid and simultaneous detection of bacteria plus the determination of their physiological activity in water and other environmental samples. The present version of our method involves the concentration of organisms by membrane filtration or immunomagnetic separation and combines an intracellular fluorochrome (CTC) for assessment of respiratory activity plus fluorescent-labelled antibody detection of specific bacteria. This approach has also been successfully used to demonstrate spatial and temporal heterogeneities of physiological activities in biofilms when coupled with cryosectioning. Candidate physiological stains include those capable of determining respiratory activity, membrane potential, membrane integrity, growth rate and cellular enzymatic activities. Results obtained thus far indicate that immunomagnetic separation can provide a high degree of sensitivity in the recovery of seeded target bacteria (Escherichia coli O157:H7) in water and hamburger. The captured and stained target bacteria are then enumerated by either conventional fluorescence microscopy or ChemScan(R), a new instrument that is very sensitive and rapid. The ChemScan(R) laser scanning instrument (Chemunex, Paris, France) provides the detection of individual fluorescently labelled bacterial cells using three emission channels in less than 5 min. A high degree of correlation has been demonstrated between results obtained with the ChemScan and traditional plate counts of mixed natural bacterial populations in water. The continuing evolution of these methods will be valuable in the rapid and accurate analysis of environmental samples.

Strain, biochemistry, and cultivation-dependent measurement variability of algal biomass composition.

PubMed

Laurens, Lieve M L; Van Wychen, Stefanie; McAllister, Jordan P; Arrowsmith, Sarah; Dempster, Thomas A; McGowen, John; Pienkos, Philip T

2014-05-01

Accurate compositional analysis in biofuel feedstocks is imperative; the yields of individual components can define the economics of an entire process. In the nascent industry of algal biofuels and bioproducts, analytical methods that have been deemed acceptable for decades are suddenly critical for commercialization. We tackled the question of how the strain and biochemical makeup of algal cells affect chemical measurements. We selected a set of six procedures (two each for lipids, protein, and carbohydrates): three rapid fingerprinting methods and three advanced chromatography-based methods. All methods were used to measure the composition of 100 samples from three strains: Scenedesmus sp., Chlorella sp., and Nannochloropsis sp. The data presented point not only to species-specific discrepancies but also to cell biochemistry-related discrepancies. There are cases where two respective methods agree but the differences are often significant with over- or underestimation of up to 90%, likely due to chemical interferences with the rapid spectrophotometric measurements. We provide background on the chemistry of interfering reactions for the fingerprinting methods and conclude that for accurate compositional analysis of algae and process and mass balance closure, emphasis should be placed on unambiguous characterization using methods where individual components are measured independently. Copyright © 2014 Elsevier Inc. All rights reserved.

Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry

PubMed Central

2010-01-01

Background Accurate identification is necessary to discriminate harmless environmental Yersinia species from the food-borne pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis and from the group A bioterrorism plague agent Yersinia pestis. In order to circumvent the limitations of current phenotypic and PCR-based identification methods, we aimed to assess the usefulness of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) protein profiling for accurate and rapid identification of Yersinia species. As a first step, we built a database of 39 different Yersinia strains representing 12 different Yersinia species, including 13 Y. pestis isolates representative of the Antiqua, Medievalis and Orientalis biotypes. The organisms were deposited on the MALDI-TOF plate after appropriate ethanol-based inactivation, and a protein profile was obtained within 6 minutes for each of the Yersinia species. Results When compared with a 3,025-profile database, every Yersinia species yielded a unique protein profile and was unambiguously identified. In the second step of analysis, environmental and clinical isolates of Y. pestis (n = 2) and Y. enterocolitica (n = 11) were compared to the database and correctly identified. In particular, Y. pestis was unambiguously identified at the species level, and MALDI-TOF was able to successfully differentiate the three biotypes. Conclusion These data indicate that MALDI-TOF can be used as a rapid and accurate first-line method for the identification of Yersinia isolates. PMID:21073689

Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.

PubMed

Ayyadurai, Saravanan; Flaudrops, Christophe; Raoult, Didier; Drancourt, Michel

2010-11-12

Accurate identification is necessary to discriminate harmless environmental Yersinia species from the food-borne pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis and from the group A bioterrorism plague agent Yersinia pestis. In order to circumvent the limitations of current phenotypic and PCR-based identification methods, we aimed to assess the usefulness of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) protein profiling for accurate and rapid identification of Yersinia species. As a first step, we built a database of 39 different Yersinia strains representing 12 different Yersinia species, including 13 Y. pestis isolates representative of the Antiqua, Medievalis and Orientalis biotypes. The organisms were deposited on the MALDI-TOF plate after appropriate ethanol-based inactivation, and a protein profile was obtained within 6 minutes for each of the Yersinia species. When compared with a 3,025-profile database, every Yersinia species yielded a unique protein profile and was unambiguously identified. In the second step of analysis, environmental and clinical isolates of Y. pestis (n = 2) and Y. enterocolitica (n = 11) were compared to the database and correctly identified. In particular, Y. pestis was unambiguously identified at the species level, and MALDI-TOF was able to successfully differentiate the three biotypes. These data indicate that MALDI-TOF can be used as a rapid and accurate first-line method for the identification of Yersinia isolates.

Laboratory Methods for the Measurement of Pollutants in Water and Waste Effluents

NASA Technical Reports Server (NTRS)

Ballinger, Dwight G.

1971-01-01

The requirement for accurate, precise, and rapid analytical procedures for the examination of water and waste samples requires the use of a variety of instruments. The instrumentation in water laboratories includes atomic absorption, UV-visible. and infrared spectrophotometers, automatic colorimetric analyzers, gas chromatographs and mass spectrometers. Because of the emphasis on regulatory action, attention is being directed toward quality control of analytical results. Among the challenging problems are the differentiation of metallic species in water at nanogram concentrations, rapid measurement of free cyanide and free ammonia, more sensitive methods for arsenic and selenium and improved characterization of organic contaminants.

Validation of Rapid Radiochemical Method for Californium ...

EPA Pesticide Factsheets

Technical Brief In the event of a radiological/nuclear contamination event, the response community would need tools and methodologies to rapidly assess the nature and the extent of contamination. To characterize a radiologically contaminated outdoor area and to inform risk assessment, large numbers of environmental samples would be collected and analyzed over a short period of time. To address the challenge of quickly providing analytical results to the field, the U.S. EPA developed a robust analytical method. This method allows response officials to characterize contaminated areas and to assess the effectiveness of remediation efforts, both rapidly and accurately, in the intermediate and late phases of environmental cleanup. Improvement in sample processing and analysis leads to increased laboratory capacity to handle the analysis of a large number of samples following the intentional or unintentional release of a radiological/nuclear contaminant.

DNA-BASED METHODS FOR MONITORING INVASIVE SPECIES: A REVIEW AND PROSPECTUS

EPA Science Inventory

The recent explosion of interest in DNA-based tools for species identification has prompted widespread speculation on the future availability of inexpensive, rapid and accurate means of identifying specimens and assessing biodiversity. One applied field that may benefit dramatic...

Determining water content of fresh concrete by microwave reflection or transmission measurement.

DOT National Transportation Integrated Search

1987-01-01

In search of a rapid and accurate method for determining the water content of fresh concrete mixes, the microwave reflection and transmission properties of fresh concrete mixes were studied to determine the extent of correlation between each of these...

A rapid method to extract Seebeck coefficient under a large temperature difference

NASA Astrophysics Data System (ADS)

Zhu, Qing; Kim, Hee Seok; Ren, Zhifeng

2017-09-01

The Seebeck coefficient is one of the three important properties in thermoelectric materials. Since thermoelectric materials usually work under large temperature difference in real applications, we propose a quasi-steady state method to accurately measure the Seebeck coefficient under large temperature gradient. Compared to other methods, this method is not only highly accurate but also less time consuming. It can measure the Seebeck coefficient in both the temperature heating up and cooling down processes. In this work, a Zintl material (Mg3.15Nb0.05Sb1.5Bi0.49Te0.01) was tested to extract the Seebeck coefficient from room temperature to 573 K. Compared with a commercialized Seebeck coefficient measurement device (ZEM-3), there is ±5% difference between those from ZEM-3 and this method.

Auto Regressive Moving Average (ARMA) Modeling Method for Gyro Random Noise Using a Robust Kalman Filter

PubMed Central

Huang, Lei

2015-01-01

To solve the problem in which the conventional ARMA modeling methods for gyro random noise require a large number of samples and converge slowly, an ARMA modeling method using a robust Kalman filtering is developed. The ARMA model parameters are employed as state arguments. Unknown time-varying estimators of observation noise are used to achieve the estimated mean and variance of the observation noise. Using the robust Kalman filtering, the ARMA model parameters are estimated accurately. The developed ARMA modeling method has the advantages of a rapid convergence and high accuracy. Thus, the required sample size is reduced. It can be applied to modeling applications for gyro random noise in which a fast and accurate ARMA modeling method is required. PMID:26437409

PconsD: ultra rapid, accurate model quality assessment for protein structure prediction.

PubMed

Skwark, Marcin J; Elofsson, Arne

2013-07-15

Clustering methods are often needed for accurately assessing the quality of modeled protein structures. Recent blind evaluation of quality assessment methods in CASP10 showed that there is little difference between many different methods as far as ranking models and selecting best model are concerned. When comparing many models, the computational cost of the model comparison can become significant. Here, we present PconsD, a fast, stream-computing method for distance-driven model quality assessment that runs on consumer hardware. PconsD is at least one order of magnitude faster than other methods of comparable accuracy. The source code for PconsD is freely available at http://d.pcons.net/. Supplementary benchmarking data are also available there. arne@bioinfo.se Supplementary data are available at Bioinformatics online.

Method development and validation of potent pyrimidine derivative by UV-VIS spectrophotometer.

PubMed

Chaudhary, Anshu; Singh, Anoop; Verma, Prabhakar Kumar

2014-12-01

A rapid and sensitive ultraviolet-visible (UV-VIS) spectroscopic method was developed for the estimation of pyrimidine derivative 6-Bromo-3-(6-(2,6-dichlorophenyl)-2-(morpolinomethylamino) pyrimidine4-yl) -2H-chromen-2-one (BT10M) in bulk form. Pyrimidine derivative was monitored at 275 nm with UV detection, and there is no interference of diluents at 275 nm. The method was found to be linear in the range of 50 to 150 μg/ml. The accuracy and precision were determined and validated statistically. The method was validated as a guideline. The results showed that the proposed method is suitable for the accurate, precise, and rapid determination of pyrimidine derivative. Graphical Abstract Method development and validation of potent pyrimidine derivative by UV spectroscopy.

Rapid Detection of Urinary Tract Infections via Bacterial Nuclease Activity.

PubMed

Flenker, Katie S; Burghardt, Elliot L; Dutta, Nirmal; Burns, William J; Grover, Julia M; Kenkel, Elizabeth J; Weaver, Tyler M; Mills, James; Kim, Hyeon; Huang, Lingyan; Owczarzy, Richard; Musselman, Catherine A; Behlke, Mark A; Ford, Bradley; McNamara, James O

2017-06-07

Rapid and accurate bacterial detection methods are needed for clinical diagnostic, water, and food testing applications. The wide diversity of bacterial nucleases provides a rich source of enzymes that could be exploited as signal amplifying biomarkers to enable rapid, selective detection of bacterial species. With the exception of the use of micrococcal nuclease activity to detect Staphylococcus aureus, rapid methods that detect bacterial pathogens via their nuclease activities have not been developed. Here, we identify endonuclease I as a robust biomarker for E. coli and develop a rapid ultrasensitive assay that detects its activity. Comparison of nuclease activities of wild-type and nuclease-knockout E. coli clones revealed that endonuclease I is the predominant DNase in E. coli lysates. Endonuclease I is detectable by immunoblot and activity assays in uropathogenic E. coli strains. A rapid assay that detects endonuclease I activity in patient urine with an oligonucleotide probe exhibited substantially higher sensitivity for urinary tract infections than that reported for rapid urinalysis methods. The 3 hr turnaround time is much shorter than that of culture-based methods, thereby providing a means for expedited administration of appropriate antimicrobial therapy. We suggest this approach could address various unmet needs for rapid detection of E. coli. Copyright © 2017 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.

A rapid and accurate method for determining protein content in dairy products based on asynchronous-injection alternating merging zone flow-injection spectrophotometry.

PubMed

Liang, Qin-Qin; Li, Yong-Sheng

2013-12-01

An accurate and rapid method and a system to determine protein content using asynchronous-injection alternating merging zone flow-injection spectrophotometry based on reaction between coomassie brilliant blue G250 (CBBG) and protein was established. Main merit of our approach is that it can avoid interferences of other nitric-compounds in samples, such as melamine and urea. Optimized conditions are as follows: Concentrations of CBBG, polyvinyl alcohol (PVA), NaCl and HCl are 150 mg/l, 30 mg/l, 0.1 mol/l and 1.0% (v/v), respectively; volumes of the sample and reagent are 150 μl and 30 μl, respectively; length of a reaction coil is 200 cm; total flow rate is 2.65 ml/min. The linear range of the method is 0.5-15 mg/l (BSA), its detection limit is 0.05 mg/l, relative standard deviation is less than 1.87% (n=11), and analytical speed is 60 samples per hour. Copyright © 2013 Elsevier Ltd. All rights reserved.

A rapid solvent accessible surface area estimator for coarse grained molecular simulations.

PubMed

Wei, Shuai; Brooks, Charles L; Frank, Aaron T

2017-06-05

The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with biophysical processes, and when combined with coarse-grained simulations, can be particularly useful for accounting for solvation effects within the framework of implicit solvent models. In such cases, a fast and accurate, residue-wise SASA predictor is highly desirable. Here, we develop a predictive model that estimates SASAs based on Cα-only protein structures. Through an extensive comparison between this method and a comparable method, POPS-R, we demonstrate that our new method, Protein-C α Solvent Accessibilities or PCASA, shows better performance, especially for unfolded conformations of proteins. We anticipate that this model will be quite useful in the efficient inclusion of SASA-based solvent free energy estimations in coarse-grained protein folding simulations. PCASA is made freely available to the academic community at https://github.com/atfrank/PCASA. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Rapid and quantitative detection of the microbial spoilage in milk using Fourier transform infrared spectroscopy and chemometrics.

PubMed

Nicolaou, Nicoletta; Goodacre, Royston

2008-10-01

Microbiological safety plays a very significant part in the quality control of milk and dairy products worldwide. Current methods used in the detection and enumeration of spoilage bacteria in pasteurized milk in the dairy industry, although accurate and sensitive, are time-consuming. FT-IR spectroscopy is a metabolic fingerprinting technique that can potentially be used to deliver results with the same accuracy and sensitivity, within minutes after minimal sample preparation. We tested this hypothesis using attenuated total reflectance (ATR), and high throughput (HT) FT-IR techniques. Three main types of pasteurized milk - whole, semi-skimmed and skimmed - were used and milk was allowed to spoil naturally by incubation at 15 degrees C. Samples for FT-IR were obtained at frequent, fixed time intervals and pH and total viable counts were also recorded. Multivariate statistical methods, including principal components-discriminant function analysis and partial least squares regression (PLSR), were then used to investigate the relationship between metabolic fingerprints and the total viable counts. FT-IR ATR data for all milks showed reasonable results for bacterial loads above 10(5) cfu ml(-1). By contrast, FT-IR HT provided more accurate results for lower viable bacterial counts down to 10(3) cfu ml(-1) for whole milk and, 4 x 10(2) cfu ml(-1) for semi-skimmed and skimmed milk. Using FT-IR with PLSR we were able to acquire a metabolic fingerprint rapidly and quantify the microbial load of milk samples accurately, with very little sample preparation. We believe that metabolic fingerprinting using FT-IR has very good potential for future use in the dairy industry as a rapid method of detection and enumeration.

Highly efficient classification and identification of human pathogenic bacteria by MALDI-TOF MS.

PubMed

Hsieh, Sen-Yung; Tseng, Chiao-Li; Lee, Yun-Shien; Kuo, An-Jing; Sun, Chien-Feng; Lin, Yen-Hsiu; Chen, Jen-Kun

2008-02-01

Accurate and rapid identification of pathogenic microorganisms is of critical importance in disease treatment and public health. Conventional work flows are time-consuming, and procedures are multifaceted. MS can be an alternative but is limited by low efficiency for amino acid sequencing as well as low reproducibility for spectrum fingerprinting. We systematically analyzed the feasibility of applying MS for rapid and accurate bacterial identification. Directly applying bacterial colonies without further protein extraction to MALDI-TOF MS analysis revealed rich peak contents and high reproducibility. The MS spectra derived from 57 isolates comprising six human pathogenic bacterial species were analyzed using both unsupervised hierarchical clustering and supervised model construction via the Genetic Algorithm. Hierarchical clustering analysis categorized the spectra into six groups precisely corresponding to the six bacterial species. Precise classification was also maintained in an independently prepared set of bacteria even when the numbers of m/z values were reduced to six. In parallel, classification models were constructed via Genetic Algorithm analysis. A model containing 18 m/z values accurately classified independently prepared bacteria and identified those species originally not used for model construction. Moreover bacteria fewer than 10(4) cells and different species in bacterial mixtures were identified using the classification model approach. In conclusion, the application of MALDI-TOF MS in combination with a suitable model construction provides a highly accurate method for bacterial classification and identification. The approach can identify bacteria with low abundance even in mixed flora, suggesting that a rapid and accurate bacterial identification using MS techniques even before culture can be attained in the near future.

A rapid method of estimating the collision frequencies between the earth and the earth-crossing bodies

NASA Technical Reports Server (NTRS)

Su, Shin-Yi; Kessler, Donald J.

1991-01-01

The present study examines a very fast method of calculating the collision frequency between two low-eccentricity orbiting bodies for evaluating the evolution of earth-orbiting objects such as space debris. The results are very accurate and the required computer time is negligible. The method is now applied without modification to calculate the collision frequencies for moderately and highly eccentric orbits.

Prosthodontics an “arsenal” in forensic dentistry

PubMed Central

Bathala, Lakshmana Rao; Rachuri, Narendra Kumar; Rayapati, Srinivas Rao; Kondaka, Sudheer

2016-01-01

After major disasters such as earthquakes, fires, floods, tsunami, bomb blasts or terrorist attacks, accurate, and early identification of the dead and injured becomes an utmost importance. Restorations, cariesteeth, missingteeth and/or prostheses are most useful aids for the dental identification. At times, only identifiable remains are a victim's partial or complete dentures. The central principle of dental identification is that postmortem dental remains can be compared with antemortem dental records which include, studycasts, radiographs, etc., to confirm the identity of the victims. Marking/labeling dentures have been considered an important aid in forensic dentistry. Other than finger printing, when compared with all the methods, the marking/labeling of dentures is an accurate and rapid method to identify the unknown victims. There are no standardized methods to follow, but dental practitioners needs to maintain some dental records of their patients. This may include documentation of the “marking of dentures.” The preparedness is the key to success in mass disaster identification. The aim of this review article is to discuss the methods of denture identification, advantages of denture labeling for the rapid identification during major disasters/accidents and the importance of maintaining the patient records. PMID:28123274

Genetic methods for detection of antibiotic resistance: focus on extended-spectrum β-lactamases.

PubMed

Chroma, Magdalena; Kolar, Milan

2010-12-01

In 1928, the first antibiotic, penicillin, was discovered. That was the beginning of a great era in the development and prescription of antibiotics. However, the introduction of these antimicrobial agents into clinical practice was accompanied by the problem of antibiotic resistance. Currently, bacterial resistance to antibiotics poses a major problem in both hospital and community settings throughout the world. This review provides examples of modern genetic methods and their practical application in the field of extended-spectrum β-lactamase detection. Since extended-spectrum β-lactamases are the main mechanism of Gram-negative bacterial resistance to oxyimino-cephalosporins, rapid and accurate detection is requested in common clinical practice. Currently, the detection of extended-spectrum β-lactamases is primarily based on the determination of bacterial phenotypes rather than genotypes. This is because therapeutic decisions are based on assessing the susceptibility rather than presence of resistance genes. One of the main disadvantages of genetic methods is high costs, including those of laboratory equipment. On the other hand, if these modern methods are introduced into diagnostics, they often help in rapid and accurate detection of certain microorganisms or their resistance and pathogenic determinants.

Rapid and accurate intraoperative pathological diagnosis by artificial intelligence with deep learning technology.

PubMed

Zhang, Jing; Song, Yanlin; Xia, Fan; Zhu, Chenjing; Zhang, Yingying; Song, Wenpeng; Xu, Jianguo; Ma, Xuelei

2017-09-01

Frozen section is widely used for intraoperative pathological diagnosis (IOPD), which is essential for intraoperative decision making. However, frozen section suffers from some drawbacks, such as time consuming and high misdiagnosis rate. Recently, artificial intelligence (AI) with deep learning technology has shown bright future in medicine. We hypothesize that AI with deep learning technology could help IOPD, with a computer trained by a dataset of intraoperative lesion images. Evidences supporting our hypothesis included the successful use of AI with deep learning technology in diagnosing skin cancer, and the developed method of deep-learning algorithm. Large size of the training dataset is critical to increase the diagnostic accuracy. The performance of the trained machine could be tested by new images before clinical use. Real-time diagnosis, easy to use and potential high accuracy were the advantages of AI for IOPD. In sum, AI with deep learning technology is a promising method to help rapid and accurate IOPD. Copyright © 2017 Elsevier Ltd. All rights reserved.

A rapid method for preparation of the cerebrospinal fluid proteome.

PubMed

Larssen, Eivind; Brede, Cato; Hjelle, Anne Bjørnstad; Øysaed, Kjell Birger; Tjensvoll, Anne Bolette; Omdal, Roald; Ruoff, Peter

2015-01-01

The cerebrospinal fluid (CSF) proteome is of great interest for investigation of diseases and conditions involving the CNS. However, the presence of high-abundance proteins (HAPs) can interfere with the detection of low-abundance proteins, potentially hindering the discovery of new biomarkers. Therefore, an assessment of the CSF subproteome composition requires depletion strategies. Existing methods are time consuming, often involving multistep protocols. Here, we present a rapid, accurate, and reproducible method for preparing the CSF proteome, which allows the identification of a high number of proteins. This method involves acetonitrile (ACN) precipitation for depleting HAPs, followed by immediate trypsination. As an example, we demonstrate that this method allows discrimination between multiple sclerosis patients and healthy subjects. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid Identification of Legionella Pathogenicity by Surface-Enhanced Raman Spectroscopy.

PubMed

Li, Jing; Qin, Tian; Jia, Xiao Xiao; Deng, Ai Hua; Zhang, Xu; Fan, Wen Hui; Huo, Shuai Dong; Wen, Ting Yi; Liu, Wen Jun

2015-06-01

To establish Surface-enhanced Raman Spectroscopy (SERS) can be used as a rapid and reliable method to distinguish virulent strain and mild strain of L. pneumophila. Mortality data were collected from company departments through administrative documents, death certificates, etc. Trend analyses of cancer mortality were performed on the basis of 925 cancer deaths between 2001 and 2010. Our results indicated that the peaks of high virulence strains reached ⋝4000. This criterion was verified by subsequent cell experiments. In addition, we also conducted SERS rapid identification on the virulence of several collected clinical strains and obtained accurate results. The present study indicates that the established SERS protocol can be used as a rapid and reliable method to distinguish virulent and mildly virulent strains of L. pneumophila, which can be further used in clinical samples. Copyright © 2015 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Rapid detection of undesired cosmetic ingredients by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

PubMed

Ouyang, Jie; An, Dongli; Chen, Tengteng; Lin, Zhiwei

2017-10-01

In recent years, cosmetic industry profits soared due to the widespread use of cosmetics, which resulted in illicit manufacturers and products of poor quality. Therefore, the rapid and accurate detection of the composition of cosmetics has become crucial. At present, numerous methods, such as gas chromatography and liquid chromatography-mass spectrometry, were available for the analysis of cosmetic ingredients. However, these methods present several limitations, such as failure to perform comprehensive and rapid analysis of the samples. Compared with other techniques, matrix-assisted laser desorption ionization time-of-flight mass spectrometry offered the advantages of wide detection range, fast speed and high accuracy. In this article, we briefly summarized how to select a suitable matrix and adjust the appropriate laser energy. We also discussed the rapid identification of undesired ingredients, focusing on antibiotics and hormones in cosmetics.

A review of rapid and field-portable analytical techniques for the diagnosis of cyanide exposure.

PubMed

Jackson, Randy; Logue, Brian A

2017-04-01

Although commonly known as a highly toxic chemical, cyanide is also an essential reagent for many industrial processes in areas such as mining, electroplating and synthetic fiber production. The "heavy" use of cyanide in these industries, along with its necessary transportation, increases the possibility of human exposure. Another relatively common, but consistently overlooked, mode of cyanide exposure is inhalation of fire smoke. Both civilians and fire rescue personnel risk exposure during the unfortunate event of a structure fire. Additionally, fire rescue personnel risk long-term effects of habitual exposure throughout their careers in fire rescue. The relatively rapid onset of cyanide toxicity and the fact that cyanide exposure symptoms mimic other medical conditions necessitate a rapid, sensitive, portable, and accurate method for the diagnosis of cyanide exposure. This review focuses on the important issues concerning accurate point-of-care diagnosis of cyanide exposure and cyanide detection technologies that may allow a commercial cyanide exposure diagnostic to become a reality. Copyright © 2017 Elsevier B.V. All rights reserved.

Development and validation of a SYBR Green real-time PCR assay for rapid and quantitative detection of goose interferons and proinflammatory cytokines.

PubMed

Zhou, Hao; Chen, Shun; Qi, Yulin; Wang, Mingshu; Jia, Renyong; Zhu, Dekang; Liu, Mafeng; Liu, Fei; Chen, Xiaoyue; Cheng, Anchun

2015-10-01

Real time quantitative polymerase chain reaction (RT-qPCR) based on SYBR-Green I binding is a quick, reliable, and easy method for analyzing small amounts of mRNA. Viral pathogens are recognized at the time of infection by pattern recognition receptors; thus, the inflammatory cytokines (IL1β, IL6, and IL18) and antiviral cytokines (IFNα, IFNγ) are secreted by innate immune cells and induced to respond to the pathogens. The objective of this study was to develop an effective and sensitive RT-qPCR assay for the rapid and accurate quantification of goose cytokines: IFNα, IFNγ, IL1β, IL6, and IL18. Subsequently, the established methods were employed to detect the immune response in agonist-stimulated goose spleen cells in vitro. These data indicated that the established RT-qPCR is a reliable method for determining relative gene expression. The results revealed that Imiquimod led to the significant upregulation of goose IFNα (P < 0.01), IFNγ (P < 0.01), IL1β (P < 0.01), IL6 (P < 0.01), and IL18 (P < 0.05). The established methods are important for scientific research and clinical applications, which require rapid and accurate results in a short period of time. The technique can potentially be used in the further research of goose molecular immunology, which will help us understand the interactions between hosts and pathogens. © 2015 Poultry Science Association Inc.

Accelerated aging: prediction of chemical stability of pharmaceuticals.

PubMed

Waterman, Kenneth C; Adami, Roger C

2005-04-11

Methods of rapidly and accurately assessing the chemical stability of pharmaceutical dosage forms are reviewed with respect to the major degradation mechanisms generally observed in pharmaceutical development. Methods are discussed, with the appropriate caveats, for accelerated aging of liquid and solid dosage forms, including small and large molecule active pharmaceutical ingredients. In particular, this review covers general thermal methods, as well as accelerated aging methods appropriate to oxidation, hydrolysis, reaction with reactive excipient impurities, photolysis and protein denaturation.

A rapid and accurate method, ventilated chamber C-history method, of measuring the emission characteristic parameters of formaldehyde/VOCs in building materials.

PubMed

Huang, Shaodan; Xiong, Jianyin; Zhang, Yinping

2013-10-15

The indoor pollution caused by formaldehyde and volatile organic compounds (VOCs) emitted from building materials poses an adverse effect on people's health. It is necessary to understand and control the behaviors of the emission sources. Based on detailed mass transfer analysis on the emission process in a ventilated chamber, this paper proposes a novel method of measuring the three emission characteristic parameters, i.e., the initial emittable concentration, the diffusion coefficient and the partition coefficient. A linear correlation between the logarithm of dimensionless concentration and time is derived. The three parameters can then be calculated from the intercept and slope of the correlation. Compared with the closed chamber C-history method, the test is performed under ventilated condition thus some commonly-used measurement instruments (e.g., GC/MS, HPLC) can be applied. While compared with other methods, the present method can rapidly and accurately measure the three parameters, with experimental time less than 12h and R(2) ranging from 0.96 to 0.99 for the cases studied. Independent experiment was carried out to validate the developed method, and good agreement was observed between the simulations based on the determined parameters and experiments. The present method should prove useful for quick characterization of formaldehyde/VOC emissions from indoor materials. Copyright © 2013 Elsevier B.V. All rights reserved.

Loop-mediated isothermal amplification (LAMP) method for detection of genetically modified maize T25.

PubMed

Xu, Junyi; Zheng, Qiuyue; Yu, Ling; Liu, Ran; Zhao, Xin; Wang, Gang; Wang, Qinghua; Cao, Jijuan

2013-11-01

The loop-mediated isothermal amplification (LAMP) assay indicates a potential and valuable means for genetically modified organism (GMO) detection especially for its rapidity, simplicity, and low cost. We developed and evaluated the specificity and sensitivity of the LAMP method for rapid detection of the genetically modified (GM) maize T25. A set of six specific primers was successfully designed to recognize six distinct sequences on the target gene, including a pair of inner primers, a pair of outer primers, and a pair of loop primers. The optimum reaction temperature and time were verified to be 65°C and 45 min, respectively. The detection limit of this LAMP assay was 5 g kg(-1) GMO component. Comparative experiments showed that the LAMP assay was a simple, rapid, accurate, and specific method for detecting the GM maize T25.

Loop-mediated isothermal amplification (LAMP) method for detection of genetically modified maize T25

PubMed Central

Xu, Junyi; Zheng, Qiuyue; Yu, Ling; Liu, Ran; Zhao, Xin; Wang, Gang; Wang, Qinghua; Cao, Jijuan

2013-01-01

The loop-mediated isothermal amplification (LAMP) assay indicates a potential and valuable means for genetically modified organism (GMO) detection especially for its rapidity, simplicity, and low cost. We developed and evaluated the specificity and sensitivity of the LAMP method for rapid detection of the genetically modified (GM) maize T25. A set of six specific primers was successfully designed to recognize six distinct sequences on the target gene, including a pair of inner primers, a pair of outer primers, and a pair of loop primers. The optimum reaction temperature and time were verified to be 65°C and 45 min, respectively. The detection limit of this LAMP assay was 5 g kg−1 GMO component. Comparative experiments showed that the LAMP assay was a simple, rapid, accurate, and specific method for detecting the GM maize T25. PMID:24804053

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

EPA Science Inventory

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

Remote-sensing-based rapid assessment of flood crop loss to support USDA flooding decision-making

NASA Astrophysics Data System (ADS)

Di, L.; Yu, G.; Yang, Z.; Hipple, J.; Shrestha, R.

2016-12-01

Floods often cause significant crop loss in the United States. Timely and objective assessment of flood-related crop loss is very important for crop monitoring and risk management in agricultural and disaster-related decision-making in USDA. Among all flood-related information, crop yield loss is particularly important. Decision on proper mitigation, relief, and monetary compensation relies on it. Currently USDA mostly relies on field surveys to obtain crop loss information and compensate farmers' loss claim. Such methods are expensive, labor intensive, and time consumptive, especially for a large flood that affects a large geographic area. Recent studies have demonstrated that Earth observation (EO) data are useful in post-flood crop loss assessment for a large geographic area objectively, timely, accurately, and cost effectively. There are three stages of flood damage assessment, including rapid assessment, early recovery assessment, and in-depth assessment. EO-based flood assessment methods currently rely on the time-series of vegetation index to assess the yield loss. Such methods are suitable for in-depth assessment but are less suitable for rapid assessment since the after-flood vegetation index time series is not available. This presentation presents a new EO-based method for the rapid assessment of crop yield loss immediately after a flood event to support the USDA flood decision making. The method is based on the historic records of flood severity, flood duration, flood date, crop type, EO-based both before- and immediate-after-flood crop conditions, and corresponding crop yield loss. It hypotheses that a flood of same severity occurring at the same pheonological stage of a crop will cause the similar damage to the crop yield regardless the flood years. With this hypothesis, a regression-based rapid assessment algorithm can be developed by learning from historic records of flood events and corresponding crop yield loss. In this study, historic records of MODIS-based flood and vegetation products and USDA/NASS crop type and crop yield data are used to train the regression-based rapid assessment algorithm. Validation of the rapid assessment algorithm indicates it can predict the yield loss at 90% accuracy, which is accurate enough to support USDA on flood-related quick response and mitigation.

Rapid Measurement of Tectonic Deformation Using Structure-from-Motion

NASA Astrophysics Data System (ADS)

Pickering, A.; DeLong, S.; Lienkaemper, J. J.; Hecker, S.; Prentice, C. S.; Schwartz, D. P.; Sickler, R. R.

2016-12-01

Rapid collection and distribution of accurate surface slip data after earthquakes can support emergency response, help coordinate scientific response, and constrain coseismic slip that can be rapidly overprinted by postseismic slip, or eliminated as evidence of surface deformation is repaired or obscured. Analysis of earthquake deformation can be achieved quickly, repeatedly and inexpensively with the use of Structure-from-Motion (SfM) photogrammetry. Traditional methods of measuring surface slip (e.g. manual measurement with tape measures) have proven inconsistent and irreproducible, and sophisticated methods such as laser scanning require specialized equipment and longer field time. Here we present a simple, cost-effective workflow for rapid, three-dimensional imaging and measurement of features affected by earthquake rupture. As part of a response drill performed by the USGS and collaborators on May 11, 2016, geologists documented offset cultural features along the creeping Hayward Fault in northern California, in simulation of a surface-rupturing earthquake. We present several photo collections from smart phones, tablets, and DSLR cameras from a number of locations along the fault collected by users with a range of experience. Using professionally calibrated photogrammetric scale bars we automatically and accurately scale our 3D models to 1 mm accuracy for precise measurement in three dimensions. We then generate scaled 3D point clouds and extract offsets from manual measurement and multiple linear regression for comparison with collected terrestrial scanner data. These results further establish dense photo collection and SfM processing as an important, low-cost, rapid means of quantifying surface deformation in the critical hours after a surface-rupturing earthquake and emphasize that researchers with minimal training can rapidly collect three-dimensional data that can be used to analyze and archive the surface effects of damaging earthquakes.

Value and Methods for Molecular Subtyping of Bacteria

NASA Astrophysics Data System (ADS)

Moorman, Mark; Pruett, Payton; Weidman, Martin

Tracking sources of microbial contaminants has been a concern since the early days of commercial food processing; however, recent advances in the development of molecular subtyping methods have provided tools that allow more rapid and highly accurate determinations of these sources. Only individuals with an understanding of the molecular subtyping methods, and the epidemiological techniques used, can evaluate the reliability of a link between a food-manufacturing plant, a food, and a foodborne disease outbreak.

Automated seamline detection along skeleton for remote sensing image mosaicking

NASA Astrophysics Data System (ADS)

Zhang, Hansong; Chen, Jianyu; Liu, Xin

2015-08-01

The automatic generation of seamline along the overlap region skeleton is a concerning problem for the mosaicking of Remote Sensing(RS) images. Along with the improvement of RS image resolution, it is necessary to ensure rapid and accurate processing under complex conditions. So an automated seamline detection method for RS image mosaicking based on image object and overlap region contour contraction is introduced. By this means we can ensure universality and efficiency of mosaicking. The experiments also show that this method can select seamline of RS images with great speed and high accuracy over arbitrary overlap regions, and realize RS image rapid mosaicking in surveying and mapping production.

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

NASA Astrophysics Data System (ADS)

Greenwood, Jeremy R.; Calkins, David; Sullivan, Arron P.; Shelley, John C.

2010-06-01

Generating the appropriate protonation states of drug-like molecules in solution is important for success in both ligand- and structure-based virtual screening. Screening collections of millions of compounds requires a method for determining tautomers and their energies that is sufficiently rapid, accurate, and comprehensive. To maximise enrichment, the lowest energy tautomers must be determined from heterogeneous input, without over-enumerating unfavourable states. While computationally expensive, the density functional theory (DFT) method M06-2X/aug-cc-pVTZ(-f) [PB-SCRF] provides accurate energies for enumerated model tautomeric systems. The empirical Hammett-Taft methodology can very rapidly extrapolate substituent effects from model systems to drug-like molecules via the relationship between pKT and pKa. Combining the two complementary approaches transforms the tautomer problem from a scientific challenge to one of engineering scale-up, and avoids issues that arise due to the very limited number of measured pKT values, especially for the complicated heterocycles often favoured by medicinal chemists for their novelty and versatility. Several hundreds of pre-calculated tautomer energies and substituent pKa effects are tabulated in databases for use in structural adjustment by the program Epik, which treats tautomers as a subset of the larger problem of the protonation states in aqueous ensembles and their energy penalties. Accuracy and coverage is continually improved and expanded by parameterizing new systems of interest using DFT and experimental data. Recommendations are made for how to best incorporate tautomers in molecular design and virtual screening workflows.

Rapid and efficient differentiation of Yersinia species using high-resolution melting analysis.

PubMed

Souza, Roberto A; Frazão, Miliane R; Almeida, Alzira M P; Falcão, Juliana P

2015-08-01

The primary goal of clinical microbiology is the accurate identification of the causative agent of the disease. Here, we describe a method for differentiation between Yersinia species using PCR-HRMA. The results revealed species-specific melting profiles. The herein developed assay can be used as an effective method to differentiate Yersinia species. Copyright © 2015 Elsevier B.V. All rights reserved.

Conventional and improved cytotoxicity test methods of newly developed biodegradable magnesium alloys

NASA Astrophysics Data System (ADS)

Han, Hyung-Seop; Kim, Hee-Kyoung; Kim, Yu-Chan; Seok, Hyun-Kwang; Kim, Young-Yul

2015-11-01

Unique biodegradable property of magnesium has spawned countless studies to develop ideal biodegradable orthopedic implant materials in the last decade. However, due to the rapid pH change and extensive amount of hydrogen gas generated during biocorrosion, it is extremely difficult to determine the accurate cytotoxicity of newly developed magnesium alloys using the existing methods. Herein, we report a new method to accurately determine the cytotoxicity of magnesium alloys with varying corrosion rate while taking in-vivo condition into the consideration. For conventional method, extract quantities of each metal ion were determined using ICP-MS and the result showed that the cytotoxicity due to pH change caused by corrosion affected the cell viability rather than the intrinsic cytotoxicity of magnesium alloy. In physiological environment, pH is regulated and adjusted within normal pH (˜7.4) range by homeostasis. Two new methods using pH buffered extracts were proposed and performed to show that environmental buffering effect of pH, dilution of the extract, and the regulation of eluate surface area must be taken into consideration for accurate cytotoxicity measurement of biodegradable magnesium alloys.

Multifunctional Collaborative Modeling and Analysis Methods in Engineering Science

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.; Broduer, Steve (Technical Monitor)

2001-01-01

Engineers are challenged to produce better designs in less time and for less cost. Hence, to investigate novel and revolutionary design concepts, accurate, high-fidelity results must be assimilated rapidly into the design, analysis, and simulation process. This assimilation should consider diverse mathematical modeling and multi-discipline interactions necessitated by concepts exploiting advanced materials and structures. Integrated high-fidelity methods with diverse engineering applications provide the enabling technologies to assimilate these high-fidelity, multi-disciplinary results rapidly at an early stage in the design. These integrated methods must be multifunctional, collaborative, and applicable to the general field of engineering science and mechanics. Multifunctional methodologies and analysis procedures are formulated for interfacing diverse subdomain idealizations including multi-fidelity modeling methods and multi-discipline analysis methods. These methods, based on the method of weighted residuals, ensure accurate compatibility of primary and secondary variables across the subdomain interfaces. Methods are developed using diverse mathematical modeling (i.e., finite difference and finite element methods) and multi-fidelity modeling among the subdomains. Several benchmark scalar-field and vector-field problems in engineering science are presented with extensions to multidisciplinary problems. Results for all problems presented are in overall good agreement with the exact analytical solution or the reference numerical solution. Based on the results, the integrated modeling approach using the finite element method for multi-fidelity discretization among the subdomains is identified as most robust. The multiple-method approach is advantageous when interfacing diverse disciplines in which each of the method's strengths are utilized. The multifunctional methodology presented provides an effective mechanism by which domains with diverse idealizations are interfaced. This capability rapidly provides the high-fidelity results needed in the early design phase. Moreover, the capability is applicable to the general field of engineering science and mechanics. Hence, it provides a collaborative capability that accounts for interactions among engineering analysis methods.

Rapid Model Fabrication and Testing for Aerospace Vehicles

NASA Technical Reports Server (NTRS)

Buck, Gregory M.

2000-01-01

Advanced methods for rapid fabrication and instrumentation of hypersonic wind tunnel models are being developed and evaluated at NASA Langley Research Center. Rapid aeroheating model fabrication and measurement techniques using investment casting of ceramic test models and thermographic phosphors are reviewed. More accurate model casting techniques for fabrication of benchmark metal and ceramic test models are being developed using a combination of rapid prototype patterns and investment casting. White light optical scanning is used for coordinate measurements to evaluate the fabrication process and verify model accuracy to +/- 0.002 inches. Higher-temperature (<210C) luminescent coatings are also being developed for simultaneous pressure and temperature mapping, providing global pressure as well as global aeroheating measurements. Together these techniques will provide a more rapid and complete experimental aerodynamic and aerothermodynamic database for future aerospace vehicles.

Agreement between a Brief Autism Observational Instrument and Established ASD Measures

ERIC Educational Resources Information Center

Ward, Samantha L.; Sullivan, Karen A.; Gilmore, Linda

2016-01-01

Objective: Limited time and resources necessitate the availability of accurate, inexpensive and rapid diagnostic aids for Autism Spectrum Disorder (ASD). The Autistic Behavioural Indicators Instrument (ABII) was developed for this purpose, but its psychometric properties have not yet been fully established. Method: The clinician-rated ABII, the…

Volumetric determination of uranium titanous sulfate as reductant before oxidimetric titration

USGS Publications Warehouse

Wahlberg, J.S.; Skinner, D.L.; Rader, L.F.

1957-01-01

Need for a more rapid volumetric method for the routine determination of uranium in uranium-rich materials has led to the development of a method that uses titanous sulfate as a reductant before oxidimetric titration. Separation of the hydrogen sulfide group is not necessary. Interfering elements precipitated by cupferron are removed by automatic filtrations made simultaneously rather than by the longer chloroform extraction method. Uranium is reduced from VI to IV by addition of an excess of titanous sulfate solution, cupric ion serving as an indicator by forming red metallic copper when reduction is complete. The copper is reoxidized by addition of mercuric perchlorate. The reduced uranium is then determined by addition of excess ferric sulfate and titration with ceric sulfate. The method has proved to be rapid, accurate, and economical.

Rapid prediction of particulate, humus and resistant fractions of soil organic carbon in reforested lands using infrared spectroscopy.

PubMed

Madhavan, Dinesh B; Baldock, Jeff A; Read, Zoe J; Murphy, Simon C; Cunningham, Shaun C; Perring, Michael P; Herrmann, Tim; Lewis, Tom; Cavagnaro, Timothy R; England, Jacqueline R; Paul, Keryn I; Weston, Christopher J; Baker, Thomas G

2017-05-15

Reforestation of agricultural lands with mixed-species environmental plantings can effectively sequester C. While accurate and efficient methods for predicting soil organic C content and composition have recently been developed for soils under agricultural land uses, such methods under forested land uses are currently lacking. This study aimed to develop a method using infrared spectroscopy for accurately predicting total organic C (TOC) and its fractions (particulate, POC; humus, HOC; and resistant, ROC organic C) in soils under environmental plantings. Soils were collected from 117 paired agricultural-reforestation sites across Australia. TOC fractions were determined in a subset of 38 reforested soils using physical fractionation by automated wet-sieving and 13 C nuclear magnetic resonance (NMR) spectroscopy. Mid- and near-infrared spectra (MNIRS, 6000-450 cm -1 ) were acquired from finely-ground soils from environmental plantings and agricultural land. Satisfactory prediction models based on MNIRS and partial least squares regression (PLSR) were developed for TOC and its fractions. Leave-one-out cross-validations of MNIRS-PLSR models indicated accurate predictions (R 2  > 0.90, negligible bias, ratio of performance to deviation > 3) and fraction-specific functional group contributions to beta coefficients in the models. TOC and its fractions were predicted using the cross-validated models and soil spectra for 3109 reforested and agricultural soils. The reliability of predictions determined using k-nearest neighbour score distance indicated that >80% of predictions were within the satisfactory inlier limit. The study demonstrated the utility of infrared spectroscopy (MNIRS-PLSR) to rapidly and economically determine TOC and its fractions and thereby accurately describe the effects of land use change such as reforestation on agricultural soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi.

PubMed

McMullen, Allison R; Wallace, Meghan A; Pincus, David H; Wilkey, Kathy; Burnham, C A

2016-08-01

Invasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (including Aspergillus amoenus [n = 2] and Aspergillus calidoustus [n = 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%) Aspergillus sp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

[Rapid determination of volatile organic compounds in workplace air by protable gas chromatography-mass spectrometer].

PubMed

Zhu, H B; Su, C J; Tang, H F; Ruan, Z; Liu, D H; Wang, H; Qian, Y L

2017-10-20

Objective: To establish a method for rapid determination of 47 volatile organic compounds in the air of workplace using portable gas chromatography - mass spectrometer(GC - MS). Methods: The mixed standard gas with different concentration levels was made by using the static gas distribution method with the high purity nitrogen as dilution gas. The samples were injected into the GC - MS by a hand - held probe. Retention time and characteristic ion were used for qualitative analysis,and the internal standard method was usd for quantitation. Results: The 47 poisonous substances were separated and determined well. The linear range of this method was 0.2 - 16.0 mg/m(3),and the relative standard deviation of 45 volatile ovganic compounds was 3.8% - 15.8%. The average recovery was 79.3% - 119.0%. Conclusion: The method is simple,accurate,sensitive,has good separation effect,short analysis period, can be used for qualitative and quantitative analysis of volatile organic compounds in the workplace, and also supports the rapid identification and detection of occupational hazards.

Rapid identification of pathogenic streptococci isolated from moribund red tilapia (Oreochromis spp.).

PubMed

Abdelsalam, Mohamed; Elgendy, Mamdouh Y; Shaalan, Mohamed; Moustafa, Mohamed; Fujino, Masayuki

2017-03-01

Accurate and rapid identification of bacterial pathogens of fish is essential for the effective treatment and speedy control of infections. Massive mortalities in market-sized red tilapia (Oreochromis spp.) were noticed in mariculture concrete ponds in northern Egypt. Histopathological examination revealed marked congestion in the central vein of the liver with the presence of bacterial aggregates inside the lumen and in the vicinity of the central vein. A total of 12 isolates of streptococci were obtained from the moribund fish. This study documented the ability of the MicroSeq 500 16S bacterial sequencing method to accurately identify Streptococcus agalactiae and S. dysgalactiae mixed infections from moribund red tilapia that were difficult to be recognised by the commercial biochemical systems. The continuously decreasing cost of the sequencing technique should encourage its application in routine diagnostic procedures.

Analysis of loxoprofen in tablets, patches, and equine urine as tert-butyldimethylsilyl derivative by gas chromatography-mass spectrometry.

PubMed

Kim, Youngbae; Seo, Chan; Oh, Suin; Kwak, Juhwan; Jung, Sumin; Sin, Eunsu; Kim, Hyunbin; Ji, Moongi; Lee, Hyeon-Seong; Park, Hyung-Jin; Lee, Gwang; Yu, Jundong; Kim, Minsoo; Lee, Wonjae; Paik, Man-Jeong

2018-04-01

Loxoprofen is a non-steroidal anti-inflammatory drug of the 2-arylpropionic acid type, which has used to treat musculoskeletal disorders in the horse racing industry. However, it has also used illicitly to mask clinical signs of inflammation and pain in racehorses. Thus, its accurate analysis has become an important issue in horse doping laboratories. In this study, an analytical method of loxoprofen was developed as tert-butyldimethylsilyl (TBDMS) derivative by gas chromatography-mass spectrometry (GC-MS). Characteristic fragment ions of [M-15], [M-57], and [M-139] permitted the accurate and selective detection of loxoprofen. Under optimal conditions, this method showed good linearity (r ≥ 0.999) in the range of 10-500 ng/mL, repeatability (% relative standard deviation = 5.6-8.5), and accuracy (% relative error = - 0.3-0.9) with a detection limit of 1.0 ng. When applied to the analysis of loxoprofen in tablet and patch products, loxoprofen was positively identified as TBDMS derivative by GC-MS. The present method provided rapid and accurate determination of loxoprofen in patch and tablet products. Levels of loxoprofen were highest in equine urine at 0.5 and 1 h after oral administration with single dose (3 mg/kg) to three horses, and then rapidly reduced to below the lower limit of quantification at 24 h. Therefore, the present method will be useful for the pharmacokinetic study and doping tests for loxoprofen and other similar acidic drugs in horses.

RapGene: a fast and accurate strategy for synthetic gene assembly in Escherichia coli

PubMed Central

Zampini, Massimiliano; Stevens, Pauline Rees; Pachebat, Justin A.; Kingston-Smith, Alison; Mur, Luis A. J.; Hayes, Finbarr

2015-01-01

The ability to assemble DNA sequences de novo through efficient and powerful DNA fabrication methods is one of the foundational technologies of synthetic biology. Gene synthesis, in particular, has been considered the main driver for the emergence of this new scientific discipline. Here we describe RapGene, a rapid gene assembly technique which was successfully tested for the synthesis and cloning of both prokaryotic and eukaryotic genes through a ligation independent approach. The method developed in this study is a complete bacterial gene synthesis platform for the quick, accurate and cost effective fabrication and cloning of gene-length sequences that employ the widely used host Escherichia coli. PMID:26062748

PCR-based Methodologies Used to Detect and Differentiate the Burkholderia pseudomallei complex: B. pseudomallei, B. mallei, and B. thailandensis.

PubMed

Lowe, Woan; March, Jordon K; Bunnell, Annette J; O'Neill, Kim L; Robison, Richard A

2014-01-01

Methods for the rapid detection and differentiation of the Burkholderia pseudomallei complex comprising B. pseudomallei, B. mallei, and B. thailandensis, have been the topic of recent research due to the high degree of phenotypic and genotypic similarities of these species. B. pseudomallei and B. mallei are recognized by the CDC as tier 1 select agents. The high mortality rates of glanders and melioidosis, their potential use as bioweapons, and their low infectious dose, necessitate the need for rapid and accurate detection methods. Although B. thailandensis is generally avirulent in mammals, this species displays very similar phenotypic characteristics to that of B. pseudomallei. Optimal identification of these species remains problematic, due to the difficulty in developing a sensitive, selective, and accurate assay. The development of PCR technologies has revolutionized diagnostic testing and these detection methods have become popular due to their speed, sensitivity, and accuracy. The purpose of this review is to provide a comprehensive overview and evaluation of the advancements in PCR-based detection and differentiation methodologies for the B. pseudomallei complex, and examine their potential uses in diagnostic and environmental testing.

Advances in thickness measurements and dynamic visualization of the tear film using non-invasive optical approaches.

PubMed

Bai, Yuqiang; Nichols, Jason J

2017-05-01

The thickness of tear film has been investigated under both invasive and non-invasive methods. While invasive methods are largely historical, more recent noninvasive methods are generally based on optical approaches that provide accurate, precise, and rapid measures. Optical microscopy, interferometry, and optical coherence tomography (OCT) have been developed to characterize the thickness of tear film or certain aspects of the tear film (e.g., the lipid layer). This review provides an in-depth overview on contemporary optical techniques used in studying the tear film, including both advantages and limitations of these approaches. It is anticipated that further developments of high-resolution OCT and other interferometric methods will enable a more accurate and precise measurement of the thickness of the tear film and its related dynamic properties. Copyright © 2017 Elsevier Ltd. All rights reserved.

Alkaloid profiling of the traditional Chinese medicine Rhizoma corydalis using high performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry

PubMed Central

Sun, Mingqian; Liu, Jianxun; Lin, Chengren; Miao, Lan; Lin, Li

2014-01-01

Since alkaloids are the major active constituents of Rhizoma corydalis (RC), a convenient and accurate analytical method is needed for their identification and characterization. Here we report a method to profile the alkaloids in RC based on liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (LC–Q-TOF-MS/MS). A total of 16 alkaloids belonging to four different classes were identified by comparison with authentic standards. The fragmentation pathway of each class of alkaloid was clarified and their differences were elucidated. Furthermore, based on an analysis of fragmentation pathways and alkaloid profiling, a rapid and accurate method for the identification of unknown alkaloids in RC is proposed. The method could also be useful for the quality control of RC. PMID:26579385

A suite of microplate reader-based colorimetric methods to quantify ammonium, nitrate, orthophosphate and silicate concentrations for aquatic nutrient monitoring.

PubMed

Ringuet, Stephanie; Sassano, Lara; Johnson, Zackary I

2011-02-01

A sensitive, accurate and rapid analysis of major nutrients in aquatic systems is essential for monitoring and maintaining healthy aquatic environments. In particular, monitoring ammonium (NH(4)(+)) concentrations is necessary for maintenance of many fish stocks, while accurate monitoring and regulation of ammonium, orthophosphate (PO(4)(3-)), silicate (Si(OH)(4)) and nitrate (NO(3)(-)) concentrations are required for regulating algae production. Monitoring of wastewater streams is also required for many aquaculture, municipal and industrial wastewater facilities to comply with local, state or federal water quality effluent regulations. Traditional methods for quantifying these nutrient concentrations often require laborious techniques or expensive specialized equipment making these analyses difficult. Here we present four alternative microcolorimetric assays that are based on a standard 96-well microplate format and microplate reader that simplify the quantification of each of these nutrients. Each method uses small sample volumes (200 µL), has a detection limit ≤ 1 µM in freshwater and ≤ 2 µM in saltwater, precision of at least 8% and compares favorably with standard analytical procedures. Routine use of these techniques in the laboratory and at an aquaculture facility to monitor nutrient concentrations associated with microalgae growth demonstrates that they are rapid, accurate and highly reproducible among different users. These techniques offer an alternative to standard nutrient analyses and because they are based on the standard 96-well format, they significantly decrease the cost and time of processing while maintaining high precision and sensitivity.

Spectrophotometric simultaneous determination of Rabeprazole Sodium and Itopride Hydrochloride in capsule dosage form

NASA Astrophysics Data System (ADS)

Sabnis, Shweta S.; Dhavale, Nilesh D.; Jadhav, Vijay. Y.; Gandhi, Santosh V.

2008-03-01

A new simple, economical, rapid, precise and accurate method for simultaneous determination of rabeprazole sodium and itopride hydrochloride in capsule dosage form has been developed. The method is based on ratio spectra derivative spectrophotometry. The amplitudes in the first derivative of the corresponding ratio spectra at 231 nm (minima) and 260 nm were selected to determine rabeprazole sodium and itopride hydrochloride, respectively. The method was validated with respect to linearity, precision and accuracy.

Spectrophotometric simultaneous determination of rabeprazole sodium and itopride hydrochloride in capsule dosage form.

PubMed

Sabnis, Shweta S; Dhavale, Nilesh D; Jadhav, Vijay Y; Gandhi, Santosh V

2008-03-01

A new simple, economical, rapid, precise and accurate method for simultaneous determination of rabeprazole sodium and itopride hydrochloride in capsule dosage form has been developed. The method is based on ratio spectra derivative spectrophotometry. The amplitudes in the first derivative of the corresponding ratio spectra at 231nm (minima) and 260nm were selected to determine rabeprazole sodium and itopride hydrochloride, respectively. The method was validated with respect to linearity, precision and accuracy.

Development of a simple chromatographic method for the determination of piracetam in human plasma and its pharmacokinetic evaluation.

PubMed

Barkat, K; Ahmad, M; Minhas, M U; Malik, M Z; Sohail, M

2014-07-01

The objective of study was to develop an accurate and reproducible HPLC method for determination of piracetam in human plasma and to evaluate pharmacokinetic parameters of 800 mg piracetam. A simple, rapid, accurate, precise and sensitive high pressure liquid chromatography method has been developed and subsequently validated for determination of piracetam. This study represents the results of a randomized, single-dose and single-period in 18 healthy male volunteers to assess pharmacokinetic parameters of 800 mg piracetam tablets. Various pharmacokinetic parameters were determined from plasma for piracetam and found to be in good agreement with previous reported values. The data was analyzed by using Kinetica® version 4.4 according to non-compartment model of pharmacokinetic analysis and after comparison with previous studies, no significant differences were found in present study of tested product. The major pharmacokinetic parameters for piracetam were as follows: t1/2 was (4.40 ± 0.179) h; Tmax value was (2.33 ± 0.105) h; Cmax was (14.53 ± 0.282) µg/mL; the AUC(0-∞) was (59.19 ± 4.402) µg · h/mL. AUMC(0-∞) was (367.23 ± 38.96) µg. (h)(2)/mL; Ke was (0.16 ± 0.006) h; MRT was (5.80 ± 0.227) h; Vd was (96.36 ± 8.917 L). A rapid, accurate and precise high pressure liquid chromatography method was developed and validated before the study. It is concluded that this method is very useful for the analysis of pharmacokinetic parameters, in human plasma and assured the safety and efficacy of piracetam, can be effectively used in medical practice. © Georg Thieme Verlag KG Stuttgart · New York.

RATT: Rapid Annotation Transfer Tool

PubMed Central

Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.; Berriman, Matthew

2011-01-01

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net. PMID:21306991

Rapid lysostaphin test to differentiate Staphylococcus and Micrococcus species.

PubMed Central

Geary, C; Stevens, M

1986-01-01

A rapid, simple lysostaphin lysis susceptibility test to differentiate the genera Staphylococcus and Micrococcus was evaluated. Of 181 strains from culture collections, 95 of 95 Staphylococcus strains were lysed, and 79 of 79 Micrococcus strains were not lysed. The seven Planococcus strains were resistant. Clinical isolates (890) were tested with lysostaphin and for the ability to produce acid from glycerol in the presence of erythromycin. Overall agreement between the methods was 99.2%. All clinical Micrococcus strains (43) were resistant to lysostaphin, and all clinical Staphylococcus strains (847) were susceptible. Seven of the Staphylococcus strains did not produce acid from glycerol in the presence of erythromycin. This lysostaphin test provides results in 2 h. It is easier to perform than previously described lysostaphin lysis methods. It is also more rapid and accurate than the glycerol-erythromycin test. PMID:3519667

Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions

NASA Astrophysics Data System (ADS)

Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

2016-11-01

Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

Selection of actuator locations for static shape control of large space structures by heuristic integer programing

NASA Technical Reports Server (NTRS)

Haftka, R. T.; Adelman, H. M.

1984-01-01

Orbiting spacecraft such as large space antennas have to maintain a highly accurate space to operate satisfactorily. Such structures require active and passive controls to mantain an accurate shape under a variety of disturbances. Methods for the optimum placement of control actuators for correcting static deformations are described. In particular, attention is focused on the case were control locations have to be selected from a large set of available sites, so that integer programing methods are called for. The effectiveness of three heuristic techniques for obtaining a near-optimal site selection is compared. In addition, efficient reanalysis techniques for the rapid assessment of control effectiveness are presented. Two examples are used to demonstrate the methods: a simple beam structure and a 55m space-truss-parabolic antenna.

On-line identification of lysergic acid diethylamide (LSD) in tablets using a combination of a sweeping technique and micellar electrokinetic chromatography/77 K fluorescence spectroscopy.

PubMed

Fang, Ching; Liu, Ju-Tsung; Lin, Cheng-Huang

2003-03-01

This work describes a novel method for the accurate determination of lysergic acid diethylamide (LSD) in tablets. A technique involving sweeping-micellar electrokinetic chromatography (MEKC) was used for the initial on-line concentration and separation, after which a cryogenic molecular fluorescence experiment was performed at 77 K. Using this approach, not only the separation of LSD from the tablet extract was achieved, but on-line spectra were readily distinguishable and could be unambiguously assigned. The results are in agreement with analyses by gas chromatography-mass spectrometry (GC-MS). Thus, this method, which was found to be accurate, sensitive and rapid, has the potential for use as a reliable complementary method to GC-MS in such analyses.

Extraction and Analysis of Traditional Chinese Medicine Crops Based on Multitemporal High Resolution Data-Taking Qiaocheng District of Bozhou as AN Example

NASA Astrophysics Data System (ADS)

Yu, H.; He, J.; Zhou, H.; Guan, F.; Li, L.; Ren, B.; Wang, Z.

2018-04-01

Remote sensing technology has become an important method to rapidly acquireing of planting layout and composition of regional crops.It is very important to accurately master the planting area of Chinese medicine crops in the Characteristic planting area because it relations to accurately master the cultivation of Chinese medicine crops, formulate related policies and adjustment of crop planting structure.The author puts forward a method of using remote sencing technology for momitoring Chinese medicine which has good applicability and generalization. This paper took Qiaocheng District of Bozhou as an example to Verify the feasibility of the method, providing a reference for solving the problem of interpretation and extraction of Chinese medicinal materials in the region.

Development of rapid phenotypic system for the identification of Gram-negative oxidase-positive bacilli in resource-limited settings.

PubMed

Kazmi, Mahmooda; Khan, Adnan; Kazmi, Shahana Urooj

2013-06-01

Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology. The diagnosis and surveillance of diseases is dependent, to a great extent, on laboratory services, which cannot function without effective reliable reagents and diagnostics. Despite the advancement in microbiology diagnosis globally, resourcelimited countries still struggle to provide an acceptable diagnosis quality which helps in clinical disease management and improve their mortality and morbidity data. During this study an indigenous product, Quick Test Strip (QTS) NE, was developed for the rapid identification of biochemically slower group of Gram-negative oxidase-positive bacilli that covers 19 different bacterial genera. Some of the members belonging to these groups are well-established human pathogens, e.g. various species of Vibrio, Pseudomonas, Burkholderia, Aeromonas, Achromobacter and Stenotrophomonas. This study also evaluates the performance of QTS-NE by comparing with genotypic characterization methods. A total of 232 clinical and reference bacterial isolates were tested by three different methods. QTSNE provides 100 percent concordant results with other rapid identification and molecular characterization methods and confirms the potential to be used in clinical diagnosis.

Rapid molecular diagnostics for multi-drug resistant tuberculosis in India.

PubMed

Ramachandran, Rajeswari; Muniyandi, M

2018-03-01

Rapid molecular diagnostic methods help in the detection of TB and Rifampicin resistance. These methods detect TB early, are accurate and play a crucial role in reducing the burden of drug resistant tuberculosis. Areas covered: This review analyses rapid molecular diagnostic tools used in the diagnosis of MDR-TB in India, such as the Line Probe Assay and GeneXpert. We have discussed the burden of MDR-TB and the impact of recent diagnostic tools on case detection and treatment outcomes. This review also discusses the costs involved in establishing these new techniques in India. Expert commentary: Molecular methods have considerable advantages for the programmatic management of drug resistant TB. These include speed, standardization of testing, potentially high throughput and reduced laboratory biosafety requirements. There is a desperate need for India to adopt modern, rapid, molecular tools with point-of-care tests being currently evaluated. New molecular diagnostic tests appear to be cost effective and also help in detecting missing cases. There is enough evidence to support the scaling up of these new tools in India.

Substoichiometric radiochemical determination of silver with potassium ethyl xanthate in photofilm washings.

PubMed

Reddy, P C; Rangamannar, B

1990-05-01

An accurate and rapid radiochemical method has been developed for the determination of microgram amount of silver employing potassium ethyl xanthate as a substoichiometric radiochemical reagent. The light yellow coloured silver ethyl xanthate formed was extracted into nitrobenzene from sulphuric acid media. The effect of foreign ions on the extraction was studied. The method was applied to the determination of silver content in photofilm washings.

Rapid detection of potyviruses from crude plant extracts.

PubMed

Silva, Gonçalo; Oyekanmi, Joshua; Nkere, Chukwuemeka K; Bömer, Moritz; Kumar, P Lava; Seal, Susan E

2018-04-01

Potyviruses (genus Potyvirus; family Potyviridae) are widely distributed and represent one of the most economically important genera of plant viruses. Therefore, their accurate detection is a key factor in developing efficient control strategies. However, this can sometimes be problematic particularly in plant species containing high amounts of polysaccharides and polyphenols such as yam (Dioscorea spp.). Here, we report the development of a reliable, rapid and cost-effective detection method for the two most important potyviruses infecting yam based on reverse transcription-recombinase polymerase amplification (RT-RPA). The developed method, named 'Direct RT-RPA', detects each target virus directly from plant leaf extracts prepared with a simple and inexpensive extraction method avoiding laborious extraction of high-quality RNA. Direct RT-RPA enables the detection of virus-positive samples in under 30 min at a single low operation temperature (37 °C) without the need for any expensive instrumentation. The Direct RT-RPA tests constitute robust, accurate, sensitive and quick methods for detection of potyviruses from recalcitrant plant species. The minimal sample preparation requirements and the possibility of storing RPA reagents without cold chain storage, allow Direct RT-RPA to be adopted in minimally equipped laboratories and with potential use in plant clinic laboratories and seed certification facilities worldwide. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Rapid analysis of scattering from periodic dielectric structures using accelerated Cartesian expansions.

PubMed

Baczewski, Andrew D; Miller, Nicholas C; Shanker, Balasubramaniam

2012-04-01

The analysis of fields in periodic dielectric structures arise in numerous applications of recent interest, ranging from photonic bandgap structures and plasmonically active nanostructures to metamaterials. To achieve an accurate representation of the fields in these structures using numerical methods, dense spatial discretization is required. This, in turn, affects the cost of analysis, particularly for integral-equation-based methods, for which traditional iterative methods require O(N2) operations, N being the number of spatial degrees of freedom. In this paper, we introduce a method for the rapid solution of volumetric electric field integral equations used in the analysis of doubly periodic dielectric structures. The crux of our method is the accelerated Cartesian expansion algorithm, which is used to evaluate the requisite potentials in O(N) cost. Results are provided that corroborate our claims of acceleration without compromising accuracy, as well as the application of our method to a number of compelling photonics applications.

Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis

NASA Astrophysics Data System (ADS)

Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

2017-08-01

In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH4+ strategy for ethylene and SO2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO2 from fruits. It was satisfied that trace ethylene and SO2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO2 during the entire LVCC sampling process were proved to be < 4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS.

Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis.

PubMed

Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

2017-08-05

In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH 4 + strategy for ethylene and SO 2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO 2 from fruits. It was satisfied that trace ethylene and SO 2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO 2 during the entire LVCC sampling process were proved to be <4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid perfusion quantification using Welch-Satterthwaite approximation and analytical spectral filtering

NASA Astrophysics Data System (ADS)

Krishnan, Karthik; Reddy, Kasireddy V.; Ajani, Bhavya; Yalavarthy, Phaneendra K.

2017-02-01

CT and MR perfusion weighted imaging (PWI) enable quantification of perfusion parameters in stroke studies. These parameters are calculated from the residual impulse response function (IRF) based on a physiological model for tissue perfusion. The standard approach for estimating the IRF is deconvolution using oscillatory-limited singular value decomposition (oSVD) or Frequency Domain Deconvolution (FDD). FDD is widely recognized as the fastest approach currently available for deconvolution of CT Perfusion/MR PWI. In this work, three faster methods are proposed. The first is a direct (model based) crude approximation to the final perfusion quantities (Blood flow, Blood volume, Mean Transit Time and Delay) using the Welch-Satterthwaite approximation for gamma fitted concentration time curves (CTC). The second method is a fast accurate deconvolution method, we call Analytical Fourier Filtering (AFF). The third is another fast accurate deconvolution technique using Showalter's method, we call Analytical Showalter's Spectral Filtering (ASSF). Through systematic evaluation on phantom and clinical data, the proposed methods are shown to be computationally more than twice as fast as FDD. The two deconvolution based methods, AFF and ASSF, are also shown to be quantitatively accurate compared to FDD and oSVD.

[Prediction of the side-cut product yield of atmospheric/vacuum distillation unit by NIR crude oil rapid assay].

PubMed

Wang, Yan-Bin; Hu, Yu-Zhong; Li, Wen-Le; Zhang, Wei-Song; Zhou, Feng; Luo, Zhi

2014-10-01

In the present paper, based on the fast evaluation technique of near infrared, a method to predict the yield of atmos- pheric and vacuum line was developed, combined with H/CAMS software. Firstly, the near-infrared (NIR) spectroscopy method for rapidly determining the true boiling point of crude oil was developed. With commercially available crude oil spectroscopy da- tabase and experiments test from Guangxi Petrochemical Company, calibration model was established and a topological method was used as the calibration. The model can be employed to predict the true boiling point of crude oil. Secondly, the true boiling point based on NIR rapid assay was converted to the side-cut product yield of atmospheric/vacuum distillation unit by H/CAMS software. The predicted yield and the actual yield of distillation product for naphtha, diesel, wax and residual oil were compared in a 7-month period. The result showed that the NIR rapid crude assay can predict the side-cut product yield accurately. The near infrared analytic method for predicting yield has the advantages of fast analysis, reliable results, and being easy to online operate, and it can provide elementary data for refinery planning optimization and crude oil blending.

Measuring micro-organism gas production

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Pearson, A. O.; Mills, S. M.

1973-01-01

Transducer, which senses pressure buildup, is easy to assemble and use, and rate of gas produced can be measured automatically and accurately. Method can be used in research, in clinical laboratories, and for environmental pollution studies because of its ability to detect and quantify rapidly the number of gas-producing microorganisms in water, beverages, and clinical samples.

Determining average yarding distance.

Treesearch

Roger H. Twito; Charles N. Mann

1979-01-01

Emphasis on environmental and esthetic quality in timber harvesting has brought about increased use of complex boundaries of cutting units and a consequent need for a rapid and accurate method of determining the average yarding distance and area of these units. These values, needed for evaluation of road and landing locations in planning timber harvests, are easily and...

Highly Accurate Antibody Assays for Early and Rapid Detection of Tuberculosis in African and Asian Elephants

USDA-ARS?s Scientific Manuscript database

Tuberculosis (TB) in elephants is a re-emerging zoonotic disease caused primarily by Mycobacterium tuberculosis. Current methods for screening and diagnosis rely on trunk wash culture, which has serious limitations due to low test sensitivity, slow turn-around time, and variable sample quality. Inn...

Airborne particulate discriminator

DOEpatents

Creek, Kathryn Louise [San Diego, CA; Castro, Alonso [Santa Fe, NM; Gray, Perry Clayton [Los Alamos, NM

2009-08-11

A method and apparatus for rapid and accurate detection and discrimination of biological, radiological, and chemical particles in air. A suspect aerosol of the target particulates is treated with a taggant aerosol of ultrafine particulates. Coagulation of the taggant and target particles causes a change in fluorescent properties of the cloud, providing an indication of the presence of the target.

Factors Affecting Accuracy and Time Requirements of a Glucose Oxidase-Peroxidase Assay for Determination of Glucose

USDA-ARS?s Scientific Manuscript database

Accurate and rapid assays for glucose are desirable for analysis of glucose and starch in food and feedstuffs. An established colorimetric glucose oxidase-peroxidase method for glucose was modified to reduce analysis time, and evaluated for factors that affected accuracy. Time required to perform t...

VALIDATION OF A METHOD FOR ESTIMATING POLLUTION EMISSION RATES FROM AREA SOURCES USING OPEN-PATH FTIR SEPCTROSCOPY AND DISPERSION MODELING TECHNIQUES

EPA Science Inventory

The paper describes a methodology developed to estimate emissions factors for a variety of different area sources in a rapid, accurate, and cost effective manner. he methodology involves using an open-path Fourier transform infrared (FTIR) spectrometer to measure concentrations o...

A rapid and accurate quantification method for real-time dynamic analysis of cellular lipids during microalgal fermentation processes in Chlorella protothecoides with low field nuclear magnetic resonance.

PubMed

Wang, Tao; Liu, Tingting; Wang, Zejian; Tian, Xiwei; Yang, Yi; Guo, Meijin; Chu, Ju; Zhuang, Yingping

2016-05-01

The rapid and real-time lipid determination can provide valuable information on process regulation and optimization in the algal lipid mass production. In this study, a rapid, accurate and precise quantification method of in vivo cellular lipids of Chlorella protothecoides using low field nuclear magnetic resonance (LF-NMR) was newly developed. LF-NMR was extremely sensitive to the algal lipids with the limits of the detection (LOD) of 0.0026g and 0.32g/L in dry lipid samples and algal broth, respectively, as well as limits of quantification (LOQ) of 0.0093g and 1.18g/L. Moreover, the LF-NMR signal was specifically proportional to the cellular lipids of C. protothecoides, thus the superior regression curves existing in a wide detection range from 0.02 to 0.42g for dry lipids and from 1.12 to 8.97gL(-1) of lipid concentration for in vivo lipid quantification were obtained with all R(2) higher than 0.99, irrespective of the lipid content and fatty acids profile variations. The accuracy of this novel method was further verified to be reliable by comparing lipid quantification results to those obtained by GC-MS. And the relative standard deviation (RSD) of LF-NMR results were smaller than 2%, suggesting the precision of this method. Finally, this method was successfully used in the on-line lipid monitoring during the algal lipid fermentation processes, making it possible for better understanding of the lipid accumulation mechanism and dynamic bioprocess control. Copyright © 2016 Elsevier B.V. All rights reserved.

Allele-specific HLA-DR typing by mass spectrometry: an alternative to hybridization-based typing methods.

PubMed

Worrall, T A; Schmeckpeper, B J; Corvera, J S; Cotter, R J

2000-11-01

The primer oligomer base extension (PROBE) reaction, combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, is used to characterize HLA-DR2 polymorphism. Alleles are distinguished rapidly and accurately by measuring the mass of primer extension products at every known variable region of HLA-DR2 alleles. Since differentiation of alleles by PROBE relies on measuring differences in extension product mass rather than differences in hybridization properties, mistyped alleles resulting from nonspecific hybridization are absent. The method shows considerable potential for high-throughput screening of HLA-DR polymorphism in a chip-based format, including rapid tissue typing of unrelated volunteer donors.

Tail shortening by discrete hydrodynamics

NASA Astrophysics Data System (ADS)

Kiefer, J.; Visscher, P. B.

1982-02-01

A discrete formulation of hydrodynamics was recently introduced, whose most important feature is that it is exactly renormalizable. Previous numerical work has found that it provides a more efficient and rapidly convergent method for calculating transport coefficients than the usual Green-Kubo method. The latter's convergence difficulties are due to the well-known "long-time tail" of the time correlation function which must be integrated over time. The purpose of the present paper is to present additional evidence that these difficulties are really absent in the discrete equation of motion approach. The "memory" terms in the equation of motion are calculated accurately, and shown to decay much more rapidly with time than the equilibrium time correlations do.

Statistical Methods for Rapid Aerothermal Analysis and Design Technology: Validation

NASA Technical Reports Server (NTRS)

DePriest, Douglas; Morgan, Carolyn

2003-01-01

The cost and safety goals for NASA s next generation of reusable launch vehicle (RLV) will require that rapid high-fidelity aerothermodynamic design tools be used early in the design cycle. To meet these requirements, it is desirable to identify adequate statistical models that quantify and improve the accuracy, extend the applicability, and enable combined analyses using existing prediction tools. The initial research work focused on establishing suitable candidate models for these purposes. The second phase is focused on assessing the performance of these models to accurately predict the heat rate for a given candidate data set. This validation work compared models and methods that may be useful in predicting the heat rate.

A robust and accurate center-frequency estimation (RACE) algorithm for improving motion estimation performance of SinMod on tagged cardiac MR images without known tagging parameters.

PubMed

Liu, Hong; Wang, Jie; Xu, Xiangyang; Song, Enmin; Wang, Qian; Jin, Renchao; Hung, Chih-Cheng; Fei, Baowei

2014-11-01

A robust and accurate center-frequency (CF) estimation (RACE) algorithm for improving the performance of the local sine-wave modeling (SinMod) method, which is a good motion estimation method for tagged cardiac magnetic resonance (MR) images, is proposed in this study. The RACE algorithm can automatically, effectively and efficiently produce a very appropriate CF estimate for the SinMod method, under the circumstance that the specified tagging parameters are unknown, on account of the following two key techniques: (1) the well-known mean-shift algorithm, which can provide accurate and rapid CF estimation; and (2) an original two-direction-combination strategy, which can further enhance the accuracy and robustness of CF estimation. Some other available CF estimation algorithms are brought out for comparison. Several validation approaches that can work on the real data without ground truths are specially designed. Experimental results on human body in vivo cardiac data demonstrate the significance of accurate CF estimation for SinMod, and validate the effectiveness of RACE in facilitating the motion estimation performance of SinMod. Copyright © 2014 Elsevier Inc. All rights reserved.

Rapid and accurate peripheral nerve detection using multipoint Raman imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kumamoto, Yasuaki; Minamikawa, Takeo; Kawamura, Akinori; Matsumura, Junichi; Tsuda, Yuichiro; Ukon, Juichiro; Harada, Yoshinori; Tanaka, Hideo; Takamatsu, Tetsuro

2017-02-01

Nerve-sparing surgery is essential to avoid functional deficits of the limbs and organs. Raman scattering, a label-free, minimally invasive, and accurate modality, is one of the best candidate technologies to detect nerves for nerve-sparing surgery. However, Raman scattering imaging is too time-consuming to be employed in surgery. Here we present a rapid and accurate nerve visualization method using a multipoint Raman imaging technique that has enabled simultaneous spectra measurement from different locations (n=32) of a sample. Five sec is sufficient for measuring n=32 spectra with good S/N from a given tissue. Principal component regression discriminant analysis discriminated spectra obtained from peripheral nerves (n=863 from n=161 myelinated nerves) and connective tissue (n=828 from n=121 tendons) with sensitivity and specificity of 88.3% and 94.8%, respectively. To compensate the spatial information of a multipoint-Raman-derived tissue discrimination image that is too sparse to visualize nerve arrangement, we used morphological information obtained from a bright-field image. When merged with the sparse tissue discrimination image, a morphological image of a sample shows what portion of Raman measurement points in arbitrary structure is determined as nerve. Setting a nerve detection criterion on the portion of "nerve" points in the structure as 40% or more, myelinated nerves (n=161) and tendons (n=121) were discriminated with sensitivity and specificity of 97.5%. The presented technique utilizing a sparse multipoint Raman image and a bright-field image has enabled rapid, safe, and accurate detection of peripheral nerves.

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library.

PubMed

Lee, Hyeyoung; Cuthbertson, Daniel J; Otter, Don E; Barile, Daniela

2016-08-17

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching.

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library

PubMed Central

Lee, Hyeyoung; Cuthbertson, Daniel J.; Otter, Don E.; Barile, Daniela

2018-01-01

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching. PMID:27428379

Laboratory diagnosis of Chlamydia pneumoniae infections

PubMed Central

Peeling, Rosanna W

1995-01-01

Chlamydia pneumoniae is an important cause of respiratory illness. There is a need for accurate and rapid laboratory diagnostic methods that will lead to improved patient care, appropriate use of antimicrobial therapy and a better understanding of the epidemiology of this emerging pathogen. Culture is highly specific but is technically demanding, expensive, has a long turnaround time and its sensitivity is highly dependent on transport conditions. Antigen detection tests such as enzyme immunoassay and direct fluorescent antibody assay, and molecular detection methods such as the polymerase chain reaction assay, may provide a rapid diagnosis without the requirement for stringent transport conditions. The results of these tests should be interpreted with caution until more thorough evaluation is available. Serology remains the method of choice. The limitations of different serological methods for the laboratory diagnosis of C pneumoniae are discussed. PMID:22514397

Using Multiple Barometers to Detect the Floor Location of Smart Phones with Built-in Barometric Sensors for Indoor Positioning

PubMed Central

Xia, Hao; Wang, Xiaogang; Qiao, Yanyou; Jian, Jun; Chang, Yuanfei

2015-01-01

Following the popularity of smart phones and the development of mobile Internet, the demands for accurate indoor positioning have grown rapidly in recent years. Previous indoor positioning methods focused on plane locations on a floor and did not provide accurate floor positioning. In this paper, we propose a method that uses multiple barometers as references for the floor positioning of smart phones with built-in barometric sensors. Some related studies used barometric formula to investigate the altitude of mobile devices and compared the altitude with the height of the floors in a building to obtain the floor number. These studies assume that the accurate height of each floor is known, which is not always the case. They also did not consider the difference in the barometric-pressure pattern at different floors, which may lead to errors in the altitude computation. Our method does not require knowledge of the accurate heights of buildings and stories. It is robust and less sensitive to factors such as temperature and humidity and considers the difference in the barometric-pressure change trends at different floors. We performed a series of experiments to validate the effectiveness of this method. The results are encouraging. PMID:25835189

Study on the applicability of a precise, accurate method for rapid evaluation of engine and lubricant performance. [determination of wear metal in used lubricating oils

NASA Technical Reports Server (NTRS)

Kinard, J. T.

1975-01-01

The development of a procedure for obtaining data related to wear metal determinations in used lubricants is discussed. The procedure makes it possible to obtain rapid, simultaneous determinations of a number of wear metals at levels of parts per thousand to low parts per billion using a small amount of sample. The electrode assembly and instrumentation used in the process are described. Samples of data obtained from tests conducted under controlled conditions are tabulated.

Nested PCR Assay for Eight Pathogens: A Rapid Tool for Diagnosis of Bacterial Meningitis.

PubMed

Bhagchandani, Sharda P; Kubade, Sushant; Nikhare, Priyanka P; Manke, Sonali; Chandak, Nitin H; Kabra, Dinesh; Baheti, Neeraj N; Agrawal, Vijay S; Sarda, Pankaj; Mahajan, Parikshit; Ganjre, Ashish; Purohit, Hemant J; Singh, Lokendra; Taori, Girdhar M; Daginawala, Hatim F; Kashyap, Rajpal S

2016-02-01

Bacterial meningitis is a dreadful infectious disease with a high mortality and morbidity if remained undiagnosed. Traditional diagnostic methods for bacterial meningitis pose a challenge in accurate identification of pathogen, making prognosis difficult. The present study is therefore aimed to design and evaluate a specific and sensitive nested 16S rDNA genus-based polymerase chain reaction (PCR) assay using clinical cerebrospinal fluid (CSF) for rapid diagnosis of eight pathogens causing the disease. The present work was dedicated to development of an in-house genus specific 16S rDNA nested PCR covering pathogens of eight genera responsible for causing bacterial meningitis using newly designed as well as literature based primers for respective genus. A total 150 suspected meningitis CSF obtained from the patients admitted to Central India Institute of Medical Sciences (CIIMS), India during the period from August 2011 to May 2014, were used to evaluate clinical sensitivity and clinical specificity of optimized PCR assays. The analytical sensitivity and specificity of our newly designed genus-specific 16S rDNA PCR were found to be ≥92%. With such a high sensitivity and specificity, our in-house nested PCR was able to give 100% sensitivity in clinically confirmed positive cases and 100% specificity in clinically confirmed negative cases indicating its applicability in clinical diagnosis. Our in-house nested PCR system therefore can diagnose the accurate pathogen causing bacterial meningitis and therefore be useful in selecting a specific treatment line to minimize morbidity. Results are obtained within 24 h and high sensitivity makes this nested PCR assay a rapid and accurate diagnostic tool compared to traditional culture-based methods.

Development of a Combined Human Transferrin-Hemoglobin Lateral Immunochromatographic Assay for Accurate and Rapid Fecal Occult Blood Test.

PubMed

Ye, Yuanyuan; Deng, Yin; Mao, Jinju; Yan, Qin; Huang, Yidan; Zhang, Jun; Zheng, Jian; Li, Yue; Chen, Weixian

2018-05-01

Fecal occult bloodtest (FOBT) plays an important role in the diagnosis of gastrointestinal diseases. The sensitivities of current FOBT methods are still not satisfactory. The aim of this study is to develop a combined human transferrin (HTf)-hemoglobin (HHb) lateral flow assay (LFA) for accurate and rapid FOBT. Monoclonal antibodies (MAbs) targeting HTf were developed by conventional methods and paired using LFA strips. The best HTf MAb pair was chosen according to the overall performance on testing limit and specificity. Meanwhile, HHb LFA strips were prepared using previously developed HHb MAbs. The testing limit and specificity were characterized. Based on the selected HTf MAb pair and the verified HHb MAb pair, combined HTf-HHb strips were developed. The combined HTf-HHb strips were used for FOBT of 400 human fecal samples, including 200 gastrointestinal bleeding specimens and 200 healthy subjects. For comparison, the homemade individual HTf and HHb strips, as well as three kinds of commercial FOBT strips, were also used for the FOBT. Two MAb pairs targeting HTf were developed for LFA. Two types of HTf strips were prepared accordingly. The type I was chosen due to its lower detection limit. Using the type I HTf MAb pair and the verified HHb- MAb pair, the combined HTf-HHb strips could detect the HTf at concentrations between 1 ng/mL and 1 x 106 ng/mL and the HHb between 10 ng/mL and 2.5 x 106 ng/mL. Compared to individual HTf and HHb strips and three kinds of commercial strips, the combined strips showed the highest diagnostic sensitivity in FOBT (96.0%). The specificity was a satisfactory 99%. Our combined HTf-HHb test strips are a very promising product for accurate and rapid FOBT.

A Rapid Diagnostic Technique to Discriminate between Two Pests of Palms, Brontispa longissima and Octodonta nipae (Coleoptera: Chrysomelidae), for Quarantine Applications.

PubMed

Zhang, X; Tang, B; Hou, Y

2015-02-01

Octodonta nipae (Maulik) is morphologically and biologically similar to Brontispa longissima (Gestro), one of the most damaging pests of coconut. The two species share several palm hosts and produce similar symptoms. They are easily confused when they invade a new area, and without professional taxonomic expertise accurate identification is arduous and time-consuming. Thus, a method of rapidly distinguishing these two invasive insects rapidly is critical for quarantine. Based on the first internal transcribed spacer and the mitochondrial cytochrome oxidase I gene, two pairs of special primers and corresponding polymerase chain reaction processes have been developed to enhance a single objective band only from the O. nipae DNA template. This will quickly discriminate between these two species. The present results provide a rapid method of distinguishing O. nipae from B. longissima to help avoid misidentification, and furthermore, to facilitate rapid and appropriate quarantine decisions and effective treatments to the pest. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A computer program for the localization of small areas in roentgenological images

NASA Technical Reports Server (NTRS)

Keller, R. A.; Baily, N. A.

1976-01-01

A method and associated algorithm are presented which allow a simple and accurate determination to be made of the location of small symmetric areas presented in roentgenological images. The method utilizes an operator to visually spot object positions but eliminates the need for critical positioning accuracy on the operator's part. The rapidity of measurement allows results to be evaluated on-line. Parameters associated with the algorithm have been analyzed, and methods to facilitate an optimum choice for any particular experimental setup are presented.

Cytopathology in the post mortem room.

PubMed Central

Walker, E; Going, J J

1994-01-01

AIM--To demonstrate the role of cytopathology in examining tumours found at post mortem examination. METHODS--Tumour deposits were found in 25 hospital necropsies. Cytological diagnosis made at the time of necropsy was compared with subsequent paraffin wax embedded histological sections. RESULTS--In 19 out of 20 cases with no previous histological diagnosis, cytology at the time of necropsy provided rapid and accurate assessment of tumour type. Subsequent histological examination of formalin fixed material merely refined the diagnosis in some cases. In the remaining five cases in which tumour type was known, cytological examination of deposits found at necropsy provided extra information that was useful for compiling a provisional report. CONCLUSIONS--Rapid cytological examination of tumours found during post mortem examinations provides accurate relevant information which can be used to produce a more comprehensive provisional necropsy report. The technique has advantages over frozen section histology and can provide useful cytological experience for histopathology trainees. Images PMID:7962623

Rapid, Reliable Shape Setting of Superelastic Nitinol for Prototyping Robots

PubMed Central

Gilbert, Hunter B.; Webster, Robert J.

2016-01-01

Shape setting Nitinol tubes and wires in a typical laboratory setting for use in superelastic robots is challenging. Obtaining samples that remain superelastic and exhibit desired precurvatures currently requires many iterations, which is time consuming and consumes a substantial amount of Nitinol. To provide a more accurate and reliable method of shape setting, in this paper we propose an electrical technique that uses Joule heating to attain the necessary shape setting temperatures. The resulting high power heating prevents unintended aging of the material and yields consistent and accurate results for the rapid creation of prototypes. We present a complete algorithm and system together with an experimental analysis of temperature regulation. We experimentally validate the approach on Nitinol tubes that are shape set into planar curves. We also demonstrate the feasibility of creating general space curves by shape setting a helical tube. The system demonstrates a mean absolute temperature error of 10°C. PMID:27648473

Rapid, Reliable Shape Setting of Superelastic Nitinol for Prototyping Robots.

PubMed

Gilbert, Hunter B; Webster, Robert J

Shape setting Nitinol tubes and wires in a typical laboratory setting for use in superelastic robots is challenging. Obtaining samples that remain superelastic and exhibit desired precurvatures currently requires many iterations, which is time consuming and consumes a substantial amount of Nitinol. To provide a more accurate and reliable method of shape setting, in this paper we propose an electrical technique that uses Joule heating to attain the necessary shape setting temperatures. The resulting high power heating prevents unintended aging of the material and yields consistent and accurate results for the rapid creation of prototypes. We present a complete algorithm and system together with an experimental analysis of temperature regulation. We experimentally validate the approach on Nitinol tubes that are shape set into planar curves. We also demonstrate the feasibility of creating general space curves by shape setting a helical tube. The system demonstrates a mean absolute temperature error of 10°C.

[Computer-aided method and rapid prototyping for the personalized fabrication of a silicone bandage digital prosthesis].

PubMed

Ventura Ferreira, Nuno; Leal, Nuno; Correia Sá, Inês; Reis, Ana; Marques, Marisa

2014-01-01

The fabrication of digital prostheses has acquired growing importance not only for the possibility for the patient to overcome psychosocial trauma but also to promote grip functionality. An application method of three dimensional-computer-aided design technologies for the production of passive prostheses is presented by means of a fifth finger amputee clinical case following bilateral hand replantation.Three-dimensional-computerized tomography was used for the collection of anthropometric images of the hands. Computer-aided design techniques were used to develop the digital file-based prosthesis from the reconstruction images by inversion and superimposing the contra-lateral finger images. The rapid prototyping manufacturing method was used for the production of a silicone bandage prosthesis prototype. This approach replaces the traditional manual method by a virtual method that is basis for the optimization of a high speed, accurate and innovative process.

DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.

PubMed

Kelly, Steven; Maini, Philip K

2013-01-01

The rapidly growing availability of genome information has created considerable demand for both fast and accurate phylogenetic inference algorithms. We present a novel method called DendroBLAST for reconstructing phylogenetic dendrograms/trees from protein sequences using BLAST. This method differs from other methods by incorporating a simple model of sequence evolution to test the effect of introducing sequence changes on the reliability of the bipartitions in the inferred tree. Using realistic simulated sequence data we demonstrate that this method produces phylogenetic trees that are more accurate than other commonly-used distance based methods though not as accurate as maximum likelihood methods from good quality multiple sequence alignments. In addition to tests on simulated data, we use DendroBLAST to generate input trees for a supertree reconstruction of the phylogeny of the Archaea. This independent analysis produces an approximate phylogeny of the Archaea that has both high precision and recall when compared to previously published analysis of the same dataset using conventional methods. Taken together these results demonstrate that approximate phylogenetic trees can be produced in the absence of multiple sequence alignments, and we propose that these trees will provide a platform for improving and informing downstream bioinformatic analysis. A web implementation of the DendroBLAST method is freely available for use at http://www.dendroblast.com/.

Lymph node micrometastasis in gastrointestinal tract cancer--a clinical aspect.

PubMed

Natsugoe, Shoji; Arigami, Takaaki; Uenosono, Yoshikazu; Yanagita, Shigehiro; Nakajo, Akihiro; Matsumoto, Masataka; Okumura, Hiroshi; Kijima, Yuko; Sakoda, Masahiko; Mataki, Yuko; Uchikado, Yasuto; Mori, Shinichiro; Maemura, Kosei; Ishigami, Sumiya

2013-10-01

Lymph node micrometastasis (LNM) can now be detected thanks to the development of various biological methods such as immunohistochemistry (IHC) and reverse transcription-polymerase chain reaction (RT-PCR). Although several reports have examined LNM in various carcinomas, including gastrointestinal (GI) cancer, the clinical significance of LNM remains controversial. Clinically, the presence of LNM is particularly important in patients without nodal metastasis on routine histological examination (pN0), because patients with pN0 but with LNM already in fact have metastatic potential. However, at present, several technical obstacles are impeding the detection of LNM using methods such as IHC or RT-PCR. Accurate evaluation should be carried out using the same antibody or primer and the same technique in a large number of patients. The clinical importance of the difference between LNM and isolated tumor cells (≤0.2 mm in diameter) will also be gradually clarified. It is important that the results of basic studies on LNM are prospectively introduced into the clinical field. Rapid diagnosis of LNM using IHC and RT-PCR during surgery would be clinically useful. Currently, minimally invasive treatments such as endoscopic submucosal dissection and laparoscopic surgery with individualized lymphadenectomy are increasingly being performed. Accurate diagnosis of LNM would clarify issues of curability and safety when performing such treatments. In the near future, individualized lymphadenectomy will develop based on the establishment of rapid, accurate diagnosis of LNM.

Use of Lean response to improve pandemic influenza surge in public health laboratories.

PubMed

Isaac-Renton, Judith L; Chang, Yin; Prystajecky, Natalie; Petric, Martin; Mak, Annie; Abbott, Brendan; Paris, Benjamin; Decker, K C; Pittenger, Lauren; Guercio, Steven; Stott, Jeff; Miller, Joseph D

2012-01-01

A novel influenza A (H1N1) virus detected in April 2009 rapidly spread around the world. North American provincial and state laboratories have well-defined roles and responsibilities, including providing accurate, timely test results for patients and information for regional public health and other decision makers. We used the multidisciplinary response and rapid implementation of process changes based on Lean methods at the provincial public health laboratory in British Columbia, Canada, to improve laboratory surge capacity in the 2009 influenza pandemic. Observed and computer simulating evaluation results from rapid processes changes showed that use of Lean tools successfully expanded surge capacity, which enabled response to the 10-fold increase in testing demands.

High Order Accurate Algorithms for Shocks, Rapidly Changing Solutions and Multiscale Problems

DTIC Science & Technology

2014-11-13

for front propagation with obstacles, and homotopy method for steady states. Applications include high order simulations for 3D gaseous detonations ...obstacles, and homotopy method for steady states. Applications include high order simulations for 3D gaseous detonations , sound generation study via... detonation waves, Combustion and Flame, (02 2013): 0. doi: 10.1016/j.combustflame.2012.10.002 Yang Yang, Ishani Roy, Chi-Wang Shu, Li-Zhi Fang. THE

The RAPID method for blood processing yields new insight in plasma concentrations and molecular forms of circulating gut peptides.

PubMed

Stengel, Andreas; Keire, David; Goebel, Miriam; Evilevitch, Lena; Wiggins, Brian; Taché, Yvette; Reeve, Joseph R

2009-11-01

The correct identification of circulating molecular forms and measurement of peptide levels in blood entails that the endocrine peptide being studied is stable and recovered in good yields during blood processing. However, it is not clear whether this is achieved in studies using standard blood processing. Therefore, we compared peptide concentration and form of 12 (125)I-labeled peptides using the standard procedure (EDTA-blood on ice) and a new method employing Reduced temperatures, Acidification, Protease inhibition, Isotopic exogenous controls, and Dilution (RAPID). During standard processing there was at least 80% loss for calcitonin-gene-related peptide and cholecystokinin-58 (CCK-58) and more than 35% loss for amylin, insulin, peptide YY forms (PYY((1-36)) and PYY((3-36))), and somatostatin-28. In contrast, the RAPID method significantly improved the recovery for 11 of 12 peptides (P < 0.05) and eliminated the breakdown of endocrine peptides occurring after standard processing as reflected in radically changed molecular forms for CCK-58, gastrin-releasing peptide, somatostatin-28, and ghrelin. For endogenous ghrelin, this led to an acyl/total ghrelin ratio of 1:5 instead of 1:19 by the standard method. These results show that the RAPID method enables accurate assessment of circulating gut peptide concentrations and forms such as CCK-58, acylated ghrelin, and somatostatin-28. Therefore, the RAPID method represents an efficacious means to detect circulating variations in peptide concentrations and form relevant to the understanding of physiological function of endocrine peptides.

Determination of molybenum in soils and rocks: A geochemical semimicro field method

USGS Publications Warehouse

Ward, F.N.

1951-01-01

Reconnaissance work in geochemical prospecting requires a simple, rapid, and moderately accurate method for the determination of small amounts of molybdenum in soils and rocks. The useful range of the suggested procedure is from 1 to 32 p.p.m. of molybdenum, but the upper limit can be extended. Duplicate determinations on eight soil samples containing less than 10 p.p.m. of molybdenum agree within 1 p.p.m., and a comparison of field results with those obtained by a conventional laboratory procedure shows that the method is sufficiently accurate for use in geochemical prospecting. The time required for analysis and the quantities of reagents needed have been decreased to provide essentially a "test tube" method for the determination of molybdenum in soils and rocks. With a minimum amount of skill, one analyst can make 30 molybdenum determinations in an 8-hour day.

Analysis of Glycosaminoglycans Using Mass Spectrometry

PubMed Central

Staples, Gregory O.; Zaia, Joseph

2015-01-01

The glycosaminoglycans (GAGs) are linear polysaccharides expressed on animal cell surfaces and in extracellular matrices. Their biosynthesis is under complex control and confers a domain structure that is essential to their ability to bind to protein partners. Key to understanding the functions of GAGs are methods to determine accurately and rapidly patterns of sulfation, acetylation and uronic acid epimerization that correlate with protein binding or other biological activities. Mass spectrometry (MS) is particularly suitable for the analysis of GAGs for biomedical purposes. Using modern ionization techniques it is possible to accurately determine molecular weights of GAG oligosaccharides and their distributions within a mixture. Methods for direct interfacing with liquid chromatography have been developed to permit online mass spectrometric analysis of GAGs. New tandem mass spectrometric methods for fine structure determination of GAGs are emerging. This review summarizes MS-based approaches for analysis of GAGs, including tissue extraction and chromatographic methods compatible with LC/MS and tandem MS. PMID:25705143

Automated DNA extraction from genetically modified maize using aminosilane-modified bacterial magnetic particles.

PubMed

Ota, Hiroyuki; Lim, Tae-Kyu; Tanaka, Tsuyoshi; Yoshino, Tomoko; Harada, Manabu; Matsunaga, Tadashi

2006-09-18

A novel, automated system, PNE-1080, equipped with eight automated pestle units and a spectrophotometer was developed for genomic DNA extraction from maize using aminosilane-modified bacterial magnetic particles (BMPs). The use of aminosilane-modified BMPs allowed highly accurate DNA recovery. The (A(260)-A(320)):(A(280)-A(320)) ratio of the extracted DNA was 1.9+/-0.1. The DNA quality was sufficiently pure for PCR analysis. The PNE-1080 offered rapid assay completion (30 min) with high accuracy. Furthermore, the results of real-time PCR confirmed that our proposed method permitted the accurate determination of genetically modified DNA composition and correlated well with results obtained by conventional cetyltrimethylammonium bromide (CTAB)-based methods.

A SCILAB Program for Computing General-Relativistic Models of Rotating Neutron Stars by Implementing Hartle's Perturbation Method

NASA Astrophysics Data System (ADS)

Papasotiriou, P. J.; Geroyannis, V. S.

We implement Hartle's perturbation method to the computation of relativistic rigidly rotating neutron star models. The program has been written in SCILAB (© INRIA ENPC), a matrix-oriented high-level programming language. The numerical method is described in very detail and is applied to many models in slow or fast rotation. We show that, although the method is perturbative, it gives accurate results for all practical purposes and it should prove an efficient tool for computing rapidly rotating pulsars.

Minimum impulse three-body trajectories.

NASA Technical Reports Server (NTRS)

D'Amario, L.; Edelbaum, T. N.

1973-01-01

A rapid and accurate method of calculating optimal impulsive transfers in the restricted problem of three bodies has been developed. The technique combines a multi-conic method of trajectory integration with primer vector theory and an accelerated gradient method of trajectory optimization. A unique feature is that the state transition matrix and the primer vector are found analytical without additional integrations or differentiations. The method has been applied to the determination of optimal two and three impulse transfers between the L2 libration point and circular orbits about both the earth and the moon.

A rapid method for counting nucleated erythrocytes on stained blood smears by digital image analysis

USGS Publications Warehouse

Gering, E.; Atkinson, C.T.

2004-01-01

Measures of parasitemia by intraerythrocytic hematozoan parasites are normally expressed as the number of infected erythrocytes per n erythrocytes and are notoriously tedious and time consuming to measure. We describe a protocol for generating rapid counts of nucleated erythrocytes from digital micrographs of thin blood smears that can be used to estimate intensity of hematozoan infections in nonmammalian vertebrate hosts. This method takes advantage of the bold contrast and relatively uniform size and morphology of erythrocyte nuclei on Giemsa-stained blood smears and uses ImageJ, a java-based image analysis program developed at the U.S. National Institutes of Health and available on the internet, to recognize and count these nuclei. This technique makes feasible rapid and accurate counts of total erythrocytes in large numbers of microscope fields, which can be used in the calculation of peripheral parasitemias in low-intensity infections.

Forensic 3D Scene Reconstruction

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

LITTLE,CHARLES Q.; PETERS,RALPH R.; RIGDON,J. BRIAN

Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a feasible prototype of a fast, accurate, 3Dmore » measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.« less

Rapid jetting status inspection and accurate droplet volume measurement for a piezo drop-on-demand inkjet print head using a scanning mirror for display applications

NASA Astrophysics Data System (ADS)

Shin, Dong-Youn; Kim, Minsung

2017-02-01

Despite the inherent fabrication simplicity of piezo drop-on-demand inkjet printing, the non-uniform deposition of colourants or electroluminescent organic materials leads to faulty display products, and hence, the importance of rapid jetting status inspection and accurate droplet volume measurement increases from a process perspective. In this work, various jetting status inspections and droplet volume measurement methods are reviewed by discussing their advantages and disadvantages, and then, the opportunities for the developed prototype with a scanning mirror are explored. This work demonstrates that jetting status inspection of 384 fictitious droplets can be performed within 17 s with maximum and minimum measurement accuracies of 0.2 ± 0.5 μ m for the fictitious droplets of 50 μ m in diameter and -1.2 ± 0.3 μ m for the fictitious droplets of 30 μ m in diameter, respectively. In addition to the new design of an inkjet monitoring instrument with a scanning mirror, two novel methods to accurately measure the droplet volume by amplifying a minute droplet volume difference and then converting to other physical properties are suggested and the droplet volume difference of ±0.3% is demonstrated to be discernible using numerical simulations, even with the low measurement accuracy of 1 μ m . When the fact is considered that the conventional vision-based method with a CCD camera requires the optical measurement accuracy less than 25 nm to measure the volume of an in-flight droplet in the nominal diameter of 50 μ m at the same volume measurement accuracy, the suggested method with the developed prototype offers a whole new opportunity to inkjet printing for display applications.

Rapid jetting status inspection and accurate droplet volume measurement for a piezo drop-on-demand inkjet print head using a scanning mirror for display applications.

PubMed

Shin, Dong-Youn; Kim, Minsung

2017-02-01

Despite the inherent fabrication simplicity of piezo drop-on-demand inkjet printing, the non-uniform deposition of colourants or electroluminescent organic materials leads to faulty display products, and hence, the importance of rapid jetting status inspection and accurate droplet volume measurement increases from a process perspective. In this work, various jetting status inspections and droplet volume measurement methods are reviewed by discussing their advantages and disadvantages, and then, the opportunities for the developed prototype with a scanning mirror are explored. This work demonstrates that jetting status inspection of 384 fictitious droplets can be performed within 17 s with maximum and minimum measurement accuracies of 0.2 ± 0.5 μm for the fictitious droplets of 50 μm in diameter and -1.2 ± 0.3 μm for the fictitious droplets of 30 μm in diameter, respectively. In addition to the new design of an inkjet monitoring instrument with a scanning mirror, two novel methods to accurately measure the droplet volume by amplifying a minute droplet volume difference and then converting to other physical properties are suggested and the droplet volume difference of ±0.3% is demonstrated to be discernible using numerical simulations, even with the low measurement accuracy of 1 μm. When the fact is considered that the conventional vision-based method with a CCD camera requires the optical measurement accuracy less than 25 nm to measure the volume of an in-flight droplet in the nominal diameter of 50 μm at the same volume measurement accuracy, the suggested method with the developed prototype offers a whole new opportunity to inkjet printing for display applications.

Salient man-made structure detection in infrared images

NASA Astrophysics Data System (ADS)

Li, Dong-jie; Zhou, Fu-gen; Jin, Ting

2013-09-01

Target detection, segmentation and recognition is a hot research topic in the field of image processing and pattern recognition nowadays, among which salient area or object detection is one of core technologies of precision guided weapon. Many theories have been raised in this paper; we detect salient objects in a series of input infrared images by using the classical feature integration theory and Itti's visual attention system. In order to find the salient object in an image accurately, we present a new method to solve the edge blur problem by calculating and using the edge mask. We also greatly improve the computing speed by improving the center-surround differences method. Unlike the traditional algorithm, we calculate the center-surround differences through rows and columns separately. Experimental results show that our method is effective in detecting salient object accurately and rapidly.

Implementing targeted region capture sequencing for the clinical detection of Alagille syndrome: An efficient and cost‑effective method.

PubMed

Huang, Tianhong; Yang, Guilin; Dang, Xiao; Ao, Feijian; Li, Jiankang; He, Yizhou; Tang, Qiyuan; He, Qing

2017-11-01

Alagille syndrome (AGS) is a highly variable, autosomal dominant disease that affects multiple structures including the liver, heart, eyes, bones and face. Targeted region capture sequencing focuses on a panel of known pathogenic genes and provides a rapid, cost‑effective and accurate method for molecular diagnosis. In a Chinese family, this method was used on the proband and Sanger sequencing was applied to validate the candidate mutation. A de novo heterozygous mutation (c.3254_3255insT p.Leu1085PhefsX24) of the jagged 1 gene was identified as the potential disease‑causing gene mutation. In conclusion, the present study suggested that target region capture sequencing is an efficient, reliable and accurate approach for the clinical diagnosis of AGS. Furthermore, these results expand on the understanding of the pathogenesis of AGS.

Rapid identification of clinical mycobacterial isolates by protein profiling using matrix assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Panda, A; Kurapati, S; Samantaray, J C; Myneedu, V P; Verma, A; Srinivasan, A; Ahmad, H; Behera, D; Singh, U B

2013-01-01

The purpose of this study was to evaluate the identification of Mycobacterium tuberculosis which is often plagued with ambiguity. It is a time consuming process requiring 4-8 weeks after culture positivity, thereby delaying therapeutic intervention. For a successful treatment and disease management, timely diagnosis is imperative. We evaluated a rapid, proteomic based technique for identification of clinical mycobacterial isolates by protein profiling using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Freshly grown mycobacterial isolates were used. Acetonitrile/trifluoroacetic acid extraction procedure was carried out, following which cinnamic acid charged plates were subjected to identification by MALDI-TOF MS. A comparative analysis of 42 clinical mycobacterial isolates using the MALDI-TOF MS and conventional techniques was carried out. Among these, 97.61% were found to corroborate with the standard methods at genus level and 85.36% were accurate till the species level. One out of 42 was not in accord with the conventional assays because MALDI-TOF MS established it as Mycobacterium tuberculosis (log (score)>2.0) and conventional methods established it to be non-tuberculous Mycobacterium. MALDI-TOF MS was found to be an accurate, rapid, cost effective and robust system for identification of mycobacterial species. This innovative approach holds promise for early therapeutic intervention leading to better patient care.

Rapid and on-site analysis of illegal drugs on the nano-microscale using a deep ultraviolet-visible reflected optical fiber sensor.

PubMed

Li, Qiang; Qiu, Tian; Hao, Hongxia; Zhou, Hong; Wang, Tongzhou; Zhang, Ye; Li, Xin; Huang, Guoliang; Cheng, Jing

2012-04-07

A deep ultraviolet-visible (DUV-Vis) reflected optical fiber sensor was developed for use in a simple spectrophotometric detection system to detect the absorption of various illegal drugs at wavelengths between 180 and 800 nm. Quantitative analyses performed using the sensor revealed a high specificity and sensitivity for drug detection at a wavelength of approximately 200 nm. Using a double-absorption optical path length, extremely small sample volumes were used (32 to 160 nL), which allowed the use of minimal amounts of samples. A portable spectrophotometric system was established based on our optical fiber sensor for the on-site determination and quantitative analysis of common illegal drugs, such as 3,4-methylenedioxymethamphetamine (MDMA), ketamine hydrochloride, cocaine hydrochloride, diazepam, phenobarbital, and barbital. By analyzing the absorbance spectra, six different drugs were quantified at concentrations that ranged from 0.1 to 1000 μg mL(-1) (16 pg-0.16 μg). A novel Matching Algorithm of Spectra Space (MASS) was used to accurately distinguish between each drug in a mixture. As an important supplement to traditional methods, such as mass spectrometry or chromatography, our optical fiber sensor offers rapid and low-cost on-site detection using trace amounts of sample. This rapid and accurate analytical method has wide-ranging applications in forensic science, law enforcement, and medicine.

Validation and clinical application of a molecular method for the identification of Cryptococcus neoformans/Cryptococcus gattii complex DNA in human clinical specimens.

PubMed

Rivera, Vanessa; Gaviria, Marcela; Muñoz-Cadavid, Cesar; Cano, Luz; Naranjo, Tonny

2015-01-01

The diagnosis of cryptococcosis is usually performed based on cultures of tissue or body fluids and isolation of the fungus, but this method may require several days. Direct microscopic examination, although rapid, is relatively insensitive. Biochemical and immunodiagnostic rapid tests are also used. However, all of these methods have limitations that may hinder final diagnosis. The increasing incidence of fungal infections has focused attention on tools for rapid and accurate diagnosis using molecular biological techniques. Currently, PCR-based methods, particularly nested, multiplex and real-time PCR, provide both high sensitivity and specificity. In the present study, we evaluated a nested PCR targeting the gene encoding the ITS-1 and ITS-2 regions of rDNA in samples from a cohort of patients diagnosed with cryptococcosis. The results showed that in our hands, this Cryptococcus nested PCR assay has 100% specificity and 100% sensitivity and was able to detect until 2 femtograms of Cryptococcus DNA. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

Rocket Immunoelectrophoresis of the Entomocidal Parasporal Crystal of Bacillus thuringiensis subsp. kurstaki†

PubMed Central

Andrews, R. E.; Iandolo, J. J.; Campbell, B. S.; Davidson, L. I.; Bulla, L. A.

1980-01-01

Rocket immunoelectrophoresis was used to quantitate the soluble parasporal crystal of Bacillus thuringiensis subsp. kurstaki. The method described is rapid, reliable, specific, and extremely accurate, and it can be used to measure crystal toxin in commercial microbial insecticides that contain a mixture of spores, vegetative cells, and carrier materials. Images PMID:16345656

Deep feature representation with stacked sparse auto-encoder and convolutional neural network for hyperspectral imaging-based detection of cucumber defects

USDA-ARS?s Scientific Manuscript database

It is challenging to achieve rapid and accurate processing of large amounts of hyperspectral image data. This research was aimed to develop a novel classification method by employing deep feature representation with the stacked sparse auto-encoder (SSAE) and the SSAE combined with convolutional neur...

Teaching Mental Abacus Calculation to Students with Mental Retardation

ERIC Educational Resources Information Center

Shen, Hong

2006-01-01

The abacus is a calculating tool that has been used in Asia for thousands of years. Mental abacus calculation is a skill in which an abacus image in the mind is used without the actual physical manipulation of the abacus. Using this method, people can perform extremely rapid and accurate mental calculations. Research indicates that abacus training…

A Hybrid On-line Verification Method of Relay Setting

NASA Astrophysics Data System (ADS)

Gao, Wangyuan; Chen, Qing; Si, Ji; Huang, Xin

2017-05-01

Along with the rapid development of the power industry, grid structure gets more sophisticated. The validity and rationality of protective relaying are vital to the security of power systems. To increase the security of power systems, it is essential to verify the setting values of relays online. Traditional verification methods mainly include the comparison of protection range and the comparison of calculated setting value. To realize on-line verification, the verifying speed is the key. The verifying result of comparing protection range is accurate, but the computation burden is heavy, and the verifying speed is slow. Comparing calculated setting value is much faster, but the verifying result is conservative and inaccurate. Taking the overcurrent protection as example, this paper analyses the advantages and disadvantages of the two traditional methods above, and proposes a hybrid method of on-line verification which synthesizes the advantages of the two traditional methods. This hybrid method can meet the requirements of accurate on-line verification.

Multi-wavelength dye concentration determination for enzymatic assays: evaluation of chromogenic para-nitrophenol over a wide pH range.

PubMed

Max, Jean-Joseph; Meddeb-Mouelhi, Fatma; Beauregard, Marc; Chapados, Camille

2012-12-01

Enzymatic assays need robust, rapid colorimetric methods that can follow ongoing reactions. For this, we developed a highly accurate, multi-wavelength detection method that could be used for several systems. Here, it was applied to the detection of para-nitrophenol (pNP) in basic and acidic solutions. First, we confirmed by factor analysis that pNP has two forms, with unique spectral characteristics in the 240 to 600 nm range: Phenol in acidic conditions absorbs in the lower range, whereas phenolate in basic conditions absorbs in the higher range. Thereafter, the method was used for the determination of species concentration. For this, the intensity measurements were made at only two wavelengths with a microtiter plate reader. This yielded total dye concentration, species relative abundance, and solution pH value. The method was applied to an enzymatic assay. For this, a chromogenic substrate that generates pNP after hydrolysis catalyzed by a lipase from the fungus Yarrowia lipolytica was used. Over the pH range of 3-11, accurate amounts of acidic and basic pNP were determined at 340 and 405 nm, respectively. This method surpasses the commonly used single-wavelength assay at 405 nm, which does not detect pNP acidic species, leading to activity underestimations. Moreover, alleviation of this pH-related problem by neutralization is not necessary. On the whole, the method developed is readily applicable to rapid high-throughput of enzymatic activity measurements over a wide pH range.

Direct identification of bacteria causing urinary tract infections by combining matrix-assisted laser desorption ionization-time of flight mass spectrometry with UF-1000i urine flow cytometry.

PubMed

Wang, X-H; Zhang, G; Fan, Y-Y; Yang, X; Sui, W-J; Lu, X-X

2013-03-01

Rapid identification of bacterial pathogens from clinical specimens is essential to establish an adequate empirical antibiotic therapy to treat urinary tract infections (UTIs). We used matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) combined with UF-1000i urine flow cytometry of urine specimens to quickly and accurately identify bacteria causing UTIs. We divided each urine sample into three aliquots for conventional identification, UF-1000i, and MALDI-TOF MS, respectively. We compared the results of the conventional method with those of MALDI-TOF MS combined with UF-1000i, and discrepancies were resolved by 16S rRNA gene sequencing. We analyzed 1456 urine samples from patients with UTI symptoms, and 932 (64.0%) were negative using each of the three testing methods. The combined method used UF-1000i to eliminate negative specimens and then MALDI-TOF MS to identify the remaining positive samples. The combined method was consistent with the conventional method in 1373 of 1456 cases (94.3%), and gave the correct result in 1381 of 1456 cases (94.8%). Therefore, the combined method described here can directly provide a rapid, accurate, definitive bacterial identification for the vast majority of urine samples, though the MALDI-TOF MS software analysis capabilities should be improved, with regard to mixed bacterial infection. Copyright © 2012 Elsevier B.V. All rights reserved.

[Rapid analysis on phenolic compounds in Rheum palmatum based on UPLC-Q-TOF/MSE combined with diagnostic ions filter].

PubMed

Wang, Qing; Lu, Zhi-Wei; Liu, Yue-Hong; Wang, Ming-Ling; Fu, Shuang; Zhang, Qing-Qing; Zhao, Hui-Zhen; Zhang, Zhi-Xin; Xie, Zi-Ye; Huang, Zheng-Hai; Yu, Hong-Hong; Zhou, Wen-Juan; Gao, Xiao-Yan

2017-05-01

Diagnostic ions filter method was used to rapidly detect and identify the phenolic compounds in Rheum palmatum based on ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MSE). The representative authentic standards of phenolic compounds, including gallic acid, (+)-catechin, (－)-epicatechin, (－)-epicatechin-3-O-gallate and procyanidin B2, were subjected to analysis by UPLC-Q-TOF/MSE system with negative ion mode. Fragmentation patterns of each standard were summarized based on assigned fragment ions. The prominent product ions were selected as diagnostic ions. Subsequently, diagnostic ions filter was employed to rapidly recognize analogous skeletons. Combined with retention time, accurate mass, characteristic fragments and previous literature data, the structures of the filtered compounds were identified or tentatively characterized. A total 63 phenolic compounds (36 phenolic acid derivatives, 8 flavonoid derivatives and 19 tennis derivatives) in R. palmatum were identified, including 6 potential new compounds. The method of diagnostic ions filter could rapidly detect and identify phenolic compounds in R. palmatum This study provides a method for rapid detection of phenolic compounds in R. palmatum and is expected to complete the material basis of rhubarb. Copyright© by the Chinese Pharmaceutical Association.

Comparing rapid methods for detecting Listeria in seafood and environmental samples using the most probably number (MPN) technique.

PubMed

Cruz, Cristina D; Win, Jessicah K; Chantarachoti, Jiraporn; Mutukumira, Anthony N; Fletcher, Graham C

2012-02-15

The standard Bacteriological Analytical Manual (BAM) protocol for detecting Listeria in food and on environmental surfaces takes about 96 h. Some studies indicate that rapid methods, which produce results within 48 h, may be as sensitive and accurate as the culture protocol. As they only give presence/absence results, it can be difficult to compare the accuracy of results generated. We used the Most Probable Number (MPN) technique to evaluate the performance and detection limits of six rapid kits for detecting Listeria in seafood and on an environmental surface compared with the standard protocol. Three seafood products and an environmental surface were inoculated with similar known cell concentrations of Listeria and analyzed according to the manufacturers' instructions. The MPN was estimated using the MPN-BAM spreadsheet. For the seafood products no differences were observed among the rapid kits and efficiency was similar to the BAM method. On the environmental surface the BAM protocol had a higher recovery rate (sensitivity) than any of the rapid kits tested. Clearview™, Reveal®, TECRA® and VIDAS® LDUO detected the cells but only at high concentrations (>10(2) CFU/10 cm(2)). Two kits (VIP™ and Petrifilm™) failed to detect 10(4) CFU/10 cm(2). The MPN method was a useful tool for comparing the results generated by these presence/absence test kits. There remains a need to develop a rapid and sensitive method for detecting Listeria in environmental samples that performs as well as the BAM protocol, since none of the rapid tests used in this study achieved a satisfactory result. Copyright © 2011 Elsevier B.V. All rights reserved.

A rapid and non-invasive method for measuring the peak positive pressure of HIFU fields by a laser beam.

PubMed

Wang, Hua; Zeng, Deping; Chen, Ziguang; Yang, Zengtao

2017-04-12

Based on the acousto-optic interaction, we propose a laser deflection method for rapidly, non-invasively and quantitatively measuring the peak positive pressure of HIFU fields. In the characterization of HIFU fields, the effect of nonlinear propagation is considered. The relation between the laser deflection length and the peak positive pressure is derived. Then the laser deflection method is assessed by comparing it with the hydrophone method. The experimental results show that the peak positive pressure measured by laser deflection method is little higher than that obtained by the hydrophone, confirming that they are in reasonable agreement. Considering that the peak pressure measured by hydrophones is always underestimated, the laser deflection method is assumed to be more accurate than the hydrophone method due to the absence of the errors in hydrophone spatial-averaging measurement and the influence of waveform distortion on hydrophone corrections. Moreover, noting that the Lorentz formula still remains applicable to high-pressure environments, the laser deflection method exhibits a great potential for measuring HIFU field under high-pressure amplitude. Additionally, the laser deflection method provides a rapid way for measuring the peak positive pressure, without the scan time, which is required by the hydrophones.

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks

PubMed Central

Walsh, Aaron M.; Crispie, Fiona; Daari, Kareem; O'Sullivan, Orla; Martin, Jennifer C.; Arthur, Cornelius T.; Claesson, Marcus J.; Scott, Karen P.

2017-01-01

ABSTRACT The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization. IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products. PMID:28625983

Proof-of-principle rapid noninvasive prenatal diagnosis of autosomal recessive founder mutations

PubMed Central

Zeevi, David A.; Altarescu, Gheona; Weinberg-Shukron, Ariella; Zahdeh, Fouad; Dinur, Tama; Chicco, Gaya; Herskovitz, Yair; Renbaum, Paul; Elstein, Deborah; Levy-Lahad, Ephrat; Rolfs, Arndt; Zimran, Ari

2015-01-01

BACKGROUND. Noninvasive prenatal testing can be used to accurately detect chromosomal aneuploidies in circulating fetal DNA; however, the necessity of parental haplotype construction is a primary drawback to noninvasive prenatal diagnosis (NIPD) of monogenic disease. Family-specific haplotype assembly is essential for accurate diagnosis of minuscule amounts of circulating cell-free fetal DNA; however, current haplotyping techniques are too time-consuming and laborious to be carried out within the limited time constraints of prenatal testing, hampering practical application of NIPD in the clinic. Here, we have addressed this pitfall and devised a universal strategy for rapid NIPD of a prevalent mutation in the Ashkenazi Jewish (AJ) population. METHODS. Pregnant AJ couples, carrying mutation(s) in GBA, which encodes acid β-glucosidase, were recruited at the SZMC Gaucher Clinic. Targeted next-generation sequencing of GBA-flanking SNPs was performed on peripheral blood samples from each couple, relevant mutation carrier family members, and unrelated individuals who are homozygotes for an AJ founder mutation. Allele-specific haplotypes were constructed based on linkage, and a consensus Gaucher disease–associated founder mutation–flanking haplotype was fine mapped. Together, these haplotypes were used for NIPD. All test results were validated by conventional prenatal or postnatal diagnostic methods. RESULTS. Ten parental alleles in eight unrelated fetuses were diagnosed successfully based on the noninvasive method developed in this study. The consensus mutation–flanking haplotype aided diagnosis for 6 of 9 founder mutation alleles. CONCLUSIONS. The founder NIPD method developed and described here is rapid, economical, and readily adaptable for prenatal testing of prevalent autosomal recessive disease-causing mutations in an assortment of worldwide populations. FUNDING. SZMC, Protalix Biotherapeutics Inc., and Centogene AG. PMID:26426075

Rapid identification of apolipoprotein E genotypes by high-resolution melting analysis in Chinese Han and African Fang populations.

PubMed

Zhan, Xiu-Hui; Zha, Guang-Cai; Jiao, Ji-Wei; Yang, Li-Ye; Zhan, Xiao-Fen; Chen, Jiang-Tao; Xie, Dong-DE; Eyi, Urbano Monsuy; Matesa, Rocio Apicante; Obono, Maximo Miko Ondo; Ehapo, Carlos Sala; Wei, Er-Jia; Zheng, Yu-Zhong; Yang, Hui; Lin, Min

2015-02-01

Apolipoprotein E (APOE) gene polymorphism can affect APOE gene transcription, serum lipid levels and repair of tissue damage, which could place individuals at serious risk of cardiovascular disease or certain infectious diseases. Recently, high-resolution melting (HRM) analysis was reported to be a simple, inexpensive, accurate and sensitive method for the genotyping or/and scanning of rare mutations. For this reason, an HRM analysis was used in the present study for APOE genotyping in the Southern Chinese Han and African Fang populations. A total of 100 healthy Southern Chinese Han and 175 healthy African Fang individuals attended the study. Polymerase chain reaction-DNA sequencing was used as a reference method for the genotyping of these samples. The six APOE genotypes could all be rapidly and efficiently identified by HRM analysis, and 100% concordance was found between the HRM analysis and the reference method. The allele frequencies of APOE in the Southern Chinese Han population were 7.0, 87.5 and 5.5% for ɛ2, ɛ3 and ɛ4, respectively. In the African Fang population, the allele frequencies of APOE were 24.3, 65.7 and 10.0% for ɛ2, ɛ3 and ɛ4, respectively. A statistically significant difference was found between the allele frequencies between the populations (P<0.05). In conclusion, the present study revealed the molecular characterization of APOE gene polymorphism in the Han population from the Chaozhou region of Southern China and the Fang population from Equatorial Guinea. The findings of the study indicated that HRM analysis could be used as an accurate and sensitive method for the rapid screening and identification of APOE genotypes in prospective clinical and population genetic analyses.

PCR analysis of the cryI insecticidal crystal family genes from Bacillus thuringiensis.

PubMed Central

Ceron, J; Covarrubias, L; Quintero, R; Ortiz, A; Ortiz, M; Aranda, E; Lina, L; Bravo, A

1994-01-01

A method allowing rapid and accurate identification of different subgroups within the insecticidal crystal CryI protein-producing family of Bacillus thuringiensis strains was established by using PCR technology. Thirteen highly homologous primers specific to regions within genes encoding seven different subgroups of B. thuringiensis CryI proteins were described. Differentiation among these strains was determined on the basis of the electrophoretic patterns of PCR products. B. thuringiensis strains, isolated from soil samples, were analyzed by PCR technology. Small amounts of bacterial lysates were assayed in two reaction mixtures containing six to eight primers. This method can be applied to rapidly detect the subgroups of CryI proteins that correspond with toxicity to various lepidopteran insects. Images PMID:8117089

Method and apparatus for fringe-scanning chromosome analysis

DOEpatents

Norgren, R.M.; Gray, J.W.; Hirschfeld, T.B.

1983-08-31

Apparatus and method are provided for analyzing sub-micron-sized features of microscopic particles. Two central features of the invention are (1) constraining microscopic particles to flow with substantially constant orientation through a predetermined interference fringe pattern, and (2) estimating particle structure by analyzing its fringe profile. The invention allows nearly an order of magnitude higher resolution of chromosome structure than possible with currently available flow system techniques. The invention allows rapid and accurate flow karyotyping of chromosomes.

Automatic identification of the reference system based on the fourth ventricular landmarks in T1-weighted MR images.

PubMed

Fu, Yili; Gao, Wenpeng; Chen, Xiaoguang; Zhu, Minwei; Shen, Weigao; Wang, Shuguo

2010-01-01

The reference system based on the fourth ventricular landmarks (including the fastigial point and ventricular floor plane) is used in medical image analysis of the brain stem. The objective of this study was to develop a rapid, robust, and accurate method for the automatic identification of this reference system on T1-weighted magnetic resonance images. The fully automated method developed in this study consisted of four stages: preprocessing of the data set, expectation-maximization algorithm-based extraction of the fourth ventricle in the region of interest, a coarse-to-fine strategy for identifying the fastigial point, and localization of the base point. The method was evaluated on 27 Brain Web data sets qualitatively and 18 Internet Brain Segmentation Repository data sets and 30 clinical scans quantitatively. The results of qualitative evaluation indicated that the method was robust to rotation, landmark variation, noise, and inhomogeneity. The results of quantitative evaluation indicated that the method was able to identify the reference system with an accuracy of 0.7 +/- 0.2 mm for the fastigial point and 1.1 +/- 0.3 mm for the base point. It took <6 seconds for the method to identify the related landmarks on a personal computer with an Intel Core 2 6300 processor and 2 GB of random-access memory. The proposed method for the automatic identification of the reference system based on the fourth ventricular landmarks was shown to be rapid, robust, and accurate. The method has potentially utility in image registration and computer-aided surgery.

Performance of commercial platforms for rapid genotyping of polymorphisms affecting warfarin dose.

PubMed

King, Cristi R; Porche-Sorbet, Rhonda M; Gage, Brian F; Ridker, Paul M; Renaud, Yannick; Phillips, Michael S; Eby, Charles

2008-06-01

Initiation of warfarin therapy is associated with bleeding owing to its narrow therapeutic window and unpredictable therapeutic dose. Pharmacogenetic-based dosing algorithms can improve accuracy of initial warfarin dosing but require rapid genotyping for cytochrome P-450 2C9 (CYP2C9) *2 and *3 single nucleotide polymorphisms (SNPs) and a vitamin K epoxide reductase (VKORC1) SNP. We evaluated 4 commercial systems: INFINITI analyzer (AutoGenomics, Carlsbad, CA), Invader assay (Third Wave Technologies, Madison, WI), Tag-It Mutation Detection assay (Luminex Molecular Diagnostics, formerly Tm Bioscience, Toronto, Canada), and Pyrosequencing (Biotage, Uppsala, Sweden). We genotyped 112 DNA samples and resolved any discrepancies with bidirectional sequencing. The INFINITI analyzer was 100% accurate for all SNPs and required 8 hours. Invader and Tag-It were 100% accurate for CYP2C9 SNPs, 99% accurate for VKORC1 -1639/3673 SNP, and required 3 hours and 8 hours, respectively. Pyrosequencing was 99% accurate for CYP2C9 *2, 100% accurate for CYP2C9 *3, and 100% accurate for VKORC1 and required 4 hours. Current commercial platforms provide accurate and rapid genotypes for pharmacogenetic dosing during initiation of warfarin therapy.

Rapid Harmonic Analysis of Piezoelectric MEMS Resonators.

PubMed

Puder, Jonathan M; Pulskamp, Jeffrey S; Rudy, Ryan Q; Cassella, Cristian; Rinaldi, Matteo; Chen, Guofeng; Bhave, Sunil A; Polcawich, Ronald G

2018-06-01

This paper reports on a novel simulation method combining the speed of analytical evaluation with the accuracy of finite-element analysis (FEA). This method is known as the rapid analytical-FEA technique (RAFT). The ability of the RAFT to accurately predict frequency response orders of magnitude faster than conventional simulation methods while providing deeper insights into device design not possible with other types of analysis is detailed. Simulation results from the RAFT across wide bandwidths are compared to measured results of resonators fabricated with various materials, frequencies, and topologies with good agreement. These include resonators targeting beam extension, disk flexure, and Lamé beam modes. An example scaling analysis is presented and other applications enabled are discussed as well. The supplemental material includes example code for implementation in ANSYS, although any commonly employed FEA package may be used.

A new measurement method of coatings thickness based on lock-in thermography

NASA Astrophysics Data System (ADS)

Zhang, Jin-Yu; Meng, Xiang-bin; Ma, Yong-chao

2016-05-01

Coatings have been widely used in modern industry and it plays an important role. Coatings thickness is directly related to the performance of the functional coatings, therefore, rapid and accurate coatings thickness inspection has great significance. Existing coatings thickness measurement method is difficult to achieve fast and accurate on-site non-destructive coatings inspection due to cost, accuracy, destruction during inspection and other reasons. This paper starts from the introduction of the principle of lock-in thermography, and then performs an in-depth study on the application of lock-in thermography in coatings inspection through numerical modeling and analysis. The numerical analysis helps explore the relationship between coatings thickness and phase, and the relationship lays the foundation for accurate calculation of coatings thickness. The author sets up a lock-in thermography inspection system and uses thermal barrier coatings specimens to conduct an experiment. The specimen coatings thickness is measured and calibrated to verify the quantitative inspection. Experiment results show that the lock-in thermography method can perform fast coatings inspection and the inspection accuracy is about 95%. Therefore, the method can meet the field testing requirements for engineering projects.

Analytical Fuselage and Wing Weight Estimation of Transport Aircraft

NASA Technical Reports Server (NTRS)

Chambers, Mark C.; Ardema, Mark D.; Patron, Anthony P.; Hahn, Andrew S.; Miura, Hirokazu; Moore, Mark D.

1996-01-01

A method of estimating the load-bearing fuselage weight and wing weight of transport aircraft based on fundamental structural principles has been developed. This method of weight estimation represents a compromise between the rapid assessment of component weight using empirical methods based on actual weights of existing aircraft, and detailed, but time-consuming, analysis using the finite element method. The method was applied to eight existing subsonic transports for validation and correlation. Integration of the resulting computer program, PDCYL, has been made into the weights-calculating module of the AirCraft SYNThesis (ACSYNT) computer program. ACSYNT has traditionally used only empirical weight estimation methods; PDCYL adds to ACSYNT a rapid, accurate means of assessing the fuselage and wing weights of unconventional aircraft. PDCYL also allows flexibility in the choice of structural concept, as well as a direct means of determining the impact of advanced materials on structural weight. Using statistical analysis techniques, relations between the load-bearing fuselage and wing weights calculated by PDCYL and corresponding actual weights were determined.

Rapid analysis of scattering from periodic dielectric structures using accelerated Cartesian expansions

DOE PAGES

Baczewski, Andrew David; Miller, Nicholas C.; Shanker, Balasubramaniam

2012-03-22

Here, the analysis of fields in periodic dielectric structures arise in numerous applications of recent interest, ranging from photonic bandgap structures and plasmonically active nanostructures to metamaterials. To achieve an accurate representation of the fields in these structures using numerical methods, dense spatial discretization is required. This, in turn, affects the cost of analysis, particularly for integral-equation-based methods, for which traditional iterative methods require Ο(Ν 2) operations, Ν being the number of spatial degrees of freedom. In this paper, we introduce a method for the rapid solution of volumetric electric field integral equations used in the analysis of doubly periodicmore » dielectric structures. The crux of our method is the accelerated Cartesian expansion algorithm, which is used to evaluate the requisite potentials in Ο(Ν) cost. Results are provided that corroborate our claims of acceleration without compromising accuracy, as well as the application of our method to a number of compelling photonics applications.« less

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

PubMed

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

2012-11-01

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

Use of Lean Response to Improve Pandemic Influenza Surge in Public Health Laboratories

PubMed Central

Chang, Yin; Prystajecky, Natalie; Petric, Martin; Mak, Annie; Abbott, Brendan; Paris, Benjamin; Decker, K.C.; Pittenger, Lauren; Guercio, Steven; Stott, Jeff; Miller, Joseph D.

2012-01-01

A novel influenza A (H1N1) virus detected in April 2009 rapidly spread around the world. North American provincial and state laboratories have well-defined roles and responsibilities, including providing accurate, timely test results for patients and information for regional public health and other decision makers. We used the multidisciplinary response and rapid implementation of process changes based on Lean methods at the provincial public health laboratory in British Columbia, Canada, to improve laboratory surge capacity in the 2009 influenza pandemic. Observed and computer simulating evaluation results from rapid processes changes showed that use of Lean tools successfully expanded surge capacity, which enabled response to the 10-fold increase in testing demands. PMID:22257385

High-Throughput Phenotyping of Maize Leaf Physiological and Biochemical Traits Using Hyperspectral Reflectance1[OPEN

PubMed Central

Yendrek, Craig R.; Tomaz, Tiago; Montes, Christopher M.; Cao, Youyuan; Morse, Alison M.; Brown, Patrick J.; McIntyre, Lauren M.; Leakey, Andrew D.B.

2017-01-01

High-throughput, noninvasive field phenotyping has revealed genetic variation in crop morphological, developmental, and agronomic traits, but rapid measurements of the underlying physiological and biochemical traits are needed to fully understand genetic variation in plant-environment interactions. This study tested the application of leaf hyperspectral reflectance (λ = 500–2,400 nm) as a high-throughput phenotyping approach for rapid and accurate assessment of leaf photosynthetic and biochemical traits in maize (Zea mays). Leaf traits were measured with standard wet-laboratory and gas-exchange approaches alongside measurements of leaf reflectance. Partial least-squares regression was used to develop a measure of leaf chlorophyll content, nitrogen content, sucrose content, specific leaf area, maximum rate of phosphoenolpyruvate carboxylation, [CO2]-saturated rate of photosynthesis, and leaf oxygen radical absorbance capacity from leaf reflectance spectra. Partial least-squares regression models accurately predicted five out of seven traits and were more accurate than previously used simple spectral indices for leaf chlorophyll, nitrogen content, and specific leaf area. Correlations among leaf traits and statistical inferences about differences among genotypes and treatments were similar for measured and modeled data. The hyperspectral reflectance approach to phenotyping was dramatically faster than traditional measurements, enabling over 1,000 rows to be phenotyped during midday hours over just 2 to 4 d, and offers a nondestructive method to accurately assess physiological and biochemical trait responses to environmental stress. PMID:28049858

Detection of plant quarantine pathogen Ralstonia solanacearum r3b2 with portable POCKIT™ and BLItz® systems

USDA-ARS?s Scientific Manuscript database

Ralstonia solanacearum (Rs) race 3 biovar 2 (r3b2) is designated as a quarantine pathogen in many countries and additionally as a Select Agent in the United States. Rapid, sensitive and accurate detection methods are urgently needed. We report here the development of two portable platforms for r3b...

The Role of Color Cues in Facilitating Accurate and Rapid Location of Aided Symbols by Children with and without Down Syndrome

ERIC Educational Resources Information Center

Wilkinson, Krista; Carlin, Michael; Thistle, Jennifer

2008-01-01

Purpose: This research examined how the color distribution of symbols within a visual aided augmentative and alternative communication array influenced the speed and accuracy with which participants with and without Down syndrome located a target picture symbol. Method: Eight typically developing children below the age of 4 years, 8 typically…

Has the promise of DNA barcoding been achieved? a critical look at the application of eDNA barcoding to biomonitoring

Treesearch

Carolina Penalva-Arana; Erik P. Pilgrim; John Martinson

2016-01-01

Biological monitoring programs aim to assess the health of waters and determine the direct impact anthropogenic activities are having on the ecosystems. There is a need for the development of accurate and reproducible methods that can assess biodiversity rapidly and in a cost-effective manner.

A brief review of machine vision in the context of automated wood identification systems

Treesearch

John C. Hermanson; Alex C. Wiedenhoeft

2011-01-01

The need for accurate and rapid field identification of wood to combat illegal logging around the world is outpacing the ability to train personnel to perform this task. Despite increased interest in non-anatomical (DNA, spectroscopic, chemical) methods for wood identification, anatomical characteristics are the least labile data that can be extracted from solid wood...

Identifying the Method for Effective Combat Marksmanship Training Using Site Optics and Packaged Sensor Feedback

DTIC Science & Technology

2011-09-01

accurately displaying the point of aim to a precision of two minutes of angle. • At the distance of approximately 240 inches from the muzzle of the SRS...line, rapid stage, shooters will engage a static Dog (D)-target firing ten rounds, referenced in Figure 12. Shooters will prepare for this stage by

DNAzyme based gap-LCR detection of single-nucleotide polymorphism.

PubMed

Zhou, Li; Du, Feng; Zhao, Yongyun; Yameen, Afshan; Chen, Haodong; Tang, Zhuo

2013-07-15

Fast and accurate detection of single-nucleotide polymorphism (SNP) is thought more and more important for understanding of human physiology and elucidating the molecular based diseases. A great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. However most of those methods developed to date incorporate complicated probe labeling and depend on advanced equipment. The DNAzyme based Gap-LCR detection method averts any chemical modification on probes and circumvents those problems by incorporating a short functional DNA sequence into one of LCR primers. Two kinds of exonuclease are utilized in our strategy to digest all the unreacted probes and release the DNAzymes embedded in the LCR product. The DNAzyme applied in our method is a versatile tool to report the result of SNP detection in colorimetric or fluorometric ways for different detection purposes. Copyright © 2013 Elsevier B.V. All rights reserved.

Simultaneous and Rapid Detection of Salmonella typhi, Bacillus anthracis, and Yersinia pestis by Using Multiplex Polymerase Chain Reaction (PCR)

PubMed Central

Safari Foroshani, Nargess; Karami, Ali; Pourali, Fatemeh

2013-01-01

Background Salmonella typhi, Bacillus anthracis, and Yersinia pestis are some serious human pathogens, which their early diagnosis is of great importance. Salmonella typhi, Bacillus anthracis, and Yersinia pestis cause typhoid fever, anthrax, and plague respectively. These bacteria can be used to make biologic weapons. Objectives In this study, we designed a new and rapid diagnostic method based on Uniplex and Multiplex PCR method. Materials and Methods Uniplex and multiplex Polymerase Chain Reaction (PCR) were conducted on virulent genes of hp and invA of Salmonella typhimurium, Pa and chr of Bacillus anthracis, and pla of Yersinia pestis. A genome from other bacteria was used to study the specificity of the primer and the PCR test. Results Standard strains used in this study showed that primers were specific. As for sensitivity, it was shown that this method can diagnose 1-10 copies of the genome, or 1-10 Colony Forming Units (CFU) for each of the bacteria. All pieces except anthrax were sequenced in PCR to validate the product. DNA fragment resulted from Bacillus anthracis was confirmed by restriction enzyme digestions. Conclusion The designed methods are accurate, rapid, and inexpensive to find and differentiate these bacteria from similar bacteria. They can be applied for rapid diagnosis of these agents in different specimens, and bioterrorism cases. PMID:24719692

Evaluation of an inhouse rapid ELISA test for detection of giardia in domestic sheep (Ovis aries).

PubMed

Wilson, Jolaine M; Hankenson, F Claire

2010-11-01

Sheep (Ovis aries) are increasingly used at our institution as models of human disease. Within the research environment, routine husbandry and handling of sheep has potential for transmission of zoonotic agents, including Giardia. The prevalence of Giardia in sheep may approach 68%. Classic diagnostic testing involves microscopic examination for fecal cysts or trophozoites; however, limitations of microscopy include time, labor, and potential false-negative results due to intermittent shedding. We wished to determine whether a commercial rapid ELISA used for Giardia detection in dogs and cats could be used in sheep. Fecal samples collected from sheep (n = 93) were tested with a combination of 6 methods: reference laboratory fecal flotation, reference laboratory ELISA, inhouse fecal flotation, and commercially available tests (enzyme immunoassay, direct fluorescence antibody assay, and rapid ELISA). Prevalence of Giardia infection in facility sheep was 11.8% (11 of 93 animals). Of the 11 samples considered positive, 3 were confirmed by multiple testing methods, and 5 were positive by microscopy alone. Inhouse fecal flotation for 8 samples was positive on only 1 of 2 consecutive testing days. The rapid ELISA test exhibited 0% sensitivity for sheep giardiasis. Overall, the examined methods had low sensitivities and low positive predictive values. Despite limitations, microscopic analysis of repeat fecal samples remained the most accurate diagnostic method for ovine giardiasis among the methods tested.

Lessons learned from implementing a wet laboratory molecular training workshop for beach water quality monitoring.

PubMed

Verhougstraete, Marc Paul; Brothers, Sydney; Litaker, Wayne; Blackwood, A Denene; Noble, Rachel

2015-01-01

Rapid molecular testing methods are poised to replace many of the conventional, culture-based tests currently used in fields such as water quality and food science. Rapid qPCR methods have the benefit of being faster than conventional methods and provide a means to more accurately protect public health. However, many scientists and technicians in water and food quality microbiology laboratories have limited experience using these molecular tests. To ensure that practitioners can use and implement qPCR techniques successfully, we developed a week long workshop to provide hands-on training and exposure to rapid molecular methods for water quality management. This workshop trained academic professors, government employees, private industry representatives, and graduate students in rapid qPCR methods for monitoring recreational water quality. Attendees were immersed in these new methods with hands-on laboratory sessions, lectures, and one-on-one training. Upon completion, the attendees gained sufficient knowledge and practice to teach and share these new molecular techniques with colleagues at their respective laboratories. Key findings from this workshop demonstrated: 1) participants with no prior experience could be effectively trained to conduct highly repeatable qPCR analysis in one week; 2) participants with different desirable outcomes required exposure to a range of different platforms and sample processing approaches; and 3) the collaborative interaction amongst newly trained practitioners, workshop leaders, and members of the water quality community helped foster a cohesive cohort of individuals which can advocate powerful cohort for proper implementation of molecular methods.

Lessons Learned from Implementing a Wet Laboratory Molecular Training Workshop for Beach Water Quality Monitoring

PubMed Central

Verhougstraete, Marc Paul; Brothers, Sydney; Litaker, Wayne; Blackwood, A. Denene; Noble, Rachel

2015-01-01

Rapid molecular testing methods are poised to replace many of the conventional, culture-based tests currently used in fields such as water quality and food science. Rapid qPCR methods have the benefit of being faster than conventional methods and provide a means to more accurately protect public health. However, many scientists and technicians in water and food quality microbiology laboratories have limited experience using these molecular tests. To ensure that practitioners can use and implement qPCR techniques successfully, we developed a week long workshop to provide hands-on training and exposure to rapid molecular methods for water quality management. This workshop trained academic professors, government employees, private industry representatives, and graduate students in rapid qPCR methods for monitoring recreational water quality. Attendees were immersed in these new methods with hands-on laboratory sessions, lectures, and one-on-one training. Upon completion, the attendees gained sufficient knowledge and practice to teach and share these new molecular techniques with colleagues at their respective laboratories. Key findings from this workshop demonstrated: 1) participants with no prior experience could be effectively trained to conduct highly repeatable qPCR analysis in one week; 2) participants with different desirable outcomes required exposure to a range of different platforms and sample processing approaches; and 3) the collaborative interaction amongst newly trained practitioners, workshop leaders, and members of the water quality community helped foster a cohesive cohort of individuals which can advocate powerful cohort for proper implementation of molecular methods. PMID:25822486

Seasonal performance of a malaria rapid diagnosis test at community health clinics in a malaria-hyperendemic region of Burkina Faso

PubMed Central

2012-01-01

Backgound Treatment of confirmed malaria patients with Artemisinin-based Combination Therapy (ACT) at remote areas is the goal of many anti-malaria programs. Introduction of effective and affordable malaria Rapid Diagnosis Test (RDT) in remote areas could be an alternative tool for malaria case management. This study aimed to assess performance of the OptiMAL dipstick for rapid malaria diagnosis in children under five. Methods Malaria symptomatic and asymptomatic children were recruited in a passive manner in two community clinics (CCs). Malaria diagnosis by microscopy and RDT were performed. Performance of the tests was determined. Results RDT showed similar ability (61.2%) to accurately diagnose malaria as microscopy (61.1%). OptiMAL showed a high level of sensitivity and specificity, compared with microscopy, during both transmission seasons (high & low), with a sensitivity of 92.9% vs. 74.9% and a specificity of 77.2% vs. 87.5%. Conclusion By improving the performance of the test through accurate and continuous quality control of the device in the field, OptiMAL could be suitable for use at CCs for the management and control of malaria. PMID:22647557

Rapid separation and characterization of diterpenoid alkaloids in processed roots of Aconitum carmichaeli using ultra high performance liquid chromatography coupled with hybrid linear ion trap-Orbitrap tandem mass spectrometry.

PubMed

Xu, Wen; Zhang, Jing; Zhu, Dayuan; Huang, Juan; Huang, Zhihai; Bai, Junqi; Qiu, Xiaohui

2014-10-01

The lateral root of Aconitum carmichaeli, a popular traditional Chinese medicine, has been widely used to treat rheumatic diseases. For decades, diterpenoid alkaloids have dominated the phytochemical and biomedical research on this plant. In this study, a rapid and sensitive method based on ultra high performance liquid chromatography coupled with linear ion trap-Orbitrap tandem mass spectrometry was developed to characterize the diterpenoid alkaloids in Aconitum carmichaeli. Based on an optimized chromatographic condition, more than 120 diterpenoid alkaloids were separated with good resolution. Using a systematic strategy that combines high resolution separation, highly accurate mass measurements and a good understanding of the diagnostic fragment-based fragmentation patterns, these diterpenoid alkaloids were identified or tentatively identified. The identification of these chemicals provided essential data for further phytochemical studies and toxicity research of Aconitum carmichaeli. Moreover, the ultra high performance liquid chromatography with linear ion trap-Orbitrap mass spectrometry platform was an effective and accurate tool for rapid qualitative analysis of secondary metabolite productions from natural resources. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photogrammetry-Based Head Digitization for Rapid and Accurate Localization of EEG Electrodes and MEG Fiducial Markers Using a Single Digital SLR Camera.

PubMed

Clausner, Tommy; Dalal, Sarang S; Crespo-García, Maité

2017-01-01

The performance of EEG source reconstruction has benefited from the increasing use of advanced head modeling techniques that take advantage of MRI together with the precise positions of the recording electrodes. The prevailing technique for registering EEG electrode coordinates involves electromagnetic digitization. However, the procedure adds several minutes to experiment preparation and typical digitizers may not be accurate enough for optimal source reconstruction performance (Dalal et al., 2014). Here, we present a rapid, accurate, and cost-effective alternative method to register EEG electrode positions, using a single digital SLR camera, photogrammetry software, and computer vision techniques implemented in our open-source toolbox, janus3D . Our approach uses photogrammetry to construct 3D models from multiple photographs of the participant's head wearing the EEG electrode cap. Electrodes are detected automatically or semi-automatically using a template. The rigid facial features from these photo-based models are then surface-matched to MRI-based head reconstructions to facilitate coregistration to MRI space. This method yields a final electrode coregistration error of 0.8 mm, while a standard technique using an electromagnetic digitizer yielded an error of 6.1 mm. The technique furthermore reduces preparation time, and could be extended to a multi-camera array, which would make the procedure virtually instantaneous. In addition to EEG, the technique could likewise capture the position of the fiducial markers used in magnetoencephalography systems to register head position.

Photogrammetry-Based Head Digitization for Rapid and Accurate Localization of EEG Electrodes and MEG Fiducial Markers Using a Single Digital SLR Camera

PubMed Central

Clausner, Tommy; Dalal, Sarang S.; Crespo-García, Maité

2017-01-01

The performance of EEG source reconstruction has benefited from the increasing use of advanced head modeling techniques that take advantage of MRI together with the precise positions of the recording electrodes. The prevailing technique for registering EEG electrode coordinates involves electromagnetic digitization. However, the procedure adds several minutes to experiment preparation and typical digitizers may not be accurate enough for optimal source reconstruction performance (Dalal et al., 2014). Here, we present a rapid, accurate, and cost-effective alternative method to register EEG electrode positions, using a single digital SLR camera, photogrammetry software, and computer vision techniques implemented in our open-source toolbox, janus3D. Our approach uses photogrammetry to construct 3D models from multiple photographs of the participant's head wearing the EEG electrode cap. Electrodes are detected automatically or semi-automatically using a template. The rigid facial features from these photo-based models are then surface-matched to MRI-based head reconstructions to facilitate coregistration to MRI space. This method yields a final electrode coregistration error of 0.8 mm, while a standard technique using an electromagnetic digitizer yielded an error of 6.1 mm. The technique furthermore reduces preparation time, and could be extended to a multi-camera array, which would make the procedure virtually instantaneous. In addition to EEG, the technique could likewise capture the position of the fiducial markers used in magnetoencephalography systems to register head position. PMID:28559791

Comparison among four proposed direct blood culture microbial identification methods using MALDI-TOF MS.

PubMed

Bazzi, Ali M; Rabaan, Ali A; El Edaily, Zeyad; John, Susan; Fawarah, Mahmoud M; Al-Tawfiq, Jaffar A

Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry facilitates rapid and accurate identification of pathogens, which is critical for sepsis patients. In this study, we assessed the accuracy in identification of both Gram-negative and Gram-positive bacteria, except for Streptococcus viridans, using four rapid blood culture methods with Vitek MALDI-TOF-MS. We compared our proposed lysis centrifugation followed by washing and 30% acetic acid treatment method (method 2) with two other lysis centrifugation methods (washing and 30% formic acid treatment (method 1); 100% ethanol treatment (method 3)), and picking colonies from 90 to 180min subculture plates (method 4). Methods 1 and 2 identified all organisms down to species level with 100% accuracy, except for Streptococcus viridans, Streptococcus pyogenes, Enterobacter cloacae and Proteus vulgaris. The latter two were identified to genus level with 100% accuracy. Each method exhibited excellent accuracy and precision in terms of identification to genus level with certain limitations. Copyright © 2016 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

[An integrated segmentation method for 3D ultrasound carotid artery].

PubMed

Yang, Xin; Wu, Huihui; Liu, Yang; Xu, Hongwei; Liang, Huageng; Cai, Wenjuan; Fang, Mengjie; Wang, Yujie

2013-07-01

An integrated segmentation method for 3D ultrasound carotid artery was proposed. 3D ultrasound image was sliced into transverse, coronal and sagittal 2D images on the carotid bifurcation point. Then, the three images were processed respectively, and the carotid artery contours and thickness were obtained finally. This paper tries to overcome the disadvantages of current computer aided diagnosis method, such as high computational complexity, easily introduced subjective errors et al. The proposed method could get the carotid artery overall information rapidly, accurately and completely. It could be transplanted into clinical usage for atherosclerosis diagnosis and prevention.

Serum protein measurement using a tapered fluorescent fibre-optic evanescent wave-based biosensor

NASA Astrophysics Data System (ADS)

Preejith, P. V.; Lim, C. S.; Chia, T. F.

2006-12-01

A novel method to measure the total serum protein concentration is described in this paper. The method is based on the principles of fibre-optic evanescent wave spectroscopy. The biosensor applies a fluorescent dye-immobilized porous glass coating on a multi-mode optical fibre. The evanescent wave's intensity at the fibre-optic core-cladding interface is used to monitor the protein-induced changes in the sensor element. The sensor offers a rapid, single-step method for quantifying protein concentrations without destroying the sample. This unique sensing method presents a sensitive and accurate platform for the quantification of protein.

Optimal Cluster Mill Pass Scheduling With an Accurate and Rapid New Strip Crown Model

NASA Astrophysics Data System (ADS)

Malik, Arif S.; Grandhi, Ramana V.; Zipf, Mark E.

2007-05-01

Besides the requirement to roll coiled sheet at high levels of productivity, the optimal pass scheduling of cluster-type reversing cold mills presents the added challenge of assigning mill parameters that facilitate the best possible strip flatness. The pressures of intense global competition, and the requirements for increasingly thinner, higher quality specialty sheet products that are more difficult to roll, continue to force metal producers to commission innovative flatness-control technologies. This means that during the on-line computerized set-up of rolling mills, the mathematical model should not only determine the minimum total number of passes and maximum rolling speed, it should simultaneously optimize the pass-schedule so that desired flatness is assured, either by manual or automated means. In many cases today, however, on-line prediction of strip crown and corresponding flatness for the complex cluster-type rolling mills is typically addressed either by trial and error, by approximate deflection models for equivalent vertical roll-stacks, or by non-physical pattern recognition style models. The abundance of the aforementioned methods is largely due to the complexity of cluster-type mill configurations and the lack of deflection models with sufficient accuracy and speed for on-line use. Without adequate assignment of the pass-schedule set-up parameters, it may be difficult or impossible to achieve the required strip flatness. In this paper, we demonstrate optimization of cluster mill pass-schedules using a new accurate and rapid strip crown model. This pass-schedule optimization includes computations of the predicted strip thickness profile to validate mathematical constraints. In contrast to many of the existing methods for on-line prediction of strip crown and flatness on cluster mills, the demonstrated method requires minimal prior tuning and no extensive training with collected mill data. To rapidly and accurately solve the multi-contact problem and predict the strip crown, a new customized semi-analytical modeling technique that couples the Finite Element Method (FEM) with classical solid mechanics was developed to model the deflection of the rolls and strip while under load. The technique employed offers several important advantages over traditional methods to calculate strip crown, including continuity of elastic foundations, non-iterative solution when using predetermined foundation moduli, continuous third-order displacement fields, simple stress-field determination, and a comparatively faster solution time.

Rapid and precise determination of total sulphur in soda-lime-silica glasses.

PubMed

Beesley, W J; Chamberlain, B R

1974-04-01

A method is described for the determination of total sulphur in small amounts of soda-lime-silica glasses (100 mg or less). The crushed glass is mixed with vanadium pentoxide and decomposed at 1450 degrees under oxygen. The sulphur is quantitatively removed from the glass and determined by a conductometric technique. The method is standardized by accurately injecting sulphur dioxide into the furnace tube. The analysis time is about 10 min and the overall precision (2s) is of the order of 5%.

Sensing and Active Flow Control for Advanced BWB Propulsion-Airframe Integration Concepts

NASA Technical Reports Server (NTRS)

Fleming, John; Anderson, Jason; Ng, Wing; Harrison, Neal

2005-01-01

In order to realize the substantial performance benefits of serpentine boundary layer ingesting diffusers, this study investigated the use of enabling flow control methods to reduce engine-face flow distortion. Computational methods and novel flow control modeling techniques were utilized that allowed for rapid, accurate analysis of flow control geometries. Results were validated experimentally using the Techsburg Ejector-based wind tunnel facility; this facility is capable of simulating the high-altitude, high subsonic Mach number conditions representative of BWB cruise conditions.

Efficient hybrid-symbolic methods for quantum mechanical calculations

NASA Astrophysics Data System (ADS)

Scott, T. C.; Zhang, Wenxing

2015-06-01

We present hybrid symbolic-numerical tools to generate optimized numerical code for rapid prototyping and fast numerical computation starting from a computer algebra system (CAS) and tailored to any given quantum mechanical problem. Although a major focus concerns the quantum chemistry methods of H. Nakatsuji which has yielded successful and very accurate eigensolutions for small atoms and molecules, the tools are general and may be applied to any basis set calculation with a variational principle applied to its linear and non-linear parameters.

GRAVIMETRIC DETERMINATION OF PLATINIUM, PALLADIUM, RUTHENIUM, RHODIUM AS TlPtS$sub 3$, TlPd$sub 2$S$sub 3$, TlRu$sub 2$S$sub 6$, TlRh$sub 2$S$sub 4$ (in Russian)

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

Rudnev, N.A.; Malofeeva, G.I.

1963-07-01

Gravimetric methods were developed for the determination of microamounts of Ru, Rh, Pt, and Pd as TlRu/sub 2/S/sub 6/, TlRh/sub 2/S/sub 4/ TlPtS/sub 3/, and TlPd/sub 2/S/sub 3/. The methods are simpl e, rapid, and satisfactorily accurate. (auth)

Development of Advanced Methods of Structural and Trajectory Analysis for Transport Aircraft

NASA Technical Reports Server (NTRS)

Ardema, Mark D.

1996-01-01

In this report the author describes: (1) development of advanced methods of structural weight estimation, and (2) development of advanced methods of flight path optimization. A method of estimating the load-bearing fuselage weight and wing weight of transport aircraft based on fundamental structural principles has been developed. This method of weight estimation represents a compromise between the rapid assessment of component weight using empirical methods based on actual weights of existing aircraft and detailed, but time-consuming, analysis using the finite element method. The method was applied to eight existing subsonic transports for validation and correlation. Integration of the resulting computer program, PDCYL, has been made into the weights-calculating module of the AirCraft SYNThesis (ACSYNT) computer program. ACSYNT bas traditionally used only empirical weight estimation methods; PDCYL adds to ACSYNT a rapid, accurate means of assessing the fuselage and wing weights of unconventional aircraft. PDCYL also allows flexibility in the choice of structural concept, as well as a direct means of determining the impact of advanced materials on structural weight.

Indirect enzyme-linked immunosorbent assay method based on Streptococcus agalactiae rSip-Pgk-FbsA fusion protein for detection of bovine mastitis.

PubMed

Bu, Ri-E; Wang, Jin-Liang; Wu, Jin-Hua; Xilin, Gao-Wa; Chen, Jin-Long; Wang, Hua

2017-03-01

The aim of this study was to establish a rapid and accurate method for the detection of the Streptococcus agalactiae antibody (SA-Ab) to determine the presence of the bovine mastitis (BM)-causative pathogen. The multi-subunit fusion protein rSip-Pgk-FbsA was prokaryotically expressed and purified. The triple activities of the membrane surface-associated proteins Sip, phosphoglycerate kinase (Pgk), and fibronectin (FbsA) were used as the diagnostic antigens to establish an indirect enzyme-linked immunosorbent assay (ELISA) method for the detection of SA-Ab in BM. The optimal antigen coating concentration was 2 μg/mL, the optimal serum dilution was 1:160, and the optimal dilution of the enzyme-labeled secondary antibody was 1:6000. The sensitivity, specificity, and repeatability tests showed that the method established in this study had no cross-reaction with antibodies to Streptococcus pyogenes, Escherichia coli, Staphylococcus aureus, and Staphylococcus epidermidis in the sera. The results of the sensitivity test showed that a positive result could be obtained even if the serum dilution reached 1:12,800, indicating the high sensitivity and good repeatability of the method. The positive coincidence rate of this method was 98.6%, which is higher than that of previous tests established with the Sip or Pgk mono-antigen fusion protein, respectively, demonstrating the relatively higher sensitivity of this newly established method. The detection rate for 389 clinical samples was 46.53%. The indirect ELISA method established in this study could provide a more accurate and reliable serological method for the rapid detection of S. agalactiae in cases of BM.

Prediction of packaging seal life using thermoanalytical techniques

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

Nigrey, P.J.

1997-11-01

In this study, Thermogravimetric Analysis (TGA) has been used to study silicone, Viton and Ethylene Propylene (EPDM) rubber. The studies have shown that TGA accurately predicts the relative order of thermo-oxidative stability of these three materials from the calculated activation energies. As expected, the greatest thermal stability was found in silicone rubber followed by Viton and EPDM rubber. The calculated lifetimes for these materials were in relatively close agreement with published values. The preliminary results also accurately reflect decreased thermal stability and lifetime for EPDM rubber exposed to radiation and chemicals. These results suggest TGA provides a rapid method tomore » evaluate material stability.« less

A Rapid Method for the Determination of Fucoxanthin in Diatom

PubMed Central

Wang, Li-Juan; Fan, Yong; Parsons, Ronald L.; Hu, Guang-Rong; Zhang, Pei-Yu

2018-01-01

Fucoxanthin is a natural pigment found in microalgae, especially diatoms and Chrysophyta. Recently, it has been shown to have anti-inflammatory, anti-tumor, and anti-obesityactivity in humans. Phaeodactylum tricornutum is a diatom with high economic potential due to its high content of fucoxanthin and eicosapentaenoic acid. In order to improve fucoxanthin production, physical and chemical mutagenesis could be applied to generate mutants. An accurate and rapid method to assess the fucoxanthin content is a prerequisite for a high-throughput screen of mutants. In this work, the content of fucoxanthin in P. tricornutum was determined using spectrophotometry instead of high performance liquid chromatography (HPLC). This spectrophotometric method is easier and faster than liquid chromatography and the standard error was less than 5% when compared to the HPLC results. Also, this method can be applied to other diatoms, with standard errors of 3–14.6%. It provides a high throughput screening method for microalgae strains producing fucoxanthin. PMID:29361768

Rapid screening and determination of 11 new psychoactive substances by direct analysis in real time mass spectrometry and liquid chromatography/quadrupole time-of-flight mass spectrometry.

PubMed

Nie, Honggang; Li, Xianjiang; Hua, Zhendong; Pan, Wei; Bai, Yanping; Fu, Xiaofang

2016-08-01

With the amounts and types of new psychoactive substances (NPSs) increasing rapidly in recent years, an excellent high-throughput method for the analysis of these compounds is urgently needed. In this article, a rapid screening method and a quantitative analysis method for 11 NPSs are described and compared, respectively. A simple direct analysis in real time mass spectrometry (DART-MS) method was developed for the analysis of 11 NPSs including three categories of these substances present on the global market such as four cathinones, one phenylethylamine, and six synthetic cannabinoids. In order to analyze these compounds quantitatively with better accuracy and sensitivity, another rapid analytical method with a low limit of detection (LOD) was also developed using liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry (LC/QTOFMS). The 11 NPSs could be determined within 0.5 min by DART-MS. Furthermore, they could also be separated and determined within 5 min by the LC/QTOFMS method. The two methods both showed good linearity with correlation coefficients (r(2) ) higher than 0.99. The LODs for all these target NPSs by DART-MS and LC/QTOFMS ranged from 5 to 40 ng mL(-1) and 0.1 to 1 ng mL(-1) , respectively. Confiscated samples, named as "music vanilla" and "bath salt", and 11 spiked samples were firstly screened by DART-MS and then determined by LC/QTOFMS. The identification of NPSs in confiscated materials was successfully achieved, and the proposed analytical methodology could offer rapid screening and accurate analysis results. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Nuclear Magnetic Resonance Spectroscopy-Based Identification of Yeast.

PubMed

Himmelreich, Uwe; Sorrell, Tania C; Daniel, Heide-Marie

2017-01-01

Rapid and robust high-throughput identification of environmental, industrial, or clinical yeast isolates is important whenever relatively large numbers of samples need to be processed in a cost-efficient way. Nuclear magnetic resonance (NMR) spectroscopy generates complex data based on metabolite profiles, chemical composition and possibly on medium consumption, which can not only be used for the assessment of metabolic pathways but also for accurate identification of yeast down to the subspecies level. Initial results on NMR based yeast identification where comparable with conventional and DNA-based identification. Potential advantages of NMR spectroscopy in mycological laboratories include not only accurate identification but also the potential of automated sample delivery, automated analysis using computer-based methods, rapid turnaround time, high throughput, and low running costs.We describe here the sample preparation, data acquisition and analysis for NMR-based yeast identification. In addition, a roadmap for the development of classification strategies is given that will result in the acquisition of a database and analysis algorithms for yeast identification in different environments.

Scalable Algorithms for Global Scale Remote Sensing Applications

NASA Astrophysics Data System (ADS)

Vatsavai, R. R.; Bhaduri, B. L.; Singh, N.

2015-12-01

Recent decade has witnessed major changes on the Earth, for example, deforestation, varying cropping and human settlement patterns, and crippling damages due to disasters. Accurate damage assessment caused by major natural and anthropogenic disasters is becoming critical due to increases in human and economic loss. This increase in loss of life and severe damages can be attributed to the growing population, as well as human migration to the disaster prone regions of the world. Rapid assessment of these changes and dissemination of accurate information is critical for creating an effective emergency response. Change detection using high-resolution satellite images is a primary tool in assessing damages, monitoring biomass and critical infrastructures, and identifying new settlements. Existing change detection methods suffer from registration errors and often based on pixel (location) wise comparison of spectral observations from single sensor. In this paper we present a novel probabilistic change detection framework based on patch comparison and a GPU implementation that supports near real-time rapid damage exploration capability.

Direct quantification of lipopeptide biosurfactants in biological samples via HPLC and UPLC-MS requires sample modification with an organic solvent.

PubMed

Biniarz, Piotr; Łukaszewicz, Marcin

2017-06-01

The rapid and accurate quantification of biosurfactants in biological samples is challenging. In contrast to the orcinol method for rhamnolipids, no simple biochemical method is available for the rapid quantification of lipopeptides. Various liquid chromatography (LC) methods are promising tools for relatively fast and exact quantification of lipopeptides. Here, we report strategies for the quantification of the lipopeptides pseudofactin and surfactin in bacterial cultures using different high- (HPLC) and ultra-performance liquid chromatography (UPLC) systems. We tested three strategies for sample pretreatment prior to LC analysis. In direct analysis (DA), bacterial cultures were injected directly and analyzed via LC. As a modification, we diluted the samples with methanol and detected an increase in lipopeptide recovery in the presence of methanol. Therefore, we suggest this simple modification as a tool for increasing the accuracy of LC methods. We also tested freeze-drying followed by solvent extraction (FDSE) as an alternative for the analysis of "heavy" samples. In FDSE, the bacterial cultures were freeze-dried, and the resulting powder was extracted with different solvents. Then, the organic extracts were analyzed via LC. Here, we determined the influence of the extracting solvent on lipopeptide recovery. HPLC methods allowed us to quantify pseudofactin and surfactin with run times of 15 and 20 min per sample, respectively, whereas UPLC quantification was as fast as 4 and 5.5 min per sample, respectively. Our methods provide highly accurate measurements and high recovery levels for lipopeptides. At the same time, UPLC-MS provides the possibility to identify lipopeptides and their structural isoforms.

Identification of Low-Level Vancomycin Resistance in Staphylococcus aureus in the Era of Informatics.

PubMed

Ford, Bradley A

2016-04-01

Vancomycin-intermediateStaphylococcus aureus(VISA) and heteroresistant VISA (hVISA) are pathogens for which accurate antimicrobial susceptibility testing (AST) would rule out standard treatment with vancomycin. Unfortunately, AST for vancomycin is relatively slow and standard methods are unable to reliably detect VISA and hVISA. An article in this issue (C. A. Mather, B. J. Werth, S. Sivagnanam, D. J. SenGupta, and S. M. Butler-Wu, J Clin Microbiol 54:883-890, 2016, doi:http://dx.doi.org/10.1128/JCM.02428-15) describes a rapid whole-cell matrix-assisted laser desorption ionization-time of flight proxy susceptibility method that highlights current innovations and challenges with rapid AST, VISA/hVISA identification, and clinical bioinformatics. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

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

2018-06-01

Rapid and accurate identification and classification of microorganisms is of paramount importance to public health and safety. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is complicating correct microbial identification even in a simple sample due to the large number of candidates present. To properly untwine candidate microbes in samples containing one or more microbes, one needs to go beyond apparent morphology or simple "fingerprinting"; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptide-centric representations of microbes to better separate them and by augmenting our earlier analysis method that yields accurate statistical significance. Here, we present an updated analysis workflow that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using 226 MS/MS publicly available data files (each containing from 2500 to nearly 100,000 MS/MS spectra) and 4000 additional MS/MS data files, that the updated workflow can correctly identify multiple microbes at the genus and often the species level for samples containing more than one microbe. We have also shown that the proposed workflow computes accurate statistical significances, i.e., E values for identified peptides and unified E values for identified microbes. Our updated analysis workflow MiCId, a freely available software for Microorganism Classification and Identification, is available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry.

PubMed

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

2018-06-05

Rapid and accurate identification and classification of microorganisms is of paramount importance to public health and safety. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is complicating correct microbial identification even in a simple sample due to the large number of candidates present. To properly untwine candidate microbes in samples containing one or more microbes, one needs to go beyond apparent morphology or simple "fingerprinting"; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptide-centric representations of microbes to better separate them and by augmenting our earlier analysis method that yields accurate statistical significance. Here, we present an updated analysis workflow that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using 226 MS/MS publicly available data files (each containing from 2500 to nearly 100,000 MS/MS spectra) and 4000 additional MS/MS data files, that the updated workflow can correctly identify multiple microbes at the genus and often the species level for samples containing more than one microbe. We have also shown that the proposed workflow computes accurate statistical significances, i.e., E values for identified peptides and unified E values for identified microbes. Our updated analysis workflow MiCId, a freely available software for Microorganism Classification and Identification, is available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html . Graphical Abstract ᅟ.

[Flow injection biamperometric analysis of isoniazid].

PubMed

Zhang, J C; Zhao, C; Song, J F

2001-09-01

To establish a simple, rapid, and accurate electrochemical method for on-line determination of isoniazid. Based on the flow injection biamperometry for irreversible couple system, and using two preanodized platinum electrodes with the applied potential difference of 0 V, the biamperometric method for the determination of isoniazid has been proposed by coupling the catalytic oxidation of isoniazid and the reduction of platinum oxide. Common excipients, inorganic ions, amino acids, vitamins and proteins do not interfere with the determination. Linear relationship between current and the concentration of isoniazid is obtained in the range of 1.0 x 10(-6)-1.0 x 10(-4) mol.L-1 (gamma = 0.998, n = 11). The RSD of 1.8% was obtained for 8 successive determinations of 1.0 x 10(-5) mol.L-1 isoniazid. The proposed method has been shown to be sensitive, selective, rapid (120 samples.h-1), and suitable for the on-line direct determination of isoniazid.

Rapid and reliable quantitation of amino acids and myo-inositol in mouse brain by high performance liquid chromatography and tandem mass spectrometry.

PubMed

Bathena, Sai P; Huang, Jiangeng; Epstein, Adrian A; Gendelman, Howard E; Boska, Michael D; Alnouti, Yazen

2012-04-15

Amino acids and myo-inositol have long been proposed as putative biomarkers for neurodegenerative diseases. Accurate measures and stability have precluded their selective use. To this end, a sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) method based on multiple reaction monitoring was developed to simultaneously quantify glutamine, glutamate, γ-aminobutyric acid (GABA), aspartic acid, N-acetyl aspartic acid, taurine, choline, creatine, phosphocholine and myo-inositol in mouse brain by methanol extractions. Chromatography was performed using a hydrophilic interaction chromatography silica column within in a total run time of 15 min. The validated method is selective, sensitive, accurate, and precise. The method has a limit of quantification ranging from 2.5 to 20 ng/ml for a range of analytes and a dynamic range from 2.5-20 to 500-4000 ng/ml. This LC-MS/MS method was validated for biomarker discovery in models of human neurological disorders. Copyright © 2012 Elsevier B.V. All rights reserved.

A scanning PIV method for fine-scale turbulence measurements

NASA Astrophysics Data System (ADS)

Lawson, John M.; Dawson, James R.

2014-12-01

A hybrid technique is presented that combines scanning PIV with tomographic reconstruction to make spatially and temporally resolved measurements of the fine-scale motions in turbulent flows. The technique uses one or two high-speed cameras to record particle images as a laser sheet is rapidly traversed across a measurement volume. This is combined with a fast method for tomographic reconstruction of the particle field for use in conjunction with PIV cross-correlation. The method was tested numerically using DNS data and with experiments in a large mixing tank that produces axisymmetric homogeneous turbulence at . A parametric investigation identifies the important parameters for a scanning PIV set-up and provides guidance to the interested experimentalist in achieving the best accuracy. Optimal sheet spacings and thicknesses are reported, and it was found that accurate results could be obtained at quite low scanning speeds. The two-camera method is the most robust to noise, permitting accurate measurements of the velocity gradients and direct determination of the dissipation rate.

Evaluation of the pulse-contour method of determining stroke volume in man.

NASA Technical Reports Server (NTRS)

Alderman, E. L.; Branzi, A.; Sanders, W.; Brown, B. W.; Harrison, D. C.

1972-01-01

The pulse-contour method for determining stroke volume has been employed as a continuous rapid method of monitoring the cardiovascular status of patients. Twenty-one patients with ischemic heart disease and 21 patients with mitral valve disease were subjected to a variety of hemodynamic interventions. The pulse-contour estimations, using three different formulas derived by Warner, Kouchoukos, and Herd, were compared with indicator-dilution outputs. A comparison of the results of the two methods for determining stroke volume yielded correlation coefficients ranging from 0.59 to 0.84. The better performing Warner formula yielded a coefficient of variation of about 20%. The type of hemodynamic interventions employed did not significantly affect the results using the pulse-contour method. Although the correlation of the pulse-contour and indicator-dilution stroke volumes is high, the coefficient of variation is such that small changes in stroke volume cannot be accurately assessed by the pulse-contour method. However, the simplicity and rapidity of this method compared to determination of cardiac output by Fick or indicator-dilution methods makes it a potentially useful adjunct for monitoring critically ill patients.

Holographic deep learning for rapid optical screening of anthrax spores

PubMed Central

Jo, YoungJu; Park, Sangjin; Jung, JaeHwang; Yoon, Jonghee; Joo, Hosung; Kim, Min-hyeok; Kang, Suk-Jo; Choi, Myung Chul; Lee, Sang Yup; Park, YongKeun

2017-01-01

Establishing early warning systems for anthrax attacks is crucial in biodefense. Despite numerous studies for decades, the limited sensitivity of conventional biochemical methods essentially requires preprocessing steps and thus has limitations to be used in realistic settings of biological warfare. We present an optical method for rapid and label-free screening of Bacillus anthracis spores through the synergistic application of holographic microscopy and deep learning. A deep convolutional neural network is designed to classify holographic images of unlabeled living cells. After training, the network outperforms previous techniques in all accuracy measures, achieving single-spore sensitivity and subgenus specificity. The unique “representation learning” capability of deep learning enables direct training from raw images instead of manually extracted features. The method automatically recognizes key biological traits encoded in the images and exploits them as fingerprints. This remarkable learning ability makes the proposed method readily applicable to classifying various single cells in addition to B. anthracis, as demonstrated for the diagnosis of Listeria monocytogenes, without any modification. We believe that our strategy will make holographic microscopy more accessible to medical doctors and biomedical scientists for easy, rapid, and accurate point-of-care diagnosis of pathogens. PMID:28798957

Rapid automated classification of anesthetic depth levels using GPU based parallelization of neural networks.

PubMed

Peker, Musa; Şen, Baha; Gürüler, Hüseyin

2015-02-01

The effect of anesthesia on the patient is referred to as depth of anesthesia. Rapid classification of appropriate depth level of anesthesia is a matter of great importance in surgical operations. Similarly, accelerating classification algorithms is important for the rapid solution of problems in the field of biomedical signal processing. However numerous, time-consuming mathematical operations are required when training and testing stages of the classification algorithms, especially in neural networks. In this study, to accelerate the process, parallel programming and computing platform (Nvidia CUDA) facilitates dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU) was utilized. The system was employed to detect anesthetic depth level on related electroencephalogram (EEG) data set. This dataset is rather complex and large. Moreover, the achieving more anesthetic levels with rapid response is critical in anesthesia. The proposed parallelization method yielded high accurate classification results in a faster time.

Comparison of spot esculin hydrolysis with the PathoTec strip test for rapid differentiation of anaerobic bacteria.

PubMed Central

Qadri, S M; Johnson, S; Smith, J C; Zubairi, S; Gillum, R L

1981-01-01

The ability of several anaerobic bacteria to hydrolyze esculin to esculetin is used by clinical microbiologists and taxonomists in the differentiation and identification of both gram-positive and gram-negative microorganisms. Conventional methods used for determining esculin hydrolysis by anaerobic bacteria require 24 to 48 h for completion. In this paper we evaluate two procedures which yield rapid results. A total of 738 anaerobic bacteria were used in this study. A total of 99% of the esculin-hydrolyzing anaerobic bacteria gave positive results with the spot test in 1 h, whereas the other test method, the PathoTec strip test (General Diagnostics, Morris Plains, N.J.), required 4 h for 96% of the strains tested to yield positive reactions. Both tests showed a 100% specificity when compared with the standard broth test and are easy to perform, accurate, and economical. The spot test is superior to the PathoTec strip test in yielding results more rapidly. PMID:7016896

PATtyFams: Protein families for the microbial genomes in the PATRIC database

DOE PAGES

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.; ...

2016-02-08

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based functionmore » assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.« less

Rapid and accurate identification of in vivo-induced haploid seeds based on oil content in maize

PubMed Central

Melchinger, Albrecht E.; Schipprack, Wolfgang; Würschum, Tobias; Chen, Shaojiang; Technow, Frank

2013-01-01

The needs of a growing human population require rapid and efficient development of improved cultivars by plant breeders. The doubled haploid (DH) technology enables generating completely homozygous lines in a single step and, thus, is central to modern genetics and breeding approaches. Rapid and reliable identification of seeds with a haploid embryo after in vivo haploid induction is elementary in the method utilized in maize but current systems have severe shortcomings preventing their use in many germplasm types. Here, we describe an alternative method for discrimination of haploid from diploid seeds based on differences in their oil content stemming from pollination with high oil inducers. After presenting some fundamental theory, we provide a proof-of-concept with experimental results, demonstrating acceptable error rates across different germplasm. Our approach represents a breakthrough in DH technology in maize, because it is amenable to automated high-throughput screening and applicable to any maize germplasm worldwide. PMID:23820577

PATtyFams: Protein families for the microbial genomes in the PATRIC database

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

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based functionmore » assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.« less

UPLC/Q-TOFMS/MS as a powerful technique for rapid identification of polymethoxylated flavones in Fructus aurantii.

PubMed

Zhou, Da-Yong; Zhang, Xiu-Li; Xu, Qing; Xue, Xing-Ya; Zhang, Fei-Fang; Liang, Xin-Miao

2009-08-15

Polymethoxylated flavones (PMFs), as potential cancer chemopreventive agents, are widely distributed in Citrus genus. In this study, a selected ion monitoring-tandem mass (SIM-MS/MS) method for the rapid identification of PMFs in Fructus aurantii (F. aurantii) with ultra-performance liquid chromatography (UPLC) coupled to quadrupole, hybrid orthogonal acceleration time-of-flight tandem mass spectrometer (Q-TOFMS/MS) was proposed. The MS data for candidates, containing accurate mass and isotopic patterns for both precursors and their fragment ions, were acquired selectively. Based on the MS data, the mass spectrometric fingerprint (MSFP) for candidates, consisting of chemical formula and dissociation pattern, was determined. Comparing the MSFPs of the observed compounds with the diagnostic MSFP of the species, 44 PMFs were tentatively identified. The method was validated by tangeretin and sinensetin, two representative compounds of PMFs, and was considered to be suitable for the rapid screening of PMFs in crude and partially purified samples.

Rapid in situ identification of bioactive compounds in plants by in vivo nanospray high-resolution mass spectrometry.

PubMed

Chang, Qing; Peng, Yue'e; Dan, Conghui; Shuai, Qin; Hu, Shenghong

2015-03-25

A method for the rapid in situ identification of bioactive compounds in fresh plants has been developed using in vivo nanospray coupled to high-resolution mass spectrometry (HR-MS). Using a homemade in vivo nanospray ion source, the plant liquid was drawn out from a target region and ionized in situ. The ionized bioactive compounds were then identified using Q-Orbitrap HR-MS. The accurate mass measurements of these bioactive compounds were performed by full-scan or selected ion monitoring (SIM), and tandem mass spectrometry (MS/MS) was used in the structural elucidation. Without sample pretreatment, 12 bioactive compounds in 7 different plant species were identified, namely, isoalliin in onion; butylphthalide in celery; N-methylpelletierine, pelletierine, and pseudopelletierine in pomegranate; chlorogenic acid in crabapple; solamargine, solasonine, and solasodine in nightshade; aloin and aloe-emodin in aloe; and menthone in mint. This work demonstrates that in vivo nanospray HR-MS is a good method for rapid in situ identification of bioactive compounds in plants.

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

PubMed Central

2015-01-01

Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. PMID:25182276

[Rapid screening and identification of 22 allergenic disperse dyes in ecological textiles by high performance liquid chromatography-linear ion trap/orbitrap mass spectrometry].

PubMed

Niu, Zengyuan; Luo, Xin; Ye, Xiwen; Xiu, Xiaoli; Zhang, Li; Wang, Xin; Chen, Jing

2015-10-01

A rapid screening method based on high performance liquid chromatography-linear ion trap/orbitrap high-resolution mass spectrometry (HPLC-LTQ/Orbitrap MS) for 22 disperse dyes in ecological textiles has been established. The target compounds were extracted by pyridine/water (1:1, v/v) by shaking extraction in 90 degrees C water bath. The extracts were then separated by a CAPCELL PAK C18 column (100 mm x 2.0 mm, 5 μm) using gradient elution with acetonitrile-5 mmol/L ammonium acetate containing 0.01% (v/v) formic acid as mobile phases, and finally analyzed by HPLC-LTQ/Orbitrap in positive and negative ESI modes. The retention time and accurate mass of parent ion were used for fast screening of 22 disperse dyes, while the confirmatory analysis was obtained by fragments generated by collision-induced dissociation (CID) MS/MS. Target analysis exhibited high mass accuracy (< 5 x 10(-6)). Each target showed a good linearity in its own concentration range and the correlation coefficient was higher than 0.99. The LOQs were 0.125-2.5 mg/kg. Except for Disperse Yellow 49, the average recoveries of most disperse dyes at three spiked levels were 65%-120%, and the relative standard deviations (n = 6) were less than 15%. The method was applied for screening 40 different kinds of textiles, and Disperse Orange 37/76 was detected in one of them. With high selectivity and strong anti-jamming ability, this method is simple, rapid, accurate, and it can be used for the inspection of disperse dyes in textiles.

Rapid and quantitative detection of the microbial spoilage in chicken meat by diffuse reflectance spectroscopy (600-1100 nm).

PubMed

Lin, M; Al-Holy, M; Mousavi-Hesary, M; Al-Qadiri, H; Cavinato, A G; Rasco, B A

2004-01-01

To evaluate the feasibility of visible and short-wavelength near-infrared (SW-NIR) diffuse reflectance spectroscopy (600-1100 nm) to quantify the microbial loads in chicken meat and to develop a rapid methodology for monitoring the onset of spoilage. Twenty-four prepackaged fresh chicken breast muscle samples were prepared and stored at 21 degrees C for 24 h. Visible and SW-NIR was used to detect and quantify the microbial loads in chicken breast muscle at time intervals of 0, 2, 4, 6, 8, 10, 12 and 24 h. Spectra were collected in the diffuse reflectance mode (600-1100 nm). Total aerobic plate count (APC) of each sample was determined by the spread plate method at 32 degrees C for 48 h. Principal component analysis (PCA) and partial least squares (PLS) based prediction models were developed. PCA analysis showed clear segregation of samples held 8 h or longer compared with 0-h control. An optimum PLS model required eight latent variables for chicken muscle (R = 0.91, SEP = 0.48 log CFU g(-1)). Visible and SW-NIR combined with PCA is capable of perceiving the change of the microbial loads in chicken muscle once the APC increases slightly above 1 log cycle. Accurate quantification of the bacterial loads in chicken muscle can be calculated from the PLS-based prediction method. Visible and SW-NIR spectroscopy is a technique with a considerable potential for monitoring food safety and food spoilage. Visible and SW-NIR can acquire a metabolic snapshot and quantify the microbial loads of food samples rapidly, accurately, and noninvasively. This method would allow for more expeditious applications of quality control in food industries.

The use of quantitative real-time reverse transcriptase PCR for 5' and 3' portions of ALK transcripts to detect ALK rearrangements in lung cancers.

PubMed

Wang, Rui; Pan, Yunjian; Li, Chenguang; Hu, Haichuan; Zhang, Yang; Li, Hang; Luo, Xiaoyang; Zhang, Jie; Fang, Zhaoyuan; Li, Yuan; Shen, Lei; Ji, Hongbin; Garfield, David; Sun, Yihua; Chen, Haiquan

2012-09-01

Approximately 3% to 7% of non-small cell lung cancers (NSCLC) harbor an ALK fusion gene, thus defining a tumor group that may be responsive to targeted therapy. The breakpoint in ALK consistently occurs at exon 20 and EML4 or other fusion partners, thus driving a strong expression of ALK kinase domain and resulting in an unbalanced expression in 5' and 3' portions of ALK transcripts. We have developed a rapid and accurate method by simultaneously detecting the expression in 5' and 3' portions of ALK mRNA. Quantitative real-time reverse transcriptase PCR (qRT-PCR) was used to examine expression levels of the 5' and 3' portions of ALK transcripts in177 NSCLCs, in which EGFR, KRAS, HER2, and BRAF mutations were absent. If unbalanced ALK mRNA expression was seen, ALK rearrangement was assumed to exist. ALK FISH was used to confirm the accuracy of qRT-PCR. RT-PCR and 5' RACE coupling sequencing identified the fusion variants. Real-time RT-PCR showed excellent sensitivity and specificity (100% and 100%, respectively) for detection of ALK rearrangements in resected specimens. In addition, six novel ALK fusion variants were identified, including one KIF5B-ALK (E17;A20) and five EML4-ALK variants (E6a;A19, E6a/b ins 18;A20, E17b ins 39;A20, E10a/b, E13;A20, and E17 ins 65;A20). Real-time RT-PCR is a rapid and accurate method for diagnosing ALK-rearranged lung cancers. Coupling of 5' RACE to this method should further facilitate rapid identification of novel ALK fusion genes. ©2012 AACR.

Energy dispersive X-ray fluorescence and scattering assessment of soil quality via partial least squares and artificial neural networks analytical modeling approaches.

PubMed

Kaniu, M I; Angeyo, K H; Mwala, A K; Mwangi, F K

2012-08-30

Soil quality assessment (SQA) calls for rapid, simple and affordable but accurate analysis of soil quality indicators (SQIs). Routine methods of soil analysis are tedious and expensive. Energy dispersive X-ray fluorescence and scattering (EDXRFS) spectrometry in conjunction with chemometrics is a potentially powerful method for rapid SQA. In this study, a 25 m Ci (109)Cd isotope source XRF spectrometer was used to realize EDXRFS spectrometry of soils. Glycerol (a simulate of "organic" soil solution) and kaolin (a model clay soil) doped with soil micro (Fe, Cu, Zn) and macro (NO(3)(-), SO(4)(2-), H(2)PO(4)(-)) nutrients were used to train multivariate chemometric calibration models for direct (non-invasive) analysis of SQIs based on partial least squares (PLS) and artificial neural networks (ANN). The techniques were compared for each SQI with respect to speed, robustness, correction ability for matrix effects, and resolution of spectral overlap. The method was then applied to perform direct rapid analysis of SQIs in field soils. A one-way ANOVA test showed no statistical difference at 95% confidence interval between PLS and ANN results compared to reference soil nutrients. PLS was more accurate analyzing C, N, Na, P and Zn (R(2)>0.9) and low SEP of (0.05%, 0.01%, 0.01%, and 1.98 μg g(-1)respectively), while ANN was better suited for analysis of Mg, Cu and Fe (R(2)>0.9 and SEP of 0.08%, 4.02 μg g(-1), and 0.88 μg g(-1) respectively). Copyright © 2012 Elsevier B.V. All rights reserved.

Efficient quantification of water content in edible oils by headspace gas chromatography with vapour phase calibration.

PubMed

Xie, Wei-Qi; Gong, Yi-Xian; Yu, Kong-Xian

2018-06-01

An automated and accurate headspace gas chromatographic (HS-GC) technique was investigated for rapidly quantifying water content in edible oils. In this method, multiple headspace extraction (MHE) procedures were used to analyse the integrated water content from the edible oil sample. A simple vapour phase calibration technique with an external vapour standard was used to calibrate both the water content in the gas phase and the total weight of water in edible oil sample. After that the water in edible oils can be quantified. The data showed that the relative standard deviation of the present HS-GC method in the precision test was less than 1.13%, the relative differences between the new method and a reference method (i.e. the oven-drying method) were no more than 1.62%. The present HS-GC method is automated, accurate, efficient, and can be a reliable tool for quantifying water content in edible oil related products and research. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Rapid analysis of the main components of the total glycosides of Ranunculus japonicus by UPLC/Q-TOF-MS.

PubMed

Rui, Wen; Chen, Hongyuan; Tan, Yuzhi; Zhong, Yanmei; Feng, Yifan

2010-05-01

A rapid method for the analysis of the main components of the total glycosides of Ranunculus japonicus (TGOR) was developed using ultra-performance liquid chromatography with quadrupole-time-of-flight mass spectrometry (UPLC/Q-TOF-MS). The separation analysis was performed on a Waters Acquity UPLC system and the accurate mass of molecules and their fragment ions were determined by Q-TOF MS. Twenty compounds, including lactone glycosides, flavonoid glycosides and flavonoid aglycones, were identified and tentatively deduced on the basis of their elemental compositions, MS/MS data and relevant literature. The results demonstrated that lactone glycosides and flavonoids were the main constituents of TGOR. Furthermore, an effective and rapid pattern was established allowing for the comprehensive and systematic characterization of the complex samples.

Identification of Escherichia coli O157 by Using a Novel Colorimetric Detection Method with DNA Microarrays

PubMed Central

Swimley, Michelle S.; Taylor, Amber W.; Dawson, Erica D.

2011-01-01

Abstract Shiga toxin–producing Escherichia coli O157 is a leading cause of foodborne illness worldwide. To evaluate better methods to rapidly detect and genotype E. coli O157 strains, the present study evaluated the use of ampliPHOX, a novel colorimetric detection method based on photopolymerization, for pathogen identification with DNA microarrays. A low-density DNA oligonucleotide microarray was designed to target stx1 and stx2 genes encoding Shiga toxin production, the eae gene coding for adherence membrane protein, and the per gene encoding the O157-antigen perosamine synthetase. Results from the validation experiments demonstrated that the use of ampliPHOX allowed the accurate genotyping of the tested E. coli strains, and positive hybridization signals were observed for only probes targeting virulence genes present in the reference strains. Quantification showed that the average signal-to-noise ratio values ranged from 47.73 ± 7.12 to 76.71 ± 8.33, whereas average signal-to-noise ratio values below 2.5 were determined for probes where no polymer was formed due to lack of specific hybridization. Sensitivity tests demonstrated that the sensitivity threshold for E. coli O157 detection was 100–1000 CFU/mL. Thus, the use of DNA microarrays in combination with photopolymerization allowed the rapid and accurate genotyping of E. coli O157 strains. PMID:21288130

Free surface profiles in river flows: Can standard energy-based gradually-varied flow computations be pursued?

NASA Astrophysics Data System (ADS)

Cantero, Francisco; Castro-Orgaz, Oscar; Garcia-Marín, Amanda; Ayuso, José Luis; Dey, Subhasish

2015-10-01

Is the energy equation for gradually-varied flow the best approximation for the free surface profile computations in river flows? Determination of flood inundation in rivers and natural waterways is based on the hydraulic computation of flow profiles. This is usually done using energy-based gradually-varied flow models, like HEC-RAS, that adopts a vertical division method for discharge prediction in compound channel sections. However, this discharge prediction method is not so accurate in the context of advancements over the last three decades. This paper firstly presents a study of the impact of discharge prediction on the gradually-varied flow computations by comparing thirteen different methods for compound channels, where both energy and momentum equations are applied. The discharge, velocity distribution coefficients, specific energy, momentum and flow profiles are determined. After the study of gradually-varied flow predictions, a new theory is developed to produce higher-order energy and momentum equations for rapidly-varied flow in compound channels. These generalized equations enable to describe the flow profiles with more generality than the gradually-varied flow computations. As an outcome, results of gradually-varied flow provide realistic conclusions for computations of flow in compound channels, showing that momentum-based models are in general more accurate; whereas the new theory developed for rapidly-varied flow opens a new research direction, so far not investigated in flows through compound channels.

[Screening and confirmation of 24 hormones in cosmetics by ultra high performance liquid chromatography-linear ion trap/orbitrap high resolution mass spectrometry].

PubMed

Li, Zhaoyong; Wang, Fengmei; Niu, Zengyuan; Luo, Xin; Zhang, Gang; Chen, Junhui

2014-05-01

A method of ultra high performance liquid chromatography-linear ion trap/orbitrap high resolution mass spectrometry (UPLC-LTQ/Orbitrap MS) was established to screen and confirm 24 hormones in cosmetics. Various cosmetic samples were extracted with methanol. The extract was loaded onto a Waters ACQUITY UPLC BEH C18 column (50 mm x 2.1 mm, 1.7 microm) using a gradient elution of acetonitrile/water containing 0.1% (v/v) formic acid for the separation. The accurate mass of quasi-molecular ion was acquired by full scanning of electrostatic field orbitrap. The rapid screening was carried out by the accurate mass of quasi-molecular ion. The confirmation analysis for targeted compounds was performed with the retention time and qualitative fragments obtained by data dependent scan mode. Under the optimal conditions, the 24 hormones were routinely detected with mass accuracy error below 3 x 10(-6) (3 ppm), and good linearities were obtained in their respective linear ranges with correlation coefficients higher than 0.99. The LODs (S/N = 3) of the 24 compounds were < or = 10 microg/kg, which can meet the requirements for the actual screening of cosmetic samples. The developed method was applied to screen the hormones in 50 cosmetic samples. The results demonstrate that the method is a useful tool for the rapid screening and identification of the hormones in cosmetics.

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

Dustin Popp; Zander Mausolff; Sedat Goluoglu

We are proposing to use the code, TDKENO, to model TREAT. TDKENO solves the time dependent, three dimensional Boltzmann transport equation with explicit representation of delayed neutrons. Instead of directly integrating this equation, the neutron flux is factored into two components – a rapidly varying amplitude equation and a slowly varying shape equation and each is solved separately on different time scales. The shape equation is solved using the 3D Monte Carlo transport code KENO, from Oak Ridge National Laboratory’s SCALE code package. Using the Monte Carlo method to solve the shape equation is still computationally intensive, but the operationmore » is only performed when needed. The amplitude equation is solved deterministically and frequently, so the solution gives an accurate time-dependent solution without having to repeatedly We have modified TDKENO to incorporate KENO-VI so that we may accurately represent the geometries within TREAT. This paper explains the motivation behind using generalized geometry, and provides the results of our modifications. TDKENO uses the Improved Quasi-Static method to accomplish this. In this method, the neutron flux is factored into two components. One component is a purely time-dependent and rapidly varying amplitude function, which is solved deterministically and very frequently (small time steps). The other is a slowly varying flux shape function that weakly depends on time and is only solved when needed (significantly larger time steps).« less

Joint water-fat separation and deblurring for spiral imaging.

PubMed

Wang, Dinghui; Zwart, Nicholas R; Pipe, James G

2018-06-01

Most previous approaches to spiral Dixon water-fat imaging perform the water-fat separation and deblurring sequentially based on the assumption that the phase accumulation and blurring as a result of off-resonance are separable. This condition can easily be violated in regions where the B 0 inhomogeneity varies rapidly. The goal of this work is to present a novel joint water-fat separation and deblurring method for spiral imaging. The proposed approach is based on a more accurate signal model that takes into account the phase accumulation and blurring simultaneously. A conjugate gradient method is used in the image domain to reconstruct the deblurred water and fat iteratively. Spatially varying convolutions with a local convergence criterion are used to reduce the computational demand. Both simulation and high-resolution brain imaging have demonstrated that the proposed joint method consistently improves the quality of reconstructed water and fat images compared with the sequential approach, especially in regions where the field inhomogeneity changes rapidly in space. The loss of signal-to-noise-ratio as a result of deblurring is minor at optimal echo times. High-quality water-fat spiral imaging can be achieved with the proposed joint approach, provided that an accurate field map of B 0 inhomogeneity is available. Magn Reson Med 79:3218-3228, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Rapid tests for diagnosis of leptospirosis: current tools and emerging technologies.

PubMed

Picardeau, Mathieu; Bertherat, Eric; Jancloes, Michel; Skouloudis, Andreas N; Durski, Kara; Hartskeerl, Rudy A

2014-01-01

Leptospirosis is an emerging zoonosis with a worldwide distribution but is more commonly found in impoverished populations in developing countries and tropical regions with frequent flooding. The rapid detection of leptospirosis is a critical step to effectively manage the disease and to control outbreaks in both human and animal populations. Therefore, there is a need for accurate and rapid diagnostic tests and appropriate surveillance and alert systems to identify outbreaks. This review describes current in-house methods and commercialized tests for the rapid diagnosis of acute leptospirosis. It focuses on diagnostic tests that can be performed with minimal training and limited equipment in less-developed and newly industrialized countries, particularly in resource-limited settings and with results in minutes to less than 4 hours. We also describe recent technological advances in the field of diagnostic tests that could allow for the development of innovative rapid tests in the near future. © 2013 Elsevier Inc. All rights reserved.

Accurate phase extraction algorithm based on Gram–Schmidt orthonormalization and least square ellipse fitting method

NASA Astrophysics Data System (ADS)

Lei, Hebing; Yao, Yong; Liu, Haopeng; Tian, Yiting; Yang, Yanfu; Gu, Yinglong

2018-06-01

An accurate algorithm by combing Gram-Schmidt orthonormalization and least square ellipse fitting technology is proposed, which could be used for phase extraction from two or three interferograms. The DC term of background intensity is suppressed by subtraction operation on three interferograms or by high-pass filter on two interferograms. Performing Gram-Schmidt orthonormalization on pre-processing interferograms, the phase shift error is corrected and a general ellipse form is derived. Then the background intensity error and the corrected error could be compensated by least square ellipse fitting method. Finally, the phase could be extracted rapidly. The algorithm could cope with the two or three interferograms with environmental disturbance, low fringe number or small phase shifts. The accuracy and effectiveness of the proposed algorithm are verified by both of the numerical simulations and experiments.

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

PubMed Central

Maples, Brian K.; Gravel, Simon; Kenny, Eimear E.; Bustamante, Carlos D.

2013-01-01

Local-ancestry inference is an important step in the genetic analysis of fully sequenced human genomes. Current methods can only detect continental-level ancestry (i.e., European versus African versus Asian) accurately even when using millions of markers. Here, we present RFMix, a powerful discriminative modeling approach that is faster (∼30×) and more accurate than existing methods. We accomplish this by using a conditional random field parameterized by random forests trained on reference panels. RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians. Finally, we demonstrate that African Americans in HapMap contain modest (but nonzero) levels of Native American ancestry (∼0.4%). PMID:23910464

Local Debonding and Fiber Breakage in Composite Materials Modeled Accurately

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2001-01-01

A prerequisite for full utilization of composite materials in aerospace components is accurate design and life prediction tools that enable the assessment of component performance and reliability. Such tools assist both structural analysts, who design and optimize structures composed of composite materials, and materials scientists who design and optimize the composite materials themselves. NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) software package (http://www.grc.nasa.gov/WWW/LPB/mac) addresses this need for composite design and life prediction tools by providing a widely applicable and accurate approach to modeling composite materials. Furthermore, MAC/GMC serves as a platform for incorporating new local models and capabilities that are under development at NASA, thus enabling these new capabilities to progress rapidly to a stage in which they can be employed by the code's end users.

A drone detection with aircraft classification based on a camera array

NASA Astrophysics Data System (ADS)

Liu, Hao; Qu, Fangchao; Liu, Yingjian; Zhao, Wei; Chen, Yitong

2018-03-01

In recent years, because of the rapid popularity of drones, many people have begun to operate drones, bringing a range of security issues to sensitive areas such as airports and military locus. It is one of the important ways to solve these problems by realizing fine-grained classification and providing the fast and accurate detection of different models of drone. The main challenges of fine-grained classification are that: (1) there are various types of drones, and the models are more complex and diverse. (2) the recognition test is fast and accurate, in addition, the existing methods are not efficient. In this paper, we propose a fine-grained drone detection system based on the high resolution camera array. The system can quickly and accurately recognize the detection of fine grained drone based on hd camera.

Determination of Porosity in Shale by Double Headspace Extraction GC Analysis.

PubMed

Zhang, Chun-Yun; Li, Teng-Fei; Chai, Xin-Sheng; Xiao, Xian-Ming; Barnes, Donald

2015-11-03

This paper reports on a novel method for the rapid determination of the shale porosity by double headspace extraction gas chromatography (DHE-GC). Ground core samples of shale were placed into headspace vials and DHE-GC measurements of released methane gas were performed at a given time interval. A linear correlation between shale porosity and the ratio of consecutive GC signals was established both theoretically and experimentally by comparing with the results from the standard helium pycnometry method. The results showed that (a) the porosity of ground core samples of shale can be measured within 30 min; (b) the new method is not significantly affected by particle size of the sample; (c) the uncertainties of measured porosities of nine shale samples by the present method range from 0.31 to 0.46 p.u.; and (d) the results obtained by the DHE-GC method are in a good agreement with those from the standard helium pycnometry method. In short, the new DHE-GC method is simple, rapid, and accurate, making it a valuable tool for shale gas-related research and applications.

Rapid prototyping polymers for microfluidic devices and high pressure injections.

PubMed

Sollier, Elodie; Murray, Coleman; Maoddi, Pietro; Di Carlo, Dino

2011-11-21

Multiple methods of fabrication exist for microfluidic devices, with different advantages depending on the end goal of industrial mass production or rapid prototyping for the research laboratory. Polydimethylsiloxane (PDMS) has been the mainstay for rapid prototyping in the academic microfluidics community, because of its low cost, robustness and straightforward fabrication, which are particularly advantageous in the exploratory stages of research. However, despite its many advantages and its broad use in academic laboratories, its low elastic modulus becomes a significant issue for high pressure operation as it leads to a large alteration of channel geometry. Among other consequences, such deformation makes it difficult to accurately predict the flow rates in complex microfluidic networks, change flow speed quickly for applications in stop-flow lithography, or to have predictable inertial focusing positions for cytometry applications where an accurate alignment of the optical system is critical. Recently, other polymers have been identified as complementary to PDMS, with similar fabrication procedures being characteristic of rapid prototyping but with higher rigidity and better resistance to solvents; Thermoset Polyester (TPE), Polyurethane Methacrylate (PUMA) and Norland Adhesive 81 (NOA81). In this review, we assess these different polymer alternatives to PDMS for rapid prototyping, especially in view of high pressure injections with the specific example of inertial flow conditions. These materials are compared to PDMS, for which magnitudes of deformation and dynamic characteristics are also characterized. We provide a complete and systematic analysis of these materials with side-by-side experiments conducted in our lab that also evaluate other properties, such as biocompatibility, solvent compatibility, and ease of fabrication. We emphasize that these polymer alternatives, TPE, PUMA and NOA, have some considerable strengths for rapid prototyping when bond strength, predictable operation at high pressure, or transitioning to commercialization are considered important for the application.

Laser triangulation method for measuring the size of parking claw

NASA Astrophysics Data System (ADS)

Liu, Bo; Zhang, Ming; Pang, Ying

2017-10-01

With the development of science and technology and the maturity of measurement technology, the 3D profile measurement technology has been developed rapidly. Three dimensional measurement technology is widely used in mold manufacturing, industrial inspection, automatic processing and manufacturing, etc. There are many kinds of situations in scientific research and industrial production. It is necessary to transform the original mechanical parts into the 3D data model on the computer quickly and accurately. At present, many methods have been developed to measure the contour size, laser triangulation is one of the most widely used methods.

Improvement of Gaofen-3 Absolute Positioning Accuracy Based on Cross-Calibration

PubMed Central

Deng, Mingjun; Li, Jiansong

2017-01-01

The Chinese Gaofen-3 (GF-3) mission was launched in August 2016, equipped with a full polarimetric synthetic aperture radar (SAR) sensor in the C-band, with a resolution of up to 1 m. The absolute positioning accuracy of GF-3 is of great importance, and in-orbit geometric calibration is a key technology for improving absolute positioning accuracy. Conventional geometric calibration is used to accurately calibrate the geometric calibration parameters of the image (internal delay and azimuth shifts) using high-precision ground control data, which are highly dependent on the control data of the calibration field, but it remains costly and labor-intensive to monitor changes in GF-3’s geometric calibration parameters. Based on the positioning consistency constraint of the conjugate points, this study presents a geometric cross-calibration method for the rapid and accurate calibration of GF-3. The proposed method can accurately calibrate geometric calibration parameters without using corner reflectors and high-precision digital elevation models, thus improving absolute positioning accuracy of the GF-3 image. GF-3 images from multiple regions were collected to verify the absolute positioning accuracy after cross-calibration. The results show that this method can achieve a calibration accuracy as high as that achieved by the conventional field calibration method. PMID:29240675

Screening of the binding of small molecules to proteins by desorption electrospray ionization mass spectrometry combined with protein microarray.

PubMed

Yao, Chenxi; Wang, Tao; Zhang, Buqing; He, Dacheng; Na, Na; Ouyang, Jin

2015-11-01

The interaction between bioactive small molecule ligands and proteins is one of the important research areas in proteomics. Herein, a simple and rapid method is established to screen small ligands that bind to proteins. We designed an agarose slide to immobilize different proteins. The protein microarrays were allowed to interact with different small ligands, and after washing, the microarrays were screened by desorption electrospray ionization mass spectrometry (DESI MS). This method can be applied to screen specific protein binding ligands and was shown for seven proteins and 34 known ligands for these proteins. In addition, a high-throughput screening was achieved, with the analysis requiring approximately 4 s for one sample spot. We then applied this method to determine the binding between the important protein matrix metalloproteinase-9 (MMP-9) and 88 small compounds. The molecular docking results confirmed the MS results, demonstrating that this method is suitable for the rapid and accurate screening of ligands binding to proteins. Graphical Abstract ᅟ.

Are rapid population estimates accurate? A field trial of two different assessment methods.

PubMed

Grais, Rebecca F; Coulombier, Denis; Ampuero, Julia; Lucas, Marcelino E S; Barretto, Avertino T; Jacquier, Guy; Diaz, Francisco; Balandine, Serge; Mahoudeau, Claude; Brown, Vincent

2006-09-01

Emergencies resulting in large-scale displacement often lead to populations resettling in areas where basic health services and sanitation are unavailable. To plan relief-related activities quickly, rapid population size estimates are needed. The currently recommended Quadrat method estimates total population by extrapolating the average population size living in square blocks of known area to the total site surface. An alternative approach, the T-Square, provides a population estimate based on analysis of the spatial distribution of housing units taken throughout a site. We field tested both methods and validated the results against a census in Esturro Bairro, Beira, Mozambique. Compared to the census (population: 9,479), the T-Square yielded a better population estimate (9,523) than the Quadrat method (7,681; 95% confidence interval: 6,160-9,201), but was more difficult for field survey teams to implement. Although applicable only to similar sites, several general conclusions can be drawn for emergency planning.

Fast skin dose estimation system for interventional radiology

PubMed Central

Takata, Takeshi; Kotoku, Jun’ichi; Maejima, Hideyuki; Kumagai, Shinobu; Arai, Norikazu; Kobayashi, Takenori; Shiraishi, Kenshiro; Yamamoto, Masayoshi; Kondo, Hiroshi; Furui, Shigeru

2018-01-01

Abstract To minimise the radiation dermatitis related to interventional radiology (IR), rapid and accurate dose estimation has been sought for all procedures. We propose a technique for estimating the patient skin dose rapidly and accurately using Monte Carlo (MC) simulation with a graphical processing unit (GPU, GTX 1080; Nvidia Corp.). The skin dose distribution is simulated based on an individual patient’s computed tomography (CT) dataset for fluoroscopic conditions after the CT dataset has been segmented into air, water and bone based on pixel values. The skin is assumed to be one layer at the outer surface of the body. Fluoroscopic conditions are obtained from a log file of a fluoroscopic examination. Estimating the absorbed skin dose distribution requires calibration of the dose simulated by our system. For this purpose, a linear function was used to approximate the relation between the simulated dose and the measured dose using radiophotoluminescence (RPL) glass dosimeters in a water-equivalent phantom. Differences of maximum skin dose between our system and the Particle and Heavy Ion Transport code System (PHITS) were as high as 6.1%. The relative statistical error (2 σ) for the simulated dose obtained using our system was ≤3.5%. Using a GPU, the simulation on the chest CT dataset aiming at the heart was within 3.49 s on average: the GPU is 122 times faster than a CPU (Core i7–7700K; Intel Corp.). Our system (using the GPU, the log file, and the CT dataset) estimated the skin dose more rapidly and more accurately than conventional methods. PMID:29136194

Fast skin dose estimation system for interventional radiology.

PubMed

Takata, Takeshi; Kotoku, Jun'ichi; Maejima, Hideyuki; Kumagai, Shinobu; Arai, Norikazu; Kobayashi, Takenori; Shiraishi, Kenshiro; Yamamoto, Masayoshi; Kondo, Hiroshi; Furui, Shigeru

2018-03-01

To minimise the radiation dermatitis related to interventional radiology (IR), rapid and accurate dose estimation has been sought for all procedures. We propose a technique for estimating the patient skin dose rapidly and accurately using Monte Carlo (MC) simulation with a graphical processing unit (GPU, GTX 1080; Nvidia Corp.). The skin dose distribution is simulated based on an individual patient's computed tomography (CT) dataset for fluoroscopic conditions after the CT dataset has been segmented into air, water and bone based on pixel values. The skin is assumed to be one layer at the outer surface of the body. Fluoroscopic conditions are obtained from a log file of a fluoroscopic examination. Estimating the absorbed skin dose distribution requires calibration of the dose simulated by our system. For this purpose, a linear function was used to approximate the relation between the simulated dose and the measured dose using radiophotoluminescence (RPL) glass dosimeters in a water-equivalent phantom. Differences of maximum skin dose between our system and the Particle and Heavy Ion Transport code System (PHITS) were as high as 6.1%. The relative statistical error (2 σ) for the simulated dose obtained using our system was ≤3.5%. Using a GPU, the simulation on the chest CT dataset aiming at the heart was within 3.49 s on average: the GPU is 122 times faster than a CPU (Core i7-7700K; Intel Corp.). Our system (using the GPU, the log file, and the CT dataset) estimated the skin dose more rapidly and more accurately than conventional methods.

MBTH: A novel approach to rapid, spectrophotometric quantitation of total algal carbohydrates

DOE PAGES

Van Wychen, Stefanie; Long, William; Black, Stuart K.; ...

2016-11-24

A high-throughput and robust application of the 3-methyl-2-benzothiazolinone hydrazone (MBTH) method was developed for carbohydrate determination in microalgae. The traditional phenol-sulfuric acid method to quantify carbohydrates is strongly affected by algal biochemical components and exhibits a highly variable response to microalgal monosaccharides. We present a novel use of the MBTH method to accurately quantify carbohydrates in hydrolyzate after acid hydrolysis of algal biomass, without a need for neutralization. As a result, the MBTH method demonstrated consistent and sensitive quantitation of algae-specific monosaccharides down to 5 ug mL -1 without interference from other algae acidic hydrolyzate components.

Increasing role of arthropod bites in tularaemia transmission in Poland - case reports and diagnostic methods.

PubMed

Formińska, Kamila; Zasada, Aleksandra A; Rastawicki, Waldemar; Śmietańska, Karolina; Bander, Dorota; Wawrzynowicz-Syczewska, Marta; Yanushevych, Mariya; Niścigórska-Olsen, Jolanta; Wawszczak, Marek

2015-01-01

The study describes four cases of tularaemia - one developed after contact with rabbits and three developed after an arthropod bite. Due to non-specific clinical symptoms, accurate diagnosis of tularaemia may be difficult. The increasing contribution of the arthropod vectors in the transmission of the disease indicates that special effort should be made to apply sensitive and specific diagnostic methods for tularaemia, and to remind health-care workers about this route of Francisella tularensis infections. The advantages and disadvantages of various diagnostic methods - molecular, serological and microbiological culture - are discussed. The PCR as a rapid and proper diagnostic method for ulceroglandular tularaemia is presented.

MBTH: A novel approach to rapid, spectrophotometric quantitation of total algal carbohydrates

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

Van Wychen, Stefanie; Long, William; Black, Stuart K.

A high-throughput and robust application of the 3-methyl-2-benzothiazolinone hydrazone (MBTH) method was developed for carbohydrate determination in microalgae. The traditional phenol-sulfuric acid method to quantify carbohydrates is strongly affected by algal biochemical components and exhibits a highly variable response to microalgal monosaccharides. We present a novel use of the MBTH method to accurately quantify carbohydrates in hydrolyzate after acid hydrolysis of algal biomass, without a need for neutralization. As a result, the MBTH method demonstrated consistent and sensitive quantitation of algae-specific monosaccharides down to 5 ug mL -1 without interference from other algae acidic hydrolyzate components.

Rapid mapping of schistosomiasis and other neglected tropical diseases in the context of integrated control programmes in Africa

PubMed Central

BROOKER, S.; KABATEREINE, N. B.; GYAPONG, J. O.; STOTHARD, J. R.; UTZINGER, J.

2009-01-01

SUMMARY There is growing interest and commitment to the control of schistosomiasis and other so-called neglected tropical diseases (NTDs). Resources for control are inevitably limited, necessitating assessment methods that can rapidly and accurately identify and map high-risk communities so that interventions can be targeted in a spatially-explicit and cost-effective manner. Here, we review progress made with (i) mapping schistosomiasis across Africa using available epidemiological data and more recently, climate-based risk prediction; (ii) the development and use of morbidity questionnaires for rapid identification of high-risk communities of urinary schistosomiasis; and (iii) innovative sampling-based approaches for intestinal schistosomiasis, using the lot quality assurance sampling technique. Experiences are also presented for the rapid mapping of other NTDs, including onchocerciasis, loiasis and lymphatic filariasis. Future directions for an integrated rapid mapping approach targeting multiple NTDs simultaneously are outlined, including potential challenges in developing an integrated survey tool. The lessons from the mapping of human helminth infections may also be relevant for the rapid mapping of malaria as its control efforts are intensified. PMID:19450373

Star tracking method based on multiexposure imaging for intensified star trackers.

PubMed

Yu, Wenbo; Jiang, Jie; Zhang, Guangjun

2017-07-20

The requirements for the dynamic performance of star trackers are rapidly increasing with the development of space exploration technologies. However, insufficient knowledge of the angular acceleration has largely decreased the performance of the existing star tracking methods, and star trackers may even fail to track under highly dynamic conditions. This study proposes a star tracking method based on multiexposure imaging for intensified star trackers. The accurate estimation model of the complete motion parameters, including the angular velocity and angular acceleration, is established according to the working characteristic of multiexposure imaging. The estimation of the complete motion parameters is utilized to generate the predictive star image accurately. Therefore, the correct matching and tracking between stars in the real and predictive star images can be reliably accomplished under highly dynamic conditions. Simulations with specific dynamic conditions are conducted to verify the feasibility and effectiveness of the proposed method. Experiments with real starry night sky observation are also conducted for further verification. Simulations and experiments demonstrate that the proposed method is effective and shows excellent performance under highly dynamic conditions.

Photographic Analysis Technique for Assessing External Tank Foam Loss Events

NASA Technical Reports Server (NTRS)

Rieckhoff, T. J.; Covan, M.; OFarrell, J. M.

2001-01-01

A video camera and recorder were placed inside the solid rocket booster forward skirt in order to view foam loss events over an area on the external tank (ET) intertank surface. In this Technical Memorandum, a method of processing video images to allow rapid detection of permanent changes indicative of foam loss events on the ET surface was defined and applied to accurately count, categorize, and locate such events.

Isolation and molecular characterization of multiresistant Staphylococcus sciuri and Staphylococcus haemolyticus associated with skin and soft-tissue infections.

PubMed

Shittu, Adebayo; Lin, Johnson; Morrison, Donald; Kolawole, Deboye

2004-01-01

The isolation, molecular identification and genotyping of multiresistant Staphylococcus sciuri and Staphylococcus haemolyticus from skin and soft-tissue infections are reported. Accurate and full identification of three coagulase-negative staphylococcal isolates was achieved using PCR, while the API STAPH method failed to identify an isolate of S. haemolyticus fully. The PCR assay, which detects polymorphism in the 16S-23S rRNA spacer region, is shown to be potentially useful for rapid and accurate identification of coagulase-negative staphylococci. Identical PFGE type and antibiotic-resistance profiles of two methicillin-resistant S. haemolyticus isolates in this study suggest the existence of a multiresistant community clone.

Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia)

PubMed Central

Marescaux, Jonathan; Van Doninck, Karine

2013-01-01

Abstract The zebra mussel (Dreissena polymorpha) and the quagga mussel (Dreissena rostriformis bugensis) are considered as the most competitive invaders in freshwaters of Europe and North America. Although shell characteristics exist to differentiate both species, phenotypic plasticity in the genus Dreissena does not always allow a clear identification. Therefore, the need to find an accurate identification method is essential. DNA barcoding has been proven to be an adequate procedure to discriminate species. The cytochrome c oxidase subunit I mitochondrial gene (COI) is considered as the standard barcode for animals. We tested the use of this gene as an efficient DNA barcode and found that it allow rapid and accurate identification of adult Dreissena individuals. PMID:24453560

Attrition Rate of Oxygen Carriers in Chemical Looping Combustion Systems

NASA Astrophysics Data System (ADS)

Feilen, Harry Martin

This project developed an evaluation methodology for determining, accurately and rapidly, the attrition resistance of oxygen carrier materials used in chemical looping technologies. Existing test protocols, to evaluate attrition resistance of granular materials, are conducted under non-reactive and ambient temperature conditions. They do not accurately reflect the actual behavior under the unique process conditions of chemical looping, including high temperatures and cyclic operation between oxidizing and reducing atmospheres. This project developed a test method and equipment that represented a significant improvement over existing protocols. Experimental results obtained from this project have shown that hematite exhibits different modes of attrition, including both due to mechanical stresses and due to structural changes in the particles due to chemical reaction at high temperature. The test methodology has also proven effective in providing reactivity changes of the material with continued use, a property, which in addition to attrition, determines material life. Consumption/replacement cost due to attrition or loss of reactivity is a critical factor in the economic application of the chemical looping technology. This test method will allow rapid evaluation of a wide range of materials that are best suited for this technology. The most important anticipated public benefit of this project is the acceleration of the development of chemical looping technology for lowering greenhouse gas emissions from fossil fuel combustion.

Microbial genomic island discovery, visualization and analysis.

PubMed

Bertelli, Claire; Tilley, Keith E; Brinkman, Fiona S L

2018-06-03

Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Over the past decade, numerous computational tools have been developed to tackle the challenges inherent in accurate GI prediction. We review here the main types of GI prediction methods and discuss their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing. An assessment is provided of 20 GI prediction software methods that use sequence-composition bias to identify the GIs, using a reference GI data set from 104 genomes obtained using an independent comparative genomics approach. Finally, we present guidelines to assist researchers in effectively identifying these key genomic regions.

Interactive numerical flow visualization using stream surfaces

NASA Technical Reports Server (NTRS)

Hultquist, J. P. M.

1990-01-01

Particle traces and ribbons are often used to depict the structure of three-dimensional flowfields, but images produced using these models can be ambiguous. Stream surfaces offer a more visually intuitive method for the depiction of flowfields, but interactive response is needed to allow the user to place surfaces which reveal the essential features of a given flowfield. FLORA, a software package which supports the interactive calculation and display of stream surfaces on silicon graphics workstations, is described. Alternative methods for the integration of particle traces are examined, and calculation through computational space is found to provide rapid results with accuracy adequate for most purposes. Rapid calculation of traces is teamed with progressive refinement of appoximated surfaces. An initial approximation provides immediate user feedback, and subsequent improvement of the surface ensures that the final image is an accurate representation of the flowfield.

[Methods of high-throughput plant phenotyping for large-scale breeding and genetic experiments].

PubMed

Afonnikov, D A; Genaev, M A; Doroshkov, A V; Komyshev, E G; Pshenichnikova, T A

2016-07-01

Phenomics is a field of science at the junction of biology and informatics which solves the problems of rapid, accurate estimation of the plant phenotype; it was rapidly developed because of the need to analyze phenotypic characteristics in large scale genetic and breeding experiments in plants. It is based on using the methods of computer image analysis and integration of biological data. Owing to automation, new approaches make it possible to considerably accelerate the process of estimating the characteristics of a phenotype, to increase its accuracy, and to remove a subjectivism (inherent to humans). The main technologies of high-throughput plant phenotyping in both controlled and field conditions, their advantages and disadvantages, and also the prospects of their use for the efficient solution of problems of plant genetics and breeding are presented in the review.

[Determination of acetochlor and oxyfluorfen by capillary gas chromatography].

PubMed

Xiang, Wen-Sheng; Wang, Xiang-Jing; Wang, Jing; Wang, Qing

2002-09-01

A method is described for the determination of acetochlor and oxyfluorfen by capillary gas chromatography with FID and an SE-30 capillary column (60 m x 0.53 mm i. d., 1.5 microm), using dibutyl phthalate as the internal standard. The standard deviations for acetochlor and oxyfluorfen concentration(mass fraction) were 0.44% and 0.47% respectively. The relative standard deviations for acetochlor and oxyfluorfen were 0.79% and 0.88% and the average recoveries for acetochlor and oxyfluorfen were 99.3% and 101.1% respectively. The method is simple, rapid and accurate.

Immunosensors using a quartz crystal microbalance

NASA Astrophysics Data System (ADS)

Kurosawa, Shigeru; Aizawa, Hidenobu; Tozuka, Mitsuhiro; Nakamura, Miki; Park, Jong-Won

2003-11-01

Better analytical technology has been demanded for accurate and rapid determination of trace amounts of chemical compounds, such as marker proteins for disease or endocrine disrupters like dioxin, which might be contained in blood, food and the environment. The study of immunosensors using a quartz crystal microbalance (QCM) has recently focused on conventional detection methods for the determination of chemical compounds together with the development of reagents and processes. This paper introduces the principle of the detection method of QCM immunosensors developed at AIST and its application to the detection of trace amounts of chemical compounds.

A numerical method for solving systems of linear ordinary differential equations with rapidly oscillating solutions

NASA Technical Reports Server (NTRS)

Bernstein, Ira B.; Brookshaw, Leigh; Fox, Peter A.

1992-01-01

The present numerical method for accurate and efficient solution of systems of linear equations proceeds by numerically developing a set of basis solutions characterized by slowly varying dependent variables. The solutions thus obtained are shown to have a computational overhead largely independent of the small size of the scale length which characterizes the solutions; in many cases, the technique obviates series solutions near singular points, and its known sources of error can be easily controlled without a substantial increase in computational time.

Use and limitations of malaria rapid diagnostic testing by community health workers in war-torn Democratic Republic of Congo

PubMed Central

2009-01-01

Background Accurate and practical malaria diagnostics, such as immunochromatographic rapid diagnostic tests (RDTs), have the potential to avert unnecessary treatments and save lives. Volunteer community health workers (CHWs) represent a potentially valuable human resource for expanding this technology to where it is most needed, remote rural communities in sub-Saharan Africa with limited health facilities and personnel. This study reports on a training programme for CHWs to incorporate RDTs into their management strategy for febrile children in the Democratic Republic of Congo, a tropical African setting ravaged by human conflict. Methods Prospective cohort study, satisfaction questionnaire and decision analysis. Results Twelve CHWs were trained to safely and accurately perform and interpret RDTs, then successfully implemented rapid diagnostic testing in their remote community in a cohort of 357 febrile children. CHWs were uniformly positive in evaluating RDTs for their utility and ease of use. However, high malaria prevalence in this cohort (93% by RDTs, 88% by light microscopy) limited the cost-effectiveness of RDTs compared to presumptive treatment of all febrile children, as evidenced by findings from a simplified decision analysis. Conclusions CHWs can safely and effectively use RDTs in their management of febrile children; however, cost-effectiveness of RDTs is limited in zones of high malaria prevalence. PMID:20028563

Use of Enzyme Tests in Characterization and Identification of Aerobic and Facultatively Anaerobic Gram-Positive Cocci

PubMed Central

Bascomb, Shoshana; Manafi, Mammad

1998-01-01

The contribution of enzyme tests to the accurate and rapid routine identification of gram-positive cocci is introduced. The current taxonomy of the genera of aerobic and facultatively anaerobic cocci based on genotypic and phenotypic characterization is reviewed. The clinical and economic importance of members of these taxa is briefly summarized. Tables summarizing test schemes and kits available for the identification of staphylococci, enterococci, and streptococci on the basis of general requirements, number of tests, number of taxa, test classes, and completion times are discussed. Enzyme tests included in each scheme are compared on the basis of their synthetic moiety. The current understanding of the activity of enzymes important for classification and identification of the major groups, methods of testing, and relevance to the ease and speed of identification are reviewed. Publications describing the use of different identification kits are listed, and overall identification successes and problems are discussed. The relationships between the results of conventional biochemical and rapid enzyme tests are described and considered. The use of synthetic substrates for the detection of glycosidases and peptidases is reviewed, and the advantages of fluorogenic synthetic moieties are discussed. The relevance of enzyme tests to accurate and meaningful rapid routine identification is discussed. PMID:9564566

disLocate: tools to rapidly quantify local intermolecular structure to assess two-dimensional order in self-assembled systems.

PubMed

Bumstead, Matt; Liang, Kunyu; Hanta, Gregory; Hui, Lok Shu; Turak, Ayse

2018-01-24

Order classification is particularly important in photonics, optoelectronics, nanotechnology, biology, and biomedicine, as self-assembled and living systems tend to be ordered well but not perfectly. Engineering sets of experimental protocols that can accurately reproduce specific desired patterns can be a challenge when (dis)ordered outcomes look visually similar. Robust comparisons between similar samples, especially with limited data sets, need a finely tuned ensemble of accurate analysis tools. Here we introduce our numerical Mathematica package disLocate, a suite of tools to rapidly quantify the spatial structure of a two-dimensional dispersion of objects. The full range of tools available in disLocate give different insights into the quality and type of order present in a given dispersion, accessing the translational, orientational and entropic order. The utility of this package allows for researchers to extract the variation and confidence range within finite sets of data (single images) using different structure metrics to quantify local variation in disorder. Containing all metrics within one package allows for researchers to easily and rapidly extract many different parameters simultaneously, allowing robust conclusions to be drawn on the order of a given system. Quantifying the experimental trends which produce desired morphologies enables engineering of novel methods to direct self-assembly.

The Tropospheric Products of the International VLBI Service for Geodesy and Astrometry

NASA Technical Reports Server (NTRS)

Heinkelmann, Robert; Schwatke, Christian

2010-01-01

The IVS runs two tropospheric products: The IVS tropospheric parameter rapid combination monitors the zenith wet delay (ZWD) and zenith total delay (ZTD) of the rapid turnaround sessions R1 and R4. Goal of the combination is the identification and the exclusion of outliers by comparison and the assessment of the precision of current VLBI solutions in terms of tropospheric parameters. The rapid combination is done on a weekly basis four weeks after the observation files are released on IVS Data Centers. Since tropospheric and geodetic parameters, such as vertical station components, can significantly correlate, the consistency of the ZTD can be a measure of the consistency of the corresponding TRF as well. The ZWD mainly rely on accurate atmospheric pressure data. Thus, besides estimation techniques, modeling and analyst s noise, ZWD reflects differences in the atmospheric pressure data applied to the VLBI analysis. The second product, called tropospheric parameter long-term combination, aims for an accurate determination of climatological signals, such as trends of the atmospheric water vapor observed by VLBI. Therefore, the long-term homogeneity of atmospheric pressure data plays a crucial role for this product. The paper reviews the methods applied and results achieved so far and describes the new maintenance through DGFI.

Cost Savings Realized by Implementation of Routine Microbiological Identification by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Alby, Kevin; Kerr, Alan; Jones, Melissa; Gilligan, Peter H.

2015-01-01

Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is an emerging technology for rapid identification of bacterial and fungal isolates. In comparison to conventional methods, this technology is much less labor intensive and can provide accurate and reliable results in minutes from a single isolated colony. We compared the cost of performing the bioMérieux Vitek MALDI-TOF MS with conventional microbiological methods to determine the amount saved by the laboratory by converting to the new technology. Identification costs for 21,930 isolates collected between April 1, 2013, and March 31, 2014, were directly compared for MALDI-TOF MS and conventional methodologies. These isolates were composed of commonly isolated organisms, including commonly encountered aerobic and facultative bacteria and yeast but excluding anaerobes and filamentous fungi. Mycobacterium tuberculosis complex and rapidly growing mycobacteria were also evaluated for a 5-month period during the study. Reagent costs and a total cost analysis that included technologist time in addition to reagent expenses and maintenance service agreement costs were analyzed as part of this study. The use of MALDI-TOF MS equated to a net savings of $69,108.61, or 87.8%, in reagent costs annually compared to traditional methods. When total costs are calculated to include technologist time and maintenance costs, traditional identification would have cost $142,532.69, versus $68,886.51 with the MALDI-TOF MS method, resulting in a laboratory savings of $73,646.18, or 51.7%, annually by adopting the new technology. The initial cost of the instrument at our usage level would be offset in about 3 years. MALDI-TOF MS not only represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates, it also provides a significant cost savings for the laboratory. PMID:25994167

Rapid detection of the CYP2A6*12 hybrid allele by Pyrosequencing technology.

PubMed

Koontz, Deborah A; Huckins, Jacqueline J; Spencer, Antonina; Gallagher, Margaret L

2009-08-24

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. 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. 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. 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.

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks.

PubMed

Walsh, Aaron M; Crispie, Fiona; Daari, Kareem; O'Sullivan, Orla; Martin, Jennifer C; Arthur, Cornelius T; Claesson, Marcus J; Scott, Karen P; Cotter, Paul D

2017-08-15

The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization. IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products. Copyright © 2017 American Society for Microbiology.

Cost Savings Realized by Implementation of Routine Microbiological Identification by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Tran, Anthony; Alby, Kevin; Kerr, Alan; Jones, Melissa; Gilligan, Peter H

2015-08-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is an emerging technology for rapid identification of bacterial and fungal isolates. In comparison to conventional methods, this technology is much less labor intensive and can provide accurate and reliable results in minutes from a single isolated colony. We compared the cost of performing the bioMérieux Vitek MALDI-TOF MS with conventional microbiological methods to determine the amount saved by the laboratory by converting to the new technology. Identification costs for 21,930 isolates collected between April 1, 2013, and March 31, 2014, were directly compared for MALDI-TOF MS and conventional methodologies. These isolates were composed of commonly isolated organisms, including commonly encountered aerobic and facultative bacteria and yeast but excluding anaerobes and filamentous fungi. Mycobacterium tuberculosis complex and rapidly growing mycobacteria were also evaluated for a 5-month period during the study. Reagent costs and a total cost analysis that included technologist time in addition to reagent expenses and maintenance service agreement costs were analyzed as part of this study. The use of MALDI-TOF MS equated to a net savings of $69,108.61, or 87.8%, in reagent costs annually compared to traditional methods. When total costs are calculated to include technologist time and maintenance costs, traditional identification would have cost $142,532.69, versus $68,886.51 with the MALDI-TOF MS method, resulting in a laboratory savings of $73,646.18, or 51.7%, annually by adopting the new technology. The initial cost of the instrument at our usage level would be offset in about 3 years. MALDI-TOF MS not only represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates, it also provides a significant cost savings for the laboratory. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Automatic tracking of labeled red blood cells in microchannels.

PubMed

Pinho, Diana; Lima, Rui; Pereira, Ana I; Gayubo, Fernando

2013-09-01

The current study proposes an automatic method for the segmentation and tracking of red blood cells flowing through a 100- μm glass capillary. The original images were obtained by means of a confocal system and then processed in MATLAB using the Image Processing Toolbox. The measurements obtained with the proposed automatic method were compared with the results determined by a manual tracking method. The comparison was performed by using both linear regressions and Bland-Altman analysis. The results have shown a good agreement between the two methods. Therefore, the proposed automatic method is a powerful way to provide rapid and accurate measurements for in vitro blood experiments in microchannels. Copyright © 2012 John Wiley & Sons, Ltd.

Proximal sensing for soil carbon accounting

NASA Astrophysics Data System (ADS)

England, Jacqueline R.; Viscarra Rossel, Raphael A.

2018-05-01

Maintaining or increasing soil organic carbon (C) is vital for securing food production and for mitigating greenhouse gas (GHG) emissions, climate change, and land degradation. Some land management practices in cropping, grazing, horticultural, and mixed farming systems can be used to increase organic C in soil, but to assess their effectiveness, we need accurate and cost-efficient methods for measuring and monitoring the change. To determine the stock of organic C in soil, one requires measurements of soil organic C concentration, bulk density, and gravel content, but using conventional laboratory-based analytical methods is expensive. Our aim here is to review the current state of proximal sensing for the development of new soil C accounting methods for emissions reporting and in emissions reduction schemes. We evaluated sensing techniques in terms of their rapidity, cost, accuracy, safety, readiness, and their state of development. The most suitable method for measuring soil organic C concentrations appears to be visible-near-infrared (vis-NIR) spectroscopy and, for bulk density, active gamma-ray attenuation. Sensors for measuring gravel have not been developed, but an interim solution with rapid wet sieving and automated measurement appears useful. Field-deployable, multi-sensor systems are needed for cost-efficient soil C accounting. Proximal sensing can be used for soil organic C accounting, but the methods need to be standardized and procedural guidelines need to be developed to ensure proficient measurement and accurate reporting and verification. These are particularly important if the schemes use financial incentives for landholders to adopt management practices to sequester soil organic C. We list and discuss requirements for developing new soil C accounting methods based on proximal sensing, including requirements for recording, verification, and auditing.

Nanomechanical sensor applied to blood culture pellets: a fast approach to determine the antibiotic susceptibility against agents of bloodstream infections.

PubMed

Stupar, P; Opota, O; Longo, G; Prod'hom, G; Dietler, G; Greub, G; Kasas, S

2017-06-01

The management of bloodstream infection, a life-threatening disease, largely relies on early detection of infecting microorganisms and accurate determination of their antibiotic susceptibility to reduce both mortality and morbidity. Recently we developed a new technique based on atomic force microscopy capable of detecting movements of biologic samples at the nanoscale. Such sensor is able to monitor the response of bacteria to antibiotic's pressure, allowing a fast and versatile susceptibility test. Furthermore, rapid preparation of a bacterial pellet from a positive blood culture can improve downstream characterization of the recovered pathogen as a result of the increased bacterial concentration obtained. Using artificially inoculated blood cultures, we combined these two innovative procedures and validated them in double-blind experiments to determine the susceptibility and resistance of Escherichia coli strains (ATCC 25933 as susceptible and a characterized clinical isolate as resistant strain) towards a selection of antibiotics commonly used in clinical settings. On the basis of the variance of the sensor movements, we were able to positively discriminate the resistant from the susceptible E. coli strains in 16 of 17 blindly investigated cases. Furthermore, we defined a variance change threshold of 60% that discriminates susceptible from resistant strains. By combining the nanomotion sensor with the rapid preparation method of blood culture pellets, we obtained an innovative, rapid and relatively accurate method for antibiotic susceptibility test directly from positive blood culture bottles, without the need for bacterial subculture. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Molecular Identification of an Invasive Wood-Boring Insect Lyctus brunneus (Coleoptera: Bostrichidae: Lyctinae) Using Frass by Loop-Mediated Isothermal Amplification and Nested PCR Assays.

PubMed

Ide, Tatsuya; Kanzaki, Natsumi; Ohmura, Wakako; Okabe, Kimiko

2016-03-27

Lyctus brunneus(Stephens) is one of the most destructive and worldwide invasive pests of seasoned woods for wooden products. This and other pestLyctusspecies have had their distribution expanded by international and domestic human transportation of infested wood and wood products. Rapid detection and accurate identification ofLyctusspecies are effective tools for helping to eradicate them in new introduction sites. The accurate species-level identification of adults requires expert knowledge about their morphology. However, it takes much time and effort to recover suitable adult specimens because they are borers inside wood. Frass ofLyctusspecies can easily be detected and recovered in and around infested wood. Thus, frass was tested to see if it was a suitable sample to allow development of a rapid and technically easy molecular detection and identification method forL.brunneus.Species-specific primers were designed from the cytochrome c oxidase subunit I region ofL.brunneusand used in development and testing of methods for successfully identifying them from their frass using the loop-mediated isothermal amplification (LAMP) or species-specific nested polymerase chain reaction (PCR) assays. The LAMP assay was faster and more sensitive for detecting the presence of DNA derived fromL.brunneusin their frass than the nested PCR assay. These methodologies will be applicable for the rapid detection and identification of other wood-boring invasive pests in regulatory applications. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Measurement of bedload transport in sand-bed rivers: a look at two indirect sampling methods

USGS Publications Warehouse

Holmes, Robert R.; Gray, John R.; Laronne, Jonathan B.; Marr, Jeffrey D.G.

2010-01-01

Sand-bed rivers present unique challenges to accurate measurement of the bedload transport rate using the traditional direct sampling methods of direct traps (for example the Helley-Smith bedload sampler). The two major issues are: 1) over sampling of sand transport caused by “mining” of sand due to the flow disturbance induced by the presence of the sampler and 2) clogging of the mesh bag with sand particles reducing the hydraulic efficiency of the sampler. Indirect measurement methods hold promise in that unlike direct methods, no transport-altering flow disturbance near the bed occurs. The bedform velocimetry method utilizes a measure of the bedform geometry and the speed of bedform translation to estimate the bedload transport through mass balance. The bedform velocimetry method is readily applied for the estimation of bedload transport in large sand-bed rivers so long as prominent bedforms are present and the streamflow discharge is steady for long enough to provide sufficient bedform translation between the successive bathymetric data sets. Bedform velocimetry in small sandbed rivers is often problematic due to rapid variation within the hydrograph. The bottom-track bias feature of the acoustic Doppler current profiler (ADCP) has been utilized to accurately estimate the virtual velocities of sand-bed rivers. Coupling measurement of the virtual velocity with an accurate determination of the active depth of the streambed sediment movement is another method to measure bedload transport, which will be termed the “virtual velocity” method. Much research remains to develop methods and determine accuracy of the virtual velocity method in small sand-bed rivers.

Fast-tracking determination of homozygous transgenic lines and transgene stacking using a reliable quantitative real-time PCR assay.

PubMed

Wang, Xianghong; Jiang, Daiming; Yang, Daichang

2015-01-01

The selection of homozygous lines is a crucial step in the characterization of newly generated transgenic plants. This is particularly time- and labor-consuming when transgenic stacking is required. Here, we report a fast and accurate method based on quantitative real-time PCR with a rice gene RBE4 as a reference gene for selection of homozygous lines when using multiple transgenic stacking in rice. Use of this method allowed can be used to determine the stacking of up to three transgenes within four generations. Selection accuracy reached 100 % for a single locus and 92.3 % for two loci. This method confers distinct advantages over current transgenic research methodologies, as it is more accurate, rapid, and reliable. Therefore, this protocol could be used to efficiently select homozygous plants and to expedite time- and labor-consuming processes normally required for multiple transgene stacking. This protocol was standardized for determination of multiple gene stacking in molecular breeding via marker-assisted selection.

Determination of main components and anaerobic rumen digestibility of aquatic plants in vitro using near-infrared-reflectance spectroscopy.

PubMed

Yue, Zheng-Bo; Zhang, Meng-Lin; Sheng, Guo-Ping; Liu, Rong-Hua; Long, Ying; Xiang, Bing-Ren; Wang, Jin; Yu, Han-Qing

2010-04-01

A near-infrared-reflectance (NIR) spectroscopy-based method is established to determine the main components of aquatic plants as well as their anaerobic rumen biodegradability. The developed method is more rapid and accurate compared to the conventional chemical analysis and biodegradability tests. Moisture, volatile solid, Klason lignin and ash in entire aquatic plants could be accurately predicted using this method with coefficient of determination (r(2)) values of 0.952, 0.916, 0.939 and 0.950, respectively. In addition, the anaerobic rumen biodegradability of aquatic plants, represented as biogas and methane yields, could also be predicted well. The algorithm of continuous wavelet transform for the NIR spectral data pretreatment is able to greatly enhance the robustness and predictive ability of the NIR spectral analysis. These results indicate that NIR spectroscopy could be used to predict the main components of aquatic plants and their anaerobic biodegradability. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

A stable high-order perturbation of surfaces method for numerical simulation of diffraction problems in triply layered media

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

Hong, Youngjoon, E-mail: hongy@uic.edu; Nicholls, David P., E-mail: davidn@uic.edu

The accurate numerical simulation of linear waves interacting with periodic layered media is a crucial capability in engineering applications. In this contribution we study the stable and high-order accurate numerical simulation of the interaction of linear, time-harmonic waves with a periodic, triply layered medium with irregular interfaces. In contrast with volumetric approaches, High-Order Perturbation of Surfaces (HOPS) algorithms are inexpensive interfacial methods which rapidly and recursively estimate scattering returns by perturbation of the interface shape. In comparison with Boundary Integral/Element Methods, the stable HOPS algorithm we describe here does not require specialized quadrature rules, periodization strategies, or the solution ofmore » dense non-symmetric positive definite linear systems. In addition, the algorithm is provably stable as opposed to other classical HOPS approaches. With numerical experiments we show the remarkable efficiency, fidelity, and accuracy one can achieve with an implementation of this algorithm.« less

Quantification of urinary zwitterionic organic acids using weak-anion exchange chromatography with tandem MS detection.

PubMed

Bishop, Michael Jason; Crow, Brian S; Kovalcik, Kasey D; George, Joe; Bralley, James A

2007-04-01

A rapid and accurate quantitative method was developed and validated for the analysis of four urinary organic acids with nitrogen containing functional groups, formiminoglutamic acid (FIGLU), pyroglutamic acid (PYRGLU), 5-hydroxyindoleacetic acid (5-HIAA), and 2-methylhippuric acid (2-METHIP) by liquid chromatography tandem mass spectrometry (LC/MS/MS). The chromatography was developed using a weak anion-exchange amino column that provided mixed-mode retention of the analytes. The elution gradient relied on changes in mobile phase pH over a concave gradient, without the use of counter-ions or concentrated salt buffers. A simple sample preparation was used, only requiring the dilution of urine prior to instrumental analysis. The method was validated based on linearity (r2>or=0.995), accuracy (85-115%), precision (C.V.<12%), sample preparation stability (

Some Interesting Applications of Probabilistic Techiques in Structural Dynamic Analysis of Rocket Engines

NASA Technical Reports Server (NTRS)

Brown, Andrew M.

2014-01-01

Numerical and Analytical methods developed to determine damage accumulation in specific engine components when speed variation included. Dither Life Ratio shown to be well over factor of 2 for specific example. Steady-State assumption shown to be accurate for most turbopump cases, allowing rapid calculation of DLR. If hot-fire speed data unknown, Monte Carlo method developed that uses speed statistics for similar engines. Application of techniques allow analyst to reduce both uncertainty and excess conservatism. High values of DLR could allow previously unacceptable part to pass HCF criteria without redesign. Given benefit and ease of implementation, recommend that any finite life turbomachine component analysis adopt these techniques. Probability Values calculated, compared, and evaluated for several industry-proposed methods for combining random and harmonic loads. Two new excel macros written to calculate combined load for any specific probability level. Closed form Curve fits generated for widely used 3(sigma) and 2(sigma) probability levels. For design of lightweight aerospace components, obtaining accurate, reproducible, statistically meaningful answer critical.

Assessing rare earth elements in quartz rich geological samples.

PubMed

Santoro, A; Thoss, V; Ribeiro Guevara, S; Urgast, D; Raab, A; Mastrolitti, S; Feldmann, J

2016-01-01

Sodium peroxide (Na2O2) fusion coupled to Inductively Coupled Plasma Tandem Mass Spectrometry (ICP-MS/MS) measurements was used to rapidly screen quartz-rich geological samples for rare earth element (REE) content. The method accuracy was checked with a geological reference material and Instrumental Neutron Activation Analysis (INAA) measurements. The used mass-mode combinations presented accurate results (only exception being (157)Gd in He gas mode) with recovery of the geological reference material QLO-1 between 80% and 98% (lower values for Lu, Nd and Sm) and in general comparable to INAA measurements. Low limits of detection for all elements were achieved, generally below 10 pg g(-1), as well as measurement repeatability below 15%. Overall, the Na2O2/ICP-MS/MS method proved to be a suitable lab-based method to quickly and accurately screen rock samples originating from quartz-rich geological areas for rare earth element content; particularly useful if checking commercial viability. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Rapid prenatal genetic diagnosis of a fetus with a high risk for Morquio A syndrome].

PubMed

Guo, Yi-bin; Ai, Yang; Zhao, Yan; Tang, Jia; Jiang, Wei-ying; Du, Min-lian; Ma, Hua-mei; Zhong, Yan-fang

2012-04-01

To provide rapid and accurate prenatal genetic diagnosis for a fetus with high risk of Morquio A syndrome. Based on ascertained etiology of the proband and genotypes of the parents, particular mutations of the GALNS gene were screened at 10th gestational week with amplification refractory mutation system (ARMS), denaturing high performance liquid chromatography (DHPLC), and direct DNA sequencing. DHPLC screening has identified abnormal double peaks in the PCR products of exons 1 and 10, whilst only a single peak was detected in normal controls. Amplification of ARMS specific primers derived a specific product for the fetus's gene, whilst no similar product was detected in normal controls. Sequencing of PCR products confirmed that exons 1 and 10 of the GALNS gene from the fetus contained a heterozygous paternal c.106-111 del (p.L36-L37 del) deletion and a heterozygous maternal c.1097 T>C (p.L366P) missense mutation, which resulted in a compound heterozygote status. The fetus was diagnosed with Morquio A syndrome and a genotype similar to the proband. Termination of the pregnancy was recommended. Combined ARMS, DHPLC and DNA sequencing are effective for rapid and accurate prenatal diagnosis for fetus with a high risk for Morquio A syndrome. Such methods are particularly suitable for early diagnosis when pathogenesis is clear. Furthermore, combined ARMS and DHPLC are suitable for rapid processing of large numbers of samples for the identification of new mutations.

The rapid identification of human influenza neuraminidase N1 and N2 subtypes by ELISA.

PubMed

Barr, I G; McCaig, M; Durrant, C; Shaw, R

2006-11-10

An ELISA assay was developed to allow the rapid and accurate identification of human influenza A N1 and N2 neuraminidases. Initial testing using a fetuin pre-coating of wells correctly identified 81.7% of the neuraminidase type from a series of human A(H1N1), A(H1N2) and A(H3N2) viruses. This result could be improved to detect the neuraminidase subtype of almost all human influenza A viruses from a large panel of viruses isolated from 2000 to 2005, if the fetuin pre-coating was removed and the viruses were coated directly onto wells. This method is simple, rapid and can be used to screen large numbers of currently circulating human influenza A viruses for their neurraminidase subtype and is a good alternative to RT-PCR.

Real-time PCR for rapidly detecting aniline-degrading bacteria in activated sludge.

PubMed

Kayashima, Takakazu; Suzuki, Hisako; Maeda, Toshinari; Ogawa, Hiroaki I

2013-05-01

We developed a detection method that uses quantitative real-time PCR (qPCR) and the TaqMan system to easily and rapidly assess the population of aniline-degrading bacteria in activated sludge prior to conducting a biodegradability test on a chemical compound. A primer and probe set for qPCR was designed by a multiple alignment of conserved amino acid sequences encoding the large (α) subunit of aniline dioxygenase. PCR amplification tests showed that the designed primer and probe set targeted aniline-degrading strains such as Acidovorax sp., Gordonia sp., Rhodococcus sp., and Pseudomonas putida, thereby suggesting that the developed method can detect a wide variety of aniline-degrading bacteria. There was a strong correlation between the relative copy number of the α-aniline dioxygenase gene in activated sludge obtained with the developed qPCR method and the number of aniline-degrading bacteria measured by the Most Probable Number method, which is the conventional method, and a good correlation with the lag time of the BOD curve for aniline degradation produced by the biodegradability test in activated sludge samples collected from eight different wastewater treatment plants in Japan. The developed method will be valuable for the rapid and accurate evaluation of the activity of inocula prior to conducting a ready biodegradability test. Copyright © 2013 Elsevier Ltd. All rights reserved.

Kinetic determinations of accurate relative oxidation potentials of amines with reactive radical cations.

PubMed

Gould, Ian R; Wosinska, Zofia M; Farid, Samir

2006-01-01

Accurate oxidation potentials for organic compounds are critical for the evaluation of thermodynamic and kinetic properties of their radical cations. Except when using a specialized apparatus, electrochemical oxidation of molecules with reactive radical cations is usually an irreversible process, providing peak potentials, E(p), rather than thermodynamically meaningful oxidation potentials, E(ox). In a previous study on amines with radical cations that underwent rapid decarboxylation, we estimated E(ox) by correcting the E(p) from cyclic voltammetry with rate constants for decarboxylation obtained using laser flash photolysis. Here we use redox equilibration experiments to determine accurate relative oxidation potentials for the same amines. We also describe an extension of these experiments to show how relative oxidation potentials can be obtained in the absence of equilibrium, from a complete kinetic analysis of the reversible redox kinetics. The results provide support for the previous cyclic voltammetry/laser flash photolysis method for determining oxidation potentials.

Efficient isoparametric integration over arbitrary space-filling Voronoi polyhedra for electronic structure calculations

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

Alam, Aftab; Khan, S. N.; Wilson, Brian G.

2011-07-06

A numerically efficient, accurate, and easily implemented integration scheme over convex Voronoi polyhedra (VP) is presented for use in ab initio electronic-structure calculations. We combine a weighted Voronoi tessellation with isoparametric integration via Gauss-Legendre quadratures to provide rapidly convergent VP integrals for a variety of integrands, including those with a Coulomb singularity. We showcase the capability of our approach by first applying it to an analytic charge-density model achieving machine-precision accuracy with expected convergence properties in milliseconds. For contrast, we compare our results to those using shape-functions and show our approach is greater than 10 5 times faster and 10more » 7 times more accurate. Furthermore, a weighted Voronoi tessellation also allows for a physics-based partitioning of space that guarantees convex, space-filling VP while reflecting accurate atomic size and site charges, as we show within KKR methods applied to Fe-Pd alloys.« less

Accurate quantitative CF-LIBS analysis of both major and minor elements in alloys via iterative correction of plasma temperature and spectral intensity

NASA Astrophysics Data System (ADS)

Shuxia, ZHAO; Lei, ZHANG; Jiajia, HOU; Yang, ZHAO; Wangbao, YIN; Weiguang, MA; Lei, DONG; Liantuan, XIAO; Suotang, JIA

2018-03-01

The chemical composition of alloys directly determines their mechanical behaviors and application fields. Accurate and rapid analysis of both major and minor elements in alloys plays a key role in metallurgy quality control and material classification processes. A quantitative calibration-free laser-induced breakdown spectroscopy (CF-LIBS) analysis method, which carries out combined correction of plasma temperature and spectral intensity by using a second-order iterative algorithm and two boundary standard samples, is proposed to realize accurate composition measurements. Experimental results show that, compared to conventional CF-LIBS analysis, the relative errors for major elements Cu and Zn and minor element Pb in the copper-lead alloys has been reduced from 12%, 26% and 32% to 1.8%, 2.7% and 13.4%, respectively. The measurement accuracy for all elements has been improved substantially.

A hypersonic aeroheating calculation method based on inviscid outer edge of boundary layer parameters

NASA Astrophysics Data System (ADS)

Meng, ZhuXuan; Fan, Hu; Peng, Ke; Zhang, WeiHua; Yang, HuiXin

2016-12-01

This article presents a rapid and accurate aeroheating calculation method for hypersonic vehicles. The main innovation is combining accurate of numerical method with efficient of engineering method, which makes aeroheating simulation more precise and faster. Based on the Prandtl boundary layer theory, the entire flow field is divided into inviscid and viscid flow at the outer edge of the boundary layer. The parameters at the outer edge of the boundary layer are numerically calculated from assuming inviscid flow. The thermodynamic parameters of constant-volume specific heat, constant-pressure specific heat and the specific heat ratio are calculated, the streamlines on the vehicle surface are derived and the heat flux is then obtained. The results of the double cone show that at the 0° and 10° angle of attack, the method of aeroheating calculation based on inviscid outer edge of boundary layer parameters reproduces the experimental data better than the engineering method. Also the proposed simulation results of the flight vehicle reproduce the viscid numerical results well. Hence, this method provides a promising way to overcome the high cost of numerical calculation and improves the precision.

Simultaneous Determination of Ofloxacin and Flavoxate Hydrochloride by Absorption Ratio and Second Derivative UV Spectrophotometry

PubMed Central

Attimarad, Mahesh

2010-01-01

The objective of this study was to develop simple, precise, accurate and sensitive UV spectrophotometric methods for the simultaneous determination of ofloxacin (OFX) and flavoxate HCl (FLX) in pharmaceutical formulations. The first method is based on absorption ratio method, by formation of Q absorbance equation at 289 nm (λmax of OFX) and 322.4 nm (isoabsorptive point). The linearity range was found to be 1 to 30 μg/ml for FLX and OFX. In the method-II second derivative absorption at 311.4 nm for OFX (zero crossing for FLX) and at 246.2 nm for FLX (zero crossing for OFX) was used for the determination of the drugs and the linearity range was found to be 2 to 30 μg/ml for OFX and 2-75 μg /ml for FLX. The accuracy and precision of the methods were determined and validated statistically. Both the methods showed good reproducibility and recovery with % RSD less than 1.5%. Both the methods were found to be rapid, specific, precise and accurate and can be successfully applied for the routine analysis of OFX and FLX in combined dosage form PMID:24826003

Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level.

PubMed

Jarocki, Piotr; Podleśny, Marcin; Komoń-Janczara, Elwira; Kucharska, Jagoda; Glibowska, Agnieszka; Targoński, Zdzisław

2016-07-22

Members of the genus Bifidobacterium are anaerobic Gram-positive Actinobacteria, which are natural inhabitants of human and animal gastrointestinal tract. Certain bifidobacteria are frequently used as food additives and probiotic pharmaceuticals, because of their various health-promoting properties. Due to the enormous demand on probiotic bacteria, manufacture of high-quality products containing living microorganisms requires rapid and accurate identification of specific bacteria. Additionally, isolation of new industrial bacteria from various environments may lead to multiple isolations of the same strain, therefore, it is important to apply rapid, low-cost and effective procedures differentiating bifidobacteria at the intra-species level. The identification of new isolates using microbiological and biochemical methods is difficult, but the accurate characterization of isolated strains may be achieved using a polyphasic approach that includes classical phenotypic methods and molecular procedures. However, some of these procedures are time-consuming and cumbersome, particularly when a large group of new isolates is typed, while some other approaches may have too low discriminatory power to distinguish closely related isolates obtained from similar sources. This work presents the evaluation of the discriminatory power of four molecular methods (ARDRA, RAPD-PCR, rep-PCR and SDS-PAGE fingerprinting) that are extensively used for fast differentiation of bifidobacteria up to the strain level. Our experiments included 17 reference strains and showed that in comparison to ARDRA, genotypic fingerprinting procedures (RAPD and rep-PCR) seemed to be less reproducible, however, they allowed to differentiate the tested microorganisms even at the intra-species level. In general, RAPD and rep-PCR have similar discriminatory power, though, in some instances more than one oligonucleotide needs to be used in random amplified polymorphic DNA analysis. Moreover, the results also demonstrated a high discriminatory power of SDS-PAGE fingerprinting of whole-cell proteins. On the other hand, the protein profiles obtained were rather complex, and therefore, difficult to analyze. Among the tested procedures, rep-PCR proved to be the most effective and reliable method allowing rapid differentiation of Bifidobacterium strains. Additionally, the use of the BOXA1R primer in the differentiation of 21 Bifidobacterium strains, newly isolated from infant feces, demonstrated slightly better discriminatory power in comparison to PCR reactions with the (GTG)5 oligonucleotide. Thus, BOX-PCR turned out to be the most appropriate and convenient molecular technique in differentiating Bifidobacterium strains at all taxonomic levels.

Advantages of utilizing DMD based rapid manufacturing systems in mass customization applications

NASA Astrophysics Data System (ADS)

El-Siblani, A.

2010-02-01

The Use of DMD based Rapid Manufacturing Systems has proven to be very advantageous in the production of highly accurate plastic based components for use in mass customization market such as hearing aids, and dental markets. The voxelization process currently afforded with the DLP technology eliminates any layering effect associated with all existing additive Rapid Manufacturing technologies. The smooth accurate surfaces produced in an additive process utilizing DLP technology, through the voxelization approach, allow for the production of custom finished products. The implementation of DLP technology in rapid prototyping and rapid manufacturing systems allow for the usage of highly viscous photopolymer based liquid and paste composites for rapid manufacturing that could not be used in any other additive process prior to implementation of DLP technology in RP and RM systems. It also allowed for the greater throughput in production without sacrificing quality and accuracy.

Fast auto-focus scheme based on optical defocus fitting model

NASA Astrophysics Data System (ADS)

Wang, Yeru; Feng, Huajun; Xu, Zhihai; Li, Qi; Chen, Yueting; Cen, Min

2018-04-01

An optical defocus fitting model-based (ODFM) auto-focus scheme is proposed. Considering the basic optical defocus principle, the optical defocus fitting model is derived to approximate the potential-focus position. By this accurate modelling, the proposed auto-focus scheme can make the stepping motor approach the focal plane more accurately and rapidly. Two fitting positions are first determined for an arbitrary initial stepping motor position. Three images (initial image and two fitting images) at these positions are then collected to estimate the potential-focus position based on the proposed ODFM method. Around the estimated potential-focus position, two reference images are recorded. The auto-focus procedure is then completed by processing these two reference images and the potential-focus image to confirm the in-focus position using a contrast based method. Experimental results prove that the proposed scheme can complete auto-focus within only 5 to 7 steps with good performance even under low-light condition.

Remote sensing techniques for prediction of watershed runoff

NASA Technical Reports Server (NTRS)

Blanchard, B. J.

1975-01-01

Hydrologic parameters of watersheds for use in mathematical models and as design criteria for flood detention structures are sometimes difficult to quantify using conventional measuring systems. The advent of remote sensing devices developed in the past decade offers the possibility that watershed characteristics such as vegetative cover, soils, soil moisture, etc., may be quantified rapidly and economically. Experiments with visible and near infrared data from the LANDSAT-1 multispectral scanner indicate a simple technique for calibration of runoff equation coefficients is feasible. The technique was tested on 10 watersheds in the Chickasha area and test results show more accurate runoff coefficients were obtained than with conventional methods. The technique worked equally as well using a dry fall scene. The runoff equation coefficients were then predicted for 22 subwatersheds with flood detention structures. Predicted values were again more accurate than coefficients produced by conventional methods.

A rapid leaf-disc sampler for psychrometric water potential measurements.

PubMed

Wullschleger, S D; Oosterhuis, D M

1986-06-01

An instrument was designed which facilitates faster and more accurate sampling of leaf discs for psychrometric water potential measurements. The instrument consists of an aluminum housing, a spring-loaded plunger, and a modified brass-plated cork borer. The leaf-disc sampler was compared with the conventional method of sampling discs for measurement of leaf water potential with thermocouple psychrometers on a range of plant material including Gossypium hirsutum L., Zea mays L., and Begonia rex-cultorum L. The new sampler permitted a leaf disc to be excised and inserted into the psychrometer sample chamber in less than 7 seconds, which was more than twice as fast as the conventional method. This resulted in more accurate determinations of leaf water potential due to reduced evaporative water losses. The leaf-disc sampler also significantly reduced sample variability between individual measurements. This instrument can be used for many other laboratory and field measurements that necessitate leaf disc sampling.

Measurement of lung volumes from supine portable chest radiographs.

PubMed

Ries, A L; Clausen, J L; Friedman, P J

1979-12-01

Lung volumes in supine nonambulatory patients are physiological parameters often difficult to measure with current techniques (plethysmograph, gas dilution). Existing radiographic methods for measuring lung volumes require standard upright chest radiographs. Accordingly, in 31 normal supine adults, we determined helium-dilution functional residual and total lung capacities and measured planimetric lung field areas (LFA) from corresponding portable anteroposterior and lateral radiographs. Low radiation dose methods, which delivered less than 10% of that from standard portable X-ray technique, were utilized. Correlation between lung volume and radiographic LFA was highly significant (r = 0.96, SEE = 10.6%). Multiple-step regressions using height and chest diameter correction factors reduced variance, but weight and radiographic magnification factors did not. In 17 additional subjects studied for validation, the regression equations accurately predicted radiographic lung volume. Thus, this technique can provide accurate and rapid measurement of lung volume in studies involving supine patients.

Characterizing the Frequency and Elevation of Rapid Drainage Events in West Greenland

NASA Astrophysics Data System (ADS)

Cooley, S.; Christoffersen, P.

2016-12-01

Rapid drainage of supraglacial lakes on the Greenland Ice Sheet is critical for the establishment of surface-to-bed hydrologic connections and the subsequent transfer of water from surface to bed. Yet, estimates of the number and spatial distribution of rapidly draining lakes vary widely due to limitations in the temporal frequency of image collection and obscureness by cloud. So far, no study has assessed the impact of these observation biases. In this study, we examine the frequency and elevation of rapidly draining lakes in central West Greenland, from 68°N to 72.6°N, and we make a robust statistical analysis to estimate more accurately the likelihood of lakes draining rapidly. Using MODIS imagery and a fully automated lake detection method, we map more than 500 supraglacial lakes per year over a 63000 km2 study area from 2000-2015. Through testing four different definitions of rapidly draining lakes from previously published studies, we find that the number of rapidly draining lakes varies from 3% to 38%. Logistic regression between rapid drainage events and image sampling frequency demonstrates that the number of rapid drainage events is strongly dependent on cloud-free observation percentage. We then develop three new drainage criteria and apply an observation bias correction that suggests a true rapid drainage probability between 36% and 45%, considerably higher than previous studies without bias assessment have reported. We find rapid-draining lakes are on average larger and disappear earlier than slow-draining lakes, and we also observe no elevation differences for the lakes detected as rapidly draining. We conclude a) that methodological problems in rapid drainage research caused by observation bias and varying detection methods have obscured large-scale rapid drainage characteristics and b) that the lack of evidence for an elevation limit on rapid drainage suggests surface-to-bed hydrologic connections may continue to propagate inland as climate warms.

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

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

Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.

Here, the accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. Herein, a novel photographic method is described that uses biomolecular staining and image analysis to enhance contrast of early stage biofouling. A robust algorithm was developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs and results weremore » compared to independent measurements of cell density. Results from image analysis quantified biofilm growth intensity accurately and with approximately the same precision of the more laborious cell counting method. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field. Broad spectrum staining highlights fouling biomass, photography quickly captures a large area of interest, and image analysis rapidly quantifies fouling in the image.« less

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

DOE PAGES

Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.; ...

2015-12-07

Here, the accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. Herein, a novel photographic method is described that uses biomolecular staining and image analysis to enhance contrast of early stage biofouling. A robust algorithm was developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs and results weremore » compared to independent measurements of cell density. Results from image analysis quantified biofilm growth intensity accurately and with approximately the same precision of the more laborious cell counting method. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field. Broad spectrum staining highlights fouling biomass, photography quickly captures a large area of interest, and image analysis rapidly quantifies fouling in the image.« less

Toward a high-throughput method for determining vicine and convicine levels in faba bean seeds using flow injection analysis combined with tandem mass spectrometry.

PubMed

Purves, Randy W; Khazaei, Hamid; Vandenberg, Albert

2018-08-01

Although faba bean provides environmental and health benefits, vicine and convicine (v-c) limit its use as a source of vegetable protein. Crop improvement efforts to minimize v-c concentration require low-cost, rapid screening methods to distinguish between high and low v-c genotypes to accelerate development of new cultivars and to detect out-crossing events. To assist crop breeders, we developed a unique and rapid screening method that uses a 60 s instrumental analysis step to accurately distinguish between high and low v-c genotypes. The method involves flow injection analysis (FIA) coupled with tandem mass spectrometry (i.e., selective reaction monitoring, SRM). Using seeds with known v-c levels as calibrants, measured v-c levels were comparable with liquid chromatography (LC)-SRM results and the method was used to screen 370 faba bean genotypes. Widespread use of FIA-SRM will accelerate breeding of low v-c faba bean, thereby alleviating concerns about anti-nutritional effects of v-c in this crop. Copyright © 2018 Elsevier Ltd. All rights reserved.

Rapid Method for the Determination of 5-Hydroxymethylfurfural and Levulinic Acid Using a Double-Wavelength UV Spectroscopy

PubMed Central

Xue, Guoxin

2013-01-01

This study reports on a rapid method for the determination of levulinic acid (LA) and 5-hydroxymethylfurfural (HMF) in acid hydrolyze system of glucose based on UV spectroscopy. It was found that HMF and LA have a maximum absorption at the wavelengths of 284 nm and 266 nm, respectively, in a water medium, and the absorptions of HMF and LA at 284 nm and 266 nm follow Beer's law very well. However, it was found that a major spectral interference species will arise in the quantification of HMF and LA; nonetheless, this interference can be eliminated through the absorption treatment of charcoal. Therefore, both HMF and LA can be quantified with a double-wavelength technique. The repeatability of the method had a relative standard deviation of less than 4.47% for HMF and 2.25% for LA; the limit of quantification (LOQ) was 0.017 mmol/L for HMF and 4.68 mmol/L for LA, and the recovery ranged from 88% to 116% for HMF and from 94% to 105% for LA. The present method is simple, rapid, and accurate. It is suitable to use in the research of the preparation of HMF and LA in biorefinery area. PMID:24228006

What I make up when I wake up: anti-experience views and narrative fabrication of dreams.

PubMed

Rosen, Melanie G

2013-01-01

I propose a narrative fabrication thesis of dream reports, according to which dream reports are often not accurate representations of experiences that occur during sleep. I begin with an overview of anti-experience theses of Norman Malcolm and Daniel Dennett who reject the received view of dreams, that dreams are experiences we have during sleep which are reported upon waking. Although rejection of the first claim of the received view, that dreams are experiences that occur during sleep, is implausible, I evaluate in more detail the second assumption of the received view, that dream reports are generally accurate. I then propose a "narrative fabrication" view of dreams as an alternative to the received view. Dream reports are often confabulated or fabricated because of poor memory, bizarre dream content, and cognitive deficits. It is well documented that narratives can be altered between initial rapid eye movement sleep awakenings and subsequent reports. I argue that we have reason to suspect that initial reports are prone to inaccuracy. Experiments demonstrate that subjects rationalize strange elements in narratives, leaving out supernatural or bizarre components when reporting waking memories of stories. Inaccuracies in dream reports are exacerbated by rapid memory loss and bizarre dream content. Waking memory is a process of reconstruction and blending of elements, but unlike waking memory, we cannot reality-test for dream memories. Dream experiences involve imaginative elements, and dream content cannot be verified with external evidence. Some dreams may involve wake-like higher cognitive functions, such as lucid dreams. Such dreams are more likely to elicit accurate reports than cognitively deficient dreams. However, dream reports are generally less accurate than waking reports. I then propose methods which could verify the narrative fabrication view, and argue that although the theory cannot be tested with current methods, new techniques and technologies may be able to do so in the future.

What I make up when I wake up: anti-experience views and narrative fabrication of dreams

PubMed Central

Rosen, Melanie G.

2013-01-01

I propose a narrative fabrication thesis of dream reports, according to which dream reports are often not accurate representations of experiences that occur during sleep. I begin with an overview of anti-experience theses of Norman Malcolm and Daniel Dennett who reject the received view of dreams, that dreams are experiences we have during sleep which are reported upon waking. Although rejection of the first claim of the received view, that dreams are experiences that occur during sleep, is implausible, I evaluate in more detail the second assumption of the received view, that dream reports are generally accurate. I then propose a “narrative fabrication” view of dreams as an alternative to the received view. Dream reports are often confabulated or fabricated because of poor memory, bizarre dream content, and cognitive deficits. It is well documented that narratives can be altered between initial rapid eye movement sleep awakenings and subsequent reports. I argue that we have reason to suspect that initial reports are prone to inaccuracy. Experiments demonstrate that subjects rationalize strange elements in narratives, leaving out supernatural or bizarre components when reporting waking memories of stories. Inaccuracies in dream reports are exacerbated by rapid memory loss and bizarre dream content. Waking memory is a process of reconstruction and blending of elements, but unlike waking memory, we cannot reality-test for dream memories. Dream experiences involve imaginative elements, and dream content cannot be verified with external evidence. Some dreams may involve wake-like higher cognitive functions, such as lucid dreams. Such dreams are more likely to elicit accurate reports than cognitively deficient dreams. However, dream reports are generally less accurate than waking reports. I then propose methods which could verify the narrative fabrication view, and argue that although the theory cannot be tested with current methods, new techniques and technologies may be able to do so in the future. PMID:23964260

Reproducible surface-enhanced Raman quantification of biomarkers in multicomponent mixtures.

PubMed

De Luca, Anna Chiara; Reader-Harris, Peter; Mazilu, Michael; Mariggiò, Stefania; Corda, Daniela; Di Falco, Andrea

2014-03-25

Direct and quantitative detection of unlabeled glycerophosphoinositol (GroPIns), an abundant cytosolic phosphoinositide derivative, would allow rapid evaluation of several malignant cell transformations. Here we report label-free analysis of GroPIns via surface-enhanced Raman spectroscopy (SERS) with a sensitivity of 200 nM, well below its apparent concentration in cells. Crucially, our SERS substrates, based on lithographically defined gold nanofeatures, can be used to predict accurately the GroPIns concentration even in multicomponent mixtures, avoiding the preliminary separation of individual compounds. Our results represent a critical step toward the creation of SERS-based biosensor for rapid, label-free, and reproducible detection of specific molecules, overcoming limits of current experimental methods.

Rapid assessment of rice seed availability for wildlife in harvested fields

USGS Publications Warehouse

Halstead, B.J.; Miller, M.R.; Casazza, Michael L.; Coates, P.S.; Farinha, M.A.; Benjamin, Gustafson K.; Yee, J.L.; Fleskes, J.P.

2011-01-01

Rice seed remaining in commercial fields after harvest (waste rice) is a critical food resource for wintering waterfowl in rice-growing regions of North America. Accurate and precise estimates of the seed mass density of waste rice are essential for planning waterfowl wintering habitat extents and management. In the Sacramento Valley of California, USA, the existing method for obtaining estimates of availability of waste rice in harvested fields produces relatively precise estimates, but the labor-, time-, and machineryintensive process is not practical for routine assessments needed to examine long-term trends in waste rice availability. We tested several experimental methods designed to rapidly derive estimates that would not be burdened with disadvantages of the existing method. We first conducted a simulation study of the efficiency of each method and then conducted field tests. For each approach, methods did not vary in root mean squared error, although some methods did exhibit bias for both simulations and field tests. Methods also varied substantially in the time to conduct each sample and in the number of samples required to detect a standard trend. Overall, modified line-intercept methods performed well for estimating the density of rice seeds. Waste rice in the straw, although not measured directly, can be accounted for by a positive relationship with density of rice on the ground. Rapid assessment of food availability is a useful tool to help waterfowl managers establish and implement wetland restoration and agricultural habitat-enhancement goals for wintering waterfowl. ?? 2011 The Wildlife Society.

Rapid Titration of Measles and Other Viruses: Optimization with Determination of Replication Cycle Length

PubMed Central

Grigorov, Boyan; Rabilloud, Jessica; Lawrence, Philip; Gerlier, Denis

2011-01-01

Background Measles virus (MV) is a member of the Paramyxoviridae family and an important human pathogen causing strong immunosuppression in affected individuals and a considerable number of deaths worldwide. Currently, measles is a re-emerging disease in developed countries. MV is usually quantified in infectious units as determined by limiting dilution and counting of plaque forming unit either directly (PFU method) or indirectly from random distribution in microwells (TCID50 method). Both methods are time-consuming (up to several days), cumbersome and, in the case of the PFU assay, possibly operator dependent. Methods/Findings A rapid, optimized, accurate, and reliable technique for titration of measles virus was developed based on the detection of virus infected cells by flow cytometry, single round of infection and titer calculation according to the Poisson's law. The kinetics follow up of the number of infected cells after infection with serial dilutions of a virus allowed estimation of the duration of the replication cycle, and consequently, the optimal infection time. The assay was set up to quantify measles virus, vesicular stomatitis virus (VSV), and human immunodeficiency virus type 1 (HIV-1) using antibody labeling of viral glycoprotein, virus encoded fluorescent reporter protein and an inducible fluorescent-reporter cell line, respectively. Conclusion Overall, performing the assay takes only 24–30 hours for MV strains, 12 hours for VSV, and 52 hours for HIV-1. The step-by-step procedure we have set up can be, in principle, applicable to accurately quantify any virus including lentiviral vectors, provided that a virus encoded gene product can be detected by flow cytometry. PMID:21915289

Accurate Reading with Sequential Presentation of Single Letters

PubMed Central

Price, Nicholas S. C.; Edwards, Gemma L.

2012-01-01

Rapid, accurate reading is possible when isolated, single words from a sentence are sequentially presented at a fixed spatial location. We investigated if reading of words and sentences is possible when single letters are rapidly presented at the fovea under user-controlled or automatically controlled rates. When tested with complete sentences, trained participants achieved reading rates of over 60 wpm and accuracies of over 90% with the single letter reading (SLR) method and naive participants achieved average reading rates over 30 wpm with greater than 90% accuracy. Accuracy declined as individual letters were presented for shorter periods of time, even when the overall reading rate was maintained by increasing the duration of spaces between words. Words in the lexicon that occur more frequently were identified with higher accuracy and more quickly, demonstrating that trained participants have lexical access. In combination, our data strongly suggest that comprehension is possible and that SLR is a practicable form of reading under conditions in which normal scanning of text is not possible, or for scenarios with limited spatial and temporal resolution such as patients with low vision or prostheses. PMID:23115548

A Rapid Survival Assay to Measure Drug-Induced Cytotoxicity and Cell Cycle Effects

PubMed Central

Valiathan, Chandni; McFaline, Jose L.

2012-01-01

We describe a rapid method to accurately measure the cytotoxicity of mammalian cells upon exposure to various drugs. Using this assay, we obtain survival data in a fraction of the time required to perform the traditional clonogenic survival assay, considered the gold standard. The dynamic range of the assay allows sensitivity measurements on a multi-log scale allowing better resolution of comparative sensitivities. Moreover, the results obtained contain additional information on cell cycle effects of the drug treatment. Cell survival is obtained from a quantitative comparison of proliferation between drug-treated and untreated cells. During the assay, cells are treated with a drug and, following a recovery period, allowed to proliferate in the presence of BrdU. Cells that synthesize DNA in the presence of bromodeoxyuridine (BrdU) exhibit quenched Hoechst fluorescence easily detected by flow cytometry; quenching is used to determine relative proliferation in treated versus untreated cells. Finally, the multi-well setup of this assay allows the simultaneous screening of multiple cell lines, multiple doses, or multiple drugs to accurately measure cell survival and cell cycle changes after drug treatment. PMID:22133811

Recent advances in diagnostic microbiology.

PubMed

Bravo, Lulette Tricia C; Procop, Gary W

2009-07-01

The past decade has seen a surge in the development of a variety of molecular diagnostics designed to rapidly identify or characterize medically important microorganisms. We briefly review important advances in molecular microbiology, and then discuss specific assays that have been implemented in clinical microbiology laboratories throughout the country. We also discuss emerging methods and technologies that will soon be more widely used for the prompt and accurate detection of the agents of infectious diseases.

Cyclic voltammetry using silver as cathode material: a simple method for determining electro and chemical features and solubility values of CO2 in ionic liquids.

PubMed

Reche, Irene; Gallardo, Iluminada; Guirado, Gonzalo

2015-01-28

A report is presented on the use of cyclic voltammetry using silver as a working electrode. The combined electrocatalytic properties of silver and ionic liquids allow cyclic voltammetry to be turned into an ideal tool for the rapid and accurate access to diffusion coefficient values and solubility values of carbon dioxide in ionic liquids under standard conditions.

Isolation of infectious chikungunya virus and dengue virus using anionic polymer-coated magnetic beads.

PubMed

Patramool, Sirilaksana; Bernard, Eric; Hamel, Rodolphe; Natthanej, Luplertlop; Chazal, Nathalie; Surasombatpattana, Pornapat; Ekchariyawat, Peeraya; Daoust, Simon; Thongrungkiat, Supatra; Thomas, Frédéric; Briant, Laurence; Missé, Dorothée

2013-10-01

Mosquitoes-borne viruses are a major threat for human populations. Among them, chikungunya virus (CHIKV) and dengue virus (DENV) cause thousands of cases worldwide. The recent propagation of mosquito vectors competent to transmit these viruses to temperate areas increases their potential impact on susceptible human populations. The development of sensitive methods allowing the detection and isolation of infectious viruses is of crucial interest for determination of virus contamination in humans and in competent mosquito vectors. However, simple and rapid method allowing the capture of infectious CHIKV and DENV from samples with low viral titers useful for further genetic and functional characterization of circulating strains is lacking. The present study reports a fast and sensitive isolation technique based on viral particles adsorption on magnetic beads coated with anionic polymer, poly(methyl vinyl ether-maleic anhydrate) and suitable for isolation of infectious CHIKV and DENV from the four serotypes. Starting from quite reduced biological material, this method was accurate to combine with conventional detection techniques, including qRT-PCR and immunoblotting and allowed isolation of infectious particles without resorting to a step of cultivation. The use of polymer-coated magnetic beads is therefore of high interest for rapid detection and isolation of CHIKV and DENV from samples with reduced viral loads and represents an accurate approach for the surveillance of mosquito vector in area at risk for arbovirus outbreaks. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Single-Step qPCR and dPCR Detection of Diverse CRISPR-Cas9 Gene Editing Events In Vivo.

PubMed

Falabella, Micol; Sun, Linqing; Barr, Justin; Pena, Andressa Z; Kershaw, Erin E; Gingras, Sebastien; Goncharova, Elena A; Kaufman, Brett A

2017-10-05

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based technology is currently the most flexible means to create targeted mutations by recombination or indel mutations by nonhomologous end joining. During mouse transgenesis, recombinant and indel alleles are often pursued simultaneously. Multiple alleles can be formed in each animal to create significant genetic complexity that complicates the CRISPR-Cas9 approach and analysis. Currently, there are no rapid methods to measure the extent of on-site editing with broad mutation sensitivity. In this study, we demonstrate the allelic diversity arising from targeted CRISPR editing in founder mice. Using this DNA sample collection, we validated specific quantitative and digital PCR methods (qPCR and dPCR, respectively) for measuring the frequency of on-target editing in founder mice. We found that locked nucleic acid (LNA) probes combined with an internal reference probe (Drop-Off Assay) provide accurate measurements of editing rates. The Drop-Off LNA Assay also detected on-target CRISPR-Cas9 gene editing in blastocysts with a sensitivity comparable to PCR-clone sequencing. Lastly, we demonstrate that the allele-specific LNA probes used in qPCR competitor assays can accurately detect recombinant mutations in founder mice. In summary, we show that LNA-based qPCR and dPCR assays provide a rapid method for quantifying the extent of on-target genome editing in vivo , testing RNA guides, and detecting recombinant mutations. Copyright © 2017 Falabella et al.

Rapid, accurate, and direct determination of total lycopene content in tomato paste

NASA Astrophysics Data System (ADS)

Bicanic, D.; Anese, M.; Luterotti, S.; Dadarlat, D.; Gibkes, J.; Lubbers, M.

2003-01-01

Lycopene that imparts red color to the tomato fruit is the most potent antioxidant among carotenes, an important nutrient and also used as a color ingredient in many food formulations. Since cooked and processed foods derived from tomatoes were shown to provide optimal lycopene boost, products such as paste, puree, juice, etc. are nowadays gaining popularity as dietary sources. The analysis of lycopene in tomato paste (partially dehydrated product prepared by vacuum concentrating tomato juice) is carried out using either high pressure liquid chromatography (HPLC), spectrophotometry, or by evaluating the color. The instability of lycopene during processes of extraction, etc., handling, and disposal of organic solvents makes the preparation of a sample for the analysis a delicate task. Despite a recognized need for accurate and rapid assessment of lycopene in tomato products no such method is available at present. The study described here focuses on a direct determination of a total lycopene content in different tomato pastes by means of the laser optothermal window (LOW) method at 502 nm. The concentration of lycopene in tomato paste ranged between 25 and 150 mg per 100 g product; the results are in excellent agreement with those obtained by spectrophotometry. The time needed to complete LOW analysis is very short, so that decomposition of pigment and the formation of artifacts are minimized. Preliminary results indicate a good degree of reproducibility making the LOW method suitable for routine assays of lycopene content in tomato paste.

Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling.

PubMed

Hird, Sarah; Kubatko, Laura; Carstens, Bryan

2010-11-01

We describe a method for estimating species trees that relies on replicated subsampling of large data matrices. One application of this method is phylogeographic research, which has long depended on large datasets that sample intensively from the geographic range of the focal species; these datasets allow systematicists to identify cryptic diversity and understand how contemporary and historical landscape forces influence genetic diversity. However, analyzing any large dataset can be computationally difficult, particularly when newly developed methods for species tree estimation are used. Here we explore the use of replicated subsampling, a potential solution to the problem posed by large datasets, with both a simulation study and an empirical analysis. In the simulations, we sample different numbers of alleles and loci, estimate species trees using STEM, and compare the estimated to the actual species tree. Our results indicate that subsampling three alleles per species for eight loci nearly always results in an accurate species tree topology, even in cases where the species tree was characterized by extremely rapid divergence. Even more modest subsampling effort, for example one allele per species and two loci, was more likely than not (>50%) to identify the correct species tree topology, indicating that in nearly all cases, computing the majority-rule consensus tree from replicated subsampling provides a good estimate of topology. These results were supported by estimating the correct species tree topology and reasonable branch lengths for an empirical 10-locus great ape dataset. Copyright © 2010 Elsevier Inc. All rights reserved.

A Solution Adaptive Structured/Unstructured Overset Grid Flow Solver with Applications to Helicopter Rotor Flows

NASA Technical Reports Server (NTRS)

Duque, Earl P. N.; Biswas, Rupak; Strawn, Roger C.

1995-01-01

This paper summarizes a method that solves both the three dimensional thin-layer Navier-Stokes equations and the Euler equations using overset structured and solution adaptive unstructured grids with applications to helicopter rotor flowfields. The overset structured grids use an implicit finite-difference method to solve the thin-layer Navier-Stokes/Euler equations while the unstructured grid uses an explicit finite-volume method to solve the Euler equations. Solutions on a helicopter rotor in hover show the ability to accurately convect the rotor wake. However, isotropic subdivision of the tetrahedral mesh rapidly increases the overall problem size.

Rapid design and optimization of low-thrust rendezvous/interception trajectory for asteroid deflection missions

NASA Astrophysics Data System (ADS)

Li, Shuang; Zhu, Yongsheng; Wang, Yukai

2014-02-01

Asteroid deflection techniques are essential in order to protect the Earth from catastrophic impacts by hazardous asteroids. Rapid design and optimization of low-thrust rendezvous/interception trajectories is considered as one of the key technologies to successfully deflect potentially hazardous asteroids. In this paper, we address a general framework for the rapid design and optimization of low-thrust rendezvous/interception trajectories for future asteroid deflection missions. The design and optimization process includes three closely associated steps. Firstly, shape-based approaches and genetic algorithm (GA) are adopted to perform preliminary design, which provides a reasonable initial guess for subsequent accurate optimization. Secondly, Radau pseudospectral method is utilized to transcribe the low-thrust trajectory optimization problem into a discrete nonlinear programming (NLP) problem. Finally, sequential quadratic programming (SQP) is used to efficiently solve the nonlinear programming problem and obtain the optimal low-thrust rendezvous/interception trajectories. The rapid design and optimization algorithms developed in this paper are validated by three simulation cases with different performance indexes and boundary constraints.

Development and Validation of Liquid Chromatographic Method for Estimation of Naringin in Nanoformulation

PubMed Central

Musmade, Kranti P.; Trilok, M.; Dengale, Swapnil J.; Bhat, Krishnamurthy; Reddy, M. S.; Musmade, Prashant B.; Udupa, N.

2014-01-01

A simple, precise, accurate, rapid, and sensitive reverse phase high performance liquid chromatography (RP-HPLC) method with UV detection has been developed and validated for quantification of naringin (NAR) in novel pharmaceutical formulation. NAR is a polyphenolic flavonoid present in most of the citrus plants having variety of pharmacological activities. Method optimization was carried out by considering the various parameters such as effect of pH and column. The analyte was separated by employing a C18 (250.0 × 4.6 mm, 5 μm) column at ambient temperature in isocratic conditions using phosphate buffer pH 3.5: acetonitrile (75 : 25% v/v) as mobile phase pumped at a flow rate of 1.0 mL/min. UV detection was carried out at 282 nm. The developed method was validated according to ICH guidelines Q2(R1). The method was found to be precise and accurate on statistical evaluation with a linearity range of 0.1 to 20.0 μg/mL for NAR. The intra- and interday precision studies showed good reproducibility with coefficients of variation (CV) less than 1.0%. The mean recovery of NAR was found to be 99.33 ± 0.16%. The proposed method was found to be highly accurate, sensitive, and robust. The proposed liquid chromatographic method was successfully employed for the routine analysis of said compound in developed novel nanopharmaceuticals. The presence of excipients did not show any interference on the determination of NAR, indicating method specificity. PMID:26556205

Rapid quantification of live/dead lactic acid bacteria in probiotic products using high-sensitivity flow cytometry

NASA Astrophysics Data System (ADS)

He, Shengbin; Hong, Xinyi; Huang, Tianxun; Zhang, Wenqiang; Zhou, Yingxing; Wu, Lina; Yan, Xiaomei

2017-06-01

A laboratory-built high-sensitivity flow cytometer (HSFCM) was employed for the rapid and accurate detection of lactic acid bacteria (LAB) and their viability in probiotic products. LAB were stained with both the cell membrane-permeable SYTO 9 green-fluorescent nucleic acid stain and the red-fluorescent nucleic acid stain, propidium iodide, which penetrates only bacteria with compromised membranes. The side scatter and dual-color fluorescence signals of single bacteria were detected simultaneously by the HSFCM. Ultra-high temperature processing milk and skim milk spiked with Lactobacillus casei were used as the model systems for the optimization of sample pretreatment and staining. The viable LAB counts measured by the HSFCM were in good agreement with those of the plate count method, and the measured ratios between the live and dead LAB matched well with the theoretical ratios. The established method was successfully applied to the rapid quantification of live/dead LAB in yogurts and fermented milk beverages of different brands. Moreover, the concentration and viability status of LAB in ambient yogurt, a relatively new yet popular milk product in China, are also reported.

Development of a nested-PCR assay for the rapid detection of Pilidiella granati in pomegranate fruit

PubMed Central

Yang, Xue; Hameed, Uzma; Zhang, Ai-Fang; Zang, Hao-Yu; Gu, Chun-Yan; Chen, Yu; Xu, Yi-Liu

2017-01-01

Pilidiella granati, a causal agent of twig blight and crown rot of pomegranate, is an emerging threat that may cause severe risk to the pomegranate industry in the future. Development of a rapid assay for the timely and accurate detection of P. granati will be helpful in the active surveillance and management of the disease caused by this pathogen. In this study, a nested PCR method was established for the detection of P. granati. Comparative analysis of genetic diversity within 5.8S rDNA internal transcribed spacer (ITS) sequences of P. granati and 21 other selected fungal species was performed to design species-specific primers (S1 and S2). This primer pair successfully amplified a 450 bp product exclusively from the genomic DNA of P. granati. The developed method can detect 10 pg genomic DNA of the pathogen in about 6 h. This technique was successfully applied to detect the natural infection of P. granati in the pomegranate fruit. The designed protocol is rapid and precise with a high degree of sensitivity. PMID:28106107

Development of Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Detection of Cannabis sativa.

PubMed

Kitamura, Masashi; Aragane, Masako; Nakamura, Kou; Watanabe, Kazuhito; Sasaki, Yohei

2016-07-01

In many parts of the world, the possession and cultivation of Cannabis sativa L. are restricted by law. As chemical or morphological analyses cannot identify the plant in some cases, a simple yet accurate DNA-based method for identifying C. sativa is desired. We have developed a loop-mediated isothermal amplification (LAMP) assay for the rapid identification of C. sativa. By optimizing the conditions for the LAMP reaction that targets a highly conserved region of tetrahydrocannabinolic acid (THCA) synthase gene, C. sativa was identified within 50 min at 60-66°C. The detection limit was the same as or higher than that of conventional PCR. The LAMP assay detected all 21 specimens of C. sativa, showing high specificity. Using a simple protocol, the identification of C. sativa could be accomplished within 90 min from sample treatment to detection without use of special equipment. A rapid, sensitive, highly specific, and convenient method for detecting and identifying C. sativa has been developed and is applicable to forensic investigations and industrial quality control.

Rapid Screening of Ergot Alkaloids in Sclerotia by MALDI-TOF Mass Spectrometry.

PubMed

Sivagnanam, Kumaran; Komatsu, Emy; Patrick, Susan; Rampitsch, Christoph; Perreault, Hélène; Gräfenhan, Tom

2016-07-01

Ergot is a common disease of wheat and other cereal grains that is predominantly caused by Claviceps purpurea in the field, often affecting crop yield in addition to the environment. Infected grain can be contaminated with dark sclerotia, which contain fungal metabolites such as ergot alkaloids. The occurrence of ergot alkaloids in cereal grain is a major health concern for humans and livestock. Effective and rapid screening of these mycotoxins is crucial for producers, processors, and consumers of cereal-based food and feed grain. Established methods of ergot alkaloid screening based on LC-MS or GC-MS require laborious processes. A novel method using matrix-assisted laser desorption ionization (MALDI)-time-of-flight (TOF) MS was developed to identify four ergot alkaloids. Using dihydroxybenzoic acid as the matrix, ergosine, ergocornine, ergocryptine, and ergocristine were readily detected in individual sclerotia of C. purpurea. The accuracy of the identified ergot alkaloids was further confirmed by tandem MS analysis. MALDI-TOF MS is suitable for high-throughput screening of ergot alkaloids because it permits rapid and accurate identification, simple sample preparation, and no derivatization or chromatographic separation.

Amperometric immunosensor for rapid detection of Mycobacterium tuberculosis

NASA Astrophysics Data System (ADS)

Hiraiwa, Morgan; Kim, Jong-Hoon; Lee, Hyun-Boo; Inoue, Shinnosuke; Becker, Annie L.; Weigel, Kris M.; Cangelosi, Gerard A.; Lee, Kyong-Hoon; Chung, Jae-Hyun

2015-05-01

Tuberculosis (TB) has been a major public health problem, which can be better controlled by using accurate and rapid diagnosis in low-resource settings. A simple, portable, and sensitive detection method is required for point-of-care (POC) settings. This paper studies an amperometric biosensor using a microtip immunoassay for a rapid and low-cost detection of Mycobacterium tuberculosis (MTB) in sputum. MTB in sputum is specifically captured on the functionalized microtip surface and detected by electric current. According to the numerical study, the current signal on the microtip surface is linearly changed with increasing immersion depth. Using a reference microtip, the immersion depth is compensated for a sensing microtip. On the microtip surface, target bacteria are concentrated and organized by a coffee-ring effect, which amplifies the electric current. To enhance the signal-to-noise ratio, both the sample processing and rinsing steps are presented with the use of deionized water as a medium for the amperometric measurement. When applied to cultured MTB cells spiked into human sputum, the detection limit was 100 CFU mL-1, comparable to a more labor-intensive fluorescence detection method reported previously.

A comparative approach to computer aided design model of a dog femur.

PubMed

Turamanlar, O; Verim, O; Karabulut, A

2016-01-01

Computer assisted technologies offer new opportunities in medical imaging and rapid prototyping in biomechanical engineering. Three dimensional (3D) modelling of soft tissues and bones are becoming more important. The accuracy of the analysis in modelling processes depends on the outline of the tissues derived from medical images. The aim of this study is the evaluation of the accuracy of 3D models of a dog femur derived from computed tomography data by using point cloud method and boundary line method on several modelling software. Solidworks, Rapidform and 3DSMax software were used to create 3D models and outcomes were evaluated statistically. The most accurate 3D prototype of the dog femur was created with stereolithography method using rapid prototype device. Furthermore, the linearity of the volumes of models was investigated between software and the constructed models. The difference between the software and real models manifests the sensitivity of the software and the devices used in this manner.

MBTH: A novel approach to rapid, spectrophotometric quantitation of total algal carbohydrates.

PubMed

Van Wychen, Stefanie; Long, William; Black, Stuart K; Laurens, Lieve M L

2017-02-01

A high-throughput and robust application of the 3-methyl-2-benzothiazolinone hydrazone (MBTH) method was developed for carbohydrate determination in microalgae. The traditional phenol-sulfuric acid method to quantify carbohydrates is strongly affected by algal biochemical components and exhibits a highly variable response to microalgal monosaccharides. We present a novel use of the MBTH method to accurately quantify carbohydrates in hydrolyzate after acid hydrolysis of algal biomass, without a need for neutralization. The MBTH method demonstrated consistent and sensitive quantitation of algae-specific monosaccharides down to 5 μg mL -1 without interference from other algae acidic hydrolyzate components. Copyright © 2016 Elsevier Inc. All rights reserved.

Real-time airborne gamma-ray background estimation using NASVD with MLE and radiation transport for calibration

NASA Astrophysics Data System (ADS)

Kulisek, J. A.; Schweppe, J. E.; Stave, S. C.; Bernacki, B. E.; Jordan, D. V.; Stewart, T. N.; Seifert, C. E.; Kernan, W. J.

2015-06-01

Helicopter-mounted gamma-ray detectors can provide law enforcement officials the means to quickly and accurately detect, identify, and locate radiological threats over a wide geographical area. The ability to accurately distinguish radiological threat-generated gamma-ray signatures from background gamma radiation in real time is essential in order to realize this potential. This problem is non-trivial, especially in urban environments for which the background may change very rapidly during flight. This exacerbates the challenge of estimating background due to the poor counting statistics inherent in real-time airborne gamma-ray spectroscopy measurements. To address this challenge, we have developed a new technique for real-time estimation of background gamma radiation from aerial measurements without the need for human analyst intervention. The method can be calibrated using radiation transport simulations along with data from previous flights over areas for which the isotopic composition need not be known. Over the examined measured and simulated data sets, the method generated accurate background estimates even in the presence of a strong, 60Co source. The potential to track large and abrupt changes in background spectral shape and magnitude was demonstrated. The method can be implemented fairly easily in most modern computing languages and environments.

Mapping land cover through time with the Rapid Land Cover Mapper—Documentation and user manual

USGS Publications Warehouse

Cotillon, Suzanne E.; Mathis, Melissa L.

2017-02-15

The Rapid Land Cover Mapper is an Esri ArcGIS® Desktop add-in, which was created as an alternative to automated or semiautomated mapping methods. Based on a manual photo interpretation technique, the tool facilitates mapping over large areas and through time, and produces time-series raster maps and associated statistics that characterize the changing landscapes. The Rapid Land Cover Mapper add-in can be used with any imagery source to map various themes (for instance, land cover, soils, or forest) at any chosen mapping resolution. The user manual contains all essential information for the user to make full use of the Rapid Land Cover Mapper add-in. This manual includes a description of the add-in functions and capabilities, and step-by-step procedures for using the add-in. The Rapid Land Cover Mapper add-in was successfully used by the U.S. Geological Survey West Africa Land Use Dynamics team to accurately map land use and land cover in 17 West African countries through time (1975, 2000, and 2013).

VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

PubMed

Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

2014-07-01

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.

A high-throughput detection method for invasive fruit fly (Diptera: Tephritidae) species based on microfluidic dynamic array.

PubMed

Jiang, Fan; Fu, Wei; Clarke, Anthony R; Schutze, Mark Kurt; Susanto, Agus; Zhu, Shuifang; Li, Zhihong

2016-11-01

Invasive species can be detrimental to a nation's ecology, economy and human health. Rapid and accurate diagnostics are critical to limit the establishment and spread of exotic organisms. The increasing rate of biological invasions relative to the taxonomic expertise available generates a demand for high-throughput, DNA-based diagnostics methods for identification. We designed species-specific qPCR primer and probe combinations for 27 economically important tephritidae species in six genera (Anastrepha, Bactrocera, Carpomya, Ceratitis, Dacus and Rhagoletis) based on 935 COI DNA barcode haplotypes from 181 fruit fly species publically available in BOLD, and then tested the specificity for each primer pair and probe through qPCR of 35 of those species. We then developed a standardization reaction system for detecting the 27 target species based on a microfluidic dynamic array and also applied the method to identify unknown immature samples from port interceptions and field monitoring. This method led to a specific and simultaneous detection for all 27 species in 7.5 h, using only 0.2 μL of reaction system in each reaction chamber. The approach successfully discriminated among species within complexes that had genetic similarities of up to 98.48%, while it also identified all immature samples consistent with the subsequent results of morphological examination of adults which were reared from larvae of cohorts from the same samples. We present an accurate, rapid and high-throughput innovative approach for detecting fruit flies of quarantine concern. This is a new method which has broad potential to be one of international standards for plant quarantine and invasive species detection. © 2016 John Wiley & Sons Ltd.

A segmentation method for lung nodule image sequences based on superpixels and density-based spatial clustering of applications with noise

PubMed Central

Zhang, Wei; Zhang, Xiaolong; Qiang, Yan; Tian, Qi; Tang, Xiaoxian

2017-01-01

The fast and accurate segmentation of lung nodule image sequences is the basis of subsequent processing and diagnostic analyses. However, previous research investigating nodule segmentation algorithms cannot entirely segment cavitary nodules, and the segmentation of juxta-vascular nodules is inaccurate and inefficient. To solve these problems, we propose a new method for the segmentation of lung nodule image sequences based on superpixels and density-based spatial clustering of applications with noise (DBSCAN). First, our method uses three-dimensional computed tomography image features of the average intensity projection combined with multi-scale dot enhancement for preprocessing. Hexagonal clustering and morphological optimized sequential linear iterative clustering (HMSLIC) for sequence image oversegmentation is then proposed to obtain superpixel blocks. The adaptive weight coefficient is then constructed to calculate the distance required between superpixels to achieve precise lung nodules positioning and to obtain the subsequent clustering starting block. Moreover, by fitting the distance and detecting the change in slope, an accurate clustering threshold is obtained. Thereafter, a fast DBSCAN superpixel sequence clustering algorithm, which is optimized by the strategy of only clustering the lung nodules and adaptive threshold, is then used to obtain lung nodule mask sequences. Finally, the lung nodule image sequences are obtained. The experimental results show that our method rapidly, completely and accurately segments various types of lung nodule image sequences. PMID:28880916

Fast and accurate determination of arsenobetaine in fish tissues using accelerated solvent extraction and HPLC-ICP-MS determination.

PubMed

Wahlen, Raimund

2004-04-01

A high-performance liquid chromatography-inductively coupled plasma-mass spectrometry (HPLC-ICP-MS) method has been developed for the fast and accurate analysis of arsenobetaine (AsB) in fish samples extracted by accelerated solvent extraction. The combined extraction and analysis approach is validated using certified reference materials for AsB in fish and during a European intercomparison exercise with a blind sample. Up to six species of arsenic (As) can be separated and quantitated in the extracts within a 10-min isocratic elution. The method is optimized so as to minimize time-consuming sample preparation steps and allow for automated extraction and analysis of large sample batches. A comparison of standard addition and external calibration show no significant difference in the results obtained, which indicates that the LC-ICP-MS method is not influenced by severe matrix effects. The extraction procedure can process up to 24 samples in an automated manner, yet the robustness of the developed HPLC-ICP-MS approach is highlighted by the capability to run more than 50 injections per sequence, which equates to a total run-time of more than 12 h. The method can therefore be used to rapidly and accurately assess the proportion of nontoxic AsB in fish samples with high total As content during toxicological screening studies.

Rapid Antimicrobial Susceptibility Testing Using Forward Laser Light Scatter Technology

PubMed Central

Clinton, Lani K.; Hewitt, Carolyn; Koyamatsu, Terri; Sun, Yilun; Jamison, Ginger; Perkins, Rosalie; Tang, Li; Pounds, Stanley; Bankowski, Matthew J.

2016-01-01

The delayed reporting of antimicrobial susceptibility testing remains a limiting factor in clinical decision-making in the treatment of bacterial infection. This study evaluates the use of forward laser light scatter (FLLS) to measure bacterial growth for the early determination of antimicrobial susceptibility. Three isolates each (two clinical isolates and one reference strain) of Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa were tested in triplicate using two commercial antimicrobial testing systems, the Vitek2 and the MicroScan MIC panel, to challenge the BacterioScan FLLS. The BacterioScan FLLS showed a high degree of categorical concordance with the commercial methods. Pairwise comparison with each commercial system serving as a reference standard showed 88.9% agreement with MicroScan (two minor errors) and 72.2% agreement with Vitek (five minor errors). FLLS using the BacterioScan system shows promise as a novel method for the rapid and accurate determination of antimicrobial susceptibility. PMID:27558176

Rapid characterisation and identification of compounds in Saposhnikoviae Radix by high-performance liquid chromatography coupled with electrospray ionisation quadrupole time-of-flight mass spectrometry.

PubMed

Chen, Luxiao; Chen, Xiangyang; Su, Lei; Jiang, Yanyan; Liu, Bin

2018-04-01

Saposhnikoviae Radix (SR), the dried root of Saposhnikovia divaricata (Turcz.) Schischk. (Umbelliferae), is commonly used as a traditional Chinese medicine. In this study, a rapid and accurate method was firstly, developed for the qualitative analysis of SR by high-performance liquid chromatography coupled with electrospray ionisation quadrupole time-of-flight mass spectrometry (HPLC-ESI-Q-TOF-MS/MS). A total of 45 compounds were identified or tentatively characterised, including 13 chromones, 28 coumarins and four others. Among them, 16 compounds were identified from SR for the first time. In addition, six chromones reference standards, including two isolated compounds of 3'-O-angeloylhamaudol and norcimifugin from the extraction of SR, were used to study the fragmentation pathways of chromones. The developed method was effective for characterising the compounds of SR, and the results of the study enriched the understanding of the chemical connotation.

[Diagnosis of tuberculosis meningitis by detection of adenosine deaminase activity and amplification of nucleotide sequences with PCR].

PubMed

Correa, M F; Armas, E; Díaz, D; de Elguezabal, K; De la Rosa, M L; Calles, G; Adjounian, H; Pedroza, R

2001-01-01

Tuberculous meningitis (TBM) is the most severe and lethal form of tuberculosis. The rapid bacteriological diagnosis with the conventional techniques is nearly impossible in TBM. There for many patients are treated with anti-TBC drugs without a definitive diagnosis. A more fast and accurate diagnostic method is necessary, in order to initiate the treatment on time to prevent the irreversible neurologic sequel or death. We evaluated the use of two rapid methods: Adenosine deaminase activity (ADA) and polymerase chain reaction (PCR) for IS6110 and mtp40 sequences on cerebrospinal fluid (CSF) from chronic meningitis patients. For ADA activity > 8.0 U/L the sensibility and specificity was 80% and 91%. PCR sensibility was 80% and specificity 97%. ADA activity and PCR on CSF could be specially useful as complementary tools in the early diagnosis of TBM.

A rapid and efficient branched DNA hybridization assay to titer lentiviral vectors.

PubMed

Nair, Ayyappan; Xie, Jinger; Joshi, Sarasijam; Harden, Paul; Davies, Joan; Hermiston, Terry

2008-11-01

A robust assay to titer lentiviral vectors is imperative to qualifying their use in drug discovery, target validation and clinical applications. In this study, a novel branched DNA based hybridization assay was developed to titer lentiviral vectors by quantifying viral RNA genome copy numbers from viral lysates without having to purify viral RNA, and this approach was compared with other non-functional (p24 protein ELISA and viral RT-qPCR) and a functional method (reporter gene expression) used commonly. The RT-qPCR method requires purification of viral RNA and the accuracy of titration therefore depends on the efficiency of purification; this requirement is ameliorated in the hybridization assay as RNA is measured directly in viral lysates. The present study indicates that the hybridization based titration assay performed on viral lysates was more accurate and has additional advantages of being rapid, robust and not dependent on transduction efficiency in different cell types.

Development of a PCR-based assay for rapid and reliable identification of pathogenic Fusaria.

PubMed

Mishra, Prashant K; Fox, Roland T V; Culham, Alastair

2003-01-28

Identification of Fusarium species has always been difficult due to confusing phenotypic classification systems. We have developed a fluorescent-based polymerase chain reaction assay that allows for rapid and reliable identification of five toxigenic and pathogenic Fusarium species. The species includes Fusarium avenaceum, F. culmorum, F. equiseti, F. oxysporum and F. sambucinum. The method is based on the PCR amplification of species-specific DNA fragments using fluorescent oligonucleotide primers, which were designed based on sequence divergence within the internal transcribed spacer region of nuclear ribosomal DNA. Besides providing an accurate, reliable, and quick diagnosis of these Fusaria, another advantage with this method is that it reduces the potential for exposure to carcinogenic chemicals as it substitutes the use of fluorescent dyes in place of ethidium bromide. Apart from its multidisciplinary importance and usefulness, it also obviates the need for gel electrophoresis.

Protein solubilities determined by a rapid technique and modification of that technique to a micro-method

NASA Technical Reports Server (NTRS)

Cacioppo, Elizabeth; Pusey, Marc Lee; Munson, Sibyl

1989-01-01

A simple, rapid method for determination of protein solubilities has been developed which is based upon maximization of the free solution volume to be brought into equilibrium. The tetragonal lysozome solubility diagram has been determined from pH 4.0 to 5.2 (0.1 M sodium acetate), 2-7 percent NaCl, 3-25 C, and portions of the orthorhombic solubility diagram using this technique. Both tetragonal and orthorhombic solubilities were found to increase smoothly with decreasing salt concentration and increasing temperature; no retrograde solubilities were observed. Using column volumes of 75, 300, and 900 microliters, identical tetragonal lysozyme solubility diagrams were obtained. Chymotrypsinogen solubilities have also been determined using this apparatus, being retrograde over the temperature range tested. It is noted that the primary limiting factor in reducing the crystalline volume is the minimum solution sample size needed to accurately quantitate the protein.

Rapid multiplexed genotyping for hereditary thrombophilia by SELDI-TOF mass spectrometry.

PubMed

Yang, Shangbin; Xu, Lihui; Wu, Haifeng M

2010-03-01

Approximately 50% of patients with venous thromboembolism also present with hereditary predisposition. The most common genetic factors are single nucleotide polymorphisms (SNPs) of factor V Leiden, prothrombin G20210A, and methylenetetrahydrofolate reductase C677T. Genotyping these SNPs helps clinicians to correctly diagnose the disease and properly manage patients. In this study, we report a novel method using surface-enhanced laser desorption and ionization time of flight mass spectrometry to rapidly genotype, in a multiplex fashion, 3 SNPs that predispose patients to thrombosis. First, patient DNA samples were subjected to polymerase chain reaction to amplify and extend the DNA products with masses corresponding to specific genotypes. Polymerase chain reaction products were then applied to Q10 anionic protein chips, undergoing on-chip sample enrichment and clean-up. Finally, the genotypes of the SNPs were determined by surface-enhanced laser desorption and ionization time of flight mass spectrometry. This method offers a rapid turnaround time of less than 5 hours from sample collection to result reporting. The analytical accuracy of each SNP genotyping result has been confirmed by DNA sequencing. In addition, the genotype results produced by this method were validated by comparing them with results obtained by the approved method in the clinical reference laboratory. This novel method is fast, accurate, and reproducible, and thus provides an excellent platform to promote personalized medicine in the management of clotting disorders.

Evaluation of a novel immunochromatographic device for rapid and accurate clinical detection of Porphyromonas gingivalis in subgingival plaque.

PubMed

Imamura, K; Takayama, S; Saito, A; Inoue, E; Nakayama, Y; Ogata, Y; Shirakawa, S; Nagano, T; Gomi, K; Morozumi, T; Akiishi, K; Watanabe, K; Yoshie, H

2015-10-01

An important goal for the improved diagnosis and management of infectious and inflammatory diseases, such as periodontitis, is the development of rapid and accurate technologies for the decentralized detection of bacterial pathogens. The aim of this prospective multicenter study was to evaluate the clinical use of a novel immunochromatographic device with monoclonal antibodies for the rapid point-of-care detection and semi-quantification of Porphyromonas gingivalis in subgingival plaque. Sixty-three patients with chronic periodontitis and 28 periodontally healthy volunteers were subjected to clinical and microbiological examinations. Subgingival plaque samples were analyzed for the presence of P. gingivalis using a novel immunochromatography based device DK13-PG-001, designed to detect the 40k-outer membrane protein of P. gingivalis, and compared with a PCR-Invader method. In the periodontitis group, a significant strong positive correlation in detection results was found between the test device score and the PCR-Invader method (Spearman rank correlation, r=0.737, p<0.0001). The sensitivity, specificity, and positive and negative predictive values of the test device were 96.2%, 91.8%, 90.4% and 96.7%, respectively. The detection threshold of the test device was determined to be approximately 10(4) (per two paper points). There were significant differences in the bacterial counts by the PCR-Invader method among groups with different ranges of device scores. With a cut-off value of ≥0.25 in device score, none of periodontally healthy volunteers were tested positive for the subgingival presence of P. gingivalis, whereas 76% (n=48) of periodontitis subjects were tested positive. There was a significant positive correlation between device scores for P. gingivalis and periodontal parameters including probing pocket depth and clinical attachment level (r=0.317 and 0.281, respectively, p<0.01). The results suggested that the DK13-PG-001 device kit can be effectively used for rapid, chair-side detection and semi-quantification of P. gingivalis in subgingival plaque. UMIN Clinical Trials Registry (UMIN-CTR) UMIN000011943. Copyright © 2015 Elsevier B.V. All rights reserved.

Calculation method for laser radar cross sections of rotationally symmetric targets.

PubMed

Cao, Yunhua; Du, Yongzhi; Bai, Lu; Wu, Zhensen; Li, Haiying; Li, Yanhui

2017-07-01

The laser radar cross section (LRCS) is a key parameter in the study of target scattering characteristics. In this paper, a practical method for calculating LRCSs of rotationally symmetric targets is presented. Monostatic LRCSs for four kinds of rotationally symmetric targets (cone, rotating ellipsoid, super ellipsoid, and blunt cone) are calculated, and the results verify the feasibility of the method. Compared with the results for the triangular patch method, the correctness of the method is verified, and several advantages of the method are highlighted. For instance, the method does not require geometric modeling and patch discretization. The method uses a generatrix model and double integral, and its calculation is concise and accurate. This work provides a theory analysis for the rapid calculation of LRCS for common basic targets.

Real-Time Onboard Global Nonlinear Aerodynamic Modeling from Flight Data

NASA Technical Reports Server (NTRS)

Brandon, Jay M.; Morelli, Eugene A.

2014-01-01

Flight test and modeling techniques were developed to accurately identify global nonlinear aerodynamic models onboard an aircraft. The techniques were developed and demonstrated during piloted flight testing of an Aermacchi MB-326M Impala jet aircraft. Advanced piloting techniques and nonlinear modeling techniques based on fuzzy logic and multivariate orthogonal function methods were implemented with efficient onboard calculations and flight operations to achieve real-time maneuver monitoring and analysis, and near-real-time global nonlinear aerodynamic modeling and prediction validation testing in flight. Results demonstrated that global nonlinear aerodynamic models for a large portion of the flight envelope were identified rapidly and accurately using piloted flight test maneuvers during a single flight, with the final identified and validated models available before the aircraft landed.

Catalyzing Novel Approaches to Rapid, Accurate, and Affordable Early Cancer Detection.

PubMed

Dhar, Asif; Meagher, Beth; Ryscavage, Andrew

Inspired by the Cancer Moonshot, a dedicated team of professionals worked with leaders across the cancer ecosystem to look for an opportunity to radically reduce cancer mortality globally by focusing on early cancer detection. After an initial survey of cancer innovation, progress, and pitfalls, the team believed that if new rapid, affordable, and accurate early detection solutions were appropriately brought to market, it would be possible to intervene earlier when cancer is most treatable.An extensive process began, informed by dozens of experts in the cancer ecosystem. The Cancer XPRIZE team designed a prize competition where "the winning team will develop a means to rapidly, accurately, and affordably screen for early cancers where intervention can reduce human suffering."The following outlines the Cancer XPRIZE's experience using a powerful approach-the radical prize design-to catch more cancers in time to make a difference saving lives, dollars, and suffering.

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

PubMed

Li, Fuyi; Li, Chen; Marquez-Lago, Tatiana T; Leier, André; Akutsu, Tatsuya; Purcell, Anthony W; Smith, A Ian; Lithgow, Trevor; Daly, Roger J; Song, Jiangning; Chou, Kuo-Chen

2018-06-27

Kinase-regulated phosphorylation is a ubiquitous type of post-translational modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signalling defects caused by aberrant phosphorylation are highly associated with a variety of human diseases, especially cancers. In light of this, a number of computational methods aiming to accurately predict protein kinase family-specific or kinase-specific phosphorylation sites have been established, thereby facilitating phosphoproteomic data analysis. In this work, we present Quokka, a novel bioinformatics tool that allows users to rapidly and accurately identify human kinase family-regulated phosphorylation sites. Quokka was developed by using a variety of sequence scoring functions combined with an optimized logistic regression algorithm. We evaluated Quokka based on well-prepared up-to-date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively. The independent test demonstrates that Quokka improves the prediction performance compared with state-of-the-art computational tools for phosphorylation prediction. In summary, our tool provides users with high-quality predicted human phosphorylation sites for hypothesis generation and biological validation. The Quokka webserver and datasets are freely available at http://quokka.erc.monash.edu/. Supplementary data are available at Bioinformatics online.

A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth

PubMed Central

Ross, James D.; Cullen, D. Kacy; Harris, James P.; LaPlaca, Michelle C.; DeWeerth, Stephen P.

2015-01-01

Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identification of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classifying features in 2-D and merging these classifications into 3-D objects; the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the platform provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological complexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥95%. We demonstrated the robustness of these algorithms in a more complex arena through the automated segmentation of neural cells in ex vivo brain slices. These novel methods surpass previous techniques by improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions. PMID:26257609

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

PubMed

Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

2012-01-01

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor model is uninformative in the worst possible sense. For all inputs, all trees optimize the likelihood score. Second, we show that a greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree can produce very poor alignments and trees. Therefore, the excellent performance of SATé-II and SATé-I is not because ML is used as an optimization criterion for choosing the best tree/alignment pair but rather due to the particular divide-and-conquer realignment techniques employed.

Neutral Fragment Filtering for Rapid Identification of New Diester-Diterpenoid Alkaloids in Roots of Aconitum carmichaeli by Ultra-High-Pressure Liquid Chromatography Coupled with Linear Ion Trap-Orbitrap Mass Spectrometry

PubMed Central

Qiu, Xiao Hui; Yang, Yi Ming; Zhu, Da Yuan; Xu, Wen

2012-01-01

A rapid and effective method was developed for separation and identification of diester-diterpenoid alkaloids (DDA) in the roots of Aconitum carmichaeli by ultra-high-pressure liquid chromatography coupled with high resolution LTQ-Orbitrap tandem mass spectrometry (UHPLC-LTQ-Orbitrap-MSn). According to accurate mass measurement and the characteristic neutral loss filtering strategy, a total of 42 diester-diterpenoid alkaloids (DDA) were rapidly detected and characterized or tentatively identified. Meanwhile, the proposed fragmentation pathways and the major diagnostic fragment ions of aconitine, mesaconitine and hypaconitine were investigated to trace DDA derivatives in crude plant extracts. 23 potential new compounds were successfully screened and characterized in Aconitum carmichaeli, including 16 short chain fatty acyls DDA, 4 N-dealkyl DDA and several isomers of aconitine, mesaconitine and hypaconitine. PMID:23285005

MALDI-TOF MS Profiling-Advances in Species Identification of Pests, Parasites, and Vectors.

PubMed

Murugaiyan, Jayaseelan; Roesler, Uwe

2017-01-01

Invertebrate pests and parasites of humans, animals, and plants continue to cause serious diseases and remain as a high treat to agricultural productivity and storage. The rapid and accurate species identification of the pests and parasites are needed for understanding epidemiology, monitoring outbreaks, and designing control measures. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as a rapid, cost effective, and high throughput technique of microbial species identification in modern diagnostic laboratories. The development of soft ionization techniques and the release of commercial pattern matching software platforms has resulted in the exponential growth of applications in higher organisms including parasitology. The present review discusses the proof-of-principle experiments and various methods of MALDI MS profiling in rapid species identification of both laboratory and field isolates of pests, parasites and vectors.

MALDI-TOF MS Profiling-Advances in Species Identification of Pests, Parasites, and Vectors

PubMed Central

Murugaiyan, Jayaseelan; Roesler, Uwe

2017-01-01

Invertebrate pests and parasites of humans, animals, and plants continue to cause serious diseases and remain as a high treat to agricultural productivity and storage. The rapid and accurate species identification of the pests and parasites are needed for understanding epidemiology, monitoring outbreaks, and designing control measures. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as a rapid, cost effective, and high throughput technique of microbial species identification in modern diagnostic laboratories. The development of soft ionization techniques and the release of commercial pattern matching software platforms has resulted in the exponential growth of applications in higher organisms including parasitology. The present review discusses the proof-of-principle experiments and various methods of MALDI MS profiling in rapid species identification of both laboratory and field isolates of pests, parasites and vectors. PMID:28555175

Noise Whitening in Airborne Wind Profiling With a Pulsed 2-Micron Coherent Doppler Lidar at NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Beyon, Jeffrey Y.; Arthur, Grant E.; Koch, Grady J.; Kavaya, Michael J.

2012-01-01

Two different noise whitening methods in airborne wind profiling with a pulsed 2-micron coherent Doppler lidar system at NASA Langley Research Center in Virginia are presented. In order to provide accurate wind parameter estimates from the airborne lidar data acquired during the NASA Genesis and Rapid Intensification Processes (GRIP) campaign in 2010, the adverse effects of background instrument noise must be compensated properly in the early stage of data processing. The results of the two methods are presented using selected GRIP data and compared with the dropsonde data for verification purposes.

Ultrasonic technique for characterizing skin burns

DOEpatents

Goans, Ronald E.; Cantrell, Jr., John H.; Meyers, F. Bradford; Stambaugh, Harry D.

1978-01-01

This invention, a method for ultrasonically determining the depth of a skin burn, is based on the finding that the acoustical impedance of burned tissue differs sufficiently from that of live tissue to permit ultrasonic detection of the interface between the burn and the underlying unburned tissue. The method is simple, rapid, and accurate. As compared with conventional practice, it provides the important advantage of permitting much earlier determination of whether a burn is of the first, second, or third degree. In the case of severe burns, the usual two - to three-week delay before surgery may be reduced to about 3 days or less.

Polarographic determination of tungsten in rocks

USGS Publications Warehouse

Reichen, L.E.

1954-01-01

This work was undertaken to develop a simpler and faster method than the classical gravimetric procedure for the determination of tungsten in rocks and ores. A new polarographic wave of tungsten is obtained in a supporting electrolyte of dilute hydrochloric acid containing tartrate ion. This permits the determination of tungsten both rapidly and accurately. No precipitation of the tungsten is necessary, and only the iron need be separated from the tungsten. The accuracy is within the limits of a polarographic procedure; comparison of polarographic and gravimetric results is given. The method reduces appreciably the amount of time ordinarily consumed in determination of tungsten.

[A practical method of numerical evaluation applicable to miniaturized technics of plaque assay].

PubMed

Beytout, D; Laveran, H; Reynaud, M P

1975-01-01

When one wishes to titrate viruses by counting the number of infective foci on small surfaces of observation, one is rapidly limited by confluences which render counting impossible. Between the use of an all or nothing system which is not accurate and a total field of count, often impossible, there is an intermediate method already described and studied by Tippett, which is very little used in practice. We have performed the calculations again, drawn up reference values and given rules for choice of the field. Two examples show their practical use.

A simple video-based timing system for on-ice team testing in ice hockey: a technical report.

PubMed

Larson, David P; Noonan, Benjamin C

2014-09-01

The purpose of this study was to describe and evaluate a newly developed on-ice timing system for team evaluation in the sport of ice hockey. We hypothesized that this new, simple, inexpensive, timing system would prove to be highly accurate and reliable. Six adult subjects (age 30.4 ± 6.2 years) performed on ice tests of acceleration and conditioning. The performance times of the subjects were recorded using a handheld stopwatch, photocell, and high-speed (240 frames per second) video. These results were then compared to allow for accuracy calculations of the stopwatch and video as compared with filtered photocell timing that was used as the "gold standard." Accuracy was evaluated using maximal differences, typical error/coefficient of variation (CV), and intraclass correlation coefficients (ICCs) between the timing methods. The reliability of the video method was evaluated using the same variables in a test-retest analysis both within and between evaluators. The video timing method proved to be both highly accurate (ICC: 0.96-0.99 and CV: 0.1-0.6% as compared with the photocell method) and reliable (ICC and CV within and between evaluators: 0.99 and 0.08%, respectively). This video-based timing method provides a very rapid means of collecting a high volume of very accurate and reliable on-ice measures of skating speed and conditioning, and can easily be adapted to other testing surfaces and parameters.

An Evaluation of Fractal Surface Measurement Methods for Characterizing Landscape Complexity from Remote-Sensing Imagery

NASA Technical Reports Server (NTRS)

Lam, Nina Siu-Ngan; Qiu, Hong-Lie; Quattrochi, Dale A.; Emerson, Charles W.; Arnold, James E. (Technical Monitor)

2001-01-01

The rapid increase in digital data volumes from new and existing sensors necessitates the need for efficient analytical tools for extracting information. We developed an integrated software package called ICAMS (Image Characterization and Modeling System) to provide specialized spatial analytical functions for interpreting remote sensing data. This paper evaluates the three fractal dimension measurement methods: isarithm, variogram, and triangular prism, along with the spatial autocorrelation measurement methods Moran's I and Geary's C, that have been implemented in ICAMS. A modified triangular prism method was proposed and implemented. Results from analyzing 25 simulated surfaces having known fractal dimensions show that both the isarithm and triangular prism methods can accurately measure a range of fractal surfaces. The triangular prism method is most accurate at estimating the fractal dimension of higher spatial complexity, but it is sensitive to contrast stretching. The variogram method is a comparatively poor estimator for all of the surfaces, particularly those with higher fractal dimensions. Similar to the fractal techniques, the spatial autocorrelation techniques are found to be useful to measure complex images but not images with low dimensionality. These fractal measurement methods can be applied directly to unclassified images and could serve as a tool for change detection and data mining.

Detection of shigella in lettuce by the use of a rapid molecular assay with increased sensitivity

PubMed Central

Jiménez, Kenia Barrantes; McCoy², Clyde B.; Achí, Rosario

2010-01-01

A Multiplex Polymerase Chain Reaction (PCR) assay to be used as an alternative to the conventional culture method in detecting Shigella and enteroinvasive Escherichia coli (EIEC) virulence genes ipaH and ial in lettuce was developed. Efficacy and rapidity of the molecular method were determined as compared to the conventional culture. Lettuce samples were inoculated with different Shigella flexneri concentrations (from 10 CFU/ml to 107 CFU/ml). DNA was extracted directly from lettuce after inoculation (direct-PCR) and after an enrichment step (enrichment PCR). Multiplex PCR detection limit was 104CFU/ml, diagnostic sensitivity and specificity were 100% accurate. An internal amplification control (IAC) of 100 bp was used in order to avoid false negative results. This method produced results in 1 to 2 days while the conventional culture method required 5 to 6 days. Also, the culture method detection limit was 106 CFU/ml, diagnostic sensitivity was 53% and diagnostic specificity was 100%. In this study a Multiplex PCR method for detection of virulence genes in Shigella and EIEC was shown to be effective in terms of diagnostic sensitivity, detection limit and amount of time as compared to Shigella conventional culture. PMID:24031579

Rapid Screening of Cancer Margins in Tissue with Multimodal Confocal Microscopy

PubMed Central

Gareau, Daniel S.; Jeon, Hana; Nehal, Kishwer S.; Rajadhyaksha, Milind

2012-01-01

Background Complete and accurate excision of cancer is guided by the examination of histopathology. However, preparation of histopathology is labor intensive and slow, leading to insufficient sampling of tissue and incomplete and/or inaccurate excision of margins. We demonstrate the potential utility of multimodal confocal mosaicing microscopy for rapid screening of cancer margins, directly in fresh surgical excisions, without the need for conventional embedding, sectioning or processing. Materials/Methods A multimodal confocal mosaicing microscope was developed to image basal cell carcinoma margins in surgical skin excisions, with resolution that shows nuclear detail. Multimodal contrast is with fluorescence for imaging nuclei and reflectance for cellular cytoplasm and dermal collagen. Thirtyfive excisions of basal cell carcinomas from Mohs surgery were imaged, and the mosaics analyzed by comparison to the corresponding frozen pathology. Results Confocal mosaics are produced in about 9 minutes, displaying tissue in fields-of-view of 12 mm with 2X magnification. A digital staining algorithm transforms black and white contrast to purple and pink, which simulates the appearance of standard histopathology. Mosaicing enables rapid digital screening, which mimics the examination of histopathology. Conclusions Multimodal confocal mosaicing microscopy offers a technology platform to potentially enable real-time pathology at the bedside. The imaging may serve as an adjunct to conventional histopathology, to expedite screening of margins and guide surgery toward more complete and accurate excision of cancer. PMID:22721570

Development of a fluorescence-based sensor for rapid diagnosis of cyanide exposure.

PubMed

Jackson, Randy; Oda, Robert P; Bhandari, Raj K; Mahon, Sari B; Brenner, Matthew; Rockwood, Gary A; Logue, Brian A

2014-02-04

Although commonly known as a highly toxic chemical, cyanide is also an essential reagent for many industrial processes in areas such as mining, electroplating, and synthetic fiber production. The "heavy" use of cyanide in these industries, along with its necessary transportation, increases the possibility of human exposure. Because the onset of cyanide toxicity is fast, a rapid, sensitive, and accurate method for the diagnosis of cyanide exposure is necessary. Therefore, a field sensor for the diagnosis of cyanide exposure was developed based on the reaction of naphthalene dialdehyde, taurine, and cyanide, yielding a fluorescent β-isoindole. An integrated cyanide capture "apparatus", consisting of sample and cyanide capture chambers, allowed rapid separation of cyanide from blood samples. Rabbit whole blood was added to the sample chamber, acidified, and the HCN gas evolved was actively transferred through a stainless steel channel to the capture chamber containing a basic solution of naphthalene dialdehyde (NDA) and taurine. The overall analysis time (including the addition of the sample) was <3 min, the linear range was 3.13-200 μM, and the limit of detection was 0.78 μM. None of the potential interferents investigated (NaHS, NH4OH, NaSCN, and human serum albumin) produced a signal that could be interpreted as a false positive or a false negative for cyanide exposure. Most importantly, the sensor was 100% accurate in diagnosing cyanide poisoning for acutely exposed rabbits.

A semi-automated method for rapid detection of ripple events on interictal voltage discharges in the scalp electroencephalogram

PubMed Central

Chu, Catherine. J.; Chan, Arthur; Song, Dan; Staley, Kevin J.; Stufflebeam, Steven M.; Kramer, Mark A.

2017-01-01

Summary Background High frequency oscillations are emerging as a clinically important indicator of epileptic networks. However, manual detection of these high frequency oscillations is difficult, time consuming, and subjective, especially in the scalp EEG, thus hindering further clinical exploration and application. Semi-automated detection methods augment manual detection by reducing inspection to a subset of time intervals. We propose a new method to detect high frequency oscillations that co-occur with interictal epileptiform discharges. New Method The new method proceeds in two steps. The first step identifies candidate time intervals during which high frequency activity is increased. The second step computes a set of seven features for each candidate interval. These features require that the candidate event contain a high frequency oscillation approximately sinusoidal in shape, with at least three cycles, that co-occurs with a large amplitude discharge. Candidate events that satisfy these features are stored for validation through visual analysis. Results We evaluate the detector performance in simulation and on ten examples of scalp EEG data, and show that the proposed method successfully detects spike-ripple events, with high positive predictive value, low false positive rate, and high intra-rater reliability. Comparison with Existing Method The proposed method is less sensitive than the existing method of visual inspection, but much faster and much more reliable. Conclusions Accurate and rapid detection of high frequency activity increases the clinical viability of this rhythmic biomarker of epilepsy. The proposed spike-ripple detector rapidly identifies candidate spike-ripple events, thus making clinical analysis of prolonged, multielectrode scalp EEG recordings tractable. PMID:27988323

Accurate, rapid identification of dislocation lines in coherent diffractive imaging via a min-max optimization formulation

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

Ulvestad, A.; Menickelly, M.; Wild, S. M.

Defects such as dislocations impact materials properties and their response during external stimuli. Imaging these defects in their native operating conditions to establish the structure-function relationship and, ultimately, to improve performance via defect engineering has remained a considerable challenge for both electron-based and x-ray-based imaging techniques. While Bragg coherent x-ray diffractive imaging (BCDI) is successful in many cases, nuances in identifying the dislocations has left manual identification as the preferred method. Derivative-based methods are also used, but they can be inaccurate and are computationally inefficient. Here we demonstrate a derivative-free method that is both more accurate and more computationally efficientmore » than either derivative-or human-based methods for identifying 3D dislocation lines in nanocrystal images produced by BCDI. We formulate the problem as a min-max optimization problem and show exceptional accuracy for experimental images. We demonstrate a 227x speedup for a typical experimental dataset with higher accuracy over current methods. We discuss the possibility of using this algorithm as part of a sparsity-based phase retrieval process. We also provide MATLAB code for use by other researchers.« less

Accurate, rapid identification of dislocation lines in coherent diffractive imaging via a min-max optimization formulation

NASA Astrophysics Data System (ADS)

Ulvestad, A.; Menickelly, M.; Wild, S. M.

2018-01-01

Defects such as dislocations impact materials properties and their response during external stimuli. Imaging these defects in their native operating conditions to establish the structure-function relationship and, ultimately, to improve performance via defect engineering has remained a considerable challenge for both electron-based and x-ray-based imaging techniques. While Bragg coherent x-ray diffractive imaging (BCDI) is successful in many cases, nuances in identifying the dislocations has left manual identification as the preferred method. Derivative-based methods are also used, but they can be inaccurate and are computationally inefficient. Here we demonstrate a derivative-free method that is both more accurate and more computationally efficient than either derivative- or human-based methods for identifying 3D dislocation lines in nanocrystal images produced by BCDI. We formulate the problem as a min-max optimization problem and show exceptional accuracy for experimental images. We demonstrate a 227x speedup for a typical experimental dataset with higher accuracy over current methods. We discuss the possibility of using this algorithm as part of a sparsity-based phase retrieval process. We also provide MATLAB code for use by other researchers.

International Conference on Hyperbolic Problems (2nd). Theory, Numerical Methods and Applications, 14-18 March 1988

DTIC Science & Technology

1988-01-01

of this abstract got a spontaneous development of a transverse wave-strucure in a shock-oriented coordinate system without per- turbing the global ...We develop a formal asymptotic theory for hyperbolic conservation laws with large amplitude, rapidly varying initial data [1]. For small times, the...HUnefelderstr. 1-S, D-2800 Bremen 1 Today the most accurate and cost effective industrial codes used for aircraft design are based on full potential equations

Enhanced Reliability and Accuracy for Field Deployable Bioforensic Detection and Discrimination of Xylella fastidiosa subsp. pauca, Causal Agent of Citrus Variegated Chlorosis Using Razor Ex Technology and TaqMan Quantitative PCR

PubMed Central

Fletcher, Jacqueline; Melcher, Ulrich; Ochoa Corona, Francisco Manuel

2013-01-01

A reliable, accurate and rapid multigene-based assay combining real time quantitative PCR (qPCR) and a Razor Ex BioDetection System (Razor Ex) was validated for detection of Xylella fastidiosa subsp. pauca (Xfp, a xylem-limited bacterium that causes citrus variegated chlorosis [CVC]). CVC, which is exotic to the United States, has spread through South and Central America and could significantly impact U.S. citrus if it arrives. A method for early, accurate and sensitive detection of Xfp in plant tissues is needed by plant health officials for inspection of products from quarantined locations, and by extension specialists for detection, identification and management of disease outbreaks and reservoir hosts. Two sets of specific PCR primers and probes, targeting Xfp genes for fimbrillin and the periplasmic iron-binding protein were designed. A third pair of primers targeting the conserved cobalamin synthesis protein gene was designed to detect all possible X. fastidiosa (Xf) strains. All three primer sets detected as little as 1 fg of plasmid DNA carrying X. fastidiosa target sequences and genomic DNA of Xfp at as little as 1 - 10 fg. The use of Razor Ex facilitates a rapid (about 30 min) in-field assay capability for detection of all Xf strains, and for specific detection of Xfp. Combined use of three primer sets targeting different genes increased the assay accuracy and broadened the range of detection. To our knowledge, this is the first report of a field-deployable rapid and reliable bioforensic detection and discrimination method for a bacterial phytopathogen based on multigene targets. PMID:24312333

Rapid colorimetric assay for gentamicin injection.

PubMed

Tarbutton, P

1987-01-01

A rapid colorimetric method for determining gentamicin concentration in commercial preparations of gentamicin sulfate injection was developed. Methods currently available for measuring gentamicin concentration via its colored complex with cupric ions in alkaline solution were modified to reduce the time required for a single analysis. The alkaline copper tartrate (ACT) reagent solution was prepared such that each milliliter contained 100 mumol cupric sulfate, 210 mumol potassium sodium tartrate, and 1.25 mmol sodium hydroxide. The assay involves mixing 0.3 mL gentamicin sulfate injection 40 mg/mL (of gentamicin), 1.0 mL ACT reagent, and 0.7 mL water; the absorbance of the resulting solution at 560 nm was used to calculate the gentamicin concentration in the sample. For injections containing 10 mg/mL of gentamicin, the amount of the injection was increased to 0.5 mL and water decreased to 0.5 mL. The concentration of gentamicin in samples representing 11 lots of gentamicin sulfate injection 40 mg/mL and 8 lots of gentamicin sulfate injection 10 mg/mL was determined. The specificity, reproducibility, and accuracy of the assay were assessed. The colored complex was stable for at least two hours. Gentamicin concentration ranged from 93.7 to 108% and from 95 to 109% of the stated label value of the 40 mg/mL and the 10 mg/mL injections, respectively. No components of the preservative system present in the injections interfered with the assay. Since other aminoglycosides produced a colored complex, the assay is not specific for gentamicin. The assay was accurate and reproducible over the range of 4-20 mg of gentamicin. This rapid and accurate assay can be easily applied in the hospital pharmacy setting.

Enhanced reliability and accuracy for field deployable bioforensic detection and discrimination of Xylella fastidiosa subsp. pauca, causal agent of citrus variegated chlorosis using razor ex technology and TaqMan quantitative PCR.

PubMed

Ouyang, Ping; Arif, Mohammad; Fletcher, Jacqueline; Melcher, Ulrich; Ochoa Corona, Francisco Manuel

2013-01-01

A reliable, accurate and rapid multigene-based assay combining real time quantitative PCR (qPCR) and a Razor Ex BioDetection System (Razor Ex) was validated for detection of Xylella fastidiosa subsp. pauca (Xfp, a xylem-limited bacterium that causes citrus variegated chlorosis [CVC]). CVC, which is exotic to the United States, has spread through South and Central America and could significantly impact U.S. citrus if it arrives. A method for early, accurate and sensitive detection of Xfp in plant tissues is needed by plant health officials for inspection of products from quarantined locations, and by extension specialists for detection, identification and management of disease outbreaks and reservoir hosts. Two sets of specific PCR primers and probes, targeting Xfp genes for fimbrillin and the periplasmic iron-binding protein were designed. A third pair of primers targeting the conserved cobalamin synthesis protein gene was designed to detect all possible X. fastidiosa (Xf) strains. All three primer sets detected as little as 1 fg of plasmid DNA carrying X. fastidiosa target sequences and genomic DNA of Xfp at as little as 1 - 10 fg. The use of Razor Ex facilitates a rapid (about 30 min) in-field assay capability for detection of all Xf strains, and for specific detection of Xfp. Combined use of three primer sets targeting different genes increased the assay accuracy and broadened the range of detection. To our knowledge, this is the first report of a field-deployable rapid and reliable bioforensic detection and discrimination method for a bacterial phytopathogen based on multigene targets.

Rapid and high-precision measurement of sulfur isotope and sulfur concentration in sediment pore water by multi-collector inductively coupled plasma mass spectrometry.

PubMed

Bian, Xiao-Peng; Yang, Tao; Lin, An-Jun; Jiang, Shao-Yong

2015-01-01

We have developed a technique for the rapid, precise and accurate determination of sulfur isotopes (δ(34)S) by MC-ICP-MS applicable to a range of sulfur-bearing solutions of different sulfur content. The 10 ppm Alfa-S solution (ammonium sulfate solution, working standard of the lab of the authors) was used to bracket other Alfa-S solutions of different concentrations and the measured δ(34)SV-CDT values of Alfa-S solutions deviate from the reference value to varying degrees (concentration effect). The stability of concentration effect has been verified and a correction curve has been constructed based on Alfa-S solutions to correct measured δ(34)SV-CDT values. The curve has been applied to AS solutions (dissolved ammonium sulfate from the lab of the authors) and pore water samples successfully, validating the reliability of our analytical method. This method also enables us to measure the sulfur concentration simultaneously when analyzing the sulfur isotope composition. There is a strong linear correlation (R(2)>0.999) between the sulfur concentrations and the intensity ratios of samples and the standard. We have constructed a regression curve based on Alfa-S solutions and this curve has been successfully used to determine sulfur concentrations of AS solutions and pore water samples. The analytical technique presented here enable rapid, precise and accurate S isotope measurement for a wide range of sulfur-bearing solutions - in particular for pore water samples with complex matrix and varying sulfur concentrations. Also, simultaneous measurement of sulfur concentrations is available. Copyright © 2014 Elsevier B.V. All rights reserved.

[Manufacture method and clinical application of minimally invasive dental implant guide template based on registration technology].

PubMed

Lin, Zeming; He, Bingwei; Chen, Jiang; D u, Zhibin; Zheng, Jingyi; Li, Yanqin

2012-08-01

To guide doctors in precisely positioning surgical operation, a new production method of minimally invasive implant guide template was presented. The mandible of patient was scanned by CT scanner, and three-dimensional jaw bone model was constructed based on CT images data The professional dental implant software Simplant was used to simulate the plant based on the three-dimensional CT model to determine the location and depth of implants. In the same time, the dental plaster models were scanned by stereo vision system to build the oral mucosa model. Next, curvature registration technology was used to fuse the oral mucosa model and the CT model, then the designed position of implant in the oral mucosa could be determined. The minimally invasive implant guide template was designed in 3-Matic software according to the design position of implant and the oral mucosa model. Finally, the template was produced by rapid prototyping. The three-dimensional registration technology was useful to fuse the CT data and the dental plaster data, and the template was accurate that could provide the doctors a guidance in the actual planting without cut-off mucosa. The guide template which fabricated by comprehensive utilization of three-dimensional registration, Simplant simulation and rapid prototyping positioning are accurate and can achieve the minimally invasive and accuracy implant surgery, this technique is worthy of clinical use.

Characterization and delineation of caribou habitat on Unimak Island using remote sensing techniques

NASA Astrophysics Data System (ADS)

Atkinson, Brain M.

The assessment of herbivore habitat quality is traditionally based on quantifying the forages available to the animal across their home range through ground-based techniques. While these methods are highly accurate, they can be time-consuming and highly expensive, especially for herbivores that occupy vast spatial landscapes. The Unimak Island caribou herd has been decreasing in the last decade at rates that have prompted discussion of management intervention. Frequent inclement weather in this region of Alaska has provided for little opportunity to study the caribou forage habitat on Unimak Island. The overall objectives of this study were two-fold 1) to assess the feasibility of using high-resolution color and near-infrared aerial imagery to map the forage distribution of caribou habitat on Unimak Island and 2) to assess the use of a new high-resolution multispectral satellite imagery platform, RapidEye, and use of the "red-edge" spectral band on vegetation classification accuracy. Maximum likelihood classification algorithms were used to create land cover maps in aerial and satellite imagery. Accuracy assessments and transformed divergence values were produced to assess vegetative spectral information and classification accuracy. By using RapidEye and aerial digital imagery in a hierarchical supervised classification technique, we were able to produce a high resolution land cover map of Unimak Island. We obtained overall accuracy rates of 71.4 percent which are comparable to other land cover maps using RapidEye imagery. The "red-edge" spectral band included in the RapidEye imagery provides additional spectral information that allows for a more accurate overall classification, raising overall accuracy 5.2 percent.

Rapid detection of Pseudomonas aeruginosa biomarkers in biological fluids using surface-enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Wu, Xiaomeng; Chen, Jing; Zhao, Yiping; Zughaier, Susu M.

2014-05-01

Pseudomonas aeruginosa (PA) is an opportunistic pathogen that causes major infection not only in Cystic Fibrosis patients but also in chronic obstructive pulmonary disease and in critically ill patients in intensive care units. Successful antibiotic treatment of the infection relies on accurate and rapid identification of the infectious agents. Conventional microbiological detection methods usually take more than 3 days to obtain accurate results. We have developed a rapid diagnostic technique based on surface-enhanced Raman scattering to directly identify PA from biological fluids. P. aeruginosa strains, PAO1 and PA14, are cultured in lysogeny broth, and the SERS spectra of the broth show the signature Raman peaks from pyocyanin and pyoverdine, two major biomarkers that P. aeruginosa secretes during its growth, as well as lipopolysaccharides. This provides the evidence that the presence of these biomarkers can be used to indicate P. aeruginosa infection. A total of 22 clinical exhaled breath condensates (EBC) samples were obtained from subjects with CF disease and from non-CF healthy donors. SERS spectra of these EBC samples were obtained and further analyzed by both principle component analysis and partial least square-discriminant analysis (PLS-DA). PLS-DA can discriminate the samples with P. aeruginosa infection and the ones without P. aeruginosa infection at 99.3% sensitivity and 99.6% specificity. In addition, this technique can also discriminate samples from subject with CF disease and healthy donor with 97.5% sensitivity and 100% specificity. These results demonstrate the potential of using SERS of EBC samples as a rapid diagnostic tool to detect PA infection.

Rapid diagnosis of sepsis with TaqMan-Based multiplex real-time PCR.

PubMed

Liu, Chang-Feng; Shi, Xin-Ping; Chen, Yun; Jin, Ye; Zhang, Bing

2018-02-01

The survival rate of septic patients mainly depends on a rapid and reliable diagnosis. A rapid, broad range, specific and sensitive quantitative diagnostic test is the urgent need. Thus, we developed a TaqMan-Based Multiplex real-time PCR assays to identify bloodstream pathogens within a few hours. Primers and TaqMan probes were designed to be complementary to conserved regions in the 16S rDNA gene of different kinds of bacteria. To evaluate accurately, sensitively, and specifically, the known bacteria samples (Standard strains, whole blood samples) are determined by TaqMan-Based Multiplex real-time PCR. In addition, 30 blood samples taken from patients with clinical symptoms of sepsis were tested by TaqMan-Based Multiplex real-time PCR and blood culture. The mean frequency of positive for Multiplex real-time PCR was 96% at a concentration of 100 CFU/mL, and it was 100% at a concentration greater than 1000 CFU/mL. All the known blood samples and Standard strains were detected positively by TaqMan-Based Multiplex PCR, no PCR products were detected when DNAs from other bacterium were used in the multiplex assay. Among the 30 patients with clinical symptoms of sepsis, 18 patients were confirmed positive by Multiplex real-time PCR and seven patients were confirmed positive by blood culture. TaqMan-Based Multiplex real-time PCR assay with highly sensitivity, specificity and broad detection range, is a rapid and accurate method in the detection of bacterial pathogens of sepsis and should have a promising usage in the diagnosis of sepsis. © 2017 Wiley Periodicals, Inc.

An alternative method of fabricating sub-micron resolution masks using excimer laser ablation

NASA Astrophysics Data System (ADS)

Hayden, C. J.; Eijkel, J. C. T.; Dalton, C.

2004-06-01

In the work presented here, an excimer laser micromachining system has been used successfully to fabricate high-resolution projection and contact masks. The contact masks were subsequently used to produce chrome-gold circular ac electro-osmotic pump (cACEOP) microelectrode arrays on glass substrates, using a conventional contact photolithography process. The contact masks were produced rapidly (~15 min each) and were found to be accurate to sub-micron resolution, demonstrating an alternative route for mask fabrication. Laser machined masks were also used in a laser-projection system, demonstrating that such fabrication techniques are also suited to projection lithography. The work addresses a need for quick reproduction of high-resolution contact masks, given their rapid degradation when compared to non-contact masks.

Application of MALDI-TOF MS for the Identification of Food Borne Bacteria

PubMed Central

Pavlovic, Melanie; Huber, Ingrid; Konrad, Regina; Busch, Ulrich

2013-01-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful tool for the routine identification of clinical isolates. MALDI-TOF MS based identification of bacteria has been shown to be more rapid, accurate and cost-efficient than conventional phenotypic techniques or molecular methods. Rapid and reliable identification of food-associated bacteria is also of crucial importance for food processing and product quality. This review is concerned with the applicability of MALDI-TOF MS for routine identification of foodborne bacteria taking the specific requirements of food microbiological laboratories and the food industry into account. The current state of knowledge including recent findings and new approaches are discussed. PMID:24358065

Subsonic Wing Optimization for Handling Qualities Using ACSYNT

NASA Technical Reports Server (NTRS)

Soban, Danielle Suzanne

1996-01-01

The capability to accurately and rapidly predict aircraft stability derivatives using one comprehensive analysis tool has been created. The PREDAVOR tool has the following capabilities: rapid estimation of stability derivatives using a vortex lattice method, calculation of a longitudinal handling qualities metric, and inherent methodology to optimize a given aircraft configuration for longitudinal handling qualities, including an intuitive graphical interface. The PREDAVOR tool may be applied to both subsonic and supersonic designs, as well as conventional and unconventional, symmetric and asymmetric configurations. The workstation-based tool uses as its model a three-dimensional model of the configuration generated using a computer aided design (CAD) package. The PREDAVOR tool was applied to a Lear Jet Model 23 and the North American XB-70 Valkyrie.

Rapid determination of cell mass and density using digitally controlled electric field in a microfluidic chip.

PubMed

Zhao, Yuliang; Lai, Hok Sum Sam; Zhang, Guanglie; Lee, Gwo-Bin; Li, Wen Jung

2014-11-21

The density of a single cell is a fundamental property of cells. Cells in the same cycle phase have similar volume, but the differences in their mass and density could elucidate each cell's physiological state. Here we report a novel technique to rapidly measure the density and mass of a single cell using an optically induced electrokinetics (OEK) microfluidic platform. Presently, single cellular mass and density measurement devices require a complicated fabrication process and their output is not scalable, i.e., it is extremely difficult to measure the mass and density of a large quantity of cells rapidly. The technique reported here operates on a principle combining sedimentation theory, computer vision, and microparticle manipulation techniques in an OEK microfluidic platform. We will show in this paper that this technique enables the measurement of single-cell volume, density, and mass rapidly and accurately in a repeatable manner. The technique is also scalable - it allows simultaneous measurement of volume, density, and mass of multiple cells. Essentially, a simple time-controlled projected light pattern is used to illuminate the selected area on the OEK microfluidic chip that contains cells to lift the cells to a particular height above the chip's surface. Then, the cells are allowed to "free fall" to the chip's surface, with competing buoyancy, gravitational, and fluidic drag forces acting on the cells. By using a computer vision algorithm to accurately track the motion of the cells and then relate the cells' motion trajectory to sedimentation theory, the volume, mass, and density of each cell can be rapidly determined. A theoretical model of micro-sized spheres settling towards an infinite plane in a microfluidic environment is first derived and validated experimentally using standard micropolystyrene beads to demonstrate the viability and accuracy of this new technique. Next, we show that the yeast cell volume, mass, and density could be rapidly determined using this technology, with results comparable to those using the existing method suspended microchannel resonator.

Development and validation of a rapid stability indicating HPLC-method using monolithic stationary phase and two spectrophotometric methods for determination of antihistaminic acrivastine in capsules

NASA Astrophysics Data System (ADS)

Gouda, Ayman A.; Hashem, Hisham; Jira, Thomas

2014-09-01

Simple, rapid and accurate high performance liquid chromatographic (HPLC) and spectrophotometric methods are described for determination of antihistaminic acrivastine in capsules. The first method (method A) is based on accurate, sensitive and stability indicating chromatographic separation method. Chromolith® Performance RP-18e column, a relatively new packing material consisting of monolithic rods of highly porous silica, was used as stationary phase applying isocratic binary mobile phase of ACN and 25 mM NaH2PO4 pH 4.0 in the ratio of 22.5:77.5 at flow rate of 5.0 mL/min and 40 °C. A diode array detector was used at 254 nm for detection. The elution time of acrivastine was found to be 2.080 ± 0.032. The second and third methods (methods B and C) are based on the oxidation of acrivastine with excess N-bromosuccinimide (NBS) and determination of the unconsumed NBS with, metol-sulphanilic acid (λmax: 520 nm) or amaranth dye (λmax: 530 nm). The reacted oxidant corresponds to the drug content. Beer’s law is obeyed over the concentration range 1.563-50, 2.0-20 and 1.0-10 μg mL-1 for methods A, B and C, respectively. The limits of detection and quantitation were 0.40, 0.292 and 0.113 μg mL-1 and 0.782, 0.973 and 0.376 μg mL-1 for methods A, B and C, respectively. The HPLC method was validated for system suitability, linearity, precision, limits of detection and quantitation, specificity, stability and robustness. Stability tests were done through exposure of the analyte solution for four different stress conditions and the results indicate no interference of degradants with HPLC-method. The proposed methods was favorably applied for determination of acrivastine in capsules formulation. Statistical comparison of the obtained results from the analysis of the studied drug to those of the reported method using t- and F-tests showed no significant difference between them.

A Rapid and Specific Assay for the Detection of MERS-CoV

PubMed Central

Huang, Pei; Wang, Hualei; Cao, Zengguo; Jin, Hongli; Chi, Hang; Zhao, Jincun; Yu, Beibei; Yan, Feihu; Hu, Xingxing; Wu, Fangfang; Jiao, Cuicui; Hou, Pengfei; Xu, Shengnan; Zhao, Yongkun; Feng, Na; Wang, Jianzhong; Sun, Weiyang; Wang, Tiecheng; Gao, Yuwei; Yang, Songtao; Xia, Xianzhu

2018-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel human coronavirus that can cause human respiratory disease. The development of a detection method for this virus that can lead to rapid and accurate diagnosis would be significant. In this study, we established a nucleic acid visualization technique that combines the reverse transcription loop-mediated isothermal amplification technique and a vertical flow visualization strip (RT-LAMP-VF) to detect the N gene of MERS-CoV. The RT-LAMP-VF assay was performed in a constant temperature water bath for 30 min, and the result was visible by the naked eye within 5 min. The RT-LAMP-VF assay was capable of detecting 2 × 101 copies/μl of synthesized RNA transcript and 1 × 101 copies/μl of MERS-CoV RNA. The method exhibits no cross-reactivities with multiple CoVs including SARS-related (SARSr)-CoV, HKU4, HKU1, OC43 and 229E, and thus exhibits high specificity. Compared to the real-time RT-PCR (rRT-PCR) method recommended by the World Health Organization (WHO), the RT-LAMP-VF assay is easy to handle, does not require expensive equipment and can rapidly complete detection within 35 min. PMID:29896174

Rapid detection method for Bacillus anthracis using a combination of multiplexed real-time PCR and pyrosequencing and its application for food biodefense.

PubMed

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

2015-02-01

Bacillus anthracis, the causative agent of anthrax, has the capacity to form highly resilient spores as part of its life cycle. The potential for the dissemination of these spores using food as a vehicle is a huge public health concern and, hence, requires the development of a foodborne bioterrorism response approach. In this work, we address a critical gap in food biodefense by presenting a novel, combined, sequential method involving the use of real-time PCR and pyrosequencing for the rapid, specific detection of B. anthracis spores in three food matrices: milk, apple juice, and bottled water. The food samples were experimentally inoculated with 40 CFU ml(-1), and DNA was extracted from the spores and analyzed after immunomagnetic separation. Applying the combination of multiplex real-time PCR and pyrosequencing, we successfully detected the presence of targets on both of the virulence plasmids and the chromosome. The results showed that DNA amplicons generated from a five-target multiplexed real-time PCR detection using biotin-labeled primers can be used for single-plex pyrosequencing detection. The combined use of multiplexed real-time PCR and pyrosequencing is a novel, rapid detection method for B. anthracis from food and provides a tool for accurate, quantitative identification with potential biodefense applications.

Development and application of loop-mediated isothermal amplification (LAMP) for detection of Plasmopara viticola

PubMed Central

Kong, Xiangjiu; Qin, Wentao; Huang, Xiaoqing; Kong, Fanfang; Schoen, Cor D.; Feng, Jie; Wang, Zhongyue; Zhang, Hao

2016-01-01

A rapid LAMP (loop-mediated isothermal amplification) detection method was developed on the basis of the ITS sequence of P. viticola, the major causal agent of grape downy mildew. Among the 38 fungal and oomycete species tested, DNA isolated exclusively from P. viticola resulted in a specific product after LAMP amplification. This assay had high sensitivity and was able to detect the presence of less than 33 fg of genomic DNA per 25-μL reaction within 30 min. The infected leaves may produce sporangia that serve as a secondary inoculum. The developed LAMP assay is efficient for estimating the latent infection of grape leaves by P. viticola. When combined with the rapid and simple DNA extraction method, this assay’s total detection time is shortened to approximately one hour; therefore it is suitable for on-site detection of latent infection in the field. The sporangia levels in the air are strongly associated with disease severity. The LAMP method was also demonstrated to be able to estimate the level of sporangia released in the air in a certain period. This assay should make disease forecasting more accurate and rapid and should be helpful in decision-making regarding the control of grape downy mildew. PMID:27363943

[Rapid determination of COD in aquaculture water based on LS-SVM with ultraviolet/visible spectroscopy].

PubMed

Liu, Xue-Mei; Zhang, Hai-Liang

2014-10-01

Ultraviolet/visible (UV/Vis) spectroscopy was studied for the rapid determination of chemical oxygen demand (COD), which was an indicator to measure the concentration of organic matter in aquaculture water. In order to reduce the influence of the absolute noises of the spectra, the extracted 135 absorbance spectra were preprocessed by Savitzky-Golay smoothing (SG), EMD, and wavelet transform (WT) methods. The preprocessed spectra were then used to select latent variables (LVs) by partial least squares (PLS) methods. Partial least squares (PLS) was used to build models with the full spectra, and back- propagation neural network (BPNN) and least square support vector machine (LS-SVM) were applied to build models with the selected LVs. The overall results showed that BPNN and LS-SVM models performed better than PLS models, and the LS-SVM models with LVs based on WT preprocessed spectra obtained the best results with the determination coefficient (r2) and RMSE being 0. 83 and 14. 78 mg · L(-1) for calibration set, and 0.82 and 14.82 mg · L(-1) for the prediction set respectively. The method showed the best performance in LS-SVM model. The results indicated that it was feasible to use UV/Vis with LVs which were obtained by PLS method, combined with LS-SVM calibration could be applied to the rapid and accurate determination of COD in aquaculture water. Moreover, this study laid the foundation for further implementation of online analysis of aquaculture water and rapid determination of other water quality parameters.

Rapid comparison of protein binding site surfaces with Property Encoded Shape Distributions (PESD)

PubMed Central

Das, Sourav; Kokardekar, Arshad

2009-01-01

Patterns in shape and property distributions on the surface of binding sites are often conserved across functional proteins without significant conservation of the underlying amino-acid residues. To explore similarities of these sites from the viewpoint of a ligand, a sequence and fold-independent method was created to rapidly and accurately compare binding sites of proteins represented by property-mapped triangulated Gauss-Connolly surfaces. Within this paradigm, signatures for each binding site surface are produced by calculating their property-encoded shape distributions (PESD), a measure of the probability that a particular property will be at a specific distance to another on the molecular surface. Similarity between the signatures can then be treated as a measure of similarity between binding sites. As postulated, the PESD method rapidly detected high levels of similarity in binding site surface characteristics even in cases where there was very low similarity at the sequence level. In a screening experiment involving each member of the PDBBind 2005 dataset as a query against the rest of the set, PESD was able to retrieve a binding site with identical E.C. (Enzyme Commission) numbers as the top match in 79.5% of cases. The ability of the method in detecting similarity in binding sites with low sequence conservations were compared with state-of-the-art binding site comparison methods. PMID:19919089

Rapid diagnosis of Theileria annulata by recombinase polymerase amplification combined with a lateral flow strip (LF-RPA) in epidemic regions.

PubMed

Yin, Fangyuan; Liu, Junlong; Liu, Aihong; Li, Youquan; Luo, Jianxun; Guan, Guiquan; Yin, Hong

2017-04-15

Rapid and accurate diagnosis of Theileria annulata infection contributes to the formulation of strategies to eradicate this parasite. A simple and efficient diagnostic tool, recombinase polymerase amplification (RPA) combined with a lateral flow (LF) strip, was used in detection of Theileria and compared to other methods that require expensive instruments and skilled personnel. Herein, we established and optimized an LF-RPA method to detect the cytochrome b gene of T. annulata mitochondrial DNA from experimentally infected and field-collected blood samples. This method has many unparalleled characteristics, including that it is rapid (clear detection in 5min at constant temperature), sensitive (the limitation of detection is at least 2pg genomic DNA), and specific (no cross-reaction with other piroplasms that infect cattle). The LF-RPA assay was evaluated via testing 17 field blood samples and comparing the results of that of a PCR, showing 100% agreement, which demonstrates the ability of the LF-RPA assay to detect T. annulata infections in small number of samples (n=17). Taken together, the results indicate that this method could be used as an ideal diagnostic tool for detecting T. annulata in endemic regions with limited to fewer and local resources and could also be a potential technique for the surveillance and control of blood protozoa. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantification of strontium in human serum by ICP-MS using alternate analyte-free matrix and its application to a pilot bioequivalence study of two strontium ranelate oral formulations in healthy Chinese subjects.

PubMed

Zhang, Dan; Wang, Xiaolin; Liu, Man; Zhang, Lina; Deng, Ming; Liu, Huichen

2015-01-01

A rapid, sensitive and accurate ICP-MS method using alternate analyte-free matrix for calibration standards preparation and a rapid direct dilution procedure for sample preparation was developed and validated for the quantification of exogenous strontium (Sr) from the drug in human serum. Serum was prepared by direct dilution (1:29, v/v) in an acidic solution consisting of nitric acid (0.1%) and germanium (Ge) added as internal standard (IS), to obtain simple and high-throughput preparation procedure with minimized matrix effect, and good repeatability. ICP-MS analysis was performed using collision cell technology (CCT) mode. Alternate matrix method by using distilled water as an alternate analyte-free matrix for the preparation of calibration standards (CS) was used to avoid the influence of endogenous Sr in serum on the quantification. The method was validated in terms of selectivity, carry-over, matrix effects, lower limit of quantification (LLOQ), linearity, precision and accuracy, and stability. Instrumental linearity was verified in the range of 1.00-500ng/mL, corresponding to a concentration range of 0.0300-15.0μg/mL in 50μL sample of serum matrix and alternate matrix. Intra- and inter-day precision as relative standard deviation (RSD) were less than 8.0% and accuracy as relative error (RE) was within ±3.0%. The method allowed a high sample throughput, and was sensitive and accurate enough for a pilot bioequivalence study in healthy male Chinese subjects following single oral administration of two strontium ranelate formulations containing 2g strontium ranelate. Copyright © 2014 Elsevier GmbH. All rights reserved.

Prevention of bacterial foodborne disease using nanobiotechnology.

PubMed

Billington, Craig; Hudson, J Andrew; D'Sa, Elaine

2014-01-01

Foodborne disease is an important source of expense, morbidity, and mortality for society. Detection and control constitute significant components of the overall management of foodborne bacterial pathogens, and this review focuses on the use of nanosized biological entities and molecules to achieve these goals. There is an emphasis on the use of organisms called bacteriophages (phages: viruses that infect bacteria), which are increasingly being used in pathogen detection and biocontrol applications. Detection of pathogens in foods by conventional techniques is time-consuming and expensive, although it can also be sensitive and accurate. Nanobiotechnology is being used to decrease detection times and cost through the development of biosensors, exploiting specific cell-recognition properties of antibodies and phage proteins. Although sensitivity per test can be excellent (eg, the detection of one cell), the very small volumes tested mean that sensitivity per sample is less compelling. An ideal detection method needs to be inexpensive, sensitive, and accurate, but no approach yet achieves all three. For nanobiotechnology to displace existing methods (culture-based, antibody-based rapid methods, or those that detect amplified nucleic acid) it will need to focus on improving sensitivity. Although manufactured nonbiological nanoparticles have been used to kill bacterial cells, nanosized organisms called phages are increasingly finding favor in food safety applications. Phages are amenable to protein and nucleic acid labeling, and can be very specific, and the typical large "burst size" resulting from phage amplification can be harnessed to produce a rapid increase in signal to facilitate detection. There are now several commercially available phages for pathogen control, and many reports in the literature demonstrate efficacy against a number of foodborne pathogens on diverse foods. As a method for control of pathogens, nanobiotechnology is therefore flourishing.

[Determination of Total Iron and Fe2+ in Basalt].

PubMed

Liu, Jian-xun; Chen, Mei-rong; Jian, Zheng-guo; Wu, Gang; Wu, Zhi-shen

2015-08-01

Basalt is the raw material of basalt fiber. The content of FeO and Fe2O3 has a great impact on the properties of basalt fibers. ICP-OES and dichromate method were used to test total Fe and Fe(2+) in basalt. Suitable instrument parameters and analysis lines of Fe were chosen for ICP-OES. The relative standard deviation (RSD) of ICP-OES is 2.2%, and the recovery is in the range of 98%~101%. The method shows simple, rapid and highly accurate for determination of total Fe and Fe(2+) in basalt. The RSD of ICP-OES and dichromate method is 0.42% and 1.4%, respectively.

Simple and sensitive method for quantification of fluorescent enzymatic mature and senescent crosslinks of collagen in bone hydrolysate using single-column high performance liquid chromatography.

PubMed

Viguet-Carrin, S; Gineyts, E; Bertholon, C; Delmas, P D

2009-01-01

A rapid high performance liquid chromatographic method was developed including an internal standard for the measurement of mature and senescent crosslinks concentration in non-demineralized bone hydrolysates. To avoid the demineralization which is a tedious step, we developed a method based on the use of a solid-phase extraction procedure to clean-up the samples. It resulted in sensitive and accurate measurements: the detection limits as low as 0.2 pmol for the pyridimium crosslinks and 0.02 pmol for the pentosidine. The inter- and intra-assay coefficients of variation were as low as 5% and 2%, respectively, for all crosslinks.

Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

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

Bingol, Kerem; Brüschweiler, Rafael

Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexitymore » of these tasks.« less

A Consistency Evaluation and Calibration Method for Piezoelectric Transmitters.

PubMed

Zhang, Kai; Tan, Baohai; Liu, Xianping

2017-04-28

Array transducer and transducer combination technologies are evolving rapidly. While adapting transmitter combination technologies, the parameter consistencies between each transmitter are extremely important because they can determine a combined effort directly. This study presents a consistency evaluation and calibration method for piezoelectric transmitters by using impedance analyzers. Firstly, electronic parameters of transmitters that can be measured by impedance analyzers are introduced. A variety of transmitter acoustic energies that are caused by these parameter differences are then analyzed and certified and, thereafter, transmitter consistency is evaluated. Lastly, based on the evaluations, consistency can be calibrated by changing the corresponding excitation voltage. Acoustic experiments show that this method accurately evaluates and calibrates transducer consistencies, and is easy to realize.

Elasticity measurement of nasal cartilage as a function of temperature using optical coherence elastography

NASA Astrophysics Data System (ADS)

Liu, Chih Hao; Skryabina, M. N.; Singh, Manmohan; Li, Jiasong; Wu, Chen; Sobol, E.; Larin, Kirill V.

2015-03-01

Current clinical methods of reconstruction surgery involve laser reshaping of nasal cartilage. The process of stress relaxation caused by laser heating is the primary method to achieve nasal cartilage reshaping. Based on this, a rapid, non-destructive and accurate elasticity measurement would allow for a more robust reshaping procedure. In this work, we have utilized a phase-stabilized swept source optical coherence elastography (PhSSSOCE) to quantify the Young's modulus of porcine nasal septal cartilage during the relaxation process induced by heating. The results show that PhS-SSOCE was able to monitor changes in elasticity of hyaline cartilage, and this method could potentially be applied in vivo during laser reshaping therapies.

Automated Development of Accurate Algorithms and Efficient Codes for Computational Aeroacoustics

NASA Technical Reports Server (NTRS)

Goodrich, John W.; Dyson, Rodger W.

1999-01-01

The simulation of sound generation and propagation in three space dimensions with realistic aircraft components is a very large time dependent computation with fine details. Simulations in open domains with embedded objects require accurate and robust algorithms for propagation, for artificial inflow and outflow boundaries, and for the definition of geometrically complex objects. The development, implementation, and validation of methods for solving these demanding problems is being done to support the NASA pillar goals for reducing aircraft noise levels. Our goal is to provide algorithms which are sufficiently accurate and efficient to produce usable results rapidly enough to allow design engineers to study the effects on sound levels of design changes in propulsion systems, and in the integration of propulsion systems with airframes. There is a lack of design tools for these purposes at this time. Our technical approach to this problem combines the development of new, algorithms with the use of Mathematica and Unix utilities to automate the algorithm development, code implementation, and validation. We use explicit methods to ensure effective implementation by domain decomposition for SPMD parallel computing. There are several orders of magnitude difference in the computational efficiencies of the algorithms which we have considered. We currently have new artificial inflow and outflow boundary conditions that are stable, accurate, and unobtrusive, with implementations that match the accuracy and efficiency of the propagation methods. The artificial numerical boundary treatments have been proven to have solutions which converge to the full open domain problems, so that the error from the boundary treatments can be driven as low as is required. The purpose of this paper is to briefly present a method for developing highly accurate algorithms for computational aeroacoustics, the use of computer automation in this process, and a brief survey of the algorithms that have resulted from this work. A review of computational aeroacoustics has recently been given by Lele.

A Radioactivity Based Quantitative Analysis of the Amount of Thorium Present in Ores and Metallurgical Products; ANALYSE QUANTITATIVE DU THORIUM DANS LES MINERAIS ET LES PRODUITS THORIFERES PAR UNE METHODE BASEE SUR LA RADIOACTIVITE

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

Collee, R.; Govaerts, J.; Winand, L.

1959-10-31

A brief resume of the classical methods of quantitative determination of thorium in ores and thoriferous products is given to show that a rapid, accurate, and precise physical method based on the radioactivity of thorium would be of great utility. A method based on the utilization of the characteristic spectrum of the thorium gamma radiation is presented. The preparation of the samples and the instruments needed for the measurements is discussed. The experimental results show that the reproducibility is very satisfactory and that it is possible to detect Th contents of 1% or smaller. (J.S.R.)

Comparison of different methods for radiochemical purity testing of [99mTc-EDDA-HYNIC-D-Phe1,Tyr3]-octreotide.

PubMed

von Guggenberg, Elisabeth; Penz, Barbara; Kemmler, Georg; Virgolini, Irene; Decristoforo, Clemens

2006-02-01

[99mTc-EDDA-HYNIC-D-Phe1,Tyr3]-octreotide (99mTc-EDDA-HYNIC-TOC) is an alternative radioligand for somatostatin receptor (SSTR) scintigraphy of neuroendocrine tumours. In order to allow a rapid and accurate determination of the quality in the clinical routine the aim of this study was to evaluate different methods of radiochemical purity (RCP) testing. Three different methods of RCP testing were compared: high-performance liquid chromatography (HPLC), thin layer chromatography (TLC) and minicolumn (Sep-Pak purification = SPE). HPLC was shown to be the most effective method for the quality control. The use of TLC and SPE is only recommended after sufficient practical labelling experience.

Direct differentiation of the quasi-incompressible fluid formulation of fluid-structure interaction using the PFEM

NASA Astrophysics Data System (ADS)

Zhu, Minjie; Scott, Michael H.

2017-07-01

Accurate and efficient response sensitivities for fluid-structure interaction (FSI) simulations are important for assessing the uncertain response of coastal and off-shore structures to hydrodynamic loading. To compute gradients efficiently via the direct differentiation method (DDM) for the fully incompressible fluid formulation, approximations of the sensitivity equations are necessary, leading to inaccuracies of the computed gradients when the geometry of the fluid mesh changes rapidly between successive time steps or the fluid viscosity is nonzero. To maintain accuracy of the sensitivity computations, a quasi-incompressible fluid is assumed for the response analysis of FSI using the particle finite element method and DDM is applied to this formulation, resulting in linearized equations for the response sensitivity that are consistent with those used to compute the response. Both the response and the response sensitivity can be solved using the same unified fractional step method. FSI simulations show that although the response using the quasi-incompressible and incompressible fluid formulations is similar, only the quasi-incompressible approach gives accurate response sensitivity for viscous, turbulent flows regardless of time step size.

Semiautomated Segmentation of Polycystic Kidneys in T2-Weighted MR Images.

PubMed

Kline, Timothy L; Edwards, Marie E; Korfiatis, Panagiotis; Akkus, Zeynettin; Torres, Vicente E; Erickson, Bradley J

2016-09-01

The objective of the present study is to develop and validate a fast, accurate, and reproducible method that will increase and improve institutional measurement of total kidney volume and thereby avoid the higher costs, increased operator processing time, and inherent subjectivity associated with manual contour tracing. We developed a semiautomated segmentation approach, known as the minimal interaction rapid organ segmentation (MIROS) method, which results in human interaction during measurement of total kidney volume on MR images being reduced to a few minutes. This software tool automatically steps through slices and requires rough definition of kidney boundaries supplied by the user. The approach was verified on T2-weighted MR images of 40 patients with autosomal dominant polycystic kidney disease of varying degrees of severity. The MIROS approach required less than 5 minutes of user interaction in all cases. When compared with the ground-truth reference standard, MIROS showed no significant bias and had low variability (mean ± 2 SD, 0.19% ± 6.96%). The MIROS method will greatly facilitate future research studies in which accurate and reproducible measurements of cystic organ volumes are needed.

Analyzing forensic evidence based on density with magnetic levitation.

PubMed

Lockett, Matthew R; Mirica, Katherine A; Mace, Charles R; Blackledge, Robert D; Whitesides, George M

2013-01-01

This paper describes a method for determining the density of contact trace objects with magnetic levitation (MagLev). MagLev measurements accurately determine the density (± 0.0002 g/cm(3) ) of a diamagnetic object and are compatible with objects that are nonuniform in shape and size. The MagLev device (composed of two permanent magnets with like poles facing) and the method described provide a means of accurately determining the density of trace objects. This method is inexpensive, rapid, and verifiable and provides numerical values--independent of the specific apparatus or analyst--that correspond to the absolute density of the sample that may be entered into a searchable database. We discuss the feasibility of MagLev as a possible means of characterizing forensic-related evidence and demonstrate the ability of MagLev to (i) determine the density of samples of glitter and gunpowder, (ii) separate glitter particles of different densities, and (iii) determine the density of a glitter sample that was removed from a complex sample matrix. © 2012 American Academy of Forensic Sciences.

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

PubMed Central

Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.; Chain, Patrick S. G.

2015-01-01

A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools. PMID:25765641

The single water-surface sweep estimation method accurately estimates very low (n = 4) to low-moderate (n = 25-100) and high (n > 100) Aedes aegypti (Diptera: Culicidae) pupae numbers in large water containers up to 13 times faster than the exhaustive sweep and total count method and without any sediment contamination.

PubMed

Romero-Vivas, C M; Llinás, H; Falconar, A K

2015-03-01

To confirm that a single water-surface sweep-net collection coupled with three calibration factors (2.6, 3.0 and 3.5 for 1/3, 2/3 and 3/3 water levels, respectively) (WSCF) could accurately estimate very low to high Aedes aegypti pupae numbers in water containers more rapidly than the exhaustive 5-sweep and total count (ESTC) method recommended by WHO. Both methods were compared in semi-field trials using low (n = 25) to moderate (n = 50-100) pupae numbers in a 250-l drum at 1/3, 2/3 and 3/3 water levels, and by their mean-time determinations using 200 pupae in three 220- to 1024-l water containers at these water levels. Accuracy was further assessed using 69.1% (393/569) of the field-based drums and tanks which contained <100 pupae. The WSCF method accurately estimated total populations in the semi-field trials up to 13.0 times faster than the ESTC method (all P < 0.001); no significant differences (all P-values ≥ 0.05) were obtained between the methods for very low (n = 4) to low-moderate (n = 25-100) and high (n > 100) pupae numbers/container and without sediment disturbance. The simple WSCF method sensitively, accurately and robustly estimated total pupae numbers in their principal breeding sites worldwide, containers with >20 l water volumes, significantly (2.7- to 13.0-fold: all P-values <0.001) faster than the ESTC method for very low to high pupae numbers/container without contaminating the clean water by sediment disturbance which is generated using the WHO-recommended ESTC method. The WSCF method seems ideal for global community-based surveillance and control programmes. © 2014 John Wiley & Sons Ltd.

Rapid Transient Pressure Field Computations in the Nearfield of Circular Transducers using Frequency Domain Time-Space Decomposition

PubMed Central

Alles, E. J.; Zhu, Y.; van Dongen, K. W. A.; McGough, R. J.

2013-01-01

The fast nearfield method, when combined with time-space decomposition, is a rapid and accurate approach for calculating transient nearfield pressures generated by ultrasound transducers. However, the standard time-space decomposition approach is only applicable to certain analytical representations of the temporal transducer surface velocity that, when applied to the fast nearfield method, are expressed as a finite sum of products of separate temporal and spatial terms. To extend time-space decomposition such that accelerated transient field simulations are enabled in the nearfield for an arbitrary transducer surface velocity, a new transient simulation method, frequency domain time-space decomposition (FDTSD), is derived. With this method, the temporal transducer surface velocity is transformed into the frequency domain, and then each complex-valued term is processed separately. Further improvements are achieved by spectral clipping, which reduces the number of terms and the computation time. Trade-offs between speed and accuracy are established for FDTSD calculations, and pressure fields obtained with the FDTSD method for a circular transducer are compared to those obtained with Field II and the impulse response method. The FDTSD approach, when combined with the fast nearfield method and spectral clipping, consistently achieves smaller errors in less time and requires less memory than Field II or the impulse response method. PMID:23160476

Rapid Detection and Identification of Human Hookworm Infections through High Resolution Melting (HRM) Analysis

PubMed Central

Ngui, Romano; Lim, Yvonne A. L.; Chua, Kek Heng

2012-01-01

Background Hookworm infections are still endemic in low and middle income tropical countries with greater impact on the socioeconomic and public health of the bottom billion of the world's poorest people. In this study, a real-time polymerase chain reaction (PCR) coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on the five human hookworm species. Methods Real-time PCR coupled with HRM analysis targeting the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA as the genetic marker was used to identify and distinguish hookworm species in human samples. Unique and distinct characteristics of HRM patterns were produced for each of the five hookworm species. The melting curves were characterized by peaks of 79.24±0.05°C and 83.00±0.04°C for Necator americanus, 79.12±0.10°C for Ancylostoma duodenale, 79.40±0.10°C for Ancylostoma ceylanicum, 79.63±0.05°C for Ancylostoma caninum and 79.70±0.14°C for Ancylostoma braziliense. An evaluation of the method's sensitivity and specificity revealed that this assay was able to detect as low as 0.01 ng/µl hookworm DNA and amplification was only recorded for hookworm positive samples. Conclusion The HRM assay developed in this study is a rapid and straightforward method for the diagnosis, identification and discrimination of five human hookworms. This assay is simple compared to other probe-based genotyping methods as it does not require multiplexing, DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of human hookworm species. PMID:22844538

Rapid screening and quantification of residual pesticides and illegal adulterants in red wine by direct analysis in real time mass spectrometry.

PubMed

Guo, Tianyang; Fang, Pingping; Jiang, Juanjuan; Zhang, Feng; Yong, Wei; Liu, Jiahui; Dong, Yiyang

2016-11-04

A rapid method to screen and quantify multi-class analytic targets in red wine has been developed by direct analysis in real time (DART) coupled with triple quadruple tandem mass spectrometry (QqQ-MS). A modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) procedure was used for increasing analytical speed and reducing matrix effect, and the multiple reaction monitoring (MRM) in DART-MS/MS ensured accurate analysis. One bottle of wine containing 50 pesticides and 12 adulterants, i.e., preservatives, antioxidant, sweeteners, and azo dyes, could be totally determined less than 12min. This method exhibited proper linearity (R 2 ≥0.99) in the range of 1-1000ng/mL for pesticides and 10-5000ng/mL for adulterants. The limits of detection (LODs) were obtained in a 0.5-50ng/mL range for pesticides and 5-50ng/mL range for adulterants, and the limits of quantification (LOQs) were in a 1-100ng/mL range for pesticides and 10-250ng/mL range for adulterants. Three spiked levels for each analyte in wine were evaluated, and the recoveries were in a scope of 75-120%. The results demonstrated DART-MS/MS was a rapid and simple method, and could be applied to rapid analyze residual pesticides and illegal adulterants in a large quantities of red wine. Copyright © 2016 Elsevier B.V. All rights reserved.

A rapid Salmonella detection method involving thermophilic helicase-dependent amplification and a lateral flow assay.

PubMed

Du, Xin-Jun; Zhou, Tian-Jiao; Li, Ping; Wang, Shuo

2017-08-01

Salmonella is a major foodborne pathogen that is widespread in the environment and can cause serious human and animal disease. Since conventional culture methods to detect Salmonella are time-consuming and laborious, rapid and accurate techniques to detect this pathogen are critically important for food safety and diagnosing foodborne illness. In this study, we developed a rapid, simple and portable Salmonella detection strategy that combines thermophilic helicase-dependent amplification (tHDA) with a lateral flow assay to provide a detection result based on visual signals within 90 min. Performance analyses indicated that the method had detection limits for DNA and pure cultured bacteria of 73.4-80.7 fg and 35-40 CFU, respectively. Specificity analyses showed no cross reactions with Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Enterobacter aerogenes, Shigella and Campylobacter jejuni. The results for detection in real food samples showed that 1.3-1.9 CFU/g or 1.3-1.9 CFU/mL of Salmonella in contaminated chicken products and infant nutritional cereal could be detected after 2 h of enrichment. The same amount of Salmonella in contaminated milk could be detected after 4 h of enrichment. This tHDA-strip can be used for the rapid detection of Salmonella in food samples and is particularly suitable for use in areas with limited equipment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Towards improved characterization of northern wetlands (or other landscapes) by remote sensing - a rapid approach to collect ground truth data

NASA Astrophysics Data System (ADS)

Gålfalk, Magnus; Karlson, Martin; Crill, Patrick; Bastviken, David

2017-04-01

The calibration and validation of remote sensing land cover products is highly dependent on accurate ground truth data, which are costly and practically challenging to collect. This study evaluates a novel and efficient alternative to field surveys and UAV imaging commonly applied for this task. The method consists of i) a light weight, water proof, remote controlled RGB-camera mounted on an extendable monopod used for acquiring wide-field images of the ground from a height of 4.5 meters, and ii) a script for semi-automatic image classification. In the post-processing, the wide-field images are corrected for optical distortion and geometrically rectified so that the spatial resolution is the same over the surface area used for classification. The script distinguishes land surface components by color, brightness and spatial variability. The method was evaluated in wetland areas located around Abisko, northern Sweden. Proportional estimates of the six main surface components in the wetlands (wet and dry Sphagnum, shrub, grass, water, rock) were derived for 200 images, equivalent to 10 × 10 m field plots. These photo plots were then used as calibration data for a regional scale satellite based classification which separates the six wetland surface components using a Sentinel-1 time series. The method presented in this study is accurate, rapid, robust and cost efficient in comparison to field surveys (time consuming) and drone mapping (which require low wind speeds and no rain, suffer from battery limited flight times, have potential GPS/compass errors far north, and in some areas are prohibited by law).

Toward Automating HIV Identification: Machine Learning for Rapid Identification of HIV-Related Social Media Data.

PubMed

Young, Sean D; Yu, Wenchao; Wang, Wei

2017-02-01

"Social big data" from technologies such as social media, wearable devices, and online searches continue to grow and can be used as tools for HIV research. Although researchers can uncover patterns and insights associated with HIV trends and transmission, the review process is time consuming and resource intensive. Machine learning methods derived from computer science might be used to assist HIV domain experts by learning how to rapidly and accurately identify patterns associated with HIV from a large set of social data. Using an existing social media data set that was associated with HIV and coded by an HIV domain expert, we tested whether 4 commonly used machine learning methods could learn the patterns associated with HIV risk behavior. We used the 10-fold cross-validation method to examine the speed and accuracy of these models in applying that knowledge to detect HIV content in social media data. Logistic regression and random forest resulted in the highest accuracy in detecting HIV-related social data (85.3%), whereas the Ridge Regression Classifier resulted in the lowest accuracy. Logistic regression yielded the fastest processing time (16.98 seconds). Machine learning can enable social big data to become a new and important tool in HIV research, helping to create a new field of "digital HIV epidemiology." If a domain expert can identify patterns in social data associated with HIV risk or HIV transmission, machine learning models could quickly and accurately learn those associations and identify potential HIV patterns in large social data sets.

Rapid measurement of perchlorate in polar ice cores down to sub-ng L(-1) levels without pre-concentration.

PubMed

Peterson, Kari; Cole-Dai, Jihong; Brandis, Derek; Cox, Thomas; Splett, Scott

2015-10-01

An ion chromatography-electrospray ionization-tandem mass spectrometry (IC-ESI-MS/MS) method has been developed for rapid and accurate measurement of perchlorate in polar snow and ice core samples in which perchlorate concentrations are expected to be as low as 0.1 ng L(-1). Separation of perchlorate from major inorganic species in snow is achieved with an ion chromatography system interfaced to an AB SCIEX triple quadrupole mass spectrometer operating in multiple reaction monitoring mode. Under optimized conditions, the limit of detection and lower limit of quantification without pre-concentration have been determined to be 0.1 and 0.3 ng L(-1), respectively, with a linear dynamic range of 0.3-10.0 ng L(-1) in routine measurement. These represent improvements over previously reported methods using similar analytical techniques. The improved method allows fast, accurate, and reproducible perchlorate quantification down to the sub-ng L(-1) level and will facilitate perchlorate measurement in the study of natural perchlorate production with polar ice cores in which perchlorate concentrations are anticipated to vary in the low and sub-ng L(-1) range. Initial measurements of perchlorate in ice core samples from central Greenland show that typical perchlorate concentrations in snow dated prior to the Industrial Revolution are about 0.8 ng L(-1), while perchlorate concentrations are significantly higher in recent (post-1980) snow, suggesting that anthropogenic sources are a significant contributor to perchlorate in the current environment.

Rapid measurement of plasma free fatty acid concentration and isotopic enrichment using LC/MS

PubMed Central

Persson, Xuan-Mai T.; Błachnio-Zabielska, Agnieszka Urszula; Jensen, Michael D.

2010-01-01

Measurements of plasma free fatty acids (FFA) concentration and isotopic enrichment are commonly used to evaluate FFA metabolism. Until now, gas chromatography-combustion-isotope ratio mass spectrometry (GC/C/IRMS) was the best method to measure isotopic enrichment in the methyl derivatives of 13C-labeled fatty acids. Although IRMS is excellent for analyzing enrichment, it requires time-consuming derivatization steps and is not optimal for measuring FFA concentrations. We developed a new, rapid, and reliable method for simultaneous quantification of 13C-labeled fatty acids in plasma using high-performance liquid chromatography-mass spectrometry (HPLC/MS). This method involves a very quick Dole extraction procedure and direct injection of the samples on the HPLC system. After chromatographic separation, the samples are directed to the mass spectrometer for electrospray ionization (ESI) and analysis in the negative mode using single ion monitoring. By employing equipment with two columns connected parallel to a mass spectrometer, we can double the throughput to the mass spectrometer, reducing the analysis time per sample to 5 min. Palmitate flux measured using this approach agreed well with the GC/C/IRMS method. This HPLC/MS method provides accurate and precise measures of FFA concentration and enrichment. PMID:20526002

Scene Segmentation For Autonomous Robotic Navigation Using Sequential Laser Projected Structured Light

NASA Astrophysics Data System (ADS)

Brown, C. David; Ih, Charles S.; Arce, Gonzalo R.; Fertell, David A.

1987-01-01

Vision systems for mobile robots or autonomous vehicles navigating in an unknown terrain environment must provide a rapid and accurate method of segmenting the scene ahead into regions of pathway and background. A major distinguishing feature between the pathway and background is the three dimensional texture of these two regions. Typical methods of textural image segmentation are very computationally intensive, often lack the required robustness, and are incapable of sensing the three dimensional texture of various regions of the scene. A method is presented where scanned laser projected lines of structured light, viewed by a stereoscopically located single video camera, resulted in an image in which the three dimensional characteristics of the scene were represented by the discontinuity of the projected lines. This image was conducive to processing with simple regional operators to classify regions as pathway or background. Design of some operators and application methods, and demonstration on sample images are presented. This method provides rapid and robust scene segmentation capability that has been implemented on a microcomputer in near real time, and should result in higher speed and more reliable robotic or autonomous navigation in unstructured environments.

Analysis of lignans in Magnoliae Flos by turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry.

PubMed

Zhou, Xuan; Chen, Cen; Ye, Xiaolan; Song, Fenyun; Fan, Guorong; Wu, Fuhai

2016-04-01

In this study, a method coupling turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry was developed for analyzing the lignans in Magnoliae Flos. By the online pretreatment of turbulent flow chromatography solid-phase extraction, the impurities removal and analytes concentration were automatically processed, and the lignans were separated rapidly and well. Seven lignans of Magnoliae Flos including epieudesmin, magnolin, 1-irioresinol-B-dimethyl ether, epi-magnolin, fargesin aschantin, and demethoxyaschantin were identified by comparing their retention behavior, UV spectra, and mass spectra with those of reference substances or literature data. The developed method was validated, and the good results showed that the method was not only automatic and rapid, but also accurate and reliable. The turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry method holds a high potential to become an effective method for the quality control of lignans in Magnoliae Flos and a useful tool for the analysis of other complex mixtures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A method for rapid 3D scanning and replication of large paleontological specimens

PubMed Central

Das, Anshuman J.; Murmann, Denise C.; Cohrn, Kenneth; Raskar, Ramesh

2017-01-01

We demonstrate a fast and cost-effective technique to perform three dimensional (3D) scanning and replication of large paleontological specimens, in this case the entire skull of a Tyrannosaurus rex (T.rex) with a volume in the range of 2 m3. The technique involves time-of-flight (TOF) depth sensing using the Kinect scanning module commonly used in gesture recognition in gaming. Raw data from the Kinect sensor was captured using open source software and the reconstruction was done rapidly making this a viable method that can be adopted by museums and researchers in paleontology. The current method has the advantage of being low-cost as compared to industrial scanners and photogrammetric methods but also of accurately scanning a substantial volume range which is well suited for large specimens. The depth resolution from the Kinect sensor was measured to be around 0.6 mm which is ideal for scanning large specimens with reasonable structural detail. We demonstrate the efficacy of this method on the skull of FMNH PR 2081, also known as SUE, a near complete T.rex at the Field Museum of Natural History. PMID:28678817

A method for rapid 3D scanning and replication of large paleontological specimens.

PubMed

Das, Anshuman J; Murmann, Denise C; Cohrn, Kenneth; Raskar, Ramesh

2017-01-01

We demonstrate a fast and cost-effective technique to perform three dimensional (3D) scanning and replication of large paleontological specimens, in this case the entire skull of a Tyrannosaurus rex (T.rex) with a volume in the range of 2 m3. The technique involves time-of-flight (TOF) depth sensing using the Kinect scanning module commonly used in gesture recognition in gaming. Raw data from the Kinect sensor was captured using open source software and the reconstruction was done rapidly making this a viable method that can be adopted by museums and researchers in paleontology. The current method has the advantage of being low-cost as compared to industrial scanners and photogrammetric methods but also of accurately scanning a substantial volume range which is well suited for large specimens. The depth resolution from the Kinect sensor was measured to be around 0.6 mm which is ideal for scanning large specimens with reasonable structural detail. We demonstrate the efficacy of this method on the skull of FMNH PR 2081, also known as SUE, a near complete T.rex at the Field Museum of Natural History.

Hartree-Fock implementation using a Laguerre-based wave function for the ground state and correlation energies of two-electron atoms.

PubMed

King, Andrew W; Baskerville, Adam L; Cox, Hazel

2018-03-13

An implementation of the Hartree-Fock (HF) method using a Laguerre-based wave function is described and used to accurately study the ground state of two-electron atoms in the fixed nucleus approximation, and by comparison with fully correlated (FC) energies, used to determine accurate electron correlation energies. A variational parameter A is included in the wave function and is shown to rapidly increase the convergence of the energy. The one-electron integrals are solved by series solution and an analytical form is found for the two-electron integrals. This methodology is used to produce accurate wave functions, energies and expectation values for the helium isoelectronic sequence, including at low nuclear charge just prior to electron detachment. Additionally, the critical nuclear charge for binding two electrons within the HF approach is calculated and determined to be Z HF C =1.031 177 528.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Author(s).

Fast and accurate automated cell boundary determination for fluorescence microscopy

NASA Astrophysics Data System (ADS)

Arce, Stephen Hugo; Wu, Pei-Hsun; Tseng, Yiider

2013-07-01

Detailed measurement of cell phenotype information from digital fluorescence images has the potential to greatly advance biomedicine in various disciplines such as patient diagnostics or drug screening. Yet, the complexity of cell conformations presents a major barrier preventing effective determination of cell boundaries, and introduces measurement error that propagates throughout subsequent assessment of cellular parameters and statistical analysis. State-of-the-art image segmentation techniques that require user-interaction, prolonged computation time and specialized training cannot adequately provide the support for high content platforms, which often sacrifice resolution to foster the speedy collection of massive amounts of cellular data. This work introduces a strategy that allows us to rapidly obtain accurate cell boundaries from digital fluorescent images in an automated format. Hence, this new method has broad applicability to promote biotechnology.

Emergency department patient perceptions and preferences on opt-in rapid HIV screening program components

PubMed Central

Merchant, Roland C.; Clark, Melissa A.; Seage, George R.; Mayer, Kenneth H.; DeGruttola, Victor G.; Becker, Bruce M.

2011-01-01

The aim of this investigation was to assess emergency department (ED) patients’ perceptions and preferences about an opt-in, universal, rapid HIV screening program and identify patient groups who expressed stronger beliefs about components of the testing program. From July 2005 to July 2006, ED patients in the opt-in, universal, rapid HIV screening program were interviewed in person. Multivariable regression models were used to compare participants on their beliefs about the program components. Of the 561 participants, 62.0% had previously been tested for HIV. The majority of participants (58.8%) believed the rapid and standard/conventional HIV tests to be equally accurate, 27.7% believed the rapid test to be less or much less accurate, and 8.7% believed the rapid test to be more or much more accurate. Almost two-thirds (65.1%) favored having a rapid instead of a standard/conventional HIV test, 94.6% wanted the test results within one hour, and 61.3% would be likely or very likely to undergo testing in the ED if it prolonged their ED visit. Almost all (92.5%) believed that their medical care was “not at all” delayed because of being tested, 94.1% believed that testing did “not at all” divert attention from the reason for their ED visit, and 80.9% thought that testing in the ED was “not at all” stressful. In multivariable logistic regression models, males and those with more than 12 years of formal education showed greater concerns about the rapid HIV test’s accuracy. Hispanic/Latinos, participants with governmental insurance, and those previously HIV tested were more apt to be screened for HIV even if testing delayed their ED departure. Overall, participants were highly accepting of the components of this opt-in rapid HIV screening program. However, concerns regarding the accuracy of the rapid HIV test might limit test acceptance and should be addressed during pre-test information procedures. PMID:19283644

Metabolite identification of triptolide by data-dependent accurate mass spectrometric analysis in combination with online hydrogen/deuterium exchange and multiple data-mining techniques.

PubMed

Du, Fuying; Liu, Ting; Liu, Tian; Wang, Yongwei; Wan, Yakun; Xing, Jie

2011-10-30

Triptolide (TP), the primary active component of the herbal medicine Tripterygium wilfordii Hook F, has shown promising antileukemic and anti-inflammatory activity. The pharmacokinetic profile of TP indicates an extensive metabolic elimination in vivo; however, its metabolic data is rarely available partly because of the difficulty in identifying it due to the absence of appropriate ultraviolet chromophores in the structure and the presence of endogenous interferences in biological samples. In the present study, the biotransformation of TP was investigated by improved data-dependent accurate mass spectrometric analysis, using an LTQ/Orbitrap hybrid mass spectrometer in conjunction with the online hydrogen (H)/deuterium (D) exchange technique for rapid structural characterization. Accurate full-scan MS and MS/MS data were processed with multiple post-acquisition data-mining techniques, which were complementary and effective in detecting both common and uncommon metabolites from biological matrices. As a result, 38 phase I, 9 phase II and 8 N-acetylcysteine (NAC) metabolites of TP were found in rat urine. Accurate MS/MS data were used to support assignments of metabolite structures, and online H/D exchange experiments provided additional evidence for exchangeable hydrogen atoms in the structure. The results showed the main phase I metabolic pathways of TP are hydroxylation, hydrolysis and desaturation, and the resulting metabolites subsequently undergo phase II processes. The presence of NAC conjugates indicated the capability of TP to form reactive intermediate species. This study also demonstrated the effectiveness of LC/HR-MS(n) in combination with multiple post-acquisition data-mining methods and the online H/D exchange technique for the rapid identification of drug metabolites. Copyright © 2011 John Wiley & Sons, Ltd.

Development of improved enzyme-based and lateral flow immunoassays for rapid and accurate serodiagnosis of canine brucellosis.

PubMed

Cortina, María E; Novak, Analía; Melli, Luciano J; Elena, Sebastián; Corbera, Natalia; Romero, Juan E; Nicola, Ana M; Ugalde, Juan E; Comerci, Diego J; Ciocchini, Andrés E

2017-09-01

Brucellosis is a widespread zoonotic disease caused by Brucella spp. Brucella canis is the etiological agent of canine brucellosis, a disease that can lead to sterility in bitches and dogs causing important economic losses in breeding kennels. Early and accurate diagnosis of canine brucellosis is central to control the disease and lower the risk of transmission to humans. Here, we develop and validate enzyme and lateral flow immunoassays for improved serodiagnosis of canine brucellosis using as antigen the B. canis rough lipopolysaccharide (rLPS). The method used to obtain the rLPS allowed us to produce more homogeneous batches of the antigen that facilitated the standardization of the assays. To validate the assays, 284 serum samples obtained from naturally infected dogs and healthy animals were analyzed. For the B. canis-iELISA and B. canis-LFIA the diagnostic sensitivity was of 98.6%, and the specificity 99.5% and 100%, respectively. We propose the implementation of the B. canis-LFIA as a screening test in combination with the highly accurate laboratory g-iELISA. The B. canis-LFIA is a rapid, accurate and easy to use test, characteristics that make it ideal for the serological surveillance of canine brucellosis in the field or veterinary laboratories. Finally, a blind study including 1040 serum samples obtained from urban dogs showed a prevalence higher than 5% highlighting the need of new diagnostic tools for a more effective control of the disease in dogs and therefore to reduce the risk of transmission of this zoonotic pathogen to humans. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular quenching and relaxation in a plasmonic tunable system

NASA Astrophysics Data System (ADS)

Baffou, Guillaume; Girard, Christian; Dujardin, Erik; Colas Des Francs, Gérard; Martin, Olivier J. F.

2008-03-01

Molecular fluorescence decay is significantly modified when the emitting molecule is located near a plasmonic structure. When the lateral sizes of such structures are reduced to nanometer-scale cross sections, they can be used to accurately control and amplify the emission rate. In this Rapid Communication, we extend Green’s dyadic method to quantitatively investigate both radiative and nonradiative decay channels experienced by a single fluorescent molecule confined in an adjustable dielectric-metal nanogap. The technique produces data in excellent agreement with current experimental work.

Compressing random microstructures via stochastic Wang tilings.

PubMed

Novák, Jan; Kučerová, Anna; Zeman, Jan

2012-10-01

This Rapid Communication presents a stochastic Wang tiling-based technique to compress or reconstruct disordered microstructures on the basis of given spatial statistics. Unlike the existing approaches based on a single unit cell, it utilizes a finite set of tiles assembled by a stochastic tiling algorithm, thereby allowing to accurately reproduce long-range orientation orders in a computationally efficient manner. Although the basic features of the method are demonstrated for a two-dimensional particulate suspension, the present framework is fully extensible to generic multidimensional media.

Debris Examination Using Ballistic and Radar Integrated Software

NASA Technical Reports Server (NTRS)

Griffith, Anthony; Schottel, Matthew; Lee, David; Scully, Robert; Hamilton, Joseph; Kent, Brian; Thomas, Christopher; Benson, Jonathan; Branch, Eric; Hardman, Paul;

A semi-automated method for rapid detection of ripple events on interictal voltage discharges in the scalp electroencephalogram.

PubMed

Chu, Catherine J; Chan, Arthur; Song, Dan; Staley, Kevin J; Stufflebeam, Steven M; Kramer, Mark A

2017-02-01

High frequency oscillations are emerging as a clinically important indicator of epileptic networks. However, manual detection of these high frequency oscillations is difficult, time consuming, and subjective, especially in the scalp EEG, thus hindering further clinical exploration and application. Semi-automated detection methods augment manual detection by reducing inspection to a subset of time intervals. We propose a new method to detect high frequency oscillations that co-occur with interictal epileptiform discharges. The new method proceeds in two steps. The first step identifies candidate time intervals during which high frequency activity is increased. The second step computes a set of seven features for each candidate interval. These features require that the candidate event contain a high frequency oscillation approximately sinusoidal in shape, with at least three cycles, that co-occurs with a large amplitude discharge. Candidate events that satisfy these features are stored for validation through visual analysis. We evaluate the detector performance in simulation and on ten examples of scalp EEG data, and show that the proposed method successfully detects spike-ripple events, with high positive predictive value, low false positive rate, and high intra-rater reliability. The proposed method is less sensitive than the existing method of visual inspection, but much faster and much more reliable. Accurate and rapid detection of high frequency activity increases the clinical viability of this rhythmic biomarker of epilepsy. The proposed spike-ripple detector rapidly identifies candidate spike-ripple events, thus making clinical analysis of prolonged, multielectrode scalp EEG recordings tractable. Copyright © 2016 Elsevier B.V. All rights reserved.

A Rapid Leaf-Disc Sampler for Psychrometric Water Potential Measurements 1

PubMed Central

Wullschleger, Stan D.; Oosterhuis, Derrick M.

1986-01-01

An instrument was designed which facilitates faster and more accurate sampling of leaf discs for psychrometric water potential measurements. The instrument consists of an aluminum housing, a spring-loaded plunger, and a modified brass-plated cork borer. The leaf-disc sampler was compared with the conventional method of sampling discs for measurement of leaf water potential with thermocouple psychrometers on a range of plant material including Gossypium hirsutum L., Zea mays L., and Begonia rex-cultorum L. The new sampler permitted a leaf disc to be excised and inserted into the psychrometer sample chamber in less than 7 seconds, which was more than twice as fast as the conventional method. This resulted in more accurate determinations of leaf water potential due to reduced evaporative water losses. The leaf-disc sampler also significantly reduced sample variability between individual measurements. This instrument can be used for many other laboratory and field measurements that necessitate leaf disc sampling. PMID:16664879

Performance improvement of the one-dot lateral flow immunoassay for aflatoxin B1 by using a smartphone-based reading system.

PubMed

Lee, Sangdae; Kim, Giyoung; Moon, Jihea

2013-04-18

This study was conducted to develop a simple, rapid, and accurate lateral flow immunoassay (LFIA) detection method for point-of-care diagnosis. The one-dot LFIA for aflatoxin B1 (AFB1) was based on the modified competitive binding format using competition between AFB1 and colloidal gold-AFB1-BSA conjugate for antibody binding sites in the test zone. A Smartphone-based reading system consisting of a Samsung Galaxy S2 Smartphone, a LFIA reader, and a Smartphone application for the image acquisition and data analysis. The detection limit of one-dot LFIA for AFB1 is 5 μg/kg. This method provided semi-quantitative analysis of AFB1 samples in the range of 5 to 1,000 μg/kg. Using combination of the one-dot LFIA and the Smartphone-based reading system, it is possible to conduct a more fast and accurate point-of-care diagnosis.

Performance Improvement of the One-Dot Lateral Flow Immunoassay for Aflatoxin B1 by Using a Smartphone-Based Reading System

PubMed Central

Lee, Sangdae; Kim, Giyoung; Moon, Jihea

2013-01-01

This study was conducted to develop a simple, rapid, and accurate lateral flow immunoassay (LFIA) detection method for point-of-care diagnosis. The one-dot LFIA for aflatoxin B1 (AFB1) was based on the modified competitive binding format using competition between AFB1 and colloidal gold-AFB1-BSA conjugate for antibody binding sites in the test zone. A Smartphone-based reading system consisting of a Samsung Galaxy S2 Smartphone, a LFIA reader, and a Smartphone application for the image acquisition and data analysis. The detection limit of one-dot LFIA for AFB1 is 5 μg/kg. This method provided semi-quantitative analysis of AFB1 samples in the range of 5 to 1,000 μg/kg. Using combination of the one-dot LFIA and the Smartphone-based reading system, it is possible to conduct a more fast and accurate point-of-care diagnosis. PMID:23598499

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.

PubMed

Ionescu, Crina-Maria; Geidl, Stanislav; Svobodová Vařeková, Radka; Koča, Jaroslav

2013-10-28

We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.

High-order space charge effects using automatic differentiation

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

Reusch, Michael F.; Bruhwiler, David L.; Computer Accelerator Physics Conference Williamsburg, Virginia 1996

1997-02-01

The Northrop Grumman Topkark code has been upgraded to Fortran 90, making use of operator overloading, so the same code can be used to either track an array of particles or construct a Taylor map representation of the accelerator lattice. We review beam optics and beam dynamics simulations conducted with TOPKARK in the past and we present a new method for modeling space charge forces to high-order with automatic differentiation. This method generates an accurate, high-order, 6-D Taylor map of the phase space variable trajectories for a bunched, high-current beam. The spatial distribution is modeled as the product of amore » Taylor Series times a Gaussian. The variables in the argument of the Gaussian are normalized to the respective second moments of the distribution. This form allows for accurate representation of a wide range of realistic distributions, including any asymmetries, and allows for rapid calculation of the space charge fields with free space boundary conditions. An example problem is presented to illustrate our approach.« less

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

PubMed

Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

2016-07-08

The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Numerical modeling of turbulent swirling flow in a multi-inlet vortex nanoprecipitation reactor using dynamic DDES

NASA Astrophysics Data System (ADS)

Hill, James C.; Liu, Zhenping; Fox, Rodney O.; Passalacqua, Alberto; Olsen, Michael G.

2015-11-01

The multi-inlet vortex reactor (MIVR) has been developed to provide a platform for rapid mixing in the application of flash nanoprecipitation (FNP) for manufacturing functional nanoparticles. Unfortunately, commonly used RANS methods are unable to accurately model this complex swirling flow. Large eddy simulations have also been problematic, as expensive fine grids to accurately model the flow are required. These dilemmas led to the strategy of applying a Delayed Detached Eddy Simulation (DDES) method to the vortex reactor. In the current work, the turbulent swirling flow inside a scaled-up MIVR has been investigated by using a dynamic DDES model. In the DDES model, the eddy viscosity has a form similar to the Smagorinsky sub-grid viscosity in LES and allows the implementation of a dynamic procedure to determine its coefficient. The complex recirculating back flow near the reactor center has been successfully captured by using this dynamic DDES model. Moreover, the simulation results are found to agree with experimental data for mean velocity and Reynolds stresses.

Numerical simulation of the rapid intensification of Hurricane Katrina (2005): Sensitivity to boundary layer parameterization schemes

NASA Astrophysics Data System (ADS)

Liu, Jianjun; Zhang, Feimin; Pu, Zhaoxia

2017-04-01

Accurate forecasting of the intensity changes of hurricanes is an important yet challenging problem in numerical weather prediction. The rapid intensification of Hurricane Katrina (2005) before its landfall in the southern US is studied with the Advanced Research version of the WRF (Weather Research and Forecasting) model. The sensitivity of numerical simulations to two popular planetary boundary layer (PBL) schemes, the Mellor-Yamada-Janjic (MYJ) and the Yonsei University (YSU) schemes, is investigated. It is found that, compared with the YSU simulation, the simulation with the MYJ scheme produces better track and intensity evolution, better vortex structure, and more accurate landfall time and location. Large discrepancies (e.g., over 10 hPa in simulated minimum sea level pressure) are found between the two simulations during the rapid intensification period. Further diagnosis indicates that stronger surface fluxes and vertical mixing in the PBL from the simulation with the MYJ scheme lead to enhanced air-sea interaction, which helps generate more realistic simulations of the rapid intensification process. Overall, the results from this study suggest that improved representation of surface fluxes and vertical mixing in the PBL is essential for accurate prediction of hurricane intensity changes.

Infectious helminth ova in wastewater and sludge: A review on public health issues and current quantification practices.

PubMed

Gyawali, P

2018-02-01

Raw and partially treated wastewater has been widely used to maintain the global water demand. Presence of viable helminth ova and larvae in the wastewater raised significant public health concern especially when used for agriculture and aquaculture. Depending on the prevalence of helminth infections in communities, up to 1.0 × 10 3 ova/larvae can be presented per litre of wastewater and 4 gm (dry weight) of sludge. Multi-barrier approaches including pathogen reduction, risk assessment, and exposure reduction have been suggested by health regulators to minimise the potential health risk. However, with a lack of a sensitive and specific method for the quantitative detection of viable helminth ova from wastewater, an accurate health risk assessment is difficult to achieve. As a result, helminth infections are difficult to control from the communities despite two decades of global effort (mass drug administration). Molecular methods can be more sensitive and specific than currently adapted culture-based and vital stain methods. The molecular methods, however, required more and thorough investigation for its ability with accurate quantification of viable helminth ova/larvae from wastewater and sludge samples. Understanding different cell stages and corresponding gene copy numbers is pivotal for accurate quantification of helminth ova/larvae in wastewater samples. Identifying specific genetic markers including protein, lipid, and metabolites using multiomics approach could be utilized for cheap, rapid, sensitive, specific and point of care detection tools for helminth ova and larva in the wastewater.

Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

PubMed Central

Garcia Lopez, Sebastian; Kim, Philip M.

2014-01-01

Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT) algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases. PMID:25243403

Use of an automated chromium reduction system for hydrogen isotope ratio analysis of physiological fluids applied to doubly labeled water analysis.

PubMed

Schoeller, D A; Colligan, A S; Shriver, T; Avak, H; Bartok-Olson, C

2000-09-01

The doubly labeled water method is commonly used to measure total energy expenditure in free-living subjects. The method, however, requires accurate and precise deuterium abundance determinations, which can be laborious. The aim of this study was to evaluate a fully automated, high-throughput, chromium reduction technique for the measurement of deuterium abundances in physiological fluids. The chromium technique was compared with an off-line zinc bomb reduction technique and also subjected to test-retest analysis. Analysis of international water standards demonstrated that the chromium technique was accurate and had a within-day precision of <1 per thousand. Addition of organic matter to water samples demonstrated that the technique was sensitive to interference at levels between 2 and 5 g l(-1). Physiological samples could be analyzed without this interference, plasma by 10000 Da exclusion filtration, saliva by sedimentation and urine by decolorizing with carbon black. Chromium reduction of urine specimens from doubly labeled water studies indicated no bias relative to zinc reduction with a mean difference in calculated energy expenditure of -0.2 +/- 3.9%. Blinded reanalysis of urine specimens from a second doubly labeled water study demonstrated a test-retest coefficient of variation of 4%. The chromium reduction method was found to be a rapid, accurate and precise method for the analysis of urine specimens from doubly labeled water. Copyright 2000 John Wiley & Sons, Ltd.

Rapid detection of Streptococcus pneumoniae by real-time fluorescence loop-mediated isothermal amplification

PubMed Central

Guo, Xu-Guang; Zhou, Shan

2014-01-01

Background and aim of study A significant human pathogenic bacterium, Streptococcus pneumoniae was recognized as a major cause of pneumonia, and is the subject of many humoral immunity studies. Diagnosis is generally made based on clinical suspicion along with a positive culture from a sample from virtually any place in the body. But the testing time is too long. This study is to establish a rapid diagnostic method to identification of Streptococcus pneumoniae. Methods Our laboratory has recently developed a new platform called real-amp, which combines loop-mediated isothermal amplification (LAMP) with a portable tube scanner real-time isothermal instrument for the rapid detection of Streptococcus pneumonia. Two pairs of amplification primers required for this method were derived from a conserved DNA sequence unique to the Streptococcus pneumoniae. The amplification was carried out at 63 degree Celsius using SYBR Green for 60 minutes with the tube scanner set to collect fluorescence signals. Clinical samples of Streptococcus pneumoniae and other bacteria were used to determine the sensitivity and specificity of the primers by comparing with traditional culture method. Results The new set of primers consistently detected in laboratory-maintained isolates of Streptococcus pneumoniae from our hospital. The new primers also proved to be more sensitive than the published species-specific primers specifically developed for the LAMP method in detecting Streptococcus pneumoniae. Conclusions This study demonstrates that the Streptococcus pneumoniae LAMP primers developed here have the ability to accurately detect Streptococcus pneumoniae infections by real-time fluorescence LAMP. PMID:25276360

Fabrication of spherical microlens array by combining lapping on silicon wafer and rapid surface molding

NASA Astrophysics Data System (ADS)

Liu, Xiaohua; Zhou, Tianfeng; Zhang, Lin; Zhou, Wenchen; Yu, Jianfeng; Lee, L. James; Yi, Allen Y.

2018-07-01

Silicon is a promising mold material for compression molding because of its properties of hardness and abrasion resistance. Silicon wafers with carbide-bonded graphene coating and micro-patterns were evaluated as molds for the fabrication of microlens arrays. This study presents an efficient but flexible manufacturing method for microlens arrays that combines a lapping method and a rapid molding procedure. Unlike conventional processes for microstructures on silicon wafers, such as diamond machining and photolithography, this research demonstrates a unique approach by employing precision steel balls and diamond slurries to create microlenses with accurate geometry. The feasibility of this method was demonstrated by the fabrication of several microlens arrays with different aperture sizes and pitches on silicon molds. The geometrical accuracy and surface roughness of the microlens arrays were measured using an optical profiler. The measurement results indicated good agreement with the optical profile of the design. The silicon molds were then used to copy the microstructures onto polymer substrates. The uniformity and quality of the samples molded through rapid surface molding were also assessed and statistically quantified. To further evaluate the optical functionality of the molded microlens arrays, the focal lengths of the microlens arrays were measured using a simple optical setup. The measurements showed that the microlens arrays molded in this research were compatible with conventional manufacturing methods. This research demonstrated an alternative low-cost and efficient method for microstructure fabrication on silicon wafers, together with the follow-up optical molding processes.

Rapid and interference-free analysis of nine B-group vitamins in energy drinks using trilinear component modeling of liquid chromatography-mass spectrometry data.

PubMed

Hu, Yong; Wu, Hai-Long; Yin, Xiao-Li; Gu, Hui-Wen; Xiao, Rong; Xie, Li-Xia; Liu, Zhi; Fang, Huan; Wang, Li; Yu, Ru-Qin

2018-04-01

The aim of the present work was to develop a rapid and interference-free method based on liquid chromatography-mass spectrometry (LC-MS) for the simultaneous determination of nine B-group vitamins in various energy drinks. A smart and green strategy that modeled the three-way data array of LC-MS with second-order calibration methods based on alternating trilinear decomposition (ATLD) and alternating penalty trilinear decomposition (APTLD) algorithms was developed. By virtue of "mathematical separation" and "second-order advantage", the proposed strategy successfully solved the co-eluted peaks and unknown interferents in LC-MS analysis with the elution time less than 4.5min and simple sample preparation. Satisfactory quantitative results were obtained by the ATLD-LC-MS and APTLD-LC-MS methods for the spiked recovery assays, with the average spiked recoveries ranging from 87.2-113.9% to 92.0-111.7%, respectively. These results acquired from the proposed methods were confirmed by the LC-MS/MS method, which shows a quite good consistency with each other. All these results demonstrated that the developed chemometrics-assisted LC-MS strategy had advantages of being rapid, green, accurate and low-cost, and it could be an attractive alternative for the determination of multiple vitamins in complex food matrices, which required no laborious sample preparation, tedious condition optimization or more sophisticated instrumentations. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

PubMed

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.

Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.

PubMed

Bhaskar, Anand; Wang, Y X Rachel; Song, Yun S

2015-02-01

With the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency spectrum. In addition to inferring demography, our method can also accurately estimate locus-specific mutation rates. We perform extensive validation of our method on simulated data and show that it can accurately infer multiple recent epochs of rapid exponential growth, a signal that is difficult to pick up with small sample sizes. Lastly, we use our method to analyze data from recent sequencing studies, including a large-sample exome-sequencing data set of tens of thousands of individuals assayed at a few hundred genic regions. © 2015 Bhaskar et al.; Published by Cold Spring Harbor Laboratory Press.

State space truncation with quantified errors for accurate solutions to discrete Chemical Master Equation

PubMed Central

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-01-01

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEG), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of 1) the birth and death model, 2) the single gene expression model, 3) the genetic toggle switch model, and 4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate out theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks. PMID:27105653

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

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

Cao, Youfang; Terebus, Anna; Liang, Jie

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. Wemore » further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.« less

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

DOE PAGES

Cao, Youfang; Terebus, Anna; Liang, Jie

2016-04-22

The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. Wemore » further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space truncation and error analysis methods developed here can be used to ensure accurate direct solutions to the dCME for a large number of stochastic networks.« less

Current and Developing Technologies for Monitoring Agents of Bioterrorism and Biowarfare

PubMed Central

Lim, Daniel V.; Simpson, Joyce M.; Kearns, Elizabeth A.; Kramer, Marianne F.

2005-01-01

Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents. PMID:16223949

Colorimetric microdetermination of captopril in pure form and in pharmaceutical formulations

NASA Astrophysics Data System (ADS)

Shama, Sayed Ahmed; El-Sayed Amin, Alla; Omara, Hany

2006-11-01

A simple, rapid, accurate, precise and sensitive colorimetric method for the determination of captopril (CAP) in bulk sample and in dosage forms is described. The method is based on oxidation of the drug by potassium permanganate in acidic medium and determination of the unreacted oxidant by measuring the decrease in absorbance for five different dyes; methylene blue (MB); acid blue 74 (AB), acid red 73 (AR), amaranth dye (AM) and acid orange 7 (AO) at a suitable λmax (660, 610, 510, 520, and 485 nm), respectively. Regression analysis of Beer's plots showed good correlation in the concentration ranges (0.4 12.5, 0.3 10, 0.5 11, 0.4 8.3 and 0.5 9.3 μg ml-1), respectively. The apparent molar absorbtivity, Sandell sensitivity, detection and quantitation limits were calculated. For more accurate results, Ringbom optimum concentration ranges were 0.5 12, 0.5 9.6, 0.6 10.5, 0.5 8.0 and 0.7 9.0 μg ml-1, respectively. The validity of the proposed method was tested by analyzing in pure and dosage forms containing CAP whether alone or in combination with hydrochlorothiazide. Statistical analysis of the results reflects that the proposed procedures are precise, accurate and easily applicable for the determination of CAP in pure form and in pharmaceutical preparations. Also, the stability constant was determined and the free energy change was calculated potentiometrically.

Measurement of marine picoplankton cell size by using a cooled, charge-coupled device camera with image-analyzed fluorescence microscopy.

PubMed Central

Viles, C L; Sieracki, M E

1992-01-01

Accurate measurement of the biomass and size distribution of picoplankton cells (0.2 to 2.0 microns) is paramount in characterizing their contribution to the oceanic food web and global biogeochemical cycling. Image-analyzed fluorescence microscopy, usually based on video camera technology, allows detailed measurements of individual cells to be taken. The application of an imaging system employing a cooled, slow-scan charge-coupled device (CCD) camera to automated counting and sizing of individual picoplankton cells from natural marine samples is described. A slow-scan CCD-based camera was compared to a video camera and was superior for detecting and sizing very small, dim particles such as fluorochrome-stained bacteria. Several edge detection methods for accurately measuring picoplankton cells were evaluated. Standard fluorescent microspheres and a Sargasso Sea surface water picoplankton population were used in the evaluation. Global thresholding was inappropriate for these samples. Methods used previously in image analysis of nanoplankton cells (2 to 20 microns) also did not work well with the smaller picoplankton cells. A method combining an edge detector and an adaptive edge strength operator worked best for rapidly generating accurate cell sizes. A complete sample analysis of more than 1,000 cells averages about 50 min and yields size, shape, and fluorescence data for each cell. With this system, the entire size range of picoplankton can be counted and measured. Images PMID:1610183

Accurate Mass Fragment Library for Rapid Analysis of Pesticides on Produce Using Ambient Pressure Desorption Ionization with High-Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Kern, Sara E.; Lin, Lora A.; Fricke, Frederick L.

2014-08-01

U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]+) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]+ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]+ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli. The minimal sample preparation and absence of chromatography has shortened the analysis time to about 15 min per sample, and the simplicity and robustness of the technique make it ideal for rapid screening.

Comparison of susceptibility test methods to detect penicillin susceptibility in Streptococcus pneumoniae isolates.

PubMed

Mohd Nasir, Mohd Desa; Parasakthi, Navaratnam

2004-06-01

The increasing prevalence of penicillin-resistant Streptococuus pneumoniae urges for fast and accurate susceptibility testing methods. This study evaluated the comparability of three commonly used techniques; disk diffusion, E-test and agar dilution, to detect penicillin susceptibility in clinical isolates of S. pneumoniae. Fifty pneumococcal isolates, obtained from patients at the University of Malaya Medical Centre, were selected to include both penicillin-susceptible strains and those that had decreased susceptibility (resistant and intermediate) to penicillin. The minimum inhibitory concentration (MIC) values of penicillin to serve as the reference was determined by the agar dilution method in which, based on the MIC breakpoints recommended by the National Committee for Clinical Laboratory Standards (NCCLS), 27 strains had decreased susceptibility to penicillin with 17 strains resistant and 10 intermediate. Comparing to the agar dilution method, oxacillin disk diffusion test detected all strains with decreased penicillin susceptibility as such while E-test showed a close agreement of susceptibility (92%) of the isolates to penicillin. This confirmed that oxacillin is a good screening test for S. pneumoniae isolates with decreased susceptibility to penicillin while E-test is very reliable for rapid and accurate detection of penicillin susceptibility.

Identification of Eight Synthetic Cannabinoids, Including 5F-AKB48 in Seized Herbal Products Using DART-TOF-MS and LC-QTOF-MS as Nontargeted Screening Methods.

PubMed

Moore, Katherine N; Garvin, Demetra; Thomas, Brian F; Grabenauer, Megan

2017-09-01

Synthetic cannabinoids are sprayed onto plant material and smoked for their marijuana-like effects. Clandestine manufacturers modify synthetic cannabinoid structures by creating closely related analogs. Forensic laboratories are tasked with detection of these analog compounds, but targeted analytical methods are often thwarted by the structural modifications. Here, direct analysis in real time coupled to accurate mass time-of-flight mass spectrometry (DART-TOF-MS) in combination with liquid chromatography quadruple time-of-flight mass spectrometry (LC-QTOF-MS) are presented as a screening and nontargeted confirmation method, respectively. Methanol extracts of herbal material were run using both methods. Spectral data from four different herbal products were evaluated by comparing fragmentation pattern, accurate mass and retention time to available reference standards. JWH-018, JWH-019, AM2201, JWH-122, 5F-AKB48, AKB48-N-(4-pentenyl) analog, UR144, and XLR11 were identified in the products. Results demonstrate that DART-TOF-MS affords a useful approach for rapid screening of herbal products for the presence and identification of synthetic cannabinoids. © 2017 American Academy of Forensic Sciences.

Review of Angiotensin-converting Enzyme Inhibitory Assay: Rapid Method in Drug Discovery of Herbal Plants

PubMed Central

Ahmad, Islamudin; Yanuar, Arry; Mulia, Kamarza; Mun’im, Abdul

2017-01-01

The renin-angiotensin-aldosterone system is a signaling pathway which responsible in the blood pressure regulation. Angiotensin-converting enzyme (ACE) is one of the key elements responsible for the hypertensive mechanism. It converts angiotensin-I to angiotensin-II. The discovery history of the ACE inhibitory activity assay method has been through a long stage for decades and development continues until today. The ACE inhibitory activity has become an effective screening method in the search for new antihypertensive agents from herbal plants. Some of in vitro assay methods were used to examine the activity of ACE inhibitors based on the substrate usage, such as; Cushman and Cheung Method using a substrate hippuryl-histidyl-leucine (HHL), Holmquist method using a substrate furanacryloyl-tripeptide, Elbl and Wagner method using a substrate benzoil-[l-14C] glicyl-L-histidine-L-leucine, Carmel and Yaron method using a substrate o-aminobenzoylglycyl-p-nitrophenylalanilproline, and Lam method using 3-hydroxybutyrylglycyl-glycyl-glycine as substrate. Several different methods to measure the results of enzymatic reactions or separating substrate with products, including spectrophotometric, fluorometric, high-performance liquid chromatography, electrophoresis, and radiochemistry. Application of the test method for screening the ACE inhibitors activity and investigation of active compounds from natural products can be done easily with this method, it is very helpful in research because the results obtained are simple, accurate, and rapid. PMID:28503045

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

Negrete, Oscar A.; Branda, Catherine; Hardesty, Jasper O. E.

In the response to and recovery from a critical homeland security event involving deliberate or accidental release of biological agents, initial decontamination efforts are necessarily followed by tests for the presence of residual live virus or bacteria. Such 'clearance sampling' should be rapid and accurate, to inform decision makers as they take appropriate action to ensure the safety of the public and of operational personnel. However, the current protocol for clearance sampling is extremely time-intensive and costly, and requires significant amounts of laboratory space and capacity. Detection of residual live virus is particularly problematic and time-consuming, as it requires evaluationmore » of replication potential within a eukaryotic host such as chicken embryos. The intention of this project was to develop a new method for clearance sampling, by leveraging Sandia's expertise in the biological and material sciences in order to create a C. elegans-based foam that could be applied directly to the entire contaminated area for quick and accurate detection of any and all residual live virus by means of a fluorescent signal. Such a novel technology for rapid, on-site detection of live virus would greatly interest the DHS, DoD, and EPA, and hold broad commercial potential, especially with regard to the transportation industry.« less

Assessment of cell concentration and viability of isolated hepatocytes using flow cytometry.

PubMed

Wigg, Alan J; Phillips, John W; Wheatland, Loretta; Berry, Michael N

2003-06-01

The assessment of cell concentration and viability of freshly isolated hepatocyte preparations has been traditionally performed using manual counting with a Neubauer counting chamber and staining for trypan blue exclusion. Despite the simple and rapid nature of this assessment, concerns about the accuracy of these methods exist. Simple flow cytometry techniques which determine cell concentration and viability are available yet surprisingly have not been extensively used or validated with isolated hepatocyte preparations. We therefore investigated the use of flow cytometry using TRUCOUNT Tubes and propidium iodide staining to measure cell concentration and viability of isolated rat hepatocytes in suspension. Analysis using TRUCOUNT Tubes provided more accurate and reproducible measurement of cell concentration than manual cell counting. Hepatocyte viability, assessed using propidium iodide, correlated more closely than did trypan blue exclusion with all indicators of hepatocyte integrity and function measured (lactate dehydrogenase leakage, cytochrome p450 content, cellular ATP concentration, ammonia and lactate removal, urea and albumin synthesis). We conclude that flow cytometry techniques can be used to measure cell concentration and viability of isolated hepatocyte preparations. The techniques are simple, rapid, and more accurate than manual cell counting and trypan blue staining and the results are not affected by protein-containing media.