Pull-in instability tuning in imperfect nonlinear circular microplates under electrostatic actuation

Energy Technology Data Exchange (ETDEWEB)

Jallouli, A.; Kacem, N., E-mail: najib.kacem@univ-fcomte.fr; Bourbon, G.; Le Moal, P.; Walter, V.; Lardies, J.

2016-12-01

Highlights: • Dynamic range improvement of electrostatically actuated circular microplates. • Pull-in instability tuning based on geometric nonlinearity and imperfections. • Predictive computational model for the nonlinear behavior of circular microplates. - Abstract: Dynamic range improvement based on geometric nonlinearity and initial deflection is demonstrated with imperfect circular microplates under electrostatic actuation. Depending on design parameters, we prove how the von Kármán nonlinearity and the plate imperfections lead to a significant delay in pull-in occurrence. These promising results open the way towards an accurate identification of static parameters of circular microplates and the development of a predictive model for the nonlinear dynamics of imperfect capacitive micromachined ultrasonic transducers.

Microplates with adaptive surfaces.

Science.gov (United States)

Akbulut, Meshude; Lakshmi, Dhana; Whitcombe, Michael J; Piletska, Elena V; Chianella, Iva; Güven, Olgun; Piletsky, Sergey A

2011-11-14

Here we present a new and versatile method for the modification of the well surfaces of polystyrene microtiter plates (microplates) with poly(N-phenylethylene diamine methacrylamide), (poly-NPEDMA). The chemical grafting of poly-NPEDMA to the surface of microplates resulted in the formation of thin layers of a polyaniline derivative bearing pendant methacrylamide double bonds. These were used as the attachment point for various functional polymers through photochemical grafting of various, for example, acrylate and methacrylate, polymers with different functionalities. In a model experiment, we have modified poly-NPEDMA-coated microplates with a small library of polymers containing different functional groups using a two-step approach. In the first step, double bonds were activated by UV irradiation in the presence of N,N-diethyldithiocarbamic acid benzyl ester (iniferter). This enabled grafting of the polymer library in the second step by UV irradiation of solutions of the corresponding monomers in the microplate wells. The uniformity of coatings was confirmed spectrophotometrically, by microscopic imaging and by contact angle measurements (CA). The feasibility of the current technology has been shown by the generation of a small library of polymers grafted to the microplate well surfaces and screening of their affinity to small molecules, such as atrazine, a trio of organic dyes, and a model protein, bovine serum albumin (BSA). The stability of the polymers, reproducibility of measurement, ease of preparation, and cost-effectiveness make this approach suitable for applications in high-throughput screening in the area of materials research.

Comparability of slack water and Lagrangian flow respirometry methods for community metabolic measurements.

Directory of Open Access Journals (Sweden)

Emily C Shaw

Full Text Available Coral reef calcification is predicted to decline as a result of ocean acidification and other anthropogenic stressors. The majority of studies predicting declines based on in situ relationships between environmental parameters and net community calcification rate have been location-specific, preventing accurate predictions for coral reefs globally. In this study, net community calcification and production were measured on a coral reef flat at One Tree Island, Great Barrier Reef, using Lagrangian flow respirometry and slack water methods. Net community calcification, daytime net photosynthesis and nighttime respiration were higher under the flow respirometry method, likely due to increased water flow relative to the slack water method. The two methods also varied in the degrees to which they were influenced by potential measurement uncertainties. The difference in the results from these two commonly used methods implies that some of the location-specific differences in coral reef community metabolism may be due to differences in measurement methods.

Size-dependent vibrations of post-buckled functionally graded Mindlin rectangular microplates

Directory of Open Access Journals (Sweden)

R. Ansari

Full Text Available In this paper, the free vibration behavior of post-buckled functionally graded (FG Mindlin rectangular microplates are described based on the modified couple stress theory (MCST. This theory enables the consideration of the size-effect through introducing material length scale parameters. The FG microplates made of a mixture of metal and ceramic are considered whose volume fraction of components is expressed by a power law function. By means of Hamilton's principle, the nonlinear governing equations and associated boundary conditions are derived for FG micro-plates in the postbuckling domain. The governing equations and boundary conditions are then discretized by using the generalized differential quadrature (GDQ method before solving numerically by the pseudo-arclength continuation technique. In the solution procedure, the postbuckling problem of microplates is investigated first. Afterwards, the free vibration of microplates around the buckled configuration is discussed. The effects of dimensionless length scale parameter, material gradient index and aspect ratio on the on the postbuckling path and frequency of FG microplates subject to arbitrary edge supports are thoroughly discussed.

Initially Imperfect MEMS Microplates Under Electrostatic Actuation: Theory and Experiment

KAUST Repository

Saghir, Shahid

2016-12-05

Microplates are building blocks of many Micro-Electro-Mechanical Systems (MEMS). It is common for them to undergo imperfections due to residual stresses caused by the micro fabrication process. Such plates are essentially different from perfectly flat plates and cannot be modeled using the governing equations of flat plates. In this article, we adopt the governing equations of imperfect plates employing the modified von-Karman strains. These equations then are used to develop a Reduced Order Model based on the Galerkin procedure to simulate the static and dynamic behavior of an electrostatically actuated microplate. Also, microplates made of silicon nitride are fabricated and tested. First, the static behaviour of the microplate is investigated when applying a static voltage Vdc. To study the dynamic behaviour we apply a harmonic voltage, Vac, superimposed to Vdc. Simulation results show good agreement with the experimentally measured responses.

Photosensitizer Adhered to Cell Culture Microplates Induces Phototoxicity in Carcinoma Cells

Directory of Open Access Journals (Sweden)

Verena Ziegler

2013-01-01

Full Text Available In vitro experiments in plastic receptacles are the basis of characterization of new photosensitizers (PSs for the photodynamic therapy. We recently reported that lipophilic PSs adhere to cell culture microplates in a kinetic-like manner (Engelhardt et al., 2011. In the current study, we examined the interaction and phototoxic effects of the microplate-adhered PS in cancer cells. Therefore, we preloaded microplates with hypericin, Foscan, PVP-hypericin, or aluminum (III phthalocyanine tetrasulfonate chloride (AlPCS4 for 24 hours and measured the PS distribution after addition of A431 human carcinoma cells: following another 24 hours up to 68% of hypericin were detected in the cell fraction. The hydrophilic PVP-hypericin and AlPCS4 also diffused into the cells, but the quantities of PS adherence were considerably lower. Microplate-adhered Foscan appeared not to be redistributed. In contrast to the hydrophilic PSs, the cellular phototoxicity of microplate-adhered lipophilic PS was high, independent of whether the PS (i was pre-loaded onto microplates or (ii added simultaneously with the cells or (iii one day after cell seeding. Based on these results, we suggest testing lipophilic PS dyes for their adherence to microplates. Furthermore, the ability of plastic materials to (reversibly store PSs might represent a new approach for the PS delivery or the development of antimicrobial coatings.

Photometric Determination of Ammonium and Phosphate in Seawater Medium Using a Microplate Reader.

Science.gov (United States)

Ruppersberg, Hanna S; Goebel, Maren R; Kleinert, Svea I; Wünsch, Daniel; Trautwein, Kathleen; Rabus, Ralf

2017-01-01

To more efficiently process the large sample numbers for quantitative determination of ammonium (NH4+) and phosphate (orthophosphate, PO43-) generated during comprehensive growth experiments with the marine Roseobacter group member Phaeobacter inhibens DSM 17395, specific colorimetric assays employing a microplate reader (MPR) were established. The NH4+ assay is based on the reaction of NH4+ with hypochlorite and salicylate, yielding a limit of detection of 14 µM, a limit of quantitation of 36 µM, and a linear range for quantitative determination up to 200 µM. The PO43-assay is based on the complex formation of PO43- with ammonium molybdate in the presence of ascorbate and zinc acetate, yielding a limit of detection of 13 µM, a limit of quantitation of 50 µM, and a linear range for quantitative determination up to 1 mM. Both MPR-based assays allowed for fast (significantly lower than 1 h) analysis of 21 samples plus standards for calibration (all measured in triplicates) and showed only low variation across a large collection of biological samples. © 2017 S. Karger AG, Basel.

Resonant frequency analysis on an electrostatically actuated microplate under uniform hydrostatic pressure

International Nuclear Information System (INIS)

Li Zhikang; Zhao Libo; Ye Zhiying; Zhao Yulong; Jiang Zhuangde; Wang Hongyan

2013-01-01

The resonant frequency of a microplate is influenced by various physical parameters such as mass, surface stress, hydrostatic pressure and electrostatic force. In this paper, the effects of both electrostatic force and uniform hydrostatic pressure on the resonant frequency of a clamped circular microplate are investigated. An approximate solution is derived for the fundamental resonance frequency of the mciroplate under both types of loads using an energy equivalent method. It is found that both electrostatic force and uniform hydrostatic pressure decrease the resonant frequency of the microplate under small deflections. Additionally, the linearized expression of this solution shows that the resonant frequency varies linearly with pressure in the low and ultra-low range, and the corresponding pressure sensitivity depends on the voltage applied to the microplate. The analytical results are well validated by the finite element method. This study may be helpful for the design and optimization of electrostatically actuated resonance devices based on microplates, especially electrostatically actuated low- or ultra-low-pressure sensors. (paper)

Portable Microplate Analyzer with a Thermostatic Chamber Based on a Smartphone for On-site Rapid Detection.

Science.gov (United States)

Wan, Zijian; Zhong, Longjie; Pan, Yuxiang; Li, Hongbo; Zou, Quchao; Su, Kaiqi; Wang, Ping

2017-01-01

A microplate method provides an efficient way to use modern detection technology. However, there are some difficulties concerning on-site detection, such as being non-portable and time-consuming. In this work, a novel portable microplate analyzer with a thermostatic chamber based on a smartphone was designed for rapid on-site detection. An analyzer with a wide-angle lens and an optical filter provides a proper environment for the microplate. A smartphone app-iPlate Monitor was used for RGB analyze of image. After a consistency experiment with a microtiter plate reader (MTPR), the normalized calibration curves were y = 0.7276x + 0.0243 (R 2 = 0.9906) and y = 0.3207x + 0.0094 (R 2 = 0.9917) with a BCA protein kit as well as y = 0.182x + 0.0134 (R 2 = 0.994) and y = 0.0674x + 0.0003 (R 2 = 0.9988) with a glucose kit. The times for obtaining the detection requirement were 15 and 10 min for the BCA protein kit and the glucose kit at 37°C; in contrast, it required more than 30 and 20 min at ambient temperature. Meanwhile, it also showed good repeatability for detections.

Further analysis of open-respirometry systems: an a-compartmental mechanistic approach

Directory of Open Access Journals (Sweden)

Chaui-Berlinck J.G.

2000-01-01

Full Text Available A system is said to be "instantaneous" when for a given constant input an equilibrium output is obtained after a while. In the meantime, the output is changing from its initial value towards the equilibrium one. This is the transient period of the system and transients are important features of open-respirometry systems. During transients, one cannot compute the input amplitude directly from the output. The existing models (e.g., first or second order dynamics cannot account for many of the features observed in real open-respirometry systems, such as time lag. Also, these models do not explain what should be expected when a system is speeded up or slowed down. The purpose of the present study was to develop a mechanistic approach to the dynamics of open-respirometry systems, employing basic thermodynamic concepts. It is demonstrated that all the main relevant features of the output dynamics are due to and can be adequately explained by a distribution of apparent velocities within the set of molecules travelling along the system. The importance of the rate at which the molecules leave the sensor is explored for the first time. The study approaches the difference in calibrating a system with a continuous input and with a "unit impulse": the former truly reveals the dynamics of the system while the latter represents the first derivative (in time of the former and, thus, cannot adequately be employed in the apparent time-constant determination. Also, we demonstrate why the apparent order of the output changes with volume or flow.

An investigation of the mechanical behavior of initially curved microplates under electrostatic actuation

KAUST Repository

Saghir, Shahid

2018-03-28

In this article, we investigate the mechanical behavior of initially curved microplates under electrostatic actuation. Microplates are essential components of many Micro-Electro-Mechanical System devices; however, they commonly undergo an initial curvature imperfection, due to the microfabrication process. Initial curvature imperfection significantly affects the mechanical behavior of microplates. In this work, we derive a dynamic analogue of the von Kármán governing equation for such plates. These equations are then used to develop a reduced order model based on the Galerkin procedure to simulate the static and dynamic behavior of the microplate. Two profiles of initial curvature commonly encountered in microfabricated structures are considered, where one assumes a variation in shape along one dimension of the plate only (cylindrical bending shape) while the other assumes a variation in shape along both dimensions of the plate. Their effects on both the static and dynamic responses of the microplates are examined and compared. We validate the reduced order model by comparing the calculated static behavior and the fundamental natural frequency with those computed by a finite element model over a range of the initial plate rise. The static behavior of the microplate is investigated when varying the DC voltage. Then, the dynamic behavior of the microplate is examined under the application of a harmonic AC voltage superimposed to a DC voltage.

Magmatic evolution of the Easter microplate-Crough Seamount region (South East Pacific)

Science.gov (United States)

Hekinian, R.; Stoffers, P.; Akermand, D.; Binard, N.; Francheteau, Jean; Devey, C.; Garbe-Schonberg, D.

1995-01-01

The Easter microplate-Crough Seamount region located between 25?? S-116?? W and 25?? S-122?? W consists of a chain of seamounts forming isolated volcanoes and elongated (100-200 km in length) en echelon volcanic ridges oriented obliquely NE (N 065??), to the present day general spreading direction (N 100??) of the Pacific-Nazca plates. The extension of this seamount chain into the southwestern edge of the Easter microplate near 26??30??? S-115?? W was surveyed and sampled. The southern boundary including the Orongo fracture zone and other shallow ridges ( 0.25) MORBs which are similar in composition to other more recent basalts from the Southwest and East Rifts spreading axes of the Easter microplate. Incompatible element ratios normalized to chondrite values [(Ce/Yb)N = 1-2.5}, {(La/Sm)N = 0.4-1.2} and {(Zr/Y)N = 0.7-2.5} of the basalts are also similar to present day volcanism found in the Easter microplate. The volcanics from the Easter microplate-Crough region are unrelated to other known South Pacific intraplate magmatism (i.e. Society, Pitcairn, and Salas y Gomez Islands). Instead their range in incompatible element ratios is comparable to the submarine basalts from the recently investigated Ahu and Umu volcanic field (Easter hotspot) (Scientific Party SO80, 1993) and centered at about 80 km west of Easter Island. The oblique ridges and their associated seamounts are likely to represent ancient leaky transform faults created during the initial stage of the Easter microplate formation (??? 5 Ma). It appears that volcanic activity on seamounts overlying the oblique volcanic ridges has continued during their westward drift from the microplate as shown by the presence of relatively fresh lava observed on one of these structures, namely the first Oblique Volcanic Ridge near 25?? S-118?? W at about 160 km west of the Easter microplate West Rift. Based on a reconstruction of the Easter microplate, it is suggested that the Crough seamount (Easter Island. ?? 1995

Nonlinear Mechanics of MEMS Rectangular Microplates under Electrostatic Actuation

KAUST Repository

Saghir, Shahid

2016-12-01

The first objective of the dissertation is to develop a suitable reduced order model capable of investigating the nonlinear mechanical behavior of von-Karman plates under electrostatic actuation. The second objective is to investigate the nonlinear static and dynamic behavior of rectangular microplates under small and large actuating forces. In the first part, we present and compare various approaches to develop reduced order models for the nonlinear von-Karman rectangular microplates actuated by nonlinear electrostatic forces. The reduced-order models aim to investigate the static and dynamic behavior of the plate under small and large actuation forces. A fully clamped microplate is considered. Different types of basis functions are used in conjunction with the Galerkin method to discretize the governing equations. First we investigate the convergence with the number of modes retained in the model. Then for validation purpose, a comparison of the static results is made with the results calculated by a nonlinear finite element model. The linear eigenvalue problem for the plate under the electrostatic force is solved for a wide range of voltages up to pull-in. In the second part, we present an investigation of the static and dynamic behavior of a fully clamped microplate. We investigate the effect of different non-dimensional design parameters on the static response. The forced-vibration response of the plate is then investigated when the plate is excited by a harmonic AC load superimposed to a DC load. The dynamic behavior is examined near the primary and secondary (superharmonic and subharmonic) resonances. The microplate shows a strong hardening behavior due to the cubic nonlinearity of midplane stretching. However, the behavior switches to softening as the DC load is increased. Next, near-square plates are studied to understand the effect of geometric imperfections of microplates. In the final part of the dissertation, we investigate the mechanical behavior of

High-throughput microplate technique for enzymatic hydrolysis of lignocellulosic biomass.

Science.gov (United States)

Chundawat, Shishir P S; Balan, Venkatesh; Dale, Bruce E

2008-04-15

Several factors will influence the viability of a biochemical platform for manufacturing lignocellulosic based fuels and chemicals, for example, genetically engineering energy crops, reducing pre-treatment severity, and minimizing enzyme loading. Past research on biomass conversion has focused largely on acid based pre-treatment technologies that fractionate lignin and hemicellulose from cellulose. However, for alkaline based (e.g., AFEX) and other lower severity pre-treatments it becomes critical to co-hydrolyze cellulose and hemicellulose using an optimized enzyme cocktail. Lignocellulosics are appropriate substrates to assess hydrolytic activity of enzyme mixtures compared to conventional unrealistic substrates (e.g., filter paper, chromogenic, and fluorigenic compounds) for studying synergistic hydrolysis. However, there are few, if any, high-throughput lignocellulosic digestibility analytical platforms for optimizing biomass conversion. The 96-well Biomass Conversion Research Lab (BCRL) microplate method is a high-throughput assay to study digestibility of lignocellulosic biomass as a function of biomass composition, pre-treatment severity, and enzyme composition. The most suitable method for delivering milled biomass to the microplate was through multi-pipetting slurry suspensions. A rapid bio-enzymatic, spectrophotometric assay was used to determine fermentable sugars. The entire procedure was automated using a robotic pipetting workstation. Several parameters that affect hydrolysis in the microplate were studied and optimized (i.e., particle size reduction, slurry solids concentration, glucan loading, mass transfer issues, and time period for hydrolysis). The microplate method was optimized for crystalline cellulose (Avicel) and ammonia fiber expansion (AFEX) pre-treated corn stover. Copyright 2008 Wiley Periodicals, Inc.

Cutaneous respirometry by dynamic measurement of mitochondrial oxygen tension for monitoring mitochondrial function in vivo.

Science.gov (United States)

Harms, Floor A; Voorbeijtel, Wilhelmina J; Bodmer, Sander I A; Raat, Nicolaas J H; Mik, Egbert G

2013-09-01

Progress in diagnosis and treatment of mitochondrial dysfunction in chronic and acute disease could greatly benefit from techniques for monitoring of mitochondrial function in vivo. In this study we demonstrate the feasibility of in vivo respirometry in skin. Mitochondrial oxygen measurements by means of oxygen-dependent delayed fluorescence of protoporphyrin IX are shown to provide a robust basis for measurement of local oxygen disappearance rate (ODR). The fundamental principles behind the technology are described, together with an analysis method for retrievel of respirometry data. The feasibility and reproducibility of this clinically useful approach are demonstrated in a series of rats. Copyright © 2012 Elsevier B.V. All rights reserved.

Design and characterization of AlN-based in-plane microplate resonators

International Nuclear Information System (INIS)

Ruiz-Díez, V; Manzaneque, T; Hernando-García, J; Sánchez-Rojas, J L; Ababneh, A; Kucera, M; Schmid, U; Seidel, H

2013-01-01

In this paper, a design procedure to perform an efficient actuation of in-plane modes in piezoelectric resonators is presented. This procedure is applied to different microplate structures, paying attention to two in-plane mode families: contour modes and flexure-actuated modes. A representative set of devices from both families were used as illustrative examples. These devices were characterized electrically by measuring the impedance and their in-plane modal shapes were measured with a novel technique based on speckle-pattern interferometry. Figures of merit such as the quality factor or the motional resistance were obtained and used to evaluate the different design approaches. (paper)

Finite element analysis to determine the stress distribution, displacement and safety factor on a microplate for the fractured jaw case

Science.gov (United States)

Pratama, Juan; Mahardika, Muslim

2018-03-01

Microplate is a connecting plate that can be used for jaw bone fixation. In the last two decades, microplate has been used so many times to help reconstruction of fractured jaw bone which is called mandibular bone or mandible bone. The plate is used to provide stable fixation of the fractured bone tissue during healing and reconstruction process. In this study Finite Element Analysis was used to predict the stress concentration and distribution on a microplate, displacement on the microplate and also to determine the safety factor of the microplate based on maximum allowable stress value, and finally to ascertain whether microplate is safe to use or not. The microplate was produced from punching process using titanium grade 1 (pure titanium) as material with a thickness of 500 µm. The results of the research indicated that the microplate was safe to use according to the maximum stress around the hole, displacement around the hole and also the safety factor of the microplate.

Simple extraction-solvothermal synthesis of single-crystalline silver microplates

Energy Technology Data Exchange (ETDEWEB)

You, Ting; Sun, Sixiu; Song, Xinyu; Xu, Shuling [Department of Chemistry and Chemical Engineering, Shandong University (China)

2009-08-15

Single-crystalline silver microplates, with average edge length of about 1.5{mu}m and thickness of 100 nm, have been synthesized by a simple extraction-solvothermal method. Samples were characterized in detail by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM) and High-resolution transmission electron microscopy (HRTEM) technologies. Extractant primary amine N1923 can also act as reducing agent. It has been found that microstructure of the silver can be controlled by the n-octanol during the solvothermal treatment. Based on a series of experimental analysis, the possible formation mechanism of these microplates was discussed briefly. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Noninvasive diagnostics of mitochondrial disorders in isolated lymphocytes with high resolution respirometry

Czech Academy of Sciences Publication Activity Database

Pecina, Petr; Houšťková, H.; Mráček, Tomáš; Pecinová, Alena; Nůsková, Hana; Tesařová, M.; Hansíková, H.; Janota, J.; Zeman, J.; Houštěk, Josef

2014-01-01

Roč. 2, Dec (2014), s. 62-71 ISSN 2214-6474 R&D Projects: GA MZd(CZ) NT12370; GA ČR(CZ) GAP303/11/0970; GA ČR(CZ) GB14-36804G Institutional support: RVO:67985823 Keywords : lymphocytes * respirometry * oxidative phosphorylation * mitochondrial diseases * diagnostics Subject RIV: FG - Pediatrics

A direct heating model to overcome the edge effect in microplates.

Science.gov (United States)

Lau, Chun Yat; Zahidi, Alifa Afiah Ahmad; Liew, Oi Wah; Ng, Tuck Wah

2015-01-01

Array-based tests in a microplate format are complicated by the regional variation in results of the outer against the inner wells of the plate. Analysis of the evaporation mechanics of sessile drops showed that evaporation rate increase with temperature was due to changes in the heat of vaporization, density and diffusion coefficient. In simulations of direct bottom heating of standard microplates, considerable heat transfer via conduction from the side walls was found to be responsible for lower temperatures in the liquid in wells close to the edge. Applying a two temperature heating mode, 304 K at the side compared to 310 K at the bottom, allowed for a more uniform temperature distribution. Transparency microplates were found to inherently possess immunity to the edge effect problem due to the presence of air between the liquid and solid wall. Copyright © 2014 Elsevier B.V. All rights reserved.

Microplate-based high throughput screening procedure for the isolation of lipid-rich marine microalgae

Directory of Open Access Journals (Sweden)

Pereira Hugo

2011-12-01

Full Text Available Abstract We describe a new selection method based on BODIPY (4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene staining, fluorescence activated cell sorting (FACS and microplate-based isolation of lipid-rich microalgae from an environmental sample. Our results show that direct sorting onto solid medium upon FACS can save about 3 weeks during the scale-up process as compared with the growth of the same cultures in liquid medium. This approach enabled us to isolate a biodiverse collection of several axenic and unialgal cultures of different phyla.

Visual detection and microplate assay for Staphylococcus aureus based on aptamer recognition coupled to tyramine signal amplification

International Nuclear Information System (INIS)

Yuan, Jinglei; Li, Can; Ma, Xiaoyuan; Xia, Yu; Chen, Jie; Wang, Zhouping; Yu, Ye

2014-01-01

We have developed a specific method for the visual detection of Staphylococcus aureus based on aptamer recognition coupled to tyramine signal amplification technology. A biotinylated aptamer specific for S. aureus was immobilized on the surface of the wells of a microplate via biotin-avidin binding. Then, the target bacteria (S. aureus), the biotinylated-aptamer-streptavidin-HRP conjugates, biotinylated tyramine, hydrogen peroxide and streptavidin-HRP were successively placed in the wells of the microplate. After adding TMB reagent and stop solution, the intensity of the yellow reaction product can be visually inspected or measured with a plate reader. Under optimized conditions, there is a linear relationship between absorbance at 450 nm and the concentration of S. aureus in the 10 to 107 cfu mL −1 concentration range (with an R 2 of 0.9976). The limit of detection is 8 cfu mL −1 . (author)

Identification and quantification of nitrogen nutrient deficiency in the activated sludge process using respirometry

NARCIS (Netherlands)

Ning, Z.; Patry, G.G.; Spanjers, H.

2000-01-01

Experimental protocols to identify and quantify nitrogen nutrient deficiency in the activated sludge process were developed and tested using respirometry. Respirometric experiments showed that when a nitrogen nutrient deficient sludge is exposed to ammonia nitrogen, the oxygen uptake rate (OUR) of

Microplate Heat Exchanger, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — We propose a microplate heat exchanger for cryogenic cooling systems used for continuous flow distributed cooling systems, large focal plane arrays, multiple cooling...

Forecastable and Guidable Bubble-Propelled Microplate Motors for Cell Transport.

Science.gov (United States)

Hu, Narisu; Zhang, Bin; Gai, Meiyu; Zheng, Ce; Frueh, Johannes; He, Qiang

2017-06-01

Cell transport is important to renew body functions and organs with stem cells, or to attack cancer cells with immune cells. The main hindrances of this method are the lack of understanding of cell motion as well as proper transport systems. In this publication, bubble-propelled polyelectrolyte microplates are used for controlled transport and guidance of HeLa cells. Cells survive attachment on the microplates and up to 22 min in 5% hydrogen peroxide solution. They can be guided by a magnetic field whereby increased friction of cells attached to microplates decreases the speed by 90% compared to pristine microplates. The motion direction of the cell-motor system is easier to predict due to the cell being opposite to the bubbles. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inline chemical process analysis in micro-plants based on thermoelectric flow and impedimetric sensors

International Nuclear Information System (INIS)

Jacobs, T; Kutzner, C; Hauptmann, P; Kropp, M; Lang, W; Brokmann, G; Steinke, A; Kienle, A

2010-01-01

In micro-plants, as used in chemical micro-process engineering, an integrated inline analytics is regarded as an important factor for the development and optimization of chemical processes. Up to now, there is a lack of sensitive, robust and low-priced micro-sensors for monitoring mixing and chemical conversion in micro-fluidic channels. In this paper a novel sensor system combining an impedimetric sensor and a novel pressure stable thermoelectric flow sensor for monitoring chemical reactions in micro-plants is presented. The CMOS-technology-based impedimetric sensor mainly consists of two capacitively coupled interdigital electrodes on a silicon chip. The thermoelectric flow sensor consists of a heater in between two thermopiles on a perforated membrane. The pulsed and constant current feeds of the heater were analyzed. Both sensors enable the analysis of chemical conversion by means of changes in the thermal and electrical properties of the liquid. The homogeneously catalyzed synthesis of n-butyl acetate as a chemical model system was studied. Experimental results revealed that in an overpressure regime, relative changes of less than 1% in terms of thermal and electrical properties can be detected. Furthermore, the transition from one to two liquid phases accompanied by the change in slug flow conditions could be reproducibly detected

Absorbance and fluorometric sensing with capillary wells microplates

International Nuclear Information System (INIS)

Tan, Han Yen; Cheong, Brandon Huey-Ping; Neild, Adrian; Wah Ng, Tuck; Liew, Oi Wah

2010-01-01

Detection and readout from small volume assays in microplates are a challenge. The capillary wells microplate approach [Ng et al., Appl. Phys. Lett. 93, 174105 (2008)] offers strong advantages in small liquid volume management. An adapted design is described and shown here to be able to detect, in a nonimaging manner, fluorescence and absorbance assays minus the error often associated with meniscus forming at the air-liquid interface. The presence of bubbles in liquid samples residing in microplate wells can cause inaccuracies. Pipetting errors, if not adequately managed, can result in misleading data and wrong interpretations of assay results; particularly in the context of high throughput screening. We show that the adapted design is also able to detect for bubbles and pipetting errors during actual assay runs to ensure accuracy in screening.

Absorbance and fluorometric sensing with capillary wells microplates

Energy Technology Data Exchange (ETDEWEB)

Tan, Han Yen; Cheong, Brandon Huey-Ping; Neild, Adrian; Wah Ng, Tuck [Laboratory for Optics, Acoustics, and Mechanics, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, Victoria 3800 (Australia); Liew, Oi Wah [Cardiovascular Biomarkers Laboratory, Cardiovascular Research Institute, 30 Medical Drive, Singapore 117609 (Singapore)

2010-12-15

Detection and readout from small volume assays in microplates are a challenge. The capillary wells microplate approach [Ng et al., Appl. Phys. Lett. 93, 174105 (2008)] offers strong advantages in small liquid volume management. An adapted design is described and shown here to be able to detect, in a nonimaging manner, fluorescence and absorbance assays minus the error often associated with meniscus forming at the air-liquid interface. The presence of bubbles in liquid samples residing in microplate wells can cause inaccuracies. Pipetting errors, if not adequately managed, can result in misleading data and wrong interpretations of assay results; particularly in the context of high throughput screening. We show that the adapted design is also able to detect for bubbles and pipetting errors during actual assay runs to ensure accuracy in screening.

Cutaneous respirometry as novel technique to monitor mitochondrial function: A feasibility study in healthy volunteers

NARCIS (Netherlands)

F.A. Harms (Floor A.); R.J. Stolker (Robert); E.G. Mik (Egbert)

2016-01-01

textabstractBackground: The protoporphyrin IX-triplet state lifetime technique (PpIX-TSLT) is proposed as a potential clinical non-invasive tool to monitor mitochondrial function. This technique has been evaluated in several animal studies. Mitochondrial respirometry allows measurement in vivo of

Presencia de microplásticos en cuatro playas arenosas de Perú

Directory of Open Access Journals (Sweden)

Sara Purca

2017-04-01

Full Text Available Se presenta el número y peso por metro cuadrado de fragmentos de microplásticos presentes en cuatro playas arenosas de la costa peruana. Las muestras fueron colectadas entre junio de 2014 y mayo 2015. Fragmentos de plástico duro mayores a 1 mm fueron encontrados en más del 80% de las muestras de las cuatro playas. La playa Costa Azul (~ 12°S presentó 522 fragmentos por metro cuadrado (items/m2 de microplásticos, de los cuales, 463.33 items/m2 y 2.6 g/m2 fueron plásticos duros. La playa Albúfera de Medio Mundo (~ 11°S presentó el menor número y peso de microplásticos (4.67 items/m2 y 0.50 g/m2. Una muestra aleatoria de la playa Costa Azul fue analizada por el espectroscopio FT-IR. Se encontró 5 fragmentos con poliuretano (PE, dos fragmentos con polipropileno (PP y un fragmento con estireno (EPS. Pocos estudios mencionan al plástico duro como la mayor fracción de los microplásticos, se sugiere nuevas fuentes de intrusión y vías de microbasura en los hábitas, los cuales podrían estar afectando desde la base de trama trófica marina en el Perú.

Approaches for Reduced Order Modeling of Electrically Actuated von Karman Microplates

KAUST Repository

Saghir, Shahid

2016-07-25

This article presents and compares different approaches to develop reduced order models for the nonlinear von Karman rectangular microplates actuated by nonlinear electrostatic forces. The reduced-order models aim to investigate the static and dynamic behavior of the plate under small and large actuation forces. A fully clamped microplate is considered. Different types of basis functions are used in conjunction with the Galerkin method to discretize the governing equations. First we investigate the convergence with the number of modes retained in the model. Then for validation purpose, a comparison of the static results is made with the results calculated by a nonlinear finite element model. The linear eigenvalue problem for the plate under the electrostatic force is solved for a wide range of voltages up to pull-in. Results among the various reduced-order modes are compared and are also validated by comparing to results of the finite-element model. Further, the reduced order models are employed to capture the forced dynamic response of the microplate under small and large vibration amplitudes. Comparison of the different approaches are made for this case. Keywords: electrically actuated microplates, static analysis, dynamics of microplates, diaphragm vibration, large amplitude vibrations, nonlinear dynamics

Assessment of Equipment for the Determination of Nutrients in Marine Waters: A Case Study of the Microplate Technique

Science.gov (United States)

Aminot, A.

1996-09-01

An essential prerequisite for quality assurance of the colorimetric determination of nutrients in seawater is the use of suitable photometric equipment. Based on a knowledge of the optical characteristics of a particular system and the absorption coefficient of the analyte, a statistical approach can be used to predict the limit of detection and the limit of quantitation for a given determinand. The microplate technique, widely used for bioassays, is applicable to colorimetric analysis in general, and its use for the determination of nutrients in seawater has been suggested. This paper reports a theoretical assessment of its capabilities in this context and a practical check on its performance, taking the determination of nitrite in seawater as typical. The conclusion is that short optical path length and insufficient repeatability of the absorbance measurement render it unsuitable for the determination of the low concentrations generally encountered in marine work, with the possible exception of nitrate. The perceived advantage of high-speed analysis is a secondary consideration in the overall process of determining nutrients, and the microplate technique's small scale of operation is a definite disadvantage as this increases the risk of exposure to contamination problems, in comparison with conventional techniques.

An experimental and theoretical investigation of the mechanical behavior of multilayer initially curved microplates under electrostatic actuation

KAUST Repository

Saghir, Shahid

2017-04-07

We investigate the static and dynamic behavior of a multilayer clamped-free-clamped-free (CFCF) microplate, which is made of polyimide, gold, chromium, and nickel. The microplate is slightly curved away from a stationary electrode and is electrostatically actuated. The free and forced vibrations of the microplate are examined. First, we experimentally investigate the variation of the first natural frequency under the electrostatic DC load. Then, the forced dynamic behavior is investigated by applying a harmonic AC voltage superimposed to a DC voltage. Results are shown demonstrating the transition of the dynamic response of the microplate from hardening to softening as the DC voltage is changed as well the dynamic pull-in phenomenon. For theoretical model, we adopt a dynamic analog of the von-Karman governing equations accounting for initial curvature imperfection. These equations are then used to develop a reduced order model based on the Galerkin procedure to simulate the mechanical behavior of the microplate. We compare the theoretical results with experimental data and show excellent agreement among the results. We also examine the effect of the initial rise on the natural frequencies of first three symmetric-symmetric modes of the plate.

Customizable PCR-microplate array for differential identification of multiple pathogens.

Science.gov (United States)

Woubit, Abdela; Yehualaeshet, Teshome; Roberts, Sherrelle; Graham, Martha; Kim, Moonil; Samuel, Temesgen

2013-11-01

Customizable PCR-microplate arrays were developed for the rapid identification of Salmonella Typhimurium, Salmonella Saintpaul, Salmonella Typhi, Shigella dysenteriae, Escherichia coli O157:H7, Francisella tularensis subsp. tularensis, Francisella tularensis subsp. novicida, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis, and Yersinia pseudotuberculosis. Previously, we identified highly specific primers targeting each of these pathogens. Here, we report the development of customizable PCR-microplate arrays for simultaneous identification of the pathogens using the primers identified. A mixed aliquot of genomic DNA from 38 strains was used to validate three PCR-microplate array formats. Identical PCR conditions were used to run all the samples on the three formats. Specific amplifications were obtained on all three custom plates. In preliminary tests performed to evaluate the sensitivity of these assays in samples inoculated in the laboratory with Salmonella Typhimurium, amplifications were obtained from 1 g of beef hot dog inoculated at as low as 9 CFU/ml or from milk inoculated at as low as 78 CFU/ml. Such microplate arrays could be valuable tools for initial identification or secondary confirmation of contamination by these pathogens.

The “Flexi-Chamber”: A Novel Cost-Effective In Situ Respirometry Chamber for Coral Physiological Measurements

Science.gov (United States)

Camp, Emma F.; Krause, Sophie-Louise; Santos, Lourianne M. F.; Naumann, Malik S.; Kikuchi, Ruy K. P.; Smith, David J.; Wild, Christian; Suggett, David J.

2015-01-01

Coral reefs are threatened worldwide, with environmental stressors increasingly affecting the ability of reef-building corals to sustain growth from calcification (G), photosynthesis (P) and respiration (R). These processes support the foundation of coral reefs by directly influencing biogeochemical nutrient cycles and complex ecological interactions and therefore represent key knowledge required for effective reef management. However, metabolic rates are not trivial to quantify and typically rely on the use of cumbersome in situ respirometry chambers and/or the need to remove material and examine ex situ, thereby fundamentally limiting the scale, resolution and possibly the accuracy of the rate data. Here we describe a novel low-cost in situ respirometry bag that mitigates many constraints of traditional glass and plexi-glass incubation chambers. We subsequently demonstrate the effectiveness of our novel “Flexi-Chamber” approach via two case studies: 1) the Flexi-Chamber provides values of P, R and G for the reef-building coral Siderastrea cf. stellata collected from reefs close to Salvador, Brazil, which were statistically similar to values collected from a traditional glass respirometry vessel; and 2) wide-scale application of obtaining P, R and G rates for different species across different habitats to obtain inter- and intra-species differences. Our novel cost-effective design allows us to increase sampling scale of metabolic rate measurements in situ without the need for destructive sampling and thus significantly expands on existing research potential, not only for corals as we have demonstrated here, but also other important benthic groups. PMID:26448294

Analytical determination of size-dependent natural frequencies of fully clamped rectangular microplates based on the modified couple stress theory

Energy Technology Data Exchange (ETDEWEB)

Askari, Amir R.; Tahani, Masoud [Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of)

2015-05-15

This paper presents an analytical and size-dependent model for vibrational analysis of fully clamped rectangular microplates. Modified couple stress theory (MCST) and the Kirchhoff plate model are considered, and Hamilton's principle is employed to derive the size dependent equation of motion that accounts for the effect of residual stresses. The natural frequencies of the microplate are extracted analytically by extended Kantorovich method. The present findings are validated with the available results in the literature, and an excellent agreement is observed between them. In addition, a parametric study is conducted to demonstrate the significant effects of couple stress components on the natural frequencies of fully clamped microplates. The ratio of MCST natural frequencies to those obtained with classical theory depends only on the Poisson's ratio of the plate and is independent of the aspect ratio of the plate for cases with no residual stresses.

Analytical determination of size-dependent natural frequencies of fully clamped rectangular microplates based on the modified couple stress theory

International Nuclear Information System (INIS)

Askari, Amir R.; Tahani, Masoud

2015-01-01

This paper presents an analytical and size-dependent model for vibrational analysis of fully clamped rectangular microplates. Modified couple stress theory (MCST) and the Kirchhoff plate model are considered, and Hamilton's principle is employed to derive the size dependent equation of motion that accounts for the effect of residual stresses. The natural frequencies of the microplate are extracted analytically by extended Kantorovich method. The present findings are validated with the available results in the literature, and an excellent agreement is observed between them. In addition, a parametric study is conducted to demonstrate the significant effects of couple stress components on the natural frequencies of fully clamped microplates. The ratio of MCST natural frequencies to those obtained with classical theory depends only on the Poisson's ratio of the plate and is independent of the aspect ratio of the plate for cases with no residual stresses.

Euler-Vector Clustering of GPS Velocities Defines Microplate Geometry in Southwest Japan

Science.gov (United States)

Savage, J. C.

2018-02-01

I have used Euler-vector clustering to assign 469 GEONET stations in southwest Japan to k clusters (k = 2, 3,..., 9) so that, for any k, the velocities of stations within each cluster are most consistent with rigid-block motion on a sphere. That is, I attempt to explain the raw (i.e., uncorrected for strain accumulation), 1996-2006 velocities of those 469 Global Positioning System stations by rigid motion of k clusters on the surface of a spherical Earth. Because block geometry is maintained as strain accumulates, Euler-vector clustering may better approximate the block geometry than the values of the associated Euler vectors. The microplate solution for each k is constructed by merging contiguous clusters that have closely similar Euler vectors. The best solution consists of three microplates arranged along the Nankaido Trough-Ryukyu Trench between the Amurian and Philippine Sea Plates. One of these microplates, the South Kyushu Microplate (an extension of the Ryukyu forearc into the southeast corner of Kyushu), had previously been identified from paleomagnetic rotations. Relative to ITRF2000 the three microplates rotate at different rates about neighboring poles located close to the northwest corner of Shikoku. The microplate model is identical to that proposed in the block model of Wallace et al. (2009, https://doi.org/10.1130/G2522A.1) except in southernmost Kyushu. On Shikoku and Honshu, but not Kyushu, the microplate model is consistent with that proposed in the block models of Nishimura and Hashimoto (2006, https://doi.org/10.1016/j.tecto.2006.04.017) and Loveless and Meade (2010, https://doi.org/10.1029/2008JB006248) without the low-slip-rate boundaries proposed in the latter.

An investigation of the static and dynamic behavior of electrically actuated rectangular microplates

KAUST Repository

Saghir, S.

2016-06-16

We present an investigation of the static and dynamic behavior of the nonlinear von-Karman plates when actuated by the nonlinear electrostatic forces. The investigation is based on a reduced order model developed using the Galerkin method, which rely on modeshapes and in-plane shape functions extracted using a finite element method. In this study, a fully clamped microplate is considered. We investigate the static behavior and the effect of different non-dimensional design parameters. The static results are validated by comparison with the results calculated by a finite element model. The forced-vibration response of the plate is then investigated when the plate is excited by a harmonic AC load superimposed to a DC load. The dynamic behavior is examined near the primary and secondary (superharmonic and subharmonic) resonances. The microplate shows a strong hardening behavior due to the cubic nonlinearity of mid-plane stretching. However, the behavior switches to softening as the DC load is increased. Finally, near-square plates are studied to understand the effect of geometric imperfections of microplates.

An investigation of the static and dynamic behavior of electrically actuated rectangular microplates

KAUST Repository

Saghir, Shahid; Younis, Mohammad I.

2016-01-01

We present an investigation of the static and dynamic behavior of the nonlinear von-Karman plates when actuated by the nonlinear electrostatic forces. The investigation is based on a reduced order model developed using the Galerkin method, which rely on modeshapes and in-plane shape functions extracted using a finite element method. In this study, a fully clamped microplate is considered. We investigate the static behavior and the effect of different non-dimensional design parameters. The static results are validated by comparison with the results calculated by a finite element model. The forced-vibration response of the plate is then investigated when the plate is excited by a harmonic AC load superimposed to a DC load. The dynamic behavior is examined near the primary and secondary (superharmonic and subharmonic) resonances. The microplate shows a strong hardening behavior due to the cubic nonlinearity of mid-plane stretching. However, the behavior switches to softening as the DC load is increased. Finally, near-square plates are studied to understand the effect of geometric imperfections of microplates.

Reliability of maximal mitochondrial oxidative phosphorylation in permeabilized fibers from the vastus lateralis employing high-resolution respirometry

DEFF Research Database (Denmark)

Cardinale, Daniele A; Gejl, Kasper D; Ørtenblad, Niels

2018-01-01

The purpose was to assess the impact of various factors on methodological errors associated with measurement of maximal oxidative phosphorylation (OXPHOS) in human skeletal muscle determined by high-resolution respirometry in saponin-permeabilized fibers. Biopsies were collected from 25 men...

Micro-plate radiobinding assay of autoantibody to glutamic acid decarboxylase

International Nuclear Information System (INIS)

Huang Gan; Jin Helai; Wang Xia; Li Hui; Zhang Song; Zhou Zhiguang

2008-01-01

Objective: The purpose of this study was to develop a high-throughput micro-plate radiobinding assay (RBA) of glutamic acid decarboxylase antibody (CAD-Ab) and to evaluate its clinical application. Methods: 35 S labeled GAD 65 antigen was incubated with sera for 24 h on a 96-well plate, and then transferred to the Millipore plate coated with protein A, which was washed with 4 degree C PBS buffer, and then counted by a liquid scintillation counter. The CAD-Ab results were expressed by WHO standard unit (U/ml). A total of 224 healthy controls, 162 patients with type 1 diabetes mellitus (T1DM) and 210 patients with newly diagnosed type 2 diabetes (T2DM) were recruited. A total of 119 T1DM and healthy eases with gradually changing GAD-Ab levels were selected to compare the consistency of micro-plate RBA with conventional radioligand assay (RLA). Blood samples were obtained from the peripheral vein and finger tip in 32 healthy controls, 35 T1DM and 24 T2DM patients, and tested with micro-plate RBA and then compared with the conventional RLA to investigate the reliability of finger tip sampling. Linear correlation, student's t-test, variance analysis and receiver operating characteristic (ROC) curve were performed using SPSS 11.5. Results: (1) The optimized conditions of micro-plate RBA included 2 μl serum incubated with 3 x 10 4 counts/min 35 S-CAD for 24 h under slow vibration, antigen-antibody compounds washed 10 times by 4 degree C PBS buffer, and radioactivity counted with Optiphase Supermix scintillation liquid. (2)The intra-batch CV of the micro-plate RBA was 3.8%-10.2%, and the inter-batch CV was 5.6%-11.9%. The linearity analysis showed a good correlation when the GAD-Ab in serum samples ranged from 40.3 to 664 U/ml and the detection limit of measurement was 3.6 U/ml. The results from Diabetes Autoantibody Standardization Program (DASP) 2005 showed that the sensitivity and specificity for GAD-Ab were 78% (39 positive among 50 new-onset T1DM) and 98% (2 positive

Correction of Microplate Data from High-Throughput Screening.

Science.gov (United States)

Wang, Yuhong; Huang, Ruili

2016-01-01

High-throughput screening (HTS) makes it possible to collect cellular response data from a large number of cell lines and small molecules in a timely and cost-effective manner. The errors and noises in the microplate-formatted data from HTS have unique characteristics, and they can be generally grouped into three categories: run-wise (temporal, multiple plates), plate-wise (background pattern, single plate), and well-wise (single well). In this chapter, we describe a systematic solution for identifying and correcting such errors and noises, mainly basing on pattern recognition and digital signal processing technologies.

Application of 60Co γ-ray irradiated polystyrene microplate for anti-HCV ELISA

International Nuclear Information System (INIS)

Feng Bo; Zeng Hongyan; Tang Yufang; Wang Lu

2005-01-01

In order to explore the effect of 60 Co γ-ray irradiation on minor polypeptides absorption of polystyrene microplate, an indirect ELISA detection of anti-HCV was established, 60 Co γ-ray irradiated polystyrene microplates and the controls (without irradiation or UV-irradiated) were applied to absorb recombinant HCV antigens respectively. Cooperated with Bovine antihuman IgG labelled HRP, their related indices of sensitivity, specificity, homogeneity and stability were determinate. The results indicated that, optimum dose of the γ-ray irradiation is 8 kGy, and compared with the controls, detection sensitivity and homogeneity of the polystyrene microplate irradiated to 8 kGy could be improved markedly. (authors)

Microplate-compatible total internal reflection fluorescence microscopy for receptor pharmacology

Science.gov (United States)

Chen, Minghan; Zaytseva, Natalya V.; Wu, Qi; Li, Min; Fang, Ye

2013-05-01

We report the use of total internal reflection fluorescence (TIRF) microscopy for analyzing receptor pharmacology and the development of a microplate-compatible TIRF imaging system. Using stably expressed green fluorescence protein tagged β2-adrenergic receptor as the reporter, we found that the activation of different receptors results in distinct kinetic signatures of the TIRF intensity of cells. These TIRF signatures closely resemble the characteristics of their respective label-free dynamic mass redistribution signals in the same cells. This suggests that TIRF in microplate can be used for profiling and screening drugs.

Coupling HPLC-SPE-NMR with a microplate-based high-resolution antioxidant assay for efficient analysis of antioxidants in food--validation and proof-of-concept study with caper buds.

Science.gov (United States)

Wiese, Stefanie; Wubshet, Sileshi G; Nielsen, John; Staerk, Dan

2013-12-15

This work describes the coupling of a microplate-based antioxidant assay with a hyphenated system consisting of high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy, i.e., HPLC-SPE-NMR/high-resolution antioxidant assay, for the analysis of complex food extracts. The applicability of the microplate-based antioxidant assay for high-resolution screening of common food phenolics as well as parameters related to their trapping efficiency, elution behavior, and recovery on/from SPE cartridges are described. It was found that the microplate-based high-resolution antioxidant assay is an attractive and easy implementable alternative to direct on-line screening methods. Furthermore, it was shown that Resin SH and Resin GP SPE material are superior to RP C18HD for trapping of phenolic compounds. Proof-of-concept study was performed with caper bud extract, revealing the most important antioxidants to be quercetin, kaempferol, rutin, kaempferol-3-O-β-rutinoside and N(1),N(5),N(10)-triphenylpropenoyl spermidine amides. Targeted isolation of the latter, and comprehensive NMR experiments showed them to be N(1),N(10)-di-(E)-caffeoyl-N(5)-p-(E)-coumaroyl spermidine, N(1)-(E)-caffeoyl-N(5),N(10)-di-p-(E)-coumaroyl spermidine, N(10)-(E)-caffeoyl-N(1),N(5)-di-p-(E)-coumaroyl spermidine, and N(1),N(5),N(10)-tri-p-(E)-coumaroyl spermidine amides. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mitochondrial Stress Tests Using Seahorse Respirometry on Intact Dictyostelium discoideum Cells.

Science.gov (United States)

Lay, Sui; Sanislav, Oana; Annesley, Sarah J; Fisher, Paul R

2016-01-01

Mitochondria not only play a critical and central role in providing metabolic energy to the cell but are also integral to the other cellular processes such as modulation of various signaling pathways. These pathways affect many aspects of cell physiology, including cell movement, growth, division, differentiation, and death. Mitochondrial dysfunction which affects mitochondrial bioenergetics and causes oxidative phosphorylation defects can thus lead to altered cellular physiology and manifest in disease. The assessment of the mitochondrial bioenergetics can thus provide valuable insights into the physiological state, and the alterations to the state of the cells. Here, we describe a method to successfully use the Seahorse XF(e)24 Extracellular Flux Analyzer to assess the mitochondrial respirometry of the cellular slime mold Dictyostelium discoideum.

Application of microplate spectrophotometer in determination of apparent amylose content and mutant selection in rice

International Nuclear Information System (INIS)

Zhu Xiaoyang; Shen Shengquan; Chen Wenyue; Shu Qingyao

2004-01-01

The application of automatic microplate spectrophotometer (SpectraMax 190, Sunnyvale, USA) was investigated for measurement of apparent amylose content (AAC) of rice grains. By using five rice varieties (IR24, Iri371, Z413, KMD1 and Xiushui 11), a microplate spectrophotometer-facilitated AAC measurement system was established with similar accuracy to that of standard protocol (NY147-88). In this system, sample was treated as NY147-88, but directly stained in a microplate and the OD values of each sample were determined by a microplate spectrophotometer. A regression equation was established by using the AAC and OD value of standard samples, and the AAC of test samples were estimated by using the equation. The system is simple, accurate and high-throughput. By using this system, about 1500 progenies of M 3 seeds (harvested from individual M 2 plants) were screened for putative AAC mutants, from which one mutant line ZXY16 was developed with a middle AAC of about 16%

Initially curved microplates under electrostatic actuation: theory and experiment

KAUST Repository

Saghir, Shahid; Bellaredj, Mohammed Lamine Faycal; Ramini, Abdallah; Younis, Mohammad I.

2016-01-01

Microplates are the building blocks of many micro-electro-mechanical systems. It is common for them to experience initial curvature imperfection due to residual stresses caused by the micro fabrication process. Such plates are essentially different

Establishment and validation of a method for multi-dose irradiation of cells in 96-well microplates

International Nuclear Information System (INIS)

Abatzoglou, Ioannis; Zois, Christos E.; Pouliliou, Stamatia; Koukourakis, Michael I.

2013-01-01

Highlights: ► We established a method for multi-dose irradiation of cell cultures within a 96-well plate. ► Equations to adjust to preferable dose levels are produced and provided. ► Up to eight different dose levels can be tested in one microplate. ► This method results in fast and reliable estimation of radiation dose–response curves. -- Abstract: Microplates are useful tools in chemistry, biotechnology and molecular biology. In radiobiology research, these can be also applied to assess the effect of a certain radiation dose delivered to the whole microplate, to test radio-sensitivity, radio-sensitization or radio-protection. Whether different radiation doses can be accurately applied to a single 96-well plate to further facilitate and accelerated research by one hand and spare funds on the other, is a question dealt in the current paper. Following repeated ion-chamber, TLD and radiotherapy planning dosimetry we established a method for multi-dose irradiation of cell cultures within a 96-well plate, which allows an accurate delivery of desired doses in sequential columns of the microplate. Up to eight different dose levels can be tested in one microplate. This method results in fast and reliable estimation of radiation dose–response curves

Investigation of the nonlinear static and dynamic behaviour of rectangular microplates under electrostatic actuation

KAUST Repository

Saghir, Shahid; Younis, Mohammad I.

2016-01-01

We present an investigation of the static and dynamic behavior of the nonlinear von-Karman plates when actuated by the nonlinear electrostatic forces. The investigation is based on a reduced order model developed using the Galerkin method, which rely on modeshapes and in-plane shape functions extracted using a finite element method. In this study, a fully clamped microplate is considered. We investigate the static behavior and the results are validated by comparison with the results calculated by a finite element model. The forced-vibration response of the plate is then investigated when the plate is excited by a harmonic AC load superimposed to a DC load. The dynamic behavior is examined near the primary resonance. The microplate shows a strong hardening behavior due to the cubic nonlinearity of mid-plane stretching. However, the behavior switches to softening as the DC load is increased.

Investigation of the nonlinear static and dynamic behaviour of rectangular microplates under electrostatic actuation

KAUST Repository

Saghir, Shahid

2016-11-16

We present an investigation of the static and dynamic behavior of the nonlinear von-Karman plates when actuated by the nonlinear electrostatic forces. The investigation is based on a reduced order model developed using the Galerkin method, which rely on modeshapes and in-plane shape functions extracted using a finite element method. In this study, a fully clamped microplate is considered. We investigate the static behavior and the results are validated by comparison with the results calculated by a finite element model. The forced-vibration response of the plate is then investigated when the plate is excited by a harmonic AC load superimposed to a DC load. The dynamic behavior is examined near the primary resonance. The microplate shows a strong hardening behavior due to the cubic nonlinearity of mid-plane stretching. However, the behavior switches to softening as the DC load is increased.

Initially Imperfect MEMS Microplates Under Electrostatic Actuation: Theory and Experiment

KAUST Repository

Saghir, Shahid; Bellaredj, Mohammed Lamine Faycal; Younis, Mohammad I.

2016-01-01

Microplates are building blocks of many Micro-Electro-Mechanical Systems (MEMS). It is common for them to undergo imperfections due to residual stresses caused by the micro fabrication process. Such plates are essentially different from perfectly

Presencia de microplásticos en cuatro playas arenosas de Perú

OpenAIRE

Purca, Sara; Henostroza, Aida

2017-01-01

Se presenta el número y peso por metro cuadrado de fragmentos de microplásticos presentes en cuatro playas arenosas de la costa peruana. Las muestras fueron colectadas entre junio de 2014 y mayo 2015. Fragmentos de plástico duro mayores a 1 mm fueron encontrados en más del 80% de las muestras de las cuatro playas. La playa Costa Azul (~ 12°S) presentó 522 fragmentos por metro cuadrado (items/m2) de microplásticos, de los cuales, 463.33 items/m2 y 2.6 g/m2 fueron plásticos duros. La playa Albú...

Synthesis and structure of large single crystalline silver hexagonal microplates suitable for micromachining

Energy Technology Data Exchange (ETDEWEB)

Lyutov, Dimitar L.; Genkov, Kaloyan V.; Zyapkov, Anton D.; Tsutsumanova, Gichka G.; Tzonev, Atanas N. [Department of Solid State Physics and Microelectronics, Faculty of Physics, University of Sofia, 5, J. Bouchier Blvd, Sofia (Bulgaria); Lyutov, Lyudmil G. [Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Sofia, 1, J. Bouchier Blvd, Sofia (Bulgaria); Russev, Stoyan C., E-mail: scr@phys.uni-sofia.bg [Department of Solid State Physics and Microelectronics, Faculty of Physics, University of Sofia, 5, J. Bouchier Blvd, Sofia (Bulgaria)

2014-01-15

We report a simple one-step synthesis method of large single crystalline Ag (111) hexagonal microplates with sharp edges and a size of up to tens of microns. Single silver crystals were produced by reduction silver nitrate aqueous solution with 4-(methylamino)phenol sulfate. Scanning and transmission electron microscopy, energy-dispersive X-ray spectroscopy, selected area electron diffraction and optical microscopy techniques were combined to characterize the crystals. It is shown that the microplates can be easily dispersed and transferred as single objects onto different substrates and subsequently used as a high quality plasmonic starting material for micromachining of future nanocomponents, using modern top-down techniques like focused-ion beam milling and gas injection deposition. - Highlights: • Synthesis of large Ag hexagonal microplates with high crystallinity. • It is shown and discussed the role of twinning for the anisotropic 2D growth. • The Ag plates are stable in water and can be dispersed onto different substrates. • Their positioning and subsequent micromachining with FIB/GIS is demonstrated. • Suitable starting material for future plasmonic nanocomponents.

High resolution respirometry analysis of polyethylenimine-mediated mitochondrial energy crisis and cellular stress

DEFF Research Database (Denmark)

Hall, Arnaldur; Larsen, Anna Karina; Parhamifar, Ladan

2013-01-01

and spectrophotometry analysis of cytochrome c oxidase activity we were able to identify complex IV (cytochrome c oxidase) as a likely specific site of PEI mediated inhibition within the electron transport system. Unraveling the mechanisms of PEI-mediated mitochondrial energy crisis is central for combinatorial design...... of PEI-mediated plasma membrane damage and subsequent ATP leakage to the extracellular medium. Studies with freshly isolated mouse liver mitochondria corroborated with bioenergetic findings and demonstrated parallel polycation concentration- and time-dependent changes in state 2 and state 4o oxygen flux...... as well as lowered ADP phosphorylation (state 3) and mitochondrial ATP synthesis. Polycation-mediated reduction of electron transport system activity was further demonstrated in 'broken mitochondria' (freeze-thawed mitochondrial preparations). Moreover, by using both high-resolution respirometry...

Anaerobic microplate assay for direct microbial conversion of switchgrass and Avicel using Clostridium thermocellum

Energy Technology Data Exchange (ETDEWEB)

Oguntimein, Gbekeloluwa B. [Morgan State Univ., Baltimore, MD (United States); Rodriguez, Jr., Miguel [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Lab., Oak Ridge, TN (United States). BioEnergy Science Center; Dumitrache, Alexandru [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Lab., Oak Ridge, TN (United States). BioEnergy Science Center; Shollenberger, Todd [National Renewable Energy Lab. (NREL), Golden, CO (United States); Decker, Stephen R. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Davison, Brian H. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Lab., Oak Ridge, TN (United States). BioEnergy Science Center; Brown, Steven D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Lab., Oak Ridge, TN (United States). BioEnergy Science Center; LanzaTech, Inc., Skokie, IL (United States)

2017-11-09

Here, to develop and prototype a high-throughput microplate assay to assess anaerobic microorganisms and lignocellulosic biomasses in a rapid, cost-effective screen for consolidated bioprocessing potential. Clostridium thermocellum parent Δhpt strain deconstructed Avicel to cellobiose, glucose, and generated lactic acid, formic acid, acetic acid and ethanol as fermentation products in titers and ratios similar to larger scale fermentations confirming the suitability of a plate-based method for C. thermocellum growth studies. C. thermocellum strain LL1210, with gene deletions in the key central metabolic pathways, produced higher ethanol titers in the Consolidated Bioprocessing (CBP) plate assay for both Avicel and switchgrass fermentations when compared to the Δhpt strain. A prototype microplate assay system is developed that will facilitate high-throughput bioprospecting for new lignocellulosic biomass types, genetic variants and new microbial strains for bioethanol production.

Approaches for Reduced Order Modeling of Electrically Actuated von Karman Microplates

KAUST Repository

Saghir, Shahid; Younis, Mohammad I.

2016-01-01

and dynamic behavior of the plate under small and large actuation forces. A fully clamped microplate is considered. Different types of basis functions are used in conjunction with the Galerkin method to discretize the governing equations. First we investigate

Microplate Ames MPF™ test use in assessment of mutagenic properties of dust pollution

Directory of Open Access Journals (Sweden)

Agnieszka Kozłowska

2012-09-01

Full Text Available Background: Highly industrialized Upper Silesia Region is particularly polluted by both anthropogenic and natural airborne particulate matters, which may lead to negative health effects in human. Materials and methods: The aim of the study was to assess the mutagenic properties of dust extracts which were collected in six cities in the Silesian Voivodeship. Dust samples were collected on glass fiber filters by the aspirator with air flow ca. 1 m3/min. Extraction of pollution was carried out using dichlorometane. The extracted samples were dissolved in dimethylsulfoxide (DMSO. The mutagenic properties were assessed using microplate Ames assay MPFTM with the use of bacteria Salmonella typhimurium strain TA98 and TA100. Results: In microplate Ames assay MPFTM there was observed a linear dose-response relationship in both metabolic variants of TA98 strain. Similar relationship was observed for TA100 strain with metabolic activation (S9. Mutagenic activity (AM of 100% extracts for TA98 strain in both metabolic variants (S9 exceeded 2, what indicate highly mutagenic effects of dust extracts. There was no mutagenic activity observed in the assay with TA100 (S9, AM 1. In the variant with exogenous metabolic activation (S9 in TA100 strain AM values ranged from AM1,160,15 to AM9,671,02. Mutagenic activity varied between different cities. Conclusions: The study demonstrated that microplate Ames assay MPFTM is fast and complex method of assessing the mutagenic properties of dust pollution, which exert toxic effect on organisms. The use of microplate Ames assay MPFTM together with chemical analyses of air dust pollution may evaluate the level of exposure in the environment and enable to perform health risk assessment in populations exposed to mutagenic, toxic and cytotoxic substances.

Microplate Bioassay for Determining Substrate Selectivity of "Candida rugosa" Lipase

Science.gov (United States)

Wang, Shi-zhen; Fang, Bai-shan

2012-01-01

Substrate selectivity of "Candida rugosa" lipase was tested using "p"-nitrophenyl esters of increasing chain length (C[subscript 1], C[subscript 7], C[subscript 15]) using the high-throughput screening method. A fast and easy 96-well microplate bioassay was developed to help students learn and practice biotechnological specificity screen. The…

Visual and microplate detection of aflatoxin B2 based on NaCl-induced aggregation of aptamer-modified gold nanoparticles

International Nuclear Information System (INIS)

Luan, Yunxia; Chen, Jiayi; Li, Cheng; Ping, Hua; Ma, Zhihong; Lu, Anxiang; Xie, Gang

2015-01-01

We describe a fast and sensitive method for the detection of aflatoxin B2 (AFB2) that is based on the addition of AFB2-sensitive aptamers to a colloidal solution of gold nanoparticles (AuNPs). Subsequent addition of AFB2 and NaCl to the solution causes a color change from wine-red to blue-purple. Best results are obtained at a pH value of 7.0, a 10 mM aptamer concentration, and a 2 M concentration of NaCl. The method has a linear dynamic range that extends from 0.025 to 10 ng∙mL −1 of AFB2, and the detection limit is 25 pg∙mL −1 . The method is simple, fast, highly sensitive, and enables both visual and microplate readout. (author)

Variabilidad en la eliminación de metales pesados en aguas residuales debido a contaminación por microplásticos

OpenAIRE

Muñoz Cava, José Angel

2016-01-01

Abordamos el tema de los microplásticos contenidos en las cremas cosméticas, en un estudio que tiene como fin el comportamiento de esos microplásticos en presencia de aguas residuales. Estos pueden producir procesos de adsorción de posibles metales pesados contenidos en dichas aguas, pudiendo ser una vía de conducción de las mismas hasta diversos seres vivos llegando incluso a mamíferos de grandes dimensiones. Estos tipos de microplásticos se han incrementado en los últimos años, ya que la...

Impact of electrochemical treatment of soil washing solution on PAH degradation efficiency and soil respirometry

International Nuclear Information System (INIS)

Mousset, Emmanuel; Huguenot, David; Hullebusch, Eric D. van; Oturan, Nihal; Guibaud, Gilles; Esposito, Giovanni; Oturan, Mehmet A.

2016-01-01

The remediation of a genuinely PAH-contaminated soil was performed, for the first time, through a new and complete investigation, including PAH extraction followed by advanced oxidation treatment of the washing solution and its recirculation, and an analysis of the impact of the PAH extraction on soil respirometry. The study has been performed on the remediation of genuine PAH-contaminated soil, in the following three steps: (i) PAH extraction with soil washing (SW) techniques, (ii) PAH degradation with an electro-Fenton (EF) process, and (iii) recirculation of the partially oxidized effluent for another SW cycle. The following criteria were monitored during the successive washing cycles: PAH extraction efficiency, PAH oxidation rates and yields, extracting agent recovery, soil microbial activity, and pH of soil. Two representative extracting agents were compared: hydroxypropyl-beta-cyclodextrin (HPCD) and a non-ionic surfactant, Tween"® 80. Six PAH with different numbers of rings were monitored: acenaphthene (ACE), phenanthrene (PHE), fluoranthene (FLA), pyrene (PYR), benzo(a)pyrene (BaP), and benzo(g,h,i)perylene (BghiP). Tween"® 80 showed much better PAH extraction efficiency (after several SW cycles) than HPCD, regardless of the number of washing cycles. Based on successive SW experiments, a new mathematical relation taking into account the soil/water partition coefficient (Kd*) was established, and could predict the amount of each PAH extracted by the surfactant with a good correlation with experimental results (R"2 > 0.975). More HPCD was recovered (89%) than Tween"® 80 (79%), while the monitored pollutants were completely degraded (>99%) after 4 h and 8 h, respectively. Even after being washed with partially oxidized solutions, the Tween"® 80 solutions extracted significantly more PAH than HPCD and promoted better soil microbial activity, with higher oxygen consumption rates. Moreover, neither the oxidation by-products nor the acidic media (p

Enterococcus faecalis Infection Causes Inflammation, Intracellular Oxphos-Independent ROS Production, and DNA Damage in Human Gastric Cancer Cells

DEFF Research Database (Denmark)

Strickertsson, Jesper A. B; Desler, Claus; Martin-Bertelsen, Tomas

2013-01-01

Background Achlorhydria caused by e.g. atrophic gastritis allows for bacterial overgrowth, which induces chronic inflammation and damage to the mucosal cells of infected individuals driving gastric malignancies and cancer. Enterococcus faecalis (E. faecalis) can colonize achlohydric stomachs and we...... therefore wanted to study the impact of E. faecalis infection on inflammatory response, reactive oxygen species (ROS) formation, mitochondrial respiration, and mitochondrial genetic stability in gastric mucosal cells. Methods To separate the changes induced by bacteria from those of the inflammatory cells...... we established an in vitro E. faecalis infection model system using the gastric carcinoma cell line MKN74. Total ROS and superoxide was measured by fluorescence microscopy. Cellular oxygen consumption was characterized non-invasively using XF24 microplate based respirometry. Gene expression...

The use of a single titanium microplate in displaced pediatric parasymphysial mandibular fractures.

Science.gov (United States)

Abdullah, Walid A

2009-07-01

The objective of this study was to evaluate the use of one titanium microplate in the fixation of displaced pediatric parasymphysial mandibular fractures. The study was conducted on 7 children in the mixed dentition stage with displaced parasymphysial fracture. Patients' age ranged between 5 years 9 months and 8 years 4 months with an average of 7 years 1 month. Fractured bone segments were exposed, reduced and then fixed using 1.5 linear microplates at the inferior border of the mandible using monocortical screws, with 1.5 mm in diameter and 5 mm in length. Stainless steel wire was used as a tension band by ligating the teeth around the fracture line. Patients were followed up for occlusion and stability clinically and radiographically (panoramic X-ray and CT). According to clinical and radiographic post-operative follow-up, none of the patients showed displacement of the fixed bony segments. The present study concluded that using one microplate with 1.5 monocortical microscrews and dental tension band by a stainless steel wire could be adequate for fixing displaced pediatric parasymphysial mandibular fractures. This technique has the following advantages: decreases the amount of titanium used, decreases the risk of injury of the roots and teeth buds, and decreases the cost and time of surgery.

Evaluation of Biostimulation (Nutrients) in hydrocarbons contaminated soils by respirometry

International Nuclear Information System (INIS)

Garcia, Erika; Roldan, Fabio; Garzon, Laura

2011-01-01

The biostimulation process was evaluated in a hydrocarbon contaminated soil by respirometry after amendment with inorganic compound fertilizer (ICF) (N: P: K 28:12:7) and simple inorganic salts (SIS) (NH 4 NO 3 and K 2 HPO 4 ). The soil was contaminated with oily sludge (40.000 MgTPH/Kgdw). The oxygen uptake was measured using two respirometers (HACH 2173b and OXITOP PF 600) during thirteen days (n=3). Two treatments (ICF and SIS) and three controls (abiotic, reference substance and without nutrients) were evaluated during the study. Physicochemical (pH, nutrients, and TPH) and microbiological analysis (heterotrophic and hydrocarbon-utilizing microorganisms) were obtained at the beginning and at the end of each assay. Higher respiration rates were recorded in sis and without nutrient control. Results were 802.28 and 850.72- 1 d-1, MgO 2 kgps - 1d i n HACH, while in OXITOP were 936.65 and 502.05 MgO 2 Kgps respectively. These data indicate that amendment of nutrients stimulated microbial metabolism. ICF had lower respiration rates (188.18 and 139.87 MgO 2 kgps - 1d - 1 i n HACH and OXITOP, respectively) as well as counts; this could be attributed to ammonia toxicity.

HNO₃-assisted polyol synthesis of ultralarge single-crystalline Ag microplates and their far propagation length of surface plasmon polariton.

Science.gov (United States)

Chang, Cheng-Wei; Lin, Fan-Cheng; Chiu, Chun-Ya; Su, Chung-Yi; Huang, Jer-Shing; Perng, Tsong-Pyng; Yen, Ta-Jen

2014-07-23

We developed a HNO3-assisted polyol reduction method to synthesize ultralarge single-crystalline Ag microplates routinely. The edge length of the synthesized Ag microplates reaches 50 μm, and their top facets are (111). The mechanism for dramatically enlarging single-crystalline Ag structure stems from a series of competitive anisotropic growths, primarily governed by carefully tuning the adsorption of Ag(0) by ethylene glycol and the desorption of Ag(0) by a cyanide ion on Ag(100). Finally, we measured the propagation length of surface plasmon polaritons along the air/Ag interface under 534 nm laser excitation. Our single-crystalline Ag microplate exhibited a propagation length (11.22 μm) considerably greater than that of the conventional E-gun deposited Ag thin film (5.27 μm).

Free vibration and biaxial buckling analysis of magneto-electro-elastic microplate resting on visco-Pasternak substrate via modified strain gradient theory

Science.gov (United States)

Jamalpoor, A.; Ahmadi-Savadkoohi, A.; Hosseini-Hashemi, Sh

2016-10-01

This paper deals with the theoretical analysis of free vibration and biaxial buckling of magneto-electro-elastic (MEE) microplate resting on Kelvin-Voigt visco-Pasternak foundation and subjected to initial external electric and magnetic potentials, using modified strain gradient theory (MSGT). Kirchhoff plate model and Hamilton’s principle are employed to extract the governing equations of motion. Governing equations were analytically solved to obtain clear closed-form expression for complex natural frequencies and buckling loads using Navier’s approach. Numerical results are presented to reveal variations of natural frequency and buckling load ratio of MEE microplate against different amounts of the length scale parameter, initial external electric and magnetic potentials, aspect ratio, damping and transverse and shear stiffness parameters of the visco-Pasternak foundation, length to thickness ratio, microplate thickness and higher modes. Numerical results of this study illustrate that by increasing thickness-to-material length scale parameter ratio, both natural frequency and buckling load ratio predicted by MSGT and modified couple stress theory are reduced because the non-dimensional length scale parameter tends to decrease the stiffness of structures and make them more flexible. In addition, results show that initial external electric and initial external magnetic potentials have no considerable influence on the buckling load ratio and frequency of MEE microplate as the microplate thickness increases.

Evaluation of the Alexon-Trend ProSpecT Campylobacter Microplate Assay

Science.gov (United States)

Tolcin, Rita; LaSalvia, Margaret M.; Kirkley, Barbara A.; Vetter, Emily A.; Cockerill, Franklin R.; Procop, Gary W.

2000-01-01

We evaluated stool specimens known to contain or be free of Campylobacter by traditional culture, using the ProSpecT Campylobacter microplate assay (Alexon-Trend, Ramsey, Minn.). This rapid enzyme immunoassay for the detection of Campylobacter-specific antigens demonstrated 96% sensitivity and 99% specificity and is an acceptable alternative method of Campylobacter detection. PMID:11015419

Graduated characterization method using a multi-well microplate for reducing reactivity of nanoscale zero valent iron materials

DEFF Research Database (Denmark)

Hwang, Yuhoon; Salatas, Apostolos; Mines, Paul D.

2015-01-01

Even though nanoscale zero valent iron (nZVI) has been intensively studied for the treatment of a plethora of pollutants through reductive reaction, quantification of nZVI reactivity has not yet been standardized. Here, we adapted colorimetric assays for determining reductive activity of n...... with different compounds, combined with the use of a multi-well microplate based color assay, promises to be a useful and simple tool in various nZVI related research topics....

Rapid 2,2'-bicinchoninic-based xylanase assay compatible with high throughput screening

Science.gov (United States)

William R. Kenealy; Thomas W. Jeffries

2003-01-01

High-throughput screening requires simple assays that give reliable quantitative results. A microplate assay was developed for reducing sugar analysis that uses a 2,2'-bicinchoninic-based protein reagent. Endo-1,4-â-D-xylanase activity against oat spelt xylan was detected at activities of 0.002 to 0.011 IU ml−1. The assay is linear for sugar...

An investigation of the mechanical behavior of initially curved microplates under electrostatic actuation

KAUST Repository

Saghir, Shahid; Younis, Mohammad I.

2018-01-01

of the microplates are examined and compared. We validate the reduced order model by comparing the calculated static behavior and the fundamental natural frequency with those computed by a finite element model over a range of the initial plate rise. The static

Microplate-reader method for the rapid analysis of copper in natural waters with chemiluminescence detection

Directory of Open Access Journals (Sweden)

Axel eDurand

2013-01-01

Full Text Available We have developed a method for the determination of copper in natural waters at nanomolar levels. The use of a microplate-reader minimises sample processing time (~ 25 sec per sample, reagent consumption (~ 120 μL per sample and sample volume (~ 700 μL. Copper is detected by chemiluminescence. This technique is based on the formation of a complex between copper and 1,10-phenanthroline and the subsequent emission of light during the oxidation of the complex by hydrogen peroxide. Samples are acidified to pH 1.7 and then introduced directly into a 24-well plate. Reagents are added during data acquisition via two reagent injectors. When trace metal clean protocols are employed, the reproducibility is generally less then 7% on blanks and the detection limit is 0.7 nM for seawater and 0.4 nM for freshwater. More than 100 samples per hour can be analyzed with this technique, which is simple, robust, and amenable to at-sea analysis. Seawater samples from Storm Bay in Tasmania illustrate the utility of the method for environmental science. Indeed other trace metals for which optical detection methods exist (e.g. chemiluminescence, fluorescence and absorbance could be adapted to the microplate-reader.

A dynamic regression analysis tool for quantitative assessment of bacterial growth written in Python.

Science.gov (United States)

Hoeflinger, Jennifer L; Hoeflinger, Daniel E; Miller, Michael J

2017-01-01

Herein, an open-source method to generate quantitative bacterial growth data from high-throughput microplate assays is described. The bacterial lag time, maximum specific growth rate, doubling time and delta OD are reported. Our method was validated by carbohydrate utilization of lactobacilli, and visual inspection revealed 94% of regressions were deemed excellent. Copyright © 2016 Elsevier B.V. All rights reserved.

Fabrication of single phase 2D homologous perovskite microplates by mechanical exfoliation

Science.gov (United States)

Li, Junze; Wang, Jun; Zhang, Yingjun; Wang, Haizhen; Lin, Gaoming; Xiong, Xuan; Zhou, Weihang; Luo, Hongmei; Li, Dehui

2018-04-01

The two-dimensional (2D) Ruddlesden-Popper type perovskites have attracted intensive interest for their great environmental stability and various potential optoelectronic applications. Fundamental understanding of the photophysical and electronic properties of the 2D perovskites with pure single phase is essential for improving the performance of the optoelectronic devices and designing devices with new architectures. Investigating the optical and electronic properties of these materials with pure single phase is required to obtain pure single phase 2D perovskites. Here, we report on an alternative approach to fabricate (C4H9NH3)2(CH3NH3) n-1Pb n I3n+1 microplates with pure single n-number perovskite phase for n  >  2 by mechanical exfoliation. Micro-photoluminescence and absorption spectroscopy studies reveal that the as-synthesized 2D perovskite plates for n  >  2 are comprised by dominant n-number phase and small inclusions of hybrid perovskite phases with different n values, which is supported by excitation power dependent photoluminescence. By mechanical exfoliation method, 2D perovskite microplates with the thickness of around 20 nm are obtained, which surprisingly have single n-number perovskite phase for n  =  2-5. In addition, we have demonstrated that the exfoliated 2D perovskite microplates can be integrated with other 2D layered materials such as boron nitride, and are able to be transferred to prefabricated electrodes for photodetections. Our studies not only provide a strategy to prepare 2D perovskites with a single n-number perovskite phase allowing us to extract the basic optical and electronic parameters of pure phase perovskites, but also demonstrate the possibility to integrate the 2D perovskites with other 2D layered materials to extend the device’s functionalities.

Assessing honeybee and wasp thermoregulation and energetics-New insights by combination of flow-through respirometry with infrared thermography

Energy Technology Data Exchange (ETDEWEB)

Stabentheiner, Anton, E-mail: anton.stabentheiner@uni-graz.at [Institut fuer Zoologie, Karl-Franzens-Universitaet Graz, Universitaetsplatz 2, A-8010 Graz (Austria); Kovac, Helmut, E-mail: he.kovac@uni-graz.at [Institut fuer Zoologie, Karl-Franzens-Universitaet Graz, Universitaetsplatz 2, A-8010 Graz (Austria); Hetz, Stefan K. [Department of Animal Physiology/Systems Neurobiology and Neural Computation, Philippstrasse 13-Leonor Michaelis Haus, Humboldt-Universitaet zu Berlin, 10115 Berlin (Germany); Kaefer, Helmut; Stabentheiner, Gabriel [Institut fuer Zoologie, Karl-Franzens-Universitaet Graz, Universitaetsplatz 2, A-8010 Graz (Austria)

2012-04-20

Highlights: Black-Right-Pointing-Pointer We demonstrate the benefits of a combined use of infrared thermography with respiratory measurements in insect ecophysiological research. Black-Right-Pointing-Pointer Infrared thermography enables repeated investigation of behaviour and thermoregulation without behavioural impairment. Black-Right-Pointing-Pointer Comparison with respirometry brings new insights into the mechanisms of energetic optimisation of bee and wasp foraging. Black-Right-Pointing-Pointer Combination of methods improves interpretation of respiratory traces in determinations of insect critical thermal limits. - Abstract: Endothermic insects like honeybees and some wasps have to cope with an enormous heat loss during foraging because of their small body size in comparison to endotherms like mammals and birds. The enormous costs of thermoregulation call for optimisation. Honeybees and wasps differ in their critical thermal maximum, which enables the bees to kill the wasps by heat. We here demonstrate the benefits of a combined use of body temperature measurement with infrared thermography, and respiratory measurements of energy turnover (O{sub 2} consumption or CO{sub 2} production via flow-through respirometry) to answer questions of insect ecophysiological research, and we describe calibrations to receive accurate results. To assess the question of what foraging honeybees optimise, their body temperature was compared with their energy turnover. Honeybees foraging from an artificial flower with unlimited sucrose flow increased body surface temperature and energy turnover with profitability of foraging (sucrose content of the food; 0.5 or 1.5 mol/L). Costs of thermoregulation, however, were rather independent of ambient temperature (13-30 Degree-Sign C). External heat gain by solar radiation was used to increase body temperature. This optimised foraging energetics by increasing suction speed. In determinations of insect respiratory critical thermal limits

Vibration and buckling of orthotropic functionally graded micro-plates on the basis of a re-modified couple stress theory

Directory of Open Access Journals (Sweden)

Zihao Yang

Full Text Available A microstructure-dependent model for the free vibration and buckling analysis of an orthotropic functionally graded micro-plate was proposed on the basis of a re-modified couple stress theory. The macro- and microscopic anisotropy were simultaneously taken into account by introducing two material length scale parameters. The material attributes were assumed to vary continuously through the thickness direction by a power law. The governing equations and corresponding boundary conditions were derived through Hamilton’s principle. The Navier method was used to calculate the natural frequencies and buckling loads of a simply supported micro-plate. The numerical results indicated that the present model predicts higher natural frequencies and critical buckling loads than the classical model, particular when the geometric size of the micro-plates is comparable to the material length scale parameters, i.e., the scale effect is well represented. The scale effect becomes more noticeable as the material length scale parameters increase, the anisotropy weaken or the power law index increases, and vice versa. Keywords: Free vibration, Buckling, Functionally graded materials, Modified couple stress theory, Scale effect

Enzyme activity assay of glycoprotein enzymes based on a boronate affinity molecularly imprinted 96-well microplate.

Science.gov (United States)

Bi, Xiaodong; Liu, Zhen

2014-12-16

Enzyme activity assay is an important method in clinical diagnostics. However, conventional enzyme activity assay suffers from apparent interference from the sample matrix. Herein, we present a new format of enzyme activity assay that can effectively eliminate the effects of the sample matrix. The key is a 96-well microplate modified with molecularly imprinted polymer (MIP) prepared according to a newly proposed method called boronate affinity-based oriented surface imprinting. Alkaline phosphatase (ALP), a glycoprotein enzyme that has been routinely used as an indicator for several diseases in clinical tests, was taken as a representative target enzyme. The prepared MIP exhibited strong affinity toward the template enzyme (with a dissociation constant of 10(-10) M) as well as superb tolerance for interference. Thus, the enzyme molecules in a complicated sample matrix could be specifically captured and cleaned up for enzyme activity assay, which eliminated the interference from the sample matrix. On the other hand, because the boronate affinity MIP could well retain the enzymatic activity of glycoprotein enzymes, the enzyme captured by the MIP was directly used for activity assay. Thus, additional assay time and possible enzyme or activity loss due to an enzyme release step required by other methods were avoided. Assay of ALP in human serum was successfully demonstrated, suggesting a promising prospect of the proposed method in real-world applications.

Eficiência dos testes COPAN (Microplate e Single na detecção de resíduos de antimicrobianos no leite Efficacy of COPAN (Microplate and Single kits in detection of antimicrobials residues in milk

Directory of Open Access Journals (Sweden)

C.G.M.S.C. Tenório

2009-04-01

Full Text Available Avaliou-se a eficiência dos testes microbiológicos COPAN (Microplate e Single para detecção de resíduos de 13 antimicrobianos inoculados em leite isento de resíduos. Foram utilizadas quatro concentrações, sendo a primeira equivalente à metade do limite de detecção declarado pelo fabricante (C1; a segunda equivalente ao limite máximo de resíduos (LMR estabelecido pela legislação brasileira (C2; a terceira equivalente ao limite de detecção declarado pelo fabricante (C3; e a quarta equivalente ao dobro do limite de detecção declarado pelo fabricante (C4. Os testes apresentaram 100% de sensibilidade na detecção de amoxicilina, ampicilina, cloxacilina, penicilina, tilosina, sulfadiazina, sulfametoxazol, e 96,7% na detecção de oxacilina para as concentrações informadas pelo fabricante como limite de detecção. Em relação às concentrações estabelecidas pela legislação brasileira, verificou-se que os testes foram capazes de detectá-las para a maioria dos antimicrobianos avaliados. Os testes não se mostraram eficientes na detecção das concentrações estabelecidas pela legislação para eritromicina, oxitetraciclina, tetraciclina, trimetoprim e gentamicina (Microplate.The efficacy of the microbiological kits COPAN (Microplate and Single for detection of antimicrobials residues was tested. Thirteen drugs were inoculated into milk without residues at four concentration levels: C1 - half of the detection threshold declared by the manufacturer, C2 - the maximum residues threshold established by the Brazilian legislation, C3 - the detection threshold declared by the manufacturer, and C4 - two fold the detection threshold declared by the manufacturer. The tests showed 100% efficient in detection of amoxicillin, cloxacillin, penicillin, tilosin, sulfadiazine, and sulfa methoxazol; and 96.7% for oxacillin considering the concentration stated by the manufacturer as threshold level. Regarding the concentrations established by

High-resolution respirometry of fine-needle muscle biopsies in pre-manifest Huntington's disease expansion mutation carriers shows normal mitochondrial respiratory function.

Directory of Open Access Journals (Sweden)

Eva Buck

Full Text Available Alterations in mitochondrial respiration are an important hallmark of Huntington's disease (HD, one of the most common monogenetic causes of neurodegeneration. The ubiquitous expression of the disease causing mutant huntingtin gene raises the prospect that mitochondrial respiratory deficits can be detected in skeletal muscle. While this tissue is readily accessible in humans, transgenic animal models offer the opportunity to cross-validate findings and allow for comparisons across organs, including the brain. The integrated respiratory chain function of the human vastus lateralis muscle was measured by high-resolution respirometry (HRR in freshly taken fine-needle biopsies from seven pre-manifest HD expansion mutation carriers and nine controls. The respiratory parameters were unaffected. For comparison skeletal muscle isolated from HD knock-in mice (HdhQ111 as well as a broader spectrum of tissues including cortex, liver and heart muscle were examined by HRR. Significant changes of mitochondrial respiration in the HdhQ knock-in mouse model were restricted to the liver and the cortex. Mitochondrial mass as quantified by mitochondrial DNA copy number and citrate synthase activity was stable in murine HD-model tissue compared to control. mRNA levels of key enzymes were determined to characterize mitochondrial metabolic pathways in HdhQ mice. We demonstrated the feasibility to perform high-resolution respirometry measurements from small human HD muscle biopsies. Furthermore, we conclude that alterations in respiratory parameters of pre-manifest human muscle biopsies are rather limited and mirrored by a similar absence of marked alterations in HdhQ skeletal muscle. In contrast, the HdhQ111 murine cortex and liver did show respiratory alterations highlighting the tissue specific nature of mutant huntingtin effects on respiration.

Analysis of regional brain mitochondrial bioenergetics and susceptibility to mitochondrial inhibition utilizing a microplate based system

Science.gov (United States)

Sauerbeck, Andrew; Pandya, Jignesh; Singh, Indrapal; Bittman, Kevin; Readnower, Ryan; Bing, Guoying; Sullivan, Patrick

2012-01-01

The analysis of mitochondrial bioenergetic function typically has required 50–100 μg of protein per sample and at least 15 min per run when utilizing a Clark-type oxygen electrode. In the present work we describe a method utilizing the Seahorse Biosciences XF24 Flux Analyzer for measuring mitochondrial oxygen consumption simultaneously from multiple samples and utilizing only 5 μg of protein per sample. Utilizing this method we have investigated whether regionally based differences exist in mitochondria isolated from the cortex, striatum, hippocampus, and cerebellum. Analysis of basal mitochondrial bioenergetics revealed that minimal differences exist between the cortex, striatum, and hippocampus. However, the cerebellum exhibited significantly slower basal rates of Complex I and Complex II dependent oxygen consumption (p < 0.05). Mitochondrial inhibitors affected enzyme activity proportionally across all samples tested and only small differences existed in the effect of inhibitors on oxygen consumption. Investigation of the effect of rotenone administration on Complex I dependent oxygen consumption revealed that exposure to 10 pM rotenone led to a clear time dependent decrease in oxygen consumption beginning 12 min after administration (p < 0.05). These studies show that the utilization of this microplate based method for analysis of mitochondrial bioenergetics is effective at quantifying oxygen consumption simultaneously from multiple samples. Additionally, these studies indicate that minimal regional differences exist in mitochondria isolated from the cortex, striatum, or hippocampus. Furthermore, utilization of the mitochondrial inhibitors suggests that previous work indicating regionally specific deficits following systemic mitochondrial toxin exposure may not be the result of differences in the individual mitochondria from the affected regions. PMID:21402103

Modelling out-of-plane and in-plane resonant modes of microplates in liquid media

International Nuclear Information System (INIS)

Ruiz-Díez, V; Hernando-García, J; Manzaneque, T; Sánchez-Rojas, J L; Kucera, M; Schmid, U

2015-01-01

In this article, the quality factor and the resonant frequency of different vibrating modes of microplates immersed in liquid are simulated by means of a finite element method (FEM) and compared with experimental data. For the in-plane modes, we studied the first extensional mode of mid-point supported microplates, which may be efficiently actuated by a thin piezoelectric film on top of the structure. A comparison of different approaches to account for the viscous loading in computationally efficient 2D finite element models is presented. As an alternative to the harmonic response, a novel multitone excitation in the fluid–structure interaction model allows for the calculation of the frequency response of the structure. For the out-of-plane modes, different modes were simulated and compared to analytical models to validate our approach. Our 2D FEM model yields more accurate estimations of the experimental resonance frequency and quality factors than the available analytical models. With the help of these tools, the applicability of the micro-resonators as viscosity and density sensors is discussed. (paper)

Distributed Feedback Laser Based on Single Crystal Perovskite

Science.gov (United States)

Sun, Shang; Xiao, Shumin; Song, Qinghai

2017-06-01

We demonstrate a single crystal perovskite based, with grating-structured photoresist on top, highly polarized distributed feedback laser. A lower laser threshold than the Fabry-Perot mode lasers from the same single crystal CH3NH3PbBr3 microplate was obtained. Single crystal CH3NH3PbBr3 microplates was synthesized with one-step solution processed precipitation method. Once the photoresist on top of the microplate was patterned with electron beam, the device was realized. This one-step fabrication process utilized the advantage of single crystal to the greatest extend. The ultra-low defect density in single crystalline microplate offer an opportunity for lower threshold lasing action compare with poly-crystal perovskite films. In the experiment, the lasing action based on the distributed feedback grating design was found with lower threshold and higher intensity than the Fabry-Perot mode lasers supported by the flat facets of the same microplate.

Development, Optimization, and Validation of a Microplate Bioassay for Relative Potency Determination of Linezolid Using a Design Space Concept, and its Measurement Uncertainty.

Science.gov (United States)

Saviano, Alessandro Morais; Francisco, Fabiane Lacerda; Ostronoff, Celina Silva; Lourenço, Felipe Rebello

2015-01-01

The aim of this study was to develop, optimize, and validate a microplate bioassay for relative potency determination of linezolid in pharmaceutical samples using quality-by-design and design space approaches. In addition, a procedure is described for estimating relative potency uncertainty based on microbiological response variability. The influence of culture media composition was studied using a factorial design and a central composite design was adopted to study the influence of inoculum proportion and triphenyltetrazolium chloride in microbial growth. The microplate bioassay was optimized regarding the responses of low, medium, and high doses of linezolid, negative and positive controls, and the slope, intercept, and correlation coefficient of dose-response curves. According to optimization results, design space ranges were established using: (a) low (1.0 μg/mL), medium (2.0 μg/mL), and high (4.0 μg/mL) doses of pharmaceutical samples and linezolid chemical reference substance; (b) Staphylococcus aureus ATCC 653 in an inoculum proportion of 10%; (c) antibiotic No. 3 culture medium pH 7.0±0.1; (d) 6 h incubation at 37.0±0.1ºC; and (e) addition of 50 μL of 0.5% (w/v) triphenyltetrazolium chloride solution. The microplate bioassay was linear (r2=0.992), specific, precise (repeatability RSD=2.3% and intermediate precision RSD=4.3%), accurate (mean recovery=101.4%), and robust. The overall measurement uncertainty was reasonable considering the increased variability inherent in microbiological response. Final uncertainty was comparable with those obtained with other microbiological assays, as well as chemical methods.

An experimental and theoretical investigation of the mechanical behavior of multilayer initially curved microplates under electrostatic actuation

KAUST Repository

Saghir, Shahid; Ilyas, Saad; Jaber, Nizar; Younis, Mohammad I.

2017-01-01

of the microplate. We compare the theoretical results with experimental data and show excellent agreement among the results. We also examine the effect of the initial rise on the natural frequencies of first three symmetric-symmetric modes of the plate.

Assessment of mitochondrial functions in Daphnia pulex clones using high-resolution respirometry.

Science.gov (United States)

Kake-Guena, Sandrine A; Touisse, Kamal; Vergilino, Roland; Dufresne, France; Blier, Pierre U; Lemieux, Hélène

2015-06-01

The objectives of our study were to adapt a method to measure mitochondrial function in intact mitochondria from the small crustacean Daphnia pulex and to validate if this method was sensitive enough to characterize mitochondrial metabolism in clones of the pulex complex differing in ploidy levels, mitochondrial DNA haplotypes, and geographic origins. Daphnia clones belonging to the Daphnia pulex complex represent a powerful model to delineate the link between mitochondrial DNA evolution and mitochondrial phenotypes, as single genotypes with divergent mtDNA can be grown under various experimental conditions. Our study included two diploid clones from temperate environments and two triploid clones from subarctic environments. The whole animal permeabilization and measurement of respiration with high-resolution respirometry enabled the measurement of the functional capacity of specific mitochondrial complexes in four clones. When expressing the activity as ratios, our method detected significant interclonal variations. In the triploid subarctic clone from Kuujjurapik, a higher proportion of the maximal physiological oxidative phosphorylation (OXPHOS) capacity of mitochondria was supported by complex II, and a lower proportion by complex I. The triploid subarctic clone from Churchill (Manitoba) showed the lowest proportion of the maximal OXPHOS supported by complex II. Additional studies are required to determine if these differences in mitochondrial functions are related to differences in mitochondrial haplotypes or ploidy level and if they might be associated with fitness divergences and therefore selective value. © 2015 Wiley Periodicals, Inc.

Generalized viscothermoelasticity theory of dual-phase-lagging model for damping analysis in circular micro-plate resonators

Science.gov (United States)

Grover, D.; Seth, R. K.

2018-05-01

Analysis and numerical results are presented for the thermoelastic dissipation of a homogeneous isotropic, thermally conducting, Kelvin-Voigt type circular micro-plate based on Kirchhoff's Love plate theory utilizing generalized viscothermoelasticity theory of dual-phase-lagging model. The analytical expressions for thermoelastic damping of vibration and frequency shift are obtained for generalized dual-phase-lagging model and coupled viscothermoelastic plates. The scaled thermoelastic damping has been illustrated in case of circular plate and axisymmetric circular plate for fixed aspect ratio for clamped and simply supported boundary conditions. It is observed that the damping of vibrations significantly depend on time delay and mechanical relaxation times in addition to thermo-mechanical coupling in circular plate under resonance conditions and plate dimensions.

A Microplate Growth Inhibition Assay for Screening Bacteriocins against Listeria monocytogenes to Differentiate Their Mode-of-Action

Directory of Open Access Journals (Sweden)

Paul Priyesh Vijayakumar

2015-06-01

Full Text Available Lactic acid bacteria (LAB have historically been used in food fermentations to preserve foods and are generally-recognized-as-safe (GRAS by the FDA for use as food ingredients. In addition to lactic acid; some strains also produce bacteriocins that have been proposed for use as food preservatives. In this study we examined the inhibition of Listeria monocytogenes 39-2 by neutralized and non-neutralized bacteriocin preparations (Bac+ preps produced by Lactobacillus curvatus FS47; Lb. curvatus Beef3; Pediococcus acidilactici Bac3; Lactococcus lactis FLS1; Enterococcus faecium FS56-1; and Enterococcus thailandicus FS92. Activity differences between non-neutralized and neutralized Bac+ preps in agar spot assays could not readily be attributed to acid because a bacteriocin-negative control strain was not inhibitory to Listeria in these assays. When neutralized and non-neutralized Bac+ preps were used in microplate growth inhibition assays against L. monocytogenes 39-2 we observed some differences attributed to acid inhibition. A microplate growth inhibition assay was used to compare inhibitory reactions of wild-type and bacteriocin-resistant variants of L. monocytogenes to differentiate bacteriocins with different modes-of-action (MOA whereby curvaticins FS47 and Beef3, and pediocin Bac3 were categorized to be in MOA1; enterocins FS92 and FS56-1 in MOA2; and lacticin FLS1 in MOA3. The microplate bacteriocin MOA assay establishes a platform to evaluate the best combination of bacteriocin preparations for use in food applications as biopreservatives against L. monocytogenes.

A Microplate Growth Inhibition Assay for Screening Bacteriocins against Listeria monocytogenes to Differentiate Their Mode-of-Action.

Science.gov (United States)

Vijayakumar, Paul Priyesh; Muriana, Peter M

2015-06-11

Lactic acid bacteria (LAB) have historically been used in food fermentations to preserve foods and are generally-recognized-as-safe (GRAS) by the FDA for use as food ingredients. In addition to lactic acid; some strains also produce bacteriocins that have been proposed for use as food preservatives. In this study we examined the inhibition of Listeria monocytogenes 39-2 by neutralized and non-neutralized bacteriocin preparations (Bac+ preps) produced by Lactobacillus curvatus FS47; Lb. curvatus Beef3; Pediococcus acidilactici Bac3; Lactococcus lactis FLS1; Enterococcus faecium FS56-1; and Enterococcus thailandicus FS92. Activity differences between non-neutralized and neutralized Bac+ preps in agar spot assays could not readily be attributed to acid because a bacteriocin-negative control strain was not inhibitory to Listeria in these assays. When neutralized and non-neutralized Bac+ preps were used in microplate growth inhibition assays against L. monocytogenes 39-2 we observed some differences attributed to acid inhibition. A microplate growth inhibition assay was used to compare inhibitory reactions of wild-type and bacteriocin-resistant variants of L. monocytogenes to differentiate bacteriocins with different modes-of-action (MOA) whereby curvaticins FS47 and Beef3, and pediocin Bac3 were categorized to be in MOA1; enterocins FS92 and FS56-1 in MOA2; and lacticin FLS1 in MOA3. The microplate bacteriocin MOA assay establishes a platform to evaluate the best combination of bacteriocin preparations for use in food applications as biopreservatives against L. monocytogenes.

Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries.

Science.gov (United States)

Jang, Sook-Jin; Park, Eunji; Lee, Won-Kyung; Johnson, Shannon B; Vrijenhoek, Robert C; Won, Yong-Jin

2016-10-28

The Equator and Easter Microplate regions of the eastern Pacific Ocean exhibit geomorphological and hydrological features that create barriers to dispersal for a number of animals associated with deep-sea hydrothermal vent habitats. This study examined effects of these boundaries on geographical subdivision of the vent polychaete Alvinella pompejana. DNA sequences from one mitochondrial and eleven nuclear genes were examined in samples collected from ten vent localities that comprise the species' known range from 23°N latitude on the East Pacific Rise to 38°S latitude on the Pacific Antarctic Ridge. Multi-locus genotypes inferred from these sequences clustered the individual worms into three metapopulation segments - the northern East Pacific Rise (NEPR), southern East Pacific Rise (SEPR), and northeastern Pacific Antarctic Ridge (PAR) - separated by the Equator and Easter Microplate boundaries. Genetic diversity estimators were negatively correlated with tectonic spreading rates. Application of the isolation-with-migration (IMa2) model provided information about divergence times and demographic parameters. The PAR and NEPR metapopulation segments were estimated to have split roughly 4.20 million years ago (Mya) (2.42-33.42 Mya, 95 % highest posterior density, (HPD)), followed by splitting of the SEPR and NEPR segments about 0.79 Mya (0.07-6.67 Mya, 95 % HPD). Estimates of gene flow between the neighboring regions were mostly low (2 Nm  SEPR > PAR. Highly effective dispersal capabilities allow A. pompejana to overcome the temporal instability and intermittent distribution of active hydrothermal vents in the eastern Pacific Ocean. Consequently, the species exhibits very high levels of genetic diversity compared with many co-distributed vent annelids and mollusks. Nonetheless, its levels of genetic diversity in partially isolated populations are inversely correlated with tectonic spreading rates. As for many other vent taxa, this pioneering colonizer is

Sensitive microplate assay for the detection of proteolytic enzymes using radiolabeled gelatin

International Nuclear Information System (INIS)

Robertson, B.D.; Kwan-Lim, G.E.; Maizels, R.M.

1988-01-01

A sensitive, microplate assay is described for the detection of a wide range of proteolytic enzymes, using radio-iodine-labeled gelatin as substrate. The technique uses the Bolton-Hunter reagent to label the substrate, which is then coated onto the wells of polyvinyl chloride microtiter plates. By measuring the radioactivity released the assay is able to detect elastase, trypsin, and collagenase in concentrations of 1 ng/ml or less, while the microtiter format permits multiple sample handling and minimizes sample volumes required for analysis

Investigation of Mitochondrial Dysfunction by Sequential Microplate-Based Respiration Measurements from Intact and Permeabilized Neurons

Science.gov (United States)

Clerc, Pascaline; Polster, Brian M.

2012-01-01

Mitochondrial dysfunction is a component of many neurodegenerative conditions. Measurement of oxygen consumption from intact neurons enables evaluation of mitochondrial bioenergetics under conditions that are more physiologically realistic compared to isolated mitochondria. However, mechanistic analysis of mitochondrial function in cells is complicated by changing energy demands and lack of substrate control. Here we describe a technique for sequentially measuring respiration from intact and saponin-permeabilized cortical neurons on single microplates. This technique allows control of substrates to individual electron transport chain complexes following permeabilization, as well as side-by-side comparisons to intact cells. To illustrate the utility of the technique, we demonstrate that inhibition of respiration by the drug KB-R7943 in intact neurons is relieved by delivery of the complex II substrate succinate, but not by complex I substrates, via acute saponin permeabilization. In contrast, methyl succinate, a putative cell permeable complex II substrate, failed to rescue respiration in intact neurons and was a poor complex II substrate in permeabilized cells. Sequential measurements of intact and permeabilized cell respiration should be particularly useful for evaluating indirect mitochondrial toxicity due to drugs or cellular signaling events which cannot be readily studied using isolated mitochondria. PMID:22496810

Sensitive detection of oversulfated chondroitin sulfate in heparin sodium or crude heparin with a colorimetric microplate based assay.

Science.gov (United States)

Sommers, Cynthia D; Mans, Daniel J; Mecker, Laura C; Keire, David A

2011-05-01

In this work we describe a 96-well microplate assay for oversulfated chondroitin sulfate A (OSCS) in heparin, based on a water-soluble cationic polythiophene polymer (3-(2-(N-(N'-methylimidazole))ethoxy)-4-methylthiophene (LPTP)) and heparinase digestion of heparin. The assay takes advantage of several unique properties of heparin, OSCS, and LPTP, including OSCS inhibition of heparinase I and II activity, the molecular weight dependence of heparin-LPTP spectral shifts, and the distinct association of heparin fragments and OSCS to LPTP. These factors combine to enable detection of the presence of 0.003% w/w spiked OSCS in 10 μg of heparin sodium active pharmaceutical ingredient (API) using a plate reader and with visual detection to 0.1% levels. The same detection limit for OSCS was observed in the presence of 10% levels of dermatan sulfate (DS) or chondroitin sulfate A (CSA) impurities. In addition, we surveyed a selection of crude heparin samples received by the agency in 2008 and 2009 to determine average and extreme DS, CSA, and galactosamine weight percent levels. In the presence of these impurities and the variable heparin content in the crude heparin samples, spiked OSCS was reliably detected to the 0.1% w/w level using a plate reader. Finally, authentically OSCS contaminated heparin sodium API and crude samples were distinguished visually by color from control samples using the LPTP/heparinase test.

Scanometry as microplate reader for high throughput method based on DPPH dry reagent for antioxidant assay

Directory of Open Access Journals (Sweden)

Mochammad Amrun Hidayat

2017-05-01

Full Text Available The stable chromogenic radical 1,1′-diphenyl-2-picrylhydrazyl (DPPH solution was immobilized on the microwell plate as dry reagent to construct a simple antioxidant sensor. Then, a regular flatbed scanner was used as microplate reader to obtain analytical parameters for antioxidant assay using one-shot optical sensors as scanometry technique. Variables affecting the acquisition of the images were optimized and the analytical parameters are obtained from an area of the sensing zone inside microwell using the average luminosity of the sensing zone captured as the mean of red, green, and blue (RGB value using ImageJ® program. By using this RGB value as sensor response, it is possible to determine antioxidant capacity in the range 1–25 ppm as gallic acid equivalent (GAE with the response time of 9 min. The reproducibility of sensor was good (RSD<1% with recovery at 93%–96%. The antioxidant sensor was applied to the plant extracts, such as sappan wood and Turmeric Rhizome. The results are good when compared to the same procedure using a UV/Vis spectrophotometer.

Kinetic description of flow past a micro-plate

International Nuclear Information System (INIS)

Christlieb, Andrew J.; Hitchon, W. Nicholas G.; Boyd, Iain D.; Sun Quanhua

2004-01-01

In this work we discuss a novel numerical scheme and present numerical results for the problem of 'high' (of order unity) Knudsen number, Kn=λ/L, low velocity gas flow past a micro-plate. The scheme used here is similar to one employed in the past to examine heat flow, but in order to deal with momentum transport in the vicinity of a plate, new techniques had to be developed. These include a new scheme for finding 'transition probabilities', which eliminates some forms of numerical diffusion, and a method for handling reflections off surfaces which preserves the essential properties of the flow. The purpose of the paper is to present these methods and examine their performance. The method is found to function well, but the results indicate that the collision operator which is employed here must be improved in order to obtain accurate results for the drag. Low speed neutral particle transport, in long mean free path (LMFP) environments, presents challenges for well-established techniques, such as the direct simulation Monte Carlo (DSMC) method. In particular, at low flow velocities, statistical methods suffer from noise that may render them impractical in LMFP environments. Solution of the Boltzmann equation is the alternative to these statistical methods. As computing power increases, Boltzmann-based approaches become more accessible. We discuss here a novel non-statistical (no random numbers are used) kinetic model for particle transport and explore its accuracy and sensitivity to resolution and other details of its implementation. The model is an enhanced version of the transition probability matrix (TPM) method. The results generated by the TPM are compared with the information preservation (IP) method, the Navier-Stokes (NS) slip model and when applicable to DSMC. We provide a qualitative comparison of the models and then we compare the results of the different models for various Kn for flow past a plate. For Kn in the slip flow regime, the TPM, IP and NS

Utilisation of respirometry to assess organic matter reduction of effluents from the Camaçari industrial complex (BA, Brazil

Directory of Open Access Journals (Sweden)

Carla A. Oliveira

2007-03-01

Full Text Available The treatment efficiency of industrial effluents, after biological treatment by activated sludge in aeration tanks (AT, was assessed through the utilisation of respirometry tests at the Cetrel's-wastewater treatment plant (WTP. Samples of the equalised effluent (EE, prior to treatment, and of the treated effluent (TE, after treatment, were analysed. Twenty bioassays batch were carried out to AT (AT-2, AT-3 and AT-4. Each test consisted of: a basic test, a basic test with peptone added, a test using EE and a test using TE. The data showed that there was no statistically significant difference (p>0.05 in the respiration activity between the aeration tanks. Regarding the specific oxygen uptake rate there was a mean reduction of 70.8% between the tests performed with EE and TE. The results demonstratd that respirometry tests could successfully assess the efficiency of the activated sludge process and, therefore, be adopted as tool for the monitoring from the WTP.Este trabalho avaliou, através de ensaios de respirometria, a eficiência do tratamento de efluentes industriais, após tratamento por lodo ativado em tanques de aeração (TA. Foram analisadas amostras do efluente equalisado (EE, antes do tratamento, e do efluente tratado (ET. Vinte baterias de ensaios foram realizadas com cada um dos TA (TA-2, TA-3 e TA-4. Cada bateria consistiu de um ensaio básico, contendo apenas o licor misto, um ensaio com adição de peptona, um ensaio com o EE e um com o ET. Não houve diferença estatística significativa (p>0,05 na atividade respiratória dos TA. Quanto à taxa de consumo de oxigênio específica houve uma redução média de 70,8% entre os ensaios realizados com EE e ET. Os ensaios de respirometria determinaram com eficiência o nível de tratamento através de lodo ativado, e deve ser adotado no monitoramento dos efluentes da estação de tratamento de efluentes do Pólo Industrial de Camaçari.

Quantitative digital image analysis of chromogenic assays for high throughput screening of alpha-amylase mutant libraries.

Science.gov (United States)

Shankar, Manoharan; Priyadharshini, Ramachandran; Gunasekaran, Paramasamy

2009-08-01

An image analysis-based method for high throughput screening of an alpha-amylase mutant library using chromogenic assays was developed. Assays were performed in microplates and high resolution images of the assay plates were read using the Virtual Microplate Reader (VMR) script to quantify the concentration of the chromogen. This method is fast and sensitive in quantifying 0.025-0.3 mg starch/ml as well as 0.05-0.75 mg glucose/ml. It was also an effective screening method for improved alpha-amylase activity with a coefficient of variance of 18%.

Measuring maximum and standard metabolic rates using intermittent-flow respirometry: a student laboratory investigation of aerobic metabolic scope and environmental hypoxia in aquatic breathers.

Science.gov (United States)

Rosewarne, P J; Wilson, J M; Svendsen, J C

2016-01-01

Metabolic rate is one of the most widely measured physiological traits in animals and may be influenced by both endogenous (e.g. body mass) and exogenous factors (e.g. oxygen availability and temperature). Standard metabolic rate (SMR) and maximum metabolic rate (MMR) are two fundamental physiological variables providing the floor and ceiling in aerobic energy metabolism. The total amount of energy available between these two variables constitutes the aerobic metabolic scope (AMS). A laboratory exercise aimed at an undergraduate level physiology class, which details the appropriate data acquisition methods and calculations to measure oxygen consumption rates in rainbow trout Oncorhynchus mykiss, is presented here. Specifically, the teaching exercise employs intermittent flow respirometry to measure SMR and MMR, derives AMS from the measurements and demonstrates how AMS is affected by environmental oxygen. Students' results typically reveal a decline in AMS in response to environmental hypoxia. The same techniques can be applied to investigate the influence of other key factors on metabolic rate (e.g. temperature and body mass). Discussion of the results develops students' understanding of the mechanisms underlying these fundamental physiological traits and the influence of exogenous factors. More generally, the teaching exercise outlines essential laboratory concepts in addition to metabolic rate calculations, data acquisition and unit conversions that enhance competency in quantitative analysis and reasoning. Finally, the described procedures are generally applicable to other fish species or aquatic breathers such as crustaceans (e.g. crayfish) and provide an alternative to using higher (or more derived) animals to investigate questions related to metabolic physiology. © 2016 The Fisheries Society of the British Isles.

Analytical validation of an ultra low-cost mobile phone microplate reader for infectious disease testing.

Science.gov (United States)

Wang, Li-Ju; Naudé, Nicole; Demissie, Misganaw; Crivaro, Anne; Kamoun, Malek; Wang, Ping; Li, Lei

2018-07-01

Most mobile health (mHealth) diagnostic devices for laboratory tests only analyze one sample at a time, which is not suitable for large volume serology testing, especially in low-resource settings with shortage of health professionals. In this study, we developed an ultra-low-cost clinically-accurate mobile phone microplate reader (mReader), and clinically validated this optical device for 12 infectious disease tests. The mReader optically reads 96 samples on a microplate at one time. 771 de-identified patient samples were tested for 12 serology assays for bacterial/viral infections. The mReader and the clinical instrument blindly read and analyzed all tests in parallel. The analytical accuracy and the diagnostic performance of the mReader were evaluated across the clinical reportable categories by comparison with clinical laboratorial testing results. The mReader exhibited 97.59-99.90% analytical accuracy and envision the mReader can benefit underserved areas/populations and low-resource settings in rural clinics/hospitals at a low cost (~$50 USD) with clinical-level analytical quality. It has the potential to improve health access, speed up healthcare delivery, and reduce health disparities and education disparities by providing access to a low-cost spectrophotometer. Copyright © 2018 Elsevier B.V. All rights reserved.

Antibiotic microbial assay using kinetic-reading microplate system

Directory of Open Access Journals (Sweden)

Felipe Rebello Lourenço

2011-09-01

Full Text Available The aim of this study was to determine the optimal experimental conditions to develop a methodology for microbiological assay of apramycin employing microplate and kinetic reading mode, and to validate the developed method, through evaluation of parameters of selectivity, linearity, linear range, limits of detection and quantification, accuracy and precision. The turbidimetric assay principle is simple: the test solution is added to a suspension of test microorganism in culture media, the mixture is incubated under appropriate conditions and the microbial growth is measured by photometric reading. Microplate with kinetic reading mode employed in antibiotic assay is of considerable interest since it allows reduction of material and analysis time and enables a large number of samples to be analyzed simultaneously, with automated reading and calculating. Established conditions considered the standard-curve of apramycin at concentrations from 5.0 to 35.0 μg mL-1, and tryptic soy broth inoculated with 5% Escherichia coli (ATCC 8739 suspension. Satisfactory results were obtained with 2 hours of incubation. The developed method showed appropriate selectivity, linearity in the range from 5.0 to 35.0 μg mL-1, limits of detection and quantification of 0.1 and 0.4 μg mL-1, respectively, as well as satisfactory accuracy (recuperation = 98.5% and precision (RSD = 6.0%. Microplate assay combined the characteristics of microbiological (evaluation of antibiotic activity against sensitive test microorganism and physico-chemical (operationally straightforward and faster results assays.O objetivo deste trabalho é determinar as condições experimentais ideais para o desenvolvimento de metodologia para a dosagem microbiológica de apramicina empregando microplacas e modo de leitura cinético e validar o método desenvolvido, através da avaliação dos parâmetros de especificidade e seletividade, linearidade, faixa ou intervalo linear, limite de detecção e

Inducción de la brotación in vitro de microplántulas de nogal (Juglans neotropica) tratadas con Thidiazuron (TDZ) y 6-Bencilaminnopurina (BAP)

OpenAIRE

Peña Tapia, Denisse Fabiola; Rocano Curillo, Melida Noemi; Salazar, Jazmin M.; Torres, Carlos S.; Universidad de Cuenca; Dirección de Investigación de la Universidad de Cuenca; DIUC

2014-01-01

El nogal (Juglans neotropica) es una especie de gran potencial para proyectos de conservación y agro-productivos en la eco-región Andina. No obstante, su baja capacidad germinativa limita su propagación para reforestación. El objetivo de este estudio fue determinar el efecto del tratamiento con Thidiazuron (TDZ) y 6-Bencilaminopurina (BAP) en la inducción in vitro de brotes de J. neotropica. Las microplántulas tratadas con BAP produjeron más brotes que aquellas tratadas con TDZ. Las microplán...

Effects of thermal stress and nitrate enrichment on the larval performance of two Caribbean reef corals

Science.gov (United States)

Serrano, Xaymara M.; Miller, Margaret W.; Hendee, James C.; Jensen, Brittany A.; Gapayao, Justine Z.; Pasparakis, Christina; Grosell, Martin; Baker, Andrew C.

2018-03-01

The effects of multiple stressors on the early life stages of reef-building corals are poorly understood. Elevated temperature is the main physiological driver of mass coral bleaching events, but increasing evidence suggests that other stressors, including elevated dissolved inorganic nitrogen (DIN), may exacerbate the negative effects of thermal stress. To test this hypothesis, we investigated the performance of larvae of Orbicella faveolata and Porites astreoides, two important Caribbean reef coral species with contrasting reproductive and algal transmission modes, under increased temperature and/or elevated DIN. We used a fluorescence-based microplate respirometer to measure the oxygen consumption of coral larvae from both species, and also assessed the effects of these stressors on P. astreoides larval settlement and mortality. Overall, we found that (1) larvae increased their respiration in response to different factors ( O. faveolata in response to elevated temperature and P. astreoides in response to elevated nitrate) and (2) P. astreoides larvae showed a significant increase in settlement as a result of elevated nitrate, but higher mortality under elevated temperature. This study shows how microplate respirometry can be successfully used to assess changes in respiration of coral larvae, and our findings suggest that the effects of thermal stress and nitrate enrichment in coral larvae may be species specific and are neither additive nor synergistic for O. faveolata or P. astreoides. These findings may have important consequences for the recruitment and community reassembly of corals to nutrient-polluted reefs that have been impacted by climate change.

From a collage of microplates to stable continental crust - an example from Precambrian Europe

Science.gov (United States)

Korja, Annakaisa

2013-04-01

Svecofennian orogen (2.0-1.7 Ga) comprises the oldest undispersed orogenic belt on Baltica and Eurasian plate. Svecofennian orogenic belt evolved from a series of short-lived terrane accretions around Baltica's Archean nucleus during the formation of the Precambrian Nuna supercontinent. Geological and geophysical datasets indicate W-SW growth of Baltica with NE-ward dipping subduction zones. The data suggest a long-lived retreating subduction system in the southwestern parts whereas in the northern and central parts the northeasterly transport of continental fragments or microplates towards the continental nucleus is also documented. The geotectonic environment resembles that of the early stages of the Alpine-Himalayan or Indonesian orogenic system, in which dispersed continental fragments, arcs and microplates have been attached to the Eurasian plate margin. Thus the Svecofennian orogeny can be viewed as proxy for the initial stages of an internal orogenic system. Svecofennian orogeny is a Paleoproterozoic analogue of an evolved orogenic system where terrane accretion is followed by lateral spreading or collapse induced by change in the plate architecture. The exposed parts are composed of granitoid intrusions as well as highly deformed supracrustal units. Supracrustal rocks have been metamorphosed in LP-HT conditions in either paleo-lower-upper crust or paleo-upper-middle crust. Large scale seismic reflection profiles (BABEL and FIRE) across Baltica image the crust as a collage of terranes suggesting that the bedrock has been formed and thickened in sequential accretions. The profiles also image three fold layering of the thickened crust (>55 km) to transect old terrane boundaries, suggesting that the over-thickened bedrock structures have been rearranged in post-collisional spreading and/or collapse processes. The middle crust displays typical large scale flow structures: herringbone and anticlinal ramps, rooted onto large scale listric surfaces also suggestive

Intraplate Crustal Deformation Within the Northern Sinai Microplate: Evidence from Paleomagnetic Directions and Mechanical Modeling

Science.gov (United States)

Dembo, N.; Granot, R.; Hamiel, Y.

2017-12-01

The intraplate crustal deformation found in the northern part of the Sinai Microplate, located near the northern Dead Sea Fault plate boundary, is examined. Previous studies have suggested that distributed deformation in Lebanon is accommodated by regional uniform counterclockwise rigid block rotations. However, remanent magnetization directions observed near the Lebanese restraining bend are not entirely homogeneous suggesting that an unexplained and complex internal deformation pattern exists. In order to explain the variations in the amount of vertical-axis rotations we construct a mechanical model of the major active faults in the region that simulates the rotational deformation induced by motion along these faults. The rotational pattern calculated by the mechanical modeling predicts heterogeneous distribution of rotations around the faults. The combined rotation field that considers both the fault induced rotations and the already suggested regional block rotations stands in general agreement with the observed magnetization directions. Overall, the modeling results provide a more detailed and complete picture of the deformation pattern in this region and show that rotations induced by motion along the Dead Sea Fault act in parallel to rigid block rotations. Finally, the new modeling results unravel important insights as to the fashion in which crustal deformation is distributed within the northern part of the Sinai Microplate and propose an improved deformational mechanism that might be appropriate for other plate margins as well.

Characterization of Orthorhombic α-MoO3 Microplates Produced by a Microwave Plasma Process

International Nuclear Information System (INIS)

Klinbumrung, A.; Thongtem, S.; Thongtem, T.; Thongtem, S.; Thongtem, T.

2012-01-01

Orthorhombic α-MoO 3 microplates were produced from (NH 4 ) 6 Mo 7 O 24 H 2 O solid powder by a 900 W microwave plasma for 40, 50, and 60?min. Phase, morphologies, and vibration modes were characterized by X-ray diffraction (XRD), selected area electron diffraction (SAED), scanning electron microscopy (SEM), and Raman and Fourier transform infrared (FTIR) spectroscopy. Sixty min processing resulted in the best crystallization of the α-MoO 3 phase, with photoluminescence (PL) in a wavelength range of 430-440 nm.

The Impact of Situation-Based Learning to Students’ Quantitative Literacy

Science.gov (United States)

Latifah, T.; Cahya, E.; Suhendra

2017-09-01

Nowadays, the usage of quantities can be seen almost everywhere. There has been an increase of quantitative thinking, such as quantitative reasoning and quantitative literacy, within the context of daily life. However, many people today are still not fully equipped with the knowledge of quantitative thinking. There are still a lot of individuals not having enough quantitative skills to perform well within today’s society. Based on this issue, the research aims to improve students’ quantitative literacy in junior high school. The qualitative analysis of written student work and video observations during the experiment reveal that the impact of situation-based learning affects students’ quantitative literacy.

Impact of electrochemical treatment of soil washing solution on PAH degradation efficiency and soil respirometry.

Science.gov (United States)

Mousset, Emmanuel; Huguenot, David; van Hullebusch, Eric D; Oturan, Nihal; Guibaud, Gilles; Esposito, Giovanni; Oturan, Mehmet A

2016-04-01

The remediation of a genuinely PAH-contaminated soil was performed, for the first time, through a new and complete investigation, including PAH extraction followed by advanced oxidation treatment of the washing solution and its recirculation, and an analysis of the impact of the PAH extraction on soil respirometry. The study has been performed on the remediation of genuine PAH-contaminated soil, in the following three steps: (i) PAH extraction with soil washing (SW) techniques, (ii) PAH degradation with an electro-Fenton (EF) process, and (iii) recirculation of the partially oxidized effluent for another SW cycle. The following criteria were monitored during the successive washing cycles: PAH extraction efficiency, PAH oxidation rates and yields, extracting agent recovery, soil microbial activity, and pH of soil. Two representative extracting agents were compared: hydroxypropyl-beta-cyclodextrin (HPCD) and a non-ionic surfactant, Tween(®) 80. Six PAH with different numbers of rings were monitored: acenaphthene (ACE), phenanthrene (PHE), fluoranthene (FLA), pyrene (PYR), benzo(a)pyrene (BaP), and benzo(g,h,i)perylene (BghiP). Tween(®) 80 showed much better PAH extraction efficiency (after several SW cycles) than HPCD, regardless of the number of washing cycles. Based on successive SW experiments, a new mathematical relation taking into account the soil/water partition coefficient (Kd*) was established, and could predict the amount of each PAH extracted by the surfactant with a good correlation with experimental results (R(2) > 0.975). More HPCD was recovered (89%) than Tween(®) 80 (79%), while the monitored pollutants were completely degraded (>99%) after 4 h and 8 h, respectively. Even after being washed with partially oxidized solutions, the Tween(®) 80 solutions extracted significantly more PAH than HPCD and promoted better soil microbial activity, with higher oxygen consumption rates. Moreover, neither the oxidation by-products nor the acidic media (p

Lithospheric strength in the active boundary between the Pacific Plate and Baja California microplate constrained from lower crustal and upper mantle xenoliths

Science.gov (United States)

Chatzaras, Vasileios; van der Werf, Thomas; Kriegsman, Leo M.; Kronenberg, Andreas; Tikoff, Basil; Drury, Martyn R.

2017-04-01

The lower crust is the most poorly understood of the lithospheric layers in terms of its rheology, particularly at active plate boundaries. We studied naturally deformed lower crustal xenoliths within an active plate boundary, in order to link their microstructures and rheological parameters to the well-defined active tectonic context. The Baja California shear zone (BCSZ), located at the western boundary of the Baja California microplate, comprises the active boundary accommodating the relative motion between the Pacific plate and Baja California microplate. The basalts of the Holocene San Quintin volcanic field carry lower crustal and upper mantle xenoliths, which sample the Baja California microplate lithosphere in the vicinity of the BCSZ. The lower crustal xenoliths range from undeformed gabbros to granoblastic two-pyroxene granulites. Two-pyroxene geothermometry shows that the granulites equilibrated at temperatures of 690-920 oC. Phase equilibria (P-T pseudosections using Perple_X) indicate that symplectites with intergrown pyroxenes, plagioclase, olivine and spinel formed at 3.6-5.4 kbar, following decompression from pressures exceeding 6 kbar. FTIR spectroscopy shows that the water content of plagioclase varies among the analyzed xenoliths; plagioclase is relatively dry in two xenoliths while one xenolith contains hydrated plagioclase grains. Microstructural observations and analysis of the crystallographic texture provide evidence for deformation of plagioclase by a combination of dislocation creep and grain boundary sliding. To constrain the strength of the lower crust and upper mantle near the BCSZ we estimated the differential stress using plagioclase and olivine grain size paleopiezomtery, respectively. Differential stress estimates for plagioclase range from 10 to 32 MPa and for olivine are 30 MPa. Thus the active microplate boundary records elevated crustal temperatures, heterogeneous levels of hydration, and low strength in both the lower crust and

Quantitative valuation of platform technology based intangibles companies

OpenAIRE

Achleitner, Ann-Kristin; Nathusius, Eva; Schraml, Stephanie

2007-01-01

In the course of raising external equity, e.g. from venture capitalists, a quantitative valuation is usually required for entrepreneurial ventures. This paper examines the challenges of quantitatively valuing platform technology based entrepreneurial ventures. The distinct characteristics of such companies pose specific requirements on the applicability of quantitative valuation methods. The entrepreneur can choose from a wide range of potential commercialization strategies to pursue in the c...

Microplate-Based Evaluation of the Sugar Yield from Giant Reed, Giant Miscanthus and Switchgrass after Mild Chemical Pre-Treatments and Hydrolysis with Tailored Trichoderma Enzymatic Blends.

Science.gov (United States)

Cianchetta, Stefano; Bregoli, Luca; Galletti, Stefania

2017-11-01

Giant reed, miscanthus, and switchgrass are considered prominent lignocellulosic feedstocks to obtain fermentable sugars for biofuel production. The bioconversion into sugars requires a delignifying pre-treatment step followed by hydrolysis with cellulase and other accessory enzymes like xylanase, especially in the case of alkali pre-treatments, which retain the hemicellulose fraction. Blends richer in accessory enzymes than commercial mix can be obtained growing fungi on feedstock-based substrates, thus ten selected Trichoderma isolates, including the hypercellulolytic strain Trichoderma reesei Rut-C30, were grown on giant reed, miscanthus, or switchgrass-based substrates. The produced enzymes were used to saccharify the corresponding feedstocks, compared to a commercial enzymatic mix (6 FPU/g). Feedstocks were acid (H 2 SO 4 0.2-2%, w/v) or alkali (NaOH 0.02-0.2%, w/v) pre-treated. A microplate-based approach was chosen for most of the experimental steps due to the large number of samples. The highest bioconversion was generally obtained with Trichoderma harzianum Or4/99 enzymes (78, 89, and 94% final sugar yields at 48 h for giant reed, miscanthus, and switchgrass, respectively), with significant increases compared to the commercial mix, especially with alkaline pre-treatments. The differences in bioconversion yields were only partially caused by xylanases (maximum R 2  = 0.5), indicating a role for other accessory enzymes.

A microtitre-based method for measuring the haem polymerization inhibitory activity (HPIA) of antimalarial drugs.

Science.gov (United States)

Basilico, N; Pagani, E; Monti, D; Olliaro, P; Taramelli, D

1998-07-01

The malaria parasite metabolizes haemoglobin and detoxifies the resulting haem by polymerizing it to form haemozoin (malaria pigment). A polymer identical to haemozoin, beta-haematin, can be obtained in vitro from haematin at acidic pH. Quinoline-containing anti-malarials (e.g. chloroquine) inhibit the formation of either polymer. Haem polymerization is an essential and unique pharmacological target. To identify molecules with haem polymerization inhibitory activity (HPIA) and quantify their potency, we developed a simple, inexpensive, quantitative in-vitro spectrophotometric microassay of haem polymerization. The assay uses 96-well U-bottomed polystyrene microplates and requires 24 h and a microplate reader. The relative amounts of polymerized and unpolymerized haematin are determined, based on solubility in DMSO, by measuring absorbance at 405 nm in the presence of test compounds as compared with untreated controls. The final product (a solid precipitate of polymerized haematin) was validated using infrared spectroscopy and the assay proved reproducible; in this assay, activity could be partly predicted based on the compound's chemical structure. Both water-soluble and water-insoluble compounds can be quantified by this method. Although the throughput of this assay is lower than that of radiometric methods, the assay is easier to set up and cheaper, and avoids the problems related to radioactive waste disposal.

In-vitro antimycobacterial drug susceptibility testing of non-tubercular mycobacteria by tetrazolium microplate assay.

Science.gov (United States)

Sankar, Manimuthu Mani; Gopinath, Krishnamoorthy; Singla, Roopak; Singh, Sarman

2008-07-11

Non-tubercular mycobacteria (NTM) has not been given due attention till the recent epidemic of HIV. This has led to increasing interest of health care workers in their biology, epidemiology and drug resistance. However, timely detection and drug susceptibility profiling of NTM isolates are always difficult in resource poor settings like India. Furthermore, no standardized methodology or guidelines are available to reproduce the results with clinical concordance. To find an alternative and rapid method for performing the drug susceptibility assay in a resource limited settings like India, we intended to evaluate the utility of Tetrazolium microplate assay (TEMA) in comparison with proportion method for reporting the drug resistance in clinical isolates of NTM. A total of fifty-five NTM isolates were tested for susceptibility against Streptomycin, Rifampicin, Ethambutol, Ciprofloxacin, Ofloxacin, Azithromycin, and Clarithromycin by TEMA and the results were compared with agar proportion method (APM). Of the 55 isolates, 23 (41.8%) were sensitive to all the drugs and the remaining 32 (58.2%) were resistant to at least one drug. TEMA had very good concordance with APM except with minor discrepancies. Susceptibility results were obtained in the median of 5 to 9 days by TEMA. The NTM isolates were highly sensitive against Ofloxacin (98.18% sensitive) and Ciprofloxacin (90.09% sensitive). M. mucogenicum was sensitive only to Clarithromycin and resistant to all the other drugs tested. The concordance between TEMA and APM ranged between 96.4 - 100%. Tetrazolium Microplate Assay is a rapid and highly reproducible method. However, it must be performed only in tertiary level Mycobacteriology laboratories with proper bio-safety conditions.

Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP)

Science.gov (United States)

Ma, Hongyan; Delafield, Daniel G.; Wang, Zhe; You, Jianlan; Wu, Si

2017-04-01

The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated. To address this challenge, we have developed an Activity-Correlated Quantitative Proteomics Platform (ACPP) that systematically correlates protein-level enzymatic activity patterns and protein elution profiles using a label-free quantitative proteomics approach. The ACPP optimized a high performance anion exchange separation for efficiently fractionating complex protein samples while preserving enzymatic activities. The detected enzymatic activity patterns in sequential fractions using microplate-based assays were cross-correlated with protein elution profiles using a customized pattern-matching algorithm with a correlation R-score. The ACPP has been successfully applied to the identification of two types of "active" biomass-degrading enzymes (i.e., starch hydrolysis enzymes and cellulose hydrolysis enzymes) from Aspergillus niger secretome in a multiplexed fashion. By determining protein elution profiles of 156 proteins in A. niger secretome, we confidently identified the 1,4-α-glucosidase as the major "active" starch hydrolysis enzyme (R = 0.96) and the endoglucanase as the major "active" cellulose hydrolysis enzyme (R = 0.97). The results demonstrated that the ACPP facilitated the discovery of bioactive enzymes from complex protein samples in a high-throughput, multiplexing, and untargeted fashion.

Identification of odorant binding proteins and chemosensory proteins in Microplitis mediator as well as functional characterization of chemosensory protein 3.

Directory of Open Access Journals (Sweden)

Yong Peng

Full Text Available Odorant binding proteins (OBPs and chemosensory proteins (CSPs play important roles in transporting semiochemicals through the sensillar lymph to olfactory receptors in insect antennae. In the present study, twenty OBPs and three CSPs were identified from the antennal transcriptome of Microplitis mediator. Ten OBPs (MmedOBP11-20 and two CSPs (MmedCSP2-3 were newly identified. The expression patterns of these new genes in olfactory and non-olfactory tissues were investigated by real-time quantitative PCR (qPCR measurement. The results indicated that MmedOBP14, MmedOBP18, MmedCSP2 and MmedCSP3 were primarily expressed in antennae suggesting potential olfactory roles in M. mediator. However, other genes including MmedOBP11-13, 15-17, 19-20 appeared to be expressed at higher levels in body parts than in antennae. Focusing on the functional characterization of MmedCSP3, immunocytochemistry and fluorescent competitive binding assays were conducted indoors. It was found that MmedCSP3 was specifically located in the sensillum lymph of olfactory sensilla basiconca type 2. The recombinant MmedCSP3 could bind several types of host insects odors and plant volatiles. Interestingly, three sex pheromone components of Noctuidae insects, cis-11-hexadecenyl aldehyde (Z11-16: Ald, cis-11-hexadecanol (Z11-16: OH, and trans-11-tetradecenyl acetate (E11-14: Ac, showed high binding affinities (Ki = 17.24-18.77 μM. The MmedCSP3 may be involved in locating host insects. Our data provide a base for further investigating the physiological roles of OBPs and CSPs in M. mediator, and extend the function of MmedCSP3 in chemoreception of M. mediator.

Open-circuit respirometry: real-time, laboratory-based systems.

Science.gov (United States)

Ward, Susan A

2018-05-04

This review explores the conceptual and technological factors integral to the development of laboratory-based, automated real-time open-circuit mixing-chamber and breath-by-breath (B × B) gas-exchange systems, together with considerations of assumptions and limitations. Advances in sensor technology, signal analysis, and digital computation led to the emergence of these technologies in the mid-20th century, at a time when investigators were beginning to recognise the interpretational advantages of nonsteady-state physiological-system interrogation in understanding the aetiology of exercise (in)tolerance in health, sport, and disease. Key milestones include the 'Auchincloss' description of an off-line system to estimate alveolar O 2 uptake B × B during exercise. This was followed by the first descriptions of real-time automated O 2 uptake and CO 2 output B × B measurement by Beaver and colleagues and by Linnarsson and Lindborg, and mixing-chamber measurement by Wilmore and colleagues. Challenges to both approaches soon emerged: e.g., the influence of mixing-chamber washout kinetics on mixed-expired gas concentration determination, and B × B alignment of gas-concentration signals with respired flow. The challenging algorithmic and technical refinements required for gas-exchange estimation at the alveolar level have also been extensively explored. In conclusion, while the technology (both hardware and software) underpinning real-time automated gas-exchange measurement has progressively advanced, there are still concerns regarding accuracy especially under the challenging conditions of changing metabolic rate.

Large-scale preparation of shape controlled SnO and improved capacitance for supercapacitors: from nanoclusters to square microplates

Science.gov (United States)

Wang, Lu; Ji, Hongmei; Zhu, Feng; Chen, Zhi; Yang, Yang; Jiang, Xuefan; Pinto, João; Yang, Gang

2013-07-01

Here, we first provide a facile ultrasonic-assisted synthesis of SnO using SnCl2 and the organic solvent of ethanolamine (ETA). The moderate alkalinity of ETA and ultrasound play very important roles in the synthesis of SnO. After the hydrolysis of the intermediate of ETA-Sn(ii), the as-synthesized SnO nanoclusters undergo assembly, amalgamation, and preferential growth to microplates in hydrothermal treatment. The as-synthesized SnO was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), ultraviolet-visible absorption spectroscopy (UV-vis) and X-ray diffraction (XRD). To explore its potential applications in energy storage, SnO was fabricated into a supercapacitor electrode and characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and galvanostatic charge-discharge measurements. The as-synthesized SnO exhibits remarkable pseudocapacitive activity including high specific capacitance (208.9 F g-1 at 0.1 A g-1), good rate capability (65.8 F g-1 at 40 A g-1), and excellent cycling stability (retention 119.3% after 10 000 cycles) for application in supercapacitors. The capacitive behavior of SnO with various crystal morphologies was observed by fitted EIS using an equivalent circuit. The novel synthetic route for SnO is a convenient and potential way to large-scale production of microplates which is expected to be applicable in the synthesis of other metal oxide nanoparticles.Here, we first provide a facile ultrasonic-assisted synthesis of SnO using SnCl2 and the organic solvent of ethanolamine (ETA). The moderate alkalinity of ETA and ultrasound play very important roles in the synthesis of SnO. After the hydrolysis of the intermediate of ETA-Sn(ii), the as-synthesized SnO nanoclusters undergo assembly, amalgamation, and preferential growth to microplates in hydrothermal treatment. The as-synthesized SnO was characterized by scanning

Solid-phase peptide quantitation assay using labeled monoclonal antibody and glutaraldehyde fixation

International Nuclear Information System (INIS)

Kasprzyk, P.G.; Cuttitta, F.; Avis, I.; Nakanishi, Y.; Treston, A.; Wong, H.; Walsh, J.H.; Mulshine, J.L.

1988-01-01

A solid-phase radioimmunoassay utilizing iodinated peptide-specific monoclonal antibody as a detection system instead of labeled peptide has been developed. Regional specific monoclonal antibodies to either gastrin-releasing peptide or gastrin were used as models to validate the general application of our modified assay. Conditions for radioactive labeling of the monoclonal antibody were determined to minimize oxidant damage, which compromises the sensitivity of other reported peptide quantitation assays. Pretreatment of 96-well polyvinyl chloride test plates with a 5% glutaraldehyde solution resulted in consistent retention of sufficient target peptide on the solid-phase matrix to allow precise quantitation. This quantitative method is completed within 1 h of peptide solid phasing. Pretreatment of assay plates with glutaraldehyde increased binding of target peptide and maximized antibody binding by optimizing antigen presentation. The hypothesis that glutaraldehyde affects both peptide binding to the plate and orientation of the peptide was confirmed by analysis of several peptide analogs. These studies indicate that peptide binding was mediated through a free amino group leaving the carboxy-terminal portion of the target peptide accessible for antibody binding. It was observed that the length of the peptide also affects the amount of monoclonal antibody that will bind. Under the optimal conditions, results from quantitation of gastrin-releasing peptide in relevant samples agree well with those from previously reported techniques. Thus, we report here a modified microplate assay which may be generally applied for the rapid and sensitive quantitation of peptide hormones

Quantitative learning strategies based on word networks

Science.gov (United States)

Zhao, Yue-Tian-Yi; Jia, Zi-Yang; Tang, Yong; Xiong, Jason Jie; Zhang, Yi-Cheng

2018-02-01

Learning English requires a considerable effort, but the way that vocabulary is introduced in textbooks is not optimized for learning efficiency. With the increasing population of English learners, learning process optimization will have significant impact and improvement towards English learning and teaching. The recent developments of big data analysis and complex network science provide additional opportunities to design and further investigate the strategies in English learning. In this paper, quantitative English learning strategies based on word network and word usage information are proposed. The strategies integrate the words frequency with topological structural information. By analyzing the influence of connected learned words, the learning weights for the unlearned words and dynamically updating of the network are studied and analyzed. The results suggest that quantitative strategies significantly improve learning efficiency while maintaining effectiveness. Especially, the optimized-weight-first strategy and segmented strategies outperform other strategies. The results provide opportunities for researchers and practitioners to reconsider the way of English teaching and designing vocabularies quantitatively by balancing the efficiency and learning costs based on the word network.

Use of a modified microplate bioassay method to investigate antibacterial activity in the Peruvian medicinal plant Peperomia galioides.

Science.gov (United States)

Langfield, Richard D; Scarano, Frank J; Heitzman, Mary E; Kondo, Miwako; Hammond, Gerald B; Neto, Catherine C

2004-10-01

A versatile microplate bioassay for quick and sensitive determination of antibacterial activity was developed for use in screening medicinal plants and identification of their active principles. This assay can be used to determine minimum inhibitory concentrations for small quantities of organic or water-soluble plant extracts. Bioassay-guided fractionation of the stem and leaves of Peperomia galioides using this method found fractions containing grifolin and grifolic acid, which inhibited growth of Staphylococcus aureus and Staphylococcus epidermidis.

Portable smartphone based quantitative phase microscope

Science.gov (United States)

Meng, Xin; Tian, Xiaolin; Yu, Wei; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Liu, Cheng; Wang, Shouyu

2018-01-01

To realize portable device with high contrast imaging capability, we designed a quantitative phase microscope using transport of intensity equation method based on a smartphone. The whole system employs an objective and an eyepiece as imaging system and a cost-effective LED as illumination source. A 3-D printed cradle is used to align these components. Images of different focal planes are captured by manual focusing, followed by calculation of sample phase via a self-developed Android application. To validate its accuracy, we first tested the device by measuring a random phase plate with known phases, and then red blood cell smear, Pap smear, broad bean epidermis sections and monocot root were also measured to show its performance. Owing to its advantages as accuracy, high-contrast, cost-effective and portability, the portable smartphone based quantitative phase microscope is a promising tool which can be future adopted in remote healthcare and medical diagnosis.

Vibration and bending analyses of magneto-electro-thermo-elastic sandwich microplates resting on viscoelastic foundation

Science.gov (United States)

Arefi, Mohammad; Zenkour, Ashraf M.

2017-08-01

Magneto-electro-thermo-mechanical bending and free vibration analysis of a sandwich microplate using strain gradient theory is expressed in this paper. The sandwich plate is made of a core and two integrated piezo-magnetic face sheets. The structure is subjected to electric and magnetic potentials, thermal loadings, and resting on Pasternak's foundation. Electro-magnetic equations are developed by considering the variation form of Hamilton's principle. The effects of important parameters of this problem such as applied electric and magnetic potentials, direct and shear parameter of foundation, three microlength-scale parameters, and two parameters of temperature rising are investigated on the vibration and bending results of problem.

Facile construction of novel CoMoO4 microplates@CoMoO4 microprisms structures for well-stable supercapacitors

Directory of Open Access Journals (Sweden)

Xuewen Geng

2016-06-01

Full Text Available A simple and controllable strategy has been developed to fabricate CoMoO4 microplates/CoMoO4 microprisms (CMCMs structures on Ni foam via a facile, cost-effective, two-step hydrothermal route. The as-grown 3D architecture exhibited excellent areal capacitance of 4.33 F cm−2 at a galvanostatic charge-discharge current density of 50 mA cm−2 (6 A g−1 and outstanding cycle performance with only 2.8% degradation over 6500 cycles in the 3 M KOH solution. The asymmetric all-solid-state supercapacitors based on activated carbon (AC and CMCMs exhibited much better electrochemical performance than the symmetric counterpart, showing an areal capacitance of 95.22 mF cm−2 at the current density of 12 mA cm−2 and excellent cycling stability with 92.27% of the initial capacitance after 5000 cycles. These results may provide useful guidelines for materials selection and configuration designs for the novel energy storage devices based on CoMoO4 components and substrates.

Assessing honeybee and wasp thermoregulation and energetics-New insights by combination of flow-through respirometry with infrared thermography.

Science.gov (United States)

Stabentheiner, Anton; Kovac, Helmut; Hetz, Stefan K; Käfer, Helmut; Stabentheiner, Gabriel

2012-04-20

Endothermic insects like honeybees and some wasps have to cope with an enormous heat loss during foraging because of their small body size in comparison to endotherms like mammals and birds. The enormous costs of thermoregulation call for optimisation. Honeybees and wasps differ in their critical thermal maximum, which enables the bees to kill the wasps by heat. We here demonstrate the benefits of a combined use of body temperature measurement with infrared thermography, and respiratory measurements of energy turnover (O(2) consumption or CO(2) production via flow-through respirometry) to answer questions of insect ecophysiological research, and we describe calibrations to receive accurate results.To assess the question of what foraging honeybees optimise, their body temperature was compared with their energy turnover. Honeybees foraging from an artificial flower with unlimited sucrose flow increased body surface temperature and energy turnover with profitability of foraging (sucrose content of the food; 0.5 or 1.5 mol/L). Costs of thermoregulation, however, were rather independent of ambient temperature (13-30 °C). External heat gain by solar radiation was used to increase body temperature. This optimised foraging energetics by increasing suction speed.In determinations of insect respiratory critical thermal limits, the combined use of respiratory measurements and thermography made possible a more conclusive interpretation of respiratory traces.

Online identification of the antioxidant constituents of traditional Chinese medicine formula Chaihu-Shu-Gan-San by LC-LTQ-Orbitrap mass spectrometry and microplate spectrophotometer.

Science.gov (United States)

Su, Zhi-Heng; Zou, Guo-An; Preiss, Alfred; Zhang, Hong-Wu; Zou, Zhong-Mei

2010-11-02

Chaihu-Shu-Gan-San (CSGS), a traditional Chinese medicine (TCM) formula containing seven herbal medicines, has been used in treatment of gastritis, peptic ulcer, irritable bowel syndrome and depression clinically. However, the chemical constituents in CSGS had not been studied so far. To quickly identify the chemical constituents of CSGS and to understand the chemical profiles related to antioxidant activity of CSGS, liquid chromatography coupled with electrospray ionization hybrid linear trap quadrupole orbitrap (LC-LTQ-Orbitrap) mass spectrometry has been applied for online identification of chemical constituents in complex system, meanwhile, antioxidant profile of CSGS was investigated by the fraction collecting and microplate reading system. As a result, 33 chemical constituents in CSGS were identified. Among them, 13 components could be detected both in positive and in negative ion modes, 20 constituents were determined only in positive ion mode and 2 components were only detected in negative ion mode. Meanwhile, the potential antioxidant profile of CSGS was also characterized by combination of 96-well plate collection of elutes from HPLC analysis and microplate spectrophotometer, in which the scavenging activities of free radical produced by DPPH of each fraction could be directly investigated by the analysis of microplate reader. This study quickly screened the contribution of CSGS fractions to the antioxidant activity and online identified the corresponding active constituents. The results indicated that the combination of LC-MS(n) and 96-well plate assay system established in this paper would be a useful strategy for correlating the chemical profile of TCMs with their bioactivities without isolation and purification. Crown Copyright (c) 2010. Published by Elsevier B.V. All rights reserved.

[Internal fixation with one-hole microplate for the treatment of collateral ligament injuries of the metacarpophalangeal joint of the thumb combined with fracture].

Science.gov (United States)

Wang, Xi-Xun; Sun, De-Tao; Chen, Xu-Hui; Li, Jun; Cui, Yan; Hu, Ji-Chao; Shu, Zheng-Hua; He, Jian; Ding, Chao-Qi; Chen, Bo

2015-03-01

To study clinical effects of one-hole microplate internal fixation for the treatment of collateral ligament injuries of the metacarpophalangeal joint of the thumb combined with fracture. Twenty-two patients (16 males, 6 females) with collateral ligament injuries of the metacarpophalangeal joint of the thumb combined fracture were treated with one-hole microplate internal fixation. The age of the patients ranged from 18 to 53 years old with a mean age of 28.5 years old. The duration from injury to surgery ranged from 2 hours to 2 months, and the mean time was 6 days. All the patients had collateral ligament injuries combined with fracture of the metacarpophalangeal joint of the thumb. Thirteen patients had injuries in the right hand and 9 patients had injuries in the left hand. There were 18 cases of closed wound and 4 cases of open wound. Eighteen patients had fresh injuries ( 2 weeks). Sixteen patients had injuries in the ulnar collateral ligament of the thumb combined with fracture, 6 patients had radial collateral ligament injuries of the thumb combined with fracture, 4 cases of which were complicated with injuries of abductor pollicis brevis and the end of the flexor pollicis brevis tender. The size of the avulsed fragment was about 3.0 mm x 4.0 mm to 6.0 mm x 7.0 mm. The incisions of 22 patients healed by first intention. The follow-up periods ranged from 6 months to 5 years old,with an average of 2.5 years old. The thumb function was evaluated by Saetta and other evaluation criteria, and 20 patients got an excellent result and 2 good. The application of one-hole microplate internal fixation in treating collateral ligament injuries with fracture of the metacarpophalangeal joint of the thumb is an effective method.

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

Science.gov (United States)

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

2016-04-07

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

Effect of Temperature Rising on the Stygobitic Crustacean Species Diacyclops belgicus: Does Global Warming Affect Groundwater Populations?

Directory of Open Access Journals (Sweden)

Tiziana Di Lorenzo

2017-12-01

Full Text Available The average global temperature is predicted to increase by 3 °C by the end of this century due to human-induced climate change. The overall metabolism of the aquatic biota will be directly affected by rising temperatures and associated changes. Since thermal stability is a characteristic of groundwater ecosystems, global warming is expected to have a profound effect on the groundwater fauna. The prediction that stygobitic (obligate groundwater dweller species are vulnerable to climate change includes assumptions about metabolic effects that can only be tested by comparisons across a thermal gradient. To this end, we investigated the effects of two different thermal regimes on the metabolism of the stygobitic copepod species Diacyclops belgicus (Kiefer, 1936. We measured the individual-based oxygen consumption of this species as a proxy of possible metabolic reactions to temperature rising from 14 to 17 °C. We used a sealed glass microplate equipped with planar oxygen sensor spots with optical isolation glued onto the bottom of 80-μL wells integrated with a 24-channel fluorescence-based respirometry system. The tests have provided controversial results according to which the D. belgicus populations should be prudently considered at risk under a global warming scenario.

Quantitative Characterization of the Toxicities of Cd-Ni and Cd-Cr Binary Mixtures Using Combination Index Method

Directory of Open Access Journals (Sweden)

Lingyun Mo

2016-01-01

Full Text Available Direct equipartition ray design was used to construct Cd-Ni and Cd-Cr binary mixtures. Microplate toxicity analysis was used to evaluate the toxicity of individual substance and the Cd-Ni and Cd-Cr mixtures on Chlorella pyrenoidosa and Selenastrum capricornutum. The interacting toxicity of the mixture was analyzed with concentration addition (CA model. In addition, combination index method (CI was proposed and used to quantitatively characterize the toxicity of the binary mixtures of Cd-Ni and Cd-Cr observed in experiment and find the degree of deviation from the predicted outcome of the CA model, that is, the intensity of interacting toxicity. Results indicate that most of the 20 binary mixtures exhibit enhancing and synergistic effect, and only Cd-Cr-R4 and Cd-Cr-R5 mixtures have relatively high antagonistic effects against C. pyrenoidosa. Based on confidence interval, CI can compare the intensities of interaction of the mixtures under varying levels of effect. The characterization methods are applicable for analyzing binary mixture with complex interaction.

A new barrier to dispersal trapped old genetic clines that escaped the Easter Microplate tension zone of the Pacific vent mussels.

Science.gov (United States)

Plouviez, Sophie; Faure, Baptiste; Le Guen, Dominique; Lallier, François H; Bierne, Nicolas; Jollivet, Didier

2013-01-01

Comparative phylogeography of deep-sea hydrothermal vent species has uncovered several genetic breaks between populations inhabiting northern and southern latitudes of the East Pacific Rise. However, the geographic width and position of genetic clines are variable among species. In this report, we further characterize the position and strength of barriers to gene flow between populations of the deep-sea vent mussel Bathymodiolus thermophilus. Eight allozyme loci and DNA sequences of four nuclear genes were added to previously published sequences of the cytochrome c oxidase subunit I gene. Our data confirm the presence of two barriers to gene flow, one located at the Easter Microplate (between 21°33'S and 31°S) recently described as a hybrid zone, and the second positioned between 7°25'S and 14°S with each affecting different loci. Coalescence analysis indicates a single vicariant event at the origin of divergence between clades for all nuclear loci, although the clines are now spatially discordant. We thus hypothesize that the Easter Microplate barrier has recently been relaxed after a long period of isolation and that some genetic clines have escaped the barrier and moved northward where they have subsequently been trapped by a reinforcing barrier to gene flow between 7°25'S and 14°S.

Monitoring and controlling the biological purification process in a waste water treatment plant using a respirometry analyser; Vigilancia y control del proceso de la depuracion biologica en una EDAR por medio de un analizador de respirometria

Energy Technology Data Exchange (ETDEWEB)

Serrano, J. E.

2004-07-01

In a waste water biological treatment, we have to take into account that the activated sludge is a living and breathing process, and a lack of bioactivity information might cause serious confusion about control criteria on the biological reactor. For this reason, to get bioactivity information in a timely manner through the respiration analysis would be a real breakthrough in better process control. Therefore, to identify the respiration rates and calculate their derived parameters represents the guidelines of respirometry and can be considered as the most sensitive variables on the basis of which activated sludge process theory can be validated. (Author)

[Reconstituting evaluation methods based on both qualitative and quantitative paradigms].

Science.gov (United States)

Miyata, Hiroaki; Okubo, Suguru; Yoshie, Satoru; Kai, Ichiro

2011-01-01

Debate about the relationship between quantitative and qualitative paradigms is often muddled and confusing and the clutter of terms and arguments has resulted in the concepts becoming obscure and unrecognizable. In this study we conducted content analysis regarding evaluation methods of qualitative healthcare research. We extracted descriptions on four types of evaluation paradigm (validity/credibility, reliability/credibility, objectivity/confirmability, and generalizability/transferability), and classified them into subcategories. In quantitative research, there has been many evaluation methods based on qualitative paradigms, and vice versa. Thus, it might not be useful to consider evaluation methods of qualitative paradigm are isolated from those of quantitative methods. Choosing practical evaluation methods based on the situation and prior conditions of each study is an important approach for researchers.

Two types of nanoparticle-based bio-barcode amplification assays to detect HIV-1 p24 antigen

Directory of Open Access Journals (Sweden)

Dong Huahuang

2012-08-01

Full Text Available Abstract Background HIV-1 p24 antigen is a major viral component of human immunodeficiency virus type 1 (HIV-1 which can be used to identify persons in the early stage of infection and transmission of HIV-1 from infected mothers to infants. The detection of p24 is usually accomplished by using an enzyme-linked immunosorbent assay (ELISA with low detection sensitivity. Here we report the use of two bio-barcode amplification (BCA assays combined with polymerase chain reaction (PCR and gel electrophoresis to quantify HIV-1 p24 antigen. Method A pair of anti-p24 monoclonal antibodies (mAbs were used in BCA assays to capture HIV-1 p24 antigen in a sandwich format and allowed for the quantitative measurement of captured p24 using PCR and gel electrophoresis. The first 1 G12 mAb was coated on microplate wells or magnetic microparticles (MMPs to capture free p24 antigens. Captured p24 in turn captured 1D4 mAb coated gold nanoparticle probes (GNPs containing double-stranded DNA oligonucleotides. One strand of the oligonucleotides was covalently immobilized whereas the unbound complimentary bio-barcode DNA strand could be released upon heating. The released bio-barcode DNA was amplified by PCR, electrophoresed in agarose gel and quantified. Results The in-house ELISA assay was found to quantify p24 antigen with a limit of detection (LOD of 1,000 pg/ml and a linear range between 3,000 and 100,000 pg/ml. In contrast, the BCA-based microplate method yielded an LOD of 1 pg/ml and a linear detection range from 1 to 10,000 pg/ml. The BCA-based MMP method yielded an LOD of 0.1 pg/ml and a linear detection range from 0.1 to 1,000 pg/ml. Conclusions When combined with PCR and simple gel electrophoresis, BCA-based microplate and MMPs assays can be used to quantify HIV-1 p24 antigen. These methods are 3–4 orders of magnitude more sensitive than our in-house ELISA-based assay and may provide a useful approach to detect p24 in patients newly infected

A CT-based method for fully quantitative TI SPECT

International Nuclear Information System (INIS)

Willowson, Kathy; Bailey, Dale; Baldock, Clive

2009-01-01

Full text: Objectives: To develop and validate a method for quantitative 2 0 l TI SPECT data based on corrections derived from X-ray CT data, and to apply the method in the clinic for quantitative determination of recurrence of brain tumours. Method: A previously developed method for achieving quantitative SPECT with 9 9 m Tc based on corrections derived from xray CT data was extended to apply to 2 0 l Tl. Experimental validation was performed on a cylindrical phantom by comparing known injected activity and measured concentration to quantitative calculations. Further evaluation was performed on a RSI Striatal Brain Phantom containing three 'lesions' with activity to background ratios of 1: 1, 1.5: I and 2: I. The method was subsequently applied to a series of scans from patients with suspected recurrence of brain tumours (principally glioma) to determine an SUV-like measure (Standardised Uptake Value). Results: The total activity and concentration in the phantom were calculated to within 3% and I % of the true values, respectively. The calculated values for the concentration of activity in the background and corresponding lesions of the brain phantom (in increasing ratios) were found to be within 2%,10%,1% and 2%, respectively, of the true concentrations. Patient studies showed that an initial SUV greater than 1.5 corresponded to a 56% mortality rate in the first 12 months, as opposed to a 14% mortality rate for those with a SUV less than 1.5. Conclusion: The quantitative technique produces accurate results for the radionuclide 2 0 l Tl. Initial investigation in clinical brain SPECT suggests correlation between quantitative uptake and survival.

A novel multi-walled carbon nanotube-based antibody conjugate for quantitative and semi-quantitative lateral flow assays.

Science.gov (United States)

Sun, Wenjuan; Hu, Xiaolong; Liu, Jia; Zhang, Yurong; Lu, Jianzhong; Zeng, Libo

2017-10-01

In this study, the multi-walled carbon nanotubes (MWCNTs) were applied in lateral flow strips (LFS) for semi-quantitative and quantitative assays. Firstly, the solubility of MWCNTs was improved using various surfactants to enhance their biocompatibility for practical application. The dispersed MWCNTs were conjugated with the methamphetamine (MET) antibody in a non-covalent manner and then manufactured into the LFS for the quantitative detection of MET. The MWCNTs-based lateral flow assay (MWCNTs-LFA) exhibited an excellent linear relationship between the values of test line and MET when its concentration ranges from 62.5 to 1500 ng/mL. The sensitivity of the LFS was evaluated by conjugating MWCNTs with HCG antibody and the MWCNTs conjugated method is 10 times more sensitive than the one conjugated with classical colloidal gold nanoparticles. Taken together, our data demonstrate that MWCNTs-LFA is a more sensitive and reliable assay for semi-quantitative and quantitative detection which can be used in forensic analysis.

Enterococcus faecalis infection causes inflammation, intracellular oxphos-independent ROS production, and DNA damage in human gastric cancer cells.

Directory of Open Access Journals (Sweden)

Jesper A B Strickertsson

Full Text Available BACKGROUND: Achlorhydria caused by e.g. atrophic gastritis allows for bacterial overgrowth, which induces chronic inflammation and damage to the mucosal cells of infected individuals driving gastric malignancies and cancer. Enterococcus faecalis (E. faecalis can colonize achlohydric stomachs and we therefore wanted to study the impact of E. faecalis infection on inflammatory response, reactive oxygen species (ROS formation, mitochondrial respiration, and mitochondrial genetic stability in gastric mucosal cells. METHODS: To separate the changes induced by bacteria from those of the inflammatory cells we established an in vitro E. faecalis infection model system using the gastric carcinoma cell line MKN74. Total ROS and superoxide was measured by fluorescence microscopy. Cellular oxygen consumption was characterized non-invasively using XF24 microplate based respirometry. Gene expression was examined by microarray, and response pathways were identified by Gene Set Analysis (GSA. Selected gene transcripts were verified by quantitative real-time polymerase chain reaction (qRT-PCR. Mitochondrial mutations were determined by sequencing. RESULTS: Infection of MKN74 cells with E. faecalis induced intracellular ROS production through a pathway independent of oxidative phosphorylation (oxphos. Furthermore, E. faecalis infection induced mitochondrial DNA instability. Following infection, genes coding for inflammatory response proteins were transcriptionally up-regulated while DNA damage repair and cell cycle control genes were down-regulated. Cell growth slowed down when infected with viable E. faecalis and responded in a dose dependent manner to E. faecalis lysate. CONCLUSIONS: Infection by E. faecalis induced an oxphos-independent intracellular ROS response and damaged the mitochondrial genome in gastric cell culture. Finally the bacteria induced an NF-κB inflammatory response as well as impaired DNA damage response and cell cycle control gene

Quantitative tectonic reconstructions of Zealandia based on crustal thickness estimates

Science.gov (United States)

Grobys, Jan W. G.; Gohl, Karsten; Eagles, Graeme

2008-01-01

Zealandia is a key piece in the plate reconstruction of Gondwana. The positions of its submarine plateaus are major constraints on the best fit and breakup involving New Zealand, Australia, Antarctica, and associated microplates. As the submarine plateaus surrounding New Zealand consist of extended and highly extended continental crust, classic plate tectonic reconstructions assuming rigid plates and narrow plate boundaries fail to reconstruct these areas correctly. However, if the early breakup history shall be reconstructed, it is crucial to consider crustal stretching in a plate-tectonic reconstruction. We present a reconstruction of the basins around New Zealand (Great South Basin, Bounty Trough, and New Caledonia Basin) based on crustal balancing, an approach that takes into account the rifting and thinning processes affecting continental crust. In a first step, we computed a crustal thickness map of Zealandia using seismic, seismological, and gravity data. The crustal thickness map shows the submarine plateaus to have a uniform crustal thickness of 20-24 km and the basins to have a thickness of 12-16 km. We assumed that a reconstruction of Zealandia should close the basins and lead to a most uniform crustal thickness. We used the standard deviation of the reconstructed crustal thickness as a measure of uniformity. The reconstruction of the Campbell Plateau area shows that the amount of extension in the Bounty Trough and the Great South Basin is far smaller than previously thought. Our results indicate that the extension of the Bounty Trough and Great South Basin occurred simultaneously.

Cutaneous Respirometry as Novel Technique to Monitor Mitochondrial Function: A Feasibility Study in Healthy Volunteers

Science.gov (United States)

Stolker, Robert Jan; Mik, Egbert

2016-01-01

Background The protoporphyrin IX-triplet state lifetime technique (PpIX-TSLT) is proposed as a potential clinical non-invasive tool to monitor mitochondrial function. This technique has been evaluated in several animal studies. Mitochondrial respirometry allows measurement in vivo of mitochondrial oxygen tension (mitoPO2) and mitochondrial oxygen consumption (mitoVO2) in skin. This study describes the first use of a clinical prototype in skin of humans. Methods The clinical prototype was tested in 30 healthy volunteers. A self-adhesive patch containing 2 mg 5-aminolevulinic acid (ALA) was applied on the skin of the anterior chest wall (sternal) for induction of mitochondrial protoporphyrin IX and was protected from light for 5 h. MitoPO2 was measured by means of oxygen-dependent delayed fluorescence of protoporphyrin IX. MitoVO2 was determined by dynamic mitoPO2 measurements on the primed skin, while locally blocking oxygen supply by applying local pressure with the measurement probe. MitoPO2 was recorded before and during a 60-s period of compression of the microcirculation, at an interval of 1 Hz. Oxygen consumption (i.e. the local oxygen disappearance rate) was calculated from the decay of the mitoPO2 slope. Results Oxygen-dependent delayed fluorescence measurements were successfully performed in the skin of 27 volunteers. The average value (± SD) of mitoPO2 was 44 ± 17 mmHg and mean mitoVO2 values were 5.8 ± 2.3 and 6.1 ± 1.6 mmHg s-1 at a skin temperature of 34°C and 40°C, respectively. No major discomfort during measurement and no long-term dermatological abnormalities were reported in a survey performed 1 month after measurements. Conclusion These results show that the clinical prototype allows measurement of mitochondrial oxygenation and oxygen consumption in humans. The development of this clinically applicable device offers opportunities for further evaluation of the technique in humans and the start of first clinical studies. PMID:27455073

Quantitative SIMS Imaging of Agar-Based Microbial Communities.

Science.gov (United States)

Dunham, Sage J B; Ellis, Joseph F; Baig, Nameera F; Morales-Soto, Nydia; Cao, Tianyuan; Shrout, Joshua D; Bohn, Paul W; Sweedler, Jonathan V

2018-05-01

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

Establishment of Dimethyl Labeling-based Quantitative Acetylproteomics in Arabidopsis.

Science.gov (United States)

Liu, Shichang; Yu, Fengchao; Yang, Zhu; Wang, Tingliang; Xiong, Hairong; Chang, Caren; Yu, Weichuan; Li, Ning

2018-05-01

Protein acetylation, one of many types of post-translational modifications (PTMs), is involved in a variety of biological and cellular processes. In the present study, we applied both C sCl d ensity g radient (CDG) centrifugation-based protein fractionation and a dimethyl-labeling-based 4C quantitative PTM proteomics workflow in the study of dynamic acetylproteomic changes in Arabidopsis. This workflow integrates the dimethyl c hemical labeling with c hromatography-based acetylpeptide separation and enrichment followed by mass spectrometry (MS) analysis, the extracted ion chromatogram (XIC) quantitation-based c omputational analysis of mass spectrometry data to measure dynamic changes of acetylpeptide level using an in-house software program, named S table isotope-based Qua ntitation- D imethyl labeling (SQUA-D), and finally the c onfirmation of ethylene hormone-regulated acetylation using immunoblot analysis. Eventually, using this proteomic approach, 7456 unambiguous acetylation sites were found from 2638 different acetylproteins, and 5250 acetylation sites, including 5233 sites on lysine side chain and 17 sites on protein N termini, were identified repetitively. Out of these repetitively discovered acetylation sites, 4228 sites on lysine side chain ( i.e. 80.5%) are novel. These acetylproteins are exemplified by the histone superfamily, ribosomal and heat shock proteins, and proteins related to stress/stimulus responses and energy metabolism. The novel acetylproteins enriched by the CDG centrifugation fractionation contain many cellular trafficking proteins, membrane-bound receptors, and receptor-like kinases, which are mostly involved in brassinosteroid, light, gravity, and development signaling. In addition, we identified 12 highly conserved acetylation site motifs within histones, P-glycoproteins, actin depolymerizing factors, ATPases, transcription factors, and receptor-like kinases. Using SQUA-D software, we have quantified 33 ethylene hormone-enhanced and

Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples.

Science.gov (United States)

Zellner, Maria; Babeluk, Rita; Diestinger, Michael; Pirchegger, Petra; Skeledzic, Senada; Oehler, Rudolf

2008-09-01

Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.

Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity.

Science.gov (United States)

Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A; Bradford, William D; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S; Li, Rong

2015-03-30

Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein-based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. Copyright © 2015 Zhu et al.

Re-evaluating Gondwana breakup: Magmatism, movement and microplates

Science.gov (United States)

Ferraccioli, F.; Jordan, T. A.

2017-12-01

Gondwana breakup is thought to have initiated in the Early- to Mid-Jurassic between South Africa and East Antarctica. The critical stages of continental extension and magmatism which preceded breakup remain controversial. It is agreed that extensive magmatism struck this region 180 Ma, and that significant extension occurred in the Weddell Sea Rift System (WSRS) and around the Falkland Plateau. However, the timing and volume of magmatism, extent and mechanism of continental extension, and the links with the wider plate circuit are poorly constrained. Jordan et al (Gondwana Research 2017) recently proposed a two-stage model for the formation of the WSRS: initial extension and movement of the Ellsworth Whitmore Mountains microplate along the margin of the East Antarctic continent on a sinistral strike slip fault zone, followed by transtensional extension closer to the continental margin. Here we identify some key questions raised by the two-stage model, and identify regions where these can be tested. Firstly, is the magmatism inferred to have facilitated extension in the WSRS directly linked to the onshore Dufek Intrusion? This question relates to both the uncertainty in the volume of magmatism and potentially the timing of extension, and requires improved resolution of aeromagnetic data in the eastern WSRS. Secondly, did extension in the WSRS terminate against a single strike slip fault zone or into a distributed fault system? By integrating new and existing aeromagnetic data along the margin of East Antarctica we evaluate the possibility of a distributed shear zone penetrating the East Antarctic continent, and identify critical remaining data gaps. Finally we question how extension within the WSRS could fit into the wider plate circuit. By integrating the two-stage model into Gplates reconstructions we identify regions of overlap and areas where tracers of past plate motion could be identified.

Probe colorimeter for quantitating enzyme-linked immunosorbent assays and other colorimetric assays performed with microplates.

Science.gov (United States)

Ackerman, S B; Kelley, E A

1983-03-01

The performance of a fiberoptic probe colorimeter (model PC800; Brinkmann Instruments, Inc., Westbury, N.Y.) for quantitating enzymatic or colorimetric assays in 96-well microtiter plates was compared with the performances of a spectrophotometer (model 240; Gilford Instrument Laboratories, Inc., Oberlin, Ohio) and a commercially available enzyme immunoassay reader (model MR590; Dynatech Laboratories, Inc., Alexandria, Va.). Alkaline phosphatase-p-nitrophenyl phosphate in 3 M NaOH was used as the chromophore source. Six types of plates were evaluated for use with the probe colorimeter; they generated reproducibility values (100% coefficient of variation) ranging from 91 to 98% when one individual made 24 independent measurements on the same dilution of chromophore on each plate. Eleven individuals each performed 24 measurements with the colorimeter on either a visually light (absorbance of 0.10 at 420 nm) or a dark (absorbance of 0.80 at 420 nm) dilution of chromophore; reproducibilities averaged 87% for the light dilution and 97% for the dark dilution. When one individual measured the same chromophore sample at least 20 times in the colorimeter, in the spectrophotometer or in the enzyme immunoassay reader, reproducibility for each instrument was greater than 99%. Measurements of a dilution series of chromophore in a fixed volume indicated that the optical responses of each instrument were linear in a range of 0.05 to 1.10 absorbance units.

A polychromatic turbidity microplate assay to distinguish discovery stage drug molecules with beneficial precipitation properties.

Science.gov (United States)

Morrison, John; Nophsker, Michelle; Elzinga, Paul; Donoso, Maria; Park, Hyunsoo; Haskell, Roy

2017-10-05

A material sparing microplate screening assay was developed to evaluate and compare the precipitation of discovery stage drug molecules as a function of time, concentration and media composition. Polychromatic turbidity time course profiles were collected for cinnarizine, probucol, dipyridamole as well as BMS-932481, and compared with turbidity profiles of monodisperse particle size standards. Precipitation for select sample conditions were further characterized at several time points by size, morphology, amount and form via laser diffraction, microscopy, size based particle counting and X-ray diffraction respectively. Wavelength dependent turbidity was found indicative of nanoprecipitate, while wavelength independent turbidity was consistent with larger microprecipitate formation. A transition from wavelength dependent to wavelength independent turbidity occurred for nanoparticle to microparticle growth, and a decrease in wavelength independent turbidity correlated with continued growth in size of microparticles. Other sudden changes in turbidity signal over time such as rapid fluctuation, a decrease in slope or a sharp inversion were correlated with very large or aggregated macro-precipitates exceeding 100μm in diameter, a change in the rate of precipitate formation or an amorphous to crystalline form conversion respectively. The assay provides an effective method to efficiently monitor and screen the precipitation fates of drug molecules, even during the early stages of discovery with limited amounts of available material. This capability highlights molecules with beneficial precipitation properties that are able to generate and maintain solubility enabling amorphous or nanoparticle precipitates. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative Comparison of Tolerance-Based Feature Transforms

OpenAIRE

Reniers, Dennie; Telea, Alexandru

2006-01-01

Tolerance-based feature transforms (TFTs) assign to each pixel in an image not only the nearest feature pixels on the boundary (origins), but all origins from the minimum distance up to a user-defined tolerance. In this paper, we compare four simple-to-implement methods for computing TFTs for binary images. Of these, two are novel methods and two extend existing distance transform algorithms. We quantitatively and qualitatively compare all algorithms on speed and accuracy of both distance and...

MR Imaging-based Semi-quantitative Methods for Knee Osteoarthritis

Science.gov (United States)

JARRAYA, Mohamed; HAYASHI, Daichi; ROEMER, Frank Wolfgang; GUERMAZI, Ali

2016-01-01

Magnetic resonance imaging (MRI)-based semi-quantitative (SQ) methods applied to knee osteoarthritis (OA) have been introduced during the last decade and have fundamentally changed our understanding of knee OA pathology since then. Several epidemiological studies and clinical trials have used MRI-based SQ methods to evaluate different outcome measures. Interest in MRI-based SQ scoring system has led to continuous update and refinement. This article reviews the different SQ approaches for MRI-based whole organ assessment of knee OA and also discuss practical aspects of whole joint assessment. PMID:26632537

Cell mediated lympholysis: CML. A microplate technique requiring few target cells and employing a new method of supernatant collection

International Nuclear Information System (INIS)

Hirschberg, A.; Thorsby, E.

1977-01-01

A micromethod for the 51 Cr release assay is described. Allogeneically induced cytotoxic lymphocytes are generated in mixed lymphocyte microcultures in the wells of microplates. Their cytotoxic capacity is assayed by adding 51 Cr-labelled PHA derived lymphoblasts directly into the microcultures with no pooling or transfer of the cytotoxic effector cells being required. The 51 Cr isotope released into the cell supernatants is collected by inserting a cellulose acetate absorption cartridge into each well. A glass fiber filter attached to the cartridge effectively separates the supernatant from the cellular elemets. This system allows the simultaneous collection of the supernatant from 96 wells, and can be used with either adherent or non-adherent target cells

Duration of plant damage by host larvae affects attraction of two parasitoid species (Microplitis croceipes and Cotesia marginiventris) to cotton: implications for interspecific competition.

Science.gov (United States)

Morawo, Tolulope; Fadamiro, Henry

2014-12-01

Volatile organic compounds (VOCs) released by herbivore-damaged plants can guide parasitoids to their hosts. The quantity and quality of VOC blends emitted by plants may be affected by the duration of plant damage by herbivores, which could have potential ramifications on the recruitment of competing parasitoids. We used two parasitoid species, Microplitis croceipes and Cotesia marginiventris (Hymenoptera: Braconidae), to address the question of whether duration of plant damage affects parasitoid use of plant VOCs for host location. Both wasp species are larval endoparasitoids of Heliothis virescens (Lepidoptera: Noctuidae), an important pest of cotton. Attraction of the two parasitoid species to odors emitted by undamaged (UD), fresh (6 h infestation) damage (FD), and old (24 h infestation) damage (OD) cotton plants infested by H. virescens larvae was investigated using a headspace volatile collection system coupled with four-choice olfactometer bioassay. Both sexes of M. croceipes showed a preference for FD- and OD-plant odors over UD-plants. On the other hand, more C. marginiventris females were attracted to UD- and FD-plants than to OD-plants. GC/MS analyses showed qualitative and quantitative differences in the VOC profiles of UD, FD, and OD-plants, which may explain the observed preferences of the parasitoids. These results suggest a temporal partitioning in the recruitment of M. croceipes and C. marginiventris to H. virescens-damaged cotton, and may have potential implications for interspecific competition between the two parasitoid species.

Gene structure and expression characteristic of a novel odorant receptor gene cluster in the parasitoid wasp Microplitis mediator (Hymenoptera: Braconidae).

Science.gov (United States)

Wang, S-N; Shan, S; Zheng, Y; Peng, Y; Lu, Z-Y; Yang, Y-Q; Li, R-J; Zhang, Y-J; Guo, Y-Y

2017-08-01

Odorant receptors (ORs) expressed in the antennae of parasitoid wasps are responsible for detection of various lipophilic airborne molecules. In the present study, 107 novel OR genes were identified from Microplitis mediator antennal transcriptome data. Phylogenetic analysis of the set of OR genes from M. mediator and Microplitis demolitor revealed that M. mediator OR (MmedOR) genes can be classified into different subfamilies, and the majority of MmedORs in each subfamily shared high sequence identities and clear orthologous relationships to M. demolitor ORs. Within a subfamily, six MmedOR genes, MmedOR98, 124, 125, 126, 131 and 155, shared a similar gene structure and were tightly linked in the genome. To evaluate whether the clustered MmedOR genes share common regulatory features, the transcription profile and expression characteristics of the six closely related OR genes were investigated in M. mediator. Rapid amplification of cDNA ends-PCR experiments revealed that the OR genes within the cluster were transcribed as single mRNAs, and a bicistronic mRNA for two adjacent genes (MmedOR124 and MmedOR98) was also detected in female antennae by reverse transcription PCR. In situ hybridization experiments indicated that each OR gene within the cluster was expressed in a different number of cells. Moreover, there was no co-expression of the two highly related OR genes, MmedOR124 and MmedOR98, which appeared to be individually expressed in a distinct population of neurons. Overall, there were distinct expression profiles of closely related MmedOR genes from the same cluster in M. mediator. These data provide a basic understanding of the olfactory coding in parasitoid wasps. © 2017 The Royal Entomological Society.

Abundancia y distribución de microplásticos y posibles impactos sobre el rorcual común (Balaenoptera physalus) en las costas del Garraf

OpenAIRE

Tintoré Pujol-Soliano, Beatriz

2016-01-01

En este Trabajo de Final de Grado se exponen los resultados del estudio realizado con la asociación EDMAKTUB durante el “Proyecto Rorcual”, que tiene como objetivo el estudio del rorcual común (B. physalus), que puede encontrarse durante los meses de Febrero a Junio en las costas catalanas del Garraf, cerca de Barcelona. Aprovechando este proyecto, se llevo a cabo un estudio preliminar de la concentración de microplásticos en las aguas superficiales de la costa del Garraf. Los objetivos princ...

Controllable Fabrication and Tuned Electrochemical Performance of Potassium Co-Ni Phosphate Microplates as Electrodes in Supercapacitors.

Science.gov (United States)

Liang, Bo; Chen, Yule; He, Jiangyu; Chen, Chen; Liu, Wenwen; He, Yuanqing; Liu, Xiaohe; Zhang, Ning; Roy, Vellaisamy A L

2018-01-31

Most reported pristine phosphates, such as NH 4 MPO 4 ·H 2 O (M = Co, Ni), are not very stable as supercapacitor electrodes because of their chemical properties. In this work, KCo x Ni 1-x PO 4 ·H 2 O microplates were fabricated by a facile hydrothermal method at low temperature and used as electrodes in supercapacitors. The Co and Ni content could be adjusted, and optimal electrochemical performance was found in KCo 0.33 Ni 0.67 PO 4 ·H 2 O, which also possessed superior specific capacitance, rate performance, and long-term chemical stability compared with NH 4 Co 0.33 Ni 0.67 PO 4 ·H 2 O because of its unique chemical composition and microstructure. Asymmetric supercapacitor cells based on KCo 0.33 Ni 0.67 PO 4 ·H 2 O and active carbon were assembled, which produce specific capacitance of 34.7 mA h g -1 (227 F g -1 ) under current density of 1.5 A g -1 and retain 82% as initial specific capacitance after charging and discharging approximately 5000 times. The assembled asymmetric supercapacitor cells (ASCs) exhibited much higher power and energy density than most previously reported transition metal phosphate ASCs. The KCo x Ni 1-x PO 4 ·H 2 O electrodes fabricated in this work are efficient, inexpensive, and composed of naturally abundant materials, rendering them promising for energy storage device applications.

Contaminação e toxicidade de microplásticos em uma área de proteção marinha costeira

OpenAIRE

Pablo Pena Gandara e Silva

2016-01-01

Os plásticos têm trazido grandes benefícios aos humanos, sendo utilizados em diversas atividades como em aplicações médicas, entretenimento e na indústria de alimento. O uso crescente de plástico e seu descarte não adequado têm contribuído para o acúmulo deste detrito no meio ambiente, em especial nos oceanos onde tendem a acumular. Dentre os detritos de plástico de maior importância atualmente estão os microplásticos, que são partículas de plástico de tamanho entre 1 μm e 5 mm. Os princ...

Design of cinnamaldehyde amino acid Schiff base compounds based on the quantitative structure–activity relationship

Science.gov (United States)

Hui Wang; Mingyue Jiang; Shujun Li; Chung-Yun Hse; Chunde Jin; Fangli Sun; Zhuo Li

2017-01-01

Cinnamaldehyde amino acid Schiff base (CAAS) is a new class of safe, bioactive compounds which could be developed as potential antifungal agents for fungal infections. To design new cinnamaldehyde amino acid Schiff base compounds with high bioactivity, the quantitative structure–activity relationships (QSARs) for CAAS compounds against Aspergillus niger (A. niger) and...

Quantitative evaluation methods of skin condition based on texture feature parameters

Directory of Open Access Journals (Sweden)

Hui Pang

2017-03-01

Full Text Available In order to quantitatively evaluate the improvement of the skin condition after using skin care products and beauty, a quantitative evaluation method for skin surface state and texture is presented, which is convenient, fast and non-destructive. Human skin images were collected by image sensors. Firstly, the median filter of the 3 × 3 window is used and then the location of the hairy pixels on the skin is accurately detected according to the gray mean value and color information. The bilinear interpolation is used to modify the gray value of the hairy pixels in order to eliminate the negative effect of noise and tiny hairs on the texture. After the above pretreatment, the gray level co-occurrence matrix (GLCM is calculated. On the basis of this, the four characteristic parameters, including the second moment, contrast, entropy and correlation, and their mean value are calculated at 45 ° intervals. The quantitative evaluation model of skin texture based on GLCM is established, which can calculate the comprehensive parameters of skin condition. Experiments show that using this method evaluates the skin condition, both based on biochemical indicators of skin evaluation methods in line, but also fully consistent with the human visual experience. This method overcomes the shortcomings of the biochemical evaluation method of skin damage and long waiting time, also the subjectivity and fuzziness of the visual evaluation, which achieves the non-destructive, rapid and quantitative evaluation of skin condition. It can be used for health assessment or classification of the skin condition, also can quantitatively evaluate the subtle improvement of skin condition after using skin care products or stage beauty.

Quantitative evaluation methods of skin condition based on texture feature parameters.

Science.gov (United States)

Pang, Hui; Chen, Tianhua; Wang, Xiaoyi; Chang, Zhineng; Shao, Siqi; Zhao, Jing

2017-03-01

In order to quantitatively evaluate the improvement of the skin condition after using skin care products and beauty, a quantitative evaluation method for skin surface state and texture is presented, which is convenient, fast and non-destructive. Human skin images were collected by image sensors. Firstly, the median filter of the 3 × 3 window is used and then the location of the hairy pixels on the skin is accurately detected according to the gray mean value and color information. The bilinear interpolation is used to modify the gray value of the hairy pixels in order to eliminate the negative effect of noise and tiny hairs on the texture. After the above pretreatment, the gray level co-occurrence matrix (GLCM) is calculated. On the basis of this, the four characteristic parameters, including the second moment, contrast, entropy and correlation, and their mean value are calculated at 45 ° intervals. The quantitative evaluation model of skin texture based on GLCM is established, which can calculate the comprehensive parameters of skin condition. Experiments show that using this method evaluates the skin condition, both based on biochemical indicators of skin evaluation methods in line, but also fully consistent with the human visual experience. This method overcomes the shortcomings of the biochemical evaluation method of skin damage and long waiting time, also the subjectivity and fuzziness of the visual evaluation, which achieves the non-destructive, rapid and quantitative evaluation of skin condition. It can be used for health assessment or classification of the skin condition, also can quantitatively evaluate the subtle improvement of skin condition after using skin care products or stage beauty.

Microplacas de titânio em fraturas de tibiotarso em pombos domésticos Titanium microplates for treatment of tibiotarsus fractures in pigeons

Directory of Open Access Journals (Sweden)

Aline Silva Gouvêa

2011-03-01

grupo 3, houve maior precocidade no apoio do membro e menor grau de envergamento em relação aos outros grupos. Histologicamente, foi verificada a formação de calo ósseo em todos os animais e presença de tecido ósseo ao redor da microplaca e dos microparafusos. Apesar das complicações observadas, as microplacas de titânio são uma opção para osteossíntese de tibiotarso em aves de médio porte.Among the surgical problems in birds, the fractures are the most prevalent. Due to variations in size, weight, peculiar bone anatomy, high incidence of complicated fractures and functional demands of different species and individuals, it is still not possible to establish an ideal method for osteosynthesis of long bones in birds. Titanium microplates commonly used in human maxillofacial surgery have been recently employed in osteosynthesis of birds, but with few results available. The aim of this study was to evaluate the use of titanium microplates in the treatment of tibiotarsus fractures in 30 pigeons (Columba livia , adult males and females, with 7 months old, weighing from 400 to 500. The animals were divided into 3 groups with ten animals each. In group 1, a titanium microplate with 6 holes and a central spacer was used; in group 2, a titanium microplate with 8 holes without a spacer in the center was used; in group 3, a titanium microplate with 8 holes with central spacer was used. After clinical evaluation, the birds were submitted to mid-diaphyseal osteotomy in the right bone for placement of different configurations of the titanium plate, and fixed with titanium microscrews 7mm long. The animals were evaluated clinically and radiographically until 90 days postoperatively. After this period, euthanasia was performed in 2 animals from each group. In all animals was observed bone healing and in group 1 the mean and standard deviation were 32.9±9.9 days, in group 2, 30.8±6.7 days in group 3, 26.6±6.4 days. There was no statistical difference in healing time

Quantitative metagenomic analyses based on average genome size normalization

DEFF Research Database (Denmark)

Frank, Jeremy Alexander; Sørensen, Søren Johannes

2011-01-01

provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data...... marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how......). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis....

GENETIC AND MORPHOAGRONOMIC DIVERSITY OF Passiflora spp. BASED ON QUANTITATIVE MEASUREMENTS OF FLOWERS AND FRUITS

Directory of Open Access Journals (Sweden)

JAMILE DA SILVA OLIVEIRA

Full Text Available ABSTRACT The aim of this study was to characterize Passiflora spp. accessions and its genetic diversity based on quantitative morphological descriptors of flowers and fruits. The study was conducted at Embrapa Cerrados, Planaltina-DF. Fifteen Passiflora spp. accessions were characterized using 14 quantitative morphological descriptors. Genetic distances among accessions were estimated based on Mahalanobis’ generalized distance. Cluster analysis via dendrogram and graphic dispersion was analyzed. The relative contribution of characters for accession divergence was also calculated. The morphoagronomic characterization based on quantitative descriptors of flowers and fruits contributed to the differentiation of Passiflora spp. accessions, serving as an important tool for variability quantification. This information is useful to perform Passiflora spp. characterization and genetic diversity studies.

A Bayesian belief nets based quantitative software reliability assessment for PSA: COTS case study

International Nuclear Information System (INIS)

Eom, H. S.; Sung, T. Y.; Jeong, H. S.; Park, J. H.; Kang, H. G.; Lee, K. Y.; Park, J. K

2002-03-01

Current reliability assessments of safety critical software embedded in the digital systems in nuclear power plants are based on the rule-based qualitative assessment methods. Then recently practical needs require the quantitative features of software reliability for Probabilistic Safety Assessment (PSA) that is one of important methods being used in assessing the whole safety of nuclear power plant. But conventional quantitative software reliability assessment methods are not enough to get the necessary results in assessing the safety critical software used in nuclear power plants. Thus, current reliability assessment methods for these digital systems exclude the software part or use arbitrary values for the software reliability in the assessment. This reports discusses a Bayesian Belief Nets (BBN) based quantification method that models current qualitative software assessment in formal way and produces quantitative results required for PSA. Commercial Off-The-Shelf (COTS) software dedication process that KAERI developed was applied to the discussed BBN based method for evaluating the plausibility of the proposed method in PSA

Respiromics – An integrative analysis linking mitochondrial bioenergetics to molecular signatures

Directory of Open Access Journals (Sweden)

Ellen Walheim

2018-03-01

Full Text Available Objective: Energy metabolism is challenged upon nutrient stress, eventually leading to a variety of metabolic diseases that represent a major global health burden. Methods: Here, we combine quantitative mitochondrial respirometry (Seahorse technology and proteomics (LC-MS/MS-based total protein approach to understand how molecular changes translate to changes in mitochondrial energy transduction during diet-induced obesity (DIO in the liver. Results: The integrative analysis reveals that significantly increased palmitoyl-carnitine respiration is supported by an array of proteins enriching lipid metabolism pathways. Upstream of the respiratory chain, the increased capacity for ATP synthesis during DIO associates strongest to mitochondrial uptake of pyruvate, which is routed towards carboxylation. At the respiratory chain, robust increases of complex I are uncovered by cumulative analysis of single subunit concentrations. Specifically, nuclear-encoded accessory subunits, but not mitochondrial-encoded or core units, appear to be permissive for enhanced lipid oxidation. Conclusion: Our integrative analysis, that we dubbed “respiromics”, represents an effective tool to link molecular changes to functional mechanisms in liver energy metabolism, and, more generally, can be applied for mitochondrial analysis in a variety of metabolic and mitochondrial disease models. Keywords: Mitochondria, Respirometry, Proteomics, Mitochondrial pyruvate carrier, Liver disease, Bioenergetics, Obesity, Diabetes

Quantitative Determination of Plasmodium vivax Gametocytes by Real-Time Quantitative Nucleic Acid Sequence-Based Amplification in Clinical Samples

NARCIS (Netherlands)

Beurskens, Martijn; Mens, Pètra; Schallig, Henk; Syafruddin, Din; Asih, Puji Budi Setia; Hermsen, Rob; Sauerwein, Robert

2009-01-01

Microscopic detection of Plasmodium vivax gametocytes, the sexual life stage of this malaria parasite, is insensitive because P vivax parasitaemia is low. To detect and quantity gametocytes a more sensitive, quantitative realtime Pvs25-QT-NASBA based oil Pvs25 mRNA was developed and tested in two

A quantitative risk-based model for reasoning over critical system properties

Science.gov (United States)

Feather, M. S.

2002-01-01

This position paper suggests the use of a quantitative risk-based model to help support reeasoning and decision making that spans many of the critical properties such as security, safety, survivability, fault tolerance, and real-time.

Quantitative autoradiography of semiconductor base material

International Nuclear Information System (INIS)

Treutler, H.C.; Freyer, K.

1983-01-01

Autoradiographic methods for the quantitative determination of elements interesting in semiconductor technology and their distribution in silicon are described. Whereas the local concentration and distribution of phosphorus has been determined with the aid of silver halide films the neutron-induced autoradiography has been applied in the case of boron. Silicon disks containing diffused phosphorus or implanted or diffused boron have been used as standard samples. Different possibilities of the quantitative evaluation of autoradiograms are considered and compared

MilQuant: a free, generic software tool for isobaric tagging-based quantitation.

Science.gov (United States)

Zou, Xiao; Zhao, Minzhi; Shen, Hongyan; Zhao, Xuyang; Tong, Yuanpeng; Wang, Qingsong; Wei, Shicheng; Ji, Jianguo

2012-09-18

Isobaric tagging techniques such as iTRAQ and TMT are widely used in quantitative proteomics and especially useful for samples that demand in vitro labeling. Due to diversity in choices of MS acquisition approaches, identification algorithms, and relative abundance deduction strategies, researchers are faced with a plethora of possibilities when it comes to data analysis. However, the lack of generic and flexible software tool often makes it cumbersome for researchers to perform the analysis entirely as desired. In this paper, we present MilQuant, mzXML-based isobaric labeling quantitator, a pipeline of freely available programs that supports native acquisition files produced by all mass spectrometer types and collection approaches currently used in isobaric tagging based MS data collection. Moreover, aside from effective normalization and abundance ratio deduction algorithms, MilQuant exports various intermediate results along each step of the pipeline, making it easy for researchers to customize the analysis. The functionality of MilQuant was demonstrated by four distinct datasets from different laboratories. The compatibility and extendibility of MilQuant makes it a generic and flexible tool that can serve as a full solution to data analysis of isobaric tagging-based quantitation. Copyright © 2012 Elsevier B.V. All rights reserved.

Effects of propanil, tebufenozide and mefenacet on growth of four freshwater species of phytoplankton: a microplate bioassay.

Science.gov (United States)

Gómez de Barreda Ferraz, D; Sabater, C; Carrasco, J M

2004-07-01

The Albufera Natural Park situated in Valencia (Spain), with a very rich flora and fauna is surrounded by rice fields in which pesticide spraying is a regular practice. With this in mind, the sensitivity of four algal species, Scenedesmus acutus, Scenedesmus subspicatus, Chlorella vulgaris and Chlorella saccharophila to pesticides propanil, tebufenozide and mefenacet was studied using single species toxicity tests. Organisms were exposed to different concentrations of these herbicides and the algal growth was measured in a microplate reader at 410 nm, at 0, 24, 48 and 72 h. Tebufenozide appeared to be the most inhibitory to Scenedesmus and Chlorella species growth. 72 h EC50 of propanil, tebufenozide and mefenacet ranged from 0.29 to 5.98 mg/l, 0.12 to 0.15 mg/l and from 0.25 to 0.67 mg/l, respectively for the four algal species. The two species of Chlorella were more tolerant than the two species of Scenedesmus.

A Quantitative Reasoning Approach to Algebra Using Inquiry-Based Learning

Directory of Open Access Journals (Sweden)

Victor I. Piercey

2017-07-01

Full Text Available In this paper, I share a hybrid quantitative reasoning/algebra two-course sequence that challenges the common assumption that quantitative literacy and reasoning are less rigorous mathematics alternatives to algebra and illustrates that a quantitative reasoning framework can be used to teach traditional algebra. The presentation is made in two parts. In the first part, which is somewhat philosophical and theoretical, I explain my personal perspective of what I mean by “algebra” and “doing algebra.” I contend that algebra is a form of communication whose value is precision, which allows us to perform algebraic manipulations in the form of simplification and solving moves. A quantitative reasoning approach to traditional algebraic manipulations rests on intentional and purposeful use of simplification and solving moves within contextual situations. In part 2, I describe a 6-week instructional module intended for undergraduate business students that was delivered to students who had placed into beginning algebra. The perspective described in part 1 heavily informed the design of this module. The course materials, which involve the use of Excel in multiple authentic contexts, are built around the use of inquiry-based learning. Upon completion of this module, the percentage of students who successfully complete model problems in an assessment is in the same range as surveyed students in precalculus and calculus, approximately two “grade levels” ahead of their placement.

Impact of implementation choices on quantitative predictions of cell-based computational models

Science.gov (United States)

Kursawe, Jochen; Baker, Ruth E.; Fletcher, Alexander G.

2017-09-01

'Cell-based' models provide a powerful computational tool for studying the mechanisms underlying the growth and dynamics of biological tissues in health and disease. An increasing amount of quantitative data with cellular resolution has paved the way for the quantitative parameterisation and validation of such models. However, the numerical implementation of cell-based models remains challenging, and little work has been done to understand to what extent implementation choices may influence model predictions. Here, we consider the numerical implementation of a popular class of cell-based models called vertex models, which are often used to study epithelial tissues. In two-dimensional vertex models, a tissue is approximated as a tessellation of polygons and the vertices of these polygons move due to mechanical forces originating from the cells. Such models have been used extensively to study the mechanical regulation of tissue topology in the literature. Here, we analyse how the model predictions may be affected by numerical parameters, such as the size of the time step, and non-physical model parameters, such as length thresholds for cell rearrangement. We find that vertex positions and summary statistics are sensitive to several of these implementation parameters. For example, the predicted tissue size decreases with decreasing cell cycle durations, and cell rearrangement may be suppressed by large time steps. These findings are counter-intuitive and illustrate that model predictions need to be thoroughly analysed and implementation details carefully considered when applying cell-based computational models in a quantitative setting.

A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.

Science.gov (United States)

Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li

2013-01-21

A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments.

The quantitative Morse theorem

OpenAIRE

Loi, Ta Le; Phien, Phan

2013-01-01

In this paper, we give a proof of the quantitative Morse theorem stated by {Y. Yomdin} in \\cite{Y1}. The proof is based on the quantitative Sard theorem, the quantitative inverse function theorem and the quantitative Morse lemma.

Wavelength Selection Method Based on Differential Evolution for Precise Quantitative Analysis Using Terahertz Time-Domain Spectroscopy.

Science.gov (United States)

Li, Zhi; Chen, Weidong; Lian, Feiyu; Ge, Hongyi; Guan, Aihong

2017-12-01

Quantitative analysis of component mixtures is an important application of terahertz time-domain spectroscopy (THz-TDS) and has attracted broad interest in recent research. Although the accuracy of quantitative analysis using THz-TDS is affected by a host of factors, wavelength selection from the sample's THz absorption spectrum is the most crucial component. The raw spectrum consists of signals from the sample and scattering and other random disturbances that can critically influence the quantitative accuracy. For precise quantitative analysis using THz-TDS, the signal from the sample needs to be retained while the scattering and other noise sources are eliminated. In this paper, a novel wavelength selection method based on differential evolution (DE) is investigated. By performing quantitative experiments on a series of binary amino acid mixtures using THz-TDS, we demonstrate the efficacy of the DE-based wavelength selection method, which yields an error rate below 5%.

Magnetic Resonance-based Motion Correction for Quantitative PET in Simultaneous PET-MR Imaging.

Science.gov (United States)

Rakvongthai, Yothin; El Fakhri, Georges

2017-07-01

Motion degrades image quality and quantitation of PET images, and is an obstacle to quantitative PET imaging. Simultaneous PET-MR offers a tool that can be used for correcting the motion in PET images by using anatomic information from MR imaging acquired concurrently. Motion correction can be performed by transforming a set of reconstructed PET images into the same frame or by incorporating the transformation into the system model and reconstructing the motion-corrected image. Several phantom and patient studies have validated that MR-based motion correction strategies have great promise for quantitative PET imaging in simultaneous PET-MR. Copyright © 2017 Elsevier Inc. All rights reserved.

Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design.

Science.gov (United States)

Du, Qi-Shi; Huang, Ri-Bo; Wei, Yu-Tuo; Pang, Zong-Wen; Du, Li-Qin; Chou, Kuo-Chen

2009-01-30

In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" (FB-QSAR) is proposed. The essence of the new method is that the molecular framework in a family of drug candidates are divided into several fragments according to their substitutes being investigated. The bioactivities of molecules are correlated with the physicochemical properties of the molecular fragments through two sets of coefficients in the linear free energy equations. One coefficient set is for the physicochemical properties and the other for the weight factors of the molecular fragments. Meanwhile, an iterative double least square (IDLS) technique is developed to solve the two sets of coefficients in a training data set alternately and iteratively. The IDLS technique is a feedback procedure with machine learning ability. The standard Two-dimensional quantitative structure-activity relationship (2D-QSAR) is a special case, in the FB-QSAR, when the whole molecule is treated as one entity. The FB-QSAR approach can remarkably enhance the predictive power and provide more structural insights into rational drug design. As an example, the FB-QSAR is applied to build a predictive model of neuraminidase inhibitors for drug development against H5N1 influenza virus. (c) 2008 Wiley Periodicals, Inc.

A comparison of two colorimetric assays, based upon Lowry and Bradford techniques, to estimate total protein in soil extracts.

Science.gov (United States)

Redmile-Gordon, M A; Armenise, E; White, R P; Hirsch, P R; Goulding, K W T

2013-12-01

Soil extracts usually contain large quantities of dissolved humified organic material, typically reflected by high polyphenolic content. Since polyphenols seriously confound quantification of extracted protein, minimising this interference is important to ensure measurements are representative. Although the Bradford colorimetric assay is used routinely in soil science for rapid quantification protein in soil-extracts, it has several limitations. We therefore investigated an alternative colorimetric technique based on the Lowry assay (frequently used to measure protein and humic substances as distinct pools in microbial biofilms). The accuracies of both the Bradford assay and a modified Lowry microplate method were compared in factorial combination. Protein was quantified in soil-extracts (extracted with citrate), including standard additions of model protein (BSA) and polyphenol (Sigma H1675-2). Using the Lowry microplate assay described, no interfering effects of citrate were detected even with concentrations up to 5 times greater than are typically used to extract soil protein. Moreover, the Bradford assay was found to be highly susceptible to two simultaneous and confounding artefacts: 1) the colour development due to added protein was greatly inhibited by polyphenol concentration, and 2) substantial colour development was caused directly by the polyphenol addition. In contrast, the Lowry method enabled distinction between colour development from protein and non-protein origin, providing a more accurate quantitative analysis. These results suggest that the modified-Lowry method is a more suitable measure of extract protein (defined by standard equivalents) because it is less confounded by the high polyphenolic content which is so typical of soil extracts.

Multicomponent quantitative spectroscopic analysis without reference substances based on ICA modelling.

Science.gov (United States)

Monakhova, Yulia B; Mushtakova, Svetlana P

2017-05-01

A fast and reliable spectroscopic method for multicomponent quantitative analysis of targeted compounds with overlapping signals in complex mixtures has been established. The innovative analytical approach is based on the preliminary chemometric extraction of qualitative and quantitative information from UV-vis and IR spectral profiles of a calibration system using independent component analysis (ICA). Using this quantitative model and ICA resolution results of spectral profiling of "unknown" model mixtures, the absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated without reference solutions. Good recoveries generally between 95% and 105% were obtained. The method can be applied to any spectroscopic data that obey the Beer-Lambert-Bouguer law. The proposed method was tested on analysis of vitamins and caffeine in energy drinks and aromatic hydrocarbons in motor fuel with 10% error. The results demonstrated that the proposed method is a promising tool for rapid simultaneous multicomponent analysis in the case of spectral overlap and the absence/inaccessibility of reference materials.

Sieve-based device for MALDI sample preparation. III. Its power for quantitative measurements.

Science.gov (United States)

Molin, Laura; Cristoni, Simone; Seraglia, Roberta; Traldi, Pietro

2011-02-01

The solid sample inhomogeneity is a weak point of traditional MALDI deposition techniques that reflects negatively on quantitative analysis. The recently developed sieve-based device (SBD) sample deposition method, based on the electrospraying of matrix/analyte solutions through a grounded sieve, allows the homogeneous deposition of microcrystals with dimensions smaller than that of the laser spot. In each microcrystal the matrix/analyte molar ratio can be considered constant. Then, by irradiating different portions of the microcrystal distribution an identical response is obtained. This result suggests the employment of SBD in the development of quantitative procedures. For this aim, mixtures of different proteins of known molarity were analyzed, showing a good relationship between molarity and intensity ratios. This behaviour was also observed in the case of proteins with quite different ionic yields. The power of the developed method for quantitative evaluation was also tested by the measurement of the abundance of IGPP[Oxi]GPP[Oxi]GLMGPP (m/z 1219) present in the collagen-α-5(IV) chain precursor, differently expressed in urines from healthy subjects and diabetic-nephropathic patients, confirming its overexpression in the presence of nephropathy. The data obtained indicate that SBD is a particularly effective method for quantitative analysis also in biological fluids of interest. Copyright © 2011 John Wiley & Sons, Ltd.

Quantitative detection of melamine based on terahertz time-domain spectroscopy

Science.gov (United States)

Zhao, Xiaojing; Wang, Cuicui; Liu, Shangjian; Zuo, Jian; Zhou, Zihan; Zhang, Cunlin

2018-01-01

Melamine is an organic base and a trimer of cyanamide, with a 1, 3, 5-triazine skeleton. It is usually used for the production of plastics, glue and flame retardants. Melamine combines with acid and related compounds to form melamine cyanurate and related crystal structures, which have been implicated as contaminants or biomarkers in protein adulterations by lawbreakers, especially in milk powder. This paper is focused on developing an available method for quantitative detection of melamine in the fields of security inspection and nondestructive testing based on THz-TDS. Terahertz (THz) technology has promising applications for the detection and identification of materials because it exhibits the properties of spectroscopy, good penetration and safety. Terahertz time-domain spectroscopy (THz-TDS) is a key technique that is applied to spectroscopic measurement of materials based on ultrafast femtosecond laser. In this study, the melamine and its mixture with polyethylene powder in different consistence are measured using the transmission THz-TDS. And we obtained the refractive index spectra and the absorption spectrum of different concentrations of melamine on 0.2-2.8THz. In the refractive index spectra, it is obvious to see that decline trend with the decrease of concentration; and in the absorption spectrum, two peaks of melamine at 1.98THz and 2.28THz can be obtained. Based on the experimental result, the absorption coefficient and the consistence of the melamine in the mixture are determined. Finally, methods for quantitative detection of materials in the fields of nondestructive testing and quality control based on THz-TDS have been studied.

Quantitative analysis of the ATV data base, Stage 2

International Nuclear Information System (INIS)

Stenquist, C.; Kjellbert, N.A.

1981-01-01

A supplementary study of the Swedish ATV data base was carried out. The study was limited to an analysis of the quantitative coverage of component failures from 1979 through 1980. The results indicate that the coverage of component failures is about 75-80 per cent related to the failure reports and work order sheets at the reactor sites together with SKI's ''Safety Related Occurrences''. In general there has been an improvement compared to previous years. (Auth.)

Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation

Directory of Open Access Journals (Sweden)

Shen Li

2010-09-01

Full Text Available Abstract Background An exciting application of genetic network is to predict phenotypic consequences for environmental cues or genetic perturbations. However, de novo prediction for quantitative phenotypes based on network topology is always a challenging task. Results Using yeast sporulation as a model system, we have assembled a genetic network from literature and exploited Boolean network to predict sporulation efficiency change upon deleting individual genes. We observe that predictions based on the curated network correlate well with the experimentally measured values. In addition, computational analysis reveals the robustness and hysteresis of the yeast sporulation network and uncovers several patterns of sporulation efficiency change caused by double gene deletion. These discoveries may guide future investigation of underlying mechanisms. We have also shown that a hybridized genetic network reconstructed from both temporal microarray data and literature is able to achieve a satisfactory prediction accuracy of the same quantitative phenotypes. Conclusions This case study illustrates the value of predicting quantitative phenotypes based on genetic network and provides a generic approach.

Quantitative determination of pneumococcal capsular polysaccharide serotype 14 using a modification of phenol-sulfuric acid method.

Science.gov (United States)

Cuesta, Gabriela; Suarez, Norma; Bessio, Maria I; Ferreira, Fernando; Massaldi, Hugo

2003-01-01

The capsular polysaccharide of Streptococcus pneumoniae, serotype 14, is part of every pneumococcal vaccine presently in the market or under development. A strategy for the quantitative determination of this polysaccharide by the phenol-sulfuric acid method is described. The modality of acid addition is shown to be the critical step for obtaining reproducible test results between different technicians. Raising the incubation temperature above 80 degrees C increased the consistency of the method by more than 60% regardless of the acid addition modality, but at the expense of some loss of sensitivity. Incubation at 110 degrees C was found necessary to obtain reproducible results within 3% for this technique, which was used to follow the enrichment of the polysaccharide during the last steps of purification. A model mixture of the component polysaccharide sugars provided an adequate and economic standard to construct the calibration curve for this assay, with absorbance reading either in the reaction tubes or in a microplate. A similar procedure may be applied to the determination of other bacterial polysaccharides as well.

Real time quantitative phase microscopy based on single-shot transport of intensity equation (ssTIE) method

Science.gov (United States)

Yu, Wei; Tian, Xiaolin; He, Xiaoliang; Song, Xiaojun; Xue, Liang; Liu, Cheng; Wang, Shouyu

2016-08-01

Microscopy based on transport of intensity equation provides quantitative phase distributions which opens another perspective for cellular observations. However, it requires multi-focal image capturing while mechanical and electrical scanning limits its real time capacity in sample detections. Here, in order to break through this restriction, real time quantitative phase microscopy based on single-shot transport of the intensity equation method is proposed. A programmed phase mask is designed to realize simultaneous multi-focal image recording without any scanning; thus, phase distributions can be quantitatively retrieved in real time. It is believed the proposed method can be potentially applied in various biological and medical applications, especially for live cell imaging.

Paper microzone plates.

Science.gov (United States)

Carrilho, Emanuel; Phillips, Scott T; Vella, Sarah J; Martinez, Andres W; Whitesides, George M

2009-08-01

This paper describes 96- and 384-microzone plates fabricated in paper as alternatives to conventional multiwell plates fabricated in molded polymers. Paper-based plates are functionally related to plastic well plates, but they offer new capabilities. For example, paper-microzone plates are thin (approximately 180 microm), require small volumes of sample (5 microL per zone), and can be manufactured from inexpensive materials ($0.05 per plate). The paper-based plates are fabricated by patterning sheets of paper, using photolithography, into hydrophilic zones surrounded by hydrophobic polymeric barriers. This photolithography used an inexpensive formulation photoresist that allows rapid (approximately 15 min) prototyping of paper-based plates. These plates are compatible with conventional microplate readers for quantitative absorbance and fluorescence measurements. The limit of detection per zone loaded for fluorescence was 125 fmol for fluorescein isothiocyanate-labeled bovine serum albumin, and this level corresponds to 0.02 the quantity of analyte per well used to achieve comparable signal-to-noise in a 96-well plastic plate (using a solution of 25 nM labeled protein). The limits of detection for absorbance on paper was approximately 50 pmol per zone for both Coomassie Brilliant Blue and Amaranth dyes; these values were 0.4 that required for the plastic plate. Demonstration of quantitative colorimetric correlations using a scanner or camera to image the zones and to measure the intensity of color, makes it possible to conduct assays without a microplate reader.

Quantitative analysis of lead in polysulfide-based impression material

Directory of Open Access Journals (Sweden)

Aparecida Silva Braga

2007-06-01

Full Text Available Permlastic® is a polysulfide-based impression material widely used by dentists in Brazil. It is composed of a base paste and a catalyzer containing lead dioxide. The high toxicity of lead to humans is ground for much concern, since it can attack various systems and organs. The present study involved a quantitative analysis of the concentration of lead in the material Permlastic®. The lead was determined by plasma-induced optical emission spectrometry (Varian model Vista. The percentages of lead found in the two analyzed lots were 38.1 and 40.8%. The lead concentrations in the material under study were high, but the product’s packaging contained no information about these concentrations.

Method and platform standardization in MRM-based quantitative plasma proteomics.

Science.gov (United States)

Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Jackson, Angela M; Domanski, Dominik; Burkhart, Julia; Sickmann, Albert; Borchers, Christoph H

2013-12-16

There exists a growing demand in the proteomics community to standardize experimental methods and liquid chromatography-mass spectrometry (LC/MS) platforms in order to enable the acquisition of more precise and accurate quantitative data. This necessity is heightened by the evolving trend of verifying and validating candidate disease biomarkers in complex biofluids, such as blood plasma, through targeted multiple reaction monitoring (MRM)-based approaches with stable isotope-labeled standards (SIS). Considering the lack of performance standards for quantitative plasma proteomics, we previously developed two reference kits to evaluate the MRM with SIS peptide approach using undepleted and non-enriched human plasma. The first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). Here, these kits have been refined for practical use and then evaluated through intra- and inter-laboratory testing on 6 common LC/MS platforms. For an identical panel of 22 plasma proteins, similar concentrations were determined, regardless of the kit, instrument platform, and laboratory of analysis. These results demonstrate the value of the kit and reinforce the utility of standardized methods and protocols. The proteomics community needs standardized experimental protocols and quality control methods in order to improve the reproducibility of MS-based quantitative data. This need is heightened by the evolving trend for MRM-based validation of proposed disease biomarkers in complex biofluids such as blood plasma. We have developed two kits to assist in the inter- and intra-laboratory quality control of MRM experiments: the first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). In this paper, we report the use of these kits in intra- and inter-laboratory testing on 6 common LC/MS platforms. This

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

Science.gov (United States)

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

2015-11-01

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

A new microplate screening method for the simultaneous activity quantification of feruloyl esterases, tannases, and chlorogenate esterases.

Science.gov (United States)

Ramírez, L; Arrizon, J; Sandoval, G; Cardador, A; Bello-Mendoza, R; Lappe, P; Mateos-Díaz, J C

2008-12-01

Feruloyl, chlorogenate esterases, and tannases are enzymes useful in phenolic modifications of pharmaceutical relevance as protectors against several degenerative human diseases. Therefore, there is a growing interest in discovering new sources of these enzymes. However, traditional methods for their activity measurements are time-consuming and poorly adapted for high-throughput screening. In this study, a successful new microplate high-throughput screening method for the simultaneous quantification of all mentioned activities is demonstrated. This method allows the detection of activities as low as 1.7 mU ml(-1). Furthermore, reaction rates increased proportionally with the amount of enzyme added, and no interferences with the other commercial hydrolases tested were found. The utility of the method was demonstrated after simultaneously screening feruloyl, chlorogenate esterase, and tannase activities in solid state fermentation extracts obtained during the kinetics of production of 20 fungal strains. Among these, seven strains were positive for at least one of the esterase activities tested. This result shows the potential for the rapid routine screening assays for multiple samples of moderate low to high enzymatic levels.

Phase-based vascular input function: Improved quantitative DCE-MRI of atherosclerotic plaques

NARCIS (Netherlands)

van Hoof, R. H. M.; Hermeling, E.; Truijman, M. T. B.; van Oostenbrugge, R. J.; Daemen, J. W. H.; van der Geest, R. J.; van Orshoven, N. P.; Schreuder, A. H.; Backes, W. H.; Daemen, M. J. A. P.; Wildberger, J. E.; Kooi, M. E.

2015-01-01

Purpose: Quantitative pharmacokinetic modeling of dynamic contrast-enhanced (DCE)-MRI can be used to assess atherosclerotic plaque microvasculature, which is an important marker of plaque vulnerability. Purpose of the present study was (1) to compare magnitude-versus phase-based vascular input

Comparison of conventional, model-based quantitative planar, and quantitative SPECT image processing methods for organ activity estimation using In-111 agents

International Nuclear Information System (INIS)

He, Bin; Frey, Eric C

2006-01-01

Accurate quantification of organ radionuclide uptake is important for patient-specific dosimetry. The quantitative accuracy from conventional conjugate view methods is limited by overlap of projections from different organs and background activity, and attenuation and scatter. In this work, we propose and validate a quantitative planar (QPlanar) processing method based on maximum likelihood (ML) estimation of organ activities using 3D organ VOIs and a projector that models the image degrading effects. Both a physical phantom experiment and Monte Carlo simulation (MCS) studies were used to evaluate the new method. In these studies, the accuracies and precisions of organ activity estimates for the QPlanar method were compared with those from conventional planar (CPlanar) processing methods with various corrections for scatter, attenuation and organ overlap, and a quantitative SPECT (QSPECT) processing method. Experimental planar and SPECT projections and registered CT data from an RSD Torso phantom were obtained using a GE Millenium VH/Hawkeye system. The MCS data were obtained from the 3D NCAT phantom with organ activity distributions that modelled the uptake of 111 In ibritumomab tiuxetan. The simulations were performed using parameters appropriate for the same system used in the RSD torso phantom experiment. The organ activity estimates obtained from the CPlanar, QPlanar and QSPECT methods from both experiments were compared. From the results of the MCS experiment, even with ideal organ overlap correction and background subtraction, CPlanar methods provided limited quantitative accuracy. The QPlanar method with accurate modelling of the physical factors increased the quantitative accuracy at the cost of requiring estimates of the organ VOIs in 3D. The accuracy of QPlanar approached that of QSPECT, but required much less acquisition and computation time. Similar results were obtained from the physical phantom experiment. We conclude that the QPlanar method, based

Quantitative kinetics of proteolytic enzymes determined by a surface concentration-based assay using peptide arrays.

Science.gov (United States)

Jung, Se-Hui; Kong, Deok-Hoon; Park, Seoung-Woo; Kim, Young-Myeong; Ha, Kwon-Soo

2012-08-21

Peptide arrays have emerged as a key technology for drug discovery, diagnosis, and cell biology. Despite the promise of these arrays, applications of peptide arrays to quantitative analysis of enzyme kinetics have been limited due to the difficulty in obtaining quantitative information of enzymatic reaction products. In this study, we developed a new approach for the quantitative kinetics analysis of proteases using fluorescence-conjugated peptide arrays, a surface concentration-based assay with solid-phase peptide standards using dry-off measurements, and compared it with an applied concentration-based assay. For fabrication of the peptide arrays, substrate peptides of cMMP-3, caspase-3, caspase-9, and calpain-1 were functionalized with TAMRA and cysteine, and were immobilized onto amine-functionalized arrays using a heterobifunctional linker, N-[γ-maleimidobutyloxy]succinimide ester. The proteolytic activities of the four enzymes were quantitatively analyzed by calculating changes induced by enzymatic reactions in the concentrations of peptides bound to array surfaces. In addition, this assay was successfully applied for calculating the Michaelis constant (K(m,surf)) for the four enzymes. Thus, this new assay has a strong potential for use in the quantitative evaluation of proteases, and for drug discovery through kinetics studies including the determination of K(m) and V(max).

A biology-based approach for quantitative structure-activity relationships (QSARs) in ecotoxicity.

NARCIS (Netherlands)

Jager, T.; Kooijman, S.A.L.M.

2009-01-01

Quantitative structure-activity relationships (QSARs) for ecotoxicity can be used to fill data gaps and limit toxicity testing on animals. QSAR development may additionally reveal mechanistic information based on observed patterns in the data. However, the use of descriptive summary statistics for

PCA-based groupwise image registration for quantitative MRI

NARCIS (Netherlands)

Huizinga, W.; Poot, D. H. J.; Guyader, J.-M.; Klaassen, R.; Coolen, B. F.; van Kranenburg, M.; van Geuns, R. J. M.; Uitterdijk, A.; Polfliet, M.; Vandemeulebroucke, J.; Leemans, A.; Niessen, W. J.; Klein, S.

2016-01-01

Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T5 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different

Analysis of Genetic Variation across the Encapsidated Genome of Microplitis demolitor Bracovirus in Parasitoid Wasps.

Directory of Open Access Journals (Sweden)

Gaelen R Burke

Full Text Available Insect parasitoids must complete part of their life cycle within or on another insect, ultimately resulting in the death of the host insect. One group of parasitoid wasps, the 'microgastroid complex' (Hymenoptera: Braconidae, engage in an association with beneficial symbiotic viruses that are essential for successful parasitism of hosts. These viruses, known as Bracoviruses, persist in an integrated form in the wasp genome, and activate to replicate in wasp ovaries during development to ultimately be delivered into host insects during parasitism. The lethal nature of host-parasitoid interactions, combined with the involvement of viruses in mediating these interactions, has led to the hypothesis that Bracoviruses are engaged in an arms race with hosts, resulting in recurrent adaptation in viral (and host genes. Deep sequencing was employed to characterize sequence variation across the encapsidated Bracovirus genome within laboratory and field populations of the parasitoid wasp species Microplitis demolitor. Contrary to expectations, there was a paucity of evidence for positive directional selection among virulence genes, which generally exhibited signatures of purifying selection. These data suggest that the dynamics of host-parasite interactions may not result in recurrent rounds of adaptation, and that adaptation may be more variable in time than previously expected.

A family-based joint test for mean and variance heterogeneity for quantitative traits.

Science.gov (United States)

Cao, Ying; Maxwell, Taylor J; Wei, Peng

2015-01-01

Traditional quantitative trait locus (QTL) analysis focuses on identifying loci associated with mean heterogeneity. Recent research has discovered loci associated with phenotype variance heterogeneity (vQTL), which is important in studying genetic association with complex traits, especially for identifying gene-gene and gene-environment interactions. While several tests have been proposed to detect vQTL for unrelated individuals, there are no tests for related individuals, commonly seen in family-based genetic studies. Here we introduce a likelihood ratio test (LRT) for identifying mean and variance heterogeneity simultaneously or for either effect alone, adjusting for covariates and family relatedness using a linear mixed effect model approach. The LRT test statistic for normally distributed quantitative traits approximately follows χ(2)-distributions. To correct for inflated Type I error for non-normally distributed quantitative traits, we propose a parametric bootstrap-based LRT that removes the best linear unbiased prediction (BLUP) of family random effect. Simulation studies show that our family-based test controls Type I error and has good power, while Type I error inflation is observed when family relatedness is ignored. We demonstrate the utility and efficiency gains of the proposed method using data from the Framingham Heart Study to detect loci associated with body mass index (BMI) variability. © 2014 John Wiley & Sons Ltd/University College London.

Ultra-fast quantitative imaging using ptychographic iterative engine based digital micro-mirror device

Science.gov (United States)

Sun, Aihui; Tian, Xiaolin; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Wang, Shouyu; Liu, Cheng

2018-01-01

As a lensfree imaging technique, ptychographic iterative engine (PIE) method can provide both quantitative sample amplitude and phase distributions avoiding aberration. However, it requires field of view (FoV) scanning often relying on mechanical translation, which not only slows down measuring speed, but also introduces mechanical errors decreasing both resolution and accuracy in retrieved information. In order to achieve high-accurate quantitative imaging with fast speed, digital micromirror device (DMD) is adopted in PIE for large FoV scanning controlled by on/off state coding by DMD. Measurements were implemented using biological samples as well as USAF resolution target, proving high resolution in quantitative imaging using the proposed system. Considering its fast and accurate imaging capability, it is believed the DMD based PIE technique provides a potential solution for medical observation and measurements.

Smartphone based visual and quantitative assays on upconversional paper sensor.

Science.gov (United States)

Mei, Qingsong; Jing, Huarong; Li, You; Yisibashaer, Wuerzha; Chen, Jian; Nan Li, Bing; Zhang, Yong

2016-01-15

The integration of smartphone with paper sensors recently has been gain increasing attentions because of the achievement of quantitative and rapid analysis. However, smartphone based upconversional paper sensors have been restricted by the lack of effective methods to acquire luminescence signals on test paper. Herein, by the virtue of 3D printing technology, we exploited an auxiliary reusable device, which orderly assembled a 980nm mini-laser, optical filter and mini-cavity together, for digitally imaging the luminescence variations on test paper and quantitative analyzing pesticide thiram by smartphone. In detail, copper ions decorated NaYF4:Yb/Tm upconversion nanoparticles were fixed onto filter paper to form test paper, and the blue luminescence on it would be quenched after additions of thiram through luminescence resonance energy transfer mechanism. These variations could be monitored by the smartphone camera, and then the blue channel intensities of obtained colored images were calculated to quantify amounts of thiram through a self-written Android program installed on the smartphone, offering a reliable and accurate detection limit of 0.1μM for the system. This work provides an initial demonstration of integrating upconversion nanosensors with smartphone digital imaging for point-of-care analysis on a paper-based platform. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative structure-property relationship (correlation analysis) of phosphonic acid-based chelates in design of MRI contrast agent.

Science.gov (United States)

Tiwari, Anjani K; Ojha, Himanshu; Kaul, Ankur; Dutta, Anupama; Srivastava, Pooja; Shukla, Gauri; Srivastava, Rakesh; Mishra, Anil K

2009-07-01

Nuclear magnetic resonance imaging is a very useful tool in modern medical diagnostics, especially when gadolinium (III)-based contrast agents are administered to the patient with the aim of increasing the image contrast between normal and diseased tissues. With the use of soft modelling techniques such as quantitative structure-activity relationship/quantitative structure-property relationship after a suitable description of their molecular structure, we have studied a series of phosphonic acid for designing new MRI contrast agent. Quantitative structure-property relationship studies with multiple linear regression analysis were applied to find correlation between different calculated molecular descriptors of the phosphonic acid-based chelating agent and their stability constants. The final quantitative structure-property relationship mathematical models were found as--quantitative structure-property relationship Model for phosphonic acid series (Model 1)--log K(ML) = {5.00243(+/-0.7102)}- MR {0.0263(+/-0.540)}n = 12 l r l = 0.942 s = 0.183 F = 99.165 quantitative structure-property relationship Model for phosphonic acid series (Model 2)--log K(ML) = {5.06280(+/-0.3418)}- MR {0.0252(+/- .198)}n = 12 l r l = 0.956 s = 0.186 F = 99.256.

Evaluation of an automated microplate technique in the Galileo system for ABO and Rh(D) blood grouping.

Science.gov (United States)

Xu, Weiyi; Wan, Feng; Lou, Yufeng; Jin, Jiali; Mao, Weilin

2014-01-01

A number of automated devices for pretransfusion testing have recently become available. This study evaluated the Immucor Galileo System, a fully automated device based on the microplate hemagglutination technique for ABO/Rh (D) determinations. Routine ABO/Rh typing tests were performed on 13,045 samples using the Immucor automated instruments. Manual tube method was used to resolve ABO forward and reverse grouping discrepancies. D-negative test results were investigated and confirmed manually by the indirect antiglobulin test (IAT). The system rejected 70 tests for sample inadequacy. 87 samples were read as "No-type-determined" due to forward and reverse grouping discrepancies. 25 tests gave these results because of sample hemolysis. After further tests, we found 34 tests were caused by weakened RBC antibodies, 5 tests were attributable to weak A and/or B antigens, 4 tests were due to mixed-field reactions, and 8 tests had high titer cold agglutinin with blood qualifications which react only at temperatures below 34 degrees C. In the remaining 11 cases, irregular RBC antibodies were identified in 9 samples (seven anti-M and two anti-P) and two subgroups were identified in 2 samples (one A1 and one A2) by a reference laboratory. As for D typing, 2 weak D+ samples missed by automated systems gave negative results, but weak-positive reactions were observed in the IAT. The Immucor Galileo System is reliable and suited for ABO and D blood groups, some reasons may cause a discrepancy in ABO/D typing using a fully automated system. It is suggested that standardization of sample collection may improve the performance of the fully automated system.

A comparison of traditional and quantitative analysis of acid-base imbalances in hypoalbuminemic dogs.

Science.gov (United States)

Torrente, Carlos; Manzanilla, Edgar G; de Gopegui, Rafael Ruiz

2014-01-01

To compare the traditional (HH) and quantitative approaches used for the evaluation of the acid-base balance in hypoalbuminemic dogs. Prospective observational study. ICU of a veterinary teaching hospital. One hundred and five client-owned dogs. Jugular venous blood samples were collected from each patient on admission to determine: total plasma protein (TP), albumin (Alb), blood urea nitrogen (BUN), glucose (Glu), hematocrit (HCT), Na(+) , Cl(-) , K(+) , phosphate (Pi ), pH, PvCO2, bicarbonate (HCO3 (-) ), anion gap (AG), adjusted anion gap for albumin (AGalb ) or phosphate (AGalb-phos ), standardized base excess (SBE), strong ion difference (SID), concentration of nonvolatile weak buffers (Atot ), and strong ion gap (SIG). Patients were divided in 2 groups according to the severity of the hypoalbuminemia: mild (Alb = 21-25 g/L) and severe (Alb ≤20 g/L). All parameters were compared among groups. Patients with severe hypoalbuminemia showed significant decrease in TP (P = 0.011), Atot (P = 0.050), and a significant increase in adjusted AG (P = 0.048) and the magnitude of SIG (P = 0.011) compared to animals with mild hypoalbuminemia. According to the HH approach, the most frequent imbalances were simple disorders (51.4%), primarily metabolic acidosis (84.7%) associated with a high AG acidosis. However, when using the quantitative method, 58.1% of patients had complex disorders, with SIG acidosis (74.3%) and Atot alkalosis (33.3%) as the most frequent acid-base imbalances. Agreement between methods only matched in 32 cases (kappa acid-base balance was poor and many imbalances detected using the quantitative approach were missed using the HH approach. Further studies are necessary to confirm the clinical utility of using the quantitative approach in the decision-making process of the severely ill hypoalbuminemic patients. © Veterinary Emergency and Critical Care Society 2014.

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

Science.gov (United States)

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

2015-12-14

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

Quantitative analysis chemistry

International Nuclear Information System (INIS)

Ko, Wansuk; Lee, Choongyoung; Jun, Kwangsik; Hwang, Taeksung

1995-02-01

This book is about quantitative analysis chemistry. It is divided into ten chapters, which deal with the basic conception of material with the meaning of analysis chemistry and SI units, chemical equilibrium, basic preparation for quantitative analysis, introduction of volumetric analysis, acid-base titration of outline and experiment examples, chelate titration, oxidation-reduction titration with introduction, titration curve, and diazotization titration, precipitation titration, electrometric titration and quantitative analysis.

Evaluation of rapid methods for in-situ characterization of organic contaminant load and biodegradation rates in winery wastewater.

Science.gov (United States)

Carvallo, M J; Vargas, I; Vega, A; Pizarro, G; Pizarr, G; Pastén, P

2007-01-01

Rapid methods for the in-situ evaluation of the organic load have recently been developed and successfully implemented in municipal wastewater treatment systems. Their direct application to winery wastewater treatment is questionable due to substantial differences between municipal and winery wastewater. We critically evaluate the use of UV-VIS spectrometry, buffer capacity testing (BCT), and respirometry as rapid methods to determine organic load and biodegradation rates of winery wastewater. We tested three types of samples: actual and treated winery wastewater, synthetic winery wastewater, and samples from a biological batch reactor. Not surprisingly, respirometry gave a good estimation of biodegradation rates for substrate of different complexities, whereas UV-VIS and BCT did not provide a quantitative measure of the easily degradable sugars and ethanol, typically the main components of the COD in the influent. However, our results strongly suggest that UV-VIS and BCT can be used to identify and estimate the concentration of complex substrates in the influent and soluble microbial products (SMP) in biological reactors and their effluent. Furthermore, the integration of UV-VIS spectrometry, BCT, and mathematical modeling was able to differentiate between the two components of SMPs: substrate utilization associated products (UAP) and biomass associated products (BAP). Since the effluent COD in biologically treated wastewaters is composed primarily by SMPs, the quantitative information given by these techniques may be used for plant control and optimization.

Quantitative assessment of multi-isocentric radiosurgical irradiation based on the f factor

International Nuclear Information System (INIS)

Lefkopoulos, D.; Schlienger, M.; Hancilar, T.; Keraudy, K.; Touboul, E.

1995-01-01

To evaluate quantitatively the stereotactic irradiations, we defined a DVH parameter (f) resulting from the lesion underdosage and healthy tissues overdosage curves. The Lesion Underdose Factor (LUF) is the ratio of the lesion volume receiving dose inferior to a reference isodose to the lesion volume. The Healthy Tissue Overdose Factor HTOF quantitates the amount of tissue external to the lesion receiving dose equal to or greater than a given reference isodose relatively to the lesion volume. The LUF and HTOF curves represent the variation of the LUF and HTOF factors as a function of the reference isodose. The f factor is the surface situated below the intersection of the two curves. The optimization goal of the planification procedure could consist in the minimization of f. We have correlated them with clinical results (obliteration of the nidus) of a series of 34 multi-isocenters AVMs linac irradiation. The treatment dose protocol was a peripheral dose of 20 - 25 Gy (50 to 70% isodose range). According to this preliminary study, it seems that f factor provides clinically useful quantitative indices for the treatment plan evaluation. The choice of the optimal treatment plan and reference isodose is realized as follows. For a same patient different treatment plans are calculated by successive modifications of the irradiation parameters, as the number of isocenters, the distances between isocenters, the collimators diameter, the number of arcs and their angular length etc. The choice of optimal treatment plan is based on a clinically validated quantitative factor such as the f factor. According to our preliminary results one should select the treatment plan corresponding to the smallest value of f. The choice of the optimal reference isodose is based on the clinical data (lesion volume and topography, adjacent critical structures) and the LUF and HTOF factors following a well-defined protocol

An automated swimming respirometer

DEFF Research Database (Denmark)

STEFFENSEN, JF; JOHANSEN, K; BUSHNELL, PG

1984-01-01

An automated respirometer is described that can be used for computerized respirometry of trout and sharks.......An automated respirometer is described that can be used for computerized respirometry of trout and sharks....

Quantitative phase microscopy for cellular dynamics based on transport of intensity equation.

Science.gov (United States)

Li, Ying; Di, Jianglei; Ma, Chaojie; Zhang, Jiwei; Zhong, Jinzhan; Wang, Kaiqiang; Xi, Teli; Zhao, Jianlin

2018-01-08

We demonstrate a simple method for quantitative phase imaging of tiny transparent objects such as living cells based on the transport of intensity equation. The experiments are performed using an inverted bright field microscope upgraded with a flipping imaging module, which enables to simultaneously create two laterally separated images with unequal defocus distances. This add-on module does not include any lenses or gratings and is cost-effective and easy-to-alignment. The validity of this method is confirmed by the measurement of microlens array and human osteoblastic cells in culture, indicating its potential in the applications of dynamically measuring living cells and other transparent specimens in a quantitative, non-invasive and label-free manner.

Ten unique and charismatic new species of Microgastrinae wasps (Hymenoptera, Braconidae from North America

Directory of Open Access Journals (Sweden)

Jose Fernandez-Triana

2018-01-01

Full Text Available Ten new species within four genera of Microgastrinae parasitoid wasps (Hymenoptera: Braconidae are described from Canada and United States: Diolcogaster ichiroi, Diolcogaster miamensis, Glyptapanteles pseudotsugae, Microgaster archboldensis, Microgaster syntopic, Microplitis altissimus, Microplitis jorgeluisi, Microplitis juanmanueli, Microplitis julioalbertoi, and Microplitis mariamargaritae. The new taxa are significant because they represent the first North American records of a tropical group (species of the basimacula group in Diolcogaster, exemplify interesting ecological cases (niche-based host selection in Glyptapanteles, syntopic species in Microgaster, and showcase unique morphological features and/or altitudinal records (Microplitis. Most of the new species were collected in protected areas or areas with strong research programs (Archbold Biological Station and hammock forests near Miami, Florida; Great Sand Dunes National Park and Preserve, and Mount Evans Wilderness Area, Colorado; Sapelo Island, Georgia; Tonto National Forest, Arizona, and thus are also of value and interest for conservation and research efforts.

A CZT-based blood counter for quantitative molecular imaging.

Science.gov (United States)

Espagnet, Romain; Frezza, Andrea; Martin, Jean-Pierre; Hamel, Louis-André; Lechippey, Laëtitia; Beauregard, Jean-Mathieu; Després, Philippe

2017-12-01

Robust quantitative analysis in positron emission tomography (PET) and in single-photon emission computed tomography (SPECT) typically requires the time-activity curve as an input function for the pharmacokinetic modeling of tracer uptake. For this purpose, a new automated tool for the determination of blood activity as a function of time is presented. The device, compact enough to be used on the patient bed, relies on a peristaltic pump for continuous blood withdrawal at user-defined rates. Gamma detection is based on a 20 × 20 × 15 mm 3 cadmium zinc telluride (CZT) detector, read by custom-made electronics and a field-programmable gate array-based signal processing unit. A graphical user interface (GUI) allows users to select parameters and easily perform acquisitions. This paper presents the overall design of the device as well as the results related to the detector performance in terms of stability, sensitivity and energy resolution. Results from a patient study are also reported. The device achieved a sensitivity of 7.1 cps/(kBq/mL) and a minimum detectable activity of 2.5 kBq/ml for 18 F. The gamma counter also demonstrated an excellent stability with a deviation in count rates inferior to 0.05% over 6 h. An energy resolution of 8% was achieved at 662 keV. The patient study was conclusive and demonstrated that the compact gamma blood counter developed has the sensitivity and the stability required to conduct quantitative molecular imaging studies in PET and SPECT.

Problem-based learning on quantitative analytical chemistry course

Science.gov (United States)

Fitri, Noor

2017-12-01

This research applies problem-based learning method on chemical quantitative analytical chemistry, so called as "Analytical Chemistry II" course, especially related to essential oil analysis. The learning outcomes of this course include aspects of understanding of lectures, the skills of applying course materials, and the ability to identify, formulate and solve chemical analysis problems. The role of study groups is quite important in improving students' learning ability and in completing independent tasks and group tasks. Thus, students are not only aware of the basic concepts of Analytical Chemistry II, but also able to understand and apply analytical concepts that have been studied to solve given analytical chemistry problems, and have the attitude and ability to work together to solve the problems. Based on the learning outcome, it can be concluded that the problem-based learning method in Analytical Chemistry II course has been proven to improve students' knowledge, skill, ability and attitude. Students are not only skilled at solving problems in analytical chemistry especially in essential oil analysis in accordance with local genius of Chemistry Department, Universitas Islam Indonesia, but also have skilled work with computer program and able to understand material and problem in English.

The Development of Mathematical Knowledge for Teaching for Quantitative Reasoning Using Video-Based Instruction

Science.gov (United States)

Walters, Charles David

Quantitative reasoning (P. W. Thompson, 1990, 1994) is a powerful mathematical tool that enables students to engage in rich problem solving across the curriculum. One way to support students' quantitative reasoning is to develop prospective secondary teachers' (PSTs) mathematical knowledge for teaching (MKT; Ball, Thames, & Phelps, 2008) related to quantitative reasoning. However, this may prove challenging, as prior to entering the classroom, PSTs often have few opportunities to develop MKT by examining and reflecting on students' thinking. Videos offer one avenue through which such opportunities are possible. In this study, I report on the design of a mini-course for PSTs that featured a series of videos created as part of a proof-of-concept NSF-funded project. These MathTalk videos highlight the ways in which the quantitative reasoning of two high school students developed over time. Using a mixed approach to grounded theory, I analyzed pre- and postinterviews using an extant coding scheme based on the Silverman and Thompson (2008) framework for the development of MKT. This analysis revealed a shift in participants' affect as well as three distinct shifts in their MKT around quantitative reasoning with distances, including shifts in: (a) quantitative reasoning; (b) point of view (decentering); and (c) orientation toward problem solving. Using the four-part focusing framework (Lobato, Hohensee, & Rhodehamel, 2013), I analyzed classroom data to account for how participants' noticing was linked with the shifts in MKT. Notably, their increased noticing of aspects of MKT around quantitative reasoning with distances, which features prominently in the MathTalk videos, seemed to contribute to the emergence of the shifts in MKT. Results from this study link elements of the learning environment to the development of specific facets of MKT around quantitative reasoning with distances. These connections suggest that vicarious experiences with two students' quantitative

Predictive value of EEG in postanoxic encephalopathy: A quantitative model-based approach.

Science.gov (United States)

Efthymiou, Evdokia; Renzel, Roland; Baumann, Christian R; Poryazova, Rositsa; Imbach, Lukas L

2017-10-01

The majority of comatose patients after cardiac arrest do not regain consciousness due to severe postanoxic encephalopathy. Early and accurate outcome prediction is therefore essential in determining further therapeutic interventions. The electroencephalogram is a standardized and commonly available tool used to estimate prognosis in postanoxic patients. The identification of pathological EEG patterns with poor prognosis relies however primarily on visual EEG scoring by experts. We introduced a model-based approach of EEG analysis (state space model) that allows for an objective and quantitative description of spectral EEG variability. We retrospectively analyzed standard EEG recordings in 83 comatose patients after cardiac arrest between 2005 and 2013 in the intensive care unit of the University Hospital Zürich. Neurological outcome was assessed one month after cardiac arrest using the Cerebral Performance Category. For a dynamic and quantitative EEG analysis, we implemented a model-based approach (state space analysis) to quantify EEG background variability independent from visual scoring of EEG epochs. Spectral variability was compared between groups and correlated with clinical outcome parameters and visual EEG patterns. Quantitative assessment of spectral EEG variability (state space velocity) revealed significant differences between patients with poor and good outcome after cardiac arrest: Lower mean velocity in temporal electrodes (T4 and T5) was significantly associated with poor prognostic outcome (pEEG patterns such as generalized periodic discharges (pEEG analysis (state space analysis) provides a novel, complementary marker for prognosis in postanoxic encephalopathy. Copyright © 2017 Elsevier B.V. All rights reserved.

Deterministic quantitative risk assessment development

Energy Technology Data Exchange (ETDEWEB)

Dawson, Jane; Colquhoun, Iain [PII Pipeline Solutions Business of GE Oil and Gas, Cramlington Northumberland (United Kingdom)

2009-07-01

Current risk assessment practice in pipeline integrity management is to use a semi-quantitative index-based or model based methodology. This approach has been found to be very flexible and provide useful results for identifying high risk areas and for prioritizing physical integrity assessments. However, as pipeline operators progressively adopt an operating strategy of continual risk reduction with a view to minimizing total expenditures within safety, environmental, and reliability constraints, the need for quantitative assessments of risk levels is becoming evident. Whereas reliability based quantitative risk assessments can be and are routinely carried out on a site-specific basis, they require significant amounts of quantitative data for the results to be meaningful. This need for detailed and reliable data tends to make these methods unwieldy for system-wide risk k assessment applications. This paper describes methods for estimating risk quantitatively through the calibration of semi-quantitative estimates to failure rates for peer pipeline systems. The methods involve the analysis of the failure rate distribution, and techniques for mapping the rate to the distribution of likelihoods available from currently available semi-quantitative programs. By applying point value probabilities to the failure rates, deterministic quantitative risk assessment (QRA) provides greater rigor and objectivity than can usually be achieved through the implementation of semi-quantitative risk assessment results. The method permits a fully quantitative approach or a mixture of QRA and semi-QRA to suit the operator's data availability and quality, and analysis needs. For example, consequence analysis can be quantitative or can address qualitative ranges for consequence categories. Likewise, failure likelihoods can be output as classical probabilities or as expected failure frequencies as required. (author)

Applications of Microfluidics in Quantitative Biology.

Science.gov (United States)

Bai, Yang; Gao, Meng; Wen, Lingling; He, Caiyun; Chen, Yuan; Liu, Chenli; Fu, Xiongfei; Huang, Shuqiang

2018-05-01

Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future. © 2017 Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Comparison of culture-based, vital stain and PMA-qPCR methods for the quantitative detection of viable hookworm ova.

Science.gov (United States)

Gyawali, P; Sidhu, J P S; Ahmed, W; Jagals, P; Toze, S

2017-06-01

Accurate quantitative measurement of viable hookworm ova from environmental samples is the key to controlling hookworm re-infections in the endemic regions. In this study, the accuracy of three quantitative detection methods [culture-based, vital stain and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR)] was evaluated by enumerating 1,000 ± 50 Ancylostoma caninum ova in the laboratory. The culture-based method was able to quantify an average of 397 ± 59 viable hookworm ova. Similarly, vital stain and PMA-qPCR methods quantified 644 ± 87 and 587 ± 91 viable ova, respectively. The numbers of viable ova estimated by the culture-based method were significantly (P methods. Therefore, both PMA-qPCR and vital stain methods appear to be suitable for the quantitative detection of viable hookworm ova. However, PMA-qPCR would be preferable over the vital stain method in scenarios where ova speciation is needed.

Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs

Directory of Open Access Journals (Sweden)

Ye Zhi-Qiang

2011-08-01

Full Text Available Abstract Background Differential coexpression analysis (DCEA is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance. Results We developed two link-based quantitative methods, DCp and DCe, to identify differentially coexpressed genes and gene pairs (links. Bearing the uniqueness of exploiting the quantitative coexpression change of each gene pair in the coexpression networks, both methods proved to be superior to currently popular methods in simulation studies. Re-mining of a publicly available type 2 diabetes (T2D expression dataset from the perspective of differential coexpression analysis led to additional discoveries than those from differential expression analysis. Conclusions This work pointed out the critical weakness of current popular DCEA methods, and proposed two link-based DCEA algorithms that will make contribution to the development of DCEA and help extend it to a broader spectrum.

QUANTITATIVE EVALUATION METHOD OF ELEMENTS PRIORITY OF CARTOGRAPHIC GENERALIZATION BASED ON TAXI TRAJECTORY DATA

Directory of Open Access Journals (Sweden)

Z. Long

2017-09-01

Full Text Available Considering the lack of quantitative criteria for the selection of elements in cartographic generalization, this study divided the hotspot areas of passengers into parts at three levels, gave them different weights, and then classified the elements from the different hotspots. On this basis, a method was proposed to quantify the priority of elements selection. Subsequently, the quantitative priority of different cartographic elements was summarized based on this method. In cartographic generalization, the method can be preferred to select the significant elements and discard those that are relatively non-significant.

Improving quantitative dosimetry in (177)Lu-DOTATATE SPECT by energy window-based scatter corrections

DEFF Research Database (Denmark)

de Nijs, Robin; Lagerburg, Vera; Klausen, Thomas L

2014-01-01

and the activity, which depends on the collimator type, the utilized energy windows and the applied scatter correction techniques. In this study, energy window subtraction-based scatter correction methods are compared experimentally and quantitatively. MATERIALS AND METHODS: (177)Lu SPECT images of a phantom...... technique, the measured ratio was close to the real ratio, and the differences between spheres were small. CONCLUSION: For quantitative (177)Lu imaging MEGP collimators are advised. Both energy peaks can be utilized when the ESSE correction technique is applied. The difference between the calculated...

Effects of formic acid hydrolysis on the quantitative analysis of radiation-induced DNA base damage products assayed by gas chromatography/mass spectrometry

International Nuclear Information System (INIS)

Swarts, S.G.; Smith, G.S.; Miao, L.; Wheeler, K.T.

1996-01-01

Gas chromatography/mass spectrometry (GC/ MS-SIM) is an excellent technique for performing both qualitative and quantitative analysis of DNA base damage products that are formed by exposure to ionizing radiation or by the interaction of intracellular DNA with activated oxygen species. This technique commonly uses a hot formic acid hydrolysis step to degrade the DNA to individual free bases. However, due to the harsh nature of this degradation procedure, the quantitation of DNA base damage products may be adversely affected. Consequently, we examined the effects of various formic acid hydrolysis procedures on the quantitation of a number of DNA base damage products and identified several factors that can influence this quantitation. These factors included (1) the inherent acid stabilities of both the lesions and the internal standards; (2) the hydrolysis temperature; (3) the source and grade of the formic acid; and (4) the sample mass during hydrolysis. Our data also suggested that the N, O-bis (trimethylsilyl)trifluoroacetamide (BSTFA) derivatization efficiency can be adversely affected, presumably by trace contaminants either in the formic acid or from the acid-activated surface of the glass derivatization vials. Where adverse effects were noted, modifications were explored in an attempt to improve the quantitation of these DNA lesions. Although experimental steps could be taken to minimize the influence of these factors on the quantitation of some base damage products, no single procedure solved the quantitation problem for all base lesions. However, a significant improvement in the quantitation was achieved if the relative molecular response factor (RMRF) values for these lesions were generated with authentic DNA base damage products that had been treated exactly like the experimental samples. (orig.)

Quantitative high throughput analytics to support polysaccharide production process development.

Science.gov (United States)

Noyes, Aaron; Godavarti, Ranga; Titchener-Hooker, Nigel; Coffman, Jonathan; Mukhopadhyay, Tarit

2014-05-19

The rapid development of purification processes for polysaccharide vaccines is constrained by a lack of analytical tools current technologies for the measurement of polysaccharide recovery and process-related impurity clearance are complex, time-consuming, and generally not amenable to high throughput process development (HTPD). HTPD is envisioned to be central to the improvement of existing polysaccharide manufacturing processes through the identification of critical process parameters that potentially impact the quality attributes of the vaccine and to the development of de novo processes for clinical candidates, across the spectrum of downstream processing. The availability of a fast and automated analytics platform will expand the scope, robustness, and evolution of Design of Experiment (DOE) studies. This paper details recent advances in improving the speed, throughput, and success of in-process analytics at the micro-scale. Two methods, based on modifications of existing procedures, are described for the rapid measurement of polysaccharide titre in microplates without the need for heating steps. A simplification of a commercial endotoxin assay is also described that features a single measurement at room temperature. These assays, along with existing assays for protein and nucleic acids are qualified for deployment in the high throughput screening of polysaccharide feedstreams. Assay accuracy, precision, robustness, interference, and ease of use are assessed and described. In combination, these assays are capable of measuring the product concentration and impurity profile of a microplate of 96 samples in less than one day. This body of work relies on the evaluation of a combination of commercially available and clinically relevant polysaccharides to ensure maximum versatility and reactivity of the final assay suite. Together, these advancements reduce overall process time by up to 30-fold and significantly reduce sample volume over current practices. The

BBN based Quantitative Assessment of Software Design Specification

International Nuclear Information System (INIS)

Eom, Heung-Seop; Park, Gee-Yong; Kang, Hyun-Gook; Kwon, Kee-Choon; Chang, Seung-Cheol

2007-01-01

Probabilistic Safety Assessment (PSA), which is one of the important methods in assessing the overall safety of a nuclear power plant (NPP), requires quantitative reliability information of safety-critical software, but the conventional reliability assessment methods can not provide enough information for PSA of a NPP. Therefore current PSA which includes safety-critical software does not usually consider the reliability of the software or uses arbitrary values for it. In order to solve this situation this paper proposes a method that can produce quantitative reliability information of safety-critical software for PSA by making use of Bayesian Belief Networks (BBN). BBN has generally been used to model an uncertain system in many research fields including the safety assessment of software. The proposed method was constructed by utilizing BBN which can combine the qualitative and the quantitative evidence relevant to the reliability of safety critical software. The constructed BBN model can infer a conclusion in a formal and a quantitative way. A case study was carried out with the proposed method to assess the quality of software design specification (SDS) of safety-critical software that will be embedded in a reactor protection system. The intermediate V and V results of the software design specification were used as inputs to the BBN model

A Quantitative ADME-base Tool for Exploring Human ...

Science.gov (United States)

Exposure to a wide range of chemicals through our daily habits and routines is ubiquitous and largely unavoidable within modern society. The potential for human exposure, however, has not been quantified for the vast majority of chemicals with wide commercial use. Creative advances in exposure science are needed to support efficient and effective evaluation and management of chemical risks, particularly for chemicals in consumer products. The U.S. Environmental Protection Agency Office of Research and Development is developing, or collaborating in the development of, scientifically-defensible methods for making quantitative or semi-quantitative exposure predictions. The Exposure Prioritization (Ex Priori) model is a simplified, quantitative visual dashboard that provides a rank-ordered internalized dose metric to simultaneously explore exposures across chemical space (not chemical by chemical). Diverse data streams are integrated within the interface such that different exposure scenarios for “individual,” “population,” or “professional” time-use profiles can be interchanged to tailor exposure and quantitatively explore multi-chemical signatures of exposure, internalized dose (uptake), body burden, and elimination. Ex Priori has been designed as an adaptable systems framework that synthesizes knowledge from various domains and is amenable to new knowledge/information. As such, it algorithmically captures the totality of exposure across pathways. It

Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

Science.gov (United States)

Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

2006-01-01

A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

Radiation-based quantitative bioimaging at the national institute of standards and technology

Directory of Open Access Journals (Sweden)

Karam Lisa

2009-01-01

Full Text Available Building on a long history of providing physical measurements and standards for medical x rays and nuclear medicine radionuclides, the laboratory has expanded its focus to better support the extensive use of medical physics in the United States today, providing confidence in key results needed for drug and device development and marketing, therapy planning and efficacy and disease screening. In particular, to support more quantitative medical imaging, this laboratory has implemented a program to provide key measurement infrastructure to support radiation-based imaging through developing standard, benchmark phantoms, which contain radioactive sources calibrated to national measurement standards, to allow more quantitative imaging through traceable instrument calibration for clinical trials or patient management. Working closely with colleagues at the National Institutes of Health, Rensselaer Polytechnic Institute, the Food and Drug Administration and Cornell University, this laboratory has taken the initial steps in developing phantoms, and the protocols to use them, for more accurate calibration of positron emission tomography (PET or single-photon emission computed tomography (SPECT cameras, including recently standardizing 68 Ge. X-ray measurements of the laboratory′s recently developed small, resilient and inexpensive length standard phantom have shown the potential usefulness of such a "pocket" phantom for patient-based calibration of computed tomography (alone or with PET systems. The ability to calibrate diagnostic imaging tools in a way that is traceable to national standards will lead to a more quantitative approach; both physician and patient benefit from increased accuracy in treatment planning, as well as increased safety for the patient.

Contrast-enhanced spectral mammography based on a photon-counting detector: quantitative accuracy and radiation dose

Science.gov (United States)

Lee, Seungwan; Kang, Sooncheol; Eom, Jisoo

2017-03-01

Contrast-enhanced mammography has been used to demonstrate functional information about a breast tumor by injecting contrast agents. However, a conventional technique with a single exposure degrades the efficiency of tumor detection due to structure overlapping. Dual-energy techniques with energy-integrating detectors (EIDs) also cause an increase of radiation dose and an inaccuracy of material decomposition due to the limitations of EIDs. On the other hands, spectral mammography with photon-counting detectors (PCDs) is able to resolve the issues induced by the conventional technique and EIDs using their energy-discrimination capabilities. In this study, the contrast-enhanced spectral mammography based on a PCD was implemented by using a polychromatic dual-energy model, and the proposed technique was compared with the dual-energy technique with an EID in terms of quantitative accuracy and radiation dose. The results showed that the proposed technique improved the quantitative accuracy as well as reduced radiation dose comparing to the dual-energy technique with an EID. The quantitative accuracy of the contrast-enhanced spectral mammography based on a PCD was slightly improved as a function of radiation dose. Therefore, the contrast-enhanced spectral mammography based on a PCD is able to provide useful information for detecting breast tumors and improving diagnostic accuracy.

Quantitative prediction of drug side effects based on drug-related features.

Science.gov (United States)

Niu, Yanqing; Zhang, Wen

2017-09-01

Unexpected side effects of drugs are great concern in the drug development, and the identification of side effects is an important task. Recently, machine learning methods are proposed to predict the presence or absence of interested side effects for drugs, but it is difficult to make the accurate prediction for all of them. In this paper, we transform side effect profiles of drugs as their quantitative scores, by summing up their side effects with weights. The quantitative scores may measure the dangers of drugs, and thus help to compare the risk of different drugs. Here, we attempt to predict quantitative scores of drugs, namely the quantitative prediction. Specifically, we explore a variety of drug-related features and evaluate their discriminative powers for the quantitative prediction. Then, we consider several feature combination strategies (direct combination, average scoring ensemble combination) to integrate three informative features: chemical substructures, targets, and treatment indications. Finally, the average scoring ensemble model which produces the better performances is used as the final quantitative prediction model. Since weights for side effects are empirical values, we randomly generate different weights in the simulation experiments. The experimental results show that the quantitative method is robust to different weights, and produces satisfying results. Although other state-of-the-art methods cannot make the quantitative prediction directly, the prediction results can be transformed as the quantitative scores. By indirect comparison, the proposed method produces much better results than benchmark methods in the quantitative prediction. In conclusion, the proposed method is promising for the quantitative prediction of side effects, which may work cooperatively with existing state-of-the-art methods to reveal dangers of drugs.

Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe.

Science.gov (United States)

Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

2016-12-09

Accurate quantitation of intracellular pH (pH i ) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pH i sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pH i . Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pH i , in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF 4 :Yb 3+ , Tm 3+ UCNPs were used as pH i response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pH i value 3.0-7.0 with deviation less than 0.43. This approach shall facilitate the researches in pH i related areas and development of the intracellular drug delivery systems.

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

Science.gov (United States)

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

2009-07-01

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

Quantitative electromechanical impedance method for nondestructive testing based on a piezoelectric bimorph cantilever

International Nuclear Information System (INIS)

Fu, Ji; Tan, Chi; Li, Faxin

2015-01-01

The electromechanical impedance (EMI) method, which holds great promise in structural health monitoring (SHM), is usually treated as a qualitative method. In this work, we proposed a quantitative EMI method based on a piezoelectric bimorph cantilever using the sample’s local contact stiffness (LCS) as the identification parameter for nondestructive testing (NDT). Firstly, the equivalent circuit of the contact vibration system was established and the analytical relationship between the cantilever’s contact resonance frequency and the LCS was obtained. As the LCS is sensitive to typical defects such as voids and delamination, the proposed EMI method can then be used for NDT. To verify the equivalent circuit model, two piezoelectric bimorph cantilevers were fabricated and their free resonance frequencies were measured and compared with theoretical predictions. It was found that the stiff cantilever’s EMI can be well predicted by the equivalent circuit model while the soft cantilever’s cannot. Then, both cantilevers were assembled into a homemade NDT system using a three-axis motorized stage for LCS scanning. Testing results on a specimen with a prefabricated defect showed that the defect could be clearly reproduced in the LCS image, indicating the validity of the quantitative EMI method for NDT. It was found that the single-frequency mode of the EMI method can also be used for NDT, which is faster but not quantitative. Finally, several issues relating to the practical application of the NDT method were discussed. The proposed EMI-based NDT method offers a simple and rapid solution for damage evaluation in engineering structures and may also shed some light on EMI-based SHM. (paper)

Wavelet-based verification of the quantitative precipitation forecast

Science.gov (United States)

Yano, Jun-Ichi; Jakubiak, Bogumil

2016-06-01

This paper explores the use of wavelets for spatial verification of quantitative precipitation forecasts (QPF), and especially the capacity of wavelets to provide both localization and scale information. Two 24-h forecast experiments using the two versions of the Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS) on 22 August 2010 over Poland are used to illustrate the method. Strong spatial localizations and associated intermittency of the precipitation field make verification of QPF difficult using standard statistical methods. The wavelet becomes an attractive alternative, because it is specifically designed to extract spatially localized features. The wavelet modes are characterized by the two indices for the scale and the localization. Thus, these indices can simply be employed for characterizing the performance of QPF in scale and localization without any further elaboration or tunable parameters. Furthermore, spatially-localized features can be extracted in wavelet space in a relatively straightforward manner with only a weak dependence on a threshold. Such a feature may be considered an advantage of the wavelet-based method over more conventional "object" oriented verification methods, as the latter tend to represent strong threshold sensitivities. The present paper also points out limits of the so-called "scale separation" methods based on wavelets. Our study demonstrates how these wavelet-based QPF verifications can be performed straightforwardly. Possibilities for further developments of the wavelet-based methods, especially towards a goal of identifying a weak physical process contributing to forecast error, are also pointed out.

Quantitative breast tissue characterization using grating-based x-ray phase-contrast imaging

Science.gov (United States)

Willner, M.; Herzen, J.; Grandl, S.; Auweter, S.; Mayr, D.; Hipp, A.; Chabior, M.; Sarapata, A.; Achterhold, K.; Zanette, I.; Weitkamp, T.; Sztrókay, A.; Hellerhoff, K.; Reiser, M.; Pfeiffer, F.

2014-04-01

X-ray phase-contrast imaging has received growing interest in recent years due to its high capability in visualizing soft tissue. Breast imaging became the focus of particular attention as it is considered the most promising candidate for a first clinical application of this contrast modality. In this study, we investigate quantitative breast tissue characterization using grating-based phase-contrast computed tomography (CT) at conventional polychromatic x-ray sources. Different breast specimens have been scanned at a laboratory phase-contrast imaging setup and were correlated to histopathology. Ascertained tumor types include phylloides tumor, fibroadenoma and infiltrating lobular carcinoma. Identified tissue types comprising adipose, fibroglandular and tumor tissue have been analyzed in terms of phase-contrast Hounsfield units and are compared to high-quality, high-resolution data obtained with monochromatic synchrotron radiation, as well as calculated values based on tabulated tissue properties. The results give a good impression of the method’s prospects and limitations for potential tumor detection and the associated demands on such a phase-contrast breast CT system. Furthermore, the evaluated quantitative tissue values serve as a reference for simulations and the design of dedicated phantoms for phase-contrast mammography.

PCR-free quantitative detection of genetically modified organism from raw materials. An electrochemiluminescence-based bio bar code method.

Science.gov (United States)

Zhu, Debin; Tang, Yabing; Xing, Da; Chen, Wei R

2008-05-15

A bio bar code assay based on oligonucleotide-modified gold nanoparticles (Au-NPs) provides a PCR-free method for quantitative detection of nucleic acid targets. However, the current bio bar code assay requires lengthy experimental procedures including the preparation and release of bar code DNA probes from the target-nanoparticle complex and immobilization and hybridization of the probes for quantification. Herein, we report a novel PCR-free electrochemiluminescence (ECL)-based bio bar code assay for the quantitative detection of genetically modified organism (GMO) from raw materials. It consists of tris-(2,2'-bipyridyl) ruthenium (TBR)-labeled bar code DNA, nucleic acid hybridization using Au-NPs and biotin-labeled probes, and selective capture of the hybridization complex by streptavidin-coated paramagnetic beads. The detection of target DNA is realized by direct measurement of ECL emission of TBR. It can quantitatively detect target nucleic acids with high speed and sensitivity. This method can be used to quantitatively detect GMO fragments from real GMO products.

Stable isotopic labeling-based quantitative targeted glycomics (i-QTaG).

Science.gov (United States)

Kim, Kyoung-Jin; Kim, Yoon-Woo; Kim, Yun-Gon; Park, Hae-Min; Jin, Jang Mi; Hwan Kim, Young; Yang, Yung-Hun; Kyu Lee, Jun; Chung, Junho; Lee, Sun-Gu; Saghatelian, Alan

2015-01-01

Mass spectrometry (MS) analysis combined with stable isotopic labeling is a promising method for the relative quantification of aberrant glycosylation in diseases and disorders. We developed a stable isotopic labeling-based quantitative targeted glycomics (i-QTaG) technique for the comparative and quantitative analysis of total N-glycans using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We established the analytical procedure with the chemical derivatizations (i.e., sialic acid neutralization and stable isotopic labeling) of N-glycans using a model glycoprotein (bovine fetuin). Moreover, the i-QTaG using MALDI-TOF MS was evaluated with various molar ratios (1:1, 1:2, 1:5) of (13) C6 /(12) C6 -2-aminobenzoic acid-labeled glycans from normal human serum. Finally, this method was applied to direct comparison of the total N-glycan profiles between normal human sera (n = 8) and prostate cancer patient sera (n = 17). The intensities of the N-glycan peaks from i-QTaG method showed a good linearity (R(2) > 0.99) with the amount of the bovine fetuin glycoproteins. The ratios of relative intensity between the isotopically 2-AA labeled N-glycans were close to the theoretical molar ratios (1:1, 1:2, 1:5). We also demonstrated that the up-regulation of the Lewis antigen (~82%) in sera from prostate cancer patients. In this proof-of-concept study, we demonstrated that the i-QTaG method, which enables to achieve a reliable comparative quantitation of total N-glycans via MALDI-TOF MS analysis, has the potential to diagnose and monitor alterations in glycosylation associated with disease states or biotherapeutics. © 2015 American Institute of Chemical Engineers.

Kinetic microplate bioassays for relative potency of antibiotics improved by partial Least Square (PLS) regression.

Science.gov (United States)

Francisco, Fabiane Lacerda; Saviano, Alessandro Morais; Almeida, Túlia de Souza Botelho; Lourenço, Felipe Rebello

2016-05-01

Microbiological assays are widely used to estimate the relative potencies of antibiotics in order to guarantee the efficacy, safety, and quality of drug products. Despite of the advantages of turbidimetric bioassays when compared to other methods, it has limitations concerning the linearity and range of the dose-response curve determination. Here, we proposed to use partial least squares (PLS) regression to solve these limitations and to improve the prediction of relative potencies of antibiotics. Kinetic-reading microplate turbidimetric bioassays for apramacyin and vancomycin were performed using Escherichia coli (ATCC 8739) and Bacillus subtilis (ATCC 6633), respectively. Microbial growths were measured as absorbance up to 180 and 300min for apramycin and vancomycin turbidimetric bioassays, respectively. Conventional dose-response curves (absorbances or area under the microbial growth curve vs. log of antibiotic concentration) showed significant regression, however there were significant deviation of linearity. Thus, they could not be used for relative potency estimations. PLS regression allowed us to construct a predictive model for estimating the relative potencies of apramycin and vancomycin without over-fitting and it improved the linear range of turbidimetric bioassay. In addition, PLS regression provided predictions of relative potencies equivalent to those obtained from agar diffusion official methods. Therefore, we conclude that PLS regression may be used to estimate the relative potencies of antibiotics with significant advantages when compared to conventional dose-response curve determination. Copyright © 2016 Elsevier B.V. All rights reserved.

Applying quantitative adiposity feature analysis models to predict benefit of bevacizumab-based chemotherapy in ovarian cancer patients

Science.gov (United States)

Wang, Yunzhi; Qiu, Yuchen; Thai, Theresa; More, Kathleen; Ding, Kai; Liu, Hong; Zheng, Bin

2016-03-01

How to rationally identify epithelial ovarian cancer (EOC) patients who will benefit from bevacizumab or other antiangiogenic therapies is a critical issue in EOC treatments. The motivation of this study is to quantitatively measure adiposity features from CT images and investigate the feasibility of predicting potential benefit of EOC patients with or without receiving bevacizumab-based chemotherapy treatment using multivariate statistical models built based on quantitative adiposity image features. A dataset involving CT images from 59 advanced EOC patients were included. Among them, 32 patients received maintenance bevacizumab after primary chemotherapy and the remaining 27 patients did not. We developed a computer-aided detection (CAD) scheme to automatically segment subcutaneous fat areas (VFA) and visceral fat areas (SFA) and then extracted 7 adiposity-related quantitative features. Three multivariate data analysis models (linear regression, logistic regression and Cox proportional hazards regression) were performed respectively to investigate the potential association between the model-generated prediction results and the patients' progression-free survival (PFS) and overall survival (OS). The results show that using all 3 statistical models, a statistically significant association was detected between the model-generated results and both of the two clinical outcomes in the group of patients receiving maintenance bevacizumab (p<0.01), while there were no significant association for both PFS and OS in the group of patients without receiving maintenance bevacizumab. Therefore, this study demonstrated the feasibility of using quantitative adiposity-related CT image features based statistical prediction models to generate a new clinical marker and predict the clinical outcome of EOC patients receiving maintenance bevacizumab-based chemotherapy.

Slow transients recorded by the cGPS network FreDNet at the northern Adria microplate boundary (NE-Italy)

Science.gov (United States)

Rossi, Giuliana; Fabris, Paolo; Zuliani, David

2013-04-01

The northern tip of the Adria micro-plate (NE-Italy) is continuously monitored by the Friuli Regional Deformation Network (FReDNet) of OGS (Istituto Nazionale di Oceanografia e Geofisica Sperimentale), consisting of 15 GNSS permanent sites, the first eight of which were installed between 2002 and 2004. Additional information on the strain field in the region comes from the 10 GNSS permanent sites of the Marussi network of the Friuli-Venezia Giulia regional council, some of which record continuously since 1999. Having at disposal time-series of a certain length (around ten-years), it is possible to evaluate with reliability not only the plate motion direction and velocity, represented by the linear trend of the horizontal components of the records, but also the possible plate acceleration, due to the superposition of other terms of the strain field time-space variations, with different frequency. With the aim of investigating such terms, we first processed the GPS data of the longest time series from both networks, starting from 2002, using GAMIT/GLOBK, eliminated the outliers, and filled the eventual short gaps in the data through linear interpolation. A low-band pass filter allowed obtaining the time-series cleaned from the components with frequencies higher than 1.5 years, so to eliminate the annual and quasi-annual terms, and the highest frequencies. The so-obtained time-series for the two horizontal components result dominated by a linear trend, as expected, to which clear oscillations of some years of duration are superimposed. From the analysis of the linear trend, the resulting velocity field suggest crustal shortening, with values ranging between 0.6 and 2.8 mm/year, decreasing from South to North and, more slightly, from East to West. This is in agreement with preceding observations and with the geodynamic character of the region, located in the area of convergence between Adria microplate and Eurasia. As regards as the deviations from the linear trend

Gold Nanoparticle Labeling Based ICP-MS Detection/Measurement of Bacteria, and Their Quantitative Photothermal Destruction

Science.gov (United States)

Lin, Yunfeng

2015-01-01

Bacteria such as Salmonella and E. coli present a great challenge in public health care in today’s society. Protection of public safety against bacterial contamination and rapid diagnosis of infection require simple and fast assays for the detection and elimination of bacterial pathogens. After utilizing Salmonella DT104 as an example bacterial strain for our investigation, we report a rapid and sensitive assay for the qualitative and quantitative detection of bacteria by using antibody affinity binding, popcorn shaped gold nanoparticle (GNPOPs) labeling, surfance enchanced Raman spectroscopy (SERS), and inductively coupled plasma mass spectrometry (ICP-MS) detection. For qualitative analysis, our assay can detect Salmonella within 10 min by Raman spectroscopy; for quantitative analysis, our assay has the ability to measure as few as 100 Salmonella DT104 in a 1 mL sample (100 CFU/mL) within 40 min. Based on the quantitative detection, we investigated the quantitative destruction of Salmonella DT104, and the assay’s photothermal efficiency in order to reduce the amount of GNPOPs in the assay to ultimately to eliminate any potential side effects/toxicity to the surrounding cells in vivo. Results suggest that our assay may serve as a promising candidate for qualitative and quantitative detection and elimination of a variety of bacterial pathogens. PMID:26417447

Profile of Students' Creative Thinking Skills on Quantitative Project-Based Protein Testing using Local Materials

Directory of Open Access Journals (Sweden)

D. K. Sari

2017-04-01

Full Text Available The purpose of this study is to obtain a profile of students’ creative thinking skills on quantitative project-based protein testing using local materials. Implementation of the research is using quasi-experimental method pre-test post-test control group design with 40 students involved in Biochemistry lab. The research instrument is pre-test and post-test using creative thinking skills in the form of description and students’ questionnaire. The analysis was performed with SPSS 22.0 program to see the significance normality, U Mann-Whitney test for nonparametric statistics, N-Gain score, and the percentage of student responses to the practicum performed. The research result shows that the pretest rate in the experimental group is 8.25 while in the control group is 6.90. After attending a project-based practicum with local materials, the experimental group obtained the mean of posttest is 37.55 while in control class is 11.18. The students’ improvement on creative thinking skills can be seen from the average of N-Gain in the experimental class with 0.32 (medium category and in the control category with 0.05 (low category. The experimental and control class have different creative thinking skills significantly different fluency, flexibility, novelty, and detail. It can be concluded that quantitative project-based protein testing using local materials can improve students’ creative thinking skills. 71% of total students feel that quantitative project-based protein testing using local materials make them more creative in doing a practicum in the laboratory.

Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe

NARCIS (Netherlands)

Li, C.; Zuo, J.; Zhang, L.; Chang, Y.; Zhang, Y.; Tu, L.; Liu, X.; Xue, B.; Li, Q.; Zhao, H.; Zhang, H.; Kong, X.

2016-01-01

Accurate quantitation of intracellular pH (pHi) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pHi sensing. Till now,

An Amphibious Seismic Study of the Crustal Structure of the Adriatic Microplate

Science.gov (United States)

Dannowski, A.; Kopp, H.; Schurr, B.; Improta, L.; Papenberg, C. A.; Krabbenhoeft, A.; Argnani, A.; Ustaszewski, K. M.; Handy, M.; Glavatovic, B.

2016-12-01

The present-day structure of the southern Adriatic area is controlled by two oppositely-vergent fold-and-thrust belt systems (Apennines and Dinarides). The Adriatic continental domain is one of the most enigmatic segments of the Alpine-Mediterranean collision zone. It separated from the African plate during the Mesozoic extensional phase that led to the opening of the Ionian Sea. Basin widening and deepening peaked during Late Triassic-Liassic extension, resulting in the formation of the southern Adriatic basin, bounded on either side by the Dinaric and Apulian shallow water carbonate platforms. Because of its present foreland position with respect to the Dinaric part of orogenic belt, the southern Adriatic basin represents the only remnant of the Neotethyan margin and offers the unique opportunity to image a segment of Mesozoic passive margin in the Mediterranean. To study the deep crustal structure, the upper mantle and the shape of the plate margin, the German research vessel Meteor acquired 2D seismic refraction and wide-angle reflection data during an onshore-offshore experiment (cruise M86-3). We present two profiles: Profile P03 crossed Adria from the Gargano Promontory into Albania. A second profile (P01) was shot parallel to the coastlines, extending from the southern Adriatic basin to a possible mid-Adriatic strike-slip fault that purportedly segments the Adriatic microplate. Two different approaches of travel time tomography are applied to the data set: A non-linear approach is used for the shorter profile P01. A linear approach is applied to profile P03 (360 km length) and allows for the integration of the 36 ocean bottom stations and 19 land stations. First results show a good resolution of the sedimentary part of the Adriatic region. The depth of the basement as well as the depth of the Moho discontinuity vary laterally and deepen towards the North-East, consistent with the notion of flexural loading of the externally propagating orogenic wedge of the

Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women.

Science.gov (United States)

Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C; Joseph, Gabby B; Yap, Samuel P; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M

2012-07-01

The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 ± 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P infiltration of muscle commonly occurs in many metabolic and neuromuscular diseases. • Image-based semi-quantitative classifications for assessing fat infiltration are not well validated. • Quantitative MRI techniques provide an accurate assessment of muscle fat.

PCR-free quantitative detection of genetically modified organism from raw materials – A novel electrochemiluminescence-based bio-barcode method

Science.gov (United States)

Zhu, Debin; Tang, Yabing; Xing, Da; Chen, Wei R.

2018-01-01

Bio-barcode assay based on oligonucleotide-modified gold nanoparticles (Au-NPs) provides a PCR-free method for quantitative detection of nucleic acid targets. However, the current bio-barcode assay requires lengthy experimental procedures including the preparation and release of barcode DNA probes from the target-nanoparticle complex, and immobilization and hybridization of the probes for quantification. Herein, we report a novel PCR-free electrochemiluminescence (ECL)-based bio-barcode assay for the quantitative detection of genetically modified organism (GMO) from raw materials. It consists of tris-(2’2’-bipyridyl) ruthenium (TBR)-labele barcode DNA, nucleic acid hybridization using Au-NPs and biotin-labeled probes, and selective capture of the hybridization complex by streptavidin-coated paramagnetic beads. The detection of target DNA is realized by direct measurement of ECL emission of TBR. It can quantitatively detect target nucleic acids with high speed and sensitivity. This method can be used to quantitatively detect GMO fragments from real GMO products. PMID:18386909

Quantitative acid-base physiology using the Stewart model. Does it improve our understanding of what is really wrong?

NARCIS (Netherlands)

Derksen, R.; Scheffer, G.J.; Hoeven, J.G. van der

2006-01-01

Traditional theories of acid-base balance are based on the Henderson-Hasselbalch equation to calculate proton concentration. The recent revival of quantitative acid-base physiology using the Stewart model has increased our understanding of complicated acid-base disorders, but has also led to several

Comparative study of kidney function based on quantitative nuclear medicine techniques

International Nuclear Information System (INIS)

Amadou, K.

2014-07-01

The general purpose of this work was to evaluate and to compare the measurements of renal function by quantitative methods with Single Photon Emission Computed Tomography. Dynamic renal images were obtained from the database of the General University Hospital in Prague. Images of one hundred and seven (107) patients were used. Regions of Interest (ROI’s) were applied over each kidney and a background area for background activity correction using software called pmod. From the renograms, Split Renal Function (SRF) was determined using integral method. The Glomerular Filtration Rate (GFR), both as a total value and individually for each kidney using 99m-Tc MAG3 (Mercaptoactyltriglycine) was also determined using the Gate formula and Tonnesen formula for determining renal depth. For the left kidney function a strong positive association (n= 107; R² = 0.95) was found between the values obtained by calculation using integral method and that of the Czech data base. The mean difference between our calculation and Czech values was -0.91 with a standard deviation of 4.57 and the 95% limits of agreement -5.48 and 3.66. In 85 patients the difference was ≤ ±5%, in 17 patients it was between ±5% and ±10% and in 5 patients the difference was between ±10% and ±15%. For the total GFR, the accuracy is less compare to SRF (n = 60; R² = 0.66) was found between the values obtained by calculation using Gate method and that of the Czech value using MDRD methods. The mean difference between our calculation and the Czech values was -2.82 ml/min/1.73 m² with a standard deviation of 22.46 and the 95% limits of agreement -25.28 and 19.64 ml/min/1.73 m². In 21 patients the difference was 0 and ±10%, in 23 patients it was between ±10% and ±20%, in 9 patients it was between ±20% and ±30%, in 3 patients it was between ±30% and ±40%, and in 4 patients it was between ±40% and ±65%. Quantitative imaging has only recently emerged as a promising approach for diagnosis and

Effective Heart Disease Detection Based on Quantitative Computerized Traditional Chinese Medicine Using Representation Based Classifiers

Directory of Open Access Journals (Sweden)

Ting Shu

2017-01-01

Full Text Available At present, heart disease is the number one cause of death worldwide. Traditionally, heart disease is commonly detected using blood tests, electrocardiogram, cardiac computerized tomography scan, cardiac magnetic resonance imaging, and so on. However, these traditional diagnostic methods are time consuming and/or invasive. In this paper, we propose an effective noninvasive computerized method based on facial images to quantitatively detect heart disease. Specifically, facial key block color features are extracted from facial images and analyzed using the Probabilistic Collaborative Representation Based Classifier. The idea of facial key block color analysis is founded in Traditional Chinese Medicine. A new dataset consisting of 581 heart disease and 581 healthy samples was experimented by the proposed method. In order to optimize the Probabilistic Collaborative Representation Based Classifier, an analysis of its parameters was performed. According to the experimental results, the proposed method obtains the highest accuracy compared with other classifiers and is proven to be effective at heart disease detection.

[Quality evaluation of rhubarb dispensing granules based on multi-component simultaneous quantitative analysis and bioassay].

Science.gov (United States)

Tan, Peng; Zhang, Hai-Zhu; Zhang, Ding-Kun; Wu, Shan-Na; Niu, Ming; Wang, Jia-Bo; Xiao, Xiao-He

2017-07-01

This study attempts to evaluate the quality of Chinese formula granules by combined use of multi-component simultaneous quantitative analysis and bioassay. The rhubarb dispensing granules were used as the model drug for demonstrative study. The ultra-high performance liquid chromatography (UPLC) method was adopted for simultaneously quantitative determination of the 10 anthraquinone derivatives (such as aloe emodin-8-O-β-D-glucoside) in rhubarb dispensing granules; purgative biopotency of different batches of rhubarb dispensing granules was determined based on compound diphenoxylate tablets-induced mouse constipation model; blood activating biopotency of different batches of rhubarb dispensing granules was determined based on in vitro rat antiplatelet aggregation model; SPSS 22.0 statistical software was used for correlation analysis between 10 anthraquinone derivatives and purgative biopotency, blood activating biopotency. The results of multi-components simultaneous quantitative analysisshowed that there was a great difference in chemical characterizationand certain differences inpurgative biopotency and blood activating biopotency among 10 batches of rhubarb dispensing granules. The correlation analysis showed that the intensity of purgative biopotency was significantly correlated with the content of conjugated anthraquinone glycosides (Panalysis and bioassay can achieve objective quantification and more comprehensive reflection on overall quality difference among different batches of rhubarb dispensing granules. Copyright© by the Chinese Pharmaceutical Association.

Fast and quantitative differentiation of single-base mismatched DNA by initial reaction rate of catalytic hairpin assembly.

Science.gov (United States)

Li, Chenxi; Li, Yixin; Xu, Xiao; Wang, Xinyi; Chen, Yang; Yang, Xiaoda; Liu, Feng; Li, Na

2014-10-15

The widely used catalytic hairpin assembly (CHA) amplification strategy generally needs several hours to accomplish one measurement based on the prevailingly used maximum intensity detection mode, making it less practical for assays where high throughput or speed is desired. To make the best use of the kinetic specificity of toehold domain for circuit reaction initiation, we developed a mathematical model and proposed an initial reaction rate detection mode to quantitatively differentiate the single-base mismatch. Using the kinetic mode, assay time can be reduced substantially to 10 min for one measurement with the comparable sensitivity and single-base mismatch differentiating ability as were obtained by the maximum intensity detection mode. This initial reaction rate based approach not only provided a fast and quantitative differentiation of single-base mismatch, but also helped in-depth understanding of the CHA system, which will be beneficial to the design of highly sensitive and specific toehold-mediated hybridization reactions. Copyright © 2014 Elsevier B.V. All rights reserved.

Operations management research methodologies using quantitative modeling

NARCIS (Netherlands)

Bertrand, J.W.M.; Fransoo, J.C.

2002-01-01

Gives an overview of quantitative model-based research in operations management, focusing on research methodology. Distinguishes between empirical and axiomatic research, and furthermore between descriptive and normative research. Presents guidelines for doing quantitative model-based research in

Immunoliposome-PCR: a generic ultrasensitive quantitative antigen detection system

Directory of Open Access Journals (Sweden)

He Junkun

2012-06-01

Full Text Available Abstract Background The accurate quantification of antigens at low concentrations over a wide dynamic range is needed for identifying biomarkers associated with disease and detecting protein interactions in high-throughput microarrays used in proteomics. Here we report the development of an ultrasensitive quantitative assay format called immunoliposome polymerase chain reaction (ILPCR that fulfills these requirements. This method uses a liposome, with reporter DNA encapsulated inside and biotin-labeled polyethylene glycol (PEG phospholipid conjugates incorporated into the outer surface of the liposome, as a detection reagent. The antigenic target is immobilized in the well of a microplate by a capture antibody and the liposome detection reagent is then coupled to a biotin-labeled second antibody through a NeutrAvidin bridge. The liposome is ruptured to release the reporter DNA, which serves as a surrogate to quantify the protein target using real-time PCR. Results A liposome detection reagent was prepared, which consisted of a population of liposomes ~120 nm in diameter with each liposome possessing ~800 accessible biotin receptors and ~220 encapsulated reporters. This liposome detection reagent was used in an assay to quantify the concentration of carcinoembryonic antigen (CEA in human serum. This ILPCR assay exhibited a linear dose–response curve from 10-10 M to 10-16 M CEA. Within this range the assay coefficient of variance was Conclusions The ILPCR assay has several advantages over other immuno-PCR methods. The reporter DNA and biotin-labeled PEG phospholipids spontaneously incorporate into the liposomes as they form, simplifying preparation of the detection reagent. Encapsulation of the reporter inside the liposomes allows nonspecific DNA in the assay medium to be degraded with DNase I prior to quantification of the encapsulated reporter by PCR, which reduces false-positive results and improves quantitative accuracy. The ability to

Contribute to quantitative identification of casting defects based on computer analysis of X-ray images

Directory of Open Access Journals (Sweden)

Z. Ignaszak

2007-12-01

Full Text Available The forecast of structure and properties of casting is based on results of computer simulation of physical processes which are carried out during the casting processes. For the effective using of simulation system it is necessary to validate mathematica-physical models describing process of casting formation and the creation of local discontinues, witch determinate the casting properties.In the paper the proposition for quantitative validation of VP system using solidification casting defects by information sources of II group (methods of NDT was introduced. It was named the VP/RT validation (virtual prototyping/radiographic testing validation. Nowadays identification of casting defects noticeable on X-ray images bases on comparison of X-ray image of casting with relates to the ASTM. The results of this comparison are often not conclusive because based on operator’s subjective assessment. In the paper the system of quantitative identification of iron casting defects on X-ray images and classification this defects to ASTM class is presented. The methods of pattern recognition and machine learning were applied.

An Ibm PC/AT-Based Image Acquisition And Processing System For Quantitative Image Analysis

Science.gov (United States)

Kim, Yongmin; Alexander, Thomas

1986-06-01

In recent years, a large number of applications have been developed for image processing systems in the area of biological imaging. We have already finished the development of a dedicated microcomputer-based image processing and analysis system for quantitative microscopy. The system's primary function has been to facilitate and ultimately automate quantitative image analysis tasks such as the measurement of cellular DNA contents. We have recognized from this development experience, and interaction with system users, biologists and technicians, that the increasingly widespread use of image processing systems, and the development and application of new techniques for utilizing the capabilities of such systems, would generate a need for some kind of inexpensive general purpose image acquisition and processing system specially tailored for the needs of the medical community. We are currently engaged in the development and testing of hardware and software for a fairly high-performance image processing computer system based on a popular personal computer. In this paper, we describe the design and development of this system. Biological image processing computer systems have now reached a level of hardware and software refinement where they could become convenient image analysis tools for biologists. The development of a general purpose image processing system for quantitative image analysis that is inexpensive, flexible, and easy-to-use represents a significant step towards making the microscopic digital image processing techniques more widely applicable not only in a research environment as a biologist's workstation, but also in clinical environments as a diagnostic tool.

Solution identification and quantitative analysis of fiber-capacitive drop analyzer based on multivariate statistical methods

Science.gov (United States)

Chen, Zhe; Qiu, Zurong; Huo, Xinming; Fan, Yuming; Li, Xinghua

2017-03-01

A fiber-capacitive drop analyzer is an instrument which monitors a growing droplet to produce a capacitive opto-tensiotrace (COT). Each COT is an integration of fiber light intensity signals and capacitance signals and can reflect the unique physicochemical property of a liquid. In this study, we propose a solution analytical and concentration quantitative method based on multivariate statistical methods. Eight characteristic values are extracted from each COT. A series of COT characteristic values of training solutions at different concentrations compose a data library of this kind of solution. A two-stage linear discriminant analysis is applied to analyze different solution libraries and establish discriminant functions. Test solutions can be discriminated by these functions. After determining the variety of test solutions, Spearman correlation test and principal components analysis are used to filter and reduce dimensions of eight characteristic values, producing a new representative parameter. A cubic spline interpolation function is built between the parameters and concentrations, based on which we can calculate the concentration of the test solution. Methanol, ethanol, n-propanol, and saline solutions are taken as experimental subjects in this paper. For each solution, nine or ten different concentrations are chosen to be the standard library, and the other two concentrations compose the test group. By using the methods mentioned above, all eight test solutions are correctly identified and the average relative error of quantitative analysis is 1.11%. The method proposed is feasible which enlarges the applicable scope of recognizing liquids based on the COT and improves the concentration quantitative precision, as well.

[Quantitative Analysis of Heavy Metals in Water with LIBS Based on Signal-to-Background Ratio].

Science.gov (United States)

Hu, Li; Zhao, Nan-jing; Liu, Wen-qing; Fang, Li; Zhang, Da-hai; Wang, Yin; Meng, De Shuo; Yu, Yang; Ma, Ming-jun

2015-07-01

There are many influence factors in the precision and accuracy of the quantitative analysis with LIBS technology. According to approximately the same characteristics trend of background spectrum and characteristic spectrum along with the change of temperature through in-depth analysis, signal-to-background ratio (S/B) measurement and regression analysis could compensate the spectral line intensity changes caused by system parameters such as laser power, spectral efficiency of receiving. Because the measurement dates were limited and nonlinear, we used support vector machine (SVM) for regression algorithm. The experimental results showed that the method could improve the stability and the accuracy of quantitative analysis of LIBS, and the relative standard deviation and average relative error of test set respectively were 4.7% and 9.5%. Data fitting method based on signal-to-background ratio(S/B) is Less susceptible to matrix elements and background spectrum etc, and provides data processing reference for real-time online LIBS quantitative analysis technology.

[Quantitative classification-based occupational health management for electroplating enterprises in Baoan District of Shenzhen, China].

Science.gov (United States)

Zhang, Sheng; Huang, Jinsheng; Yang, Baigbing; Lin, Binjie; Xu, Xinyun; Chen, Jinru; Zhao, Zhuandi; Tu, Xiaozhi; Bin, Haihua

2014-04-01

To improve the occupational health management levels in electroplating enterprises with quantitative classification measures and to provide a scientific basis for the prevention and control of occupational hazards in electroplating enterprises and the protection of workers' health. A quantitative classification table was created for the occupational health management in electroplating enterprises. The evaluation indicators included 6 items and 27 sub-items, with a total score of 100 points. Forty electroplating enterprises were selected and scored according to the quantitative classification table. These electroplating enterprises were classified into grades A, B, and C based on the scores. Among 40 electroplating enterprises, 11 (27.5%) had scores of >85 points (grade A), 23 (57.5%) had scores of 60∼85 points (grade B), and 6 (15.0%) had scores of electroplating enterprises is a valuable attempt, which is helpful for the supervision and management by the health department and provides an effective method for the self-management of enterprises.

Quantitative Assessment of a Field-Based Course on Integrative Geology, Ecology and Cultural History

Science.gov (United States)

Sheppard, Paul R.; Donaldson, Brad A.; Huckleberry, Gary

2010-01-01

A field-based course at the University of Arizona called Sense of Place (SOP) covers the geology, ecology and cultural history of the Tucson area. SOP was quantitatively assessed for pedagogical effectiveness. Students of the Spring 2008 course were given pre- and post-course word association surveys in order to assess awareness and comprehension…

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

Directory of Open Access Journals (Sweden)

Zhang PF

2015-09-01

Full Text Available Pengfei Zhang,1,* Yan Bao,1,* Mohamed Shehata Draz,2,3,* Huiqi Lu,1 Chang Liu,1 Huanxing Han11Center for Translational Medicine, Changzheng Hospital, Second Military Medical University, Shanghai, People’s Republic of China; 2Zhejiang-California International Nanosystems Institute, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China; 3Faculty of Science, Tanta University, Tanta, Egypt*These authors contributed equally to this workAbstract: Convenient and rapid immunofiltration assays (IFAs enable on-site “yes” or “no” determination of disease markers. However, traditional IFAs are commonly qualitative or semi-quantitative and are very limited for the efficient testing of samples in field diagnostics. Here, we overcome these limitations by developing a quantum dots (QDs-based fluorescent IFA for the quantitative detection of C-reactive proteins (CRP. CRP, the well-known diagnostic marker for acute viral and bacterial infections, was used as a model analyte to demonstrate performance and sensitivity of our developed QDs-based IFA. QDs capped with both polyethylene glycol (PEG and glutathione were used as fluorescent labels for our IFAs. The presence of the surface PEG layer, which reduced the non-specific protein interactions, in conjunction with the inherent optical properties of QDs, resulted in lower background signal, increased sensitivity, and ability to detect CRP down to 0.79 mg/L with only 5 µL serum sample. In addition, the developed assay is simple, fast and can quantitatively detect CRP with a detection limit up to 200 mg/L. Clinical test results of our QD-based IFA are well correlated with the traditional latex enhance immune-agglutination aggregation. The proposed QD-based fluorescent IFA is very promising, and potentially will be adopted for multiplexed immunoassay and in field point-of-care test.Keywords: C-reactive proteins, point-of-care test, Glutathione capped QDs, PEGylation

Quantitative mass spectrometry: an overview

Science.gov (United States)

Urban, Pawel L.

2016-10-01

Mass spectrometry (MS) is a mainstream chemical analysis technique in the twenty-first century. It has contributed to numerous discoveries in chemistry, physics and biochemistry. Hundreds of research laboratories scattered all over the world use MS every day to investigate fundamental phenomena on the molecular level. MS is also widely used by industry-especially in drug discovery, quality control and food safety protocols. In some cases, mass spectrometers are indispensable and irreplaceable by any other metrological tools. The uniqueness of MS is due to the fact that it enables direct identification of molecules based on the mass-to-charge ratios as well as fragmentation patterns. Thus, for several decades now, MS has been used in qualitative chemical analysis. To address the pressing need for quantitative molecular measurements, a number of laboratories focused on technological and methodological improvements that could render MS a fully quantitative metrological platform. In this theme issue, the experts working for some of those laboratories share their knowledge and enthusiasm about quantitative MS. I hope this theme issue will benefit readers, and foster fundamental and applied research based on quantitative MS measurements. This article is part of the themed issue 'Quantitative mass spectrometry'.

Extending Theory-Based Quantitative Predictions to New Health Behaviors.

Science.gov (United States)

Brick, Leslie Ann D; Velicer, Wayne F; Redding, Colleen A; Rossi, Joseph S; Prochaska, James O

2016-04-01

Traditional null hypothesis significance testing suffers many limitations and is poorly adapted to theory testing. A proposed alternative approach, called Testing Theory-based Quantitative Predictions, uses effect size estimates and confidence intervals to directly test predictions based on theory. This paper replicates findings from previous smoking studies and extends the approach to diet and sun protection behaviors using baseline data from a Transtheoretical Model behavioral intervention (N = 5407). Effect size predictions were developed using two methods: (1) applying refined effect size estimates from previous smoking research or (2) using predictions developed by an expert panel. Thirteen of 15 predictions were confirmed for smoking. For diet, 7 of 14 predictions were confirmed using smoking predictions and 6 of 16 using expert panel predictions. For sun protection, 3 of 11 predictions were confirmed using smoking predictions and 5 of 19 using expert panel predictions. Expert panel predictions and smoking-based predictions poorly predicted effect sizes for diet and sun protection constructs. Future studies should aim to use previous empirical data to generate predictions whenever possible. The best results occur when there have been several iterations of predictions for a behavior, such as with smoking, demonstrating that expected values begin to converge on the population effect size. Overall, the study supports necessity in strengthening and revising theory with empirical data.

Quantitative assessment of Heart Rate Dynamics during meditation: An ECG based study with Multi-fractality and visibility graph

Directory of Open Access Journals (Sweden)

Anirban eBhaduri

2016-02-01

Full Text Available Abstract: Abstract: The cardiac dynamics during meditation is explored quantitatively with two chaos-based non-linear techniques viz. multi-fractal detrended fluctuation analysis and visibility network analysis techniques. The data used are the instantaneous heart rate (in beats/minute of subjects performing Kundalini Yoga and Chi meditation from PhysioNet. The results show consistent differences between the quantitative parameters obtained by both the analysis techniques. This indicates an interesting phenomenon of change in the complexity of the cardiac dynamics during meditation supported with quantitative parameters.The results also produce a preliminary evidence that these techniques can be used as a measure of physiological impact on subjects performing meditation.

Quantitative Assessment of Heart Rate Dynamics during Meditation: An ECG Based Study with Multi-Fractality and Visibility Graph.

Science.gov (United States)

Bhaduri, Anirban; Ghosh, Dipak

2016-01-01

The cardiac dynamics during meditation is explored quantitatively with two chaos-based non-linear techniques viz. multi-fractal detrended fluctuation analysis and visibility network analysis techniques. The data used are the instantaneous heart rate (in beats/minute) of subjects performing Kundalini Yoga and Chi meditation from PhysioNet. The results show consistent differences between the quantitative parameters obtained by both the analysis techniques. This indicates an interesting phenomenon of change in the complexity of the cardiac dynamics during meditation supported with quantitative parameters. The results also produce a preliminary evidence that these techniques can be used as a measure of physiological impact on subjects performing meditation.

Respirometry in activated sludge

NARCIS (Netherlands)

Spanjers, H.

1993-01-01

The purpose of the study was (1) to develop a respiration meter capable of continuously measuring, using different procedures, the oxygen uptake rate of activated sludge and (2) to expand knowledge about respiration related characteristics of wastewater and activated sludge.

A

Electrical impedance tomography-based sensing skin for quantitative imaging of damage in concrete

International Nuclear Information System (INIS)

Hallaji, Milad; Pour-Ghaz, Mohammad; Seppänen, Aku

2014-01-01

This paper outlines the development of a large-area sensing skin for damage detection in concrete structures. The developed sensing skin consists of a thin layer of electrically conductive copper paint that is applied to the surface of the concrete. Cracking of the concrete substrate results in the rupture of the sensing skin, decreasing its electrical conductivity locally. The decrease in conductivity is detected with electrical impedance tomography (EIT) imaging. In previous works, electrically based sensing skins have provided only qualitative information on the damage on the substrate surface. In this paper, we study whether quantitative imaging of the damage is possible. We utilize application-specific models and computational methods in the image reconstruction, including a total variation (TV) prior model for the damage and an approximate correction of the modeling errors caused by the inhomogeneity of the painted sensing skin. The developed damage detection method is tested experimentally by applying the sensing skin to polymeric substrates and a reinforced concrete beam under four-point bending. In all test cases, the EIT-based sensing skin provides quantitative information on cracks and/or other damages on the substrate surface: featuring a very low conductivity in the damage locations, and a reliable indication of the lengths and shapes of the cracks. The results strongly support the applicability of the painted EIT-based sensing skin for damage detection in reinforced concrete elements and other substrates. (paper)

Quantitative generalized ratiometric fluorescence spectroscopy for turbid media based on probe encapsulated by biologically localized embedding

International Nuclear Information System (INIS)

Yan, Xiu-Fang; Chen, Zeng-Ping; Cui, Yin-Yin; Hu, Yuan-Liang; Yu, Ru-Qin

2016-01-01

PEBBLE (probe encapsulated by biologically localized embedding) nanosensor encapsulating an intensity-based fluorescence indicator and an inert reference fluorescence dye inside the pores of stable matrix can be used as a generalized wavelength-ratiometric probe. However, the lack of an efficient quantitative model render the choices of inert reference dyes and intensity-based fluorescence indicators used in PEBBLEs based generalized wavelength-ratiometric probes rather limited. In this contribution, an extended quantitative fluorescence model was derived specifically for generalized wavelength-ratiometric probes based on PEBBLE technique (QFM GRP ) with a view to simplify the design of PEBBLEs and hence further extend their application potentials. The effectiveness of QFM GRP has been tested on the quantitative determination of free Ca 2+ in both simulated and real turbid media using a Ca 2+ sensitive PEBBLE nanosensor encapsulating Rhod-2 and eosin B inside the micropores of stable polyacrylamide matrix. Experimental results demonstrated that QFM GRP could realize precise and accurate quantification of free Ca 2+ in turbid samples, even though there is serious overlapping between the fluorescence excitation peaks of eosin B and Ca 2+ bound Rhod-2. The average relative predictive error value of QFM GRP for the test simulated turbid samples was 5.9%, about 2–4 times lower than the corresponding values of partial least squares calibration model and the empirical ratiometric model based on the ratio of fluorescence intensities at the excitation peaks of Ca 2+ bound Rhod-2 and eosin B. The recovery rates of QFM GRP for the real and spiked turbid samples varied from 93.1% to 101%, comparable to the corresponding results of atomic absorption spectrometry. - Highlights: • An advanced model was derived for generalized wavelength-ratiometric PEBBLEs. • The model can simplify the design of generalized wavelength-ratiometric PEBBLEs. • The model realized accurate

Development of High-Throughput Method for Measurement of Vascular Nitric Oxide Generation in Microplate Reader.

Science.gov (United States)

Abd El-Hay, Soad S; Colyer, Christa L

2017-01-13

Despite the importance of nitric oxide (NO) in vascular physiology and pathology, a high-throughput method for the quantification of its vascular generation is lacking. By using the fluorescent probe 4-amino-5-methylamino-2',7'-difluorofluorescein (DAF-FM), we have optimized a simple method for the determination of the generation of endothelial nitric oxide in a microplate format. A nitric oxide donor was used (3-morpholinosydnonimine hydrochloride, SIN-1). Different factors affecting the method were studied, such as the effects of dye concentration, different buffers, time of reaction, gain, and number of flashes. Beer's law was linear over a nanomolar range (1-10 nM) of SIN-1 with wavelengths of maximum excitation and emission at 495 and 525 nm; the limit of detection reached 0.897 nM. Under the optimized conditions, the generation of rat aortic endothelial NO was measured by incubating DAF-FM with serial concentrations (10-1000 µM) of acetylcholine (ACh) for 3 min. To confirm specificity, N ω -Nitro-l-arginine methyl ester (l-NAME)-the standard inhibitor of endothelial NO synthase-was found to inhibit the ACh-stimulated generation of NO. In addition, vessels pre-exposed for 1 h to 400 µM of the endothelial damaging agent methyl glyoxal showed inhibited NO generation when compared to the control stimulated by ACh. The capability of the method to measure micro-volume samples makes it convenient for the simultaneous handling of a very large number of samples. Additionally, it allows samples to be run simultaneously with their replicates to ensure identical experimental conditions, thus minimizing the effect of biological variability.

Development of High-Throughput Method for Measurement of Vascular Nitric Oxide Generation in Microplate Reader

Directory of Open Access Journals (Sweden)

Soad S. Abd El-Hay

2017-01-01

Full Text Available Background: Despite the importance of nitric oxide (NO in vascular physiology and pathology, a high-throughput method for the quantification of its vascular generation is lacking. Objective: By using the fluorescent probe 4-amino-5-methylamino-2′,7′-difluorofluorescein (DAF-FM, we have optimized a simple method for the determination of the generation of endothelial nitric oxide in a microplate format. Methods: A nitric oxide donor was used (3-morpholinosydnonimine hydrochloride, SIN-1. Different factors affecting the method were studied, such as the effects of dye concentration, different buffers, time of reaction, gain, and number of flashes. Results: Beer’s law was linear over a nanomolar range (1–10 nM of SIN-1 with wavelengths of maximum excitation and emission at 495 and 525 nm; the limit of detection reached 0.897 nM. Under the optimized conditions, the generation of rat aortic endothelial NO was measured by incubating DAF-FM with serial concentrations (10–1000 µM of acetylcholine (ACh for 3 min. To confirm specificity, Nω-Nitro-l-arginine methyl ester (l-NAME—the standard inhibitor of endothelial NO synthase—was found to inhibit the ACh-stimulated generation of NO. In addition, vessels pre-exposed for 1 h to 400 µM of the endothelial damaging agent methyl glyoxal showed inhibited NO generation when compared to the control stimulated by ACh. Conclusions: The capability of the method to measure micro-volume samples makes it convenient for the simultaneous handling of a very large number of samples. Additionally, it allows samples to be run simultaneously with their replicates to ensure identical experimental conditions, thus minimizing the effect of biological variability.

A new quantitative model of ecological compensation based on ecosystem capital in Zhejiang Province, China*

Science.gov (United States)

Jin, Yan; Huang, Jing-feng; Peng, Dai-liang

2009-01-01

Ecological compensation is becoming one of key and multidiscipline issues in the field of resources and environmental management. Considering the change relation between gross domestic product (GDP) and ecological capital (EC) based on remote sensing estimation, we construct a new quantitative estimate model for ecological compensation, using county as study unit, and determine standard value so as to evaluate ecological compensation from 2001 to 2004 in Zhejiang Province, China. Spatial differences of the ecological compensation were significant among all the counties or districts. This model fills up the gap in the field of quantitative evaluation of regional ecological compensation and provides a feasible way to reconcile the conflicts among benefits in the economic, social, and ecological sectors. PMID:19353749

An alternative to γ histograms for ROI-based quantitative dose comparisons

International Nuclear Information System (INIS)

Dvorak, P

2009-01-01

An alternative to gamma (γ) histograms for ROI-based quantitative comparisons of dose distributions using the γ concept is proposed. The method provides minimum values of dose difference and distance-to-agreement such that a pre-set fraction of the region of interest passes the γ test. Compared to standard γ histograms, the method provides more information in terms of pass rate per γ calculation. This is achieved at negligible additional calculation cost and without loss of accuracy. The presented method is proposed as a useful and complementary alternative to standard γ histograms, increasing both the quantity and quality of information for use in acceptance or rejection decisions. (note)

Understanding quantitative research: part 1.

Science.gov (United States)

Hoe, Juanita; Hoare, Zoë

This article, which is the first in a two-part series, provides an introduction to understanding quantitative research, basic statistics and terminology used in research articles. Critical appraisal of research articles is essential to ensure that nurses remain up to date with evidence-based practice to provide consistent and high-quality nursing care. This article focuses on developing critical appraisal skills and understanding the use and implications of different quantitative approaches to research. Part two of this article will focus on explaining common statistical terms and the presentation of statistical data in quantitative research.

Synthesizing Quantitative Evidence for Evidence-based Nursing: Systematic Review.

Science.gov (United States)

Oh, Eui Geum

2016-06-01

As evidence-based practice has become an important issue in healthcare settings, the educational needs for knowledge and skills for the generation and utilization of healthcare evidence are increasing. Systematic review (SR), a way of evidence generation, is a synthesis of primary scientific evidence, which summarizes the best evidence on a specific clinical question using a transparent, a priori protocol driven approach. SR methodology requires a critical appraisal of primary studies, data extraction in a reliable and repeatable way, and examination for validity of the results. SRs are considered hierarchically as the highest form of evidence as they are a systematic search, identification, and summarization of the available evidence to answer a focused clinical question with particular attention to the methodological quality of studies or the credibility of opinion and text. The purpose of this paper is to introduce an overview of the fundamental knowledge, principals and processes in SR. The focus of this paper is on SR especially for the synthesis of quantitative data from primary research studies that examines the effectiveness of healthcare interventions. To activate evidence-based nursing care in various healthcare settings, the best and available scientific evidence are essential components. This paper will include some examples to promote understandings. Copyright © 2016. Published by Elsevier B.V.

Synthesizing Quantitative Evidence for Evidence-based Nursing: Systematic Review

Directory of Open Access Journals (Sweden)

Eui Geum Oh, PhD, RN

2016-06-01

Full Text Available As evidence-based practice has become an important issue in healthcare settings, the educational needs for knowledge and skills for the generation and utilization of healthcare evidence are increasing. Systematic review (SR, a way of evidence generation, is a synthesis of primary scientific evidence, which summarizes the best evidence on a specific clinical question using a transparent, a priori protocol driven approach. SR methodology requires a critical appraisal of primary studies, data extraction in a reliable and repeatable way, and examination for validity of the results. SRs are considered hierarchically as the highest form of evidence as they are a systematic search, identification, and summarization of the available evidence to answer a focused clinical question with particular attention to the methodological quality of studies or the credibility of opinion and text. The purpose of this paper is to introduce an overview of the fundamental knowledge, principals and processes in SR. The focus of this paper is on SR especially for the synthesis of quantitative data from primary research studies that examines the effectiveness of healthcare interventions. To activate evidence-based nursing care in various healthcare settings, the best and available scientific evidence are essential components. This paper will include some examples to promote understandings.

Diagnostic performance of semi-quantitative and quantitative stress CMR perfusion analysis: a meta-analysis.

Science.gov (United States)

van Dijk, R; van Assen, M; Vliegenthart, R; de Bock, G H; van der Harst, P; Oudkerk, M

2017-11-27

Stress cardiovascular magnetic resonance (CMR) perfusion imaging is a promising modality for the evaluation of coronary artery disease (CAD) due to high spatial resolution and absence of radiation. Semi-quantitative and quantitative analysis of CMR perfusion are based on signal-intensity curves produced during the first-pass of gadolinium contrast. Multiple semi-quantitative and quantitative parameters have been introduced. Diagnostic performance of these parameters varies extensively among studies and standardized protocols are lacking. This study aims to determine the diagnostic accuracy of semi- quantitative and quantitative CMR perfusion parameters, compared to multiple reference standards. Pubmed, WebOfScience, and Embase were systematically searched using predefined criteria (3272 articles). A check for duplicates was performed (1967 articles). Eligibility and relevance of the articles was determined by two reviewers using pre-defined criteria. The primary data extraction was performed independently by two researchers with the use of a predefined template. Differences in extracted data were resolved by discussion between the two researchers. The quality of the included studies was assessed using the 'Quality Assessment of Diagnostic Accuracy Studies Tool' (QUADAS-2). True positives, false positives, true negatives, and false negatives were subtracted/calculated from the articles. The principal summary measures used to assess diagnostic accuracy were sensitivity, specificity, andarea under the receiver operating curve (AUC). Data was pooled according to analysis territory, reference standard and perfusion parameter. Twenty-two articles were eligible based on the predefined study eligibility criteria. The pooled diagnostic accuracy for segment-, territory- and patient-based analyses showed good diagnostic performance with sensitivity of 0.88, 0.82, and 0.83, specificity of 0.72, 0.83, and 0.76 and AUC of 0.90, 0.84, and 0.87, respectively. In per territory

Brain Injury Lesion Imaging Using Preconditioned Quantitative Susceptibility Mapping without Skull Stripping.

Science.gov (United States)

Soman, S; Liu, Z; Kim, G; Nemec, U; Holdsworth, S J; Main, K; Lee, B; Kolakowsky-Hayner, S; Selim, M; Furst, A J; Massaband, P; Yesavage, J; Adamson, M M; Spincemallie, P; Moseley, M; Wang, Y

2018-04-01

Identifying cerebral microhemorrhage burden can aid in the diagnosis and management of traumatic brain injury, stroke, hypertension, and cerebral amyloid angiopathy. MR imaging susceptibility-based methods are more sensitive than CT for detecting cerebral microhemorrhage, but methods other than quantitative susceptibility mapping provide results that vary with field strength and TE, require additional phase maps to distinguish blood from calcification, and depict cerebral microhemorrhages as bloom artifacts. Quantitative susceptibility mapping provides universal quantification of tissue magnetic property without these constraints but traditionally requires a mask generated by skull-stripping, which can pose challenges at tissue interphases. We evaluated the preconditioned quantitative susceptibility mapping MR imaging method, which does not require skull-stripping, for improved depiction of brain parenchyma and pathology. Fifty-six subjects underwent brain MR imaging with a 3D multiecho gradient recalled echo acquisition. Mask-based quantitative susceptibility mapping images were created using a commonly used mask-based quantitative susceptibility mapping method, and preconditioned quantitative susceptibility images were made using precondition-based total field inversion. All images were reviewed by a neuroradiologist and a radiology resident. Ten subjects (18%), all with traumatic brain injury, demonstrated blood products on 3D gradient recalled echo imaging. All lesions were visible on preconditioned quantitative susceptibility mapping, while 6 were not visible on mask-based quantitative susceptibility mapping. Thirty-one subjects (55%) demonstrated brain parenchyma and/or lesions that were visible on preconditioned quantitative susceptibility mapping but not on mask-based quantitative susceptibility mapping. Six subjects (11%) demonstrated pons artifacts on preconditioned quantitative susceptibility mapping and mask-based quantitative susceptibility mapping

A Fuzzy-Based Fusion Method of Multimodal Sensor-Based Measurements for the Quantitative Evaluation of Eye Fatigue on 3D Displays

Directory of Open Access Journals (Sweden)

Jae Won Bang

2015-05-01

Full Text Available With the rapid increase of 3-dimensional (3D content, considerable research related to the 3D human factor has been undertaken for quantitatively evaluating visual discomfort, including eye fatigue and dizziness, caused by viewing 3D content. Various modalities such as electroencephalograms (EEGs, biomedical signals, and eye responses have been investigated. However, the majority of the previous research has analyzed each modality separately to measure user eye fatigue. This cannot guarantee the credibility of the resulting eye fatigue evaluations. Therefore, we propose a new method for quantitatively evaluating eye fatigue related to 3D content by combining multimodal measurements. This research is novel for the following four reasons: first, for the evaluation of eye fatigue with high credibility on 3D displays, a fuzzy-based fusion method (FBFM is proposed based on the multimodalities of EEG signals, eye blinking rate (BR, facial temperature (FT, and subjective evaluation (SE; second, to measure a more accurate variation of eye fatigue (before and after watching a 3D display, we obtain the quality scores of EEG signals, eye BR, FT and SE; third, for combining the values of the four modalities we obtain the optimal weights of the EEG signals BR, FT and SE using a fuzzy system based on quality scores; fourth, the quantitative level of the variation of eye fatigue is finally obtained using the weighted sum of the values measured by the four modalities. Experimental results confirm that the effectiveness of the proposed FBFM is greater than other conventional multimodal measurements. Moreover, the credibility of the variations of the eye fatigue using the FBFM before and after watching the 3D display is proven using a t-test and descriptive statistical analysis using effect size.

Guidelines for reporting quantitative mass spectrometry based experiments in proteomics.

Science.gov (United States)

Martínez-Bartolomé, Salvador; Deutsch, Eric W; Binz, Pierre-Alain; Jones, Andrew R; Eisenacher, Martin; Mayer, Gerhard; Campos, Alex; Canals, Francesc; Bech-Serra, Joan-Josep; Carrascal, Montserrat; Gay, Marina; Paradela, Alberto; Navajas, Rosana; Marcilla, Miguel; Hernáez, María Luisa; Gutiérrez-Blázquez, María Dolores; Velarde, Luis Felipe Clemente; Aloria, Kerman; Beaskoetxea, Jabier; Medina-Aunon, J Alberto; Albar, Juan P

2013-12-16

Mass spectrometry is already a well-established protein identification tool and recent methodological and technological developments have also made possible the extraction of quantitative data of protein abundance in large-scale studies. Several strategies for absolute and relative quantitative proteomics and the statistical assessment of quantifications are possible, each having specific measurements and therefore, different data analysis workflows. The guidelines for Mass Spectrometry Quantification allow the description of a wide range of quantitative approaches, including labeled and label-free techniques and also targeted approaches such as Selected Reaction Monitoring (SRM). The HUPO Proteomics Standards Initiative (HUPO-PSI) has invested considerable efforts to improve the standardization of proteomics data handling, representation and sharing through the development of data standards, reporting guidelines, controlled vocabularies and tooling. In this manuscript, we describe a key output from the HUPO-PSI-namely the MIAPE Quant guidelines, which have developed in parallel with the corresponding data exchange format mzQuantML [1]. The MIAPE Quant guidelines describe the HUPO-PSI proposal concerning the minimum information to be reported when a quantitative data set, derived from mass spectrometry (MS), is submitted to a database or as supplementary information to a journal. The guidelines have been developed with input from a broad spectrum of stakeholders in the proteomics field to represent a true consensus view of the most important data types and metadata, required for a quantitative experiment to be analyzed critically or a data analysis pipeline to be reproduced. It is anticipated that they will influence or be directly adopted as part of journal guidelines for publication and by public proteomics databases and thus may have an impact on proteomics laboratories across the world. This article is part of a Special Issue entitled: Standardization and

Quantitative analysis of receptor imaging

International Nuclear Information System (INIS)

Fu Zhanli; Wang Rongfu

2004-01-01

Model-based methods for quantitative analysis of receptor imaging, including kinetic, graphical and equilibrium methods, are introduced in detail. Some technical problem facing quantitative analysis of receptor imaging, such as the correction for in vivo metabolism of the tracer and the radioactivity contribution from blood volume within ROI, and the estimation of the nondisplaceable ligand concentration, is also reviewed briefly

A GIS-based Quantitative Approach for the Search of Clandestine Graves, Italy.

Science.gov (United States)

Somma, Roberta; Cascio, Maria; Silvestro, Massimiliano; Torre, Eliana

2018-05-01

Previous research on the RAG color-coded prioritization systems for the discovery of clandestine graves has not considered all the factors influencing the burial site choice within a GIS project. The goal of this technical note was to discuss a GIS-based quantitative approach for the search of clandestine graves. The method is based on cross-referenced RAG maps with cumulative suitability factors to host a burial, leading to the editing of different search scenarios for ground searches showing high-(Red), medium-(Amber), and low-(Green) priority areas. The application of this procedure allowed several outcomes to be determined: If the concealment occurs at night, then the "search scenario without the visibility" will be the most effective one; if the concealment occurs in daylight, then the "search scenario with the DSM-based visibility" will be most appropriate; the different search scenarios may be cross-referenced with offender's confessions and eyewitnesses' testimonies to verify the veracity of their statements. © 2017 American Academy of Forensic Sciences.

Detection and quantification of Plasmodium falciparum in blood samples using quantitative nucleic acid sequence-based amplification

NARCIS (Netherlands)

Schoone, G. J.; Oskam, L.; Kroon, N. C.; Schallig, H. D.; Omar, S. A.

2000-01-01

A quantitative nucleic acid sequence-based amplification (QT-NASBA) assay for the detection of Plasmodium parasites has been developed. Primers and probes were selected on the basis of the sequence of the small-subunit rRNA gene. Quantification was achieved by coamplification of the RNA in the

A Quantitative Analysis of an EEG Epileptic Record Based on MultiresolutionWavelet Coefficients

Directory of Open Access Journals (Sweden)

Mariel Rosenblatt

2014-11-01

Full Text Available The characterization of the dynamics associated with electroencephalogram (EEG signal combining an orthogonal discrete wavelet transform analysis with quantifiers originated from information theory is reviewed. In addition, an extension of this methodology based on multiresolution quantities, called wavelet leaders, is presented. In particular, the temporal evolution of Shannon entropy and the statistical complexity evaluated with different sets of multiresolution wavelet coefficients are considered. Both methodologies are applied to the quantitative EEG time series analysis of a tonic-clonic epileptic seizure, and comparative results are presented. In particular, even when both methods describe the dynamical changes of the EEG time series, the one based on wavelet leaders presents a better time resolution.

Quantitative assessment of CA1 local circuits: knowledge base for interneuron-pyramidal cell connectivity.

Science.gov (United States)

Bezaire, Marianne J; Soltesz, Ivan

2013-09-01

In this work, through a detailed literature review, data-mining, and extensive calculations, we provide a current, quantitative estimate of the cellular and synaptic constituents of the CA1 region of the rat hippocampus. Beyond estimating the cell numbers of GABAergic interneuron types, we calculate their convergence onto CA1 pyramidal cells and compare it with the known input synapses on CA1 pyramidal cells. The convergence calculation and comparison are also made for excitatory inputs to CA1 pyramidal cells. In addition, we provide a summary of the excitatory and inhibitory convergence onto interneurons. The quantitative knowledge base assembled and synthesized here forms the basis for data-driven, large-scale computational modeling efforts. Additionally, this work highlights specific instances where the available data are incomplete, which should inspire targeted experimental projects toward a more complete quantification of the CA1 neurons and their connectivity. Copyright © 2013 Wiley Periodicals, Inc.

Enhanced cyclic stability of SnS microplates with conformal carbon coating derived from ethanol vapor deposition for sodium-ion batteries

Science.gov (United States)

Li, Xiang; Liu, Jiangwen; Ouyang, Liuzhang; Yuan, Bin; Yang, Lichun; Zhu, Min

2018-04-01

Carbon coated SnS microplates (SnS@C MPs) were prepared via a facile chemical vapor deposition method using SnS2 nanoflakes as precursor and ethanol vapor as carbon source. The carbon coating restrains the growth of SnS during the heat treatment. Furthermore, it improves the electronic conductivity as well as accommodates volume variations of SnS during the sodiation and desodiation processes. Therefore, the rate capability and cycle performance of the SnS@C MPs as anode materials for sodium-ion batteries are remarkably enhanced compared with the bare SnS and the SnS2 precursor. At current densities of 0.1, 0.2, 0.5, 1 and 2 A g-1, the optimized SnS@C MPs exhibit stable capacities of 602.9, 532.1, 512.2, 465.9 and 427.2 mAh g-1, respectively. At 1 A g-1, they show a reversible capacity of 528.8 mAh g-1 in the first cycle, and maintain 444.7 mAh g-1 after 50 cycles, with capacity retention of 84.1%. The carbon coating through chemical vapor deposition using ethanol vapor as carbon sources is green, simple and cost-effective, which shows great promise to improve the reversible Na+ storage of electrode materials.

Tracer-based laser-induced fluorescence measurement technique for quantitative fuel/air-ratio measurements in a hydrogen internal combustion engine.

Science.gov (United States)

Blotevogel, Thomas; Hartmann, Matthias; Rottengruber, Hermann; Leipertz, Alfred

2008-12-10

A measurement technique for the quantitative investigation of mixture formation processes in hydrogen internal combustion engines (ICEs) has been developed using tracer-based laser-induced fluorescence (TLIF). This technique can be employed to fired and motored engine operation. The quantitative TLIF fuel/air-ratio results have been verified by means of linear Raman scattering measurements. Exemplary results of the simultaneous investigation of mixture formation and combustion obtained at an optical accessible hydrogen ICE are shown.

Applied quantitative finance

CERN Document Server

Chen, Cathy; Overbeck, Ludger

2017-01-01

This volume provides practical solutions and introduces recent theoretical developments in risk management, pricing of credit derivatives, quantification of volatility and copula modeling. This third edition is devoted to modern risk analysis based on quantitative methods and textual analytics to meet the current challenges in banking and finance. It includes 14 new contributions and presents a comprehensive, state-of-the-art treatment of cutting-edge methods and topics, such as collateralized debt obligations, the high-frequency analysis of market liquidity, and realized volatility. The book is divided into three parts: Part 1 revisits important market risk issues, while Part 2 introduces novel concepts in credit risk and its management along with updated quantitative methods. The third part discusses the dynamics of risk management and includes risk analysis of energy markets and for cryptocurrencies. Digital assets, such as blockchain-based currencies, have become popular b ut are theoretically challenging...

Gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of Japanese encephalitis virus

International Nuclear Information System (INIS)

Huang, S-H; Tsai, M-H; Lin, C-W; Yang, T-C; Chuang, P-H; Tsai, I-S; Lu, H-C; Wan Lei; Lin, Y-J; Lai, C-H

2008-01-01

Virus isolation and antibody detection are routinely used for diagnosis of Japanese encephalitis virus (JEV) infection, but the low level of transient viremia in some JE patients makes JEV isolation from clinical and surveillance samples very difficult. We describe the use of gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of JEV from its RNA genome. We tested the effect of gold nanoparticles on four different PCR systems, including conventional PCR, reverse-transcription PCR (RT-PCR), and SYBR green real-time PCR and RT-PCR assays for diagnosis in the acute phase of JEV infection. Gold nanoparticles increased the amplification yield of the PCR product and shortened the PCR time compared to the conventional reaction. In addition, nanogold-based real-time RT-PCR showed a linear relationship between Ct and template amount using ten-fold dilutions of JEV. The nanogold-based RT-PCR and real-time quantitative RT-PCR assays were able to detect low levels (1-10 000 copies) of the JEV RNA genomes extracted from culture medium or whole blood, providing early diagnostic tools for the detection of low-level viremia in the acute-phase infection. The assays described here were simple, sensitive, and rapid approaches for detection and quantitation of JEV in tissue cultured samples as well as clinical samples

A novel microculture kinetic assay (MiCK assay) for malignant cell growth and chemosensitivity.

Science.gov (United States)

Kravtsov, V D

1994-01-01

The THERMOmax microplate reader was adapted for monitoring the growth kinetics of human leukaemic OCI/AML-2 and mouse tumour J-774.1 cell lines in continuous culture. Fluid evaporation from wells, CO2 escape and contamination were prevented by hermetic sealing of the microcultures in wells of a 96-well microplate, thus enabling the cells to grow exponentially for 72 h under the conditions of the incubated microplate reader. For both OCI/AML-2 cells, which grow in suspension, and adherent J-774.1 cells, a linear correlation was demonstrated between the number of unstained cells seeded in a given microplate well and the optical density (OD) of that well. Therefore, the OD/time curve of the culture could be deemed to be its growth curve. By the use of the linear fit equation, the actual number of the cells in the wells was computable at any time point of the assay. In the chemosensitivity test, an inhibitory effect of ARA-C on the growth of the cells could be estimated by viewing of the growth curves plotted on the screen. The maximum kinetic rates (Vmax) of the curves in the control and the ARA-C-treated wells were compared, yielding a growth inhibition index (GII). Comparison of results of the kinetic chemosensitivity assay with those of a [3H]thymidine incorporation assay revealed that the novel assay is suitable for precise quantitation of the cell chemosensitivity, is more informative and has the added technical advantage of performance without recourse to radioactive or chemically hazardous substances.

Probabilistic risk assessment of diuron and prometryn in the Gwydir River catchment, Australia, with the input of a novel bioassay based on algal growth.

Science.gov (United States)

Shi, Yajuan; Burns, Mitchell; Ritchie, Raymond J; Crossan, Angus; Kennedy, Ivan R

2014-08-01

A probabilistic risk assessment of the selected herbicides (diuron and prometryn) in the Gwydir River catchment was conducted, with the input of the EC₅₀ values derived from both literature and a novel bioassay. Laboratory test based on growth of algae exposed to herbicides assayed with a microplate reader was used to examine the toxicity of diuron and prometryn on the growth of Chlorella vulgaris. Both herbicides showed concentration dependent toxicity in inhibiting the growth of Chlorella during the exposure period of 18-72 h. Diuron caused more toxicity as judged by growth rates than prometryn. Thalaba Creek at Merrywinebone was identified as the 'hotspot' for diuron and prometryn risk in the Gwydir catchment. The use of microplate assays coupled with probabilistic risk assessment is recommended for rapid assessment of ecotoxicity of indigenous species, allowing identification of locations in river catchments requiring environmental management. Copyright © 2014 Elsevier Inc. All rights reserved.

Quantitative secondary electron detection

Science.gov (United States)

Agrawal, Jyoti; Joy, David C.; Nayak, Subuhadarshi

2018-05-08

Quantitative Secondary Electron Detection (QSED) using the array of solid state devices (SSD) based electron-counters enable critical dimension metrology measurements in materials such as semiconductors, nanomaterials, and biological samples (FIG. 3). Methods and devices effect a quantitative detection of secondary electrons with the array of solid state detectors comprising a number of solid state detectors. An array senses the number of secondary electrons with a plurality of solid state detectors, counting the number of secondary electrons with a time to digital converter circuit in counter mode.

A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples

Science.gov (United States)

Hutchins, Patrick; Sepulveda, Adam; Martin, Renee; Hopper, Lacey

2017-01-01

A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.

Quantification of dsDNA using the Hitachi F-7000 Fluorescence Spectrophotometer and PicoGreen dye.

Science.gov (United States)

Moreno, Luis A; Cox, Kendra L

2010-11-05

Quantification of DNA, especially in small concentrations, is an important task with a wide range of biological applications including standard molecular biology assays such as synthesis and purification of DNA, diagnostic applications such as quantification of DNA amplification products, and detection of DNA molecules in drug preparations. During this video we will demonstrate the capability of the Hitachi F-7000 Fluorescence Spectrophotometer equipped with a Micro Plate Reader accessory to perform dsDNA quantification using Molecular Probes Quant-it PicoGreen dye reagent kit. The F-7000 Fluorescence Spectrophotometer offers high sensitivity and high speed measurements. It is a highly flexible system capable of measuring fluorescence, luminescence, and phosphorescence. Several measuring modes are available, including wavelength scan, time scan, photometry and 3-D scan measurement. The spectrophotometer has sensitivity in the range of 50 picomoles of fluorescein when using a 300 μL sample volume in the microplate, and is capable of measuring scan speeds of 60,000 nm/minute. It also has a wide dynamic range of up to 5 orders of magnitude which allows for the use of calibration curves over a wide range of concentrations. The optical system uses all reflective optics for maximum energy and sensitivity. The standard wavelength range is 200 to 750 nm, and can be extended to 900 nm when using one of the optional near infrared photomultipliers. The system allows optional temperature control for the plate reader from 5 to 60 degrees Celsius using an optional external temperature controlled liquid circulator. The microplate reader allows for the use of 96 well microplates, and the measuring speed for 96 wells is less than 60 seconds when using the kinetics mode. Software controls for the F-7000 and Microplate Reader are also highly flexible. Samples may be set in either column or row formats, and any combination of wells may be chosen for sample measurements. This allows

Preliminary research on quantitative methods of water resources carrying capacity based on water resources balance sheet

Science.gov (United States)

Wang, Yanqiu; Huang, Xiaorong; Gao, Linyun; Guo, Biying; Ma, Kai

2018-06-01

Water resources are not only basic natural resources, but also strategic economic resources and ecological control factors. Water resources carrying capacity constrains the sustainable development of regional economy and society. Studies of water resources carrying capacity can provide helpful information about how the socioeconomic system is both supported and restrained by the water resources system. Based on the research of different scholars, major problems in the study of water resources carrying capacity were summarized as follows: the definition of water resources carrying capacity is not yet unified; the methods of carrying capacity quantification based on the definition of inconsistency are poor in operability; the current quantitative research methods of water resources carrying capacity did not fully reflect the principles of sustainable development; it is difficult to quantify the relationship among the water resources, economic society and ecological environment. Therefore, it is necessary to develop a better quantitative evaluation method to determine the regional water resources carrying capacity. This paper proposes a new approach to quantifying water resources carrying capacity (that is, through the compilation of the water resources balance sheet) to get a grasp of the regional water resources depletion and water environmental degradation (as well as regional water resources stock assets and liabilities), figure out the squeeze of socioeconomic activities on the environment, and discuss the quantitative calculation methods and technical route of water resources carrying capacity which are able to embody the substance of sustainable development.

Classification-based quantitative analysis of stable isotope labeling by amino acids in cell culture (SILAC) data.

Science.gov (United States)

Kim, Seongho; Carruthers, Nicholas; Lee, Joohyoung; Chinni, Sreenivasa; Stemmer, Paul

2016-12-01

Stable isotope labeling by amino acids in cell culture (SILAC) is a practical and powerful approach for quantitative proteomic analysis. A key advantage of SILAC is the ability to simultaneously detect the isotopically labeled peptides in a single instrument run and so guarantee relative quantitation for a large number of peptides without introducing any variation caused by separate experiment. However, there are a few approaches available to assessing protein ratios and none of the existing algorithms pays considerable attention to the proteins having only one peptide hit. We introduce new quantitative approaches to dealing with SILAC protein-level summary using classification-based methodologies, such as Gaussian mixture models with EM algorithms and its Bayesian approach as well as K-means clustering. In addition, a new approach is developed using Gaussian mixture model and a stochastic, metaheuristic global optimization algorithm, particle swarm optimization (PSO), to avoid either a premature convergence or being stuck in a local optimum. Our simulation studies show that the newly developed PSO-based method performs the best among others in terms of F1 score and the proposed methods further demonstrate the ability of detecting potential markers through real SILAC experimental data. No matter how many peptide hits the protein has, the developed approach can be applicable, rescuing many proteins doomed to removal. Furthermore, no additional correction for multiple comparisons is necessary for the developed methods, enabling direct interpretation of the analysis outcomes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Project-Based Learning in Undergraduate Environmental Chemistry Laboratory: Using EPA Methods to Guide Student Method Development for Pesticide Quantitation

Science.gov (United States)

Davis, Eric J.; Pauls, Steve; Dick, Jonathan

2017-01-01

Presented is a project-based learning (PBL) laboratory approach for an upper-division environmental chemistry or quantitative analysis course. In this work, a combined laboratory class of 11 environmental chemistry students developed a method based on published EPA methods for the extraction of dichlorodiphenyltrichloroethane (DDT) and its…

Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model.

Science.gov (United States)

Manabe, Sho; Morimoto, Chie; Hamano, Yuya; Fujimoto, Shuntaro; Tamaki, Keiji

2017-01-01

In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI) from these samples are challenging. In this study, we developed a new open-source software "Kongoh" for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1-4 persons' contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR) of a POI's contribution in true contributors and non-contributors by using 2-4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI's contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples.

Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model.

Directory of Open Access Journals (Sweden)

Sho Manabe

Full Text Available In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI from these samples are challenging. In this study, we developed a new open-source software "Kongoh" for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1-4 persons' contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR of a POI's contribution in true contributors and non-contributors by using 2-4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI's contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples.

Multi-spectral quantitative phase imaging based on filtration of light via ultrasonic wave

Science.gov (United States)

Machikhin, A. S.; Polschikova, O. V.; Ramazanova, A. G.; Pozhar, V. E.

2017-07-01

A new digital holographic microscopy scheme for multi-spectral quantitative phase imaging is proposed and implemented. It is based on acousto-optic filtration of wide-band low-coherence light at the entrance of a Mach-Zehnder interferometer, recording and digital processing of interferograms. The key requirements for the acousto-optic filter are discussed. The effectiveness of the technique is demonstrated by calculating the phase maps of human red blood cells at multiple wavelengths in the range 770-810 nm. The scheme can be used for the measurement of dispersion of thin films and biological samples.

FDTD-based quantitative analysis of terahertz wave detection for multilayered structures.

Science.gov (United States)

Tu, Wanli; Zhong, Shuncong; Shen, Yaochun; Zhou, Qing; Yao, Ligang

2014-10-01

Experimental investigations have shown that terahertz pulsed imaging (TPI) is able to quantitatively characterize a range of multilayered media (e.g., biological issues, pharmaceutical tablet coatings, layered polymer composites, etc.). Advanced modeling of the interaction of terahertz radiation with a multilayered medium is required to enable the wide application of terahertz technology in a number of emerging fields, including nondestructive testing. Indeed, there have already been many theoretical analyses performed on the propagation of terahertz radiation in various multilayered media. However, to date, most of these studies used 1D or 2D models, and the dispersive nature of the dielectric layers was not considered or was simplified. In the present work, the theoretical framework of using terahertz waves for the quantitative characterization of multilayered media was established. A 3D model based on the finite difference time domain (FDTD) method is proposed. A batch of pharmaceutical tablets with a single coating layer of different coating thicknesses and different refractive indices was modeled. The reflected terahertz wave from such a sample was computed using the FDTD method, assuming that the incident terahertz wave is broadband, covering a frequency range up to 3.5 THz. The simulated results for all of the pharmaceutical-coated tablets considered were found to be in good agreement with the experimental results obtained using a commercial TPI system. In addition, we studied a three-layered medium to mimic the occurrence of defects in the sample.

Understanding Pre-Quantitative Risk in Projects

Science.gov (United States)

Cooper, Lynne P.

2011-01-01

Standard approaches to risk management in projects depend on the ability of teams to identify risks and quantify the probabilities and consequences of these risks (e.g., the 5 x 5 risk matrix). However, long before quantification does - or even can - occur, and long after, teams make decisions based on their pre-quantitative understanding of risk. These decisions can have long-lasting impacts on the project. While significant research has looked at the process of how to quantify risk, our understanding of how teams conceive of and manage pre-quantitative risk is lacking. This paper introduces the concept of pre-quantitative risk and discusses the implications of addressing pre-quantitative risk in projects.

EBprot: Statistical analysis of labeling-based quantitative proteomics data.

Science.gov (United States)

Koh, Hiromi W L; Swa, Hannah L F; Fermin, Damian; Ler, Siok Ghee; Gunaratne, Jayantha; Choi, Hyungwon

2015-08-01

Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is not incorporated into the differential expression (DE) analysis. Here, we propose a novel probabilistic framework EBprot that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. To illustrate the wide applicability of EBprot in different experimental designs, we applied EBprot to a dataset for lung cancer subtype analysis with biological replicates and another dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells with multiplexed labeling. Through these examples, we show that the peptide-level analysis of EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets. The software suite is freely available on the Sourceforge website http://ebprot.sourceforge.net/. All MS data have been deposited in the ProteomeXchange with identifier PXD001426 (http://proteomecentral.proteomexchange.org/dataset/PXD001426/). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative Analyses about Market- and Prevalence-Based Needs for Adapted Physical Education Teachers in the Public Schools in the United States

Science.gov (United States)

Zhang, Jiabei

2011-01-01

The purpose of this study was to analyze quantitative needs for more adapted physical education (APE) teachers based on both market- and prevalence-based models. The market-based need for more APE teachers was examined based on APE teacher positions funded, while the prevalence-based need for additional APE teachers was analyzed based on students…

Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding.

Science.gov (United States)

Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

2017-01-01

Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.

Quantitative methods in psychology: inevitable and useless

Directory of Open Access Journals (Sweden)

Aaro Toomela

2010-07-01

Full Text Available Science begins with the question, what do I want to know? Science becomes science, however, only when this question is justified and the appropriate methodology is chosen for answering the research question. Research question should precede the other questions; methods should be chosen according to the research question and not vice versa. Modern quantitative psychology has accepted method as primary; research questions are adjusted to the methods. For understanding thinking in modern quantitative psychology, two epistemologies should be distinguished: structural-systemic that is based on Aristotelian thinking, and associative-quantitative that is based on Cartesian-Humean thinking. The first aims at understanding the structure that underlies the studied processes; the second looks for identification of cause-effect relationships between the events with no possible access to the understanding of the structures that underlie the processes. Quantitative methodology in particular as well as mathematical psychology in general, is useless for answering questions about structures and processes that underlie observed behaviors. Nevertheless, quantitative science is almost inevitable in a situation where the systemic-structural basis of behavior is not well understood; all sorts of applied decisions can be made on the basis of quantitative studies. In order to proceed, psychology should study structures; methodologically, constructive experiments should be added to observations and analytic experiments.

Diversity of respiratory impedance based on quantitative computed tomography in patients with COPD.

Science.gov (United States)

Wada, Yosuke; Kitaguchi, Yoshiaki; Yasuo, Masanori; Ueno, Fumika; Kawakami, Satoshi; Fukushima, Kiyoyasu; Fujimoto, Keisaku; Hanaoka, Masayuki

2018-01-01

This study was conducted in order to investigate the diversity of respiratory physiology, including the respiratory impedance and reversibility of airway obstruction, based on quantitative computed tomography (CT) in patients with COPD. Medical records of 174 stable COPD patients were retrospectively reviewed to obtain the patients' clinical data, including the pulmonary function and imaging data. According to the software-based quantification of the degree of emphysema and airway wall thickness, the patients were classified into the "normal by CT" phenotype, the airway-dominant phenotype, the emphysema-dominant phenotype, and the mixed phenotype. The pulmonary function, including the respiratory impedance evaluated by using the forced oscillation technique (FOT) and the reversibility of airway obstruction in response to inhaled short-acting β 2 -agonists, was then compared among the four phenotypes. The respiratory system resistance at 5 and 20 Hz (R5 and R20) was significantly higher, and the respiratory system reactance at 5 Hz (X5) was significantly more negative in the airway-dominant and mixed phenotypes than in the other phenotypes. The within-breath changes of X5 (ΔX5) were significantly greater in the mixed phenotype than in the "normal by CT" and emphysema-dominant phenotypes. The FOT parameters (R5, R20, and X5) were significantly correlated with indices of the degree of airway wall thickness and significantly but weakly correlated with the reversibility of airway obstruction. There was no significant correlation between the FOT parameters (R5, R20, and X5) and the degree of emphysema. There is a diversity of respiratory physiology, including the respiratory impedance and reversibility of airway obstruction, based on quantitative CT in patients with COPD. The FOT measurements may reflect the degree of airway disease and aid in detecting airway remodeling in patients with COPD.

Qualitative and quantitative feedback in the context of competency-based education.

Science.gov (United States)

Tekian, Ara; Watling, Christopher J; Roberts, Trudie E; Steinert, Yvonne; Norcini, John

2017-12-01

Research indicates the importance and usefulness of feedback, yet with the shift of medical curricula toward competencies, feedback is not well understood in this context. This paper attempts to identify how feedback fits within a competency-based curriculum. After careful consideration of the literature, the following conclusions are drawn: (1) Because feedback is predicated on assessment, the assessment should be designed to optimize and prevent inaccuracies in feedback; (2) Giving qualitative feedback in the form of a conversation would lend credibility to the feedback, address emotional obstacles and create a context in which feedback is comfortable; (3) Quantitative feedback in the form of individualized data could fulfill the demand for more feedback, help students devise strategies on how to improve, allow students to compare themselves to their peers, recognizing that big data have limitations; and (4) Faculty development needs to incorporate and promote cultural and systems changes with regard to feedback. A better understanding of the role of feedback in competency-based education could result in more efficient learning for students.

Liquid chromatography-mass spectrometry-based quantitative proteomics.

Science.gov (United States)

Linscheid, Michael W; Ahrends, Robert; Pieper, Stefan; Kühn, Andreas

2009-01-01

During the last decades, molecular sciences revolutionized biomedical research and gave rise to the biotechnology industry. During the next decades, the application of the quantitative sciences--informatics, physics, chemistry, and engineering--to biomedical research brings about the next revolution that will improve human healthcare and certainly create new technologies, since there is no doubt that small changes can have great effects. It is not a question of "yes" or "no," but of "how much," to make best use of the medical options we will have. In this context, the development of accurate analytical methods must be considered a cornerstone, since the understanding of biological processes will be impossible without information about the minute changes induced in cells by interactions of cell constituents with all sorts of endogenous and exogenous influences and disturbances. The first quantitative techniques, which were developed, allowed monitoring relative changes only, but they clearly showed the significance of the information obtained. The recent advent of techniques claiming to quantify proteins and peptides not only relative to each other, but also in an absolute fashion, promised another quantum leap, since knowing the absolute amount will allow comparing even unrelated species and the definition of parameters will permit to model biological systems much more accurate than before. To bring these promises to life, several approaches are under development at this point in time and this review is focused on those developments.

Appreciating the difference between design-based and model-based sampling strategies in quantitative morphology of the nervous system.

Science.gov (United States)

Geuna, S

2000-11-20

Quantitative morphology of the nervous system has undergone great developments over recent years, and several new technical procedures have been devised and applied successfully to neuromorphological research. However, a lively debate has arisen on some issues, and a great deal of confusion appears to exist that is definitely responsible for the slow spread of the new techniques among scientists. One such element of confusion is related to uncertainty about the meaning, implications, and advantages of the design-based sampling strategy that characterize the new techniques. In this article, to help remove this uncertainty, morphoquantitative methods are described and contrasted on the basis of the inferential paradigm of the sampling strategy: design-based vs model-based. Moreover, some recommendations are made to help scientists judge the appropriateness of a method used for a given study in relation to its specific goals. Finally, the use of the term stereology to label, more or less expressly, only some methods is critically discussed. Copyright 2000 Wiley-Liss, Inc.

Identification of targets of miR-200b by a SILAC-based quantitative proteomic approach

Directory of Open Access Journals (Sweden)

Arivusudar Marimuthu

2014-09-01

Full Text Available miRNAs regulate gene expression by binding to cognate mRNAs causing mRNA degradation or translational repression. Mass spectrometry-based proteomic analysis is being widely used to identify miRNA targets. The miR-200b miRNA cluster is often overexpressed in multiple cancer types, but the identity of the targets remains elusive. Using SILAC-based analysis, we examined the effects of overexpression of a miR-200b mimic or a control miRNA in fibrosarcoma cells. We identified around 300 potential targets of miR-200b based on a change in the expression of protein levels. We validated a subset of potential targets at the transcript level using quantitative PCR.

Multi-class parkinsonian disorders classification with quantitative MR markers and graph-based features using support vector machines.

Science.gov (United States)

Morisi, Rita; Manners, David Neil; Gnecco, Giorgio; Lanconelli, Nico; Testa, Claudia; Evangelisti, Stefania; Talozzi, Lia; Gramegna, Laura Ludovica; Bianchini, Claudio; Calandra-Buonaura, Giovanna; Sambati, Luisa; Giannini, Giulia; Cortelli, Pietro; Tonon, Caterina; Lodi, Raffaele

2018-02-01

In this study we attempt to automatically classify individual patients with different parkinsonian disorders, making use of pattern recognition techniques to distinguish among several forms of parkinsonisms (multi-class classification), based on a set of binary classifiers that discriminate each disorder from all others. We combine diffusion tensor imaging, proton spectroscopy and morphometric-volumetric data to obtain MR quantitative markers, which are provided to support vector machines with the aim of recognizing the different parkinsonian disorders. Feature selection is used to find the most important features for classification. We also exploit a graph-based technique on the set of quantitative markers to extract additional features from the dataset, and increase classification accuracy. When graph-based features are not used, the MR markers that are most frequently automatically extracted by the feature selection procedure reflect alterations in brain regions that are also usually considered to discriminate parkinsonisms in routine clinical practice. Graph-derived features typically increase the diagnostic accuracy, and reduce the number of features required. The results obtained in the work demonstrate that support vector machines applied to multimodal brain MR imaging and using graph-based features represent a novel and highly accurate approach to discriminate parkinsonisms, and a useful tool to assist the diagnosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantile-Based Permutation Thresholds for Quantitative Trait Loci Hotspots

NARCIS (Netherlands)

Neto, Elias Chaibub; Keller, Mark P.; Broman, Andrew F.; Attie, Alan D.; Jansen, Ritsert C.; Broman, Karl W.; Yandell, Brian S.; Borevitz, J.

Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key

Nonmydriatic fluorescence-based quantitative imaging of human macular pigment distributions

Science.gov (United States)

Sharifzadeh, Mohsen; Bernstein, Paul S.; Gellermann, Werner

2006-10-01

We have developed a CCD-camera-based nonmydriatic instrument that detects fluorescence from retinal lipofuscin chromophores ("autofluorescence") as a means to indirectly quantify and spatially image the distribution of macular pigment (MP). The lipofuscin fluorescence intensity is reduced at all retinal locations containing MP, since MP has a competing absorption in the blue-green wavelength region. Projecting a large diameter, 488 nm excitation spot onto the retina, centered on the fovea, but extending into the macular periphery, and comparing lipofuscin fluorescence intensities outside and inside the foveal area, it is possible to spatially map out the distribution of MP. Spectrally selective detection of the lipofuscin fluorescence reveals an important wavelength dependence of the obtainable image contrast and deduced MP optical density levels, showing that it is important to block out interfering fluorescence contributions in the detection setup originating from ocular media such as the lens. Measuring 70 healthy human volunteer subjects with no ocular pathologies, we find widely varying spatial extent of MP, distinctly differing distribution patterns of MP, and strongly differing absolute MP levels among individuals. Our population study suggests that MP imaging based on lipofuscin fluorescence is useful as a relatively simple, objective, and quantitative noninvasive optical technique suitable to rapidly screen MP levels and distributions in healthy humans with undilated pupils.

Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women

Energy Technology Data Exchange (ETDEWEB)

Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M. [University of California, San Francisco, Musculoskeletal and Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States)

2012-07-15

The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 {+-} 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. (orig.)

A Quantitative Tool for Producing DNA-Based Diagnostic Arrays

Energy Technology Data Exchange (ETDEWEB)

Tom J. Whitaker

2008-07-11

The purpose of this project was to develop a precise, quantitative method to analyze oligodeoxynucleotides (ODNs) on an array to enable a systematic approach to quality control issues affecting DNA microarrays. Two types of ODN's were tested; ODN's formed by photolithography and ODN's printed onto microarrays. Initial work in Phase I, performed in conjunction with Affymetrix, Inc. who has a patent on a photolithographic in situ technique for creating DNA arrays, was very promising but did seem to indicate that the atomization process was not complete. Soon after Phase II work was under way, Affymetrix had further developed fluorescent methods and indicated they were no longer interested in our resonance ionization technique. This was communicated to the program manager and it was decided that the project would continue and be focused on printed ODNs. The method being tested is called SIRIS, Sputter-Initiated Resonance Ionization Spectroscopy. SIRIS has been shown to be a highly sensitive, selective, and quantitative tool for atomic species. This project was aimed at determining if an ODN could be labeled in such a way that SIRIS could be used to measure the label and thus provide quantitative measurements of the ODN on an array. One of the largest problems in this study has been developing a method that allows us to know the amount of an ODN on a surface independent of the SIRIS measurement. Even though we could accurately determine the amount of ODN deposited on a surface, the amount that actually attached to the surface is very difficult to measure (hence the need for a quantitative tool). A double-labeling procedure was developed in which 33P and Pt were both used to label ODNs. The radioactive 33P could be measured by a proportional counter that maps the counts in one dimension. This gave a good measurement of the amount of ODN remaining on a surface after immobilization and washing. A second label, Pt, was attached to guanine nucleotides in the

Respirometry-based on-line model parameter estimation at a full-scale WWTP

NARCIS (Netherlands)

Spanjers, H.; Patry, G.G.; Keesman, K.J.

2002-01-01

This paper describes part of a project to develop a systematic approach to knowledge extraction from on-line respirometric measurements in support of wastewater treatment plant control and operation. The paper deals with the following issues: (1) test of the implementation of an automatic set-up

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

Science.gov (United States)

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-07

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

Science.gov (United States)

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-01

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Grid workflow validation using ontology-based tacit knowledge: A case study for quantitative remote sensing applications

Science.gov (United States)

Liu, Jia; Liu, Longli; Xue, Yong; Dong, Jing; Hu, Yingcui; Hill, Richard; Guang, Jie; Li, Chi

2017-01-01

Workflow for remote sensing quantitative retrieval is the ;bridge; between Grid services and Grid-enabled application of remote sensing quantitative retrieval. Workflow averts low-level implementation details of the Grid and hence enables users to focus on higher levels of application. The workflow for remote sensing quantitative retrieval plays an important role in remote sensing Grid and Cloud computing services, which can support the modelling, construction and implementation of large-scale complicated applications of remote sensing science. The validation of workflow is important in order to support the large-scale sophisticated scientific computation processes with enhanced performance and to minimize potential waste of time and resources. To research the semantic correctness of user-defined workflows, in this paper, we propose a workflow validation method based on tacit knowledge research in the remote sensing domain. We first discuss the remote sensing model and metadata. Through detailed analysis, we then discuss the method of extracting the domain tacit knowledge and expressing the knowledge with ontology. Additionally, we construct the domain ontology with Protégé. Through our experimental study, we verify the validity of this method in two ways, namely data source consistency error validation and parameters matching error validation.

A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR

Directory of Open Access Journals (Sweden)

Stewart Don

2008-05-01

Full Text Available Abstract Background Based upon defining a common reference point, current real-time quantitative PCR technologies compare relative differences in amplification profile position. As such, absolute quantification requires construction of target-specific standard curves that are highly resource intensive and prone to introducing quantitative errors. Sigmoidal modeling using nonlinear regression has previously demonstrated that absolute quantification can be accomplished without standard curves; however, quantitative errors caused by distortions within the plateau phase have impeded effective implementation of this alternative approach. Results Recognition that amplification rate is linearly correlated to amplicon quantity led to the derivation of two sigmoid functions that allow target quantification via linear regression analysis. In addition to circumventing quantitative errors produced by plateau distortions, this approach allows the amplification efficiency within individual amplification reactions to be determined. Absolute quantification is accomplished by first converting individual fluorescence readings into target quantity expressed in fluorescence units, followed by conversion into the number of target molecules via optical calibration. Founded upon expressing reaction fluorescence in relation to amplicon DNA mass, a seminal element of this study was to implement optical calibration using lambda gDNA as a universal quantitative standard. Not only does this eliminate the need to prepare target-specific quantitative standards, it relegates establishment of quantitative scale to a single, highly defined entity. The quantitative competency of this approach was assessed by exploiting "limiting dilution assay" for absolute quantification, which provided an independent gold standard from which to verify quantitative accuracy. This yielded substantive corroborating evidence that absolute accuracies of ± 25% can be routinely achieved. Comparison

Influence of Engineering Bacteria Quantitative Inspection on Diversity of Anpeng Alkali Mine Resources Exploitation

Directory of Open Access Journals (Sweden)

Yu Tao

2016-03-01

Full Text Available Cadmium (Cd is a heavy metal pollutant seriously threatening creatures, and highly concentrated Cd in soil severely inhibits the activity of microbial populations. Soil in Anpeng Alkali Mine area in Nanyang city (Henan province is seriously polluted by heavy metal. Both copper (Cu and Cd content are found to be over standard, in which, Cu belongs to mild contamination while Cd is a serious contamination. To detect diversity of microbial communities in soil in the process of bioremediation, Cd polluted soil samples are collected from orefield for pot experiment, Biolog micro-plate technology is used to study the influence of applying low, medium and high amount of rice straw (5.3 t/ha, 10.2 t/ha and 23.4 t/ha in polluted soil and combining low, medium and high amount of rice straw with surface displayed engineering bacteria (X4/pCIM on microbial community. In the meantime, X4/pCIM is quantitatively measured by real-time polymerase chain reaction (PCR. Biolog experimental results indicate that the combination of rice straw and engineering bacteria is able to change the composition of soil microbial community, and has a difference in influencing rhizosphere and non-rhizosphere microorganisms. Through real-time PCR, it is found that the number of engineering bacteria falls to 103 after 120 days of bioremediation. Therefore, it can be concluded that combining rice straw with engineering bacteria can change the composition of soil microbial community and have diverse influences as application rate changes, without obvious rules to follow.

Novel photoluminescence enzyme immunoassay based on supramolecular host-guest recognition using L-arginine/6-aza-2-thiothymine-stabilized gold nanocluster.

Science.gov (United States)

Wang, Youmei; Lu, Minghua; Tang, Dianping

2018-06-30

A new photoluminescence (PL) enzyme immunoassay was designed for sensitive detection of aflatoxin B 1 (AFB 1 ) via an innovative enzyme substrate, 6-aza-2-thiothymine-stabilized gold nanocluster (AAT-AuNC) with L-arginine. The enzyme substrate with strong PL intensity was formed through supramolecular host-guest assembly between guanidine group of L-arginine and AAT capped on the surface of AuNC. Upon arginase introduction, the captured L-arginine was hydrolyzed into ornithine and urea, thus resulting in the decreasing PL intensity. Based on this principle, a novel competitive-type immunoreaction was first carried out on AFB 1 -bovine serum albumin (AFB 1 -BSA) conjugate-coated microplate, using arginase-labeled anti-AFB 1 antibody as the competitor. Under the optimum conditions, the PL intensity increased with the increment of target AFB 1 , and allowed the detection of the analyte at concentrations as low as 3.2 pg mL -1 (ppt). Moreover, L-arginine-AAT-AuNC-based PL enzyme immunoassay afforded good reproducibility and acceptable specificity. In addition, the accuracy of this methodology, referring to commercial AFB 1 ELISA kit, was evaluated to analyze naturally contaminated or spiked peanut samples, giving well-matched results between two methods, thus representing a useful scheme for practical application in quantitative monitoring of mycotoxins in foodstuff. Copyright © 2018 Elsevier B.V. All rights reserved.

Genetic programming based quantitative structure-retention relationships for the prediction of Kovats retention indices.

Science.gov (United States)

Goel, Purva; Bapat, Sanket; Vyas, Renu; Tambe, Amruta; Tambe, Sanjeev S

2015-11-13

The development of quantitative structure-retention relationships (QSRR) aims at constructing an appropriate linear/nonlinear model for the prediction of the retention behavior (such as Kovats retention index) of a solute on a chromatographic column. Commonly, multi-linear regression and artificial neural networks are used in the QSRR development in the gas chromatography (GC). In this study, an artificial intelligence based data-driven modeling formalism, namely genetic programming (GP), has been introduced for the development of quantitative structure based models predicting Kovats retention indices (KRI). The novelty of the GP formalism is that given an example dataset, it searches and optimizes both the form (structure) and the parameters of an appropriate linear/nonlinear data-fitting model. Thus, it is not necessary to pre-specify the form of the data-fitting model in the GP-based modeling. These models are also less complex, simple to understand, and easy to deploy. The effectiveness of GP in constructing QSRRs has been demonstrated by developing models predicting KRIs of light hydrocarbons (case study-I) and adamantane derivatives (case study-II). In each case study, two-, three- and four-descriptor models have been developed using the KRI data available in the literature. The results of these studies clearly indicate that the GP-based models possess an excellent KRI prediction accuracy and generalization capability. Specifically, the best performing four-descriptor models in both the case studies have yielded high (>0.9) values of the coefficient of determination (R(2)) and low values of root mean squared error (RMSE) and mean absolute percent error (MAPE) for training, test and validation set data. The characteristic feature of this study is that it introduces a practical and an effective GP-based method for developing QSRRs in gas chromatography that can be gainfully utilized for developing other types of data-driven models in chromatography science

Affordable, automatic quantitative fall risk assessment based on clinical balance scales and Kinect data.

Science.gov (United States)

Colagiorgio, P; Romano, F; Sardi, F; Moraschini, M; Sozzi, A; Bejor, M; Ricevuti, G; Buizza, A; Ramat, S

2014-01-01

The problem of a correct fall risk assessment is becoming more and more critical with the ageing of the population. In spite of the available approaches allowing a quantitative analysis of the human movement control system's performance, the clinical assessment and diagnostic approach to fall risk assessment still relies mostly on non-quantitative exams, such as clinical scales. This work documents our current effort to develop a novel method to assess balance control abilities through a system implementing an automatic evaluation of exercises drawn from balance assessment scales. Our aim is to overcome the classical limits characterizing these scales i.e. limited granularity and inter-/intra-examiner reliability, to obtain objective scores and more detailed information allowing to predict fall risk. We used Microsoft Kinect to record subjects' movements while performing challenging exercises drawn from clinical balance scales. We then computed a set of parameters quantifying the execution of the exercises and fed them to a supervised classifier to perform a classification based on the clinical score. We obtained a good accuracy (~82%) and especially a high sensitivity (~83%).

NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

DEFF Research Database (Denmark)

Andreatta, Massimo; Schafer-Nielsen, Claus; Lund, Ole

2011-01-01

Recent advances in high-throughput technologies have made it possible to generate both gene and protein sequence data at an unprecedented rate and scale thereby enabling entirely new "omics"-based approaches towards the analysis of complex biological processes. However, the amount and complexity...... to interpret large data sets. We have recently developed a method, NNAlign, which is generally applicable to any biological problem where quantitative peptide data is available. This method efficiently identifies underlying sequence patterns by simultaneously aligning peptide sequences and identifying motifs...... associated with quantitative readouts. Here, we provide a web-based implementation of NNAlign allowing non-expert end-users to submit their data (optionally adjusting method parameters), and in return receive a trained method (including a visual representation of the identified motif) that subsequently can...

Optimisation of the microplate resazurin assay for screening and bioassay-guided fractionation of phytochemical extracts against Mycobacterium tuberculosis.

Science.gov (United States)

O'Neill, Taryn E; Li, Haoxin; Colquhoun, Caitlyn D; Johnson, John A; Webster, Duncan; Gray, Christopher A

2014-01-01

Because of increased resistance to current drugs, there is an urgent need to discover new anti-mycobacterial compounds for the development of novel anti-tuberculosis drugs. The microplate resazurin assay (MRA) is commonly used to evaluate natural products and synthetic compounds for anti-mycobacterial activity. However, the assay can be problematic and unreliable when screening methanolic phytochemical extracts. To optimise the MRA for the screening and bioassay-guided fractionation of phytochemical extracts using Mycobacterium tuberculosis H37Ra. The effects of varying assay duration, resazurin solution composition, solvent (dimethyl sulphoxide - DMSO) concentration and type of microtitre plate used on the results and reliability of the MRA were investigated. The optimal bioassay protocol was applied to methanolic extracts of medicinal plants that have been reported to possess anti-mycobacterial activity. The variables investigated were found to have significant effects on the results obtained with the MRA. A standardised procedure that can reliably quantify anti-mycobacterial activity of phytochemical extracts in as little as 48 h was identified. The optimised MRA uses 2% aqueous DMSO, with an indicator solution of 62.5 µg/mL resazurin in 5% aqueous Tween 80 over 96 h incubation. The study has identified an optimal procedure for the MRA when used with M. tuberculosis H37Ra that gives rapid, reliable and consistent results. The assay procedure has been used successfully for the screening and bioassay-guided fractionation of anti-mycobacterial compounds from methanol extracts of Canadian medicinal plants. Copyright © 2014 John Wiley & Sons, Ltd.

Towards quantitative PET/MRI: a review of MR-based attenuation correction techniques.

Science.gov (United States)

Hofmann, Matthias; Pichler, Bernd; Schölkopf, Bernhard; Beyer, Thomas

2009-03-01

Positron emission tomography (PET) is a fully quantitative technology for imaging metabolic pathways and dynamic processes in vivo. Attenuation correction of raw PET data is a prerequisite for quantification and is typically based on separate transmission measurements. In PET/CT attenuation correction, however, is performed routinely based on the available CT transmission data. Recently, combined PET/magnetic resonance (MR) has been proposed as a viable alternative to PET/CT. Current concepts of PET/MRI do not include CT-like transmission sources and, therefore, alternative methods of PET attenuation correction must be found. This article reviews existing approaches to MR-based attenuation correction (MR-AC). Most groups have proposed MR-AC algorithms for brain PET studies and more recently also for torso PET/MR imaging. Most MR-AC strategies require the use of complementary MR and transmission images, or morphology templates generated from transmission images. We review and discuss these algorithms and point out challenges for using MR-AC in clinical routine. MR-AC is work-in-progress with potentially promising results from a template-based approach applicable to both brain and torso imaging. While efforts are ongoing in making clinically viable MR-AC fully automatic, further studies are required to realize the potential benefits of MR-based motion compensation and partial volume correction of the PET data.

Towards quantitative PET/MRI: a review of MR-based attenuation correction techniques

International Nuclear Information System (INIS)

Hofmann, Matthias; Pichler, Bernd; Schoelkopf, Bernhard; Beyer, Thomas

2009-01-01

Positron emission tomography (PET) is a fully quantitative technology for imaging metabolic pathways and dynamic processes in vivo. Attenuation correction of raw PET data is a prerequisite for quantification and is typically based on separate transmission measurements. In PET/CT attenuation correction, however, is performed routinely based on the available CT transmission data. Recently, combined PET/magnetic resonance (MR) has been proposed as a viable alternative to PET/CT. Current concepts of PET/MRI do not include CT-like transmission sources and, therefore, alternative methods of PET attenuation correction must be found. This article reviews existing approaches to MR-based attenuation correction (MR-AC). Most groups have proposed MR-AC algorithms for brain PET studies and more recently also for torso PET/MR imaging. Most MR-AC strategies require the use of complementary MR and transmission images, or morphology templates generated from transmission images. We review and discuss these algorithms and point out challenges for using MR-AC in clinical routine. MR-AC is work-in-progress with potentially promising results from a template-based approach applicable to both brain and torso imaging. While efforts are ongoing in making clinically viable MR-AC fully automatic, further studies are required to realize the potential benefits of MR-based motion compensation and partial volume correction of the PET data. (orig.)

Towards quantitative PET/MRI: a review of MR-based attenuation correction techniques

Energy Technology Data Exchange (ETDEWEB)

Hofmann, Matthias [Max Planck Institute for Biological Cybernetics, Tuebingen (Germany); University of Tuebingen, Laboratory for Preclinical Imaging and Imaging Technology of the Werner Siemens-Foundation, Department of Radiology, Tuebingen (Germany); University of Oxford, Wolfson Medical Vision Laboratory, Department of Engineering Science, Oxford (United Kingdom); Pichler, Bernd [University of Tuebingen, Laboratory for Preclinical Imaging and Imaging Technology of the Werner Siemens-Foundation, Department of Radiology, Tuebingen (Germany); Schoelkopf, Bernhard [Max Planck Institute for Biological Cybernetics, Tuebingen (Germany); Beyer, Thomas [University Hospital Duisburg-Essen, Department of Nuclear Medicine, Essen (Germany); Cmi-Experts GmbH, Zurich (Switzerland)

2009-03-15

Positron emission tomography (PET) is a fully quantitative technology for imaging metabolic pathways and dynamic processes in vivo. Attenuation correction of raw PET data is a prerequisite for quantification and is typically based on separate transmission measurements. In PET/CT attenuation correction, however, is performed routinely based on the available CT transmission data. Recently, combined PET/magnetic resonance (MR) has been proposed as a viable alternative to PET/CT. Current concepts of PET/MRI do not include CT-like transmission sources and, therefore, alternative methods of PET attenuation correction must be found. This article reviews existing approaches to MR-based attenuation correction (MR-AC). Most groups have proposed MR-AC algorithms for brain PET studies and more recently also for torso PET/MR imaging. Most MR-AC strategies require the use of complementary MR and transmission images, or morphology templates generated from transmission images. We review and discuss these algorithms and point out challenges for using MR-AC in clinical routine. MR-AC is work-in-progress with potentially promising results from a template-based approach applicable to both brain and torso imaging. While efforts are ongoing in making clinically viable MR-AC fully automatic, further studies are required to realize the potential benefits of MR-based motion compensation and partial volume correction of the PET data. (orig.)

Quantitative imaging methods in osteoporosis.

Science.gov (United States)

Oei, Ling; Koromani, Fjorda; Rivadeneira, Fernando; Zillikens, M Carola; Oei, Edwin H G

2016-12-01

Osteoporosis is characterized by a decreased bone mass and quality resulting in an increased fracture risk. Quantitative imaging methods are critical in the diagnosis and follow-up of treatment effects in osteoporosis. Prior radiographic vertebral fractures and bone mineral density (BMD) as a quantitative parameter derived from dual-energy X-ray absorptiometry (DXA) are among the strongest known predictors of future osteoporotic fractures. Therefore, current clinical decision making relies heavily on accurate assessment of these imaging features. Further, novel quantitative techniques are being developed to appraise additional characteristics of osteoporosis including three-dimensional bone architecture with quantitative computed tomography (QCT). Dedicated high-resolution (HR) CT equipment is available to enhance image quality. At the other end of the spectrum, by utilizing post-processing techniques such as the trabecular bone score (TBS) information on three-dimensional architecture can be derived from DXA images. Further developments in magnetic resonance imaging (MRI) seem promising to not only capture bone micro-architecture but also characterize processes at the molecular level. This review provides an overview of various quantitative imaging techniques based on different radiological modalities utilized in clinical osteoporosis care and research.

Plant-wide quantitative assessment of a process industry system's operating state based on color-spectrum

Science.gov (United States)

Kai, Sun; Jianmin, Gao; Zhiyong, Gao; Hongquan, Jiang; Xu, Gao

2015-08-01

This paper presents a general theoretical framework to assess the operating state of a process industry system quantitatively based on meshing the theory of scientific data visualization and digital image processing. First, a series of color-spectrum, which represent the operating state of the system, is formed by mapping the monitor data set to a group of digital color images. Second, the common feature of color-spectrum, which is named benchmark-color-spectrum, is extracted as a standard of the normal state. Third, the abnormal degree can be quantified by calculating the difference of the benchmark-color-spectrum with observed color-spectrum. At last, a plant-wide operating state of the system in a period of time can be shown by plotting quantitative abnormal degree. Two case is included to illustrate the proposed method and its appropriateness. One is a general process industry system simulator named Tennessee Eastman Process. Another is an air compressor group which belongs to a real chemical plant.

Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

Directory of Open Access Journals (Sweden)

Yong-Bi Fu

2017-07-01

Full Text Available Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.

Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

Science.gov (United States)

Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

2017-01-01

Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

Bringing quality and meaning to quantitative data - Bringing quantitative evidence to qualitative observation

DEFF Research Database (Denmark)

Karpatschof, Benny

2007-01-01

Based on the author's methodological theory defining the distinctive properties of quantitative and qualitative method the article demonstrates the possibilities and advantages of combining the two types of investigation in the same research project. The project being an effect study...

Quantitative Outline-based Shape Analysis and Classification of Planetary Craterforms using Supervised Learning Models

Science.gov (United States)

Slezak, Thomas Joseph; Radebaugh, Jani; Christiansen, Eric

2017-10-01

The shapes of craterform morphology on planetary surfaces provides rich information about their origins and evolution. While morphologic information provides rich visual clues to geologic processes and properties, the ability to quantitatively communicate this information is less easily accomplished. This study examines the morphology of craterforms using the quantitative outline-based shape methods of geometric morphometrics, commonly used in biology and paleontology. We examine and compare landforms on planetary surfaces using shape, a property of morphology that is invariant to translation, rotation, and size. We quantify the shapes of paterae on Io, martian calderas, terrestrial basaltic shield calderas, terrestrial ash-flow calderas, and lunar impact craters using elliptic Fourier analysis (EFA) and the Zahn and Roskies (Z-R) shape function, or tangent angle approach to produce multivariate shape descriptors. These shape descriptors are subjected to multivariate statistical analysis including canonical variate analysis (CVA), a multiple-comparison variant of discriminant analysis, to investigate the link between craterform shape and classification. Paterae on Io are most similar in shape to terrestrial ash-flow calderas and the shapes of terrestrial basaltic shield volcanoes are most similar to martian calderas. The shapes of lunar impact craters, including simple, transitional, and complex morphology, are classified with a 100% rate of success in all models. Multiple CVA models effectively predict and classify different craterforms using shape-based identification and demonstrate significant potential for use in the analysis of planetary surfaces.

A bench-scale biotreatability methodology to evaluate field bioremediation

International Nuclear Information System (INIS)

Saberiyan, A.G.; MacPherson, J.R. Jr.; Moore, R.; Pruess, A.J.; Andrilenas, J.S.

1995-01-01

A bench-scale biotreatability methodology was designed to assess field bioremediation of petroleum contaminated soil samples. This methodology was performed successfully on soil samples from more than 40 sites. The methodology is composed of two phases, characterization and experimentation. The first phase is physical, chemical, and biological characterization of the contaminated soil sample. This phase determines soil parameters, contaminant type, presence of indigenous contaminant-degrading bacteria, and bacterial population size. The second phase, experimentation, consists of a respirometry test to measure the growth of microbes indirectly (via generation of CO 2 ) and the consumption of their food source directly (via contaminant loss). Based on a Monod kinetic analysis, the half-life of a contaminant can be calculated. Abiotic losses are accounted for based on a control test. The contaminant molecular structure is used to generate a stoichiometric equation. The stoichiometric equation yields a theoretical ratio for mg of contaminant degraded per mg of CO 2 produced. Data collected from the respirometry test are compared to theoretical values to evaluate bioremediation feasibility

Facile high-throughput forward chemical genetic screening by in situ monitoring of glucuronidase-based reporter gene expression in Arabidopsis thaliana

Directory of Open Access Journals (Sweden)

Vivek eHalder

2015-01-01

Full Text Available The use of biologically active small molecules to perturb biological functions holds enormous potential for investigating complex signaling networks. However, in contrast to animal systems, the search for and application of chemical tools for basic discovery in the plant sciences, generally referred to as ‘chemical genetics’, has only recently gained momentum. In addition to cultured cells, the well-characterized, small-sized model plant Arabidopsis thaliana is suitable for cultivation in microplates, which allows employing diverse cell- or phenotype-based chemical screens. In such screens, a chemical’s bioactivity is typically assessed either through scoring its impact on morphological traits or quantifying molecular attributes such as enzyme or reporter activities. Here, we describe a facile forward chemical screening methodology for intact Arabidopsis seedlings harboring the β-glucuronidase (GUS reporter by directly quantifying GUS activity in situ with 4-methylumbelliferyl-β-D-glucuronide (4-MUG as substrate. The quantitative nature of this screening assay has an obvious advantage over the also convenient histochemical GUS staining method, as it allows application of statistical procedures and unbiased hit selection based on threshold values as well as distinction between compounds with strong or weak bioactivity. At the same time, the in situ bioassay is very convenient requiring less effort and time for sample handling in comparison to the conventional quantitative in vitro GUS assay using 4-MUG, as validated with several Arabidopsis lines harboring different GUS reporter constructs. To demonstrate that the developed assays is particularly suitable for large-scale screening projects, we performed a pilot screen for chemical activators or inhibitors of salicylic acid-mediated defense signaling using the Arabidopsis PR1p::GUS line. Importantly, the screening methodology provided here can be adopted for any inducible GUS reporter line.

Two schemes for quantitative photoacoustic tomography based on Monte Carlo simulation

International Nuclear Information System (INIS)

Liu, Yubin; Yuan, Zhen; Jiang, Huabei

2016-01-01

Purpose: The aim of this study was to develop novel methods for photoacoustically determining the optical absorption coefficient of biological tissues using Monte Carlo (MC) simulation. Methods: In this study, the authors propose two quantitative photoacoustic tomography (PAT) methods for mapping the optical absorption coefficient. The reconstruction methods combine conventional PAT with MC simulation in a novel way to determine the optical absorption coefficient of biological tissues or organs. Specifically, the authors’ two schemes were theoretically and experimentally examined using simulations, tissue-mimicking phantoms, ex vivo, and in vivo tests. In particular, the authors explored these methods using several objects with different absorption contrasts embedded in turbid media and by using high-absorption media when the diffusion approximation was not effective at describing the photon transport. Results: The simulations and experimental tests showed that the reconstructions were quantitatively accurate in terms of the locations, sizes, and optical properties of the targets. The positions of the recovered targets were accessed by the property profiles, where the authors discovered that the off center error was less than 0.1 mm for the circular target. Meanwhile, the sizes and quantitative optical properties of the targets were quantified by estimating the full width half maximum of the optical absorption property. Interestingly, for the reconstructed sizes, the authors discovered that the errors ranged from 0 for relatively small-size targets to 26% for relatively large-size targets whereas for the recovered optical properties, the errors ranged from 0% to 12.5% for different cases. Conclusions: The authors found that their methods can quantitatively reconstruct absorbing objects of different sizes and optical contrasts even when the diffusion approximation is unable to accurately describe the photon propagation in biological tissues. In particular, their

Time-resolved quantitative phosphoproteomics

DEFF Research Database (Denmark)

Verano-Braga, Thiago; Schwämmle, Veit; Sylvester, Marc

2012-01-01

proteins involved in the Ang-(1-7) signaling, we performed a mass spectrometry-based time-resolved quantitative phosphoproteome study of human aortic endothelial cells (HAEC) treated with Ang-(1-7). We identified 1288 unique phosphosites on 699 different proteins with 99% certainty of correct peptide...

Gene-based testing of interactions in association studies of quantitative traits.

Directory of Open Access Journals (Sweden)

Li Ma

Full Text Available Various methods have been developed for identifying gene-gene interactions in genome-wide association studies (GWAS. However, most methods focus on individual markers as the testing unit, and the large number of such tests drastically erodes statistical power. In this study, we propose novel interaction tests of quantitative traits that are gene-based and that confer advantage in both statistical power and biological interpretation. The framework of gene-based gene-gene interaction (GGG tests combine marker-based interaction tests between all pairs of markers in two genes to produce a gene-level test for interaction between the two. The tests are based on an analytical formula we derive for the correlation between marker-based interaction tests due to linkage disequilibrium. We propose four GGG tests that extend the following P value combining methods: minimum P value, extended Simes procedure, truncated tail strength, and truncated P value product. Extensive simulations point to correct type I error rates of all tests and show that the two truncated tests are more powerful than the other tests in cases of markers involved in the underlying interaction not being directly genotyped and in cases of multiple underlying interactions. We applied our tests to pairs of genes that exhibit a protein-protein interaction to test for gene-level interactions underlying lipid levels using genotype data from the Atherosclerosis Risk in Communities study. We identified five novel interactions that are not evident from marker-based interaction testing and successfully replicated one of these interactions, between SMAD3 and NEDD9, in an independent sample from the Multi-Ethnic Study of Atherosclerosis. We conclude that our GGG tests show improved power to identify gene-level interactions in existing, as well as emerging, association studies.

Quantitative analysis by laser-induced breakdown spectroscopy based on generalized curves of growth

Energy Technology Data Exchange (ETDEWEB)

Aragón, C., E-mail: carlos.aragon@unavarra.es; Aguilera, J.A.

2015-08-01

A method for quantitative elemental analysis by laser-induced breakdown spectroscopy (LIBS) is proposed. The method (Cσ-LIBS) is based on Cσ graphs, generalized curves of growth which allow including several lines of various elements at different concentrations. A so-called homogeneous double (HD) model of the laser-induced plasma is used, defined by an integration over a single-region of the radiative transfer equation, combined with a separated treatment for neutral atoms (z = 0) and singly-charged ions (z = 1) in Cσ graphs and characteristic parameters. The procedure includes a criterion, based on a model limit, for eliminating data which, due to a high line intensity or concentration, are not well described by the HD model. An initial procedure provides a set of parameters (βA){sup z}, (ηNl){sup z}, T{sup z} and N{sub e}{sup z} (z = 0, 1) which characterize the plasma and the LIBS system. After characterization, two different analytical procedures, resulting in relative and absolute concentrations, may be applied. To test the method, fused glass samples prepared from certified slags and pure compounds are analyzed. We determine concentrations of Ca, Mn, Mg, V, Ti, Si and Al relative to Fe in three samples prepared from slags, and absolute concentrations of Fe, Ca and Mn in three samples prepared from Fe{sub 2}O{sub 3}, CaCO{sub 3} and Mn{sub 2}O{sub 3}. The accuracy obtained is 3.2% on the average for relative concentrations and 9.2% for absolute concentrations. - Highlights: • Method for quantitative analysis by LIBS, based on Csigma graphs • Conventional calibration is replaced with characterization of the LIBS system. • All elements are determined from measurement of one or two Csigma graphs. • The method is tested with fused glass disks prepared from slags and pure compounds. • Accurate results for relative (3.2%) and absolute concentrations (9.2%)

An Inquiry-Based Quantitative Reasoning Course for Business Students

Science.gov (United States)

Piercey, Victor; Militzer, Erin

2017-01-01

Quantitative Reasoning for Business is a two-semester sequence that serves as an alternative to elementary and intermediate algebra for first-year business students with weak mathematical preparation. Students who take the sequence have been retained at a higher rate and demonstrated a larger reduction in math anxiety than those who take the…

Quantitative analysis of glycated albumin in serum based on ATR-FTIR spectrum combined with SiPLS and SVM.

Science.gov (United States)

Li, Yuanpeng; Li, Fucui; Yang, Xinhao; Guo, Liu; Huang, Furong; Chen, Zhenqiang; Chen, Xingdan; Zheng, Shifu

2018-08-05

A rapid quantitative analysis model for determining the glycated albumin (GA) content based on Attenuated total reflectance (ATR)-Fourier transform infrared spectroscopy (FTIR) combining with linear SiPLS and nonlinear SVM has been developed. Firstly, the real GA content in human serum was determined by GA enzymatic method, meanwhile, the ATR-FTIR spectra of serum samples from the population of health examination were obtained. The spectral data of the whole spectra mid-infrared region (4000-600 cm -1 ) and GA's characteristic region (1800-800 cm -1 ) were used as the research object of quantitative analysis. Secondly, several preprocessing steps including first derivative, second derivative, variable standardization and spectral normalization, were performed. Lastly, quantitative analysis regression models were established by using SiPLS and SVM respectively. The SiPLS modeling results are as follows: root mean square error of cross validation (RMSECV T ) = 0.523 g/L, calibration coefficient (R C ) = 0.937, Root Mean Square Error of Prediction (RMSEP T ) = 0.787 g/L, and prediction coefficient (R P ) = 0.938. The SVM modeling results are as follows: RMSECV T  = 0.0048 g/L, R C  = 0.998, RMSEP T  = 0.442 g/L, and R p  = 0.916. The results indicated that the model performance was improved significantly after preprocessing and optimization of characteristic regions. While modeling performance of nonlinear SVM was considerably better than that of linear SiPLS. Hence, the quantitative analysis model for GA in human serum based on ATR-FTIR combined with SiPLS and SVM is effective. And it does not need sample preprocessing while being characterized by simple operations and high time efficiency, providing a rapid and accurate method for GA content determination. Copyright © 2018 Elsevier B.V. All rights reserved.

A novel screening method based on menadione mediated rapid reduction of tetrazolium salt for testing of anti-mycobacterial agents.

Science.gov (United States)

Singh, Upasana; Akhtar, Shamim; Mishra, Abhishek; Sarkar, Dhiman

2011-02-01

A microplate-based rapid, inexpensive and robust technique is developed by using tetrazolium salt 2,3-bis[2-methyloxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxanilide (XTT) and menadione to determine the viability of Mycobacterium tuberculosis, Mycobacterium bovis BCG and Mycobacterium smegmatis bacilli in microplate format. In general, XTT reduction is an extremely slow process which takes almost 24 h to produce a detectable signal. Menadione could drastically induce this reduction to an almost equal extent within a few minutes in a dose dependent manner. The reduction of XTT is directly proportional to the cell concentration in the presence of menadione. The standardized protocol used 200 μM of XTT and 60 μM of menadione in 250 μl of cell suspension grown either in aerobic or anaerobic conditions. The cell suspension of M. bovis BCG and M. tuberculosis were incubated for 40 min before reading the optical density at 470 nm whereas M. smegmatis was incubated for 20 min. Calculated Signal/Noise (S/N) ratios obtained by applying this protocol were 5.4, 6.4 and 9.4 using M. bovis BCG, M. tuberculosis and M. smegmatis respectively. The calculated Z' factors were >0.8 for all mycobacterium bacilli indicating the robustness of the XTT Reduction Menadione Assay (XRMA) for rapid screening of inhibitors. The assay protocol was validated by applying 10 standard anti-tubercular agents on M. tuberculosis, M. bovis BCG and M. smegmatis. The Minimum Inhibitory Concentration (MIC) values were found to be similar to reported values from Colony Forming Unit (CFU) and REMA (resazurin microplate assay) assays. Altogether, XRMA is providing a novel anti-tubercular screening protocol which could be useful in high throughput screening programs against different physiological stages of the bacilli. Copyright © 2010 Elsevier B.V. All rights reserved.

Quantitative Moessbauer analysis

International Nuclear Information System (INIS)

Collins, R.L.

1978-01-01

The quantitative analysis of Moessbauer data, as in the measurement of Fe 3+ /Fe 2+ concentration, has not been possible because of the different mean square velocities (x 2 ) of Moessbauer nuclei at chemically different sites. A method is now described which, based on Moessbauer data at several temperatures, permits the comparison of absorption areas at (x 2 )=0. (Auth.)

Study on quantitative risk assessment model of the third party damage for natural gas pipelines based on fuzzy comprehensive assessment

International Nuclear Information System (INIS)

Qiu, Zeyang; Liang, Wei; Lin, Yang; Zhang, Meng; Wang, Xue

2017-01-01

As an important part of national energy supply system, transmission pipelines for natural gas are possible to cause serious environmental pollution, life and property loss in case of accident. The third party damage is one of the most significant causes for natural gas pipeline system accidents, and it is very important to establish an effective quantitative risk assessment model of the third party damage for reducing the number of gas pipelines operation accidents. Against the third party damage accident has the characteristics such as diversity, complexity and uncertainty, this paper establishes a quantitative risk assessment model of the third party damage based on Analytic Hierarchy Process (AHP) and Fuzzy Comprehensive Evaluation (FCE). Firstly, risk sources of third party damage should be identified exactly, and the weight of factors could be determined via improved AHP, finally the importance of each factor is calculated by fuzzy comprehensive evaluation model. The results show that the quantitative risk assessment model is suitable for the third party damage of natural gas pipelines and improvement measures could be put forward to avoid accidents based on the importance of each factor. (paper)

A new liquid chromatography-mass spectrometry-based method to quantitate exogenous recombinant transferrin in cerebrospinal fluid: a potential approach for pharmacokinetic studies of transferrin-based therapeutics in the central nervous systems.

Science.gov (United States)

Wang, Shunhai; Bobst, Cedric E; Kaltashov, Igor A

2015-01-01

Transferrin (Tf) is an 80 kDa iron-binding protein that is viewed as a promising drug carrier to target the central nervous system as a result of its ability to penetrate the blood-brain barrier. Among the many challenges during the development of Tf-based therapeutics, the sensitive and accurate quantitation of the administered Tf in cerebrospinal fluid (CSF) remains particularly difficult because of the presence of abundant endogenous Tf. Herein, we describe the development of a new liquid chromatography-mass spectrometry-based method for the sensitive and accurate quantitation of exogenous recombinant human Tf in rat CSF. By taking advantage of a His-tag present in recombinant Tf and applying Ni affinity purification, the exogenous human serum Tf can be greatly enriched from rat CSF, despite the presence of the abundant endogenous protein. Additionally, we applied a newly developed (18)O-labeling technique that can generate internal standards at the protein level, which greatly improved the accuracy and robustness of quantitation. The developed method was investigated for linearity, accuracy, precision, and lower limit of quantitation, all of which met the commonly accepted criteria for bioanalytical method validation.

Quantitative method for measurement of the Goos-Hanchen effect based on source divergence considerations

International Nuclear Information System (INIS)

Gray, Jeffrey F.; Puri, Ashok

2007-01-01

In this paper we report on a method for quantitative measurement and characterization of the Goos-Hanchen effect based upon the real world performance of optical sources. A numerical model of a nonideal plane wave is developed in terms of uniform divergence properties. This model is applied to the Goos-Hanchen shift equations to determine beam shift displacement characteristics, which provides quantitative estimates of finite shifts near critical angle. As a potential technique for carrying out a meaningful comparison with experiments, a classical method of edge detection is discussed. To this end a line spread Green's function is defined which can be used to determine the effective transfer function of the near critical angle behavior of divergent plane waves. The process yields a distributed (blurred) output with a line spread function characteristic of the inverse square root nature of the Goos-Hanchen shift equation. A parameter of interest for measurement is given by the edge shift function. Modern imaging and image processing methods provide suitable techniques for exploiting the edge shift phenomena to attain refractive index sensitivities of the order of 10 -6 , comparable with the recent results reported in the literature

Investigating hyperoxic effects in the rat brain using quantitative susceptibility mapping based on MRI phase.

Science.gov (United States)

Hsieh, Meng-Chi; Kuo, Li-Wei; Huang, Yun-An; Chen, Jyh-Horng

2017-02-01

To test whether susceptibility imaging can detect microvenous oxygen saturation changes, induced by hyperoxia, in the rat brain. A three-dimensional gradient-echo with a flow compensation sequence was used to acquire T2*-weighted images of rat brains during hyperoxia and normoxia. Quantitative susceptibility mapping (QSM) and QSM-based microvenous oxygenation venography were computed from gradient-echo (GRE) phase images and compared between the two conditions. Pulse oxygen saturation (SpO 2 ) in the cortex was examined and compared with venous oxygen saturation (SvO 2 ) estimated by QSM. Oxygen saturation change calculated by a conventional Δ R2* map was also compared with the ΔSvO 2 estimated by QSM. Susceptibilities of five venous and tissue regions were quantified separately by QSM. Venous susceptibility was reduced by nearly 10%, with an SvO 2 shift of 10% during hyperoxia. A hyperoxic effect, confirmed by SpO 2 measurement, resulted in an SvO 2 increase in the cortex. The ΔSvO 2 between hyperoxia and normoxia was consistent with what was estimated by the Δ R2* map in five regions. These findings suggest that a quantitative susceptibility map is a promising technique for SvO 2 measurement. This method may be useful for quantitatively investigating oxygenation-dependent functional MRI studies. Magn Reson Med 77:592-602, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Undergraduate Students' Quantitative Reasoning in Economic Contexts

Science.gov (United States)

Mkhatshwa, Thembinkosi Peter; Doerr, Helen M.

2018-01-01

Contributing to a growing body of research on undergraduate students' quantitative reasoning, the study reported in this article used task-based interviews to investigate business calculus students' quantitative reasoning when solving two optimization tasks situated in the context of revenue and profit maximization. Analysis of verbal responses…

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

International Nuclear Information System (INIS)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir; He Yan; Xu Jianming

2010-01-01

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

Energy Technology Data Exchange (ETDEWEB)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); He Yan, E-mail: yhe2006@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); Xu Jianming, E-mail: jmxu@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China)

2010-08-15

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

Evaluation of a web based informatics system with data mining tools for predicting outcomes with quantitative imaging features in stroke rehabilitation clinical trials

Science.gov (United States)

Wang, Ximing; Kim, Bokkyu; Park, Ji Hoon; Wang, Erik; Forsyth, Sydney; Lim, Cody; Ravi, Ragini; Karibyan, Sarkis; Sanchez, Alexander; Liu, Brent

2017-03-01

Quantitative imaging biomarkers are used widely in clinical trials for tracking and evaluation of medical interventions. Previously, we have presented a web based informatics system utilizing quantitative imaging features for predicting outcomes in stroke rehabilitation clinical trials. The system integrates imaging features extraction tools and a web-based statistical analysis tool. The tools include a generalized linear mixed model(GLMM) that can investigate potential significance and correlation based on features extracted from clinical data and quantitative biomarkers. The imaging features extraction tools allow the user to collect imaging features and the GLMM module allows the user to select clinical data and imaging features such as stroke lesion characteristics from the database as regressors and regressands. This paper discusses the application scenario and evaluation results of the system in a stroke rehabilitation clinical trial. The system was utilized to manage clinical data and extract imaging biomarkers including stroke lesion volume, location and ventricle/brain ratio. The GLMM module was validated and the efficiency of data analysis was also evaluated.

RNA interference silences Microplitis demolitor bracovirus genes and implicates glc1.8 in disruption of adhesion in infected host cells

International Nuclear Information System (INIS)

Beck, Markus; Strand, Michael R.

2003-01-01

The family Polydnaviridae consists of ds-DNA viruses that are symbiotically associated with certain parasitoid wasps. PDVs are transmitted vertically but also are injected by wasps into hosts where they cause several physiological alterations including immunosuppression. The PDV genes responsible for mediating immunosuppression and other host alterations remain poorly characterized in large measure because viral mutants cannot be produced to study gene function. Here we report the use of RNA interference (RNAi) to specifically silence the glc1.8 and egf1.0 genes from Microplitis demolitor bracovirus (MdBV) in High Five cells derived from the lepidopteran Trichoplusia ni. Dose-response studies indicated that MdBV infects High Five cells and blocks the ability of these cells to adhere to culture plates. This response was very similar to what occurs in two classes of hemocytes, granular cells, and plasmatocytes, after infection by MdBV. Screening of monoclonal antibody (mAb) markers that distinguish different classes of lepidopteran hemocytes indicated that High Five cells cross-react with three mAbs that recognize granular cells from T. ni. Double-stranded RNA (dsRNA) complementary to glc1.8 specifically silenced glc1.8 expression and rescued the adhesive phenotype of High Five cells. Reciprocally, dsRNA complementary to egf1.0 silenced egf1.0 expression but had no effect on adhesion. The simplicity and potency of RNAi could be extremely useful for analysis of other PDV genes

Radar-Derived Quantitative Precipitation Estimation Based on Precipitation Classification

Directory of Open Access Journals (Sweden)

Lili Yang

2016-01-01

Full Text Available A method for improving radar-derived quantitative precipitation estimation is proposed. Tropical vertical profiles of reflectivity (VPRs are first determined from multiple VPRs. Upon identifying a tropical VPR, the event can be further classified as either tropical-stratiform or tropical-convective rainfall by a fuzzy logic (FL algorithm. Based on the precipitation-type fields, the reflectivity values are converted into rainfall rate using a Z-R relationship. In order to evaluate the performance of this rainfall classification scheme, three experiments were conducted using three months of data and two study cases. In Experiment I, the Weather Surveillance Radar-1988 Doppler (WSR-88D default Z-R relationship was applied. In Experiment II, the precipitation regime was separated into convective and stratiform rainfall using the FL algorithm, and corresponding Z-R relationships were used. In Experiment III, the precipitation regime was separated into convective, stratiform, and tropical rainfall, and the corresponding Z-R relationships were applied. The results show that the rainfall rates obtained from all three experiments match closely with the gauge observations, although Experiment II could solve the underestimation, when compared to Experiment I. Experiment III significantly reduced this underestimation and generated the most accurate radar estimates of rain rate among the three experiments.

High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis

DEFF Research Database (Denmark)

Williamson, James C; Edwards, Alistair V G; Verano-Braga, Thiago

2016-01-01

We present basic workups and quantitative comparisons for two current generation Orbitrap mass spectrometers, the Q Exactive Plus and Orbitrap Fusion Tribrid, which are widely considered two of the highest performing instruments on the market. We assessed the performance of two quantitative methods...... on both instruments, namely label-free quantitation and stable isotope labeling using isobaric tags, for studying the heat shock response in Escherichia coli. We investigated the recently reported MS3 method on the Fusion instrument and the potential of MS3-based reporter ion isolation Synchronous...... Precursor Selection (SPS) and its impact on quantitative accuracy. We confirm that the label-free approach offers a more linear response with a wider dynamic range than MS/MS-based isobaric tag quantitation and that the MS3/SPS approach alleviates but does not eliminate dynamic range compression. We...

Behavior Drift Detection Based on Anomalies Identification in Home Living Quantitative Indicators

OpenAIRE

Fabio Veronese; Andrea Masciadri; Sara Comai; Matteo Matteucci; Fabio Salice

2018-01-01

Home Automation and Smart Homes diffusion are providing an interesting opportunity to implement elderly monitoring. This is a new valid technological support to allow in-place aging of seniors by means of a detection system to notify potential anomalies. Monitoring has been implemented by means of Complex Event Processing on live streams of home automation data: this allows the analysis of the behavior of the house inhabitant through quantitative indicators. Different kinds of quantitative in...

Dynamic and quantitative method of analyzing service consistency evolution based on extended hierarchical finite state automata.

Science.gov (United States)

Fan, Linjun; Tang, Jun; Ling, Yunxiang; Li, Benxian

2014-01-01

This paper is concerned with the dynamic evolution analysis and quantitative measurement of primary factors that cause service inconsistency in service-oriented distributed simulation applications (SODSA). Traditional methods are mostly qualitative and empirical, and they do not consider the dynamic disturbances among factors in service's evolution behaviors such as producing, publishing, calling, and maintenance. Moreover, SODSA are rapidly evolving in terms of large-scale, reusable, compositional, pervasive, and flexible features, which presents difficulties in the usage of traditional analysis methods. To resolve these problems, a novel dynamic evolution model extended hierarchical service-finite state automata (EHS-FSA) is constructed based on finite state automata (FSA), which formally depict overall changing processes of service consistency states. And also the service consistency evolution algorithms (SCEAs) based on EHS-FSA are developed to quantitatively assess these impact factors. Experimental results show that the bad reusability (17.93% on average) is the biggest influential factor, the noncomposition of atomic services (13.12%) is the second biggest one, and the service version's confusion (1.2%) is the smallest one. Compared with previous qualitative analysis, SCEAs present good effectiveness and feasibility. This research can guide the engineers of service consistency technologies toward obtaining a higher level of consistency in SODSA.

Dynamic and Quantitative Method of Analyzing Service Consistency Evolution Based on Extended Hierarchical Finite State Automata

Directory of Open Access Journals (Sweden)

Linjun Fan

2014-01-01

Full Text Available This paper is concerned with the dynamic evolution analysis and quantitative measurement of primary factors that cause service inconsistency in service-oriented distributed simulation applications (SODSA. Traditional methods are mostly qualitative and empirical, and they do not consider the dynamic disturbances among factors in service’s evolution behaviors such as producing, publishing, calling, and maintenance. Moreover, SODSA are rapidly evolving in terms of large-scale, reusable, compositional, pervasive, and flexible features, which presents difficulties in the usage of traditional analysis methods. To resolve these problems, a novel dynamic evolution model extended hierarchical service-finite state automata (EHS-FSA is constructed based on finite state automata (FSA, which formally depict overall changing processes of service consistency states. And also the service consistency evolution algorithms (SCEAs based on EHS-FSA are developed to quantitatively assess these impact factors. Experimental results show that the bad reusability (17.93% on average is the biggest influential factor, the noncomposition of atomic services (13.12% is the second biggest one, and the service version’s confusion (1.2% is the smallest one. Compared with previous qualitative analysis, SCEAs present good effectiveness and feasibility. This research can guide the engineers of service consistency technologies toward obtaining a higher level of consistency in SODSA.

Development of quantitative x-ray microtomography

International Nuclear Information System (INIS)

Deckman, H.W.; Dunsmuir, J.A.; D'Amico, K.L.; Ferguson, S.R.; Flannery, B.P.

1990-01-01

The authors have developed several x-ray microtomography systems which function as quantitative three dimensional x-ray microscopes. In this paper the authors describe the evolutionary path followed from making the first high resolution experimental microscopes to later generations which can be routinely used for investigating materials. Developing the instrumentation for reliable quantitative x-ray microscopy using synchrotron and laboratory based x-ray sources has led to other imaging modalities for obtaining temporal and spatial two dimensional information

Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

International Nuclear Information System (INIS)

Lazariev, A; Graveron-Demilly, D; Allouche, A-R; Aubert-Frécon, M; Fauvelle, F; Piotto, M; Elbayed, K; Namer, I-J; Van Ormondt, D

2011-01-01

High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1 H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed

Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

Science.gov (United States)

Lazariev, A.; Allouche, A.-R.; Aubert-Frécon, M.; Fauvelle, F.; Piotto, M.; Elbayed, K.; Namer, I.-J.; van Ormondt, D.; Graveron-Demilly, D.

2011-11-01

High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed.

Evaluation of toxicity to the biological treatment and removal of recalcitrant organic compounds from oil refineries wastewaters; Avaliacao da toxicidade ao tratamento biologico e remocao de compostos organicos recalcitrantes existentes em efluentes de refinarias de petroleo

Energy Technology Data Exchange (ETDEWEB)

Barros Junior, Laerte M.; Macedo, Gorete R.; Bezerra, Marcio S.; Pereira, Franklin M.S. [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil). Dept. de Engenharia Quimica; Schmidell, Willibaldo [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil)

2004-07-01

Oil industry waste water usually contains recalcitrant chemical compounds, like phenol, benzene, toluene, xylene, naphthalene and acenaphthene. The respirometry, determination of respiration rate of an active biomass, is an adequate methodology for quantification of aerobic activity biological. This study aims evaluate the inhibition effect of phenol in the oxidation capacity of an industrial sludge. This work also intends to study the phenol removal through biological and photochemical-biological processes. The respirometry was carried out with synthetic solution, using sludge from an oil processing industry. The phenol degradation experiments were carried out in an activated sludge unit and in a photochemical reactor. This work suggests the potential of photochemical-biological treatment use, in relation to the biological process with a no-acclimated sludge, in the removal of refractory organic compounds from oil industry wastewaters. The characterization of biomass using the respirometry methodology showed which is a useful tool in evaluation of phenol toxicity to biological treatment. (author)

Quantitative method for determination of body inorganic iodine

International Nuclear Information System (INIS)

Filatov, A.A.; Tatsievskij, V.A.

1991-01-01

An original method of quantitation of body inorganic iodine, based upon a simultaneous administration of a known dose of stable and radioactive iodine with subsequent radiometry of the thyroid was proposed. The calculation is based upon the principle of the dilution of radiactive iodine in human inorganic iodine space. The method permits quantitation of the amount of inorganic iodine with regard to individual features of inorganic space. The method is characterized by simplicity and is not invasive for a patient

Medically relevant assays with a simple smartphone and tablet based fluorescence detection system.

Science.gov (United States)

Wargocki, Piotr; Deng, Wei; Anwer, Ayad G; Goldys, Ewa M

2015-05-20

Cell phones and smart phones can be reconfigured as biomedical sensor devices but this requires specialized add-ons. In this paper we present a simple cell phone-based portable bioassay platform, which can be used with fluorescent assays in solution. The system consists of a tablet, a polarizer, a smart phone (camera) and a box that provides dark readout conditions. The assay in a well plate is placed on the tablet screen acting as an excitation source. A polarizer on top of the well plate separates excitation light from assay fluorescence emission enabling assay readout with a smartphone camera. The assay result is obtained by analysing the intensity of image pixels in an appropriate colour channel. With this device we carried out two assays, for collagenase and trypsin using fluorescein as the detected fluorophore. The results of collagenase assay with the lowest measured concentration of 3.75 µg/mL and 0.938 µg in total in the sample were comparable to those obtained by a microplate reader. The lowest measured amount of trypsin was 930 pg, which is comparable to the low detection limit of 400 pg for this assay obtained in a microplate reader. The device is sensitive enough to be used in point-of-care medical diagnostics of clinically relevant conditions, including arthritis, cystic fibrosis and acute pancreatitis.

Medically Relevant Assays with a Simple Smartphone and Tablet Based Fluorescence Detection System

Directory of Open Access Journals (Sweden)

Piotr Wargocki

2015-05-01

Full Text Available Cell phones and smart phones can be reconfigured as biomedical sensor devices but this requires specialized add-ons. In this paper we present a simple cell phone-based portable bioassay platform, which can be used with fluorescent assays in solution. The system consists of a tablet, a polarizer, a smart phone (camera and a box that provides dark readout conditions. The assay in a well plate is placed on the tablet screen acting as an excitation source. A polarizer on top of the well plate separates excitation light from assay fluorescence emission enabling assay readout with a smartphone camera. The assay result is obtained by analysing the intensity of image pixels in an appropriate colour channel. With this device we carried out two assays, for collagenase and trypsin using fluorescein as the detected fluorophore. The results of collagenase assay with the lowest measured concentration of 3.75 µg/mL and 0.938 µg in total in the sample were comparable to those obtained by a microplate reader. The lowest measured amount of trypsin was 930 pg, which is comparable to the low detection limit of 400 pg for this assay obtained in a microplate reader. The device is sensitive enough to be used in point-of-care medical diagnostics of clinically relevant conditions, including arthritis, cystic fibrosis and acute pancreatitis.

The Functional Resonance Analysis Method for a systemic risk based environmental auditing in a sinter plant: A semi-quantitative approach

International Nuclear Information System (INIS)

Patriarca, Riccardo; Di Gravio, Giulio; Costantino, Francesco; Tronci, Massimo

2017-01-01

Environmental auditing is a main issue for any production plant and assessing environmental performance is crucial to identify risks factors. The complexity of current plants arises from interactions among technological, human and organizational system components, which are often transient and not easily detectable. The auditing thus requires a systemic perspective, rather than focusing on individual behaviors, as emerged in recent research in the safety domain for socio-technical systems. We explore the significance of modeling the interactions of system components in everyday work, by the application of a recent systemic method, i.e. the Functional Resonance Analysis Method (FRAM), in order to define dynamically the system structure. We present also an innovative evolution of traditional FRAM following a semi-quantitative approach based on Monte Carlo simulation. This paper represents the first contribution related to the application of FRAM in the environmental context, moreover considering a consistent evolution based on Monte Carlo simulation. The case study of an environmental risk auditing in a sinter plant validates the research, showing the benefits in terms of identifying potential critical activities, related mitigating actions and comprehensive environmental monitoring indicators. - Highlights: • We discuss the relevance of a systemic risk based environmental audit. • We present FRAM to represent functional interactions of the system. • We develop a semi-quantitative FRAM framework to assess environmental risks. • We apply the semi-quantitative FRAM framework to build a model for a sinter plant.

The Functional Resonance Analysis Method for a systemic risk based environmental auditing in a sinter plant: A semi-quantitative approach

Energy Technology Data Exchange (ETDEWEB)

Patriarca, Riccardo, E-mail: riccardo.patriarca@uniroma1.it; Di Gravio, Giulio; Costantino, Francesco; Tronci, Massimo

2017-03-15

Environmental auditing is a main issue for any production plant and assessing environmental performance is crucial to identify risks factors. The complexity of current plants arises from interactions among technological, human and organizational system components, which are often transient and not easily detectable. The auditing thus requires a systemic perspective, rather than focusing on individual behaviors, as emerged in recent research in the safety domain for socio-technical systems. We explore the significance of modeling the interactions of system components in everyday work, by the application of a recent systemic method, i.e. the Functional Resonance Analysis Method (FRAM), in order to define dynamically the system structure. We present also an innovative evolution of traditional FRAM following a semi-quantitative approach based on Monte Carlo simulation. This paper represents the first contribution related to the application of FRAM in the environmental context, moreover considering a consistent evolution based on Monte Carlo simulation. The case study of an environmental risk auditing in a sinter plant validates the research, showing the benefits in terms of identifying potential critical activities, related mitigating actions and comprehensive environmental monitoring indicators. - Highlights: • We discuss the relevance of a systemic risk based environmental audit. • We present FRAM to represent functional interactions of the system. • We develop a semi-quantitative FRAM framework to assess environmental risks. • We apply the semi-quantitative FRAM framework to build a model for a sinter plant.

First experiences with model based iterative reconstructions influence on quantitative plaque volume and intensity measurements in coronary computed tomography angiography

DEFF Research Database (Denmark)

Precht, Helle; Kitslaar, Pieter H.; Broersen, Alexander

2017-01-01

Purpose: Investigate the influence of adaptive statistical iterative reconstruction (ASIR) and the model- based IR (Veo) reconstruction algorithm in coronary computed tomography angiography (CCTA) im- ages on quantitative measurements in coronary arteries for plaque volumes and intensities. Methods...

Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics.

Science.gov (United States)

Burkhart, Julia Maria; Schumbrutzki, Cornelia; Wortelkamp, Stefanie; Sickmann, Albert; Zahedi, René Peiman

2012-02-02

Trypsin is the most frequently used proteolytic enzyme in mass spectrometry-based proteomics. Beside its good availability, it also offers some major advantages such as an optimal average peptide length of ~14 amino acids, and typically the presence of at least two defined positive charges at the N-terminus as well as the C-terminal Arg/Lys, rendering tryptic peptides well suited for CID-based LC-MS/MS. Here, we conducted a systematic study of different types of commercially available trypsin in order to qualitatively and quantitatively compare cleavage specificity, efficiency as well as reproducibility and the potential impact on quantitation and proteome coverage. We present a straightforward strategy applied to complex digests of human platelets, comprising (1) digest controls using a monolithic column HPLC-setup, (2) SCX enrichment of semitryptic/nonspecific peptides, (3) targeted MRM analysis of corresponding full cleavage/missed cleavage peptide pairs as well as (4) LC-MS analyses of complete digests with a three-step data interpretation. Thus, differences in digest performance can be readily assessed, rendering these procedures extremely beneficial to quality control not only the trypsin of choice, but also to effectively compare as well as optimize different digestion conditions and to evaluate the reproducibility of a dedicated digest protocol for all kinds of quantitative proteome studies. Copyright © 2011 Elsevier B.V. All rights reserved.

MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments

NARCIS (Netherlands)

Bustin, S.A.; Beaulieu, J.F.; Huggett, J.; Jaggi, R.; Kibenge, F.S.; Olsvik, P.A.; Penning, L.C.; Toegel, S.

2010-01-01

MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments Stephen A Bustin1 , Jean-François Beaulieu2 , Jim Huggett3 , Rolf Jaggi4 , Frederick SB Kibenge5 , Pål A Olsvik6 , Louis C Penning7 and Stefan Toegel8 1 Centre for

A method to extract quantitative information in analyzer-based x-ray phase contrast imaging

International Nuclear Information System (INIS)

Pagot, E.; Cloetens, P.; Fiedler, S.; Bravin, A.; Coan, P.; Baruchel, J.; Haertwig, J.; Thomlinson, W.

2003-01-01

Analyzer-based imaging is a powerful phase-sensitive technique that generates improved contrast compared to standard absorption radiography. Combining numerically two images taken on either side at ±1/2 of the full width at half-maximum (FWHM) of the rocking curve provides images of 'pure refraction' and of 'apparent absorption'. In this study, a similar approach is made by combining symmetrical images with respect to the peak of the analyzer rocking curve but at general positions, ±α·FWHM. These two approaches do not consider the ultrasmall angle scattering produced by the object independently, which can lead to inconsistent results. An accurate way to separately retrieve the quantitative information intrinsic to the object is proposed. It is based on a statistical analysis of the local rocking curve, and allows one to overcome the problems encountered using the previous approaches

Comparison of quantitative myocardial perfusion imaging CT to fluorescent microsphere-based flow from high-resolution cryo-images

Science.gov (United States)

Eck, Brendan L.; Fahmi, Rachid; Levi, Jacob; Fares, Anas; Wu, Hao; Li, Yuemeng; Vembar, Mani; Dhanantwari, Amar; Bezerra, Hiram G.; Wilson, David L.

2016-03-01

Myocardial perfusion imaging using CT (MPI-CT) has the potential to provide quantitative measures of myocardial blood flow (MBF) which can aid the diagnosis of coronary artery disease. We evaluated the quantitative accuracy of MPI-CT in a porcine model of balloon-induced LAD coronary artery ischemia guided by fractional flow reserve (FFR). We quantified MBF at baseline (FFR=1.0) and under moderate ischemia (FFR=0.7) using MPI-CT and compared to fluorescent microsphere-based MBF from high-resolution cryo-images. Dynamic, contrast-enhanced CT images were obtained using a spectral detector CT (Philips Healthcare). Projection-based mono-energetic images were reconstructed and processed to obtain MBF. Three MBF quantification approaches were evaluated: singular value decomposition (SVD) with fixed Tikhonov regularization (ThSVD), SVD with regularization determined by the L-Curve criterion (LSVD), and Johnson-Wilson parameter estimation (JW). The three approaches over-estimated MBF compared to cryo-images. JW produced the most accurate MBF, with average error 33.3+/-19.2mL/min/100g, whereas LSVD and ThSVD had greater over-estimation, 59.5+/-28.3mL/min/100g and 78.3+/-25.6 mL/min/100g, respectively. Relative blood flow as assessed by a flow ratio of LAD-to-remote myocardium was strongly correlated between JW and cryo-imaging, with R2=0.97, compared to R2=0.88 and 0.78 for LSVD and ThSVD, respectively. We assessed tissue impulse response functions (IRFs) from each approach for sources of error. While JW was constrained to physiologic solutions, both LSVD and ThSVD produced IRFs with non-physiologic properties due to noise. The L-curve provided noise-adaptive regularization but did not eliminate non-physiologic IRF properties or optimize for MBF accuracy. These findings suggest that model-based MPI-CT approaches may be more appropriate for quantitative MBF estimation and that cryo-imaging can support the development of MPI-CT by providing spatial distributions of MBF.

Correlation Feature Selection and Mutual Information Theory Based Quantitative Research on Meteorological Impact Factors of Module Temperature for Solar Photovoltaic Systems

Directory of Open Access Journals (Sweden)

Yujing Sun

2016-12-01

Full Text Available The module temperature is the most important parameter influencing the output power of solar photovoltaic (PV systems, aside from solar irradiance. In this paper, we focus on the interdisciplinary research that combines the correlation analysis, mutual information (MI and heat transfer theory, which aims to figure out the correlative relations between different meteorological impact factors (MIFs and PV module temperature from both quality and quantitative aspects. The identification and confirmation of primary MIFs of PV module temperature are investigated as the first step of this research from the perspective of physical meaning and mathematical analysis about electrical performance and thermal characteristic of PV modules based on PV effect and heat transfer theory. Furthermore, the quantitative description of the MIFs influence on PV module temperature is mathematically formulated as several indexes using correlation-based feature selection (CFS and MI theory to explore the specific impact degrees under four different typical weather statuses named general weather classes (GWCs. Case studies for the proposed methods were conducted using actual measurement data of a 500 kW grid-connected solar PV plant in China. The results not only verified the knowledge about the main MIFs of PV module temperatures, more importantly, but also provide the specific ratio of quantitative impact degrees of these three MIFs respectively through CFS and MI based measures under four different GWCs.

Quantitative and Label-Free Detection of Protein Kinase A Activity Based on Surface-Enhanced Raman Spectroscopy with Gold Nanostars.

Science.gov (United States)

He, Shuai; Kyaw, Yi Mon Ei; Tan, Eddie Khay Ming; Bekale, Laurent; Kang, Malvin Wei Cherng; Kim, Susana Soo-Yeon; Tan, Ivan; Lam, Kong-Peng; Kah, James Chen Yong

2018-04-26

The activity of extracellular protein kinase A (PKA) is known to be a biomarker for cancer. However, conventional PKA assays based on colorimetric, radioactive, and fluorometric techniques suffer from intensive labeling-related preparations, background interference, photobleaching, and safety concerns. While surface-enhanced Raman spectroscopy (SERS)-based assays have been developed for various enzymes to address these limitations, their use in probing PKA activity is limited due to subtle changes in the Raman spectrum with phosphorylation. Here, we developed a robust colloidal SERS-based scheme for label-free quantitative measurement of PKA activity using gold nanostars (AuNS) as a SERS substrate functionalized with bovine serum albumin (BSA)-kemptide (Kem) bioconjugate (AuNS-BSA-Kem), where BSA conferred colloidal stability and Kem is a high-affinity peptide substrate for PKA. By performing principle component analysis (PCA) on the SERS spectrum, we identified two Raman peaks at 725 and 1395 cm -1 , whose ratiometric intensity change provided a quantitative measure of Kem phosphorylation by PKA in vitro and allowed us to distinguish MDA-MB-231 and MCF-7 breast cancer cells known to overexpress extracellular PKA catalytic subunits from noncancerous human umbilical vein endothelial cells (HUVEC) based on their PKA activity in cell culture supernatant. The outcome demonstrated potential application of AuNS-BSA-Kem as a SERS probe for cancer screening based on PKA activity.

Statistical mechanics and the evolution of polygenic quantitative traits

NARCIS (Netherlands)

Barton, N.H.; De Vladar, H.P.

The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified

Simultaneous quantitative detection of multiple tumor markers with a rapid and sensitive multicolor quantum dots based immunochromatographic test strip.

Science.gov (United States)

Wang, Chunying; Hou, Fei; Ma, Yicai

2015-06-15

A novel multicolor quantum dots (QDs) based immunochromatographic test strip (ICTS) was developed for simultaneous quantitative detection of multiple tumor markers, by utilizing alpha fetoprotein (AFP) and carcinoembryonic antigen (CEA) as models. The immunosensor could realize simultaneous quantitative detection of tumor markers with only one test line and one control line on the nitrocellulose membrane (NC membrane) due to the introduction of multicolor QDs. In this method, a mixture of mouse anti-AFP McAb and mouse anti-CEA McAb was coated on NC membrane as test line and goat anti-mouse IgG antibody was coated as control line. Anti-AFP McAb-QDs546 conjugates and anti-CEA McAb-QDs620 conjugates were mixed and applied to the conjugate pad. Simultaneous quantitative detection of multiple tumor markers was achieved by detecting the fluorescence intensity of captured QDs labels on test line and control line using a test strip reader. Under the optimum conditions, AFP and CEA could be detected as low as 3 ng/mL and 2 ng/mL in 15 min with a sample volume of 80 μL, and no obvious cross-reactivity was observed. The immunosensor was validated with 130 clinical samples and in which it exhibited high sensitivity (93% for AFP and 87% for CEA) and specificity (94% for AFP and 97% for CEA). The immunosensor also demonstrated high recoveries (87.5-113% for AFP and 90-97.3% for CEA) and low relative standard deviations (RSDs) (2.8-6.2% for AFP and 4.9-9.6% for CEA) when testing spiked human serum. This novel multicolor QDs based ICTS provides an easy and rapid, simultaneous quantitative detecting strategy for point-of-care testing of tumor markers. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative Auger analysis of Nb-Ge superconducting alloys

International Nuclear Information System (INIS)

Buitrago, R.H.

1980-01-01

The feasibility of using Auger electron analysis for quantitative analysis was investigated by studying Nb 3 Ge thin-film Auger data with different approaches. A method base on elemental standards gave consistent quantitative values with reported Nb-Ge data. Alloy sputter yields were also calculated and results were consistent with those for pure elements

Quantitative analysis of fatty-acid-based biofuels produced by wild-type and genetically engineered cyanobacteria by gas chromatography-mass spectrometry.

Science.gov (United States)

Guan, Wenna; Zhao, Hui; Lu, Xuefeng; Wang, Cong; Yang, Menglong; Bai, Fali

2011-11-11

Simple and rapid quantitative determination of fatty-acid-based biofuels is greatly important for the study of genetic engineering progress for biofuels production by microalgae. Ideal biofuels produced from biological systems should be chemically similar to petroleum, like fatty-acid-based molecules including free fatty acids, fatty acid methyl esters, fatty acid ethyl esters, fatty alcohols and fatty alkanes. This study founded a gas chromatography-mass spectrometry (GC-MS) method for simultaneous quantification of seven free fatty acids, nine fatty acid methyl esters, five fatty acid ethyl esters, five fatty alcohols and three fatty alkanes produced by wild-type Synechocystis PCC 6803 and its genetically engineered strain. Data obtained from GC-MS analyses were quantified using internal standard peak area comparisons. The linearity, limit of detection (LOD) and precision (RSD) of the method were evaluated. The results demonstrated that fatty-acid-based biofuels can be directly determined by GC-MS without derivation. Therefore, rapid and reliable quantitative analysis of fatty-acid-based biofuels produced by wild-type and genetically engineered cyanobacteria can be achieved using the GC-MS method founded in this work. Copyright © 2011 Elsevier B.V. All rights reserved.

Quantitative self-assembly prediction yields targeted nanomedicines

Science.gov (United States)

Shamay, Yosi; Shah, Janki; Işık, Mehtap; Mizrachi, Aviram; Leibold, Josef; Tschaharganeh, Darjus F.; Roxbury, Daniel; Budhathoki-Uprety, Januka; Nawaly, Karla; Sugarman, James L.; Baut, Emily; Neiman, Michelle R.; Dacek, Megan; Ganesh, Kripa S.; Johnson, Darren C.; Sridharan, Ramya; Chu, Karen L.; Rajasekhar, Vinagolu K.; Lowe, Scott W.; Chodera, John D.; Heller, Daniel A.

2018-02-01

Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.

Quantitative Prediction of Coalbed Gas Content Based on Seismic Multiple-Attribute Analyses

Directory of Open Access Journals (Sweden)

Renfang Pan

2015-09-01

Full Text Available Accurate prediction of gas planar distribution is crucial to selection and development of new CBM exploration areas. Based on seismic attributes, well logging and testing data we found that seismic absorption attenuation, after eliminating the effects of burial depth, shows an evident correlation with CBM gas content; (positive structure curvature has a negative correlation with gas content; and density has a negative correlation with gas content. It is feasible to use the hydrocarbon index (P*G and pseudo-Poisson ratio attributes for detection of gas enrichment zones. Based on seismic multiple-attribute analyses, a multiple linear regression equation was established between the seismic attributes and gas content at the drilling wells. Application of this equation to the seismic attributes at locations other than the drilling wells yielded a quantitative prediction of planar gas distribution. Prediction calculations were performed for two different models, one using pre-stack inversion and the other one disregarding pre-stack inversion. A comparison of the results indicates that both models predicted a similar trend for gas content distribution, except that the model using pre-stack inversion yielded a prediction result with considerably higher precision than the other model.

PC based controlled potential coulometric titrator for quantitative analysis of nuclear materials

International Nuclear Information System (INIS)

Manna, A.; Moorthy, A.D.; Bhogale, R.G.

2001-01-01

With increased requirements for process control and accountability of nuclear materials in plutonium reprocessing plants, the PC based controlled potential coulometric titrator was developed which has the capability of automatic quantitative analysis of the samples. The instruments based on electromechanical methods, incorporates an electronic potentiostat, a digital coulometer with wide dynamic range and a PC with a control interface card. The potentiostat is required to control the potential at the working electrode surface as per predetermined controlled voltage with respect to a reference electrode under wide variations in the conductivity and double layer capacitance of the electrochemical cell. The digital coulometer precisely measures the amount of electronic charge taking part in the electrochemical reactions of interest. The software has the facility to carry out three different types of analysis, i.e., primary coulometry, secondary coulometry and coulogram curve tracing. Due to complete analysis of the samples under program control, the human related errors are minimized and a better precision in the results are obtained. It has been possible to obtain an overall precession of better than +/- 0.3% in the determination of plutonium using the instrument. (author)

A New Variable Selection Method Based on Mutual Information Maximization by Replacing Collinear Variables for Nonlinear Quantitative Structure-Property Relationship Models

Energy Technology Data Exchange (ETDEWEB)

Ghasemi, Jahan B.; Zolfonoun, Ehsan [Toosi University of Technology, Tehran (Korea, Republic of)

2012-05-15

Selection of the most informative molecular descriptors from the original data set is a key step for development of quantitative structure activity/property relationship models. Recently, mutual information (MI) has gained increasing attention in feature selection problems. This paper presents an effective mutual information-based feature selection approach, named mutual information maximization by replacing collinear variables (MIMRCV), for nonlinear quantitative structure-property relationship models. The proposed variable selection method was applied to three different QSPR datasets, soil degradation half-life of 47 organophosphorus pesticides, GC-MS retention times of 85 volatile organic compounds, and water-to-micellar cetyltrimethylammonium bromide partition coefficients of 62 organic compounds.The obtained results revealed that using MIMRCV as feature selection method improves the predictive quality of the developed models compared to conventional MI based variable selection algorithms.

A New Variable Selection Method Based on Mutual Information Maximization by Replacing Collinear Variables for Nonlinear Quantitative Structure-Property Relationship Models

International Nuclear Information System (INIS)

Ghasemi, Jahan B.; Zolfonoun, Ehsan

2012-01-01

Selection of the most informative molecular descriptors from the original data set is a key step for development of quantitative structure activity/property relationship models. Recently, mutual information (MI) has gained increasing attention in feature selection problems. This paper presents an effective mutual information-based feature selection approach, named mutual information maximization by replacing collinear variables (MIMRCV), for nonlinear quantitative structure-property relationship models. The proposed variable selection method was applied to three different QSPR datasets, soil degradation half-life of 47 organophosphorus pesticides, GC-MS retention times of 85 volatile organic compounds, and water-to-micellar cetyltrimethylammonium bromide partition coefficients of 62 organic compounds.The obtained results revealed that using MIMRCV as feature selection method improves the predictive quality of the developed models compared to conventional MI based variable selection algorithms

Virtualising the Quantitative Research Methods Course: An Island-Based Approach

Science.gov (United States)

Baglin, James; Reece, John; Baker, Jenalle

2015-01-01

Many recent improvements in pedagogical practice have been enabled by the rapid development of innovative technologies, particularly for teaching quantitative research methods and statistics. This study describes the design, implementation, and evaluation of a series of specialised computer laboratory sessions. The sessions combined the use of an…

Quantitative Decision Support Requires Quantitative User Guidance

Science.gov (United States)

Smith, L. A.

2009-12-01

Is it conceivable that models run on 2007 computer hardware could provide robust and credible probabilistic information for decision support and user guidance at the ZIP code level for sub-daily meteorological events in 2060? In 2090? Retrospectively, how informative would output from today’s models have proven in 2003? or the 1930’s? Consultancies in the United Kingdom, including the Met Office, are offering services to “future-proof” their customers from climate change. How is a US or European based user or policy maker to determine the extent to which exciting new Bayesian methods are relevant here? or when a commercial supplier is vastly overselling the insights of today’s climate science? How are policy makers and academic economists to make the closely related decisions facing them? How can we communicate deep uncertainty in the future at small length-scales without undermining the firm foundation established by climate science regarding global trends? Three distinct aspects of the communication of the uses of climate model output targeting users and policy makers, as well as other specialist adaptation scientists, are discussed. First, a brief scientific evaluation of the length and time scales at which climate model output is likely to become uninformative is provided, including a note on the applicability the latest Bayesian methodology to current state-of-the-art general circulation models output. Second, a critical evaluation of the language often employed in communication of climate model output, a language which accurately states that models are “better”, have “improved” and now “include” and “simulate” relevant meteorological processed, without clearly identifying where the current information is thought to be uninformative and misleads, both for the current climate and as a function of the state of the (each) climate simulation. And thirdly, a general approach for evaluating the relevance of quantitative climate model output

Differences in critical thermal maxima and mortality across life stages of the mealworm beetle Tenebrio molitor.

Science.gov (United States)

Vorhees, Ashley S; Bradley, Timothy J

2012-07-01

Thermal limits to activity profoundly affect the abundance and distribution of ectothermic animals. Upper thermal limits to activity are typically reported as the critical thermal maximum (CT(max)), the temperature at which activity becomes uncontrolled. Thermolimit respirometry is a new technique that allows CT(max) to be quantified in small animals, such as insects, as the point of spiracular failure by measuring CO(2) release from the animal as temperature increases. Although prior studies have reported a characteristic pattern of CO(2) release for insects during thermolimit respirometry trials, no studies have been carried out to determine the universality of this pattern across development, or at what point death occurs along this pattern. Here, we compared the CT(max) and patterns of CO(2) release among three life stages of a beetle species, Tenebrio molitor, and mapped heat death onto these patterns. Our study is the first to report distinct patterns of CO(2) release in different life stages of an insect species during thermolimit respirometry. Our results show that CT(max) was significantly higher in adult beetles than in either larvae or pupae (P<0.001) and, similarly, death occurred at higher temperatures in adults than in larvae and pupae. We also found that death during heating closely follows CT(max) in these animals, which confirms that measuring the loss of spiracular control with thermolimit respirometry successfully identifies the point of physiological limitation during heat stress.

Quantitative Structure-Retention Relationships (QSRR) for Chromatographic Separation of Disazo and Trisazo 4,4'-Diaminobenzanilide-based Dyes

OpenAIRE

Funar-Timofei, Simona; Fabian, Walter M. F.; Simu, Georgeta M.; Suzukic, Takahiro

2006-01-01

For a series of 23 disazo and trisazo 4,4'-diaminobenzanilide-based direct dye molecules, thechromatographic mobilities, extrapolated to modifier-free conditions (RM0 values), were determinedfrom reverse-phase thin-layer chromatography (RP-TLC) experiments. Traditional and rational QSAR/QSPR modelling techniques have been applied to find a quantitative structure-retention relationship (QSRR) for the dyes. Molecular dye structures were energy minimized by both molecular mechanics and quantum c...

A unique charge-coupled device/xenon arc lamp based imaging system for the accurate detection and quantitation of multicolour fluorescence.

Science.gov (United States)

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

2001-03-01

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

A Compressed Sensing-Based Wearable Sensor Network for Quantitative Assessment of Stroke Patients

Directory of Open Access Journals (Sweden)

Lei Yu

2016-02-01

Full Text Available Clinical rehabilitation assessment is an important part of the therapy process because it is the premise for prescribing suitable rehabilitation interventions. However, the commonly used assessment scales have the following two drawbacks: (1 they are susceptible to subjective factors; (2 they only have several rating levels and are influenced by a ceiling effect, making it impossible to exactly detect any further improvement in the movement. Meanwhile, energy constraints are a primary design consideration in wearable sensor network systems since they are often battery-operated. Traditionally, for wearable sensor network systems that follow the Shannon/Nyquist sampling theorem, there are many data that need to be sampled and transmitted. This paper proposes a novel wearable sensor network system to monitor and quantitatively assess the upper limb motion function, based on compressed sensing technology. With the sparse representation model, less data is transmitted to the computer than with traditional systems. The experimental results show that the accelerometer signals of Bobath handshake and shoulder touch exercises can be compressed, and the length of the compressed signal is less than 1/3 of the raw signal length. More importantly, the reconstruction errors have no influence on the predictive accuracy of the Brunnstrom stage classification model. It also indicated that the proposed system can not only reduce the amount of data during the sampling and transmission processes, but also, the reconstructed accelerometer signals can be used for quantitative assessment without any loss of useful information.

A Compressed Sensing-Based Wearable Sensor Network for Quantitative Assessment of Stroke Patients

Science.gov (United States)

Yu, Lei; Xiong, Daxi; Guo, Liquan; Wang, Jiping

2016-01-01

Clinical rehabilitation assessment is an important part of the therapy process because it is the premise for prescribing suitable rehabilitation interventions. However, the commonly used assessment scales have the following two drawbacks: (1) they are susceptible to subjective factors; (2) they only have several rating levels and are influenced by a ceiling effect, making it impossible to exactly detect any further improvement in the movement. Meanwhile, energy constraints are a primary design consideration in wearable sensor network systems since they are often battery-operated. Traditionally, for wearable sensor network systems that follow the Shannon/Nyquist sampling theorem, there are many data that need to be sampled and transmitted. This paper proposes a novel wearable sensor network system to monitor and quantitatively assess the upper limb motion function, based on compressed sensing technology. With the sparse representation model, less data is transmitted to the computer than with traditional systems. The experimental results show that the accelerometer signals of Bobath handshake and shoulder touch exercises can be compressed, and the length of the compressed signal is less than 1/3 of the raw signal length. More importantly, the reconstruction errors have no influence on the predictive accuracy of the Brunnstrom stage classification model. It also indicated that the proposed system can not only reduce the amount of data during the sampling and transmission processes, but also, the reconstructed accelerometer signals can be used for quantitative assessment without any loss of useful information. PMID:26861337

Surface-Enhanced Raman Spectroscopy Based Quantitative Bioassay on Aptamer-Functionalized Nanopillars Using Large-Area Raman Mapping

DEFF Research Database (Denmark)

Yang, Jaeyoung; Palla, Mirko; Bosco, Filippo

2013-01-01

Surface-enhanced Raman spectroscopy (SERS) has been used in a variety of biological applications due to its high sensitivity and specificity. Here, we report a SERS-based biosensing approach for quantitative detection of biomolecules. A SERS substrate bearing gold-decorated silicon nanopillars......-to-spot variation in conventional SERS quantification. Furthermore, we have developed an analytical model capable of predicting experimental intensity distributions on the substrates for reliable quantification of biomolecules. Lastly, we have calculated the minimum needed area of Raman mapping for efficient...

Quantitative Analysis of Micro-Structure in Meat Emulsions from Grating-Based Multimodal X-Ray Tomography

DEFF Research Database (Denmark)

Einarsdottir, Hildur; Nielsen, Mikkel Schou; Miklos, Rikke

2013-01-01

Using novel X-ray techniques, based on grating-interferometry, new imaging modalities can be obtained simultaneously with absorption computed tomography (CT). These modalities, called phase contrast and dark field imaging, measure the electron density and the diffusion length of the sample....... Enhanced contrast capabilities of this X-ray technique makes studies on materials with similar attenuation properties possible. In this paper the focus is set on processing grating-based X-ray tomograms of meat emulsions to quantitatively measure micro-structural changes due to heat treatment. The emulsion...... samples were imaged both in a raw and cooked state. Additionally, different fat types were used in the emulsions in order to compare micro-structural differences when either pork fat or sunflower oil was used. From the reconstructed tomograms the different ingredients in the emulsions were segmented using...

Mapping Protein-Protein Interactions by Quantitative Proteomics

DEFF Research Database (Denmark)

Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

2010-01-01

spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.......Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...

Quantitative workflow based on NN for weighting criteria in landfill suitability mapping

Science.gov (United States)

Abujayyab, Sohaib K. M.; Ahamad, Mohd Sanusi S.; Yahya, Ahmad Shukri; Ahmad, Siti Zubaidah; Alkhasawneh, Mutasem Sh.; Aziz, Hamidi Abdul

2017-10-01

Our study aims to introduce a new quantitative workflow that integrates neural networks (NNs) and multi criteria decision analysis (MCDA). Existing MCDA workflows reveal a number of drawbacks, because of the reliance on human knowledge in the weighting stage. Thus, new workflow presented to form suitability maps at the regional scale for solid waste planning based on NNs. A feed-forward neural network employed in the workflow. A total of 34 criteria were pre-processed to establish the input dataset for NN modelling. The final learned network used to acquire the weights of the criteria. Accuracies of 95.2% and 93.2% achieved for the training dataset and testing dataset, respectively. The workflow was found to be capable of reducing human interference to generate highly reliable maps. The proposed workflow reveals the applicability of NN in generating landfill suitability maps and the feasibility of integrating them with existing MCDA workflows.

Compositional and Quantitative Model Checking

DEFF Research Database (Denmark)

Larsen, Kim Guldstrand

2010-01-01

This paper gives a survey of a composition model checking methodology and its succesfull instantiation to the model checking of networks of finite-state, timed, hybrid and probabilistic systems with respect; to suitable quantitative versions of the modal mu-calculus [Koz82]. The method is based...

Evaluating a Dutch cardiology primary care plus intervention on the Triple Aim outcomes: study design of a practice-based quantitative and qualitative research.

Science.gov (United States)

Quanjel, Tessa C C; Spreeuwenberg, Marieke D; Struijs, Jeroen N; Baan, Caroline A; Ruwaard, Dirk

2017-09-06

In an attempt to deal with the pressures on the health-care system and to guarantee sustainability, changes are needed. This study focuses on a cardiology primary care plus intervention. Primary care plus (PC+) is a new health-care delivery model focused on substitution of specialist care in the hospital setting with specialist care in the primary care setting. The intervention consists of a cardiology PC+ centre in which cardiologists, supported by other health-care professionals, provide consultations in a primary care setting. The PC+ centre aims to improve the health of the population and quality of care as experienced by patients, and reduce the number of referrals to hospital-based outpatient specialist care in order to reduce health-care costs. These aims reflect the Triple Aim principle. Hence, the objectives of the study are to evaluate the cardiology PC+ centre in terms of the Triple Aim outcomes and to evaluate the process of the introduction of PC+. The study is a practice-based, quantitative study with a longitudinal observational design, and an additional qualitative study to supplement, interpret and improve the quantitative study. The study population of the quantitative part will consist of adult patients (≥18 years) with non-acute and low-complexity cardiology-related health complaints, who will be referred to the cardiology PC+ centre (intervention group) or hospital-based outpatient cardiology care (control group). All eligible patients will be asked to complete questionnaires at three different time points consisting of questions about their demographics, health status and experience of care. Additionally, quantitative data will be collected about health-care utilization and related health-care costs at the PC+ centre and the hospital. The qualitative part, consisting of semi-structured interviews, focus groups, and observations, is designed to evaluate the process as well as to amplify, clarify and explain quantitative results. This study

Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

DEFF Research Database (Denmark)

Ansari-Mahyari, S; Berg, P; Lund, M S

2009-01-01

disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across...... the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However...

The Comparison of Distributed P2P Trust Models Based on Quantitative Parameters in the File Downloading Scenarios

Directory of Open Access Journals (Sweden)

Jingpei Wang

2016-01-01

Full Text Available Varied P2P trust models have been proposed recently; it is necessary to develop an effective method to evaluate these trust models to resolve the commonalities (guiding the newly generated trust models in theory and individuality (assisting a decision maker in choosing an optimal trust model to implement in specific context issues. A new method for analyzing and comparing P2P trust models based on hierarchical parameters quantization in the file downloading scenarios is proposed in this paper. Several parameters are extracted from the functional attributes and quality feature of trust relationship, as well as requirements from the specific network context and the evaluators. Several distributed P2P trust models are analyzed quantitatively with extracted parameters modeled into a hierarchical model. The fuzzy inferring method is applied to the hierarchical modeling of parameters to fuse the evaluated values of the candidate trust models, and then the relative optimal one is selected based on the sorted overall quantitative values. Finally, analyses and simulation are performed. The results show that the proposed method is reasonable and effective compared with the previous algorithms.

A new trend to determine biochemical parameters by quantitative FRET assays.

Science.gov (United States)

Liao, Jia-yu; Song, Yang; Liu, Yan

2015-12-01

Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research because it can determine molecule or particle interactions within a range of 1-10 nm. The sensitivity and efficiency of FRET strongly depend on the distance between the FRET donor and acceptor. Historically, FRET assays have been used to quantitatively deduce molecular distances. However, another major potential application of the FRET assay has not been fully exploited, that is, the use of FRET signals to quantitatively describe molecular interactive events. In this review, we discuss the use of quantitative FRET assays for the determination of biochemical parameters, such as the protein interaction dissociation constant (K(d)), enzymatic velocity (k(cat)) and K(m). We also describe fluorescent microscopy-based quantitative FRET assays for protein interaction affinity determination in cells as well as fluorimeter-based quantitative FRET assays for protein interaction and enzymatic parameter determination in solution.

Prognostic value of pretreatment volume-based quantitative 18F-FDG PET/CT parameters in patients with malignant pleural mesothelioma

International Nuclear Information System (INIS)

Kitajima, Kazuhiro; Doi, Hiroshi; Kuribayashi, Kozo; Hashimoto, Masaki; Tsuchitani, Tatsuya; Tanooka, Masao; Fukushima, Kazuhito; Nakano, Takashi; Hasegawa, Seiki; Hirota, Shozo

2017-01-01

Purpose: To investigate the relationships between pretreatment volume-based quantitative 18 F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) parameters and overall survival (OS) in patients with malignant pleural mesothelioma (MPM). Materials and methods: We retrospectively reviewed data from 201 MPM patients, of whom 38 underwent surgical resection, and calculated the maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), and total lesion glycolysis (TLG), including primary tumors and nodal or distant metastatic lesions, on pretreatment 18 F-FDG PET/CT. Relationships between clinicopathological factors (age, sex, performance status, European Organization for Research and Treatment of Cancer [EORTC] score, histological subtype, TNM stage, and treatment strategy), volume-based quantitative PET/CT parameters, and OS were evaluated using a Cox proportional hazards model and log-rank test. Results: The median follow-up was 15 months (range, 1–96 months; median, 17 months). In a univariate analysis of all patients, older age (p < 0.05), high EORTC score (p < 0.001), non-epithelioid histological subtype (p < 0.001), high T stage (p < 0.001), positive N/M status (p < 0.05, p < 0.001), advanced TNM stage (p < 0.001), non-surgical treatment (p < 0.001), and high SUVmax (p < 0.001), MTV (p < 0.001), or TLG (p < 0.001) were associated with significantly shorter OS. A multivariate analysis confirmed non-epithelioid subtype (hazard ratio [HR]: 1.69, 95% confidence interval [CI]: 1.14–2.48; p < 0.05), non-surgical treatment (HR: 0.58, 95% CI: 0.34–0.95; p < 0.05), and high TLG (HR: 1.97, 95% CI: 1.14–3.44; p < 0.05) as independent negative predictors. Conclusions: Pretreatment volume-based quantitative 18 F-FDG PET/CT parameters, especially TLG, could serve as potential surrogate markers for MPM prognosis.

An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error

DEFF Research Database (Denmark)

Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A

2012-01-01

To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites....

Typing of unknown microorganisms based on quantitative analysis of fatty acids by mass spectrometry and hierarchical clustering

Energy Technology Data Exchange (ETDEWEB)

Li Tingting; Dai Ling; Li Lun; Hu Xuejiao; Dong Linjie; Li Jianjian; Salim, Sule Khalfan; Fu Jieying [Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079 (China); Zhong Hongying, E-mail: hyzhong@mail.ccnu.edu.cn [Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079 (China)

2011-01-17

Rapid identification of unknown microorganisms of clinical and agricultural importance is not only critical for accurate diagnosis of infections but also essential for appropriate and prompt treatment. We describe here a rapid method for microorganisms typing based on quantitative analysis of fatty acids by iFAT approach (Isotope-coded Fatty Acid Transmethylation). In this work, lyophilized cell lysates were directly mixed with 0.5 M NaOH solution in d3-methanol and n-hexane. After 1 min of ultrasonication, the top n-hexane layer was combined with a mixture of standard d0-methanol derived fatty acid methylesters with known concentration. Measurement of intensity ratios of d3/d0 labeled fragment ion and molecular ion pairs at the corresponding target fatty acids provides a quantitative basis for hierarchical clustering. In the resultant dendrogram, the Euclidean distance between unknown species and known species quantitatively reveals their differences or shared similarities in fatty acid related pathways. It is of particular interest to apply this method for typing fungal species because fungi has distinguished lipid biosynthetic pathways that have been targeted for lots of drugs or fungicides compared with bacteria and animals. The proposed method has no dependence on the availability of genome or proteome databases. Therefore, it is can be applicable for a broad range of unknown microorganisms or mutant species.

Quality control for quantitative PCR based on amplification compatibility test

Czech Academy of Sciences Publication Activity Database

Tichopád, Aleš; Bar, T.; Pecen, Ladislav; Kitchen, R.R.; Kubista, Mikael; Pfaffl, M.W.

2010-01-01

Roč. 50, č. 4 (2010), s. 308-312 ISSN 1046-2023 R&D Projects: GA AV ČR IAA500520809; GA AV ČR IAA500970904 Institutional research plan: CEZ:AV0Z50520701 Keywords : Quantitative PCR * Quality control * Amplification efficiency Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.527, year: 2010

Left atrial appendage segmentation and quantitative assisted diagnosis of atrial fibrillation based on fusion of temporal-spatial information.

Science.gov (United States)

Jin, Cheng; Feng, Jianjiang; Wang, Lei; Yu, Heng; Liu, Jiang; Lu, Jiwen; Zhou, Jie

2018-05-01

In this paper, we present an approach for left atrial appendage (LAA) multi-phase fast segmentation and quantitative assisted diagnosis of atrial fibrillation (AF) based on 4D-CT data. We take full advantage of the temporal dimension information to segment the living, flailed LAA based on a parametric max-flow method and graph-cut approach to build 3-D model of each phase. To assist the diagnosis of AF, we calculate the volumes of 3-D models, and then generate a "volume-phase" curve to calculate the important dynamic metrics: ejection fraction, filling flux, and emptying flux of the LAA's blood by volume. This approach demonstrates more precise results than the conventional approaches that calculate metrics by area, and allows for the quick analysis of LAA-volume pattern changes of in a cardiac cycle. It may also provide insight into the individual differences in the lesions of the LAA. Furthermore, we apply support vector machines (SVMs) to achieve a quantitative auto-diagnosis of the AF by exploiting seven features from volume change ratios of the LAA, and perform multivariate logistic regression analysis for the risk of LAA thrombosis. The 100 cases utilized in this research were taken from the Philips 256-iCT. The experimental results demonstrate that our approach can construct the 3-D LAA geometries robustly compared to manual annotations, and reasonably infer that the LAA undergoes filling, emptying and re-filling, re-emptying in a cardiac cycle. This research provides a potential for exploring various physiological functions of the LAA and quantitatively estimating the risk of stroke in patients with AF. Copyright © 2018 Elsevier Ltd. All rights reserved.

Proteus mirabilis biofilm - qualitative and quantitative colorimetric methods-based evaluation.

Science.gov (United States)

Kwiecinska-Piróg, Joanna; Bogiel, Tomasz; Skowron, Krzysztof; Wieckowska, Ewa; Gospodarek, Eugenia

2014-01-01

Proteus mirabilis strains ability to form biofilm is a current topic of a number of research worldwide. In this study the biofilm formation of P. mirabilis strains derived from urine of the catheterized and non-catheterized patients has been investigated. A total number of 39 P. mirabilis strains isolated from the urine samples of the patients of dr Antoni Jurasz University Hospital No. 1 in Bydgoszcz clinics between 2011 and 2012 was used. Biofilm formation was evaluated using two independent quantitative and qualitative methods with TTC (2,3,5-triphenyl-tetrazolium chloride) and CV (crystal violet) application. The obtained results confirmed biofilm formation by all the examined strains, except quantitative method with TTC, in which 7.7% of the strains did not have this ability. It was shown that P. mirabilis rods have the ability to form biofilm on the surfaces of both biomaterials applied, polystyrene and polyvinyl chloride (Nelaton catheters). The differences in ability to form biofilm observed between P. mirabilis strains derived from the urine of the catheterized and non-catheterized patients were not statistically significant.

Proteus mirabilis biofilm - Qualitative and quantitative colorimetric methods-based evaluation

Directory of Open Access Journals (Sweden)

Joanna Kwiecinska-Piróg

2014-12-01

Full Text Available Proteus mirabilis strains ability to form biofilm is a current topic of a number of research worldwide. In this study the biofilm formation of P. mirabilis strains derived from urine of the catheterized and non-catheterized patients has been investigated. A total number of 39 P. mirabilis strains isolated from the urine samples of the patients of dr Antoni Jurasz University Hospital No. 1 in Bydgoszcz clinics between 2011 and 2012 was used. Biofilm formation was evaluated using two independent quantitative and qualitative methods with TTC (2,3,5-triphenyl-tetrazolium chloride and CV (crystal violet application. The obtained results confirmed biofilm formation by all the examined strains, except quantitative method with TTC, in which 7.7% of the strains did not have this ability. It was shown that P. mirabilis rods have the ability to form biofilm on the surfaces of both biomaterials applied, polystyrene and polyvinyl chloride (Nelaton catheters. The differences in ability to form biofilm observed between P. mirabilis strains derived from the urine of the catheterized and non-catheterized patients were not statistically significant.

Potential of phytase-mediated iron release from cereal-based foods: a quantitative view

DEFF Research Database (Denmark)

Nielsen, Anne Veller Friis; Tetens, Inge; Meyer, Anne S.

2013-01-01

The major part of iron present in plant foods such as cereals is largely unavailable for direct absorption in humans due to complexation with the negatively charged phosphate groups of phytate (myo-inositol (1,2,3,4,5,6)-hexakisphosphate). Human biology has not evolved an efficient mechanism...... to naturally release iron from iron phytate complexes. This narrative review will evaluate the quantitative significance of phytase-catalysed iron release from cereal foods. In vivo studies have shown how addition of microbially derived phytases to cereal-based foods has produced increased iron absorption via...... phytate complexes, and (3) the extent of phytate dephosphorylation required for iron release from inositol phosphates is warranted. Phytase-mediated iron release can improve iron absorption from plant foods. There is a need for development of innovative strategies to obtain better effects....

Quantitative metabolomics based on gas chromatography mass spectrometry: Status and perspectives

NARCIS (Netherlands)

Koek, M.M.; Jellema, R.H.; Greef, J. van der; Tas, A.C.; Hankemeier, T.

2011-01-01

Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues (the metabolome). By analyzing differences between metabolomes using biostatistics (multivariate data analysis; pattern recognition), metabolites

Noninvasive and Quantitative Assessment of In Vivo Fetomaternal Interface Angiogenesis Using RGD-Based Fluorescence

Directory of Open Access Journals (Sweden)

M. Keramidas

2014-01-01

Full Text Available Angiogenesis is a key process for proper placental development and for the success of pregnancy. Although numerous in vitro methods have been developed for the assessment of this process, relatively few reliable in vivo methods are available to evaluate this activity throughout gestation. Here we report an in vivo technique that specifically measures placental neovascularization. The technique is based on the measurement of a fluorescent alpha v beta 3 (αvβ3 integrin-targeting molecule called Angiolone-Alexa-Fluor 700. The αvβ3 integrin is highly expressed by endothelial cells during the neovascularization and by trophoblast cells during their invasion of the maternal decidua. Angiolone was injected to gravid mice at 6.5 and 11.5 days post coitus (dpc. The fluorescence was analyzed one day later at 7.5 and 12.5 dpc, respectively. We demonstrated that (i Angiolone targets αvβ3 protein in the placenta with a strong specificity, (ii this technique is quantitative as the measurement was correlated to the increase of the placental size observed with increasing gestational age, and (iii information on the outcome is possible, as abnormal placentation could be detected early on during gestation. In conclusion, we report the validation of a new noninvasive and quantitative method to assess the placental angiogenic activity, in vivo.

Levels of reconstruction as complementarity in mixed methods research: a social theory-based conceptual framework for integrating qualitative and quantitative research.

Science.gov (United States)

Carroll, Linda J; Rothe, J Peter

2010-09-01

Like other areas of health research, there has been increasing use of qualitative methods to study public health problems such as injuries and injury prevention. Likewise, the integration of qualitative and quantitative research (mixed-methods) is beginning to assume a more prominent role in public health studies. Likewise, using mixed-methods has great potential for gaining a broad and comprehensive understanding of injuries and their prevention. However, qualitative and quantitative research methods are based on two inherently different paradigms, and their integration requires a conceptual framework that permits the unity of these two methods. We present a theory-driven framework for viewing qualitative and quantitative research, which enables us to integrate them in a conceptually sound and useful manner. This framework has its foundation within the philosophical concept of complementarity, as espoused in the physical and social sciences, and draws on Bergson's metaphysical work on the 'ways of knowing'. Through understanding how data are constructed and reconstructed, and the different levels of meaning that can be ascribed to qualitative and quantitative findings, we can use a mixed-methods approach to gain a conceptually sound, holistic knowledge about injury phenomena that will enhance our development of relevant and successful interventions.

Validation of a high-throughput fermentation system based on online monitoring of biomass and fluorescence in continuously shaken microtiter plates

Directory of Open Access Journals (Sweden)

Kensy Frank

2009-06-01

Full Text Available Abstract Background An advanced version of a recently reported high-throughput fermentation system with online measurement, called BioLector, and its validation is presented. The technology combines high-throughput screening and high-information content by applying online monitoring of scattered light and fluorescence intensities in continuously shaken microtiter plates. Various examples in calibration of the optical measurements, clone and media screening and promoter characterization are given. Results Bacterial and yeast biomass concentrations of up to 50 g/L cell dry weight could be linearly correlated to scattered light intensities. In media screening, the BioLector could clearly demonstrate its potential for detecting different biomass and product yields and deducing specific growth rates for quantitatively evaluating media and nutrients. Growth inhibition due to inappropriate buffer conditions could be detected by reduced growth rates and a temporary increase in NADH fluorescence. GFP served very well as reporter protein for investigating the promoter regulation under different carbon sources in yeast strains. A clone screening of 90 different GFP-expressing Hansenula polymorpha clones depicted the broad distribution of growth behavior and an even stronger distribution in GFP expression. The importance of mass transfer conditions could be demonstrated by varying filling volumes of an E. coli culture in 96 well MTP. The different filling volumes cause a deviation in the culture growth and acidification both monitored via scattered light intensities and the fluorescence of a pH indicator, respectively. Conclusion The BioLector technology is a very useful tool to perform quantitative microfermentations under engineered reaction conditions. With this technique, specific yields and rates can be directly deduced from online biomass and product concentrations, which is superior to existing technologies such as microplate readers or optode-based

The Quantitative Preparation of Future Geoscience Graduate Students

Science.gov (United States)

Manduca, C. A.; Hancock, G. S.

2006-12-01

. Calculus, calculus-based physics, chemistry, statistics, programming and linear algebra were viewed as important course preparation for a successful graduate experience. A set of recommendations for departments and for new community resources includes ideas for infusing quantitative reasoning throughout the undergraduate experience and mechanisms for learning from successful experiments in both geoscience and mathematics. A full list of participants, summaries of the meeting discussion and recommendations are available at http://serc.carleton.edu/quantskills/winter06/index.html. These documents, crafted by a small but diverse group can serve as a starting point for broader community discussion of the quantitative preparation of future geoscience graduate students.

Automated Quantitative Rare Earth Elements Mineralogy by Scanning Electron Microscopy

Science.gov (United States)

Sindern, Sven; Meyer, F. Michael

2016-09-01

Increasing industrial demand of rare earth elements (REEs) stems from the central role they play for advanced technologies and the accelerating move away from carbon-based fuels. However, REE production is often hampered by the chemical, mineralogical as well as textural complexity of the ores with a need for better understanding of their salient properties. This is not only essential for in-depth genetic interpretations but also for a robust assessment of ore quality and economic viability. The design of energy and cost-efficient processing of REE ores depends heavily on information about REE element deportment that can be made available employing automated quantitative process mineralogy. Quantitative mineralogy assigns numeric values to compositional and textural properties of mineral matter. Scanning electron microscopy (SEM) combined with a suitable software package for acquisition of backscatter electron and X-ray signals, phase assignment and image analysis is one of the most efficient tools for quantitative mineralogy. The four different SEM-based automated quantitative mineralogy systems, i.e. FEI QEMSCAN and MLA, Tescan TIMA and Zeiss Mineralogic Mining, which are commercially available, are briefly characterized. Using examples of quantitative REE mineralogy, this chapter illustrates capabilities and limitations of automated SEM-based systems. Chemical variability of REE minerals and analytical uncertainty can reduce performance of phase assignment. This is shown for the REE phases parisite and synchysite. In another example from a monazite REE deposit, the quantitative mineralogical parameters surface roughness and mineral association derived from image analysis are applied for automated discrimination of apatite formed in a breakdown reaction of monazite and apatite formed by metamorphism prior to monazite breakdown. SEM-based automated mineralogy fulfils all requirements for characterization of complex unconventional REE ores that will become

Quantitative (real-time) PCR

International Nuclear Information System (INIS)

Denman, S.E.; McSweeney, C.S.

2005-01-01

Many nucleic acid-based probe and PCR assays have been developed for the detection tracking of specific microbes within the rumen ecosystem. Conventional PCR assays detect PCR products at the end stage of each PCR reaction, where exponential amplification is no longer being achieved. This approach can result in different end product (amplicon) quantities being generated. In contrast, using quantitative, or real-time PCR, quantification of the amplicon is performed not at the end of the reaction, but rather during exponential amplification, where theoretically each cycle will result in a doubling of product being created. For real-time PCR, the cycle at which fluorescence is deemed to be detectable above the background during the exponential phase is termed the cycle threshold (Ct). The Ct values obtained are then used for quantitation, which will be discussed later

Quantitative materials analysis of micro devices using absorption-based thickness measurements

International Nuclear Information System (INIS)

Sim, L M; Wog, B S; Spowage, A C

2006-01-01

Preliminary work in designing an X-ray inspection machine with the capability of providing quantitative thickness analysis based on absorption measurements has been demonstrated. This study attempts to use the gray levels data to investigate the nature and thickness of occluded features and materials within devices. The investigation focused on metallic materials essential to semiconductor and MEMS technologies such as tin, aluminium, copper, silver, iron and zinc. The materials were arranged to simulate different feature thicknesses and sample geometries. The X-ray parameters were varied in-order to modify the X-ray energy spectrum with the aim of optimising the measurement conditions for each sample. The capability of the method to resolve differences in thicknesses was found to be highly dependent on the material. The thickness resolution with aluminium was the poorest due to its low radiographic density. The thickness resolutions achievable for silver and tin were significantly better and of the order of 0.015 mm and 0.025 mm respectively. From the linear relationship between the X-ray attenuation and sample thickness established, the energy dependent linear attenuation coefficient for each material was determined for a series of specific energy spectra. A decrease in the linear attenuation coefficient was observed as the applied voltage and thickness of the material increased. The results provide a platform for the development of a novel absorption-based thickness measurement system that can be optimised for a range of industrial applications

Quantitative analysis of chromium concentration in nickel based alloys by laser induced breakdown spectroscopy at atmospheric pressure using a nanosecond ultraviolet Nd:YAG laser

International Nuclear Information System (INIS)

Gupta, G.P.; Suri, B.M.; Verma, A.; Sundararaman, M.; Unnikrishnan, V.K.; Alti, K.; Kartha, V.B.; Santhosh, C.

2010-01-01

Laser-induced breakdown spectroscopy (LIBS) has been well recognized as a simple, fast and direct analytical technique of elemental analysis of multi-element materials by a number of research groups all over the world. It is based on the focusing of a high-power pulsed laser beam with a power density > 100 MW/cm 2 onto a sample surface followed by optical emission spectroscopy of the plasma produced over the surface. In the present work, they have carried out the quantitative analysis of chromium in nickel-based-alloys using laser-induced breakdown spectroscopy (LIBS) in air at atmospheric pressure. In the present work the quantitative analysis of chromium in nickel-based-alloys using laser-induced break-down spectroscopy (LIBS) in air at atmospheric pressure has been carried out

[Teaching quantitative methods in public health: the EHESP experience].

Science.gov (United States)

Grimaud, Olivier; Astagneau, Pascal; Desvarieux, Moïse; Chambaud, Laurent

2014-01-01

Many scientific disciplines, including epidemiology and biostatistics, are used in the field of public health. These quantitative sciences are fundamental tools necessary for the practice of future professionals. What then should be the minimum quantitative sciences training, common to all future public health professionals? By comparing the teaching models developed in Columbia University and those in the National School of Public Health in France, the authors recognize the need to adapt teaching to the specific competencies required for each profession. They insist that all public health professionals, whatever their future career, should be familiar with quantitative methods in order to ensure that decision-making is based on a reflective and critical use of quantitative analysis.

Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

Directory of Open Access Journals (Sweden)

Thomas Jensen

2016-01-01

Full Text Available Background: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including staining may benefit. Methods: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm are presented. Results: It is shown that the autofluorescence intensity of unstained microsections at two different wavelengths is a suitable starting point for automated digital analysis of myocytes, fibrous tissue, lipofuscin, and the extracellular compartment. The output of the method is absolute quantitation along with accurate outlines of above-mentioned components. The digital quantitations are verified by comparison to point grid quantitations performed on the microsections after Van Gieson staining. Conclusion: The presented method is amply described as a prestain multicomponent quantitation and outlining tool for histological sections of cardiac tissue. The main perspective is the opportunity for combination with digital analysis of stained microsections, for which the method may provide an accurate digital framework.

Quantitative Structure-Activity Relationship Analysis of the ...

African Journals Online (AJOL)

Erah

Quantitative Structure-Activity Relationship Analysis of the Anticonvulsant ... Two types of molecular descriptors, including the 2D autocorrelation ..... It is based on the simulation of natural .... clustering anticonvulsant, antidepressant, and.

Qualitative vs. quantitative atopic dermatitis criteria

DEFF Research Database (Denmark)

Andersen, R M; Thyssen, J P; Maibach, H I

2016-01-01

This review summarizes historical aspects, clinical expression and pathophysiology leading to coining of the terms atopy and atopic dermatitis, current diagnostic criteria and further explore the possibility of developing quantitative diagnostic criteria of atopic dermatitis (AD) based on the imp...

Quantitative analysis of psychological personality for NPP operators

International Nuclear Information System (INIS)

Gao Jia; Huang Xiangrui

1998-01-01

The author introduces the relevant personality quantitative psychological research work carried out by 'Prognoz' Laboratory and Taiwan, and presents the primary results of the research for Chinese Nuclear Power Plant (NPP) operator's psychological personality assessment, which based on the survey of MMPI, and presents the main contents for the personality quantitative psychological research in NPP of China. And emphasizes the need to carry out psychological selection and training in nuclear industry

Prognostic Value of Quantitative Stress Perfusion Cardiac Magnetic Resonance.

Science.gov (United States)

Sammut, Eva C; Villa, Adriana D M; Di Giovine, Gabriella; Dancy, Luke; Bosio, Filippo; Gibbs, Thomas; Jeyabraba, Swarna; Schwenke, Susanne; Williams, Steven E; Marber, Michael; Alfakih, Khaled; Ismail, Tevfik F; Razavi, Reza; Chiribiri, Amedeo

2018-05-01

This study sought to evaluate the prognostic usefulness of visual and quantitative perfusion cardiac magnetic resonance (CMR) ischemic burden in an unselected group of patients and to assess the validity of consensus-based ischemic burden thresholds extrapolated from nuclear studies. There are limited data on the prognostic value of assessing myocardial ischemic burden by CMR, and there are none using quantitative perfusion analysis. Patients with suspected coronary artery disease referred for adenosine-stress perfusion CMR were included (n = 395; 70% male; age 58 ± 13 years). The primary endpoint was a composite of cardiovascular death, nonfatal myocardial infarction, aborted sudden death, and revascularization after 90 days. Perfusion scans were assessed visually and with quantitative analysis. Cross-validated Cox regression analysis and net reclassification improvement were used to assess the incremental prognostic value of visual or quantitative perfusion analysis over a baseline clinical model, initially as continuous covariates, then using accepted thresholds of ≥2 segments or ≥10% myocardium. After a median 460 days (interquartile range: 190 to 869 days) follow-up, 52 patients reached the primary endpoint. At 2 years, the addition of ischemic burden was found to increase prognostic value over a baseline model of age, sex, and late gadolinium enhancement (baseline model area under the curve [AUC]: 0.75; visual AUC: 0.84; quantitative AUC: 0.85). Dichotomized quantitative ischemic burden performed better than visual assessment (net reclassification improvement 0.043 vs. 0.003 against baseline model). This study was the first to address the prognostic benefit of quantitative analysis of perfusion CMR and to support the use of consensus-based ischemic burden thresholds by perfusion CMR for prognostic evaluation of patients with suspected coronary artery disease. Quantitative analysis provided incremental prognostic value to visual assessment and

Quantitative traits and diversification.

Science.gov (United States)

FitzJohn, Richard G

2010-12-01

Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.

Improving data quality and preserving HCD-generated reporter ions with EThcD for isobaric tag-based quantitative proteomics and proteome-wide PTM studies

International Nuclear Information System (INIS)

Yu, Qing; Shi, Xudong; Feng, Yu; Kent, K. Craig; Li, Lingjun

2017-01-01

Mass spectrometry (MS)-based isobaric labeling has undergone rapid development in recent years due to its capability for high throughput quantitation. Apart from its originally designed use with collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD), isobaric tagging technique could also work with electron-transfer dissociation (ETD), which provides complementarity to CID and is preferred in sequencing peptides with post-translational modifications (PTMs). However, ETD suffers from long reaction time, reduced duty cycle and bias against peptides with lower charge states. In addition, common fragmentation mechanism in ETD results in altered reporter ion production, decreased multiplexing capability, and even loss of quantitation capability for some of the isobaric tags, including custom-designed dimethyl leucine (DiLeu) tags. Here, we demonstrate a novel electron-transfer/higher-energy collision dissociation (EThcD) approach that preserves original reporter ion channels, mitigates bias against lower charge states, improves sensitivity, and significantly improves data quality for quantitative proteomics and proteome-wide PTM studies. Systematic optimization was performed to achieve a balance between data quality and sensitivity. We provide direct comparison of EThcD with ETD and HCD for DiLeu- and TMT-labeled HEK cell lysate and IMAC enriched phosphopeptides. Results demonstrate improved data quality and phosphorylation localization accuracy while preserving sufficient reporter ion production. Biological studies were performed to investigate phosphorylation changes in a mouse vascular smooth muscle cell line treated with four different conditions. Overall, EThcD exhibits superior performance compared to conventional ETD and offers distinct advantages compared to HCD in isobaric labeling based quantitative proteomics and quantitative PTM studies. - Highlights: • EThcD was optimized for isobaric tag-labeled peptides for quantitative

Improving data quality and preserving HCD-generated reporter ions with EThcD for isobaric tag-based quantitative proteomics and proteome-wide PTM studies

Energy Technology Data Exchange (ETDEWEB)

Yu, Qing [School of Pharmacy, University of Wisconsin, Madison, WI 53705 (United States); Shi, Xudong [Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705 (United States); Feng, Yu [School of Pharmacy, University of Wisconsin, Madison, WI 53705 (United States); Kent, K. Craig [Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705 (United States); Li, Lingjun, E-mail: lingjun.li@wisc.edu [School of Pharmacy, University of Wisconsin, Madison, WI 53705 (United States); Department of Chemistry, University of Wisconsin, Madison, WI 53706 (United States)

2017-05-22

Mass spectrometry (MS)-based isobaric labeling has undergone rapid development in recent years due to its capability for high throughput quantitation. Apart from its originally designed use with collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD), isobaric tagging technique could also work with electron-transfer dissociation (ETD), which provides complementarity to CID and is preferred in sequencing peptides with post-translational modifications (PTMs). However, ETD suffers from long reaction time, reduced duty cycle and bias against peptides with lower charge states. In addition, common fragmentation mechanism in ETD results in altered reporter ion production, decreased multiplexing capability, and even loss of quantitation capability for some of the isobaric tags, including custom-designed dimethyl leucine (DiLeu) tags. Here, we demonstrate a novel electron-transfer/higher-energy collision dissociation (EThcD) approach that preserves original reporter ion channels, mitigates bias against lower charge states, improves sensitivity, and significantly improves data quality for quantitative proteomics and proteome-wide PTM studies. Systematic optimization was performed to achieve a balance between data quality and sensitivity. We provide direct comparison of EThcD with ETD and HCD for DiLeu- and TMT-labeled HEK cell lysate and IMAC enriched phosphopeptides. Results demonstrate improved data quality and phosphorylation localization accuracy while preserving sufficient reporter ion production. Biological studies were performed to investigate phosphorylation changes in a mouse vascular smooth muscle cell line treated with four different conditions. Overall, EThcD exhibits superior performance compared to conventional ETD and offers distinct advantages compared to HCD in isobaric labeling based quantitative proteomics and quantitative PTM studies. - Highlights: • EThcD was optimized for isobaric tag-labeled peptides for quantitative

Stable isotope dimethyl labelling for quantitative proteomics and beyond

Science.gov (United States)

Hsu, Jue-Liang; Chen, Shu-Hui

2016-01-01

Stable-isotope reductive dimethylation, a cost-effective, simple, robust, reliable and easy-to- multiplex labelling method, is widely applied to quantitative proteomics using liquid chromatography-mass spectrometry. This review focuses on biological applications of stable-isotope dimethyl labelling for a large-scale comparative analysis of protein expression and post-translational modifications based on its unique properties of the labelling chemistry. Some other applications of the labelling method for sample preparation and mass spectrometry-based protein identification and characterization are also summarized. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644970

Dissociative conceptual and quantitative problem solving outcomes across interactive engagement and traditional format introductory physics

Directory of Open Access Journals (Sweden)

Mark A. McDaniel

2016-11-01

Full Text Available The existing literature indicates that interactive-engagement (IE based general physics classes improve conceptual learning relative to more traditional lecture-oriented classrooms. Very little research, however, has examined quantitative problem-solving outcomes from IE based relative to traditional lecture-based physics classes. The present study included both pre- and post-course conceptual-learning assessments and a new quantitative physics problem-solving assessment that included three representative conservation of energy problems from a first-semester calculus-based college physics course. Scores for problem translation, plan coherence, solution execution, and evaluation of solution plausibility were extracted for each problem. Over 450 students in three IE-based sections and two traditional lecture sections taught at the same university during the same semester participated. As expected, the IE-based course produced more robust gains on a Force Concept Inventory than did the lecture course. By contrast, when the full sample was considered, gains in quantitative problem solving were significantly greater for lecture than IE-based physics; when students were matched on pre-test scores, there was still no advantage for IE-based physics on gains in quantitative problem solving. Further, the association between performance on the concept inventory and quantitative problem solving was minimal. These results highlight that improved conceptual understanding does not necessarily support improved quantitative physics problem solving, and that the instructional method appears to have less bearing on gains in quantitative problem solving than does the kinds of problems emphasized in the courses and homework and the overlap of these problems to those on the assessment.

Quantitation: clinical applications

International Nuclear Information System (INIS)

Britton, K.E.

1982-01-01

Single photon emission tomography may be used quantitatively if its limitations are recognized and quantitation is made in relation to some reference area on the image. Relative quantitation is discussed in outline in relation to the liver, brain and pituitary, thyroid, adrenals, and heart. (U.K.)

[Exercise Therapy in German Medical Rehabilitation - an Analysis based on Quantitative Routine Data].

Science.gov (United States)

Brüggemann, Silke; Sewöster, Daniela; Kranzmann, Angela

2018-02-01

This study describes the quantitative importance of exercise therapy in German medical rehabilitation based on 2014 routine data of the German Pension Insurance. It also shows changes in comparison with data from 2007. Data from 710012 rehabilitation discharge letters comprising 83677802 treatments from central indications in medical rehabilitation were analysed descriptively. Overall 35.4% of treatments could be classified as exercise therapy. Total and relative duration, percentage of individual treatment and kind of exercise treatment varied between indications in 2007 as well as in 2014. There were also differences between sexes, age groups and settings. During the period examined the high importance of exercise therapy in German medical rehabilitation has increased. The results point at a meaningful concept behind the composition of exercise therapy taking indications and disease related factors into account. © Georg Thieme Verlag KG Stuttgart · New York.

FPGA-based fused smart-sensor for tool-wear area quantitative estimation in CNC machine inserts.

Science.gov (United States)

Trejo-Hernandez, Miguel; Osornio-Rios, Roque Alfredo; de Jesus Romero-Troncoso, Rene; Rodriguez-Donate, Carlos; Dominguez-Gonzalez, Aurelio; Herrera-Ruiz, Gilberto

2010-01-01

Manufacturing processes are of great relevance nowadays, when there is a constant claim for better productivity with high quality at low cost. The contribution of this work is the development of a fused smart-sensor, based on FPGA to improve the online quantitative estimation of flank-wear area in CNC machine inserts from the information provided by two primary sensors: the monitoring current output of a servoamplifier, and a 3-axis accelerometer. Results from experimentation show that the fusion of both parameters makes it possible to obtain three times better accuracy when compared with the accuracy obtained from current and vibration signals, individually used.

Quantitative clinical radiobiology

International Nuclear Information System (INIS)

Bentzen, S.M.

1993-01-01

Based on a series of recent papers, a status is given of our current ability to quantify the radiobiology of human tumors and normal tissues. Progress has been made in the methods of analysis. This includes the introduction of 'direct' (maximum likelihood) analysis, incorporation of latent-time in the analyses, and statistical approaches to allow for the many factors of importance in predicting tumor-control probability of normal-tissue complications. Quantitative clinical radiobiology of normal tissues is reviewed with emphasis on fractionation sensitivity, repair kinetics, regeneration, latency, and the steepness of dose-response curves. In addition, combined modality treatment, functional endpoints, and the search for a correlation between the occurrence of different endpoints in the same individual are discussed. For tumors, quantitative analyses of fractionation sensitivity, repair kinetics, reoxygenation, and regeneration are reviewed. Other factors influencing local control are: Tumor volume, histopathologic differentiation and hemoglobin concentration. Also, the steepness of the dose-response curve for tumors is discussed. Radiobiological strategies for improving radiotherapy are discussed with emphasis on non-standard fractionation and individualization of treatment schedules. (orig.)

Genetic variability of hull-less barley accessions based on molecular and quantitative data

Directory of Open Access Journals (Sweden)

Ricardo Meneses Sayd

2015-02-01

Full Text Available The objective of this work was to characterize and quantify the genetic, molecular, and agronomic variability of hull-less barley genotypes, for the selection of parents and identification of genotypes adapted to the irrigated production system in the Brazilian Cerrado. Eighteen hull-less barley accessions were evaluated, and three covered barley accessions served as reference. The characterization was based on 157 RAPD molecular markers and ten agronomic traits. Genetic distance matrices were obtained based on molecular markers and quantitative traits. Graphic grouping and dispersion analyses were performed. Genetic, molecular, and agronomic variability was high among genotypes. Ethiopian accessions were genetically more similar, and the Brazilian ones were genetically more distant. For agronomic traits, two more consistent groupings were obtained, one with the most two-rowed materials, and the other with six-rowed materials. The more diverging materials were the two-rowed CI 13453, CN Cerrado 5, CN Cerrado 1, and CN Cerrado 2. The PI 356466, CN Cerrado 1, PI 370799, and CI 13453 genotypes show agronomic traits of interest and, as genetically different genotypes, they are indicated for crossing, in breeding programs.

Leaderless Covert Networks : A Quantitative Approach

NARCIS (Netherlands)

Husslage, B.G.M.; Lindelauf, R.; Hamers, H.J.M.

2012-01-01

Abstract: Lindelauf et al. (2009a) introduced a quantitative approach to investigate optimal structures of covert networks. This approach used an objective function which is based on the secrecy versus information trade-off these organizations face. Sageman (2008) hypothesized that covert networks

Quantitative Analysis of Variability and Uncertainty in Environmental Data and Models. Volume 1. Theory and Methodology Based Upon Bootstrap Simulation

Energy Technology Data Exchange (ETDEWEB)

Frey, H. Christopher [North Carolina State University, Raleigh, NC (United States); Rhodes, David S. [North Carolina State University, Raleigh, NC (United States)

1999-04-30

This is Volume 1 of a two-volume set of reports describing work conducted at North Carolina State University sponsored by Grant Number DE-FG05-95ER30250 by the U.S. Department of Energy. The title of the project is “Quantitative Analysis of Variability and Uncertainty in Acid Rain Assessments.” The work conducted under sponsorship of this grant pertains primarily to two main topics: (1) development of new methods for quantitative analysis of variability and uncertainty applicable to any type of model; and (2) analysis of variability and uncertainty in the performance, emissions, and cost of electric power plant combustion-based NOx control technologies. These two main topics are reported separately in Volumes 1 and 2.

Teaching Quantitative Reasoning: A Better Context for Algebra

Directory of Open Access Journals (Sweden)

Eric Gaze

2014-01-01

Full Text Available This editorial questions the preeminence of algebra in our mathematics curriculum. The GATC (Geometry, Algebra, Trigonometry, Calculus sequence abandons the fundamental middle school math topics necessary for quantitative literacy, while the standard super-abundance of algebra taught in the abstract fosters math phobia and supports a culturally acceptable stance that math is not relevant to everyday life. Although GATC is seen as a pipeline to STEM (Science, Technology, Engineering, Mathematics, it is a mistake to think that the objective of producing quantitatively literate citizens is at odds with creating more scientists and engineers. The goal must be to create a curriculum that addresses the quantitative reasoning needs of all students, providing meaningful engagement in mathematics that will simultaneously develop quantitative literacy and spark an interest in STEM fields. In my view, such a curriculum could be based on a foundation of proportional reasoning leading to higher-order quantitative reasoning via modeling (including algebraic reasoning and problem solving and statistical literacy (through the exploration and study of data.

Prognostic value of pretreatment volume-based quantitative {sup 18}F-FDG PET/CT parameters in patients with malignant pleural mesothelioma

Energy Technology Data Exchange (ETDEWEB)

Kitajima, Kazuhiro, E-mail: kitajima@med.kobe-u.ac.jp [Division of Nuclear Medicine and PET Center, Department of Radiology, Hyogo College of Medicine, Hyogo (Japan); Doi, Hiroshi, E-mail: h-doi@hyo-med.ac.jp [Department of Radiology, Hyogo College of Medicine, Hyogo (Japan); Kuribayashi, Kozo, E-mail: kuririn@hyo-med.ac.jp [Division of Respiratory Medicine, Department of Internal Medicine, Hyogo College of Medicine, Hyogo (Japan); Hashimoto, Masaki, E-mail: kogekogemasaki@gmail.com [Department of Thoracic Surgery, Hyogo College of Medicine, Hyogo (Japan); Tsuchitani, Tatsuya, E-mail: tty-823@hyo-med.ac.jp [Department of Radiological Technology, Hyogo College of Medicine College Hospital, Hyogo (Japan); Tanooka, Masao, E-mail: masao1108@gmail.com [Department of Radiological Technology, Hyogo College of Medicine College Hospital, Hyogo (Japan); Fukushima, Kazuhito, E-mail: fukuchan00106@gmail.com [Division of Nuclear Medicine and PET Center, Department of Radiology, Hyogo College of Medicine, Hyogo (Japan); Nakano, Takashi, E-mail: t-nakano@hyo-med.ac.jp [Division of Respiratory Medicine, Department of Internal Medicine, Hyogo College of Medicine, Hyogo (Japan); Hasegawa, Seiki, E-mail: hasegawa@hyo-med.ac.jp [Department of Thoracic Surgery, Hyogo College of Medicine, Hyogo (Japan); Hirota, Shozo, E-mail: hirota-s@hyo-med.ac.jp [Department of Radiology, Hyogo College of Medicine, Hyogo (Japan)

2017-01-15

Purpose: To investigate the relationships between pretreatment volume-based quantitative {sup 18}F-fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) parameters and overall survival (OS) in patients with malignant pleural mesothelioma (MPM). Materials and methods: We retrospectively reviewed data from 201 MPM patients, of whom 38 underwent surgical resection, and calculated the maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), and total lesion glycolysis (TLG), including primary tumors and nodal or distant metastatic lesions, on pretreatment {sup 18}F-FDG PET/CT. Relationships between clinicopathological factors (age, sex, performance status, European Organization for Research and Treatment of Cancer [EORTC] score, histological subtype, TNM stage, and treatment strategy), volume-based quantitative PET/CT parameters, and OS were evaluated using a Cox proportional hazards model and log-rank test. Results: The median follow-up was 15 months (range, 1–96 months; median, 17 months). In a univariate analysis of all patients, older age (p < 0.05), high EORTC score (p < 0.001), non-epithelioid histological subtype (p < 0.001), high T stage (p < 0.001), positive N/M status (p < 0.05, p < 0.001), advanced TNM stage (p < 0.001), non-surgical treatment (p < 0.001), and high SUVmax (p < 0.001), MTV (p < 0.001), or TLG (p < 0.001) were associated with significantly shorter OS. A multivariate analysis confirmed non-epithelioid subtype (hazard ratio [HR]: 1.69, 95% confidence interval [CI]: 1.14–2.48; p < 0.05), non-surgical treatment (HR: 0.58, 95% CI: 0.34–0.95; p < 0.05), and high TLG (HR: 1.97, 95% CI: 1.14–3.44; p < 0.05) as independent negative predictors. Conclusions: Pretreatment volume-based quantitative {sup 18}F-FDG PET/CT parameters, especially TLG, could serve as potential surrogate markers for MPM prognosis.

Cartilage Repair Surgery: Outcome Evaluation by Using Noninvasive Cartilage Biomarkers Based on Quantitative MRI Techniques?

Science.gov (United States)

Jungmann, Pia M.; Baum, Thomas; Bauer, Jan S.; Karampinos, Dimitrios C.; Link, Thomas M.; Li, Xiaojuan; Trattnig, Siegfried; Rummeny, Ernst J.; Woertler, Klaus; Welsch, Goetz H.

2014-01-01

Background. New quantitative magnetic resonance imaging (MRI) techniques are increasingly applied as outcome measures after cartilage repair. Objective. To review the current literature on the use of quantitative MRI biomarkers for evaluation of cartilage repair at the knee and ankle. Methods. Using PubMed literature research, studies on biochemical, quantitative MR imaging of cartilage repair were identified and reviewed. Results. Quantitative MR biomarkers detect early degeneration of articular cartilage, mainly represented by an increasing water content, collagen disruption, and proteoglycan loss. Recently, feasibility of biochemical MR imaging of cartilage repair tissue and surrounding cartilage was demonstrated. Ultrastructural properties of the tissue after different repair procedures resulted in differences in imaging characteristics. T2 mapping, T1rho mapping, delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), and diffusion weighted imaging (DWI) are applicable on most clinical 1.5 T and 3 T MR scanners. Currently, a standard of reference is difficult to define and knowledge is limited concerning correlation of clinical and MR findings. The lack of histological correlations complicates the identification of the exact tissue composition. Conclusions. A multimodal approach combining several quantitative MRI techniques in addition to morphological and clinical evaluation might be promising. Further investigations are required to demonstrate the potential for outcome evaluation after cartilage repair. PMID:24877139

Cartilage Repair Surgery: Outcome Evaluation by Using Noninvasive Cartilage Biomarkers Based on Quantitative MRI Techniques?

Directory of Open Access Journals (Sweden)

Pia M. Jungmann

2014-01-01

Full Text Available Background. New quantitative magnetic resonance imaging (MRI techniques are increasingly applied as outcome measures after cartilage repair. Objective. To review the current literature on the use of quantitative MRI biomarkers for evaluation of cartilage repair at the knee and ankle. Methods. Using PubMed literature research, studies on biochemical, quantitative MR imaging of cartilage repair were identified and reviewed. Results. Quantitative MR biomarkers detect early degeneration of articular cartilage, mainly represented by an increasing water content, collagen disruption, and proteoglycan loss. Recently, feasibility of biochemical MR imaging of cartilage repair tissue and surrounding cartilage was demonstrated. Ultrastructural properties of the tissue after different repair procedures resulted in differences in imaging characteristics. T2 mapping, T1rho mapping, delayed gadolinium-enhanced MRI of cartilage (dGEMRIC, and diffusion weighted imaging (DWI are applicable on most clinical 1.5 T and 3 T MR scanners. Currently, a standard of reference is difficult to define and knowledge is limited concerning correlation of clinical and MR findings. The lack of histological correlations complicates the identification of the exact tissue composition. Conclusions. A multimodal approach combining several quantitative MRI techniques in addition to morphological and clinical evaluation might be promising. Further investigations are required to demonstrate the potential for outcome evaluation after cartilage repair.

Newly velocity field of Sulawesi Island from GPS observation

Science.gov (United States)

Sarsito, D. A.; Susilo, Simons, W. J. F.; Abidin, H. Z.; Sapiie, B.; Triyoso, W.; Andreas, H.

2017-07-01

Sulawesi microplate Island is located at famous triple junction area of the Eurasian, India-Australian, and Philippine Sea plates. Under the influence of the northward moving Australian plate and the westward motion of the Philippine plate, the island at Eastern part of Indonesia is collide and with the Eurasian plate and Sunda Block. Those recent microplate tectonic motions can be quantitatively determine by GNSS-GPS measurement. We use combine GNSS-GPS observation types (campaign type and continuous type) from 1997 to 2015 to derive newly velocity field of the area. Several strategies are applied and tested to get the optimum result, and finally we choose regional strategy to reduce error propagation contribution from global multi baseline processing using GAMIT/GLOBK 10.5. Velocity field are analyzed in global reference frame ITRF 2008 and local reference frame by fixing with respect alternatively to Eurasian plate - Sunda block, India-Australian plate and Philippine Sea plates. Newly results show dense distribution of velocity field. This information is useful for tectonic deformation studying in geospatial era.

Experiencing teaching and learning quantitative reasoning in a project-based context

Science.gov (United States)

Muir, Tracey; Beswick, Kim; Callingham, Rosemary; Jade, Katara

2016-12-01

This paper presents the findings of a small-scale study that investigated the issues and challenges of teaching and learning about quantitative reasoning (QR) within a project-based learning (PjBL) context. Students and teachers were surveyed and interviewed about their experiences of learning and teaching QR in that context in contrast to teaching and learning mathematics in more traditional settings. The grade 9-12 student participants were characterised by a history of disengagement with mathematics and school in general, and the teacher participants were non-mathematics specialist teachers. Both students and teachers were new to the PjBL situation, which resulted in the teaching/learning relationship being a reciprocal one. The findings indicated that students and teachers viewed QR positively, particularly when compared with traditional mathematics teaching, yet tensions were identified for aspects such as implementation of curriculum and integration of relevant mathematics into projects. Both sets of participants identified situations where learning QR was particularly successful, along with concerns or difficulties about integrating QR into project work. The findings have implications for educators, who may need to examine their own approaches to mathematics teaching, particularly in terms of facilitating student engagement with the subject.

Development of a Univariate Membrane-Based Mid-Infrared Method for Protein Quantitation and Total Lipid Content Analysis of Biological Samples

Directory of Open Access Journals (Sweden)

Ivona Strug

2014-01-01

Full Text Available Biological samples present a range of complexities from homogeneous purified protein to multicomponent mixtures. Accurate qualification of such samples is paramount to downstream applications. We describe the development of an MIR spectroscopy-based analytical method offering simultaneous protein quantitation (0.25–5 mg/mL and analysis of total lipid or detergent species, as well as the identification of other biomolecules present in biological samples. The method utilizes a hydrophilic PTFE membrane engineered for presentation of aqueous samples in a dried format compatible with fast infrared analysis. Unlike classical quantification techniques, the reported method is amino acid sequence independent and thus applicable to complex samples of unknown composition. By comparison to existing platforms, this MIR-based method enables direct quantification using minimal sample volume (2 µL; it is well-suited where repeat access and limited sample size are critical parameters. Further, accurate results can be derived without specialized training or knowledge of IR spectroscopy. Overall, the simplified application and analysis system provides a more cost-effective alternative to high-throughput IR systems for research laboratories with minimal throughput demands. In summary, the MIR-based system provides a viable alternative to current protein quantitation methods; it also uniquely offers simultaneous qualification of other components, notably lipids and detergents.

A Dish-based Semi-quantitative food frequency questionnaire for assessment of dietary intakes in epidemiologic studies in Iran: Design and development

OpenAIRE

Ammar Hassanzadeh Keshteli; Ahmad Esmaillzadeh; Somayeh Rajaie; Gholamreza Askari; Christine Feinle-Bisset; Peyman Adibi

2014-01-01

Background: Earlier forms of food frequency questionnaire (FFQ) used in Iran have extensive lists of foods, traditional categories and food-based design, mostly with the interviewer-administered approach. The aim of the current paper is to describe the development of a dish-based, machine-readable, semi-quantitative food frequency questionnaire (DFQ). Methods: Within the framework of the Study on the Epidemiology of Psychological, Alimentary Health and Nutrition project, we created a nove...

Qualitative and Quantitative Integrated Modeling for Stochastic Simulation and Optimization

Directory of Open Access Journals (Sweden)

Xuefeng Yan

2013-01-01

Full Text Available The simulation and optimization of an actual physics system are usually constructed based on the stochastic models, which have both qualitative and quantitative characteristics inherently. Most modeling specifications and frameworks find it difficult to describe the qualitative model directly. In order to deal with the expert knowledge, uncertain reasoning, and other qualitative information, a qualitative and quantitative combined modeling specification was proposed based on a hierarchical model structure framework. The new modeling approach is based on a hierarchical model structure which includes the meta-meta model, the meta-model and the high-level model. A description logic system is defined for formal definition and verification of the new modeling specification. A stochastic defense simulation was developed to illustrate how to model the system and optimize the result. The result shows that the proposed method can describe the complex system more comprehensively, and the survival probability of the target is higher by introducing qualitative models into quantitative simulation.

Issues in Quantitative Analysis of Ultraviolet Imager (UV) Data: Airglow

Science.gov (United States)

Germany, G. A.; Richards, P. G.; Spann, J. F.; Brittnacher, M. J.; Parks, G. K.

1999-01-01

The GGS Ultraviolet Imager (UVI) has proven to be especially valuable in correlative substorm, auroral morphology, and extended statistical studies of the auroral regions. Such studies are based on knowledge of the location, spatial, and temporal behavior of auroral emissions. More quantitative studies, based on absolute radiometric intensities from UVI images, require a more intimate knowledge of the instrument behavior and data processing requirements and are inherently more difficult than studies based on relative knowledge of the oval location. In this study, UVI airglow observations are analyzed and compared with model predictions to illustrate issues that arise in quantitative analysis of UVI images. These issues include instrument calibration, long term changes in sensitivity, and imager flat field response as well as proper background correction. Airglow emissions are chosen for this study because of their relatively straightforward modeling requirements and because of their implications for thermospheric compositional studies. The analysis issues discussed here, however, are identical to those faced in quantitative auroral studies.

Quantitative Algebraic Reasoning

DEFF Research Database (Denmark)

Mardare, Radu Iulian; Panangaden, Prakash; Plotkin, Gordon

2016-01-01

We develop a quantitative analogue of equational reasoning which we call quantitative algebra. We define an equality relation indexed by rationals: a =ε b which we think of as saying that “a is approximately equal to b up to an error of ε”. We have 4 interesting examples where we have a quantitative...... equational theory whose free algebras correspond to well known structures. In each case we have finitary and continuous versions. The four cases are: Hausdorff metrics from quantitive semilattices; pWasserstein metrics (hence also the Kantorovich metric) from barycentric algebras and also from pointed...

Connecting qualitative observation and quantitative measurement for enhancing quantitative literacy in plant anatomy course

Science.gov (United States)

Nuraeni, E.; Rahmat, A.

2018-05-01

Forming of cognitive schemes of plant anatomy concepts is performed by processing of qualitative and quantitative data obtained from microscopic observations. To enhancing student’s quantitative literacy, strategy of plant anatomy course was modified by adding the task to analyze quantitative data produced by quantitative measurement of plant anatomy guided by material course. Participant in this study was 24 biology students and 35 biology education students. Quantitative Literacy test, complex thinking in plant anatomy test and questioner used to evaluate the course. Quantitative literacy capability data was collected by quantitative literacy test with the rubric from the Association of American Colleges and Universities, Complex thinking in plant anatomy by test according to Marzano and questioner. Quantitative literacy data are categorized according to modified Rhodes and Finley categories. The results showed that quantitative literacy of biology education students is better than biology students.

Mass Spectrometry-Based Quantitative Metabolomics Revealed a Distinct Lipid Profile in Breast Cancer Patients

Directory of Open Access Journals (Sweden)

Yun Yen

2013-04-01

Full Text Available Breast cancer accounts for the largest number of newly diagnosed cases in female cancer patients. Although mammography is a powerful screening tool, about 20% of breast cancer cases cannot be detected by this method. New diagnostic biomarkers for breast cancer are necessary. Here, we used a mass spectrometry-based quantitative metabolomics method to analyze plasma samples from 55 breast cancer patients and 25 healthy controls. A number of 30 patients and 20 age-matched healthy controls were used as a training dataset to establish a diagnostic model and to identify potential biomarkers. The remaining samples were used as a validation dataset to evaluate the predictive accuracy for the established model. Distinct separation was obtained from an orthogonal partial least squares-discriminant analysis (OPLS-DA model with good prediction accuracy. Based on this analysis, 39 differentiating metabolites were identified, including significantly lower levels of lysophosphatidylcholines and higher levels of sphingomyelins in the plasma samples obtained from breast cancer patients compared with healthy controls. Using logical regression, a diagnostic equation based on three metabolites (lysoPC a C16:0, PC ae C42:5 and PC aa C34:2 successfully differentiated breast cancer patients from healthy controls, with a sensitivity of 98.1% and a specificity of 96.0%.

SU-F-J-112: Clinical Feasibility Test of An RF Pulse-Based MRI Method for the Quantitative Fat-Water Segmentation

Energy Technology Data Exchange (ETDEWEB)

Yee, S; Wloch, J; Pirkola, M [William Beaumont Hospital, Royal Oak, MI (United States)

2016-06-15

Purpose: Quantitative fat-water segmentation is important not only because of the clinical utility of fat-suppressed MRI images in better detecting lesions of clinical significance (in the midst of bright fat signal) but also because of the possible physical need, in which CT-like images based on the materials’ photon attenuation properties may have to be generated from MR images; particularly, as in the case of MR-only radiation oncology environment to obtain radiation dose calculation or as in the case of hybrid PET/MR modality to obtain attenuation correction map for the quantitative PET reconstruction. The majority of such fat-water quantitative segmentations have been performed by utilizing the Dixon’s method and its variations, which have to enforce the proper settings (often predefined) of echo time (TE) in the pulse sequences. Therefore, such methods have been unable to be directly combined with those ultrashort TE (UTE) sequences that, taking the advantage of very low TE values (∼ 10’s microsecond), might be beneficial to directly detect bones. Recently, an RF pulse-based method (http://dx.doi.org/10.1016/j.mri.2015.11.006), termed as PROD pulse method, was introduced as a method of quantitative fat-water segmentation that does not have to depend on predefined TE settings. Here, the clinical feasibility of this method is verified in brain tumor patients by combining the PROD pulse with several sequences. Methods: In a clinical 3T MRI, the PROD pulse was combined with turbo spin echo (e.g. TR=1500, TE=16 or 60, ETL=15) or turbo field echo (e.g. TR=5.6, TE=2.8, ETL=12) sequences without specifying TE values. Results: The fat-water segmentation was possible without having to set specific TE values. Conclusion: The PROD pulse method is clinically feasible. Although not yet combined with UTE sequences in our laboratory, the method is potentially compatible with UTE sequences, and thus, might be useful to directly segment fat, water, bone and air.

Quantitative Evaluation of the Total Magnetic Moments of Colloidal Magnetic Nanoparticles: A Kinetics-based Method.

Science.gov (United States)

Liu, Haiyi; Sun, Jianfei; Wang, Haoyao; Wang, Peng; Song, Lina; Li, Yang; Chen, Bo; Zhang, Yu; Gu, Ning

2015-06-08

A kinetics-based method is proposed to quantitatively characterize the collective magnetization of colloidal magnetic nanoparticles. The method is based on the relationship between the magnetic force on a colloidal droplet and the movement of the droplet under a gradient magnetic field. Through computational analysis of the kinetic parameters, such as displacement, velocity, and acceleration, the magnetization of colloidal magnetic nanoparticles can be calculated. In our experiments, the values measured by using our method exhibited a better linear correlation with magnetothermal heating, than those obtained by using a vibrating sample magnetometer and magnetic balance. This finding indicates that this method may be more suitable to evaluate the collective magnetism of colloidal magnetic nanoparticles under low magnetic fields than the commonly used methods. Accurate evaluation of the magnetic properties of colloidal nanoparticles is of great importance for the standardization of magnetic nanomaterials and for their practical application in biomedicine. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative measurement of phase variation amplitude of ultrasonic diffraction grating based on diffraction spectral analysis

Energy Technology Data Exchange (ETDEWEB)

Pan, Meiyan, E-mail: yphantomohive@gmail.com; Zeng, Yingzhi; Huang, Zuohua, E-mail: zuohuah@163.com [Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou, Guangdong 510006 (China)

2014-09-15

A new method based on diffraction spectral analysis is proposed for the quantitative measurement of the phase variation amplitude of an ultrasonic diffraction grating. For a traveling wave, the phase variation amplitude of the grating depends on the intensity of the zeroth- and first-order diffraction waves. By contrast, for a standing wave, this amplitude depends on the intensity of the zeroth-, first-, and second-order diffraction waves. The proposed method is verified experimentally. The measured phase variation amplitude ranges from 0 to 2π, with a relative error of approximately 5%. A nearly linear relation exists between the phase variation amplitude and driving voltage. Our proposed method can also be applied to ordinary sinusoidal phase grating.

Quantitative sexing (Q-Sexing) and relative quantitative sexing (RQ ...

African Journals Online (AJOL)

samer

Key words: Polymerase chain reaction (PCR), quantitative real time polymerase chain reaction (qPCR), quantitative sexing, Siberian tiger. INTRODUCTION. Animal molecular sexing .... 43:3-12. Ellegren H (1996). First gene on the avian W chromosome (CHD) provides a tag for universal sexing of non-ratite birds. Proc.

An analytical approach based on ESI-MS, LC-MS and PCA for the quali-quantitative analysis of cycloartane derivatives in Astragalus spp.

Science.gov (United States)

Napolitano, Assunta; Akay, Seref; Mari, Angela; Bedir, Erdal; Pizza, Cosimo; Piacente, Sonia

2013-11-01

Astragalus species are widely used as health foods and dietary supplements, as well as drugs in traditional medicine. To rapidly evaluate metabolite similarities and differences among the EtOH extracts of the roots of eight commercial Astragalus spp., an approach based on direct analyses by ESI-MS followed by PCA of ESI-MS data, was carried out. Successively, quali-quantitative analyses of cycloartane derivatives in the eight Astragalus spp. by LC-ESI-MS(n) and PCA of LC-ESI-MS data were performed. This approach allowed to promptly highlighting metabolite similarities and differences among the various Astragalus spp. PCA results from LC-ESI-MS data of Astragalus samples were in reasonable agreement with both PCA results of ESI-MS data and quantitative results. This study affords an analytical method for the quali-quantitative determination of cycloartane derivatives in herbal preparations used as health and food supplements. Copyright © 2013 Elsevier B.V. All rights reserved.

Histogram-based quantitative evaluation of endobronchial ultrasonography images of peripheral pulmonary lesion.

Science.gov (United States)

Morikawa, Kei; Kurimoto, Noriaki; Inoue, Takeo; Mineshita, Masamichi; Miyazawa, Teruomi

2015-01-01

Endobronchial ultrasonography using a guide sheath (EBUS-GS) is an increasingly common bronchoscopic technique, but currently, no methods have been established to quantitatively evaluate EBUS images of peripheral pulmonary lesions. The purpose of this study was to evaluate whether histogram data collected from EBUS-GS images can contribute to the diagnosis of lung cancer. Histogram-based analyses focusing on the brightness of EBUS images were retrospectively conducted: 60 patients (38 lung cancer; 22 inflammatory diseases), with clear EBUS images were included. For each patient, a 400-pixel region of interest was selected, typically located at a 3- to 5-mm radius from the probe, from recorded EBUS images during bronchoscopy. Histogram height, width, height/width ratio, standard deviation, kurtosis and skewness were investigated as diagnostic indicators. Median histogram height, width, height/width ratio and standard deviation were significantly different between lung cancer and benign lesions (all p histogram standard deviation. Histogram standard deviation appears to be the most useful characteristic for diagnosing lung cancer using EBUS images. © 2015 S. Karger AG, Basel.

Cell origami: self-folding of three-dimensional cell-laden microstructures driven by cell traction force.

Directory of Open Access Journals (Sweden)

Kaori Kuribayashi-Shigetomi

Full Text Available This paper describes a method of generating three-dimensional (3D cell-laden microstructures by applying the principle of origami folding technique and cell traction force (CTF. We harness the CTF as a biological driving force to fold the microstructures. Cells stretch and adhere across multiple microplates. Upon detaching the microplates from a substrate, CTF causes the plates to lift and fold according to a prescribed pattern. This self-folding technique using cells is highly biocompatible and does not involve special material requirements for the microplates and hinges to induce folding. We successfully produced various 3D cell-laden microstructures by just changing the geometry of the patterned 2D plates. We also achieved mass-production of the 3D cell-laden microstructures without causing damage to the cells. We believe that our methods will be useful for biotechnology applications that require analysis of cells in 3D configurations and for self-assembly of cell-based micro-medical devices.

Cell origami: self-folding of three-dimensional cell-laden microstructures driven by cell traction force.

Science.gov (United States)

Kuribayashi-Shigetomi, Kaori; Onoe, Hiroaki; Takeuchi, Shoji

2012-01-01

This paper describes a method of generating three-dimensional (3D) cell-laden microstructures by applying the principle of origami folding technique and cell traction force (CTF). We harness the CTF as a biological driving force to fold the microstructures. Cells stretch and adhere across multiple microplates. Upon detaching the microplates from a substrate, CTF causes the plates to lift and fold according to a prescribed pattern. This self-folding technique using cells is highly biocompatible and does not involve special material requirements for the microplates and hinges to induce folding. We successfully produced various 3D cell-laden microstructures by just changing the geometry of the patterned 2D plates. We also achieved mass-production of the 3D cell-laden microstructures without causing damage to the cells. We believe that our methods will be useful for biotechnology applications that require analysis of cells in 3D configurations and for self-assembly of cell-based micro-medical devices.

Quantitative FDG in depression

Energy Technology Data Exchange (ETDEWEB)

Chua, P.; O`Keefe, G.J.; Egan, G.F.; Berlangieri, S.U.; Tochon-Danguy, H.J.; Mckay, W.J.; Morris, P.L.P.; Burrows, G.D. [Austin Hospital, Melbourne, VIC (Australia). Dept of Psychiatry and Centre for PET

1998-03-01

Full text: Studies of regional cerebral glucose metabolism (rCMRGlu) using positron emission tomography (PET) in patients with affective disorders have consistently demonstrated reduced metabolism in the frontal regions. Different quantitative and semi-quantitative rCMRGlu regions of interest (ROI) comparisons, e.g. absolute metabolic rates, ratios of dorsolateral prefrontal cortex (DLPFC) to ipsilateral hemisphere cortex, have been reported. These studies suffered from the use of a standard brain atlas to define ROls, whereas in this case study, the individual``s magnetic resonance imaging (MRI) scan was registered with the PET scan to enable accurate neuroanatomical ROI definition for the subject. The patient is a 36-year-old female with a six-week history of major depression (HAM-D = 34, MMSE = 28). A quantitative FDG PET study and an MRI scan were performed. Six MRI-guided ROls (DLPFC, PFC, whole hemisphere) were defined. The average rCMRGlu in the DLPFC (left = 28.8 + 5.8 mol/100g/min; right = 25.6 7.0 mol/100g/min) were slightly reduced compared to the ipsilateral hemispherical rate (left = 30.4 6.8 mol/100g/min; right = 29.5 7.2 mol/100g/min). The ratios of DLPFC to ipsilateral hemispheric rate were close to unity (left = 0.95 0.29; right 0.87 0.32). The right to left DLPFC ratio did not show any significant asymmetry (0.91 0.30). These results do not correlate with earlier published results reporting decreased left DLPFC rates compared to right DLPFC, although our results will need to be replicated with a group of depressed patients. Registration of PET and MRI studies is necessary in ROI-based quantitative FDG PET studies to allow for the normal anatomical variation among individuals, and thus is essential for accurate comparison of rCMRGlu between individuals.

Quantitative FDG in depression

International Nuclear Information System (INIS)

Chua, P.; O'Keefe, G.J.; Egan, G.F.; Berlangieri, S.U.; Tochon-Danguy, H.J.; Mckay, W.J.; Morris, P.L.P.; Burrows, G.D.

1998-01-01

Full text: Studies of regional cerebral glucose metabolism (rCMRGlu) using positron emission tomography (PET) in patients with affective disorders have consistently demonstrated reduced metabolism in the frontal regions. Different quantitative and semi-quantitative rCMRGlu regions of interest (ROI) comparisons, e.g. absolute metabolic rates, ratios of dorsolateral prefrontal cortex (DLPFC) to ipsilateral hemisphere cortex, have been reported. These studies suffered from the use of a standard brain atlas to define ROls, whereas in this case study, the individual''s magnetic resonance imaging (MRI) scan was registered with the PET scan to enable accurate neuroanatomical ROI definition for the subject. The patient is a 36-year-old female with a six-week history of major depression (HAM-D = 34, MMSE = 28). A quantitative FDG PET study and an MRI scan were performed. Six MRI-guided ROls (DLPFC, PFC, whole hemisphere) were defined. The average rCMRGlu in the DLPFC (left = 28.8 + 5.8 mol/100g/min; right = 25.6 7.0 mol/100g/min) were slightly reduced compared to the ipsilateral hemispherical rate (left = 30.4 6.8 mol/100g/min; right = 29.5 7.2 mol/100g/min). The ratios of DLPFC to ipsilateral hemispheric rate were close to unity (left = 0.95 0.29; right 0.87 0.32). The right to left DLPFC ratio did not show any significant asymmetry (0.91 0.30). These results do not correlate with earlier published results reporting decreased left DLPFC rates compared to right DLPFC, although our results will need to be replicated with a group of depressed patients. Registration of PET and MRI studies is necessary in ROI-based quantitative FDG PET studies to allow for the normal anatomical variation among individuals, and thus is essential for accurate comparison of rCMRGlu between individuals

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

Science.gov (United States)

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

2008-10-01

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

Questionnaire-based person trip visualization and its integration to quantitative measurements in Myanmar

Science.gov (United States)

Kimijiama, S.; Nagai, M.

2016-06-01

With telecommunication development in Myanmar, person trip survey is supposed to shift from conversational questionnaire to GPS survey. Integration of both historical questionnaire data to GPS survey and visualizing them are very important to evaluate chronological trip changes with socio-economic and environmental events. The objectives of this paper are to: (a) visualize questionnaire-based person trip data, (b) compare the errors between questionnaire and GPS data sets with respect to sex and age and (c) assess the trip behaviour in time-series. Totally, 345 individual respondents were selected through random stratification to assess person trip using a questionnaire and GPS survey for each. Conversion of trip information such as a destination from the questionnaires was conducted by using GIS. The results show that errors between the two data sets in the number of trips, total trip distance and total trip duration are 25.5%, 33.2% and 37.2%, respectively. The smaller errors are found among working-age females mainly employed with the project-related activities generated by foreign investment. The trip distant was yearly increased. The study concluded that visualization of questionnaire-based person trip data and integrating them to current quantitative measurements are very useful to explore historical trip changes and understand impacts from socio-economic events.

PIQMIe: A web server for semi-quantitative proteomics data management and analysis

NARCIS (Netherlands)

A. Kuzniar (Arnold); R. Kanaar (Roland)

2014-01-01

textabstractWe present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates

iTRAQ-Based Quantitative Proteomics Identifies Potential Regulatory Proteins Involved in Chicken Eggshell Brownness.

Directory of Open Access Journals (Sweden)

Guangqi Li

Full Text Available Brown eggs are popular in many countries and consumers regard eggshell brownness as an important indicator of egg quality. However, the potential regulatory proteins and detailed molecular mechanisms regulating eggshell brownness have yet to be clearly defined. In the present study, we performed quantitative proteomics analysis with iTRAQ technology in the shell gland epithelium of hens laying dark and light brown eggs to investigate the candidate proteins and molecular mechanisms underlying variation in chicken eggshell brownness. The results indicated 147 differentially expressed proteins between these two groups, among which 65 and 82 proteins were significantly up-regulated in the light and dark groups, respectively. Functional analysis indicated that in the light group, the down-regulated iron-sulfur cluster assembly protein (Iba57 would decrease the synthesis of protoporphyrin IX; furthermore, the up-regulated protein solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator, member 5 (SLC25A5 and down-regulated translocator protein (TSPO would lead to increased amounts of protoporphyrin IX transported into the mitochondria matrix to form heme with iron, which is supplied by ovotransferrin protein (TF. In other words, chickens from the light group produce less protoporphyrin IX, which is mainly used for heme synthesis. Therefore, the exported protoporphyrin IX available for eggshell deposition and brownness is reduced in the light group. The current study provides valuable information to elucidate variation of chicken eggshell brownness, and demonstrates the feasibility and sensitivity of iTRAQ-based quantitative proteomics analysis in providing useful insights into the molecular mechanisms underlying brown eggshell pigmentation.

A method to prioritize quantitative traits and individuals for sequencing in family-based studies.

Directory of Open Access Journals (Sweden)

Kaanan P Shah

Full Text Available Owing to recent advances in DNA sequencing, it is now technically feasible to evaluate the contribution of rare variation to complex traits and diseases. However, it is still cost prohibitive to sequence the whole genome (or exome of all individuals in each study. For quantitative traits, one strategy to reduce cost is to sequence individuals in the tails of the trait distribution. However, the next challenge becomes how to prioritize traits and individuals for sequencing since individuals are often characterized for dozens of medically relevant traits. In this article, we describe a new method, the Rare Variant Kinship Test (RVKT, which leverages relationship information in family-based studies to identify quantitative traits that are likely influenced by rare variants. Conditional on nuclear families and extended pedigrees, we evaluate the power of the RVKT via simulation. Not unexpectedly, the power of our method depends strongly on effect size, and to a lesser extent, on the frequency of the rare variant and the number and type of relationships in the sample. As an illustration, we also apply our method to data from two genetic studies in the Old Order Amish, a founder population with extensive genealogical records. Remarkably, we implicate the presence of a rare variant that lowers fasting triglyceride levels in the Heredity and Phenotype Intervention (HAPI Heart study (p = 0.044, consistent with the presence of a previously identified null mutation in the APOC3 gene that lowers fasting triglyceride levels in HAPI Heart study participants.

iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians.

Directory of Open Access Journals (Sweden)

Xiaofang Geng

Full Text Available The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. The findings of this research provide a molecular basis for further unraveling the mechanism of head regeneration initiation in planarians.

A study on quantitative V and V of safety-critical software

International Nuclear Information System (INIS)

Eom, H. S.; Kang, H. G.; Chang, S. C.; Ha, J. J.; Son, H. S.

2004-03-01

Recently practical needs have required quantitative features for the software reliability for Probabilistic Safety Assessment which is one of the important methods being used in assessing the overall safety of nuclear power plant. But the conventional assessment methods of software reliability could not provide enough information for PSA of NPP, therefore current assessments of a digital system which includes safety-critical software usually exclude the software part or use arbitrary values. This paper describes a Bayesian Belief Networks based method that models the rule-based qualitative software assessment method for a practical use and can produce quantitative results for PSA. The framework was constructed by utilizing BBN that can combine the qualitative and quantitative evidence relevant to the reliability of safety-critical software and can infer a conclusion in a formal and a quantitative way. The case study was performed by applying the method for assessing the quality of software requirement specification of safety-critical software that will be embedded in reactor protection system

A MODEL OF OXYGEN CONDITIONS IN A SCHOOL OF FISH BASED ON EXPERIMENTAL RESPIROMETRY

DEFF Research Database (Denmark)

Steffensen, John Fleng

2010-01-01

with a logging YSI CTD from a fixed position on the net cage at a depth of one meter. The data did not show lower oxygen levels in the vicinity oflhe fish compared to a position on the edge of the pen. In the near future we hope to be able to verify the model by measuring oxygen levels in large schools...... of Atlantic herring with a ROV instrumented with cameras and a logging YSJ CTD as well as an acoustic Oxyguard oxygen transmitter....

Quantitative research.

Science.gov (United States)

Watson, Roger

2015-04-01

This article describes the basic tenets of quantitative research. The concepts of dependent and independent variables are addressed and the concept of measurement and its associated issues, such as error, reliability and validity, are explored. Experiments and surveys – the principal research designs in quantitative research – are described and key features explained. The importance of the double-blind randomised controlled trial is emphasised, alongside the importance of longitudinal surveys, as opposed to cross-sectional surveys. Essential features of data storage are covered, with an emphasis on safe, anonymous storage. Finally, the article explores the analysis of quantitative data, considering what may be analysed and the main uses of statistics in analysis.

Quantitative film radiography

International Nuclear Information System (INIS)

Devine, G.; Dobie, D.; Fugina, J.; Hernandez, J.; Logan, C.; Mohr, P.; Moss, R.; Schumacher, B.; Updike, E.; Weirup, D.

1991-01-01

We have developed a system of quantitative radiography in order to produce quantitative images displaying homogeneity of parts. The materials that we characterize are synthetic composites and may contain important subtle density variations not discernible by examining a raw film x-radiograph. In order to quantitatively interpret film radiographs, it is necessary to digitize, interpret, and display the images. Our integrated system of quantitative radiography displays accurate, high-resolution pseudo-color images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. This report discusses: the method; film processor monitoring and control; verifying film and processor performance; and correction of scatter effects

Quantitative information in medical imaging

International Nuclear Information System (INIS)

Deconinck, F.

1985-01-01

When developing new imaging or image processing techniques, one constantly has in mind that the new technique should provide a better, or more optimal answer to medical tasks than existing techniques do 'Better' or 'more optimal' imply some kind of standard by which one can measure imaging or image processing performance. The choice of a particular imaging modality to answer a diagnostic task, such as the detection of coronary artery stenosis is also based on an implicit optimalisation of performance criteria. Performance is measured by the ability to provide information about an object (patient) to the person (referring doctor) who ordered a particular task. In medical imaging the task is generally to find quantitative information on bodily function (biochemistry, physiology) and structure (histology, anatomy). In medical imaging, a wide range of techniques is available. Each technique has it's own characteristics. The techniques discussed in this paper are: nuclear magnetic resonance, X-ray fluorescence, scintigraphy, positron emission tomography, applied potential tomography, computerized tomography, and compton tomography. This paper provides a framework for the comparison of imaging performance, based on the way the quantitative information flow is altered by the characteristics of the modality

Magnetoresistive biosensors for quantitative proteomics

Science.gov (United States)

Zhou, Xiahan; Huang, Chih-Cheng; Hall, Drew A.

2017-08-01

Quantitative proteomics, as a developing method for study of proteins and identification of diseases, reveals more comprehensive and accurate information of an organism than traditional genomics. A variety of platforms, such as mass spectrometry, optical sensors, electrochemical sensors, magnetic sensors, etc., have been developed for detecting proteins quantitatively. The sandwich immunoassay is widely used as a labeled detection method due to its high specificity and flexibility allowing multiple different types of labels. While optical sensors use enzyme and fluorophore labels to detect proteins with high sensitivity, they often suffer from high background signal and challenges in miniaturization. Magnetic biosensors, including nuclear magnetic resonance sensors, oscillator-based sensors, Hall-effect sensors, and magnetoresistive sensors, use the specific binding events between magnetic nanoparticles (MNPs) and target proteins to measure the analyte concentration. Compared with other biosensing techniques, magnetic sensors take advantage of the intrinsic lack of magnetic signatures in biological samples to achieve high sensitivity and high specificity, and are compatible with semiconductor-based fabrication process to have low-cost and small-size for point-of-care (POC) applications. Although still in the development stage, magnetic biosensing is a promising technique for in-home testing and portable disease monitoring.

Novel method for the study of receptor Ca2+ signalling exemplified by the NK1 receptor

DEFF Research Database (Denmark)

Heding, A; Elling, C E; Schwartz, T W

2002-01-01

We have used a novel technology (NovoStar from BMG Labtechnologies) for the study of the Ca2+ signalling of the human tackykinin NK1 (hNK-I receptor). The NovoStar is a microplate reader based on fluorescence and luminescence. The instrument implements a robotic pipettor arm and two microplate...... carriers, typically one for samples and one for cells. The robotic pipettor arm can transfer sample (agonist or antagonist) from the sample plate or other liquid containers to the cell plate, facilitating the study of Ca2+ signalling to such a degree that the instrument can be used for Medium Throughput...

Advances in establishment and analysis of three-dimensional tumor spheroid-based functional assays for target validation and drug evaluation

Directory of Open Access Journals (Sweden)

Vinci Maria

2012-03-01

Full Text Available Abstract Background There is overwhelming evidence that in vitro three-dimensional tumor cell cultures more accurately reflect the complex in vivo microenvironment than simple two-dimensional cell monolayers, not least with respect to gene expression profiles, signaling pathway activity and drug sensitivity. However, most currently available three-dimensional techniques are time consuming and/or lack reproducibility; thus standardized and rapid protocols are urgently needed. Results To address this requirement, we have developed a versatile toolkit of reproducible three-dimensional tumor spheroid models for dynamic, automated, quantitative imaging and analysis that are compatible with routine high-throughput preclinical studies. Not only do these microplate methods measure three-dimensional tumor growth, but they have also been significantly enhanced to facilitate a range of functional assays exemplifying additional key hallmarks of cancer, namely cell motility and matrix invasion. Moreover, mutual tissue invasion and angiogenesis is accommodated by coculturing tumor spheroids with murine embryoid bodies within which angiogenic differentiation occurs. Highly malignant human tumor cells were selected to exemplify therapeutic effects of three specific molecularly-targeted agents: PI-103 (phosphatidylinositol-3-kinase (PI3K-mammalian target of rapamycin (mTOR inhibitor, 17-N-allylamino-17-demethoxygeldanamycin (17-AAG (heat shock protein 90 (HSP90 inhibitor and CCT130234 (in-house phospholipase C (PLCγ inhibitor. Fully automated analysis using a Celigo cytometer was validated for tumor spheroid growth and invasion against standard image analysis techniques, with excellent reproducibility and significantly increased throughput. In addition, we discovered key differential sensitivities to targeted agents between two-dimensional and three-dimensional cultures, and also demonstrated enhanced potency of some agents against cell migration

Analysis of dextromethorphan and dextrorphan in decomposed skeletal tissues by microwave assisted extraction, microplate solid-phase extraction and gas chromatography- mass spectrometry (MAE-MPSPE-GCMS).

Science.gov (United States)

Fraser, Candice D; Cornthwaite, Heather M; Watterson, James H

2015-08-01