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1

Quantitative NMR spectroscopy of biologically active substances and excipients  

Microsoft Academic Search

Biologically active ingredients and excipients are the essentials of a drug formulation, such as a tablet, dragee, solution,\\u000a etc. Quality control of such substances thus plays a pivotal role in the production process of pharmaceutical drugs. Since\\u000a these agents often exhibit complex structures, consist of multiple components, or lack of a chromophore, traditional means\\u000a of characterization are often not feasible.

Tanja Beyer; Bernd Diehl; Ulrike Holzgrabe

2010-01-01

2

Quantitative Spectroscopy of Deneb  

Microsoft Academic Search

Context: Quantitative spectroscopy of luminous BA-type supergiants offers a high potential for modern astrophysics. Detailed studies allow the evolution of massive stars, galactochemical evolution, and the cosmic distance scale to be constrained observationally. Aims: A detailed and comprehensive understanding of the atmospheres of BA-type supergiants is required in order to use this potential properly. The degree to which we can

Florian Schiller; Norbert Przybilla

2007-01-01

3

Quantitative phase spectroscopy  

PubMed Central

Quantitative phase spectroscopy is presented as a novel method of measuring the wavelength-dependent refractive index of microscopic volumes. Light from a broadband source is filtered to an ~5 nm bandwidth and rapidly tuned across the visible spectrum in 1 nm increments by an acousto-optic tunable filter (AOTF). Quantitative phase images of semitransparent samples are recovered at each wavelength using off-axis interferometry and are processed to recover relative and absolute dispersion measurements. We demonstrate the utility of this approach by (i) spectrally averaging phase images to reduce coherent noise, (ii) measuring absorptive and dispersive features in microspheres, and (iii) quantifying bulk hemoglobin concentrations by absolute refractive index measurements. Considerations of using low coherence illumination and the extension of spectral techniques in quantitative phase measurements are discussed.

Rinehart, Matthew; Zhu, Yizheng; Wax, Adam

2012-01-01

4

Microfluidic impedance spectroscopy as a tool for quantitative biology and biotechnology  

PubMed Central

A microfluidic device that is able to perform dielectric spectroscopy is developed. The device consists of a measurement chamber that is 250??m thick and 750??m in radius. Around 1000 cells fit inside the chamber assuming average quantities for cell radius and volume fraction. This number is about 1000 folds lower than the capacity of conventional fixtures. A T-cell leukemia cell line Jurkat is tested using the microfluidic device. Measurements of deionized water and salt solutions are utilized to determine parasitic effects and geometric capacitance of the device. Physical models, including Maxwell-Wagner mixture and double shell models, are used to derive quantities for sub-cellular units. Clausius-Mossotti factor of Jurkat cells is extracted from the impedance spectrum. Effects of cellular heterogeneity are discussed and parameterized. Jurkat cells are also tested with a time domain reflectometry system for verification of the microfluidic device. Results indicate good agreement of values obtained with both techniques. The device can be used as a unique cell diagnostic tool to yield information on sub-cellular units.

Sabuncu, Ahmet C.; Zhuang, Jie; Kolb, Juergen F.; Beskok, Ali

2012-01-01

5

A Quantitative Infrared Spectroscopy Experiment.  

ERIC Educational Resources Information Center

Although infrared spectroscopy is used primarily for qualitative identifications, it is possible to use it as a quantitative tool as well. The use of a standard curve to determine percent methanol in a 2,2,2-trifluoroethanol sample is described. Background information, experimental procedures, and results obtained are provided. (JN)

Krahling, Mark D.; Eliason, Robert

1985-01-01

6

Biological applications of picosecond spectroscopy  

Microsoft Academic Search

Technological advances in picosecond spectroscopy have permitted the mechanisms of various chemical, physical and biological processes to be elucidated and understood to a greater degree than ever before. By means of picosecond emission, absorption and Raman spectroscopy, one can probe and measure directly the transient intermediates and kinetics of primary events in complex biological processes. A description of two current

E. F. Hilinski; P. M. Rentzepis

1983-01-01

7

Quantitative biology of single neurons  

PubMed Central

The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible.

Eberwine, James; Lovatt, Ditte; Buckley, Peter; Dueck, Hannah; Francis, Chantal; Kim, Tae Kyung; Lee, Jaehee; Lee, Miler; Miyashiro, Kevin; Morris, Jacqueline; Peritz, Tiina; Schochet, Terri; Spaethling, Jennifer; Sul, Jai-Yoon; Kim, Junhyong

2012-01-01

8

[Biologic artifacts in quantitative EEG].  

PubMed

We studied the influence of five biologic artifacts sources on quantitative EEG (blinking, forced eyes closure, forced jaw closure, tongue movements and pursuit eyes movements) through both visual and spectral analysis, with the purpose of verifying how do these artifacts can be seen in a cartographic way. We found that the spectrums potentials showed the same topographic display that was found through visual analysis. Visual analysis was superior than the quantitative evaluation to recognise the artifacts, as the former preserved the morphological display of the paroxysms. However it is important know how do the potentials are represented in quantitative maps, so that they can be identified as artifacts and not as pathologic EEG activity. PMID:16791367

Anghinah, Renato; Basile, Luis I; Schmidt, Magali T; Sameshima, Koichi; Gattaz, Wagner Farid

2006-06-09

9

Quantitative Analysis by Derivative Electronic Spectroscopy  

Microsoft Academic Search

Absorption and emission spectroscopy in the ultraviolet and visible regions, apart from being the earliest physical techniques of analysis, have great utility in solving a variety of structural and analytical problems [l-41. However, in many cases the quantitative determination of individual components in a mixture by UV-VIS spectroscopy becomes very difficult owing to the spectral similarities and overlapping of weak

L. Dixit; S. Ram

1985-01-01

10

QUANTITATIVE 15N NMR SPECTROSCOPY  

EPA Science Inventory

Line intensities in 15N NMR spectra are strongly influenced by spin-lattice and spin-spin relaxation times, relaxation mechanisms and experimental conditions. Special care has to be taken in using 15N spectra for quantitative purposes. Quantitative aspects are discussed for the 1...

11

Quantitative genetics in conservation biology.  

PubMed

Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations. PMID:10689801

Frankham, R

1999-12-01

12

Biomolecular Plasmonics for Quantitative Biology and Nanomedicine  

PubMed Central

Free electrons in a noble metal nanoparticle can be resonantly excited, leading to their collective oscillation termed as a surface plasmon. These surface plasmons enable nanoparticles to absorb light, generate heat, transfer energy, and re-radiate incident photons. Creative designs of nanoplasmonic optical antennae (i.e. plasmon resonant nanoparticles) have become a new foundation of quantitative biology and nanomedicine. This review focuses on the recent developments in dual-functional nanoplasmonic optical antennae for label-free biosensors and nanoplasmonic gene switches. Nanoplasmonic optical antennae, functioning as biosensors to significantly enhance biochemical-specific spectral information via plasmon resonance energy transfer (PRET) and surface-enhanced Raman spectroscopy (SERS), are discussed. Nanoplasmonic optical antennae, functioning as nanoplasmonic gene switches to enable spatiotemporal regulation of genetic activity, are also reviewed. Nanoplasmonic molecular rulers and integrated photoacoustic-photothermal contrast agents are also described.

Lee, Somin Eunice; Lee, Luke P.

2012-01-01

13

Quantitative Analysis by Auger Electron Spectroscopy  

Microsoft Academic Search

A short review is presented of the theoretical background of a physical model for the quantification of Auger electron spectroscopy (AES) for surface analysis. The recent studies on the data-base for the inelastic mean free paths (IMFP) by Seah and Dench and systematic calculations of the backscattering factors (R) by Shimizu and Ichimura have now enabled standard quantitative corrections comparable

Ryuichi Shimizu

1983-01-01

14

Outlines of a Quantitative Biology  

Microsoft Academic Search

\\u000a Recognition processes in biology started “from the top,” i.e., its basic principles and concepts were set up on the basis\\u000a of studying the most developed and thus most complex living beings. Biology had already been an advanced experimental science\\u000a when studies on simplest living systems began, and possibilities for a detailed investigation of simplest organism have only\\u000a become a reality

Tibor Gánti

15

Toward Quantitative "In Vivo Biochemistry" with Fluorescence Fluctuation Spectroscopy  

PubMed Central

Quantitative description of protein dynamics and interactions in vivo with temporal and spatial resolution is a key step in dissecting molecular mechanisms in cell biology. Fluorescence fluctuation spectroscopy (FFS) has recently emerged as a powerful in vivo tool for assessing molecular concentration and movement and formation of hetero- and homo-oligomeric complexes. This article discusses point FFS-based analysis methods that have proven useful to cell biologists, focusing on the kinds of information they provide, their pros and cons, and the basic instrumentation required. Along the way, we describe briefly a few recent examples where these analyses have helped address important biological questions.

2010-01-01

16

Quantitative Raman Spectroscopy of Biomaterials for Arthroplastic Applications  

NASA Astrophysics Data System (ADS)

Raman microprobe spectroscopy has considerable potential as an analytical tool in orthopedic science for its capability of non-destructively assessing the physical, chemical, and mechanical characteristics of load-bearing parts in arthroplastic components (i.e., artificial joints). In comparison to other assessment techniques, Raman spectroscopy offers high spatial resolution in the characterization of oxidation states, phase transformations, crystallographic textures, and residual stress/strain fields as developed at load-bearing surfaces of arthroplastic components, when embedded in biological environment. Furthermore, confocal probes can be used for non-destructively determining highly graded properties along the material subsurface. We show in this chapter a quantitative visualization of biomaterial mesostructures and, through such information, how the surfaces of orthopedic prostheses react to load bearing in biological environment.

Pezzotti, Giuseppe

17

Quantitative NIR Spectroscopy of Massive Stars  

NASA Astrophysics Data System (ADS)

Interest for near-infrared (NIR) spectroscopy of massive stars has been dramatically increasing over the last decade. Because it allows one to observe objects inaccessible at optical wavelengths due to absorption, the infrared domain offers a privileged window to study highly extinguished objects. Yet, a detailed calibration of the massive star properties at NIR wavelength is still missing. Following the lines of the work of Repolust et al. (2005), we have acquired high resolution spectroscopy of several nearby massive stars using VLT/CRIRES, focusing on spectral lines of interest in the J, H, K, and L bands. In this work, we present the earliest results of our quantitative spectroscopic analysis of the main sequence stars in our sample. Using the unique combination of a genetic algorithm approach with the state-of-the-art non-LTE atmosphere model FASTWIND, we compare the stellar and wind properties as derived from the optical and the NIR regime.

Sana, H.; Stap, F. A.; de Koter, A.; Martins, F.; Smette, A.; De Becker, M.; Nazé, Y.

2012-12-01

18

Magnetic Resonance Spectroscopy in Biological Systems.  

National Technical Information Service (NTIS)

These notes give a general view of the various methods of magnetic resonance spectroscopy and of their possible applications to biological and medical problems. After analyzing the fundamental NMR and EPR techniques, double resonance (ENDOR), pulsed NMR a...

E. Tiezzi

1971-01-01

19

Quantitative visualization in the computational biological sciences  

Microsoft Academic Search

Discoveries in computational molecular - cell biology and bioinformatics promise to provide new therapeutic interventions to disease. With the rapid growth of sequence and structural information for thousands of proteins and hundreds of cell types, computational processing are a restricting factor in obtaining quantitative understanding of molecular-cellular function. Processing and analysis is necessary both for input data (often from imaging)

Chandrajit Bajaj

2012-01-01

20

Ultrafast spectroscopy of biological photoreceptors.  

PubMed

We review recent new insights on reaction dynamics of photoreceptors proteins gained from ultrafast spectroscopy. In Blue Light sensing Using FAD (BLUF) domains, a hydrogen-bond rearrangement around the flavin chromophore proceeds through a radical-pair mechanism, by which light-induced electron and proton transfer from the protein to flavin result in rotation of a conserved glutamine that switches the hydrogen bond network. Femtosecond infrared spectroscopy has shown that in photoactive yellow protein (PYP), breaking of a hydrogen bond that connects the p-coumaric acid chromophore to the backbone is crucial for trans-cis isomerization and successful entry into the photocycle. Furthermore, isomerization reactions of phycocyanobilin in phytochrome and retinal in the rhodopsins have been revealed in detail through application of femtosecond infrared and femtosecond-stimulated Raman spectroscopy. PMID:17959372

Kennis, John T M; Groot, Marie-Louise

2007-10-23

21

Quantitative Photoacoustic Spectroscopy in the Frequency Domain  

NASA Astrophysics Data System (ADS)

In this paper, the development of a new methodology for the quantitative determination of the optical absorption coefficient in simple systems in which the light absorption follows Beer's law is described. An approximation of the heat diffusion model of the photoacoustic effect for thermally thick samples is explored. It was found that we could combine the amplitude and the phase of the photoacoustic signal to obtain a new analytical expression for the optical absorption coefficient. This expression is directly proportional to the normalized photoacoustic signal amplitude, the sine of the phase difference, and the heat capacity per unit of volume of the sample. The theoretical results were experimentally verified in the visible range (300 nm to 700 nm). The optical absorption coefficient obtained with this methodology was comparable to that obtained by UV-Vis spectroscopy.

Gutiérrez-Juárez, G.; Vela-Lira, H. A.; Yánez-Limón, J. M.; García-Rodríguez, F. J.; Polo-Parada, L.

2013-09-01

22

Quantitative Environmental and Integrative Biology (QEIB) -- Dear Colleague Letter  

NSF Publications Database

... Virginia 22230 Title: Quantitative Environmental and Integrative Biology (QEIB) Dear Colleague, We ... interface of mathematics and environmental biology. Environmental and integrative biologists are ...

23

Quantitative imaging with electrical impedance spectroscopy.  

PubMed

Electrical impedance spectroscopy (EIS) is a noninvasive modality that can be used to determine the electrical admittivity inside a body given a discrete set of current/voltage measurements made on the surface. Of particular interest is the use of EIS in the diagnosis of breast cancer, as the admittivity spectra of malignant and benign tumors differ significantly. Due to the fact that x-ray mammography is the current standard method of breast imaging to detect tumors, it is natural to see if we can use the admittivity distribution along with the mammogram image to improve the diagnosis, with the hopes that the specificity of these two methods combined will be greatly improved from using the mammogram image on its own. EIS is a highly ill-posed inverse problem, but regularization, in the form of structural prior information from the mammogram image as well as modeling error, allows for the problem to be solved for in a computationally efficient manner with improved results. To interpret the solution from the EIS inverse problem, a classification scheme is added, providing a quantitative image which maps out the tissue classification of the inside of the breast. The computational methods for solving the EIS inverse problem and the classification scheme are discussed and computed examples are presented to demonstrate the high simulated sensitivity and specificity of the method. PMID:23079558

McGivney, Debra; Calvetti, Daniela; Somersalo, Erkki

2012-10-18

24

Quantitative atomic spectroscopy for primary thermometry  

SciTech Connect

Quantitative spectroscopy has been used to measure accurately the Doppler broadening of atomic transitions in {sup 85}Rb vapor. By using a conventional platinum resistance thermometer and the Doppler thermometry technique, we were able to determine k{sub B} with a relative uncertainty of 4.1x10{sup -4} and with a deviation of 2.7x10{sup -4} from the expected value. Our experiment, using an effusive vapor, departs significantly from other Doppler-broadened thermometry (DBT) techniques, which rely on weakly absorbing molecules in a diffusive regime. In these circumstances, very different systematic effects such as magnetic sensitivity and optical pumping are dominant. Using the model developed recently by Stace and Luiten, we estimate the perturbation due to optical pumping of the measured k{sub B} value was less than 4x10{sup -6}. The effects of optical pumping on atomic and molecular DBT experiments is mapped over a wide range of beam size and saturation intensity, indicating possible avenues for improvement. We also compare the line-broadening mechanisms, windows of operation and detection limits of some recent DBT experiments.

Truong, Gar-Wing; Luiten, Andre N. [Frequency Standards and Metrology Research Group, School of Physics, University of Western Australia, Perth, Western Australia 6009 (Australia); May, Eric F. [Centre for Energy, School of Mechanical and Chemical Engineering, University of Western Australia, Perth, Western Australia 6009 (Australia); Stace, Thomas M. [School of Mathematics and Physics, University of Queensland, Brisbane, Queensland 4072 (Australia)

2011-03-15

25

Unraveling pancreatic islet biology by quantitative proteomics  

SciTech Connect

The pancreatic islets of Langerhans play a critical role in maintaining blood glucose homeostasis by secreting insulin and several other important peptide hormones. Impaired insulin secretion due to islet dysfunction is linked to the pathogenesis underlying both Type 1 and Type 2 diabetes. Over the past 5 years, emerging proteomic technologies have been applied to dissect the signaling pathways that regulate islet functions and gain an understanding of the mechanisms of islet dysfunction relevant to diabetes. Herein, we briefly review some of the recent quantitative proteomic studies involving pancreatic islets geared towards gaining a better understanding of islet biology relevant to metabolic diseases.

Zhou, Jianying; Dann, Geoffrey P.; Liew, Chong W.; Smith, Richard D.; Kulkarni, Rohit N.; Qian, Weijun

2011-08-01

26

1, 2, 3, 4: Infusing Quantitative Literacy into Introductory Biology  

ERIC Educational Resources Information Center

|Biology of the twenty-first century is an increasingly quantitative science. Undergraduate biology education therefore needs to provide opportunities for students to develop fluency in the tools and language of quantitative disciplines. Quantitative literacy (QL) is important for future scientists as well as for citizens, who need to interpret…

Bray Speth, Elena; Momsen, Jennifer L.; Moyerbrailean, Gregory A.; Ebert-May, Diane; Long, Tammy M.; Wyse, Sara; Linton, Debra

2010-01-01

27

Quantitative Optical Spectroscopy for Tissue Diagnosis  

Microsoft Academic Search

The interaction of light within tissue has been used to recognize disease since the mid-1800s. The recent developments of small light sources, detectors, and fiber optic probes provide opportunities to quantitatively measure these interactions, which yield information for diagnosis at the biochemical, structural, or (patho)physiological level within intact tissues. However, because of the strong scattering properties of tissues, the reemitted

Rebecca Richards-Kortum; Eva Sevick-Muraca

1996-01-01

28

Quantitative photoacoustic spectroscopy of cataractous human lenses.  

PubMed

Quantitative photoacoustic spectra of the nuclei of cataractous human lenses with various degrees of colouration and opacification were measured in the spectral range 250-600 nm. The lens nuclei were obtained from 20 cataractous patients through extracapsular cataract extraction. These measurements yield the light loss per unit path length in the nucleus of cataractous lenses. PMID:2111385

Bernini, U; Reccia, R; Russo, P; Scala, A

1990-03-01

29

1, 2, 3, 4: Infusing Quantitative Literacy into Introductory Biology  

PubMed Central

Biology of the twenty-first century is an increasingly quantitative science. Undergraduate biology education therefore needs to provide opportunities for students to develop fluency in the tools and language of quantitative disciplines. Quantitative literacy (QL) is important for future scientists as well as for citizens, who need to interpret numeric information and data-based claims regarding nearly every aspect of daily life. To address the need for QL in biology education, we incorporated quantitative concepts throughout a semester-long introductory biology course at a large research university. Early in the course, we assessed the quantitative skills that students bring to the introductory biology classroom and found that students had difficulties in performing simple calculations, representing data graphically, and articulating data-driven arguments. In response to students' learning needs, we infused the course with quantitative concepts aligned with the existing course content and learning objectives. The effectiveness of this approach is demonstrated by significant improvement in the quality of students' graphical representations of biological data. Infusing QL in introductory biology presents challenges. Our study, however, supports the conclusion that it is feasible in the context of an existing course, consistent with the goals of college biology education, and promotes students' development of important quantitative skills.

Momsen, Jennifer L.; Moyerbrailean, Gregory A.; Ebert-May, Diane; Long, Tammy M.; Wyse, Sara; Linton, Debra

2010-01-01

30

Quantitative Determination of Dielectric Thin-Film Properties Using Infrared Emission Spectroscopy;Applied Spectroscopy.  

National Technical Information Service (NTIS)

We have completed an experimental study to investigate the use of infrared emission spectroscopy (IRES) for the quantitative analysis of borophosphosilicate glass (BPSG) thin films on silicon monitor wafers. Experimental parameters investigated included t...

J. E. Franke D. M. Haaland T. M. Niemczyk S. Zhang

1998-01-01

31

On the Edge of Mathematics and Biology Integration: Improving Quantitative Skills in Undergraduate Biology Education  

ERIC Educational Resources Information Center

|In this paper, the authors describe how two institutions are helping their undergraduate biology students build quantitative competencies. Incorporation of quantitative skills and reasoning in biology are framed through a discussion of two cases that both concern introductory biology courses, but differ in the complexity of the mathematics and…

Feser, Jason; Vasaly, Helen; Herrera, Jose

2013-01-01

32

Quantitative Environmental and Integrative Biology (QEIB)  

NSF Publications Database

... interface of environmental and integrative biology and mathematics. Environmental and integrative ... of age and environmental conditions; 3) to foster collaboration among environmental and integrative ...

33

APD detectors for biological fluorescence spectroscopy  

NASA Astrophysics Data System (ADS)

Fluorescence spectroscopy is a very convenient and widely used method for studying the molecular background of biological processes [L. Salomé, J.L. Cazeil, A. Lopez, J.F. Tocanne, Eur. Biophys. J. 27 (1998) 391 402]. Chromophores are included in the structure under study and a flash of laser light induces fluorescence (Fluorescence Recovery After Photo-bleaching), the decay of which yields information on the polarity, the speed of rotation, and the speed of diffusion as well as on the temporal and spatial evolution of interactions between molecular species. The method can even be used to study living cells [J.F. Tocanne, L. Cézanne, A. Lopez, Prog. Lipid Res. 33 (1994) 203 237, L. Cezanne, A. Lopez, F. Loste, G. Parnaud, O. Saurel, P. Demange, J.F. Tocanne, Biochemistry 38 (1999) 2779 2786]. This is classically performed with a PM-based system. For biological reasons a decrease of the excitation of the cells is highly desirable. Because the fluorescence response then becomes fainter a significant improvement in detector capability would be welcome. We present here results obtained with an Avalanche Photo Diode (APD)-based system. The small sensitive area of detection allows a very significant improvement in signal/noise ratio, improvement in gain, and the opening-up of a new parameter space. With these new detectors we can begin the study of information transmission between cells through morphine receptors. This work involves both electronics engineers and biophysicists, so results and techniques in both fields will be presented here.

Mazères, S.; Borrel, V.; Magenc, C.; Courrech, J. L.; Bazer-Bachi, R.

2006-11-01

34

Quantitation of vitamin B 12 by first-derivative absorption spectroscopy  

NASA Astrophysics Data System (ADS)

Quantitation of vitamin B 12 by first-derivative absorption spectroscopy is described. Peak-to-peak (355 nm to 370 nm) amplitudes were measured from the first derivative spectra. The method permits rapid determination of vitamin B 12, and increases the detection limit while decreasing interference by impurities. The effects of the majority of other absorbing macromolecules which may also be present in biological samples are eliminated or very considerably minimized by this method.

Kar?ilayan, Huriye

1996-08-01

35

Quantitative analysis of the new biologically active natural substance shunlite  

Microsoft Academic Search

Methods for the quantitative determination of chemical elements contained in shunlite — a new biologically active natural\\u000a substance — have been developed. The proposed methods are characterized by high accuracy and reproducibility.

O. Yu. Vasil’eva; M. S. Goizman; G. B. Tikhomirova; A. S. Berlyand; A. S. Alikhanyan; A. V. Shevyakov

2007-01-01

36

Development of Electron Energy Loss Spectroscopy in the Biological Sciences  

PubMed Central

The high sensitivity of electron energy loss spectroscopy (EELS) for detecting light elements at the nanoscale makes it a valuable technique for application to biological systems. In particular, EELS provides quantitative information about elemental distributions within subcellular compartments, specific atoms bound to individual macromolecular assemblies, and the composition of bionanoparticles. The EELS data can be acquired either in the fixed beam energy-filtered transmission electron microscope (EFTEM) or in the scanning transmission electron microscope (STEM), and recent progress in the development of both approaches has greatly expanded the range of applications for EELS analysis. Near single atom sensitivity is now achievable for certain elements bound to isolated macromolecules, and it becomes possible to obtain three-dimensional compositional distributions from sectioned cells through EFTEM tomography.

Aronova, M.A.; Leapman, R.D.

2012-01-01

37

Quantitative Phase Microscopy of Live Biological Cell Dynamics  

NASA Astrophysics Data System (ADS)

Interferometric phase microscopy of biological cell dynamics has the potential to provide a label-free quantitative tool for cell biology, as well as for medical diagnosis and monitoring. The current state of the art of this field, the open questions, and specific solutions developed in our laboratory will be presented.

Shaked, Natan T.; Wax, Adam

2010-04-01

38

A Transformative Model for Undergraduate Quantitative Biology Education  

PubMed Central

The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions.

Driscoll, Tobin A.; Dhurjati, Prasad; Pelesko, John A.; Rossi, Louis F.; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B.

2010-01-01

39

Quantitative thermal gradient imaging of biological surfaces  

Microsoft Academic Search

Heat production in biological systems is an obligate consequence of the chemical thermodynamics of the living state. Various cellular and systemic mechanisms exist of the dissipation (or conservation) of this net heat production in a basically aqueous environment to various exchange surfaces. Besides fundamental conduction, and radiation, convective modes of heat transfer are particularly significant, the latter often establishing steady-state

Curtis J. Swanson; Christopher J. Wingard

1991-01-01

40

Quantitative and Rapid DNA Detection by Laser Transmission Spectroscopy  

PubMed Central

Laser transmission spectroscopy (LTS) is a quantitative and rapid in vitro technique for measuring the size, shape, and number of nanoparticles in suspension. Here we report on the application of LTS as a novel detection method for species-specific DNA where the presence of one invasive species was differentiated from a closely related invasive sister species. The method employs carboxylated polystyrene nanoparticles functionalized with short DNA fragments that are complimentary to a specific target DNA sequence. In solution, the DNA strands containing targets bind to the tags resulting in a sizable increase in the nanoparticle diameter, which is rapidly and quantitatively measured using LTS. DNA strands that do not contain the target sequence do not bind and produce no size change of the carboxylated beads. The results show that LTS has the potential to become a quantitative and rapid DNA detection method suitable for many real-world applications.

Li, Frank; Mahon, Andrew R.; Barnes, Matthew A.; Feder, Jeffery; Lodge, David M.; Hwang, Ching-Ting; Schafer, Robert; Ruggiero, Steven T.; Tanner, Carol E.

2011-01-01

41

Quantitative Genetic Interactions Reveal Layers of Biological Modularity  

PubMed Central

In the past, biomedical research has embraced a reductionist approach, primarily focused on characterizing the individual components that comprise a system of interest. Recent technical developments have significantly increased the size and scope of data describing biological systems. At the same time, advances in the field of systems biology have evoked a broader view of how the underlying components are interconnected. In this essay, we discuss how quantitative genetic interaction mapping has enhanced our view of biological systems, allowing a deeper functional interrogation at different biological scales.

Beltrao, Pedro; Cagney, Gerard; Krogan, Nevan J.

2010-01-01

42

X-Ray Absorption Spectroscopy Imaging of Biological Tissues  

SciTech Connect

X-ray absorption spectroscopy (XAS) is proving invaluable in determining the average chemical form of metals or metalloids in intact biological tissues. As most tissues have spatial structure, there is great additional interest in visualizing the spatial location of the metal(loid) as well as its chemical forms. XAS imaging gives the opportunity of producing maps of specific chemical types of elements in vivo in dilute biological systems. X-ray fluorescence microprobe techniques are routinely used to study samples with spatial heterogeneity. Microprobe produces elemental maps, with chemical sensitivity obtained by recording micro-XAS spectra at selected point locations on the map. Unfortunately, using these procedures spatial detail may be lost as the number of point spectra recorded generally is limited. A powerful extension of microprobe is XAS imaging or chemically specific imaging. Here, the incident energy is tuned to features in the near-edge which are characteristic of the expected chemical forms of the element. With a few simple assumptions, these XAS images can then be converted to quantitative images of specific chemical form, yielding considerable clarity in the distributions.

Pickering, I.J.; George, G.N.

2009-06-05

43

X-Ray Absorption Spectroscopy Imaging of Biological Tissues  

SciTech Connect

X-ray absorption spectroscopy (XAS) is proving invaluable in determining the average chemical form of metals or metalloids in intact biological tissues. As most tissues have spatial structure, there is great additional interest in visualizing the spatial location of the metal(loid) as well as its chemical forms. XAS imaging gives the opportunity of producing maps of specific chemical types of elements in vivo in dilute biological systems. X-ray fluorescence microprobe techniques are routinely used to study samples with spatial heterogeneity. Microprobe produces elemental maps, with chemical sensitivity obtained by recording micro-XAS spectra at selected point locations on the map. Unfortunately, using these procedures spatial detail may be lost as the number of point spectra recorded generally is limited. A powerful extension of microprobe is XAS imaging or chemically specific imaging. Here, the incident energy is tuned to features in the near-edge which are characteristic of the expected chemical forms of the element. With a few simple assumptions, these XAS images can then be converted to quantitative images of specific chemical form, yielding considerable clarity in the distributions.

Pickering, Ingrid J.; George, Graham N. [Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, SK, S7N 4R5 (Canada)

2007-02-02

44

X-Ray Absorption Spectroscopy Imaging of Biological Tissues  

NASA Astrophysics Data System (ADS)

X-ray absorption spectroscopy (XAS) is proving invaluable in determining the average chemical form of metals or metalloids in intact biological tissues. As most tissues have spatial structure, there is great additional interest in visualizing the spatial location of the metal(loid) as well as its chemical forms. XAS imaging gives the opportunity of producing maps of specific chemical types of elements in vivo in dilute biological systems. X-ray fluorescence microprobe techniques are routinely used to study samples with spatial heterogeneity. Microprobe produces elemental maps, with chemical sensitivity obtained by recording micro-XAS spectra at selected point locations on the map. Unfortunately, using these procedures spatial detail may be lost as the number of point spectra recorded generally is limited. A powerful extension of microprobe is XAS imaging or chemically specific imaging. Here, the incident energy is tuned to features in the near-edge which are characteristic of the expected chemical forms of the element. With a few simple assumptions, these XAS images can then be converted to quantitative images of specific chemical form, yielding considerable clarity in the distributions.

Pickering, Ingrid J.; George, Graham N.

2007-02-01

45

Quantitative analysis of klimont, a new natural biologically active preparation  

Microsoft Academic Search

A method for quantitative determination of silicon, aluminum, and iron, the main active components in the natural biologically\\u000a active preparation klimont, is developed that ensures good reproducibility and accuracy. The limits for the content of these\\u000a elements are established and can be introduced into the “Quantitative Determination” section of the draft manufacturer’s pharmacopoeial\\u000a monograph for klimont.

A. N. Zhuchkov; A. S. Berlyand; M. S. Goizman; G. B. Tikhomirova; V. I. Yakusheva

2009-01-01

46

Fluorescence Fluctuation Spectroscopy Enables Quantitative Imaging of Single mRNAs in Living Cells  

PubMed Central

Imaging mRNA with single-molecule sensitivity in live cells has become an indispensable tool for quantitatively studying RNA biology. The MS2 system has been extensively used due to its unique simplicity and sensitivity. However, the levels of the coat protein needed for consistent labeling of mRNAs limits the sensitivity and quantitation of this technology. Here, we applied fluorescence fluctuation spectroscopy to quantitatively characterize and enhance the MS2 system. Surprisingly, we found that a high fluorescence background resulted from inefficient dimerization of fluorescent protein (FP)-labeled MS2 coat protein (MCP). To mitigate this problem, we used a single-chain tandem dimer of MCP (tdMCP) that significantly increased the uniformity and sensitivity of mRNA labeling. Furthermore, we characterized the PP7 coat protein and the binding to its respective RNA stem loop. We conclude that the PP7 system performs better for RNA labeling. Finally, we used these improvements to study endogenous ?-actin mRNA, which has 24xMS2 binding sites inserted into the 3? untranslated region. The tdMCP-FP allowed uniform RNA labeling and provided quantitative measurements of endogenous mRNA concentration and diffusion. This work provides a foundation for quantitative spectroscopy and imaging of single mRNAs directly in live cells.

Wu, Bin; Chao, Jeffrey A.; Singer, Robert H.

2012-01-01

47

Fourier transform raman spectroscopy of synthetic and biological calcium phosphates  

Microsoft Academic Search

Fourier-transform (FT) Raman spectroscopy was used to characterize the organic and mineral components of biological and synthetic calcium phosphate minerals. Raman spectroscopy provides information on biological minerals that is complimentary to more widely used infrared methodologies as some infrared-inactive vibrational modes are Raman-active. The application of FT-Raman technology has, for the first time, enabled the problems of high sample fluorescence

G. R. Sauer; W. B. Zunic; J. R. Durig; R. E. Wuthier

1994-01-01

48

Quantitative polarized Raman spectroscopy in highly turbid bone tissue  

NASA Astrophysics Data System (ADS)

Polarized Raman spectroscopy allows measurement of molecular orientation and composition and is widely used in the study of polymer systems. Here, we extend the technique to the extraction of quantitative orientation information from bone tissue, which is optically thick and highly turbid. We discuss multiple scattering effects in tissue and show that repeated measurements using a series of objectives of differing numerical apertures can be employed to assess the contributions of sample turbidity and depth of field on polarized Raman measurements. A high numerical aperture objective minimizes the systematic errors introduced by multiple scattering. We test and validate the use of polarized Raman spectroscopy using wild-type and genetically modified (oim/oim model of osteogenesis imperfecta) murine bones. Mineral orientation distribution functions show that mineral crystallites are not as well aligned (p<0.05) in oim/oim bones (28+/-3 deg) compared to wild-type bones (22+/-3 deg), in agreement with small-angle X-ray scattering results. In wild-type mice, backbone carbonyl orientation is 76+/-2 deg and in oim/oim mice, it is 72+/-4 deg (p>0.05). We provide evidence that simultaneous quantitative measurements of mineral and collagen orientations on intact bone specimens are possible using polarized Raman spectroscopy.

Raghavan, Mekhala; Sahar, Nadder D.; Wilson, Robert H.; Mycek, Mary-Ann; Pleshko, Nancy; Kohn, David H.; Morris, Michael D.

2010-05-01

49

Optical spectroscopy for quantitative sensing in human pancreatic tissues  

NASA Astrophysics Data System (ADS)

Pancreatic adenocarcinoma has a five-year survival rate of only 6%, largely because current diagnostic methods cannot reliably detect the disease in its early stages. Reflectance and fluorescence spectroscopies have the potential to provide quantitative, minimally-invasive means of distinguishing pancreatic adenocarcinoma from normal pancreatic tissue and chronic pancreatitis. The first collection of wavelength-resolved reflectance and fluorescence spectra and time-resolved fluorescence decay curves from human pancreatic tissues was acquired with clinically-compatible instrumentation. Mathematical models of reflectance and fluorescence extracted parameters related to tissue morphology and biochemistry that were statistically significant for distinguishing between pancreatic tissue types. These results suggest that optical spectroscopy has the potential to detect pancreatic disease in a clinical setting.

Wilson, Robert H.; Chandra, Malavika; Lloyd, William; Chen, Leng-Chun; Scheiman, James; Simeone, Diane; McKenna, Barbara; Mycek, Mary-Ann

2011-06-01

50

Quantitative analysis of gallstones using laser-induced breakdown spectroscopy  

SciTech Connect

The utility of laser-induced breakdown spectroscopy (LIBS) for categorizing different types of gallbladder stone has been demonstrated by analyzing their major and minor constituents. LIBS spectra of three types of gallstone have been recorded in the 200-900 nm spectral region. Calcium is found to be the major element in all types of gallbladder stone. The spectrophotometric method has been used to classify the stones. A calibration-free LIBS method has been used for the quantitative analysis of metal elements, and the results have been compared with those obtained from inductively coupled plasma atomic emission spectroscopy (ICP-AES) measurements. The single-shot LIBS spectra from different points on the cross section (in steps of 0.5 mm from one end to the other) of gallstones have also been recorded to study the variation of constituents from the center to the surface. The presence of different metal elements and their possible role in gallstone formation is discussed.

Singh, Vivek K.; Singh, Vinita; Rai, Awadhesh K.; Thakur, Surya N.; Rai, Pradeep K.; Singh, Jagdish P

2008-11-01

51

Biological Sensing with Terahertz Circular Dichroism Spectroscopy.  

National Technical Information Service (NTIS)

We have developed a circular dichroism spectrometer working in the terahertz (THz) frequency regime. As THz spectroscopy is specific to collective vibrational modes in macromolecules (and collective modes in condensed, polar media such as water), the spec...

K. W. Plaxco S. J. Allen

2005-01-01

52

A quantitative biology of three New Zealand alpine grasshopper species  

Microsoft Academic Search

Quantitative biological data obtained in the course of a capture-recapture study are presented for three New Zealand alpine grasshopper species, Paprides nitidus, Sigaus australis, and Brachaspis nivalis. The data pertain to a mixed-species community under natural grassland conditions and include details of phenologies, longevities, ecdysis, sexual behaviour, oviposition, activity thresholds, and dispersal. Many of the details have necessarily been obtained

E. G. White

1974-01-01

53

A Transformative Model for Undergraduate Quantitative Biology Education  

ERIC Educational Resources Information Center

|The "BIO2010" report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating…

Usher, David C.; Driscoll, Tobin A.; Dhurjati, Prasad; Pelesko, John A.; Rossi, Louis F.; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B.

2010-01-01

54

Label-Free Technologies for Quantitative Multiparameter Biological Analysis  

PubMed Central

In the post-genomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We will describe the fundamental principles of these different methodologies and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application.

Qavi, Abraham J.; Washburn, Adam L.; Byeon, Ji-Yeon; Bailey, Ryan C.

2009-01-01

55

Cold Spring Harbor symposia on quantitative biology: Volume 51, Molecular biology of /ital Homo sapiens/  

SciTech Connect

This volume is the second part of a collection of papers submitted by the participants to the 1986 Cold Spring Harbor Symposium on Quantitative Biology entitled Molecular Biology of /ital Homo sapiens/. The 49 papers included in this volume are grouped by subject into receptors, human cancer genes, and gene therapy. (DT)

Not Available

1986-01-01

56

Brillouin Spectroscopy Data Base for Biological Threats.  

National Technical Information Service (NTIS)

Brillouin scattering from biological materials is conducted using a tandem Fabry-Perot interferometer. The interferometer is uniquely designed to measure small frequency shifts that are characteristic of Brillouin scattering. Brillouin scattering from DNA...

G. O. Rubel K. H. Fung

2003-01-01

57

Optimized quantitative magnetic resonance spectroscopy for clinical routine.  

PubMed

Several practical obstacles in data handling and evaluation complicate the use of quantitative localized magnetic resonance spectroscopy (qMRS) in clinical routine MR examinations. To overcome these obstacles, a clinically feasible MR pulse sequence protocol based on standard available MR pulse sequences for qMRS has been implemented along with newly added functionalities to the free software package jMRUI-v5.0 to make qMRS attractive for clinical routine. This enables (a) easy and fast DICOM data transfer from the MR console and the qMRS-computer, (b) visualization of combined MR spectroscopy and imaging, (c) creation and network transfer of spectroscopy reports in DICOM format, (d) integration of advanced water reference models for absolute quantification, and (e) setup of databases containing normal metabolite concentrations of healthy subjects. To demonstrate the work-flow of qMRS using these implementations, databases for normal metabolite concentration in different regions of brain tissue were created using spectroscopic data acquired in 55 normal subjects (age range 6-61 years) using 1.5T and 3T MR systems, and illustrated in one clinical case of typical brain tumor (primitive neuroectodermal tumor). The MR pulse sequence protocol and newly implemented software functionalities facilitate the incorporation of qMRS and reference to normal value metabolite concentration data in daily clinical routine. PMID:22907544

Scheidegger, Olivier; Wingeier, Kevin; Stefan, Dan; Graveron-Demilly, Danielle; van Ormondt, Dirk; Wiest, Roland; Slotboom, Johannes

2012-08-20

58

Quantitative spectroscopy analysis of prokaryotic cells: vegetative cells and spores.  

PubMed

Multiwavelength ultraviolet/visible (UV-Vis) spectra of microorganisms and cell suspensions contain quantitative information on properties such as number, size, shape, chemical composition, and internal structure of the suspended particles. These properties are essential for the identification and classification of microorganisms and cells. The complexity of microorganisms in terms of their chemical composition and internal structure make the interpretation of their spectral signature a difficult task. In this paper, a model is proposed for the quantitative interpretation of spectral patterns resulting from transmission measurements of prokaryotic microorganism suspensions. It is also demonstrated that different organisms give rise to spectral differences that may be used for their identification and classification. The proposed interpretation model is based on light scattering theory, spectral deconvolution techniques, and on the approximation of the frequency dependent optical properties of the basic constituents of living organisms. The quantitative deconvolution in terms of the interpretation model yields critical information necessary for the detection and identification of microorganisms, such as size, dry mass, dipicolinic acid concentration, nucleotide concentration, and an average representation of the internal scattering elements of the organisms. E. coli, P. agglomerans, B. subtilis spores, and vegetative cells and spores of Bacillus globigii are used as case studies. It is concluded that spectroscopy techniques coupled with effective interpretation models are applicable to a wide range of cell types found in diverse environments. PMID:15128109

Alupoaei, Catalina E; Olivares, Jose A; García-Rubio, Luis H

2004-03-15

59

Computational Laser Spectroscopy in a Biological Tissue  

PubMed Central

We present a numerical spectroscopic study of visible and infrared laser radiation in a biological tissue. We derive a solution of a general two-dimensional time dependent radiative transfer equation in a tissue-like medium. The used model is suitable for many situations especially when the external source is time-dependent or continuous. We use a control volume-discrete ordinate method associated with an implicit three-level second-order time differencing scheme. We consider a very thin rectangular biological-tissue-like medium submitted to a visible or a near infrared light sources. The RTE is solved for a set of different wavelength source. All sources are assumed to be monochromatic and collimated. The energetic fluence rate is computed at a set of detector points on the boundaries. According to the source type, we investigate either the steady-state or transient response of the medium. The used model is validated in the case of a heterogeneous tissue-like medium using referencing experimental results from the literature. Also, the developed model is used to study changes on transmitted light in a rat-liver tissue-like medium. Optical properties depend on the source wavelength and they are taken from the literature. In particular, light-transmission in the medium is studied for continuous wave and for short pulse.

Gantri, M.; Trabelsi, H.; Sediki, E.; Ben Salah, R.

2010-01-01

60

Raman-tweezers spectroscopy of single biological cells and organelles  

NASA Astrophysics Data System (ADS)

Raman tweezers, also called laser tweezers Raman spectroscopy (LTRS), is an instrument that combines optical tweezers and confocal Raman microscopy for simultaneous manipulation and analysis of single biological cells or organelles in a physiological solution without the need of introducing biochemical tags. The optical tweezers part of the LTRS system uses a tightly focused near-infrared beam to capture and immobilize a biological particle in a liquid medium by the gradient force. The Raman spectroscopy part can generate vibrational spectra of the trapped particle to provide composition and conformation information of molecules based on measuring molecular vibrations from the scattered light. In this talk, we will present the physical principle and instrumentation of optical tweezers and micro-Raman spectroscopy system. Applications in rapid detection and identification of microorganisms, sorting of living cells, and real-time measurement of the dynamical changes in biochemical properties of macromolecules within living cells, and detection of recombinant proteins in transgenic cells will be presented.

Li, Yongqing

2004-11-01

61

Methodologies for laboratory Laser Induced Breakdown Spectroscopy semi-quantitative and quantitative analysis—A review  

NASA Astrophysics Data System (ADS)

Since its early applications, Laser Induced Breakdown Spectroscopy has been recognized as a useful tool for solid state chemical analysis. However the quantitative accuracy of the technique depends on the complex processes involved in laser induced plasma formation, ablation, atomization, excitation and ion recombination. Problems arising from laser target coupling, matrix effect, fractionation in target vaporization, local thermodynamic equilibrium assumption and interferences from additional air ionization should be properly addressed in order to obtain reliable quantitative results in laboratory to be used as starting point during field campaigns. As selected case studies carried out within the authors' research team show, a proper selection of laser parameters and, in general of experimental conditions, for laboratory data acquisition is required in order to minimize the mentioned problems both in case of calibration curves and calibration free approaches. In particular, the choice of reference samples for measuring calibration curves is of crucial importance in laboratory experiments, in relation both to matrix effect and local thermodynamic equilibrium, to be carried out at comparable conditions in terms of temperature and electron density. A model for the ablation process aimed to the optimization of experimental conditions in some case studies (copper alloys) has been specifically developed in order to account for the target stoichiometry in the plasma. Problems related to the limit of detection for quantitative trace analysis have been considered in analyzing data collected both inside and outside the local thermodynamic equilibrium window, in cases characterized by a fixed contamination threshold.

Fantoni, R.; Caneve, L.; Colao, F.; Fornarini, L.; Lazic, V.; Spizzichino, V.

2008-10-01

62

Quantitative nanoscale water mapping in frozen-hydrated skin by low-loss electron energy-loss spectroscopy  

Microsoft Academic Search

Spatially resolved low-loss electron energy-loss spectroscopy (EELS) is a powerful method to quantitatively determine the water distribution in frozen-hydrated biological materials at high spatial resolution. However, hydrated tissue, particularly its hydrophilic protein-rich component, is very sensitive to electron radiation. This sensitivity has traditionally limited the achievable spatial resolution because of the relatively high noise associated with low-dose data acquisition. We

Sergey Yakovlev; Manoj Misra; Shanling Shi; Emre Firlar; Matthew Libera

2010-01-01

63

Lessons learned from quantitative dynamical modeling in systems biology.  

PubMed

Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A Systems Biology approach that combines quantitative experimental data with dynamic mathematical modeling promises to yield deeper insights into these processes. Nevertheless, with growing complexity and increasing amount of quantitative experimental data, building realistic and reliable mathematical models can become a challenging task: the quality of experimental data has to be assessed objectively, unknown model parameters need to be estimated from the experimental data, and numerical calculations need to be precise and efficient. Here, we discuss, compare and characterize the performance of computational methods throughout the process of quantitative dynamic modeling using two previously established examples, for which quantitative, dose- and time-resolved experimental data are available. In particular, we present an approach that allows to determine the quality of experimental data in an efficient, objective and automated manner. Using this approach data generated by different measurement techniques and even in single replicates can be reliably used for mathematical modeling. For the estimation of unknown model parameters, the performance of different optimization algorithms was compared systematically. Our results show that deterministic derivative-based optimization employing the sensitivity equations in combination with a multi-start strategy based on latin hypercube sampling outperforms the other methods by orders of magnitude in accuracy and speed. Finally, we investigated transformations that yield a more efficient parameterization of the model and therefore lead to a further enhancement in optimization performance. We provide a freely available open source software package that implements the algorithms and examples compared here. PMID:24098642

Raue, Andreas; Schilling, Marcel; Bachmann, Julie; Matteson, Andrew; Schelke, Max; Kaschek, Daniel; Hug, Sabine; Kreutz, Clemens; Harms, Brian D; Theis, Fabian J; Klingmüller, Ursula; Timmer, Jens

2013-09-30

64

Lessons Learned from Quantitative Dynamical Modeling in Systems Biology  

PubMed Central

Due to the high complexity of biological data it is difficult to disentangle cellular processes relying only on intuitive interpretation of measurements. A Systems Biology approach that combines quantitative experimental data with dynamic mathematical modeling promises to yield deeper insights into these processes. Nevertheless, with growing complexity and increasing amount of quantitative experimental data, building realistic and reliable mathematical models can become a challenging task: the quality of experimental data has to be assessed objectively, unknown model parameters need to be estimated from the experimental data, and numerical calculations need to be precise and efficient. Here, we discuss, compare and characterize the performance of computational methods throughout the process of quantitative dynamic modeling using two previously established examples, for which quantitative, dose- and time-resolved experimental data are available. In particular, we present an approach that allows to determine the quality of experimental data in an efficient, objective and automated manner. Using this approach data generated by different measurement techniques and even in single replicates can be reliably used for mathematical modeling. For the estimation of unknown model parameters, the performance of different optimization algorithms was compared systematically. Our results show that deterministic derivative-based optimization employing the sensitivity equations in combination with a multi-start strategy based on latin hypercube sampling outperforms the other methods by orders of magnitude in accuracy and speed. Finally, we investigated transformations that yield a more efficient parameterization of the model and therefore lead to a further enhancement in optimization performance. We provide a freely available open source software package that implements the algorithms and examples compared here.

Bachmann, Julie; Matteson, Andrew; Schelke, Max; Kaschek, Daniel; Hug, Sabine; Kreutz, Clemens; Harms, Brian D.; Theis, Fabian J.; Klingmuller, Ursula; Timmer, Jens

2013-01-01

65

Quantitative laser-induced breakdown spectroscopy analysis of calcified tissue samples  

NASA Astrophysics Data System (ADS)

We report on the application of laser-induced breakdown spectroscopy (LIBS) to the analysis of important minerals and the accumulation of potentially toxic elements in calcified tissue, to trace e.g. the influence of environmental exposure, and other medical or biological factors. This theme was exemplified for quantitative detection and mapping of Al, Pb and Sr in representative samples, including teeth (first teeth of infants, second teeth of children and teeth of adults) and bones (tibia and femur). In addition to identifying and quantifying major and trace elements in the tissues, one- and two-dimensional profiles and maps were generated. Such maps (a) provide time/concentration relations, (b) allow to follow mineralisation of the hydroxyapatite matrix and the migration of the elements within it and (c) enable to identify disease states, such as caries in teeth. In order to obtain quantitative calibration, reference samples in the form of pressed pellets with calcified tissue-equivalent material (majority compound of pellets is CaCO 3) were used whose physical properties closely resembled hydroxyapatite. Compounds of Al, Sr and Pb were added to the pellets, containing atomic concentrations in the range 100-10 000 ppm relative to the Ca content of the matrix. Analytical results based on this calibration against artificial samples for the trace elements under investigation agree with literature values, and with our atomic absorption spectroscopy (AAS) cross-validation measurements.

Samek, O.; Beddows, D. C. S.; Telle, H. H.; Kaiser, J.; Liška, M.; Cáceres, J. O.; Gonzáles Ureña, A.

2001-06-01

66

Molecular Biology of Homo Sapiens: Abstracts of Papers Presented at the 51ST Cold Spring Harbor Symposium on Quantitative Biology.  

National Technical Information Service (NTIS)

This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Gene...

J. D. Watson M. Siniscalco

1986-01-01

67

Cold Spring Harbor symposia on quantitative biology: Volume L, Molecular biology of development  

SciTech Connect

This volume contains contributions by contributors to the 1985 Cold Springs Harbor Symposium on Quantitative Biology. This year's theme was Molecular Biology of Development. The volume consists of 104 articles organized by content into sections entitled Nuclear/Cytoplasmic Interactions in Early Development; Lineage and Segmentation/Pattern Formation; Homeotic Mutants; Homeo Boxes; Tissue Specificity/Position Effects; Expression of Genes Introduced into Transgenic Mice; Induced Developmental Defects; Control of Gene Expression; Sex Determination; Cell-cycle Effects; Pluripotent Cells/Oncogenes; Cellular Differentiation; and Developmental Neurobiology.

Not Available

1985-01-01

68

Biological X-ray absorption spectroscopy and metalloproteomics.  

PubMed

In the past seven years the size of the known protein sequence universe has been rapidly expanding. At present, more then five million entries are included in the UniProtKB/TrEMBL protein database. In this context, a retrospective evaluation of recent X-ray absorption studies is undertaken to assess its potential role in metalloproteomics. Metalloproteomics is the structural and functional characterization of metal-binding proteins. This is a new area of active research which has particular relevance to biology and for which X-ray absorption spectroscopy is ideally suited. In the last three years, biological X-ray absorption spectroscopy (BioXAS) has been included among the techniques used in post-genomics initiatives for metalloprotein characterization. The emphasis of this review is on the progress in BioXAS that has emerged from recent meetings in 2007-2008. Developments required to enable BioXAS studies to better contribute to metalloproteomics throughput are also discussed. Overall, this paper suggests that X-ray absorption spectroscopy could have a higher impact on metalloproteomics, contributing significantly to the understanding of metal site structures and of reaction mechanisms for metalloproteins. PMID:19395808

Ascone, Isabella; Strange, Richard

2009-04-01

69

Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.  

ERIC Educational Resources Information Center

Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)

Hill, Devon W.; And Others

1988-01-01

70

Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.  

ERIC Educational Resources Information Center

|Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)|

Hill, Devon W.; And Others

1988-01-01

71

Identification and quantitative determination of lignans in Cedrus atlantica resins using 13C NMR spectroscopy.  

PubMed

Identification and quantitative determination of individual components of resin collected on the trunk of 28 Cedrus atlantica trees, grown in Corsica, has been carried out using 13C NMR spectroscopy. Eight resin acids bearing either the pimarane or abietane skeleton, two monoterpene hydrocarbons and four oxygenated neutral diterpenes have been identified, as well as three lignans, scarcely found in resins. Three groups could be distinguished within the 28 resin samples. The nine samples of Group I had their composition dominated by diterpene acids (33.7-45.8%), with abietic acid (6.2-18.7%) and isopimaric acid (5.1-12.6%) being the major components. The four samples of Group II contained resin acids (main components) and lignans in moderate amounts (up to 10.3%). Conversely, lignans (38.8-63.8%) were by far the major components of the 15 samples of Group III. Depending on the sample, the major component was pinoresinol (18.1-38.9%), lariciresinol (17.2-33.7%) or lariciresinol 9'-acetate (16.9-29.1%). Finally, due to the high biological interest in lignans, a rapid procedure, based on 1H NMR spectroscopy, was developed for quantification of lignans in resins of C. atlantica. PMID:21485279

Nam, Anne-Marie; Paoli, Mathieu; Castola, Vincent; Casanova, Joseph; Bighelli, Ange

2011-03-01

72

Qualitative and quantitative analysis of wood samples by Fourier transform infrared spectroscopy and multivariate analysis  

Microsoft Academic Search

Fourier transform infrared (FTIR) spectroscopy, in combination with multivariate analysis, enable the analysis of wood samples without time-consuming sample preparation. The aim of our work was to analysis the wood samples qualitatively and quantitatively by FTIR spectroscopy. A Van Soest method to determine the lignin, cellulose and hemicellulose content, was used as reference method. Multivariate calibration was performed based on

Huilun Chen; Carlo Ferrari; Marco Angiuli; Jun Yao; Costantino Raspi; Emilia Bramanti

2010-01-01

73

Coded Aperture Raman Spectroscopy for Quantitative Measurements of Ethanol in a Tissue Phantom  

Microsoft Academic Search

Coded aperture spectroscopy allows for sources of large etendue to be efficiently coupled into dispersive spectrometers by replacing the traditional input slit with a patterned mask. We describe a coded aperture spectrometer optimized for Raman spectroscopy of diffuse sources, (e.g., tissue). We provide design details of the Raman system, along with quantitative estimation results for ethanol at non-toxic levels in

S. T. McCain; M. E. Gehm; Y. Wang; N. P. Pitsianis; D. J. Brady

2006-01-01

74

Quantitative Determination of DNA-Ligand Binding Using Fluorescence Spectroscopy  

ERIC Educational Resources Information Center

|The effective use of fluorescence spectroscopy for determining the binding of the intercalcating agent crhidium bromide to DNA is being described. The analysis used simple measurement techniques and hence can be easily adopted by the students for a better understanding.|

Healy, Eamonn F.

2007-01-01

75

Quantitative Raman Spectroscopy of Biomaterials for Arthroplastic Applications  

Microsoft Academic Search

Raman microprobe spectroscopy has considerable potential as an analytical tool in orthopedic science for its capability of\\u000a non-destructively assessing the physical, chemical, and mechanical characteristics of load-bearing parts in arthroplastic\\u000a components (i.e., artificial joints). In comparison to other assessment techniques, Raman spectroscopy offers high spatial\\u000a resolution in the characterization of oxidation states, phase transformations, crystallographic textures, and residual stress\\/strain\\u000a fields

Giuseppe Pezzotti

76

Quantitative distinction between bound and free NADH in biological systems  

NASA Astrophysics Data System (ADS)

Without exceptions, in all living cells NADH is a key metabolite linking a large number of metabolic pathways. Flux rates through such pathways are an essential component in the understanding of the functioning of living cells. Knowledge about the way these fluxes depend on the concentrations of the metabolites involved (including NADH/NAD+) allows calculation of these fluxes. Therefore, a method to determine the concentration of free NADH is necessary. A distinction between the free and protein-bound NADH can be made on the basis of fluorescence emission spectra and fluorescence lifetimes. A method for such measurements using a microscopic set-up for time-gated fluorescence spectroscopy has been introduced by Schneckenburger and co-workers (Paul RJ, Schneckenburger H. Naturwissenschaften 83, pp. 32-35, 1996). We further improve this method by first characterizing NADH binding to model proteins by isothermal titration calorimetry and fluorescence. This allows a precise calculation of bound and free NADH and their respective spectra. An analysis of experimental data is advanced by applying two-component deconvolution and subsequent fitting. Using this method we can detect a significant proportion of free NADH in isolated potato tuber mitochondria respiring malate. Taken together these improvements allow a more accurate characterization of the NADH turnover in biological systems.

Kasimova, Marina R.; Krab, Klaas; Grigiene, Jurga; Andersen, Peter E.; Hagedorn, Peter; Flyvbjerg, Henrik K.; Moller, Ian M.

2004-07-01

77

Quantitative Infrared Spectroscopy of Minor Constituents of the Earth's Atmosphere.  

National Technical Information Service (NTIS)

We obtain quantitative laboratory spectroscopic measurements of molecular constituents which are of importance in understanding the health of the Earth's atmosphere, and, in particular, emphasize those species which are important for understanding stratos...

C. Chackerian L. P. Giver D. Goorvitch M. Spencer F. P. J. Valero

1990-01-01

78

Biological Evolution of Replicator Systems: Towards a Quantitative Approach  

NASA Astrophysics Data System (ADS)

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

Martin, Osmel; Horvath, J. E.

2013-04-01

79

Quantitative fractography of WC-Co cermets by Auger spectroscopy  

Microsoft Academic Search

A general procedure has been developed to determine the area fraction occupied by the binder on the fracture surfaces of cemented carbides. The area fraction of binder on the fracture surface was obtained from the relative peak-to-peak height ratios of elements in the binder and the carbide content was measured by Auger spectroscopy on the fracture surface and an adjacent

R. K. Viswanadham; T. S. Sun; E. F. Drake; J. A. Peck

1981-01-01

80

Quantitative Measurement of Trans-Fats by Infrared Spectroscopy  

ERIC Educational Resources Information Center

|Trans-fat is a general term, which is mainly used to describe the various trans geometric isomers present in unsaturated fatty acids. Various techniques are now used for a quantitative measurement of the amount of trans-fats present in foods and cooking oil.|

Walker, Edward B.; Davies, Don R.; Campbell, Mike

2007-01-01

81

Quantitation of Edited GABA Signals in Magnetic Resonance Spectroscopy  

Microsoft Academic Search

Amino butyric acid (GABA) is an inhibitory neurotransmitter that plays an important role in several brain disorders. Reliable detection of GABA in vivo, us- ing 1H Magnetic Resonance Spectroscopy is difficult and faces various challenges. Spectral-Editing sequences based on multiple quantum filtering techniques enable remov- ing overlapping signals. However, advanced signal pro- cessing accommodating sequence-dependence of the edited signals are

B. Tchong Len; H. Ratiney; C. Cudalbu; B. Fenet; A. R. Allouche; M. Aubert-Frecon; D. van Ormondt; D. Graveron-Demilly

82

Quantitative proton magnetic resonance spectroscopy of the cervical spinal cord.  

PubMed

Proton MR spectroscopy ((1)H-MRS) provides indices of neuronal damage in the central nervous system (CNS); however, it has not been extensively applied in the spinal cord. This work describes an optimized proton spectroscopy protocol for examination of the human cervical spinal cord. B(0) field mapping of the cord revealed periodic inhomogeneities due to susceptibility differences with surrounding tissue. By combining field maps and experimental data, we found that the optimum voxel size was 9 x 7 x 35 mm(3) placed with the inferior end of the voxel above vertebral body C2. Metabolite concentrations were determined in the cervical cord in six healthy controls by short-echo point-resolved spectroscopy (PRESS) volume localization. The results were compared with metabolite concentrations in the brainstem, cerebellum, and cortex in the same individuals. The concentrations in the cervical cord were as follows: N-acetyl-aspartate (NAA) 17.3 +/- 0.5, creatine (Cr) 9.5 +/- 0.9, and choline 2.7 +/- 0.5 mmol/l. The NAA concentration was significantly lower in the cord than in the brainstem (Mann-Whitney, P < 0.025), and higher than in the cortex (P < 0.005) and cerebellum (P < 0.005). Cr was significantly lower in the cord than in the cerebellum (P < 0.05). There were no significant differences between Cr concentrations in the spinal cord compared to the cortex and brainstem. PMID:15170831

Cooke, F J; Blamire, A M; Manners, D N; Styles, P; Rajagopalan, B

2004-06-01

83

Rapid biological agent identification by surface-enhanced Raman spectroscopy  

NASA Astrophysics Data System (ADS)

The Chemical Weapons Convention prohibits the development, production, stockpiling, and use of warfare agents (chemical and biological), and requires their destruction. Yet their use persists and has been included in the terrorist's arsenal. Currently, a number of analytical methods are being developed to perform rapid measurements of trace agents to ensure treaty compliance, as well as safe environments for military personal and the public at large. We have been investigating the ability of surface-enhanced Raman spectroscopy to detect bacterial nucleic acid-base pairs with sufficient sensitivity and selectivity to eliminate the need for enumeration used in polymerase chain reactions and culture growth, required by other measurement techniques. The design of a small volume, fiber optic coupled, electrolytic sample cell is presented along with analysis of DNA and RNA separated from non-toxic bacteria.

Farquharson, Stuart; Smith, Wayne W.; Elliott, Susan; Sperry, Jay F.

1999-11-01

84

Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology  

SciTech Connect

This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

Watson, J.D.; Siniscalco, M.

1986-01-01

85

Terahertz spectroscopy of dry, hydrated, and thermally denatured biological macromolecules  

NASA Astrophysics Data System (ADS)

Terahertz time-domain spectroscopy (THz-TDS) is an effective technique to probe the intermolecular and collective vibrational modes of biological macromolecules at THz frequencies. To date, the vast majority of spectroscopic studies have been performed on dehydrated biomolecular samples. Given the fact that all biochemical processes occur in aqueous environments and water is required for proper protein folding and function, we hypothesize that valuable information can be gained from spectroscopic studies performed on hydrated biomolecules in their native conformation. In this study, we used a THz-TDS system that exploits photoconductive techniques for THz pulse generation and freespace electro-optical sampling approaches for detection. We used the THz spectrometer to measure the time-dependent electric field of THz waves upon interaction with water, phosphate buffered saline (PBS), and collagen gels. By comparing these waveforms with references, we simultaneously determined each sample's index of refraction (n) and absorption coefficients (?a) as a function of frequency. Our data show that the properties we measure for the water, PBS and collagen are comparable to those reported in the literature. In the future, we plan to examine the effect that both temperature and pH have on the optical properties of other biological macromolecules. Studies will also be performed to compare our results to those generated using molecular dynamics simulations.

Lipscaomb, Dawn; Echchgadda, Ibtissam; Ibey, Bennett L.; Beier, Hope; Thomas, Robert J.; Peralta, Xomalin; Wilmink, Gerald J.

2012-02-01

86

Quantitative Raman Spectroscopy for the Analysis of Carrot Bioactives.  

PubMed

Rapid quantitative near-infrared Fourier transform Raman analyses of the key phytonutrients in carrots, polyacetylenes and carotenoids, are reported here for the first time. Solvent extracts of 31 carrot lines were analyzed for these phytonutrients by conventional methods, polyacetylenes by GC-FID and carotenoids by visible spectrophotometry. Carotenoid concentrations were 0-5586 ?g g(-1) dry weight (DW). Polyacetylene concentrations were 74-4846 ?g g(-1) DW, highest in wild carrots. The polyacetylenes were falcarinol, 6-1237 ?g g(-1) DW; falcarindiol, 42-3475 ?g g(-1) DW; and falcarindiol 3-acetate, 27-649 ?g g(-1) DW. Strong Raman bands for carotenoids gave good correlation to results by visible spectrophotometry. A chemometric model capable of quantitating carotenoids from Raman data was developed. A classification model for rapidly distinguishing carrots with high and low polyacetylene (limit of detection = 1400 ?g g(-1)) concentrations based on Raman spectral intensity in the region of 2250 cm(-1) was produced. PMID:23441972

Killeen, Daniel P; Sansom, Catherine E; Lill, Ross E; Eason, Jocelyn R; Gordon, Keith C; Perry, Nigel B

2013-03-11

87

Near-infrared Raman spectroscopy of single optically trapped biological cells  

Microsoft Academic Search

We report on the development and testing of a compact laser tweezers Raman spectroscopy (LTRS) system. The system combines optical trapping and near-infrared Raman spectroscopy for manipulation and identification of single biological cells in solution. A low-power diode laser at 785 nm was used for both trapping and excitation for Raman spectroscopy of the suspended microscopic particles. The design of

Changan Xie; Mumtaz A. Dinno; Yong-Qing Li

2002-01-01

88

Quantitative Analysis of Nail Polish Remover Using Nuclear Magnetic Resonance Spectroscopy Revisited  

ERIC Educational Resources Information Center

|Substantial modifications are presented for a previously described experiment using nuclear magnetic resonance (NMR) spectroscopy to quantitatively determine analytes in commercial nail polish remover. The revised experiment is intended for a second- or third-year laboratory course in analytical chemistry and can be conducted for larger…

Hoffmann, Markus M.; Caccamis, Joshua T.; Heitz, Mark P.; Schlecht, Kenneth D.

2008-01-01

89

Improved calculation of the backscattering factor for quantitative analysis by Auger electron spectroscopy  

Microsoft Academic Search

Based on a Monte Carlo simulation method, an improved calculation of the backscattering factor in quantitative analysis by Auger electron spectroscopy has been performed by integrating several aspects of recent progresses in the related fields. The calculation used a general definition of backscattering factor, more accurate ionization cross section, up-to-date Monte Carlo model of electron inelastic scattering, and a large

Z. J. Ding; W. S. Tan; Y. G. Li

2006-01-01

90

Quantitative Characterization of DNA Films by X-ray Photoelectron Spectroscopy.  

National Technical Information Service (NTIS)

We describe the use of self-assembled films of thiolated (dT)25 single-stranded DNA (ssDNA) on gold as a model system for quantitative characterization of DNA films by X-ray photoelectron spectroscopy (XPS). We evaluate the applicability of a uniform and ...

D. Y. Petrovykh H. Kimura-Suda L. J. Whitman M. J. Tarlov

2003-01-01

91

Inflammatory CNS Demyelination: Histopathologic Correlation with In Vivo Quantitative Proton MR Spectroscopy  

Microsoft Academic Search

BACKGROUND AND PURPOSE: The mechanisms behind the demyelination that is char- acteristic of multiple sclerosis (MS) are still poorly understood. The purpose of this study was to compare immunopathologic findings in demyelinating lesions of three patients with in vivo assessments obtained by quantitative proton MR spectroscopy (MRS). METHODS: Between four and seven stereotactic needle brain biopsies were performed in three

Andreas Bitsch; Harald Bruhn; Vassilios Vougioukas; Argyris Stringaris; Hans Lassmann; Jens Frahm; Wolfgang Bruck

1999-01-01

92

Rapid quantitative analysis of Dimethoate pesticide using surface enhanced raman spectroscopy  

Technology Transfer Automated Retrieval System (TEKTRAN)

A method for rapid quantitative detection of dimethoate pesticide by using surface-enhanced Raman spectroscopy (SERS) has been described. Significantly enhanced Raman signals of pesticide in low concentrations of 0.5 ~ 10 ug/mL were acquired by confocal raman micro-spectrometry with renishaw diagno...

93

Quantitative flash pyrolysis Fourier transform infrared spectroscopy of organic materials.  

PubMed

Thermal degradation is a common technique used to investigate the nature of organic materials. However, existing methods for the Fourier transform infrared (FTIR) identification and quantification of volatile products from the thermal degradation of organic materials are limited to the technique of thermogravimetric analysis (TGA)-FTIR, which utilizes relatively low heating rates. However, the thermal degradation products of organic materials are known to vary depending on the rate of heating, with lower heating rates of biomass associated with increased yields of solid char and decreased yields of volatiles, as well as a greater opportunity for secondary reactions between the residue and the pyrolysis products. Hence, it is difficult to relate the products of organic matter thermally degraded at <100 degrees C min(-1) in TGA to the products of flash pyrolysis at up to 20,000 degrees C s(-1). We have developed and applied a novel methodology for quantitative flash pyrolysis-FTIR analysis of the volatile pyrolysis products of organic-rich materials. Calibration curves of water, carbon dioxide and methane have been constructed and used to determine absolute volatile release from wood (ash, Lat. Fraxinus). This technique is quicker and simpler than comparable pyrolysis-gas chromatography-mass spectrometry techniques, and avoids errors associated with the lower rates of temperature increase associated with techniques such as thermogravimetric analysis. PMID:19345759

Court, Richard W; Sephton, Mark A

2009-03-06

94

Gas-Phase Database for Quantitative Infrared Spectroscopy  

SciTech Connect

The National Institute of Standards and Technology (NIST) and the Pacific Northwest National Laboratory (PNNL) are each creating quantitative databases containing the vapor-phase infrared spectra of pure chemicals. The digital databases have been created with both laboratory and remote-sensing applications in mind. A spectral resolution of {approx} 0.1 cm{sup -1} was selected to avoid degrading sharp spectral features, while also realizing that atmospheric broadening typically limits line widths to 0.1 cm{sup -1}. Calculated positional (wave number, cm{sup -1}) uncertainty is {le} 0.005 cm{sup -1}, while the 1{sigma} statistical uncertainty in absorbance values is <2% for most compounds. The latter was achieved by measuring multiple (typically {ge} 9) path length-concentration burdens and fitting a weighted Beer's law plot to each wave number channel. The two databases include different classes of compounds and were compared using 12 samples. Though these 12 samples span a range of polarities, absorption strengths, and vapor pressures, the data agree to within experimental uncertainties with only one exception.

Sharpe, Steven W.; Johnson, Timothy J.; Sams, Robert L.; Chu, Pamela M.; Rhoderick, G C.; Johnson, P A.

2004-12-10

95

Quantitative proton magnetic resonance spectroscopy without water suppression  

NASA Astrophysics Data System (ADS)

The suppression of the abundant water signal has been traditionally employed to decrease the dynamic range of the NMR signal in proton MRS (1H MRS) in vivo. When using this approach, if the intent is to utilize the water signal as an internal reference for the absolute quantification of metabolites, additional measurements are required for the acquisition of the water signal. This can be prohibitively time-consuming and is not desired clinically. Additionally, traditional water suppression can lead to metabolite alterations. This can be overcome by performing quantitative 1H MRS without water suppression. However, the non-water-suppressed spectra suffer from gradient-induced frequency modulations, resulting in sidebands in the spectrum. Sidebands may overlap with the metabolites, which renders the spectral analysis and quantification problematic. In this paper, we performed absolute quantification of metabolites without water suppression. Sidebands were removed by utilizing the phase of an external reference signal of single resonance to observe the time-varying the static field fluctuations induced by gradient-vibration and deconvolving this phase contamination from the desired NMR signal. The quantification of metabolites was determined after sideband correction by calibrating the metabolite signal intensities against the recorded water signal. The method was evaluated by phantom and in vivo measurements in human brain. The maximum systematic error for the quantified metabolite concentrations was found to be 10.8%, showing the feasibility of the quantification after sideband correction.

Özdemir, M. S.; DeDeene, Y.; Fieremans, E.; Lemahieu, I.

2009-06-01

96

Direct identification and quantitative determination of costunolide and dehydrocostuslactone in the fixed oil of Laurus novocanariensis by 13C-NMR spectroscopy.  

PubMed

The fixed oil of Laurus novocanariensis (previously L. azorica) contains mostly glycerides together with minor non-saponifiable compounds. The direct identification and quantitative determination of costunolide and dehydrocostuslactone, two sesquiterpene lactones components of the oil that exhibit biological activities, is described. The analysis was carried out using 13C-NMR spectroscopy (signal acquisition with inverse gated decoupling of protons; diglyme as internal standard) without separation, derivatisation or any sample preparation. PMID:15881118

Ferrari, Bernard; Castilho, Paula; Tomi, Félix; Rodrigues, Ana Isabel; do Ceu Costa, Maria; Casanova, Joseph

97

Quantitative spectroscopy of photospheric-phase type II supernovae  

NASA Astrophysics Data System (ADS)

We present first results on the quantitative spectroscopic analysis of the photospheric-phase of type II supernovae (SN). The analyses are based on the model atmosphere code, CMFGEN, of Hillier & Miller (1998) which solves the radiative transfer and statistical equilibrium equations in expanding outflows under the constraint of radiative equilibrium. A key asset of CMFGEN is its thorough treatment of line-blanketing due to metal species. From its applicability to hot star environments, the main modifications to the source code were to allow a linear velocity law, a power-law density distribution, an adaptive grid to handle the steep H recombination/ionization front occurring in some SN models, and a routine to compute the gray temperature structure in the presence of large velocities. In this first paper we demonstrate the ability of CMFGEN to reproduce, with a high level of accuracy, the UV and optical observations of a sample of well observed type II SN, i.e. SN1987A and SN1999em, at representative stages of their photospheric evolution. Two principal stages of SN are modeled that where hydrogen is fully ionized, and that in which H is only partially ionized. For models with an effective temperature below ~8000 K, hydrogen recombines and gives rise to a steep ionization front. The effect of varying the location of the outer grid radius on the spectral energy distribution (SED) is investigated. We find that going to 5-6 times the optically-thick base radius is optimal, since above that, the model becomes prohibitively large, while below this, significant differences appear because of the reduced line-blanketing (which persists even far above the photosphere) and the truncation of line-formation regions. To constrain the metallicity and the reddening of SN, the UV spectral region of early-time spectra is essential. We find that the density of the photosphere and effect of line blanketing decline as the spatial scale of the SN increases. The density distribution is found to have a strong impact on the overall flux distribution as well as line profiles. For a given base density, the faster the density drops, the higher the effective temperature of the model. We also find in cool models that the set of Ca ii lines, near 8500 Å is strongly sensitive to the density gradient. They show a weaker and narrower profile for steeper density distributions. Hydrogen Balmer lines are very well reproduced in fully or partially ionized models, but underestimated when hydrogen recombines. A reduced turbulent velocity or a flatter density layout are found to partially, but not fully, cure this persistent problem in studies of type II SN. He i lines observed in early-time spectra are very well reproduced, even for very modest helium enrichments, likely resulting from treatment of important non-LTE effects. At similar early epochs CMFGEN predicts, unambiguously, the presence of N ii lines in the blue-wing of both H? and He I 5875 Å. These lines have been observed but so far have generally been associated with peculiar emission, from locations far above the photosphere, in the strong adjacent lines. Finally, we present a pedagogical investigation on P-Cygni profile formation in type II SN. H? is found to form very close to the photosphere and thus presents a significant flux-deficit in the red, made greater by the rapidly declining density distribution. This provides a clear explanation for the noticeable blue-shift of P-Cygni profiles observed in early-time spectra of type II SN. Future studies based on CMFGEN modeling will focus on using type II SN for the calibration of distances in the Universe, as well as on detailed spectroscopic analyses for the determination of progenitor properties.

Dessart, L.; Hillier, D. J.

2005-07-01

98

Life at the Common Denominator: Mechanistic and Quantitative Biology for the Earth and Space Sciences (Invited)  

Microsoft Academic Search

The remarkable challenges and possibilities of the coming few decades will compel the biogeochemical and astrobiological sciences to characterize the interactions between biology and its environment in fundamental, mechanistic, and quantitative fashion. The clear need for integrative and scalable biology-environment models is exemplified in the Earth sciences by the challenge of effectively addressing anthropogenic global change, and in the space

T. Hoehler

2009-01-01

99

Online Interactive Teaching Modules Enhance Quantitative Proficiency of Introductory Biology Students  

ERIC Educational Resources Information Center

|There is widespread agreement within the scientific and education communities that undergraduate biology curricula fall short in providing students with the quantitative and interdisciplinary problem-solving skills they need to obtain a deep understanding of biological phenomena and be prepared fully to contribute to future scientific inquiry.…

Thompson, Katerina V.; Nelson, Karen C.; Marbach-Ad, Gili; Keller, Michael; Fagan, William F.

2010-01-01

100

Quantitative high-resolution on-line NMR spectroscopy in reaction and process monitoring.  

PubMed

On-line nuclear magnetic resonance spectroscopy (on-line NMR) is a powerful technique for reaction and process monitoring. Different set-ups for direct coupling of reaction and separation equipment with on-line NMR spectroscopy are described. NMR spectroscopy can be used to obtain both qualitative and quantitative information from complex reacting multicomponent mixtures for equilibrium or reaction kinetic studies. Commercial NMR probes can be used at pressures up to 35 MPa and temperatures up to 400 K. Applications are presented for studies of equilibria and kinetics of complex formaldehyde-containing mixtures as well as homogeneously and heterogeneously catalyzed esterification kinetics. Direct coupling of a thin-film evaporator is described as an example for the benefits of on-line NMR spectroscopy in process monitoring. PMID:14729025

Maiwald, Michael; Fischer, Holger H; Kim, Young-Kyu; Albert, Klaus; Hasse, Hans

2004-02-01

101

Quantitative stem cell biology: computational studies in the hematopoietic system  

Microsoft Academic Search

Purpose of review This review is intended to provide an overview of recently published computational methods, including bioinformatic algorithms, mathematical models and simulation studies, applied to stem cell biology, with particular reference to the hematopoietic system. Recent findings The analysis of molecular data is making an increased contribution to identify dynamic system responses. Specifically, there are promising computational approaches to

Ingo Roeder

2006-01-01

102

Quantitative Estimates of Biological Mixing Rates in Abyssal Sediments  

Microsoft Academic Search

Biological mixing in deep-sea sediments is described in terms of a time-dependent eddy diffusion model where mixing takes place to a depth L at constant eddy diffusivity D. The differential equation that describes this model has been solved for an impulse source of tracer delivered to the plane surface that forms the top of the mixed layer. The solution then

D. R. Schink

1975-01-01

103

Progress on quantitative assessment methods of biological aerosols in the atmosphere  

NASA Astrophysics Data System (ADS)

Biological aerosol is one of the most important pollutants in the air, not only influencing public health, and air quality, but also playing an important role in climate change and both chemical and physical processing regulations in the atmosphere. Therefore, the quantification of biological aerosols in the air needs to be more accurate. This article reviews the progress on quantitative assessment methods of biological aerosols in the atmosphere as well as those related merits that each method used.

Liang, L.; He, K.; Duan, F.

2012-02-01

104

Quantitative reflectance spectroscopy of buddingtonite from the Cuprite mining district, Nevada  

SciTech Connect

Buddingtonite, an ammonium-bearing feldspar diagnostic of volcanic-hosted alteration, can be identified and, in some cases, quantitatively measured using short-wave infrared (SWIR) reflectance spectroscopy. In this study over 200 samples from Cuprite, Nevada, were evaluated by X ray diffraction, chemical analysis, scanning electron microscopy, and SWIR reflectance spectroscopy with the objective of developing a quantitative remote-sensing technique for rapid determination of the amount of ammonium or buddingtonite present, and its distribution across the site. Based upon the Hapke theory of radiative transfer from particulate surfaces, spectra from quantitative, physical mixtures were compared with computed mixture spectra. We hypothesized that the concentration of ammonium in each sample is related to the size and shape of the ammonium absorption bands and tested this hypothesis for samples of relatively pure buddingtonite. We found that the band depth of the 2.12-micron NH4 feature is linearly related to the NH4 concentration for the Cuprite buddingtonite, and that the relationship is approximately exponential for a larger range of NH4 concentrations. Associated minerals such as smectite and jarosite suppress the depth of the 2.12-micron NH4 absorption band. Quantitative reflectance spectroscopy is possible when the effects of these associated minerals are also considered.

Felzer, B.; Hauff, P.; Goetz, A.F.H. [Univ. of Colorado, Boulder, CO (United States)

1994-02-01

105

Magnetic resonance microscopy and spectroscopy reveal kinetics of cryoprotectant permeation in a multicompartmental biological system.  

PubMed Central

Successful cryopreservation of most multicompartmental biological systems has not been achieved. One prerequisite for success is quantitative information on cryoprotectant permeation into and amongst the compartments. This report describes direct measurements of cryoprotectant permeation into a multicompartmental system using chemical shift selective magnetic resonance (MR) microscopy and MR spectroscopy. We used the developing zebrafish embryo as a model for studying these complex systems because these embryos are composed of two membrane-limited compartments: (i) a large yolk (surrounded by the yolk syncytial layer) and (ii) differentiating blastoderm cells (each surrounded by a plasma membrane). MR images of the spatial distribution of three cryoprotectants (dimethyl sulfoxide, propylene glycol, and methanol) demonstrated that methanol permeated the entire embryo within 15 min. In contrast, the other cryoprotectants exhibited little or no permeation over 2.5 h. MR spectroscopy and microinjections of cryoprotectants into the yolk inferred that the yolk syncytial layer plays a critical role in limiting the permeation of some cryoprotectants throughout the embryo. This study demonstrates the power of MR technology combined with micromanipulation for elucidating key physiological factors in cryobiology. Images Fig. 1 Fig. 2 Fig. 4 Fig. 5

Hagedorn, M; Hsu, E W; Pilatus, U; Wildt, D E; Rall, W R; Blackband, S J

1996-01-01

106

Fluorescence correlation spectroscopy: Statistical analysis and biological applications  

NASA Astrophysics Data System (ADS)

The experimental design and realization of an apparatus which can be used both for single molecule fluorescence detection and also fluorescence correlation and cross correlation spectroscopy is presented. A thorough statistical analysis of the fluorescence correlation functions including the analysis of bias and errors based on analytical derivations has been carried out. Using the methods developed here, the mechanism of binding and cleavage site recognition of matrix metalloproteinases (MMP) for their substrates has been studied. We demonstrate that two of the MMP family members, Collagenase (MMP-1) and Gelatinase A (MMP-2) exhibit diffusion along their substrates, the importance of this diffusion process and its biological implications are discussed. We show through truncation mutants that the hemopexin domain of the MMP-2 plays and important role in the substrate diffusion of this enzyme. Single molecule diffusion of the collagenase MMP-1 has been observed on collagen fibrils and shown to be biased. The discovered biased diffusion would make the MMP-1 molecule an active motor, thus making it the first active motor that is not coupled to ATP hydrolysis. The possible sources of energy for this enzyme and their implications are discussed. We propose that a possible source of energy for the enzyme can be in the rearrangement of the structure of collagen fibrils. In a separate application, using the methods developed here, we have observed an intermediate in the intestinal fatty acid binding protein folding process through the changes in its hydrodynamic radius also the fluctuations in the structure of the IFABP in solution were measured using FCS.

Saffarian, Saveez

2002-01-01

107

Detection of Biological Materials Using Ion Mobility Spectroscopy  

SciTech Connect

Traditionally, Ion Mobility Spectroscopy has been used to examine ions of relatively low molecular weight and high ion mobility. In recent years, however, biomolecules such as bradykinin, cytochrome c, bovine pancreatic trypsin inhibitor (BPTI), apomyoglobin, and lysozyme, have been successfully analyzed, but studies of whole bio-organisms have not been performed. In this study an attempt was made to detect and measure the mobility of two bacteriophages, {lambda}-phage and MS2 using electrospray methods to inject the viruses into the ion mobility spectrometer. Using data from Yeh, et al., which makes a comparison between the diameter of non-biologic particles and the specific particle mobility, the particle mobility for the MS2 virus was estimated to be 10{sup {minus}2} cm{sup 2}/volt-sec. From this mobility the drift time of these particles in our spectrometer was calculated to be approximately 65 msec. The particle mobility for the {lambda}-phage virus was estimated to be 10{sup {minus}3} cm{sup 2}/volt-sec. which would result in a drift time of 0.7 sec. Spectra showing the presence of a viral peak at the expected drift time were not observed. However, changes in the reactant ion peak that could be directly attributed to the presence of the viruses were observed. Virus clustering, excessive collisions, and the electrospray injection method limited the performance of this IMS. However, we believe that an instrument specifically designed to analyze such bioagents and utilizing other injection and ionization methods will succeed in directly detecting viruses and bacteria.

Rodacy, P.J.; Sterling, J.P.; Butler, M.A.

1999-03-01

108

Electrical and optical spectroscopy for quantitative screening of hepatic steatosis in donor livers  

NASA Astrophysics Data System (ADS)

Macro-steatosis in deceased donor livers is increasingly prevalent and is associated with poor or non-function of the liver upon reperfusion. Current assessment of the extent of steatosis depends upon the macroscopic assessment of the liver by the surgeon and histological examination, if available. In this paper we demonstrate electrical and optical spectroscopy techniques which quantitatively characterize fatty infiltration in liver tissue. Optical spectroscopy showed a correlation coefficient of 0.85 in humans when referenced to clinical hematoxylin and eosin (H&E) sections in 20 human samples. With further development, an optical probe may provide a comprehensive measure of steatosis across the liver at the time of procurement.

McLaughlin, B. L.; Wells, A. C.; Virtue, S.; Vidal-Puig, A.; Wilkinson, T. D.; Watson, C. J. E.; Robertson, P. A.

2010-11-01

109

Quantitative Imaging of Single Upconversion Nanoparticles in Biological Tissue  

PubMed Central

The unique luminescent properties of new-generation synthetic nanomaterials, upconversion nanoparticles (UCNPs), enabled high-contrast optical biomedical imaging by suppressing the crowded background of biological tissue autofluorescence and evading high tissue absorption. This raised high expectations on the UCNP utilities for intracellular and deep tissue imaging, such as whole animal imaging. At the same time, the critical nonlinear dependence of the UCNP luminescence on the excitation intensity results in dramatic signal reduction at (?1 cm) depth in biological tissue. Here, we report on the experimental and theoretical investigation of this trade-off aiming at the identification of optimal application niches of UCNPs e.g. biological liquids and subsurface tissue layers. As an example of such applications, we report on single UCNP imaging through a layer of hemolyzed blood. To extend this result towards in vivo applications, we quantified the optical properties of single UCNPs and theoretically analyzed the prospects of single-particle detectability in live scattering and absorbing bio-tissue using a human skin model. The model predicts that a single 70-nm UCNP would be detectable at skin depths up to 400 µm, unlike a hardly detectable single fluorescent (fluorescein) dye molecule. UCNP-assisted imaging in the ballistic regime thus allows for excellent applications niches, where high sensitivity is the key requirement.

Nadort, Annemarie; Sreenivasan, Varun K. A.; Song, Zhen; Grebenik, Ekaterina A.; Nechaev, Andrei V.; Semchishen, Vladimir A.; Panchenko, Vladislav Y.; Zvyagin, Andrei V.

2013-01-01

110

Quantitative analysis of the mixtures of illicit drugs using terahertz time-domain spectroscopy  

NASA Astrophysics Data System (ADS)

A method was proposed to quantitatively inspect the mixtures of illicit drugs with terahertz time-domain spectroscopy technique. The mass percentages of all components in a mixture can be obtained by linear regression analysis, on the assumption that all components in the mixture and their absorption features be known. For illicit drugs were scarce and expensive, firstly we used common chemicals, Benzophenone, Anthraquinone, Pyridoxine hydrochloride and L-Ascorbic acid in the experiment. Then illicit drugs and a common adulterant, methamphetamine and flour, were selected for our experiment. Experimental results were in significant agreement with actual content, which suggested that it could be an effective method for quantitative identification of illicit drugs.

Jiang, Dejun; Zhao, Shusen; Shen, Jingling

2008-03-01

111

Quantitation of cannabinoids in biological fluids by radioimmunoassay.  

PubMed

A tritium based radioimmunoassay for delta9THC and its metabolites has been developed for the use of investigators studying the epidemiological, medical, clinical, and research aspects of cannabis use. The assay is sufficiently sensitive to detect cannabinoids in the urine of marijuana smokers for several days after their last exposure to the drug. The results obtained from a 28 day study indicate that the assay reflects the administration and removal of oral doses of THC. The specificity of the antisera, as determined in cross reactivity studies, allows not only the assay of metabolites in biological samples without interference from other drugs, but also the evaluation of extracts of other kinds of samples which may contain unmetabolized delta9THC. The technique of radioimmunoassay has many advantages over other methods of analysis. It is simple to perform and can be readily applied to the rapid analysis of large numbers of samples. It can be used in the direct analysis of physiological fluids and other biological samples which ordinarily have to be processed before other techniques can be applied. The method is non-destructive abd obviates the need to use radiolabelled drugs in man during metabolic and other studies. This radioimmunoassay has been designed with particular emphasis on ease of use by other investigators. We anticipate that it will prove useful to investigators and scientists for determining the absence, or presence and amount, of THC metabolite in a biological specimen, for epidemiologists in determining the full extent of cannabis use and to the medical/clinical community for establishing the minimum effective dose of delta9THC for each patient. The widespread application of a single method of analysis should also remove a great deal of the controversy surrounding marijuana studies performed to date. PMID:987538

Chase, A R; Kelley, P R; Taunton-Rigby, A; Jones, R T; Harwood, T

1976-05-01

112

Quantitative analysis of lithium in Al-Li alloys by ionization energy loss spectroscopy  

Microsoft Academic Search

A quantitative analysis of lithium in Al-Li alloys has been carried out by ionization energy loss spectroscopy. It has been found that the power law I = A E gives the best fit to the background immediately preceding the Li-K edge, and that the optimum value of the spectrometer acceptance semi-angle ? is about 2 mrad. The Al:Li ratio on

Helen M. Chan; David B. Williams

1985-01-01

113

Quantitative determination of element concentrations in industrial oxide materials by laser-induced breakdown spectroscopy  

Microsoft Academic Search

Calibration-free laser-induced breakdown spectroscopy (CF-LIBS) method is employed for quantitative determination of oxide\\u000a concentrations in multi-component materials. Industrial oxide materials from steel industry are laser ablated in air, and\\u000a the optical plasma emission is collected by spectrometers and gated detectors. The temperature and electron number density\\u000a of laser-induced plasma are determined from measured LIBS spectra. Emission lines of aluminium (Al),

B. Praher; R. Rössler; E. Arenholz; J. Heitz; J. D. Pedarnig

114

A calculation of backscattering factor database for quantitative analysis by Auger electron spectroscopy  

Microsoft Academic Search

A systematic calculation of the backscattering factor in quantitative analysis by Auger electron spectroscopy has been performed for the primary electron beam of energy from the threshold energy of inner-shell ionization to 30 keV at the incident angle of 0°–89° and for principal Auger transition and Auger electrons emitted from over 28 pure elements at an emission angle of 0°–89°

R. G. Zeng; Z. J. Ding; Y. G. Li; S. F. Mao

2008-01-01

115

A calculation of backscattering factor database for quantitative analysis by Auger electron spectroscopy  

Microsoft Academic Search

A systematic calculation of the backscattering factor in quantitative analysis by Auger electron spectroscopy has been performed for the primary electron beam of energy from the threshold energy of inner-shell ionization to 30 keV at the incident angle of 0°-89° and for principal Auger transition and Auger electrons emitted from over 28 pure elements at an emission angle of 0°-89°

R. G. Zeng; Z. J. Ding; Y. G. Li; S. F. Mao

2008-01-01

116

An efficient method-development strategy for quantitative chemical imaging using terahertz pulse spectroscopy  

Microsoft Academic Search

The purpose of our research was to investigate efficient procedures for generating multivariate prediction vectors for quantitative\\u000a chemical analysis of solid dosage forms using terahertz pulse imaging (TPI) reflection spectroscopy. A set of calibration\\u000a development and validation tablet samples was created following a ternary mixture of anhydrous theophylline, lactose monohydrate,\\u000a and microcrystalline cellulose (MCC). Spectral images of one side of

Robert P. Cogdill; Steven M. Short; Ryanne Forcht; Zhenqi Shi; Yaochun Shen; Philip F. Taday; Carl A. Anderson; James K. Drennen

2006-01-01

117

Optimized external IR reflection spectroscopy for quantitative determination of borophosphosilicate glass parameters  

Microsoft Academic Search

Infrared (IR) external reflection spectroscopy has been optimized for the quantitative determination of composition and film thickness of borophosphosilicate glass (BPSG) deposited on silicon wafer substrates. The precision of the partial least-squares calibrations for boron and phosphorus contents and thin-film thickness were measured as the cross-validated standard error of prediction statistic. The results showed that BPSG IR reflection spectra collected

Lizhong Zhang; James E. Franke; Thomas M. Niemczyk; David M. Haaland

1997-01-01

118

Quantitative characterisation of historic paper using THz spectroscopy and multivariate data analysis  

NASA Astrophysics Data System (ADS)

THz spectroscopy in the time domain was explored in combination with multivariate data analysis, for quantitative determination of chemical and mechanical properties of historic paper, such as lignin content, tensile strength, and ash content. Using partial least squares (PLS) regression, it was shown that quantitative prediction of the material properties is possible, which indicates the potential of THz spectroscopy for chemical characterisation of complex organic materials of natural origin. In addition, the results demonstrate that THz spectra and PLS loading weights for lignin content differ significantly, which leads to the conclusion that THz spectra of composite macromolecular materials do not represent sums of spectra of the individual components. This supports the premise that THz spectra reflect intermolecular interactions. The study was carried out using 250 historical paper samples from the sixteenth century to present. Although the measurements were performed in vacuum to improve the quality of spectra, THz spectroscopy is in principle non-destructive. This research therefore reinforces the role of THz spectroscopy in characterisation of valuable historic materials, where invasive analysis is often not possible.

Trafela, Tanja; Mizuno, Maya; Fukunaga, Kaori; Strli?, Matija

2013-04-01

119

SAC-CI methodology applied to molecular spectroscopy and photo-biology  

NASA Astrophysics Data System (ADS)

The SAC-CI method was applied to the spectroscopy of radical cations and anions of various organic molecules. It was also applied to photo-biology, in particular, to elucidate the bio-molecular color-tuning mechanism of human visions and to the circular dichroism spectroscopy that is used to understand the helical structures of DNA and RNA.

Hasegawa, J.; Miyahara, T.; Nakashima, H.; Nakatsuji, H.

2012-06-01

120

Biphasic dose responses in biology, toxicology and medicine: Accounting for their generalizability and quantitative features.  

PubMed

The most common quantitative feature of the hormetic-biphasic dose response is its modest stimulatory response which at maximum is only 30-60% greater than control values, an observation that is consistently independent of biological model, level of organization (i.e., cell, organ or individual), endpoint measured, chemical/physical agent studied, or mechanism. This quantitative feature suggests an underlying "upstream" mechanism common across biological systems, therefore basic and general. Hormetic dose response relationships represent an estimate of the peak performance of integrative biological processes that are allometrically based. Hormetic responses reflect both direct stimulatory or overcompensation responses to damage induced by relatively low doses of chemical or physical agents. The integration of the hormetic dose response within an allometric framework provides, for the first time, an explanation for both the generality and the quantitative features of the hormetic dose response. PMID:23992683

Calabrese, Edward J

2013-08-29

121

The Lightning Rod Model: a Genesis for Quantitative Near-Field Spectroscopy  

NASA Astrophysics Data System (ADS)

Near-field infrared spectroscopy has the proven ability to resolve optical contrasts in materials at deeply sub-wavelength scales across a broad range of infrared frequencies. In principle, the technique enables sub-diffractional optical identification of chemical compositions within nanostructured and naturally heterogeneous samples. However current models of probe-sample optical interaction, while qualitatively descriptive, cannot quantitatively explain infrared near-field spectra, especially for strongly resonant sample materials. We present a new first-principles model of near-field interaction, and demonstrate its superb agreement with infrared near-field spectra measured for thin films of silicon dioxide and the strongly phonon-resonant material silicon carbide. Using this model we reveal the role of probe geometry and surface mode dispersion in shaping the measured near-field spectrum, establishing its quantitative relationship with the dielectric properties of the sample. This treatment offers a route to the quantitative determination of optical constants at the nano-scale.

McLeod, Alexander; Andreev, Gregory; Dominguez, Gerardo; Thiemens, Mark; Fogler, Michael; Basov, D. N.

2013-03-01

122

Quantitative {sup 29}Si MAS NMR spectroscopy of cement and silica fume containing paramagnetic impurities  

SciTech Connect

The low natural abundance and the long spin lattice relaxation time of {sup 29}Si lead to long measurement times and/or low signal-to-noise ratios using {sup 29}Si magic angle spinning NMR spectroscopy. By contrast, samples containing paramagnetic iron ions have much shorter relaxation times, making measurements up to seven times more efficient, but at the same time making quantitative analysis unreliable. To solve the problem, the spin-lattice relaxation times of ordinary Portland cement (opc) and silica fume with and without iron content has been determined with inversion recovery experiments. The effect of varying the spectrum repetition time on the quantitative analysis is demonstrated for mixtures of opc with silica fume. For opc and silica fume with iron impurities repetition times as short as 5 s has permitted accurate quantitative analysis of the silicates present in these materials.

Hilbig, H. [Center of Building Materials (CBM), Technische Universitaet Muenchen, Baumbachstr. 7, D-81245 Munich (Germany)]. E-mail: hilbig@cbm.bv.tum.de; Koehler, F.H. [Department Chemie, Technische Universitaet Muenchen, D-85747 Garching (Germany); Schiessl, P. [Center of Building Materials (CBM), Technische Universitaet Muenchen, Baumbachstr. 7, D-81245 Munich (Germany)

2006-02-15

123

Histochemical analysis of biological tissues using Raman spectroscopy  

Microsoft Academic Search

This paper reviews the application of the Raman spectroscopic technique for analysis of biological tissue. The advantages and disadvantages of visible, near-IR and UV excitations are described, and the problems and prospects of using these methodologies for disease diagnosis are addressed. In situ analysis of tissue proteins, lens, cornea, blood constituents, biological stones and several hard tissues is reviewed, and

Ramasamy Manoharan; Yang Wang; Michael S. Feld

1996-01-01

124

Determination of Calcium in Cereal with Flame Atomic Absorption Spectroscopy: An Experiment for a Quantitative Methods of Analysis Course  

ERIC Educational Resources Information Center

|An experiment for determination of calcium in cereal using two-increment standard addition method in conjunction with flame atomic absorption spectroscopy (FAAS) is demonstrated. The experiment is intended to introduce students to the principles of atomic absorption spectroscopy giving them hands on experience using quantitative methods of…

Bazzi, Ali; Kreuz, Bette; Fischer, Jeffrey

2004-01-01

125

Quantitative assessment of biological impact using transcriptomic data and mechanistic network models.  

PubMed

Exposure to biologically active substances such as therapeutic drugs or environmental toxicants can impact biological systems at various levels, affecting individual molecules, signaling pathways, and overall cellular processes. The ability to derive mechanistic insights from the resulting system responses requires the integration of experimental measures with a priori knowledge about the system and the interacting molecules therein. We developed a novel systems biology-based methodology that leverages mechanistic network models and transcriptomic data to quantitatively assess the biological impact of exposures to active substances. Hierarchically organized network models were first constructed to provide a coherent framework for investigating the impact of exposures at the molecular, pathway and process levels. We then validated our methodology using novel and previously published experiments. For both in vitro systems with simple exposure and in vivo systems with complex exposures, our methodology was able to recapitulate known biological responses matching expected or measured phenotypes. In addition, the quantitative results were in agreement with experimental endpoint data for many of the mechanistic effects that were assessed, providing further objective confirmation of the approach. We conclude that our methodology evaluates the biological impact of exposures in an objective, systematic, and quantifiable manner, enabling the computation of a systems-wide and pan-mechanistic biological impact measure for a given active substance or mixture. Our results suggest that various fields of human disease research, from drug development to consumer product testing and environmental impact analysis, could benefit from using this methodology. PMID:23933166

Thomson, Ty M; Sewer, Alain; Martin, Florian; Belcastro, Vincenzo; Frushour, Brian P; Gebel, Stephan; Park, Jennifer; Schlage, Walter K; Talikka, Marja; Vasilyev, Dmitry M; Westra, Jurjen W; Hoeng, Julia; Peitsch, Manuel C

2013-08-08

126

Ultrasensitive investigations of biological systems by fluorescence correlation spectroscopy  

Microsoft Academic Search

Fluorescence correlation spectroscopy (FCS) extracts information about molecular dynamics from the tiny fluctuations that can be observed in the emission of small ensembles of fluorescent molecules in thermodynamic equilibrium. Employing a confocal setup in conjunction with highly dilute samples, the average number of fluorescent particles simultaneously within the measurement volume (?1fl) is minimized. Among the multitude of chemical and physical

Elke Haustein; Petra Schwille

2003-01-01

127

Quantitative and qualitative analysis of urine component in the toilet set using Raman spectroscopy  

NASA Astrophysics Data System (ADS)

As a part of non-invasive and unaware measurement of physiological signal in the house of live-alone person, Raman spectroscopy was applied for urine component analysis in the toilet set. 785nm, 250-300mW output solid state diode laser and 2048 element linear silicon TE cooled CCD array were incorporated for this system. Several tests were performed for setting up Raman spectroscopy in non-constrained situation: toilet set in the house. The effect of dark current, integration time, warming up time of laser, property of probe and interference of water in the toilet were tested and controlled for appropriate measurement in this environment. The spectra were obtained immediately when the subject uses the toilet set, and they can be transmitted to the server though Bluetooth. Those spectra were pre-processed for removing or correcting the effect of undesired light scattering, sample path-length difference and baseline-effect. The preprocessed data were enhanced for more exact result of multivariate analysis. The training data was prepared for predicting unknown component and its concentration by using multivariate methods. Several kinds of multivariate methods: PCA, PCR, PLS were performed to validate what is the fittest method in this environment. Through quantitative and qualitative analysis of Raman spectroscopy"s spectra obtained in the house's toilet set, we could know the component and its concentration of urine which can be index of disease.

Chung, So Hyun; Park, Kwang Suk; Choi, Jong Min; Lee, Won Jin

2004-07-01

128

Quantitative x-ray photoelectron spectroscopy study of Al/AlOx bilayers  

NASA Astrophysics Data System (ADS)

An x-ray photoelectron spectroscopy (XPS) analysis of Nb/Al wedge bilayers, oxidized by both plasma and natural oxidation, is reported. The main goal is to show that the oxidation state--i.e., O:(oxidize)Al ratio--, structure and thickness of the surface oxide layer, as well as the thickness of the metallic Al leftover, as functions of the oxidation procedure, can be quantitatively evaluated from the XPS spectra. This is relevant to the detailed characterization of the insulating barriers in (magnetic) tunnel junctions.

Batlle, Xavier; Hattink, Bart Jan; Labarta, Amilcar; Akerman, Johan J.; Escudero, Roberto; Schuller, Ivan K.

2002-06-01

129

Quantitative Analysis for Monitoring Formulation of Lubricating Oil Using Terahertz Time-Domain Transmission Spectroscopy  

NASA Astrophysics Data System (ADS)

The quantitative analysis of zinc isopropyl-isooctyl-dithiophosphate (T204) mixed with lube base oil from Korea with viscosity index 70 (T204-Korea70) is presented by using terahertz time-domain spectroscopy (THz-TDS). Compared with the middle-infrared spectra of zinc n-butyl-isooctyl-dithiophosphate (T202) and T204, THz spectra of T202 and T204 show the weak broad absorption bands. Then, the absorption coefficients of the T204-Korea70 system follow Beer's law at the concentration from 0.124 to 4.024%. The experimental absorption spectra of T204-Korea70 agree with the calculated ones based on the standard absorption coefficients of T204 and Korea70. The quantitative analysis enables a strategy to monitor the formulation of lubricating oil in real time.

Tian, Lu; Zhao, Kun; Zhou, Qing-Li; Shi, Yu-Lei; Zhang, Cun-Lin

2012-04-01

130

Artificial neural network for on-site quantitative analysis of soils using laser induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

Nowadays, due to environmental concerns, fast on-site quantitative analyses of soils are required. Laser induced breakdown spectroscopy is a serious candidate to address this challenge and is especially well suited for multi-elemental analysis of heavy metals. However, saturation and matrix effects prevent from a simple treatment of the LIBS data, namely through a regular calibration curve. This paper details the limits of this approach and consequently emphasizes the advantage of using artificial neural networks well suited for non-linear and multi-variate calibration. This advanced method of data analysis is evaluated in the case of real soil samples and on-site LIBS measurements. The selection of the LIBS data as input data of the network is particularly detailed and finally, resulting errors of prediction lower than 20% for aluminum, calcium, copper and iron demonstrate the good efficiency of the artificial neural networks for on-site quantitative LIBS of soils.

El Haddad, J.; Villot-Kadri, M.; Ismaël, A.; Gallou, G.; Michel, K.; Bruyère, D.; Laperche, V.; Canioni, L.; Bousquet, B.

2013-01-01

131

Quantitative image analysis for the characterization of microbial aggregates in biological wastewater treatment: a review.  

PubMed

Quantitative image analysis techniques have gained an undeniable role in several fields of research during the last decade. In the field of biological wastewater treatment (WWT) processes, several computer applications have been developed for monitoring microbial entities, either as individual cells or in different types of aggregates. New descriptors have been defined that are more reliable, objective, and useful than the subjective and time-consuming parameters classically used to monitor biological WWT processes. Examples of this application include the objective prediction of filamentous bulking, known to be one of the most problematic phenomena occurring in activated sludge technology. It also demonstrated its usefulness in classifying protozoa and metazoa populations. In high-rate anaerobic processes, based on granular sludge, aggregation times and fragmentation phenomena could be detected during critical events, e.g., toxic and organic overloads. Currently, the major efforts and needs are in the development of quantitative image analysis techniques focusing on its application coupled with stained samples, either by classical or fluorescent-based techniques. The use of quantitative morphological parameters in process control and online applications is also being investigated. This work reviews the major advances of quantitative image analysis applied to biological WWT processes. PMID:23716077

Costa, J C; Mesquita, D P; Amaral, A L; Alves, M M; Ferreira, E C

2013-05-29

132

Quantitative analysis of alpha-D-glucose in an ionic liquid by using infrared spectroscopy.  

PubMed

The applicability of infrared (IR) spectroscopy for quantitative concentration measurements in mixtures of carbohydrates and ionic liquids (ILs) is investigated. The compound 1-ethyl-3-methylimidazolium acetate, [EMIM][OAc]-an "enzyme-friendly" ionic liquid with great application potential in the dissolution of various biomasses-is used as solvent in combination with alpha-D-glucose. Our study establishes a new way to monitor the concentration of sugars in ILs, thus providing a convenient method to follow the kinetics of, for example, enzymatic reactions in [EMIM][OAc]. As a first step, we present the IR spectrum of pure [EMIM][OAc] (this constitutes the first vibrational study of this particular IL). Although numerous lines overlap in the fingerprint region of the spectrum, characteristic features can be assigned to the corresponding vibrational modes of both ions. Secondly, we study different mixtures of the IL with alpha-D-glucose (in the concentration range: 0-20 mass % glucose) and analyze them by means of IR spectroscopy, followed by computational methods, thus demonstrating the great potential of this spectroscopic technique in quantitative measurements. PMID:18442034

Kiefer, Johannes; Obert, Katharina; Bösmann, Andreas; Seeger, Thomas; Wasserscheid, Peter; Leipertz, Alfred

2008-06-23

133

Quantitation of crystalline and amorphous forms of anhydrous neotame using 13C CPMAS NMR spectroscopy.  

PubMed

Although most drugs are formulated in the crystalline state, amorphous or other crystalline forms are often generated during the formulation process. The presence of other forms can dramatically affect the physical and chemical stability of the drug. The identification and quantitation of different forms of a drug is a significant analytical challenge, especially in a formulated product. The ability of solid-state 13C NMR spectroscopy with cross polarization (CP) and magic-angle spinning (MAS) to quantify the amounts of three of the multiple crystalline and amorphous forms of the artificial sweetener neotame is described. It was possible to quantify, in a mixture of two anhydrous polymorphic forms of neotame, the amount of each polymorph within 1-2%. In mixtures of amorphous and crystalline forms of neotame, the amorphous content could be determined within 5%. It was found that the crystalline standards that were used to prepare the mixtures were not pure crystalline forms, but rather a mixture of crystalline and amorphous forms. The effect of amorphous content in the crystalline standards on the overall quantitation of the two crystalline polymorphic forms is discussed. The importance of differences in relaxation parameters and CP efficiencies on quantifying mixtures of different forms using solid-state NMR spectroscopy is also addressed. PMID:16258988

Offerdahl, Thomas J; Salsbury, Jonathon S; Dong, Zedong; Grant, David J W; Schroeder, Stephen A; Prakash, Indra; Gorman, Eric M; Barich, Dewey H; Munson, Eric J

2005-12-01

134

Feasibility Study of Using Short Wave Infrared Cavity Ringdown Spectroscopy (SWIR-CRDS) for Biological Agent Detection  

SciTech Connect

This project focused on determining the feasibility of using short wave infrared (SWIR) cavity ring down spectroscopy (CRDS) as a means for real-time detection of biological aerosols. The first part of the project involved identifying biological agent signatures that could be detected with SWIR CRDS. After an exhaustive search of the open literature it was determined that whole biological spores and/or cells would not be good candidates for direct SWIR CRDS probing because they have no unique SWIR signatures. It was postulated that while whole cells or spores are not good candidates for SWIR CRDS detection, their pyrolysis break-down products might be. A literature search was then conducted to find biological pyrolysis products with low molecular weights and high symmetry since these species most likely would have overtone and combination vibrational bands that can be detected in the SWIR. It was determined that pyrrole, pyridine and picolinamide were good candidates for evaluation. These molecules are formed when proteins and porphyrins, proteins and dipicolinic acid, and dipicolinic acid are pyrolyzed, respectively. The second part of the project involved measuring quantitative SWIR spectra of pyrrole, pyridine and picolinamide in PNNL’s FTIR Spectroscopy Laboratory. Spectral information about these molecules, in the vapor phase is sparse – there were only a few prior studies that measured line positions and no information on absorption cross sections. Absorption cross sections are needed in order to estimate the SWIR CRDS detection sensitivity, and line position determines what type of laser will be needed for the sensor. The results of the spectroscopy studies allowed us to estimate the SWIR CRDS detection sensitivity for pyrrole to be 3 x 1012 molec cm-3 or 0.1 ppmv, and for pyridine it was 1.5 x 1015 molec cm-3 or 0.6 ppmv. These detection sensitivity limits are close what we have measured for ammonia. Given these detection limits we then estimated the amount of biological material that would have to be collected for analysis in a sensor that combined pyrolysis with SWIR CRDS. Using conservative estimates of pyrolysis yields and precursor species concentration we determined that it would be necessary to collect and pyrolyze biological aerosol samples in the 10’s of mg. This is a large amount and is far larger than required for current sensors. It is therefore concluded that while possible, the large amounts of material required preclude using SWIR CRDS for detecting biological agents at this time.

Aker, Pam M.; Johnson, Timothy J.; Williams, Richard M.; Valentine, Nancy B.

2007-10-01

135

Biological mineralization of iron: Studies using Mössbauer spectroscopy and complementary techniques  

NASA Astrophysics Data System (ADS)

Biological deposition of solid Fe-containing phases can be studied using57Fe Mössbauer spectroscopy. Other techniques are needed in order to understand this complex process. These include proton-induced X-ray and ?-ray emission (PIXE/PIGME), electron microscopy, electron and X-ray diffraction, infrared spectroscopy and chemical characterization of organic components. This paper reviews and evaluates the application of these techniques to biological mineralization of Fe, particularly that occurring in the radula teeth of the marine molluscs, chitons and limpets.

Webb, J.; Kim, K.-S.; Tran, K. C.; Pierre, T. G. St.

1988-02-01

136

CMOS based sensor for dielectric spectroscopy of biological cell suspension  

NASA Astrophysics Data System (ADS)

In this work we investigate the use of microwave frequency range to measure the concentration of cells in a biological cell suspension. A theoretical model is discussed and the advantage of high frequency, which is to avoid dispersion mechanisms due to the cell parameters at lower frequencies (for example membrane capacitance), has been described. Interdigitated capacitor (IDC) has been proposed as the sensor for analysing the concentration of a cell species in the suspension. The read-out circuit is a VCO using the IDC and a pair of inductors as resonator. The capacitance of the IDC which is the function of the permittivity of the biological cell suspension determines the resonant frequency of the LC tank oscillator. Thus the concentration of cells in a solution, affecting its permittivity, is read out as the frequency of the oscillator.

Guha, S.; Schmalz, K.; Meliani, C.; Wenger, Ch

2013-04-01

137

Laser-induced fluorescence-cued, laser-induced breakdown spectroscopy biological-agent detection  

Microsoft Academic Search

Methods for accurately characterizing aerosols are required for detecting biological warfare agents. Currently, fluorescence-based biological agent sensors provide adequate detection sensitivity but suffer from high false-alarm rates. Combining single-particle fluorescence analysis with laser-induced breakdown spectroscopy (LIBS) provides additional discrimination and potentially reduces false-alarm rates. A transportable UV laser-induced fluorescence-cued LIBS test bed has been developed and used to evaluate the

John D. Hybl; Shane M. Tysk; Shaun R. Berry; Michael P. Jordan

2006-01-01

138

Fast and accurate quantitation of glucans in complex mixtures by optimized heteronuclear NMR spectroscopy.  

PubMed

Nuclear magnetic resonance (NMR) spectroscopy is a widely used technique for mixture analysis, but it has shortcomings in resolving carbohydrate mixtures due to the narrow chemical shift range of glycans in general and fragments of homopolymers in particular. Here, we suggest a protocol toward fast spectroscopic glycan mixture analysis. We show that a plethora of oligosaccharides comprising only ?-glucopyranosyl residues can be resolved into distinct quantifiable signals with NMR experiments that are substantially faster than chromatographic runs. Conceptually, the approach fully exploits the narrow line widths of glycans (?1/2 < 3 Hz) in the (13)C spectral dimension while disregarding superfluous spectral information in compound identification and quantitation. The acetal (H1C1) groups suffice to spectroscopically resolve ?20 different starch fragments in optimized (1)H-(13)C NMR with a narrow (13)C spectral width (3 ppm) that allows sampling the indirect (13)C dimension at high resolution within 15 min. Rapid quantitations by high-resolution NMR data are achieved for glycans at concentrations as low as 10 ?g/mL. For validation, comparisons were made with quantitations obtained by more time-consuming chromatographic methods and yielded coefficients of determination (R(2)) above 0.99. PMID:23952648

Bøjstrup, Marie; Petersen, Bent O; Beeren, Sophie R; Hindsgaul, Ole; Meier, Sebastian

2013-08-23

139

Laser-induced fluorescence-cued, laser-induced breakdown spectroscopy biological-agent detection  

SciTech Connect

Methods for accurately characterizing aerosols are required for detecting biological warfare agents. Currently, fluorescence-based biological agent sensors provide adequate detection sensitivity but suffer from high false-alarm rates. Combining single-particle fluorescence analysis with laser-induced breakdown spectroscopy (LIBS) provides additional discrimination and potentially reduces false-alarm rates. A transportable UV laser-induced fluorescence-cued LIBS test bed has been developed and used to evaluate the utility of LIBS for biological-agent detection. Analysis of these data indicates that LIBS adds discrimination capability to fluorescence-based biological-agent detectors.However, the data also show that LIBS signatures of biological agent simulants are affected by washing. This may limit the specificity of LIBS and narrow the scope of its applicability in biological-agent detection.

Hybl, John D.; Tysk, Shane M.; Berry, Shaun R.; Jordan, Michael P

2006-12-01

140

Near infrared spectroscopy of forest soils to determine chemical and biological properties related to soil sustainability  

Microsoft Academic Search

Sustainability related soil changes due to site disturbance during forest harvesting need to be assessed. Near infrared spectroscopy (NIRS) may be useful for assessing large numbers of samples covering a landscape and dispersed over a long time span. This paper presents an evaluation of the use of NIRS to examine a number of chemical and biological soil properties. One hundred

B Ludwig; P. K Khanna; J Bauhus; P Hopmans

2002-01-01

141

Near-infrared Raman spectroscopy of single optically trapped biological cells  

NASA Astrophysics Data System (ADS)

We report on the development and testing of a compact laser tweezers Raman spectroscopy (LTRS) system. The system combines optical trapping and near-infrared Raman spectroscopy for manipulation and identification of single biological cells in solution. A low-power diode laser at 785 nm was used for both trapping and excitation for Raman spectroscopy of the suspended microscopic particles. The design of the LTRS system provides high sensitivity and permits real-time spectroscopic measurements of the biological sample. The system was calibrated by use of polystyrene microbeads and tested on living blood cells and on both living and dead yeast cells. As expected, different images and Raman spectra were observed for the different cells. The LTRS system may provide a valuable tool for the study of fundamental cellular processes and the diagnosis of cellular disorders.

Xie, Changan; Dinno, Mumtaz A.; Li, Yong-Qing

2002-02-01

142

Quantitative detection of plasma-generated radicals in liquids by electron paramagnetic resonance spectroscopy  

NASA Astrophysics Data System (ADS)

In this paper the qualitative and quantitative detection of oxygen radicals in liquids after plasma treatment with an atmospheric pressure argon plasma jet by electron paramagnetic resonance spectroscopy is investigated. Absolute values for ·OH and O_{2}^{\\cdot -} radical concentration and their net production rate in plasma-treated liquids are determined without the use of additional scavenging chemicals such as superoxide dismutase (SOD) or mannitol (D-MAN). The main oxygen-centred radical generation in PBS was found to originate from the superoxide radical. It is shown that hidden parameters such as the manufacturer of chemical components could have a big influence on the comparability and reproducibility of the results. Finally, the effect of a shielding gas device for the investigated plasma jet with a shielding gas composition of varying oxygen-to-nitrogen ratio on radical generation after plasma treatment of phosphate-buffered saline solution was investigated.

Tresp, H.; Hammer, M. U.; Winter, J.; Weltmann, K.-D.; Reuter, S.

2013-10-01

143

Quantitation of pH-induced aggregation in binary protein mixtures by dielectric spectroscopy.  

PubMed

This paper presents a quantitative approach for measuring pH-controlled protein aggregation using dielectric spectroscopy. The technique is demonstrated through two aggregation experiments, the first between ?-lactoglobulin (?-Lg) and hen lysozyme (HENL) and the second between bovine serum albumin (BSA) and HENL. In both experiments, the formation of aggregates is strongly dependent on the solution pH and is clearly indicated by a decrease in the measured permittivity when the second protein is added. A quantifiable lower-bound on the ratio of proteins involved in the aggregation process is obtained from the permittivity spectra. Lower-bound aggregation ratios of 83 % for ?-Lg/HENL at pH 6.0 and 48 % for BSA/HENL at pH 9.2 were consistent with turbidity measurements made on the same solutions. PMID:23001617

Mellor, Brett L; Wood, Stephen J; Mazzeo, Brian A

2012-12-01

144

Detection and quantitative analysis of ferrocyanide and ferricyanide: FY 93 Florida State University Raman spectroscopy report  

SciTech Connect

This report provides a summary of work to develop and investigate the feasibility of using Raman spectroscopy with tank waste materials. It contains Raman spectra from organics, such as ethylenediaminetetraacetic acid (EDTA), hydroxyethylenediaminetetraacteic acid (HEDTA), imino diacetic acid (IDA), kerosene, tributyl phosphate (TBP), acetone and butanol, anticipated to be present in tank wastes and spectra from T-107 real and BY-104 simulant materials. The results of investigating Raman for determining moisture content in tank materials are also presented. A description of software algorithms developed to process Raman spectra from a dispersive grating spectrometer system and an in initial design for a data base to support qualitative and quantitative application of remote Raman sensing with tank wastes.

Mann, C.K.; Vickers, T.J. [Florida State Univ., Tallahassee, FL (United States). Dept. of Chemistry

1994-10-11

145

Quantitative analysis of trace metal accumulation in teeth using laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

The technique of laser ablation is receiving increasing attention for applications in dentistry, specifically for the treatment of teeth (e.g. drilling of micro-holes and plaque removal). In the process of ablation a luminous micro-plasma is normally generated which may be exploited for elemental analysis. Here we report on quantitative Laser-Induced Breakdown Spectroscopy (LIBS) analysis to study the presence of trace minerals in teeth. A selection of teeth of different age groups has been investigated, ranging from the first teeth of infants, through the second teeth of children, to adults to trace the influence of environmental factors on the accumulation of a number of elements in teeth. We found a close link between elements detected in tooth fillings and toothpastes with those present in teeth.

Samek, O.; Beddows, D. C. S.; Telle, H. H.; Morris, G. W.; Liska, M.; Kaiser, J.

146

One-point calibration for calibration-free laser-induced breakdown spectroscopy quantitative analysis  

NASA Astrophysics Data System (ADS)

We present a new method for improving the reliability of quantitative analysis by laser-induced breakdown spectroscopy (LIBS). The method can be considered as a variation of the calibration-free LIBS approach; although not completely standard-less, only one standard of known composition and similar matrix to the one to be analyzed is needed. On the other hand, the one-point calibration approach allows the empirical determination of essential experimental and spectroscopic parameters, whose knowledge is often imprecise or lacking; the result is a definite improvement of the trueness of LIBS analysis with respect to the traditional calibration-free approach. The characteristics and advantages of the proposed one-point calibration LIBS approach will be demonstrated on a set of copper-based samples of known composition.

Cavalcanti, G. H.; Teixeira, D. V.; Legnaioli, S.; Lorenzetti, G.; Pardini, L.; Palleschi, V.

2013-09-01

147

Optimized external IR reflection spectroscopy for quantitative determination of borophosphosilicate glass parameters  

SciTech Connect

Infrared (IR) external reflection spectroscopy has been optimized for the quantitative determination of composition and film thickness of borophosphosilicate glass (BPSG) deposited on silicon wafer substrates. The precision of the partial least-squares calibrations for boron and phosphorus contents and thin-film thickness were measured as the cross-validated standard error of prediction statistic. The results showed that BPSG IR reflection spectra collected over a wide range of incident IR radiation angles (15{degree}, 25{degree}, 45{degree}, and 60{degree}) can be used for the simultaneous quantification of these three BPSG parameters. When high angles of incidence were employed, the measurement was found to be more sensitive to small errors in the angle of incidence. The polarization state of the incident IR radiation did not noticeably affect the prediction of the three calibrated BPSG parameters. The results achieved in this study provide guidelines for at-line process monitoring and quality control of BPSG thin films used in the fabrication of microelectronic devices. {copyright} {ital 1997} {ital Society for Applied Spectroscopy}

Zhang, L.; Franke, J.E.; Niemczyk, T.M. [Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Haaland, D.M. [Sandia National Laboratories, Albuquerque, New Mexico 87185-0342 (United States)

1997-02-01

148

[Simultaneous quantitative determination of multicomponents in tablets based on terahertz time-domain spectroscopy].  

PubMed

Terahertz time-domain spectroscopy (THz-TDS) combined with chemometric modeling methods was used to perform quantitative analysis of both active pharmaceutical ingredient (API) and excipient concentrations of multicomponent pharmaceutical mixtures. The THz spectra of ternary mixtures formulated with anhydrous theophylline, lactose monohydrate, magnesium stearate and quaternary mixtures composed of acetaminophen, lactose monohydrate, microcrystalline cellulose and soluble starch were measured using THz-TDS. Two multivariate calibration methods, principal component regression (PCR) and partial least squares (PLS) regression, were employed to correlate THz absorbance spectra with the pharmaceutical tablet concentrations. Both API and excipient concentrations of mixtures were predicted simultaneously, and the PLS method provides better result than PCR method. The correlation coefficients of calibration (Rcal) and validation (Rval) for ternary mixtures' components, anhydrous theophylline and lactose monohydrate, were all more than 0.98. The Rcal and Rval for quaternary mixtures' components, acetaminophen, lactose monohydrate, microcrystalline cellulose and soluble starch, were all more than 0.93, 0.98, 0.63 and 0.86, respectively. Experimental results show that THz-TDS combined with chemometrics is feasible in nondestructive quantitative analysis of multicomponent mixtures, and it can be widely applied in the fields of pharmaceutical analysis and others. PMID:23905323

Chen, Tao; Li, Zhi; Mo, Wei; Hu, Fang-Rong

2013-05-01

149

Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy.  

PubMed

Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure (1)H-(15)N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated (15)N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S(2) as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins. PMID:20977205

Schanda, Paul; Meier, Beat H; Ernst, Matthias

2010-10-26

150

Quantitative analysis of boron oxide in borosilicate glasses by infrared spectroscopy  

SciTech Connect

Classical multivariate least-squares methods have been applied to the quantitative analysis of boron oxide in bulk borosilicate glasses using transmission infrared spectroscopy. However, molecular interactions in the glass result in deviation from Beer's law and cause the analytical B-O overtone band at --2680 cm/sup -1/ to shift to higher energy with increased boron concentration. Therefore, in order to account for the molecular interactions and achieve higher quantitative accuracy, one must use a nonlinear model relating absorbance and concentration. It has been found that if a quadratic correction term is added to the Beer's-law equation, the observed 15 to 25 cm/sup -1/ shift in frequency of the B-O overtone band can be modeled to within the spectral noise. With the use of a model quadratic in boron oxide concentration, the least-squares analysis of boron in glass was determined with an average relative error of 3.3% for glasses with boron oxide concentrations ranging from 0.88 to 2.58%. This compares favorably with the 3% accuracy claimed for ion chromatography exculsion used for calibration. The methods described in this paper are general, and a variety of nonlinear models can be applied whenever Beer's-law deviations are present.

Haaland, D.M.

1986-11-01

151

Quantitative high-resolution photoacoustic spectroscopy by combining photoacoustic imaging with diffuse optical tomography  

NASA Astrophysics Data System (ADS)

The specificity of both molecular and functional photoacoustic (PA) images depends on the accuracy of the photoacoustic absorption spectroscopy. Because the PA signal is a product of both the optical absorption coefficient and the local light fluence, quantitative PA measurements of absorption require an accurate estimate of the optical fluence. Lightmodeling aided by diffuse optical tomography (DOT) methods can be used to provide the required fluence map and to reduce errors in traditional PA spectroscopic analysis. As a proof-ofconcept, we designed a phantom to demonstrate artifacts commonly found in photoacoustic tomography (PAT) and how fluence-related artifacts in PAT images can lead to misrepresentations of tissue properties. Specifically, we show that without accounting for fluence-related inhomogeneities in our phantom, errors in estimates of the absorption coefficient from a PAT image were as much as 33%. To correct for this problem, DOT was used to reconstruct spatial distributions of the absorption coefficients of the phantom, and along with the surface fluence distribution from the PAT system, we calculated the fluence everywhere in the phantom. This fluence map was used to correct PAT images of the phantom, reducing the error in the estimated absorption coefficient from the PAT image to less than 5%. Thus, we demonstrate experimentally that combining DOT with PAT can significantly reduce fluence-related errors in PAT images, as well as produce quantitatively accurate, highresolution images of the optical absorption coefficient.

Bauer, Adam Q.; Nothdurft, Ralph E.; Erpelding, Todd N.; Wang, Lihong V.; Culver, Joseph P.

2011-02-01

152

Social inclusion enhances biological motion processing: a functional near-infrared spectroscopy study.  

PubMed

Humans are especially tuned to the movements of other people. Neural correlates of this social attunement have been proposed to lie in and around the right posterior superior temporal sulcus (STS) region, which robustly responds to biological motion in contrast to a variety of non-biological motions. This response persists even when no form information is provided, as in point-light displays (PLDs). The aim of the current study was to assess the ability of functional near-infrared spectroscopy (fNIRS) to reliably measure brain responses to PLDs of biological motion, and determine the sensitivity of these responses to interpersonal contextual factors. To establish reliability, we measured brain activation to biological motion with fNIRS and functional magnetic resonance imaging (fMRI) during two separate sessions in an identical group of 12 participants. To establish sensitivity, brain responses to biological motion measured with fNIRS were subjected to an additional social manipulation where participants were either socially included or excluded before viewing PLDs of biological motion. Results revealed comparable brain responses to biological motion using fMRI and fNIRS in the right supramarginal gyrus. Further, social inclusion increased brain responses to biological motion in right supramarginal gyrus and posterior STS. Thus, fNIRS can reliably measure brain responses to biological motion and can detect social experience-dependent modulations of these brain responses. PMID:22941501

Bolling, Danielle Z; Pelphrey, Kevin A; Kaiser, Martha D

2012-09-02

153

Abstracts of papers presented at the LVIII Cold Spring Harbor Symposium on quantitative Biology: DNA and chromosomes  

SciTech Connect

This volume contains the abstracts of oral and poster presentations made at the LVIII Cold Spring Harbor Symposium on Quantitative Biology entitles DNA & Chromosomes. The meeting was held June 2--June 9, 1993 at Cold Spring Harbor, New York.

Not Available

1993-12-31

154

Quantitative analysis of cefalexin based on artificial neural networks combined with modified genetic algorithm using short near-infrared spectroscopy  

NASA Astrophysics Data System (ADS)

In this paper, a novel chemometric method was developed for rapid, accurate, and quantitative analysis of cefalexin in samples. The experiments were carried out by using the short near-infrared spectroscopy coupled with artificial neural networks. In order to enhancing the predictive ability of artificial neural networks model, a modified genetic algorithm was used to select fixed number of wavelength.

Huan, Yanfu; Feng, Guodong; Wang, Bin; Ren, Yulin; Fei, Qiang

2013-05-01

155

Qualitative and quantitative study of polymorphic forms in drug formulations by near infrared FT-Raman spectroscopy  

Microsoft Academic Search

Near infrared FT-Raman spectroscopy was applied for the determination of polymorphic forms in a number of commercial drug products containing the polymorphic drug compounds sorbitol, mannitol, famotidine, acemetacin, carbamazepine, meprobamate and phenylbutazone. The crystal forms present in the drug products were identified based on the position, intensity and shape of characteristic bands. Quantitative analysis of a mixture of two crystal

Martin E. Auer; Ulrich J. Griesser; Juergen Sawatzki

2003-01-01

156

Quantitative analysis of mercury in silver dental amalgam alloy using laser induced breakdown spectroscopy with a portable Echelle spectrometer  

Microsoft Academic Search

Nowadays it is commonly ascertained that, Laser- induced breakdown spectroscopy (LIBS) was investigated to evaluate the feasibility as a fast, accurate, non contact and simple technique used in both qualitative and quantitative elemental analysis of metals in various environments. The used portable Echelle spectrometer (Mechelle 7500 - Multichannel Instruments, Stockholm, Sweden) permit real simultaneous multi-elemental analysis in rang of 200-900

Walid Tawfik; Ali Saafan

157

Quantitative determination of the cubic-to-monoclinic phase transformation in fully stabilized zirconias by Raman spectroscopy  

Microsoft Academic Search

Vibrational Raman spectroscopy was used successfully for the quantitative determination of the cubic and monoclinic phases of zirconia. Pressed pellets with known composition were prepared using monoclinic and cubic powders from different manufacturers and were used as standard mixtures. An intensity ratio plot of the 617-cm[sup [minus]1] band, which is attributed to the presence of both phases, to either the

Christos G. Kontoyannis; George Carountzos

1994-01-01

158

A Quantitative Near-Infrared Spectroscopy Study: A Decrease in Cerebral Hemoglobin Oxygenation in Alzheimer's Disease and Mild Cognitive Impairment  

ERIC Educational Resources Information Center

|A newly developed quantitative near-infrared spectroscopy (NIRS) system was used to measure changes in cortical hemoglobin oxygenation during the Verbal Fluency Task in 32 healthy controls, 15 subjects with mild cognitive impairment (MCI), and 15 patients with Alzheimer's disease (AD). The amplitude of changes in the waveform, which was…

Arai, Heii; Takano, Maki; Miyakawa, Koichi; Ota, Tsuneyoshi; Takahashi, Tadashi; Asaka, Hirokazu; Kawaguchi, Tsuneaki

2006-01-01

159

A method for operative quantitative interpretation of multispectral images of biological tissues  

NASA Astrophysics Data System (ADS)

A method for operative retrieval of spatial distributions of biophysical parameters of a biological tissue by using a multispectral image of it has been developed. The method is based on multiple regressions between linearly independent components of the diffuse reflection spectrum of the tissue and unknown parameters. Possibilities of the method are illustrated by an example of determining biophysical parameters of the skin (concentrations of melanin, hemoglobin and bilirubin, blood oxygenation, and scattering coefficient of the tissue). Examples of quantitative interpretation of the experimental data are presented.

Lisenko, S. A.; Kugeiko, M. M.

2013-10-01

160

Reflective interferometric chamber for quantitative phase imaging of biological sample dynamics  

NASA Astrophysics Data System (ADS)

We introduce a new interferometric setup for single-exposure wide-field holographic phase imaging of highly dynamic biological samples. In this setup, the interferometric signal originates from a specially designed reflective interferometric chamber (InCh), creating an off-axis interferogram on the output plane of the system. The setup only requires the InCh and a simple reflection-mode two lens imaging system, without the need for additional optical elements such as gratings in the beam path. In addition, due to the close-to-common-path geometry of the setup, phase noise is greatly reduced. We experimentally compare the inherent phase stability of the system in ambient conditions to that of a conventional interferometer. We also demonstrate use of this system for wide-field quantitative phase imaging of two different highly dynamic, optically transparent biological samples: beating myocardial cells and moving unicellular microorganisms.

Shaked, Natan T.; Zhu, Yizheng; Badie, Nima; Bursac, Nenad; Wax, Adam

2010-05-01

161

Quantitative Characterization of Biological Liquids for Third-Harmonic Generation Microscopy  

PubMed Central

Third-harmonic generation (THG) microscopy provides images of unstained biological samples based on spatial variations in third-order nonlinear susceptibility, refractive index, and dispersion. In this study, we establish quantitative values for the third-order nonlinear susceptibilities of several solvents (water, ethanol, glycerol), physiological aqueous (ions, amino acids, polypeptides, bovine serum albumin, glucose) and lipid (triglycerides, cholesterol) solutions as a function of solute concentration in the 1.05–1.25 ?m excitation range. We use these data in conjunction with imaging experiments to show that THG imaging with ?1.2 ?m excitation lacks specificity and sensitivity to detect physiological ion concentration changes, and that nonaqueous structures such as lipid bodies provide a more robust source of signal. Finally, we illustrate the impact of index-matching liquids in THG images. These data provide a basis for interpreting biological THG images and for developing additional applications.

Debarre, Delphine; Beaurepaire, Emmanuel

2007-01-01

162

Quantitative analysis of chemically amplified negative photoresist using mirror-backed infrared reflection absorption spectroscopy  

NASA Astrophysics Data System (ADS)

Infrared spectroscopy is a powerful tool for studying chemical reactions which take place in photoresist films. It provides information about functional groups present in the material, is nondestructive to the sample, can be used to monitor reactions in real-time, and can be used as a monitor for real-time process control. Transmission spectroscopy has been used for determination of rate constants for the post exposure bake (PEB) step in both positive and negative chemically amplified x-ray resists, but in transmission the IR beam must pass through the wafer in order to reach the detector. Reflection spectroscopy is more suitable for on-line monitoring because all the optics are located on the same side of the wafer; however, traditional reflection spectra of thin films contain interference fringes which make quantitative analysis difficult. We have developed a method, called mirror-backed infrared reflection- absorption spectroscopy (MBIRRAS), that eliminates the problem of interference fringes in reflection spectra. The method is capable of providing quantitative information about the concentration of functional groups in resist films and produced a linear calibration curve for a commercial crosslinker (hexamethoxymethylmelamine) in a Novolac matrix over a 20% by weight range of concentrations. MBIRRAS was also used to monitor the height of an IR peak corresponding to formation of crosslinks in Shipley negative-tone resist SAL 605 at various processing conditions. The results of this experiment show that PEB time and temperature, prebake time and temperature, and delay between exposure and PEB, all have statistically significant effects on the extent of crosslinking during PEB. In order to explain the observed effect of prebake conditions on the amount of crosslinking during the PEB step and to define the acceptable range of prebaking conditions for resist/wafer adhesion studies, another experiment was performed to demonstrate that thermally generated crosslinking occurred during an additional prebake step without any exposure to x rays. In fact, an additional prebake for 60 seconds at 110 degree(s)C can generate the same number of crosslinks as an x- ray dose of 4 mJ/cm2, while baking for 60 minutes at 110 degree(s)C is equivalent to an x-ray dose that is greater than the resist sensitivity (42 mJ/cm2). Noticeable changes in crosslink concentration were detected at 30 seconds. This suggests that crosslinking occurs during the normal prebake step and explains the dependence of linewidth on prebake time. Finally, a correlation was demonstrated between printed linewidth and MBIRRAS peak height corresponding to crosslink formation in SAL 605. This correlation, along with the demonstrated precision of the MBIRRAS method (3 sigma

Gamsky, Chris J.; Dentinger, Paul M.; Howes, Glenn R.; Taylor, James W.

1995-06-01

163

Quantitative C2H2 measurements in sooty flames using mid-infrared polarization spectroscopy  

NASA Astrophysics Data System (ADS)

Quantitative measurements of acetylene (C2H2) molecules as a combustion intermediate species in a series of rich premixed C2H4/air flames were non-intrusively performed, spatially resolved, using mid-infrared polarization spectroscopy (IRPS), by probing its fundamental ro-vibrational transitions. The flat sooty C2H4/air premixed flames with different equivalence ratios varying from 1.25 to 2.50 were produced on a 6 cm diameter porous-plug McKenna type burner at atmospheric pressure, and all measurements were performed at a height of 8.5 mm above the burner surface. IRPS excitation scans in different flame conditions were performed and rotational line-resolved spectra were recorded. Spectral features of acetylene molecules were readily recognized in the spectral ranges selected, with special attention to avoid the spectral interference from the large amount of coexisting hot water and other hydrocarbon molecules. On-line calibration of the optical system was performed in a laminar C2H2/N2 gas flow at ambient conditions. Using the flame temperatures measured by coherent anti-Stokes Raman spectroscopy in a previous work, C2H2 mole fractions in different flames were evaluated with collision effects and spectral overlap between molecular line and laser source being analyzed and taken into account. C2H2 IRPS signals in two different buffering gases, N2 and CO2, had been investigated in a tube furnace in order to estimate the spectral overlap coefficients and collision effects at different temperatures. The soot-volume fractions (SVF) in the studied flames were measured using a He-Ne laser-extinction method, and no obvious degrading of the IRPS technique due to the sooty environment has been observed in the flame with SVF up to ˜2×10-7. With the increase of flame equivalence ratios not only the SVF but also the C2H2 mole fractions increased.

Sun, Z. W.; Li, Z. S.; Li, B.; Alwahabi, Z. T.; Aldén, M.

2010-10-01

164

Quantitative determination of borophosphosilicate glass thin-film properties using infrared emission spectroscopy  

SciTech Connect

We have completed an experimental study to investigate the use of infrared emission spectroscopy (IRES) for the quantitative analysis of borophosphosilicate glass (BPSG) thin films on silicon monitor wafers. Experimental parameters investigated included temperatures within the range used in the microelectronics industry to produce these films so that the potential for using the IRES technique for real-time monitoring of the film deposition process could be evaluated. The film properties that were investigated included boron content, phosphorus content, film thickness, and film temperature. The studies were conducted over two temperature ranges, 125 to 225&hthinsp;{degree}C and 300 to 400&hthinsp;{degree}C. The latter temperature range includes realistic processing temperatures for the chemical vapor deposition (CVD) of the BPSG films. Partial least-squares (PLS) multivariate calibration methods were applied to spectral and film property calibration data. The cross-validated standard errors of prediction (CVSEP) from the PLS analysis of the IRES spectra of 21 calibration samples each measured at six temperatures in the 300 to 400&hthinsp;{degree}C range were found to be 0.09 wt {percent} for B, 0.08 wt {percent} for P, 3.6 nm for film thickness, and 1.9&hthinsp;{degree}C for temperature. Upon lowering the spectral resolution from 4 to 32 cm{sup {minus}1} and decreasing the number of spectral scans from 128 to 1, we were able to determine that all the film properties could be measured in less than one second to the precision required for the manufacture and quality control of integrated circuits. Thus, real-time {ital in situ} monitoring of BPSG thin films formed by CVD deposition on Si monitor wafers is possible with the methods reported here. {copyright} {ital 1999} {ital Society for Applied Spectroscopy}

Niemczyk, T.M.; Zhang, S.; Franke, J.E. [Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131 (United States)] Haaland, D.M. [Sandia National Laboratories, Albuquerque, New Mexico 87185-0342 (United States)

1999-07-01

165

Closing the Loop: Involving Faculty in the Assessment of Scientific and Quantitative Reasoning Skills of Biology Majors  

ERIC Educational Resources Information Center

The development of scientific and quantitative reasoning skills in undergraduates majoring in science, technology, engineering, and mathematics (STEM) is an objective of many courses and curricula. The Biology Department at James Madison University (JMU) assesses these essential skills in graduating biology majors by using a multiple-choice exam…

Hurney, Carol A.; Brown, Justin; Griscom, Heather Peckham; Kancler, Erika; Wigtil, Clifton J.; Sundre, Donna

2011-01-01

166

Closing the Loop: Involving Faculty in the Assessment of Scientific and Quantitative Reasoning Skills of Biology Majors  

ERIC Educational Resources Information Center

|The development of scientific and quantitative reasoning skills in undergraduates majoring in science, technology, engineering, and mathematics (STEM) is an objective of many courses and curricula. The Biology Department at James Madison University (JMU) assesses these essential skills in graduating biology majors by using a multiple-choice exam…

Hurney, Carol A.; Brown, Justin; Griscom, Heather Peckham; Kancler, Erika; Wigtil, Clifton J.; Sundre, Donna

2011-01-01

167

LASER BIOLOGY: Laser spectroscopy technique for estimating the efficiency of photosensitisers in biological media  

NASA Astrophysics Data System (ADS)

A fast and highly informative method is presented for estimating the photodynamic activity of photosensitisers. The method makes it possible to determine the rate of photodegradation in erythrocyte-containing biological media in nearly in vivo conditions, estimate the degree of irreversible binding of oxygen dissolved in the medium during laser irradiation in the presence of photosensitisers, and determine the nature of degradation of photosensitisers exposed to light (photobleaching).

Ryabova, A. V.; Stratonnikov, Aleksandr A.; Loshchenov, V. B.

2006-06-01

168

Quantitative elemental detection of size-segregated particles using laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

In order to simulate coal combustion and develop optimal and stable boiler control systems in real power plants, it is imperative to obtain the detailed information in coal combustion processes as well as to measure species contents in fly ash, which should be controlled and analyzed for enhancing boiler efficiency and reducing environmental pollution. The fly ash consists of oxides (SiO2, Al2O3, Fe2O3, CaO, and so on), unburned carbon, and other minor elements. Recently laser-induced breakdown spectroscopy (LIBS) technique has been applied to coal combustion and other industrial fields because of the fast response, high sensitivity, real-time and non-contact features. In these applications it is important to measure controlling factors without any sample preparation to maintain the real-time measurement feature. The relation between particle content and particle diameter is also one of the vital researches, because compositions of particles are dependent on their diameter. In this study, we have detected the contents of size-segregated particles using LIBS. Particles were classified by an Anderson cascade impactor and their contents were measured using the output of 1064 nm YAG laser, a spectrograph and an ICCD camera. The plasma conditions such as plasma temperature are dependent on the size of particles and these effects must be corrected to obtain quantitative information. The plasma temperature was corrected by the emission intensity ratio from the same atom. Using this correction method, the contents of particles can be measured quantitatively in fixed experimental parameters. This method was applied to coal and fly ash from a coal-fired burner to measure unburned carbon and other contents according to the particle diameter. The acquired results demonstrate that the LIBS technique is applicable to measure size-segregated particle contents in real time and this method is useful for the analysis of coal combustion and its control because of its sensitive and fast analysis features.

Wang, Zhen Zhen; Deguchi, Yoshihiro; Kuwahara, Masakazu; Taira, Takuya; Zhang, Xiao Bo; Yan, Jun Jie; Liu, Ji Ping; Watanabe, Hiroaki; Kurose, Ryoichi

2013-09-01

169

Compound-specific, quantitative characterization of organic fluorochemicals in biological matrices.  

PubMed

Since the early 1980s, there has been a steady increase in the use of nonvolatile fluorinated organic compounds for a variety of industrial and commercial applications. The industrial use of these relatively stable compounds has initiated debate over the fate of fluorochemicals in the environment and, ultimately, the bioavailability of these compounds. In this manuscript, we present quantitative results from a study of 65 human sera samples purchased from biological supply companies that provide characterization of specific organic fluorochemicals present in the sera of nonindustrially exposed humans. Summed together, the compound-specific characterization data reported here agree closely with levels of nonspeciated organic fluorine that were originally reported to be present in sera in 1970. The compound-specific method for the extraction of extremely low levels of several commercial organic fluorochemicals from sera and liver with quantitative detection by negative ion electrospray tandem mass spectrometry described represents a robust, previously undescribed approach to quantifying specific organic fluorochemicals in biological matrices. PMID:11349290

Hansen, K J; Clemen, L A; Ellefson, M E; Johnson, H O

2001-02-15

170

A gas chromatographic-mass spectral assay for the quantitative determination of oleamide in biological fluids.  

PubMed

Oleamide is a putative endogenous sleep-inducing lipid which potently enhances currents mediated by GABAA and serotonin receptors. While a quantitative assay would aid in determining the role of oleamide in physiological processes, most of the available assays are lacking in sensitivity. We now describe a quantitative assay for measuring low nanogram amounts of oleamide in biological fluids using GC/MS in the selective ion-monitoring mode. The internal standard (13C18 oleamide) was added to known concentrations of oleamide, which were converted to the N-trimethylsilyl or N-tert-butyldimethylsilyl derivatives before analysis by GC/MS, yielding linear calibration curves over the range of 1-25 ng of oleamide when monitoring the m/z 338/356 fragments. Using this technique, oleamide levels were determined following solvent extraction of normal rat cerebrospinal fluid and plasma to be 44 and 9.9 ng/ml, respectively. This technique constitutes a sensitive and reliable method for determining low nanogram quantities of oleamide in biological fluids. PMID:10328778

Hanus, L O; Fales, H M; Spande, T F; Basile, A S

1999-05-15

171

Quantitation of biological retinoids by high-pressure liquid chromatography: primary internal standardization using tritiated retinoids  

SciTech Connect

A single method is described for quantitation of 14 retinoids found in biological material. The method consists of reversed-phase HPLC, internal standardization, and carrier extraction procedures with three synthetic retinoids. Primary standardization of HPLC uv detector is achieved using tritiated all-trans-retinoic acid, all-trans-retinol, all-trans-retinyl palmitate, and all-trans-retinyl acetate. Extraction methods are standardized by correlating the uv absorbance of retinoids at 340 nm with radioactivity of tritiated retinoids of known specific activity. Quantitation of 10 pg of tritiated or 5 ng of nonradioactive retinoid per 0.1 g sample in a polarity range from 4-oxo-retinoic acid to retinyl stearate can be achieved in a single, 50-min chromatographic run. A single HPLC pump, a C/sub 18/ reversed-phased analytical column, a multistep three-solvent gradient, and inexpensive solvents based on methanol, water, and chloroform comprise this cost-effective chromatographic system. Our primary standardization method allows investigators employing different procedures to compare results between laboratories by standardizing the HPLC uv detector with commercially available tritiated retinoids. With this method we were able to quantitate nanomolar amounts of endogenous retinoic acids and retinyl esters, that HPLC uv only conditions usually would not detect in the circulation and liver of rats under physiological conditions.

Cullum, M.E.; Zile, M.H.

1986-02-15

172

Quantitative determination of sulfur content in concrete with laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

Laser-induced breakdown spectroscopy has been employed for the investigation of the sulfur content of concrete. Sulfur compounds are a natural but minor component in building materials. The ingress of sulfates or sulfuric acid constitutes a major risk of chemical aggression for concrete. There is a need for a fast method, which can be used on-site and is able to investigate a wide range of different measuring points, so that damages can be characterized. For quantitative determination the sulfur spectral line at 921.3 nm is used. The optimum ambient atmosphere has been determined by comparison of measurements accomplished under air, argon and helium atmosphere. Reference samples have been produced and calibration curves have been determined, the results of LIBS measurements are compared with results from chemical analysis. Defining a limit for the intensity ratio of a calcium and a oxygen spectral line can reduce the influence of the heterogeneity of the material, so that only spectra with a high amount of cementitious material are evaluated. Depth profiles and spatial resolved sulfur distributions are presented measured on concrete cores originating from a highly sulfate contaminated clarifier.

Weritz, F.; Ryahi, S.; Schaurich, D.; Taffe, A.; Wilsch, G.

2005-08-01

173

Quantitative analysis of pharmaceutical products by laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

In this paper, the capabilities of laser-induced breakdown spectroscopy (LIBS) for rapid analysis of multi-component pharmaceutical tablets are illustrated using several examples. The atomic line emission from an element present only in a particular component of the tablet (for instance, emission of phosphorus from the drug, or of magnesium from the lubricant) enables the quantitative analysis of that component. It is also demonstrated that simple schemes can significantly improve the analytical performance of LIBS in this context. In particular, internal standardization with a carbon line was found to enable the correction of a matrix effect, apart from improving the precision of measurement. Furthermore, an improvement in the linearity of calibration was observed when the plasma continuum emission was used as internal standard. Finally, in the case of drugs containing halogen species (e.g. F or Cl), producing the plasma in a helium atmosphere caused a seven to eight-fold increase of the signal-to-background ratio, thus improving sensitivity. These data illustrate the strengths of LIBS for fast at-line assessment of the reliability of pharmaceutical manufacturing processes.

St-Onge, L.; Kwong, E.; Sabsabi, M.; Vadas, E. B.

2002-07-01

174

Quantitative methods for structural characterization of proteins based on deep UV resonance Raman spectroscopy.  

PubMed

Here we report on novel quantitative approaches for protein structural characterization using deep UV resonance Raman (DUVRR) spectroscopy. Specifically, we propose a new method combining hydrogen-deuterium (HD) exchange and Bayesian source separation for extracting the DUVRR signatures of various structural elements of aggregated proteins including the cross-beta core and unordered parts of amyloid fibrils. The proposed method is demonstrated using the set of DUVRR spectra of hen egg white lysozyme acquired at various stages of HD exchange. Prior information about the concentration matrix and the spectral features of the individual components was incorporated into the Bayesian equation to eliminate the ill-conditioning of the problem caused by 100% correlation of the concentration profiles of protonated and deuterated species. Secondary structure fractions obtained by partial least squares (PLS) and least squares support vector machines (LS-SVMs) were used as the initial guess for the Bayessian source separation. Advantages of the PLS and LS-SVMs methods over the classical least squares calibration (CLSC) are discussed and illustrated using the DUVRR data of the prion protein in its native and aggregated forms. PMID:20580825

Shashilov, Victor A; Sikirzhytski, Vitali; Popova, Ludmila A; Lednev, Igor K

2010-05-24

175

Non-invasive tissue temperature measurements based on quantitative diffuse optical spectroscopy (DOS) of water  

NASA Astrophysics Data System (ADS)

We describe the development of a non-invasive method for quantitative tissue temperature measurements using Broadband diffuse optical spectroscopy (DOS). Our approach is based on well-characterized opposing shifts in near-infrared (NIR) water absorption spectra that appear with temperature and macromolecular binding state. Unlike conventional reflectance methods, DOS is used to generate scattering-corrected tissue water absorption spectra. This allows us to separate the macromolecular bound water contribution from the thermally induced spectral shift using the temperature isosbestic point at 996 nm. The method was validated in intralipid tissue phantoms by correlating DOS with thermistor measurements (R = 0.96) with a difference of 1.1 ± 0.91 °C over a range of 28-48 °C. Once validated, thermal and hemodynamic (i.e. oxy- and deoxy-hemoglobin concentration) changes were measured simultaneously and continuously in human subjects (forearm) during mild cold stress. DOS-measured arm temperatures were consistent with previously reported invasive deep tissue temperature studies. These results suggest that DOS can be used for non-invasive, co-registered measurements of absolute temperature and hemoglobin parameters in thick tissues, a potentially important approach for optimizing thermal diagnostics and therapeutics.

Chung, S. H.; Cerussi, A. E.; Merritt, S. I.; Ruth, J.; Tromberg, B. J.

2010-07-01

176

[Quantitative determination of trace heavy metals in polluted soil by laser induced breakdown spectroscopy].  

PubMed

Based on laser induced breakdown spectroscopy data analysis, a quantitative determination method of elements was introduced. This method takes the advantage of Fourier analysis to study different part of the spectrum-white noise, thermal radiation and emission spectral lines. Through band-pass filter, emission spectral lines and most noise were separated, only a little white noise was missed. By calculated similarity between detected line and its corresponding unit characteristic line, convolution intensity was introduced to measure the detected line intensity. With Cu 324.75 nm as the analysis line and Ti 337.28 nm as the base line, the way of separating spectrum mentioned before was carried out to detect trace Cu pollution in soil. Results contained two bright spots. First, The correlation coefficient between Cu concentration and the spectral intensity was up to 0.997 9. Last but not the least, the detectability of Cu in soil was 44 mg x kg(-1), which is below the trace element thresholds for Class 2 soil used in the environmental quality standard for soil in China. At the same time, the relative error is always below 10%. Therefore the feasibility of this method for portable and instant detection of heavy metals in polluted soil was verified. PMID:21510402

Wu, Wen-Tao; Ma, Xiao-Hong; Zhao, Hua-Feng; Zheng, Ze-Ke; Zhang, Min; Liag, Yan-Biao

2011-02-01

177

Hypoxic encephalopathy after near-drowning studied by quantitative 1H-magnetic resonance spectroscopy.  

PubMed Central

Early prediction of outcome after global hypoxia of the brain requires accurate determination of the nature and extent of neurological injury and is cardinal for patient management. Cerebral metabolites of gray and white matter were determined sequentially after near-drowning using quantitative 1H nuclear magnetic resonance spectroscopy (MRS) in 16 children. Significant metabolite abnormalities were demonstrated in all patients compared with their age-matched normal controls. Severity of brain damage was quantified from metabolite concentrations and ratios. Loss of N-acetylaspartate, a putative neuronal marker, from gray matter preceded that observed in white matter and was more severe. Total creatine decreased, while lactate and glutamine/glutamate concentrations increased. Changes progressed with time after injury. A spectroscopic prognosis index distinguished between good outcome (n = 5) and poor outcome (n = 11) with one false negative (bad outcome after borderline MRS result) and no false positive results (100% specificity). The distinction was made with 90% sensitivity early (after 48 h) and became 100% later (by days 3 and 4). This compared with 50-75% specificity and 70-100% sensitivity based upon single clinical criteria. MRS performed sequentially in occipital gray matter provides useful objective information which can significantly enhance the ability to establish prognosis after near-drowning.

Kreis, R; Arcinue, E; Ernst, T; Shonk, T K; Flores, R; Ross, B D

1996-01-01

178

Fused glass sample preparation for quantitative laser-induced breakdown spectroscopy of geologic materials  

NASA Astrophysics Data System (ADS)

Laser-induced breakdown spectroscopy is a powerful analytical method, but LIBS is subject to a matrix effect which can limit its ability to produce quantitative results in complex materials such as geologic samples. Various methods of sample preparation, calibration, and data processing have been attempted to compensate for the matrix effect and improve LIBS precision. This study focuses on sample preparation by comparing fused glass as a preparation for powdered material to the more commonly used method of pressing powder into pellets for LIBS analysis of major elements in complex geologic materials. Pelletizing powdered material is a common and convenient method for preparing samples but problems with the physical matrix brought on by inconsistencies in the homogeneity, density, and laser absorption, coupled with the chemical matrix problem lead to spectral peak responses that are not always consistent with the absolute concentration of representative elements. Twenty-two mineral and rock samples were analyzed for eight major oxide elements. Samples were prepared under both glass and pellet methods and compared for internal precision and overall accuracy. Fused glass provided a more consistent physical matrix and yielded more reliable peak responses in the LIBS analysis than did the pressed pellet preparation. Statistical comparisons demonstrated that the glass samples expressed stronger separability between different mineral species based on the eight elements than for the pressed pellets and showed better spot-to-spot repeatability. Regression models showed substantially better correlations and predictive ability among the elements for the glass preparation than did those for the pressed pellets.

Pease, Patrick

2013-05-01

179

Quantitative analysis and detection of adulteration in pork using near-infrared spectroscopy  

NASA Astrophysics Data System (ADS)

Authenticity is an important food quality criterion. Rapid methods for confirming authenticity or detecting adulteration are increasingly demanded by food processors and consumers. Near infrared (NIR) spectroscopy has been used to detect economic adulteration in pork . Pork samples were adulterated with liver and chicken in 10% increments. Prediction and quantitative analysis were done using raw data and pretreatment spectra. The optimal prediction result was achieved by partial least aquares(PLS) regression with standard normal variate(SNV) pretreatment for pork adulterated with liver samples, and the correlation coefficient(R value), the root mean square error of calibration(RMSEC) and the root mean square error of prediction (RMSEP) were 0.97706, 0.0673 and 0.0732, respectively. The best model for pork meat adulterated with chicken samples was obtained by PLS with the raw spectra, and the correlation coefficient(R value), RMSEP and RMSEC were 0.98614, 0.0525, and 0.122, respectively. The result shows that NIR technology can be successfully used to detect adulteration in pork meat adulterated with liver and chicken.

Fan, Yuxia; Cheng, Fang; Xie, Lijuan

2010-04-01

180

Detection of biological analytes using nanomechanical infrared spectroscopy with a nanoporous microcantilever  

NASA Astrophysics Data System (ADS)

The highly sensitive nanoporous cantilever beam without immobilized receptors was combined with highly selective mid-infrared (IR) spectroscopy for molecular recognition of analytes using characteristic molecular vibrations. Unlike conventional IR spectroscopy, in addition, the detection sensitivity and resolution are drastically enhanced by combining high power tunable quantum cascade laser with a nanoporous cantilever having large surface area, low modulus, and nanowell structures. Further, analytes can be easily loaded on the porous microcantilever without receptor due to nanowells. In addition, orthogonal signals, variations in the mass and IR spectrum, provide more reliable and quantitative results including physical as well as chemical information of samples. We have used this technique to rapidly identify single and double stranded DNA.

Lee, Dongkyu; Kim, Seonghwan; Thundat, Thomas

2013-05-01

181

Quantitative assessment of hydrocarbon contamination in soil using reflectance spectroscopy: a "multipath" approach.  

PubMed

Petroleum hydrocarbons are contaminants of great significance. The commonly used analytic method for assessing total petroleum hydrocarbons (TPH) in soil samples is based on extraction with 1,1,2-Trichlorotrifluoroethane (Freon 113), a substance prohibited to use by the Environmental Protection Agency. During the past 20 years, a new quantitative methodology that uses the reflected radiation of solids has been widely adopted. By using this approach, the reflectance radiation across the visible, near infrared-shortwave infrared region (400-2500 nm) is modeled against constituents determined using traditional analytic chemistry methods and then used to predict unknown samples. This technology is environmentally friendly and permits rapid and cost-effective measurements of large numbers of samples. Thus, this method dramatically reduces chemical analytical costs and secondary pollution, enabling a new dimension of environmental monitoring. In this study we adapted this approach and developed effective steps in which hydrocarbon contamination in soils can be determined rapidly, accurately, and cost effectively solely from reflectance spectroscopy. Artificial contaminated samples were analyzed chemically and spectrally to form a database of five soils contaminated with three types of petroleum hydrocarbons (PHCs), creating 15 datasets of 48 samples each at contamination levels of 50-5000 wt% ppm (parts per million). A brute force preprocessing approach was used by combining eight different preprocessing techniques with all possible datasets, resulting in 120 different mutations for each dataset. The brute force was done based on an innovative computing system developed for this study. A new parameter for evaluating model performance scoring (MPS) is proposed based on a combination of several common statistical parameters. The effect of dividing the data into training validation and test sets on modeling accuracy is also discussed. The results of this study clearly show that predicting TPH levels at low concentrations in selected soils at high precision levels is viable. Dividing a dataset into training, validation, and test groups affects the modeling process, and different preprocessing methods, alone or in combination, need to be selected based on soil type and PHC type. MPS was found to be a better parameter for selecting the best performing model than ratio of prediction to deviation, yielding models with the same performance but less complicated and more stable. The use of the "all possibilities" system proved to be mandatory for efficient optimal modeling of reflectance spectroscopy data. PMID:24160885

Schwartz, Guy; Ben-Dor, Eyal; Eshel, Gil

2013-11-01

182

Investigation of degenerate four-wave mixing and polarization spectroscopy for quantitative measurements in combustion environments  

NASA Astrophysics Data System (ADS)

The physics of degenerate four-wave mixing (DFWM) and polarization spectroscopy (PS) and their application for quantitative concentration measurements in gas-phase media have been investigated both theoretically and experimentally. The physics of the two techniques was studied theoretically by direct numerical integration (DNI) of the time-dependent density matrix equations. Polarization effects were included by incorporation of the Zeeman structure of the upper and lower energy levels, and molecular motion effects were included by solution of the density matrix equations for numerous velocity groups. The DNI calculations demonstrated that the DFWM signal penalty for crossed-polarized configurations is decreased when the resonance is saturated. This result was explained in terms of the coupling of the various Zeeman states during the DFWM interaction for specific polarization configurations. Using the DNI approach to study PS, the low-pump- intensity PS signal was shown to be very dependent on the ratio of Doppler broadening to collisional broadening when the Doppler width is greater than the collisional width. However, at saturating pump intensities, the line- center PS signal intensity becomes nearly independent of the collision rate when the collisional width is less than the Doppler linewidth. The application of DFWM and PS for quantitative concentration measurements was investigated experimentally by measuring lineshapes and signal intensities in well-characterized hydrogen/air flames. Resonances in the A2? +-X2? (0,0) band of hydroxyl (OH) were probed with both perturbative and saturating beam intensities. Hydroxyl number densities were calculated from the DFWM and PS signal intensities in a series of near-adiabatic flames at equivalence ratios ranging from 0.5 to 1.5. The use of saturating laser intensities minimized the effects of beam absorption and variation of the collisional dynamics, providing more accurate number density measurements. The saturated DFWM results and the saturated PS results were in excellent agreement with OH absorption measurements and equilibrium calculations of OH concentration. The polarization dependence of the P1(2) and R2(l) DFWM transitions was investigated, providing experimental confirmation that the signal penalties predicted by a perturbative treatment of DFWM can be much less when the resonances are saturated.

Reichardt, Thomas Andrew

183

Final Report: Investigation of Polarization Spectroscopy and Degenerate Four-Wave Mixing for Quantitative Concentration Measurements  

SciTech Connect

Laser-induced polarization spectroscopy (LIPS), degenerate four-wave mixing (DFWM), and electronic-resonance-enhanced (ERE) coherent anti-Stokes Raman scattering (CARS) are techniques that shows great promise for sensitive measurements of transient gas-phase species, and diagnostic applications of these techniques are being pursued actively at laboratories throughout the world. However, significant questions remain regarding strategies for quantitative concentration measurements using these techniques. The primary objective of this research program is to develop and test strategies for quantitative concentration measurements in flames and plasmas using these nonlinear optical techniques. Theoretically, we are investigating the physics of these processes by direct numerical integration (DNI) of the time-dependent density matrix equations that describe the wave-mixing interaction. Significantly fewer restrictive assumptions are required when the density matrix equations are solved using this DNI approach compared with the assumptions required to obtain analytical solutions. For example, for LIPS calculations, the Zeeman state structure and hyperfine structure of the resonance and effects such as Doppler broadening can be included. There is no restriction on the intensity of the pump and probe beams in these nonperturbative calculations, and both the pump and probe beam intensities can be high enough to saturate the resonance. As computer processing speeds have increased, we have incorporated more complicated physical models into our DNI codes. During the last project period we developed numerical methods for nonperturbative calculations of the two-photon absorption process. Experimentally, diagnostic techniques are developed and demonstrated in gas cells and/or well-characterized flames for ease of comparison with model results. The techniques of two-photon, two-color H-atom LIPS and three-laser ERE CARS for NO and C{sub 2}H{sub 2} were demonstrated during the project period, and nonperturbative numerical models of both of these techniques were developed. In addition, we developed new single-mode, injection-seeded optical parametric laser sources (OPLSs) that will be used to replace multi-mode commercial dye lasers in our experimental measurements. The use of single-mode laser radiation in our experiments will increase significantly the rigor with which theory and experiment are compared.

Robert P. Lucht

2005-03-09

184

Clustering and training set selection methods for improving the accuracy of quantitative laser induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

We investigated five clustering and training set selection methods to improve the accuracy of quantitative chemical analysis of geologic samples by laser induced breakdown spectroscopy (LIBS) using partial least squares (PLS) regression. The LIBS spectra were previously acquired for 195 rock slabs and 31 pressed powder geostandards under 7 Torr CO2 at a stand-off distance of 7 m at 17 mJ per pulse to simulate the operational conditions of the ChemCam LIBS instrument on the Mars Science Laboratory Curiosity rover. The clustering and training set selection methods, which do not require prior knowledge of the chemical composition of the test-set samples, are based on grouping similar spectra and selecting appropriate training spectra for the partial least squares (PLS2) model. These methods were: (1) hierarchical clustering of the full set of training spectra and selection of a subset for use in training; (2) k-means clustering of all spectra and generation of PLS2 models based on the training samples within each cluster; (3) iterative use of PLS2 to predict sample composition and k-means clustering of the predicted compositions to subdivide the groups of spectra; (4) soft independent modeling of class analogy (SIMCA) classification of spectra, and generation of PLS2 models based on the training samples within each class; (5) use of Bayesian information criteria (BIC) to determine an optimal number of clusters and generation of PLS2 models based on the training samples within each cluster. The iterative method and the k-means method using 5 clusters showed the best performance, improving the absolute quadrature root mean squared error (RMSE) by ~ 3 wt.%. The statistical significance of these improvements was ~ 85%. Our results show that although clustering methods can modestly improve results, a large and diverse training set is the most reliable way to improve the accuracy of quantitative LIBS. In particular, additional sulfate standards and specifically fabricated analog samples with Mars-like compositions may improve the accuracy of ChemCam measurements on Mars. Refinement of the iterative method, modifications of the basic k-means clustering algorithm, and classification based on specifically selected S, C and Si emission lines may also prove beneficial and merit further study.

Anderson, Ryan B.; Bell, James F., III; Wiens, Roger C.; Morris, Richard V.; Clegg, Samuel M.

2012-04-01

185

[Localized nuclear magnetic resonance spectroscopy in vivo. Physical principles and quantitative problems].  

PubMed

Recent technological developments extended the use of nuclear magnetic resonance to clinical imaging (MRI), as well as to in vivo metabolic studies on tissues and organs by means of localized spectroscopy (MRS). The quantitative determination of absolute metabolic concentrations by in vivo MRS still represents a challenge for technological efforts and biochemical investigations. In fact, the different methodologies today available for spectral acquisition from localized regions within a body organ or pathological lesion should ideally lead to a complete suppression of signals from surrounding tissues, without any appreciable signal loss from the volume of interest. Accurate assessment of deviations of the real from the ideal case represents an essential requirement for either relative or absolute quantification of in vivo localized MR spectra. A review will be presented of the most utilized MRS methodologies, together with a discussion on their potentialities and limitations. Techniques have been classified according to the use of either r.f. (B1) and/or static magnetic field (B0) gradients. The last session will be devoted to the presentation of some results obtained in our laboratory on the use of a particular test-object (constructed at the Deft Institute of Technology) for assessing signal localization efficiency provided by a surface coil in a small scale MRS/MRI equipment (for in vivo biochemical studies on small animals). The surface coil was used in conjunction with a number of sequence (t1-90 degrees-acq; 1-D "chemical shift imaging"; "depth") of either square or adiabatic r.f. pulses. The results allow the selection, on a quantitative basis, of the most appropriate pulse sequence(s) to be used for metabolic studies on superficial experimental tumours (implanted s.c. in small animals), according to the mean area and thickness of the neoplastic lesion. The latter parameters can be non-invasively assessed by previous MRI analysis of the tumour. This study was carried out in the frame of the EC COMAC-BME Concerted Research Project on Tissue Characterization by MRS and MRI. PMID:1820740

Canese, R; Podo, F

1991-01-01

186

Quantitative Determination of Dielectric Thin-Film Properties Using Infrared Emission Spectroscopy  

SciTech Connect

We have completed an experimental study to investigate the use of infrared emission spectroscopy (IRES) for the quantitative analysis of borophosphosilicate glass (BPSG) thin films on silicon monitor wafers. Experimental parameters investigated included temperatures within the range used in the microelectronics industry to produce these films; hence the potential for using the IRES technique for real-time monitoring of the film deposition process has been evaluated. The film properties that were investigated included boron content, phosphorus content, film thickness, and film temperature. The studies were conducted over two temperature ranges, 125 to 225 *C and 300 to 400 *C. The later temperature range includes realistic processing temperatures for the chemical vapor deposition (CVD) of the BPSG films. Partial least squares (PLS) multivariate calibration methods were applied to spectral and film property calibration data. The cross-validated standard errors of prediction (CVSEP) fi-om the PLS analysis of the IRES spectraof21 calibration samples each measured at 6 temperatures in the 300 to 400 "C range were found to be 0.09 wt. `?40 for B, 0.08 wt. `%0 for P, 3.6 ~m for film thickness, and 1.9 *C for temperature. By lowering the spectral resolution fi-om 4 to 32 cm-l and decreasing the number of spectral scans fi-om 128 to 1, we were able to determine that all the film properties could be measured in less than one second to the precision required for the manufacture and quality control of integrated circuits. Thus, real-time in-situ monitoring of BPSG thin films formed by CVD deposition on Si monitor wafers is possible with the methods reported here.

Franke, J.E.; Haaland, D.M.; Niemczyk, T.M.; Zhang, S.

1998-10-14

187

Ni speciation in a New Caledonian lateritic regolith: A quantitative X-ray absorption spectroscopy investigation  

NASA Astrophysics Data System (ADS)

Changes in Ni speciation in a 64 m vertical profile of a New Caledonian saprolitic-lateritic regolith developed over ultramafic rocks under tropical weathering conditions were investigated by EXAFS spectroscopy. Quantitative analysis of the EXAFS spectra by linear combination-least squares fitting (LC-LSF) using a large set of model compound spectra showed that Ni hosted in primary silicate minerals (olivine and serpentine) in the bedrock is incorporated in secondary phyllosilicates (serpentine) and Fe-oxides (goethite) in the saprolite unit and mainly in goethite in the laterite unit. A significant concentration of Ni (up to 30% of total Ni) is also hosted by Mn-oxides in the transition laterite (i.e. the lowest part of the laterite unit which contains large amounts of Mn-oxides). However, the amount of Ni associated with Mn-oxides does not exceed 20% of the total Ni in the overlying laterite unit. This sequence of Ni species from bedrock to laterite yields information about the behavior of Ni during tropical weathering of ultramafic rocks. The different Ni distributions in phyllosilicates in the bedrock (randomly distributed) and in the saprolite unit (clustered) indicate two generations of Ni-bearing phyllosilicates. The first, which formed at higher temperature, is related to serpentinization of oceanic crust, whereas the second one, which formed at lower temperature, is associated with post-obduction weathering of ultramafic rocks. In addition, the observed decrease in the proportion of Ni hosted by Mn-oxides from the transition laterite to the upper lateritic horizons indicates dissolution of Mn-oxides during the last stages of differentiation of the lateritic regolith (i.e. lateritization). Finally, the ubiquitous occurrence of Ni-bearing goethite emphasizes the major role of this phase in Ni speciation at the different weathering stages and suggests that goethite represents the major host for Ni in the final tropical weathering stages of New Caledonian ultramafic rocks.

Dublet, Gabrielle; Juillot, Farid; Morin, Guillaume; Fritsch, Emmanuel; Fandeur, Dik; Ona-Nguema, Georges; Brown, Gordon E.

2012-10-01

188

Exploring the potential of Raman and resonance Raman spectroscopy for quantitative analysis of duplex DNA  

NASA Astrophysics Data System (ADS)

Advances in DNA microarray fabrication technologies, expanding probe libraries, and new bioinformatics methods and resources have firmly established array-based techniques as mainstream bioanalytical tools and the application space is proliferating rapidly. However, the capability of these tools to yield truly quantitative information remains limited, primarily due to problems inherent to the use of fluorescence imaging for reading the hybridized arrays. The obvious advantages of fluorescence are the unrivaled sensitivity and simplicity of the instrumentation. There are disadvantages of this approach, however, such as difficulties in achieving optimal labeling of targets and reproducible signals (due to quenching, resonance energy transfer, photobleaching effects, etc.) that undermine precision. We are exploring alternative approaches, based mainly on Raman and resonance Raman spectroscopy, that in principle permit direct analysis of structural differences between hybridized and unhybridized probes, thereby eliminating the need for labeling the target analytes. We report here on the status of efforts to evaluate the potential of these methods based on a combination of measured data and simulated experiments involving short (12-mer) ssDNA oligomer probes with varying degrees of hybridized target DNA. Preliminary results suggest that it may be possible to determine the fraction of duplex probes within a single register on a DNA microarray from 100% down to 10% (or possibly less) with a precision of +/-2 5%. Details of the methods used, their implementation, and their potential advantages and limitations are presented, along with discussion of the utility of using 2DCOS methods to emphasize small spectral changes sensitive to interstrand H bonding, backbone flexibility, hypochromicity due to base-stacking in duplex structures and solvation effects.

Schulze, H. G.; Bass, A.; Addison, C.; Hughesman, C.; So, A. P.; Haynes, C. A.; Blades, M. W.; Turner, R. F. B.

2005-09-01

189

Discrimination of edible oil products and quantitative determination of their iodine value by Fourier transform near-infrared spectroscopy  

Microsoft Academic Search

This work demonstrates the application of partial least squares (PLS) analysis as a discriminant as well as a quantitative\\u000a tool in the analysis of edible fats and oils by Fourier transform near-infrared (FT-NIR) spectroscopy. Edible fats and oils\\u000a provided by a processor were used to calibrate a FT-NIR spectrometer to discriminate between four oil formulations and to\\u000a determine iodine value

Hui Li; F. R. van de Voort; A. A. Ismail; J. Sedman; R. Cox; C. Simard; H. Buijs

2000-01-01

190

Quantitative measurements of O 2 b ? X(2,1,0?0) bands by using cavity ring-down spectroscopy  

Microsoft Academic Search

Quantitative measurements of individual rotational line intensities of molecular oxygen are made for the (0?0), (1?0), (2?0) bands of the b1?g+?X3?g? transition using highly sensitive cavity ring-down spectroscopy (CRDS). The absorption profiles of six rotational lines of the three bands of O2 are measured under pressures up to 1 atm. Corrections have been made to eliminate the effect of laser

Shucheng Xu; Dongxu Dai; Jinchun Xie; Guohe Sha; Cunhao Zhang

1999-01-01

191

Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data  

PubMed Central

Background Bayesian Network (BN) is a powerful approach to reconstructing genetic regulatory networks from gene expression data. However, expression data by itself suffers from high noise and lack of power. Incorporating prior biological knowledge can improve the performance. As each type of prior knowledge on its own may be incomplete or limited by quality issues, integrating multiple sources of prior knowledge to utilize their consensus is desirable. Results We introduce a new method to incorporate the quantitative information from multiple sources of prior knowledge. It first uses the Naïve Bayesian classifier to assess the likelihood of functional linkage between gene pairs based on prior knowledge. In this study we included cocitation in PubMed and schematic similarity in Gene Ontology annotation. A candidate network edge reservoir is then created in which the copy number of each edge is proportional to the estimated likelihood of linkage between the two corresponding genes. In network simulation the Markov Chain Monte Carlo sampling algorithm is adopted, and samples from this reservoir at each iteration to generate new candidate networks. We evaluated the new algorithm using both simulated and real gene expression data including that from a yeast cell cycle and a mouse pancreas development/growth study. Incorporating prior knowledge led to a ~2 fold increase in the number of known transcription regulations recovered, without significant change in false positive rate. In contrast, without the prior knowledge BN modeling is not always better than a random selection, demonstrating the necessity in network modeling to supplement the gene expression data with additional information. Conclusion our new development provides a statistical means to utilize the quantitative information in prior biological knowledge in the BN modeling of gene expression data, which significantly improves the performance.

2011-01-01

192

Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology.  

PubMed

Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemistry and engineering, along with a significant thrust in applications constituting areas in medicine, biology, environment and agriculture among others. In this review, we will attempt to provide a quick snapshot of the basics of SM-SERS, nanostructures and devices that can enable SM Raman measurement. We will conclude with a discussion on SERS implications in biomedical sciences. PMID:23267180

Wang, Yuling; Irudayaraj, Joseph

2012-12-24

193

Quantitative changes in sets of proteins as markers of biological response  

SciTech Connect

Exposure to either physical or chemical insults triggers a cascade of bio-chemical events within the target cell. This response requires adjustment within the protein population of the cell, some proteins becoming more abundant (those involved in the cellular response), others less abundant (those not required or counterproductive to the response). Thus, quantitative changes in the global protein population of an exposed biological system may well serve as an indicator of exposure, provided the alterations observed are selective and dose-dependent. In this paper we present results from a study in which liver protein changes induced by exposure of mice to chemicals known to cause peroxisome proliferation and subsequent hepatocellular carcinoma where monitored. Clofibrate, and its chemical analog ciprofibrate, are hypolipidemic drugs. Di-(ethylhexyl)phthalate (DEHP) is a plasticizer used widely in disposable containers for blood products. WY-14643 is a chemical shown to cause hypolipidemic and peroxisome proliferation, similar to clofibrate, ciprofibrate and DEHP, but structurally different from these three chemicals. Thus, two of the four chemicals are structurally similar while the remaining two are very distinct, although all four chemicals cause the same gross biological response. Our results show that although common protein effects are observed in mice exposed to these chemicals, each chemical also causes specific alterations in selective subsets of proteins that could serve as markers of a particular exposure. 13 refs., 4 figs., 1 tab.

Giometti, C.S.; Taylor, J.; Gemmell, M.A.; Tollaksen, S.L. (Argonne National Lab., IL (USA)); Lalwani, N.D.; Reddy, J.K. (Northwestern Univ., Chicago, IL (USA))

1990-01-01

194

The physical and biological basis of quantitative parameters derived from diffusion MRI  

PubMed Central

Diffusion magnetic resonance imaging is a quantitative imaging technique that measures the underlying molecular diffusion of protons. Diffusion-weighted imaging (DWI) quantifies the apparent diffusion coefficient (ADC) which was first used to detect early ischemic stroke. However this does not take account of the directional dependence of diffusion seen in biological systems (anisotropy). Diffusion tensor imaging (DTI) provides a mathematical model of diffusion anisotropy and is widely used. Parameters, including fractional anisotropy (FA), mean diffusivity (MD), parallel and perpendicular diffusivity can be derived to provide sensitive, but non-specific, measures of altered tissue structure. They are typically assessed in clinical studies by voxel-based or region-of-interest based analyses. The increasing recognition of the limitations of the diffusion tensor model has led to more complex multi-compartment models such as CHARMED, AxCaliber or NODDI being developed to estimate microstructural parameters including axonal diameter, axonal density and fiber orientations. However these are not yet in routine clinical use due to lengthy acquisition times. In this review, I discuss how molecular diffusion may be measured using diffusion MRI, the biological and physical bases for the parameters derived from DWI and DTI, how these are used in clinical studies and the prospect of more complex tissue models providing helpful micro-structural information.

2012-01-01

195

Application of terahertz spectroscopy to the characterization of biological samples using birefringence silicon grating  

NASA Astrophysics Data System (ADS)

We present a device and method for performing vector transmission spectroscopy on biological specimens at terahertz (THz) frequencies. The device consists of artificial dielectric birefringence obtained from silicon microfluidic grating structures. The device can measure the complex dielectric function of a liquid, across a wide THz band of 2 to 5.5 THz, using a Fourier transform infrared spectrometer. Measurement data from a range of liquid specimens, including sucrose, salmon deoxyribonucleic acid (DNA), herring DNA, and bovine serum albumin protein solution in water are presented. The specimen handling is simple, using a microfluidic channel. The transmission through the device is improved significantly and thus the measurement accuracy and bandwidth are increased.

Saha, Shimul C.; Grant, James P.; Ma, Yong; Khalid, Ata; Hong, Feng; Cumming, David R. S.

2012-06-01

196

Design of a measurement cell for low-frequency dielectric spectroscopy of biological cell suspensions  

NASA Astrophysics Data System (ADS)

Dielectric spectroscopy of biological cell suspensions has a serious problem at low frequencies, where electrode polarization (EP) effects mostly mask their dielectric spectra. This paper describes a new type of measurement cell capable of extending the available low-frequency region by shifting the EP effects toward low frequencies. Its effectiveness was evaluated by computer simulation and experimental measurement on suspensions of erythrocytes and ghosts (hypotonically lysed erythrocytes). The results showed that the available low-frequency region was extended about ten times as compared with a corresponding conventional measurement cell, and that the low-frequency dispersion (so-called ?-dispersion) of ghost suspensions was definitely observed.

Asami, Koji

2011-08-01

197

X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples.  

PubMed

As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts. PMID:23093745

George, Graham N; Pickering, Ingrid J; Pushie, M Jake; Nienaber, Kurt; Hackett, Mark J; Ascone, Isabella; Hedman, Britt; Hodgson, Keith O; Aitken, Jade B; Levina, Aviva; Glover, Christopher; Lay, Peter A

2012-10-18

198

X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples  

PubMed Central

As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts.

George, Graham N.; Pickering, Ingrid J.; Pushie, M. Jake; Nienaber, Kurt; Hackett, Mark J.; Ascone, Isabella; Hedman, Britt; Hodgson, Keith O.; Aitken, Jade B.; Levina, Aviva; Glover, Christopher; Lay, Peter A.

2012-01-01

199

Quantitative analysis of liquids from aerosols and microdrops using laser induced breakdown spectroscopy.  

PubMed

Laser induced breakdown spectroscopy (LIBS) is shown to be capable of low volume (90 pL) quantitative elemental analysis of picogram amounts of dissolved metals in solutions. Single-pulse and collinear double-pulse LIBS were investigated using a 532 nm dual head laser coupled to a spectrometer with an intensified charge coupled device (CCD) detector. Aerosols were produced using a micronebulizer, conditioned inside a concentric spray chamber, and released through an injector tube with a diameter of 1 mm such that a LIBS plasma could be formed ~2 mm from the exit of the tube. The emissions from both the aerosols and a single microdrop were then collected with a broadband high resolution spectrometer. Multielement calibration solutions were prepared, and continuing calibration verification (CCV) standards were analyzed for both aerosol and microdrop systems to calculate the precision, accuracy, and limits of detection for each system. The calibration curves produced correlation coefficients with R(2) values > 0.99 for both systems. The precision, accuracy, and limit of detection (LOD) determined for aerosol LIBS were averaged and determined for the emission lines of Sr II (421.55 nm), Mg II (279.80 nm), Ba II (493.41 nm), and Ca II (396.84 nm) to be ~3.8% RSD, 3.1% bias, 0.7 ?g/mL, respectively. A microdrop dispenser was used to deliver single drops containing 90 pL into the space where a LIBS plasma was generated with a focused laser pulse. In the single drop microdrop LIBS experiment, the analysis of a single drop, containing a total mass of 45 pg, resulted in a precision of 13% RSD and a bias of 1% for the Al I (394.40 nm) emission line. The absolute limits of detection of single drop microdrop LIBS for the emission lines Al I (394.40 nm) and Sr II (421.5 nm) were approximately 1 pg, and Ba II (493.41 nm) produced an absolute detection limit of approximately 3 pg. Overall, the precision, accuracy, and absolute LOD determined for single microdrop LIBS resulted in a typical performance of ~14% RSD, 6% bias, and 1 pg for the elements Sr II (421.55 nm), Al I(394.40 nm), Mg II (279.80), and Ba II(493.41 nm). PMID:22283515

Cahoon, Erica M; Almirall, Jose R

2012-02-10

200

Subcortical Ischemic Vascular Dementia: Assessment with Quantitative MR Imaging and 1H MR Spectroscopy  

Microsoft Academic Search

METHODS: Patients with dementia and lacunes (n 5 11), cognitive impairment and lacunes (n 5 14), and dementia without lacunes (n 5 18) and healthy age-matched control volunteers (n 5 20) underwent MR imaging and 1H MR spectroscopy. 1H MR spectroscopy data were coan- alyzed with coregistered segmented MR images to account for atrophy and tissue composition. RESULTS: Compared with

Aristides A. Capizzano; Norbert Schuff; Diane L. Amend; Jody L. Tanabe; David Norman; Andrew A. Maudsley; William Jagust; Helena C. Chui; George Fein; Mark R. Segal; Michael W. Weiner

201

Effect of biological matrix and sample preparation on qPCR quantitation of siRNA drugs in animal tissues  

Microsoft Academic Search

IntroductionQuantitative pharmacokinetic measurement of short nucleotide sequences in animal tissues is critical to the successful development of siRNA-based drugs. Stem-loop qRT-PCR is a sensitive and precise methodology, but the effect of biological matrix and purity of the input sample has yet to be investigated.

Jessica Seitzer; Hangchun Zhang; Martin Koser; Yi Pei; Marc Abrams

2011-01-01

202

Determination of quantitative distributions of heavy-metal stain in biological specimens by annular dark-field STEM  

PubMed Central

It is shown that dark-field images collected in the scanning transmission electron microscope (STEM) at two different camera lengths yield quantitative distributions of both the heavy and light atoms in a stained biological specimen. Quantitative analysis of the paired STEM images requires knowledge of the elastic scattering cross sections, which are calculated from the NIST Elastic-Scattering Cross-Section Database. The results reveal quantitative information about the distribution of fixative and stain within the biological matrix, and provide a basis for assessing detection limits for heavy metal clusters used to label intracellular proteins. In sectioned cells that have been stained only with osmium tetroxide, we find an average of 1.2 ± 0.1 Os atom per nm3, corresponding to an atomic ratio of Os:C atoms of approximately 0.02, which indicates that small heavy atom clusters of Undecagold and Nanogold can be detected in lightly stained specimens.

Sousa, A. A.; Hohmann-Marriott, M.; Aronova, M. A.; Zhang, G.; Leapman, R. D.

2009-01-01

203

Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps.  

PubMed

Where causal SNPs (single nucleotide polymorphisms) tend to accumulate within biological pathways, the incorporation of prior pathways information into a statistical model is expected to increase the power to detect true associations in a genetic association study. Most existing pathways-based methods rely on marginal SNP statistics and do not fully exploit the dependence patterns among SNPs within pathways.We use a sparse regression model, with SNPs grouped into pathways, to identify causal pathways associated with a quantitative trait. Notable features of our "pathways group lasso with adaptive weights" (P-GLAW) algorithm include the incorporation of all pathways in a single regression model, an adaptive pathway weighting procedure that accounts for factors biasing pathway selection, and the use of a bootstrap sampling procedure for the ranking of important pathways. P-GLAW takes account of the presence of overlapping pathways and uses a novel combination of techniques to optimise model estimation, making it fast to run, even on whole genome datasets.In a comparison study with an alternative pathways method based on univariate SNP statistics, our method demonstrates high sensitivity and specificity for the detection of important pathways, showing the greatest relative gains in performance where marginal SNP effect sizes are small. PMID:22499682

Silver, Matt; Montana, Giovanni

2012-01-06

204

Biological and clinical relevance of quantitative global methylation of repetitive DNA sequences in chronic lymphocytic leukemia  

PubMed Central

Global DNA hypomethylation affecting repeat sequences has been reported in different cancer types. Herein, we investigated the methylation levels of repetitive DNA elements in chronic lymphocytic leukemia (CLL), their correlation with the major cytogenetic and molecular features, and clinical relevance in predicting therapy-free survival (TFS). A quantitative bisulfite-PCR Pyrosequencing method was used to evaluate methylation of Alu, long interspersed nuclear elements-1 (LINE-1) and satellite-? (SAT-?) sequences in 77 untreated early-stage (Binet A) CLL patients. Peripheral B-cells from 7 healthy donors were used as controls. Methylation levels (median %5mC) were lower in B-CLLs compared with controls (21.4 vs. 25.9; 66.8 vs. 85.7; 84.0, vs. 88.2 for Alu, LINE-1 and SAT-?, respectively) (p < 0.001). Among CLL patients, a significant association was observed with 17p13.1 deletion (16.8 vs. 22.4; 51.2 vs. 68.5; 52.6 vs. 85.0, for Alu, LINE-1 and SAT-?) but not with other major genetic lesions, IgVH mutation status, CD38 or ZAP-70 expression. Follow-up analyses showed that lower SAT-? methylation levels appeared to be an independent prognostic marker significantly associated with shorter TFS. Our study extended previous limited evidences in methylation of repetitive sequences in CLL suggesting an important biological and clinical relevance in the disease.

Fabris, Sonia; Bollati, Valentina; Agnelli, Luca; Morabito, Fortunato; Motta, Valeria; Cutrona, Giovanna; Matis, Serena; Grazia Recchia, Anna; Gigliotti, Vincenzo; Gentile, Massimo; Deliliers, Giorgio Lambertenghi; Bertazzi, Pier Alberto; Ferrarini, Manlio; Neri, Antonino; Baccarelli, Andrea

2011-01-01

205

Fast Identification of Biological Pathways Associated with a Quantitative Trait Using Group Lasso with Overlaps  

PubMed Central

Where causal SNPs (single nucleotide polymorphisms) tend to accumulate within biological pathways, the incorporation of prior pathways information into a statistical model is expected to increase the power to detect true associations in a genetic association study. Most existing pathways-based methods rely on marginal SNP statistics and do not fully exploit the dependence patterns among SNPs within pathways. We use a sparse regression model, with SNPs grouped into pathways, to identify causal pathways associated with a quantitative trait. Notable features of our “pathways group lasso with adaptive weights” (P-GLAW) algorithm include the incorporation of all pathways in a single regression model, an adaptive pathway weighting procedure that accounts for factors biasing pathway selection, and the use of a bootstrap sampling procedure for the ranking of important pathways. P-GLAW takes account of the presence of overlapping pathways and uses a novel combination of techniques to optimise model estimation, making it fast to run, even on whole genome datasets. In a comparison study with an alternative pathways method based on univariate SNP statistics, our method demonstrates high sensitivity and specificity for the detection of important pathways, showing the greatest relative gains in performance where marginal SNP effect sizes are small.

Silver, Matt; Montana, Giovanni

2012-01-01

206

Direct visualization and quantitative analysis of water diffusion in complex biological tissues using CARS microscopy.  

PubMed

To date, it has not been possible to measure microscopic diffusive water movements in epithelia and in the interstitial space of complex tissues and organs. Diffusive water movements are essential for life because they convey physiologically important small molecules, e.g. nutrients and signaling ligands throughout the extracellular space of complex tissues. Here we report the development of a novel method for the direct observation and quantitative analysis of water diffusion dynamics in a biologically organized tissue using Coherent Anti-Stokes Raman Scattering (CARS) microscopy. Using a computer simulation model to analyze the CARS O-H bond vibration data during H2O/D2O exchange in a 3D epithelial cyst, we succeeded in measuring the diffusive water permeability of the individual luminal and basolateral water pathways and also their response to hormonal stimulation. Our technique will be applicable to the measurement of diffusive water movements in other structurally complex and medically important tissues and organs. PMID:24067894

Yu, Ying-Chun; Sohma, Yoshiro; Takimoto, Shinichi; Miyauchi, Takayuki; Yasui, Masato

2013-09-25

207

Quantitative Analysis of the TWT Cathode Impregnants Using Flame Emission Spectroscopy.  

National Technical Information Service (NTIS)

Flame emission spectroscopy (FES) is demonstrated for the determination of barium, calcium, and aluminum concentrations in barium calcium aluminate dispenser cathode impregnants. The procedure consists of dissolving the impregnant in 0.5M to 2M hydrochlor...

R. A. Lipeles

1987-01-01

208

Biological tissue characterization by magnetic induction spectroscopy (MIS): requirements and limitations.  

PubMed

Magnetic induction spectroscopy (MIS) aims at the contactless measurement of the passive electrical properties (PEP) sigma, epsilon, and mu of biological tissues via magnetic fields at multiple frequencies. Whereas previous publications focus on either the conductive or the magnetic aspect of inductive measurements, this article provides a synthesis of both concepts by discussing two different applications with the same measurement system: 1) monitoring of brain edema and 2) the estimation of hepatic iron stores in certain pathologies. We derived the equations to estimate the sensitivity of MIS as a function of the PEP of biological objects. The system requirements and possible systematic errors are analyzed for a MIS-channel using a planar gradiometer (PGRAD) as detector. We studied 4 important error sources: 1) moving conductors near the PGRAD; 2) thermal drifts of the PGRAD-parameters; 3) lateral displacements of the PGRAD; and 4) phase drifts in the receiver. All errors were compared with the desirable resolution. All errors affect the detected imaginary part (mainly related to sigma) of the measured complex field much less than the real part (mainly related to epsilon and mu). Hence, the presented technique renders possible the resolution of (patho-) physiological changes of the electrical conductivity when applying highly resolving hardware and elaborate signal processing. Changes of the magnetic permeability and permittivity in biological tissues are more complicated to deal with and may require chopping techniques, e.g., periodic movement of the object. PMID:12848355

Scharfetter, Hermann; Casañas, Roberto; Rosell, Javier

2003-07-01

209

Quantitative determination of atractylon in Atractylodis Rhizoma and Atractylodis Lanceae Rhizoma by 1H-NMR spectroscopy.  

PubMed

(1)H-NMR spectroscopy was successfully applied to the quantitative determination of atractylon in Atractylodis Rhizoma (dried rhizomes of Atractylodes ovata and A. japonica) and Atractylodis Lanceae Rhizoma (dried rhizomes of Atractylodes lancea and A. chinensis). The analysis was carried out by comparing the integral of the H-12 singlet signal of atractylon, which was well separated in the range of delta 6.95-7.05 ppm in the NMR spectrum, with the integral of a hexamethyldisilane (HMD) signal at delta 0 ppm. The atractylon contents obtained by the (1)H-NMR spectroscopy were consistent with those obtained by the conventional HPLC analysis. The present method requires neither reference compounds for calibration curves nor sample pre-purification. It also allows simultaneous determination of multiple constituents in a crude extract. Thus, it is applicable to chemical evaluation of crude drugs as a powerful alternative to various chromatographic methods. PMID:20165926

Hasada, Keiko; Yoshida, Takamitsu; Yamazaki, Takeshi; Sugimoto, Naoki; Nishimura, Tetsuji; Nagatsu, Akito; Mizukami, Hajime

2010-02-19

210

[Quantitative analysis of protein concentration by absorption peak integration method of UV spectroscopy--taking alkaline phosphatase as an example].  

PubMed

Adsorption of alkaline phosphatase (APase) on minerals (goethite, montmorillonite) and sediments from Taihu Lake was studied. However, the concentration of alkaline phosphatase in the supernatant cannot be analyzed by the adsorption at 280 nm due to that the UV spectroscopy was changed. Quantitative analysis of alkaline phosphatase in the supernatant by the absorption peak (252-305 nm) integration method of UV spectroscopy was developed. This method determined the concentrations of alkaline phosphatase well. Compared to the results of Bradford, the absorption peak integration method can determine the concentrations of supernatant fast, conveniently, and accurately. This method can also be applied to other protein solution analysis and similar experiments. The drawbacks of traditional single wavelength method (280nm) were overcome to some extent based on the method of absorption peak integration. PMID:24059187

Zhu, Yuan-Rong; Wu, Feng-Chang; Lin, Ying

2013-07-01

211

A Semi-Quantitative Analysis of Essential Micronutrient in Folium Lycii Using Laser-Induced Breakdown Spectroscopy Technique  

NASA Astrophysics Data System (ADS)

In this paper, the capabilities of laser-induced breakdown spectroscopy (LIBS) for rapid analysis to multi-component plant are illustrated using a 1064 nm laser focused onto the surface of folium lycii. Based on homogeneous plasma assumption, nine of essential micronutrients in folium lycii are identified. Using Saha equation and Boltzmann plot method electron density and plasma temperature are obtained, and their relative concentration (Ca, Mg, Al, Si, Ti, Na, K, Li, and Sr) are obtained employing a semi-quantitative method.

Sun, Duixiong; Su, Maogen; Dong, Chenzhong; Zhang, Dacheng; Ma, Xinwen

2010-08-01

212

Semi-quantitative surface analysis of Mt. St. Helens Ash by X-ray photoelectron spectroscopy (XPS)  

NASA Astrophysics Data System (ADS)

A sample of Mt. St. Helens tephra and USGS andesite rock standard (AGV-1) were analyzed by X-ray photoelectron spectroscopy (XPS). The results indicate major element surface analysis on powdered multicomponent samples (such as geological specimens) can be performed semi-quantitatively using an equation that relates XPS peak intensity with atomic surface density. The surface compositions found by XPS are in good agreement with bulk X-ray fluorescence analysis (XRF). It is interesting to note that XPS analysis of this volcanic ash did not reveal a surface enrichment of chlorine or sulphur and only trace fluorine although these volatile elements are normally abundant in volcanic gases.

Brown, J. R.; Fyfe, W. S.; Bancroft, G. M.

213

Quantitative and qualitative analysis of fluorescent substances and binary mixtures by use of shifted excitation Raman difference spectroscopy  

NASA Astrophysics Data System (ADS)

Shifted Excitation Raman Difference Spectroscopy (SERDS) implemented with two wavelength-stabilized laser diodes with fixed wavelength separation is discussed as an effective method for dealing with the effects of fluorescence in Raman spectroscopic analysis. In this presentation we discuss the results of both qualitative and quantitative SERDS analysis of a variety of strongly fluorescing samples, including binary liquid mixtures. This application is enabled by the Volume Bragg Grating® (VBG®) technology, which allows manufacturing of compact low-cost high-power laser sources, suitable for extending the SERDS methodology to portable Raman spectrometers.

Volodin, Boris L.; Dolgy, Sergei; Lieber, Chad; Wu, Huawen; Yang, William

2013-03-01

214

Monitoring of Streptomyces peucetius cultivations using FTIR/ATR spectroscopy and quantitative models based on library type data.  

PubMed

Cultivations of Streptomyces peucetius in two types of medium were monitored on-line using a Fourier transform infrared (FTIR) spectrometer combined with an attenuated total reflection probe. The quantitative measurements of the glucose, starch and acetate concentrations were implemented using partial least squares calibration models. These were regressed on spectral and concentration information obtained by adding together single constituent spectra of the main constituents in the medium according to a full factorial design. The accuracy achieved was considered to be satisfactory, with an average root mean square error of prediction of 1.5 g/l for glucose and 0.25 g/l for acetate. The methodology used is considered to be a rapid technique for generation of calibration data, and a step towards the use of library type data for calibration purposes in quantitative FTIR spectroscopy applications in bioprocesses. PMID:23242495

Dahlbacka, John; Kiviharju, Kristiina; Eerikäinen, Tero; Fagervik, Kaj

2012-12-15

215

Quantitative characterization of the mesothelioma-inducing erionite series minerals by transmission electron microscopy and energy dispersive spectroscopy.  

PubMed

Air-collected erionite series minerals from Cappadocia region of Turkey were characterized quantitatively by using transmission electron microscopy (TEM) equipped with energy dispersive spectroscopy (EDS). Field emission scanning electron microscopy aided identification of fibrous minerals. Quantitative characterization guidelines for positive identification of erionites proposed by Dogan and Dogan (2008) was applied and the modified balance error formula (E%<10) and Mg-content test <0.80 were performed for each analysis. Erionite species computation showed that the mineral is erionite-K and a mean chemical formula is proposed based upon the TEM-EDS results. Among the 60 analyses, 11 passed E% test (18.3%), 33 passed Mg-content test (55.0%), and only 3 passed both E% and Mg-content tests (5.0%). This shows difficulty of quantitative characterization of the erionite series minerals. However, as erionite is the most carcinogenic mineral known and is classified by IARC as a Group-I (human) carcinogen, it requires special attention from the mineralogical community to help establish its true mineralogical properties. Quantitatively characterized erionite data are very scarce in literature. Correctly identified erionite mineral types will be useful to medical researchers in their search to find a possible cure for the deadly disease of mesothelioma. PMID:21866558

Dogan, Meral

2011-08-22

216

Quantitative morphology for biologists and computer scientists: I. Computer-aided tutorial for biological stereology (version 1.0).  

PubMed

This paper describes a computer-aided tutorial for biological stereology. Stereology, a type of quantitative morphology, includes a collection of statistical methods that quantify the structural compartments that can be viewed in sections with light and electron microscopy. These methods provide volume, surface, length, shape, and number data, and help define the quantitative relationships among the structural compartments of biological hierarchies. Hierarchies, which connect structural data ranging in size from molecules to organs, serve as a central core to which the data of biological databases can be linked. The tutorial focuses on two objectives. It provides the user primarily interested in using quantitative morphology databases with background information, and offers a set of state-of-the-art tools to researchers wishing to use these methods in the laboratory. The main topics of the tutorial include: introduction to quantitative morphology, symbols/terms, data types, sampling, hierarchies, data interpretation, and utilities. The tutorial runs under the MS-DOS operating system and requires at least an IBM PC AT (or compatible), a color monitor (EGA, VGA), 540 KB of RAM, and 3 MB of hard disk space. PMID:1638052

Bolender, R P

1992-06-01

217

Quantitative Measurement of Superoxide Generation and Oxygen Consumption from Leukocytes Using Electron Paramagnetic Resonance Spectroscopy  

Microsoft Academic Search

In view of the important role of superoxide in cellular injury, there has been a great need for methods suitable for quantitation of superoxide production from cells. Previous methods have had limited sensitivity or specificity as well as problems with side reactions in cellular systems. Recently, we have shown that the new spin trap 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline-N-oxide has ideal properties for quantitative

Valerie Roubaud; Sornampillai Sankarapandi; Periannan Kuppusamy; Paul Tordo; Jay L. Zweier

1998-01-01

218

Application of UV-Raman spectroscopy to the detection of chemical and biological threats  

NASA Astrophysics Data System (ADS)

Brookhaven National Laboratory (BNL), Edgewood Chemical and Biological Center (ECBC) and ITT Industries Advanced Engineering and Sciences Division (AES) have been collaborating on the transitioning and subsequent development of a short-range, non-contact Raman lidar system specifically designed to detect and identify chemical agents on the battlefield. [The instrument, referred to as LISA (Laser Interrogation of Surface Agents), will the subject of an accompanying paper.] As part of this collaboration, BNL has the responsibility for developing a spectral database (library) of surrogates and precursors for use with LISA"s pattern recognition algorithms. In this paper, the authors discuss the phenomenon of UV Raman and resonance-enhanced Raman spectroscopy, the development of an instrument-independent Raman spectral library, and highlight the exploitable characteristics present in the acquired spectral signatures that suggest potential utility in our country"s efforts on Homeland Security.

Sedlacek, Arthur J., III; Christesen, Steven D.; Chyba, Tom; Ponsardin, Pat

219

Quantitative Raman spectroscopy as a tool to study the kinetics and formation mechanism of carbonates.  

PubMed

We have carried out a systematic study of abiotic precipitation at different temperatures of several Mg and Ca carbonates (calcite, nesquehonite, hydrocalcite) present in carbonaceous chondrites. This study highlights the capability of Raman spectroscopy as a primary tool for performing full mineralogical analysis. The precipitation reaction and the structure of the resulting carbonates were monitored and identified with Raman spectroscopy. Raman spectroscopy enabled us to confirm that the precipitation reaction is very fast (minutes) when Ca(II) is present in the solution, whereas for Mg(II) such reactions developed at rather slow rates (weeks). We also observed that both the composition and the reaction mechanisms depended on temperature, which might help to clarify several issues in the fields of planetology and geology, because of the environmental implications of these carbonates on both terrestrial and extraterrestrial objects. PMID:23896294

Bonales, L J; Muñoz-Iglesias, V; Santamaría-Pérez, D; Caceres, M; Fernandez-Remolar, D; Prieto-Ballesteros, O

2013-07-09

220

Assessment of Proton Microbeam Analysis of 11B for Quantitative Microdistribution Analysis of Boronated Neutron Capture Agent Analogs in Biological Tissues  

SciTech Connect

Purpose: To assess the {sup 11}B(p, {alpha}){sup 8}Be* nuclear reaction for quantitatively mapping the in-vivo sub-cellular distribution of boron within gliosarcoma tumors treated with boronated neutron capture therapy agent (NCTA) analogs. Materials and Methods: Intracranial tumors were produced in Fisher 344 rats using a 9L gliosarcoma model. Fourteen days later, the majority of rats were treated with f-boronophenylalanine and sacrificed 30 or 180 minutes after intravenous injection. Freeze dried tumor cryosections were imaged using the {sup 11}B(p, {alpha}){sup 8}Be* nuclear reaction and proton microbeams obtained from the nuclear microprobe at Lawrence Livermore National Laboratory. Results/Discussion: With{sup 11}B(p, {alpha}){sup 8}Be* analysis, {sup 11}B distributions within cells can be quantitatively imaged with spatial resolutions down to 1.5 {micro}m, minimum detection limits of 0.8 mg/kg and acquisition times of several hours. These capabilities offer advantages over alpha track autoradiography, electron energy loss spectroscopy and secondary ion mass spectrometry (SIMS) for 'B quantitation in tissues. However, the spatial resolution, multi-isotope capability and analysis times achieved with SIMS are superior to those achieved with {sup 11}B(p, {alpha}){sup 8}Be* analysis. Conclusions: When accuracy in quantitation is crucial, the assessing the microdistribution of {sup 11}B. {sup 11}B(p, {alpha}){sup 8}Be* reaction is well suited for Otherwise, SIMS may well be better suited to image the microdistribution of boron associated with NCTAs in biological tissues.

Bench, G; Grant, P G; Ueda, D L; Autry-Conwell, S A; Hou, Y; Boggan, J E

2002-12-04

221

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data.  

PubMed

Gene set enrichment analysis (GSEA) is a widely used technique in transcriptomic data analysis that uses a database of predefined gene sets to rank lists of genes from microarray studies to identify significant and coordinated changes in gene expression data. While GSEA has been playing a significant role in understanding transcriptomic data, no similar tools are currently available for understanding metabolomic data. Here, we introduce a web-based server, called Metabolite Set Enrichment Analysis (MSEA), to help researchers identify and interpret patterns of human or mammalian metabolite concentration changes in a biologically meaningful context. Key to the development of MSEA has been the creation of a library of approximately 1000 predefined metabolite sets covering various metabolic pathways, disease states, biofluids, and tissue locations. MSEA also supports user-defined or custom metabolite sets for more specialized analysis. MSEA offers three different enrichment analyses for metabolomic studies including overrepresentation analysis (ORA), single sample profiling (SSP) and quantitative enrichment analysis (QEA). ORA requires only a list of compound names, while SSP and QEA require both compound names and compound concentrations. MSEA generates easily understood graphs or tables embedded with hyperlinks to relevant pathway images and disease descriptors. For non-mammalian or more specialized metabolomic studies, MSEA allows users to provide their own metabolite sets for enrichment analysis. The MSEA server also supports conversion between metabolite common names, synonyms, and major database identifiers. MSEA has the potential to help users identify obvious as well as 'subtle but coordinated' changes among a group of related metabolites that may go undetected with conventional approaches. MSEA is freely available at http://www.msea.ca. PMID:20457745

Xia, Jianguo; Wishart, David S

2010-05-10

222

Quantitative solid-phase microextraction (SPME)-Raman spectroscopy for the detection of trace organics in water.  

PubMed

Solid-phase microextraction (SPME) was used along with Raman spectroscopy to quantify the partitioning of trace organics into polydimethylsiloxane (PDMS) matrices. PDMS has previously been utilized with SPME-Raman to pre-concentrate trace benzene, toluene, ethyl-benzene, and xylene fuel components from contaminated water, thereby enhancing detected Raman signals. Here, we show that SPME can increase Raman signals more than two orders of magnitude for the compounds investigated. We also demonstrate the quantitative features of SPME-Raman by estimating PDMS-organic partition coefficients for benzene [log(K) = 1.90 ± 10] and toluene [log(K) = 2.35 ± 20] by using linear regression fits in the dilute limit of concentrations. The K values obtained are within the range of values obtained with other quantitative SPME techniques. The method was also used to characterize quinoline, a pyridine-based organic, which yielded reasonable K values [log(K) = 1.20 ± 20]. Combining PDMS-based SPME with a technique such as Raman spectroscopy potentially enhances optical detection methods used in microfluidic systems, wherein PDMS is a common material of construction. PMID:23231913

Nwaneshiudu, Ikechukwu C; Yu, Qiuming; Schwartz, Daniel T

2012-12-01

223

Quantitative zinc speciation in soil with XAFS spectroscopy: evaluation of iterative transformation factor analysis  

Microsoft Academic Search

We employed a combination of selective sequential extractions and bulk XAFS spectroscopy, and extracted spectral XAFS components and their concentrations by iterative transformation factor analysis (ITFA), in order to determine the Zn speciation in a smelter-contaminated, acidic soil. We compared the speciation by ITFA with one we performed earlier using principal component analysis and linear combination fit. ITFA identified 4

A. C. Scheinost; A. Rossberg; M. Marcus; S. Pfister; R. Kretzschmar

2005-01-01

224

Qualitative and quantitative analysis of chlorinated solvents using Raman spectroscopy and machine learning  

Microsoft Academic Search

The unambiguous identification and quantification of hazardous materials is of increasing importance in many sectors such as waste disposal, pharmaceutical manufacturing, and environmental protection. One particular problem in waste disposal and chemical manufacturing is the identification of solvents into chlorinated or non-chlorinated. In this work we have used Raman spectroscopy as the basis for a discrimination and quantification method for

Jennifer Conroy; Alan G. Ryder; Marc N. Leger; Kenneth Hennessey; Michael G. Madden

225

The Quantitative Determination of Bis-Phenol Antioxidant Additives in Petroleum Oils by Infrared Spectroscopy.  

National Technical Information Service (NTIS)

For the determining bis-phenolic antioxidants in petroleum oils by infrared spectroscopy, the bands corresponding to the hydroxyle groups are convenient as analytical bands, i.e., 3496/cm for 2,2-methylene-bis (4-methyl-6-tert-butylphenol), 3435/cm for 2,...

A. A. Kadushin S. Korchek

1968-01-01

226

Reliable and fast quantitative analysis of active ingredient in pharmaceutical suspension using Raman spectroscopy  

Microsoft Academic Search

The concentration of acetaminophen in a turbid pharmaceutical suspension has been measured successfully using Raman spectroscopy. The spectrometer was equipped with a large spot probe which enabled the coverage of a representative area during sampling. This wide area illumination (WAI) scheme (coverage area 28.3mm2) for Raman data collection proved to be more reliable for the compositional determination of these pharmaceutical

Seok Chan Park; Minjung Kim; Jaegeun Noh; Hoeil Chung; Youngah Woo; Jonghwa Lee; Mark S. Kemper

2007-01-01

227

Longitudinal quantitative proton magnetic resonance spectroscopy of the hippocampus in Alzheimer's disease  

Microsoft Academic Search

Summary Changes in metabolites detected by proton magnetic resonance spectroscopy (1H MRS) of the brain have been demonstrated in Alzheimer's disease. Our object- ives were, first, longitudinally to measure absolute con- centrations of metabolites in both hippocampi, the sites of early Alzheimer's disease, in patients with clinical Alzheimer's disease and controls; secondly, to separate the relative contribution of atrophy and

Ruth M. Dixon; Kevin M. Bradley; Marc M. Budge; Peter Styles; A. David Smith

2002-01-01

228

[Usefulness of quantitative H-MR spectroscopy for the differentiation between radiation necrosis and recurrence of anaplastic oligodendroglioma].  

PubMed

We report a case, in which quantitative 1H-MR spectroscopy (MRS) was useful for the differentiation between radiation necrosis and a recurrent tumor. The present case is a 44-year-old man who underwent the subtotal removal of a mass lesion in the left frontal lobe. The histological diagnosis was anaplastic oligodendroglioma (WHO grade III). Postoperatively, a fractionated radiotherapy (total 64Gy) and chemotherapy were performed. MRI after the radiotherapy showed no contrast enhancing lesion. MRI, 5 years after the radiotherapy, showed a growing enhancing lesion and a T1 hypointensity lesion without enhancement, both of which indicated a recurrent tumor. MR spectroscopy was performed for the differential diagnosis of these lesions. The spectrum was acquired by the point resolved spectroscopy (PRESS) method by TR/TE=2,000 ms/68 ms, 136 ms, and 272 ms and evaluated with peak pattern and quantification value of metabolite. MRS of the enhancing lesion demonstrated a decrease of the Choline-containing compounds (Cho) concentration, disappearance of N-acetylaspartate (NAA), decrease of Creatine/ Phosphocreatine (t-Cr) and presence of Lipids (Lip) and Lactate (Lac), all of which are characteristic finding of a radiation necrosis. The histological diagnosis of this lesion showed evidence also of radiation necrosis. On the other hand, MRS of the T1 hypointensity lesion without enhancement showed, a marked high peak of the Cho concentration, which is characteristic for a recurrent tumor. The histological findings of this lesion showed a diffuse proliferation of recurrent tumor cells. Quantitative 1H-MRS is a useful tool for the differentiation between radiation necrosis and recurrent tumors. PMID:21512199

Isobe, Tomonori; Akutsu, Hiroyoshi; Yamamoto, Tetsuya; Shiigai, Masanari; Masumoto, Tomohiko; Nakai, Kei; Takano, Shingo; Anno, Izumi; Matsumura, Akira

2011-05-01

229

The quantitative monitoring of mechanochemical reaction between solid L-tartaric acid and sodium carbonate monohydrate by terahertz spectroscopy  

NASA Astrophysics Data System (ADS)

The solid-state reaction of chiral tartaric acid and alkali carbonate was studied by terahertz time-domain spectroscopy (THz-TDS). The sodium tartrate dihydrate was synthesized with high efficiency by mechanical grinding in the solid-state without waste that is particularly sustainable and environmentally benign. Distinct THz absorptions were observed for reactants and products. It indicates that THz spectroscopy is sensitive to different materials and crystal structures. The characteristic THz absorption peak at 1.09 THz of L (+)-Tartaric acid was selected for quantitative analysis. The reaction kinetics could be expressed by the Second-order equation and the Jander equation, which is consistent with a three-dimensional diffusion mechanism. The combination of multi-techniques including synchrotron radiation X-ray powder diffraction (SRXRPD), Fourier transform infrared (FT-IR) and scanning electron microscopy (SEM) was used to investigate the grinding process and presented supporting evidences. The results demonstrate that THz spectroscopy technique has great potential applications in process monitoring and analysis in pharmaceutical and chemical synthesis industry.

Liu, Xiaohong; Liu, Guifeng; Zhao, Hongwei; Zhang, Zengyang; Wei, Yongbo; Liu, Min; Wen, Wen; Zhou, Xingtai

2011-11-01

230

Rapid and quantitative detection of ethanol proportion in ethanol–gasoline mixtures by Raman spectroscopy  

Microsoft Academic Search

The paper reports a Raman spectral in-situ detection technique to measure the ethanol proportion in an ethanol–gasoline mixture rapidly and quantitatively. The transformed information of Raman spectra for different mixtures of gasoline and ethanol have been observed and recorded. The relative intensity ratio of two typical Raman peaks for ethanol and gasoline satisfies a linear relation with a variation in

Qing Ye; Qinfeng Xu; Yongai Yu; Ronghui Qu; Zujie Fang

2009-01-01

231

[Quantitative analysis of surface composition of polypropylene blends using attenuated total reflectance FTIR spectroscopy].  

PubMed

The surface composition and structure of solid organic polymers influence many of their properties and applications. Oligomers such as poly(ethylene glycol) (PEG), poly(methyl methacrylate) (PMMA) poly(butyl methacrylate) (PBMA) and their graft copolymers of polybutadiene and polypropylene were used as the macromolecular surface modifiers of polypropylene. The compositions on surface and in bulk of the polypropylene (PP) blends were determined quantitatively using attenuated total reflectance FTIR spectroscopic (ATR-FTIR) technique with a variable-angle multiple-reflection ATR accessory and FTIR measurements, respectively. By validating by Lambert-Beer law, 1103 and 1733 cm(-1) can be used to represent modifiers characteristic absorbance band to determine quantitatively the surface composition of modifiers including poly(ethylene glycol) and carbonyl segment in PP blends, respectively. The determination error can be effectively eliminated by calibrating wavelength and using absorption peak area ratio as the calibrating basis for the quantitative analysis. To minimize the effect of contact between the polymer film and the internal reflection element on the results of absolute absorbance, the technique of "band ratioing" was developed, and it was testified that the error of the peak area ratios of interest can be reduced to 5% or below, which was suitable for ATR-FTIR used as a determining quantitative tool for surface composition. The working curves were then established and used to calculate the composition of the responding functional groups in the film surface of the PP blends. The depth distribution of modifiers on the surface of blend films also can be determined by changing the incident angle of interest on the basis of the equation of the depth of penetration of the excursion wave in ATR spectra. The results indicated that ATR-FTIR can be used to determine quantitatively the surface composition and distribution of modifiers with reproducible and reliable measurement results. PMID:18975806

Chen, Han-jia; Zhu, Ya-fei; Zhang, Yi; Xu, Jia-rui

2008-08-01

232

Quantitative redox biology: an approach to understand the role of reactive species in defining the cellular redox environment.  

PubMed

Systems biology is now recognized as a needed approach to understand the dynamics of inter- and intra-cellular processes. Redox processes are at the foundation of nearly all aspects of biology. Free radicals, related oxidants, and antioxidants are central to the basic functioning of cells and tissues. They set the cellular redox environment and, therefore, are the key to regulation of biochemical pathways and networks, thereby influencing organism health. To understand how short-lived, quasi-stable species, such as superoxide, hydrogen peroxide, and nitric oxide, connect to the metabolome, proteome, lipidome, and genome we need absolute quantitative information on all redox active compounds as well as thermodynamic and kinetic information on their reactions, i.e., knowledge of the complete redoxome. Central to the state of the redoxome are the interactive details of the superoxide/peroxide formation and removal systems. Quantitative information is essential to establish the dynamic mathematical models needed to reveal the temporal evolution of biochemical pathways and networks. This new field of Quantitative Redox Biology will allow researchers to identify new targets for intervention to advance our efforts to achieve optimal human health. PMID:22161621

Buettner, Garry R; Wagner, Brett A; Rodgers, Victor G J

2013-11-01

233

Quantitative Redox Biology: An approach to understanding the role of reactive species in defining the cellular redox environment  

PubMed Central

Systems biology is now recognized as a needed approach to understand the dynamics of inter- and intra-cellular processes. Redox processes are at the foundation of nearly all aspects of biology. Free radicals, related oxidants, and antioxidants are central to the basic functioning of cells and tissues. They set the cellular redox environment and therefore are key to regulation of biochemical pathways and networks, thereby influencing organism health. To understand how short-lived, quasi-stable species, such as superoxide, hydrogen peroxide, and nitric oxide, connect to the metabolome, proteome, lipidome, and genome we need absolute quantitative information on all redox active compounds as well as thermodynamic and kinetic information on their reactions, i.e. knowledge of the complete redoxome. Central to the state of the redoxome are the interactive details of the superoxide/peroxide formation and removal systems. Quantitative information is essential to establish the dynamic mathematical models needed to reveal the temporal evolution of biochemical pathways and networks. This new field of Quantitative Redox Biology will allow researchers to identify new targets for intervention to advance our efforts to achieve optimal human health.

Buettner, Garry R.; Wagner, Brett A; Rodgers, Victor G. J.

2012-01-01

234

A semi-quantitative standard-less analysis method for laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

We report on recently developed analytical software to model laser-induced breakdown spectroscopy emission spectra and predict sample composition using a proposed calibration-free algorithm. The model uses a database of atomic emission lines to create a theoretical emission spectrum for selected elements using defined plasma parameters. The resulting theoretical spectrum is fitted to experimental data obtained from a laser-induced breakdown spectroscopy instrument comprising of four compact spectrometers that image the plasma emission. Elemental concentrations are obtained by comparing observed and predicted spectra while varying the plasma temperature and relative elemental concentrations. The use of the model for analysis of major elements in bauxites, brass and mineral samples as well as the analysis of laboratory air is demonstrated. For the majority of elements investigated agreement within 25% is achieved between estimated and certified values.

Yaroshchyk, Pavel; Body, Doug; Morrison, Richard J. S.; Chadwick, Bruce L.

2006-02-01

235

Terahertz time-domain spectroscopy and the quantitative monitoring of mechanochemical cocrystal formation  

NASA Astrophysics Data System (ADS)

Terahertz (THz) radiation probes intermolecular interactions through crystal lattice vibrations, allowing the characterization of solid materials. Thus, THz spectroscopy is a promising alternative to mainstream solid-state analytical tools such as X-ray diffraction or thermal analysis. The method provides the benefits of online measurement, remote sampling and three-dimensional imaging, all of which are attractive for quality control and security applications. In the context of pharmaceutical solids, THz spectroscopy can differentiate and quantify different forms of active pharmaceutical ingredients. Here, we apply this technique to monitor a dynamic process involving two molecular crystals. In particular, we follow the mechanochemical construction of a two-component cocrystal by grinding together phenazine (phen) and mesaconic acid (mes). To rationalize the observed changes in the spectra, we conduct lattice dynamics calculations that lead to the tentative assignment of at least one feature in the cocrystal THz spectrum.

Lien Nguyen, K.; Friš?i?, Tomislav; Day, Graeme M.; Gladden, Lynn F.; Jones, William

2007-03-01

236

Quantitative Diffuse Reflectance and Fluorescence Spectroscopy: A Tool to Monitor Tumor Physiology In Vivo  

PubMed Central

This study demonstrates the use of optical spectroscopy for monitoring tumor oxygenation and metabolism in response to hyperoxic gas breathing. Hemoglobin saturation and redox ratio were quantified for a set of 14 and 9 mice, respectively, measured at baseline and during carbogen breathing (95% O2, 5% CO2). In particular, significant increases in hemoglobin saturation and fluorescence redox ratio were observed upon carbogen breathing. These data were compared to that obtained concurrently using an established invasive technique, the OxyLite pO2 system, which also showed a significant increase in pO2. It was found that the direction of changes were generally the same between all of the methods, but that the OxyLite system was much more variable in general, suggesting that optical techniques may provide a better assessment of global tumor physiology. Optical spectroscopy measurements are demonstrated to provide a reliable, reproducible indication of changes in tumor physiology in response to physiologic manipulation.

Palmer, Gregory M.; Viola, Ronald J.; Schroeder, Thies; Yarmolenko, Pavel S.; Dewhirst, Mark W.; Ramanujam, Nirmala

2009-01-01

237

Quantitative analysis of ?-pinene and ?-myrcene in mastic gum oil using FT-Raman spectroscopy  

Microsoft Academic Search

?-Pinene and ?-myrcene are compounds that are contained in mastic gum in high concentrations. The ?-myrcene percentage determines the marketability of mastic gums. The chemical composition of mastic gum oil of a representative resin quality was evaluated by gas chromatography–mass spectrometry (GC–MS) technique. FT-Raman spectroscopy, based on band intensity measurements, was used for the determination of ?-pinene and ?-myrcene content

D. Daferera; C. Pappas; P. A. Tarantilis; M. Polissiou

2002-01-01

238

In situ monitoring by quantitative Raman spectroscopy of alcoholic fermentation by Saccharomyces cerevisiae under high pressure  

Microsoft Academic Search

We monitored alcoholic fermentation in Saccharomyces cerevisiae as a function of high hydrostatic pressure. Ethanol production from 0.15 M glucose was measured by Raman spectroscopy in\\u000a situ in a diamond-anvil cell. At 10 MPa, fermentation proceeds three times faster than at ambient pressure and the fermentation\\u000a yield is enhanced by 5% after 24 h. Above 20 MPa, the reaction kinetics slows down with increasing

A. Picard; I. Daniel; G. Montagnac; P. Oger

2007-01-01

239

Quantitative analysis of borophosphosilicate glass films on silicon using infrared external reflection--absorption spectroscopy  

Microsoft Academic Search

Borophosphosilicate glass (BPSG) dielectric thin films deposited on both bare and oxide-coated undoped silicon wafers have been analyzed using infrared external reflection--absorption spectroscopy (IRRAS). The partial least-squares (PLS1) algorithm was used to simultaneously determine boron content, phosphorous content, and film thickness, with standard errors of prediction of 0.08 wt %, 0.11 wt %, and 24 A, respectively, in the BPSG

James E. Franke; L. Zhang; T. M. Niemczyk; D. M. Haaland; K. J. Radigan

1995-01-01

240

Saturated polarization spectroscopy with a picosecond laser for quantitative concentration measurements  

SciTech Connect

The collisional dependence of saturated polarization spectroscopy with a picosecond laser is investigated by probing hydroxyl in a flow cell. While nanosecond lasers have been used often for nonlinear diagnostic measurements of flame composition, picosecond lasers provide a potentially superior source for such techniques. Compared to a nanosecond laser, picosecond lasers produce significantly greater peak power for the same pulse energy, and this could improve the signal strength of multi-photon techniques such as degenerate four-wave mixing (DFWM) and polarization spectroscopy (PS). It has been suggested that the signal produced by such lasers would be less dependent on the collisional environment because the behavior of the molecular system probed by short-pulse lasers is governed more by the spectral width of the laser and the Doppler effect. To investigate the collisional dependence of the polarization spectroscopy signal generated with a picosecond laser, the authors probe the A{sup 2}{Sigma}{sup +}-X{sup 2}{Pi} (0,0) band of OH in a flow cell. In this well-controlled environment, the authors monitor the change in signal strength as they vary the buffer gas pressure by a factor of 50. Hydroxyl (OH) is created by photolysis of hydrogen peroxide using a Nd:YAG laser.

T. A. Reichardt; R. L. Farrow; F. D. Teodoro; R. P. Lucht

2000-02-11

241

Spectroscopic characterization of biological agents using FTIR, normal Raman and surface-enhanced Raman spectroscopies  

NASA Astrophysics Data System (ADS)

FTIR, Raman spectroscopy and Surface Enhanced Raman Scattering (SERS) requires a minimum of sample allows fast identification of microorganisms. The use of this technique for characterizing the spectroscopic signatures of these agents and their stimulants has recently gained considerable attention due to the fact that these techniques can be easily adapted for standoff detection from considerable distances. The techniques also show high sensitivity and selectivity and offer near real time detection duty cycles. This research focuses in laying the grounds for the spectroscopic differentiation of Staphylococcus spp., Pseudomonas spp., Bacillus spp., Salmonella spp., Enterobacter aerogenes, Proteus mirabilis, Klebsiella pneumoniae, and E. coli, together with identification of their subspecies. In order to achieve the proponed objective, protocols to handle, cultivate and analyze the strains have been developed. Spectroscopic similarities and marked differences have been found for Spontaneous or Normal Raman spectra and for SERS using silver nanoparticles have been found. The use of principal component analysis (PCA), discriminate factor analysis (DFA) and a cluster analysis were used to evaluate the efficacy of identifying potential threat bacterial from their spectra collected on single bacteria. The DFA from the bacteria Raman spectra show a little discrimination between the diverse bacterial species however the results obtained from the SERS demonstrate to be high discrimination technique. The spectroscopic study will be extended to examine the spores produced by selected strains since these are more prone to be used as Biological Warfare Agents due to their increased mobility and possibility of airborne transport. Micro infrared spectroscopy as well as fiber coupled FTIR will also be used as possible sensors of target compounds.

Luna-Pineda, Tatiana; Soto-Feliciano, Kristina; De La Cruz-Montoya, Edwin; Pacheco Londoño, Leonardo C.; Ríos-Velázquez, Carlos; Hernández-Rivera, Samuel P.

2007-05-01

242

Infrared spectroscopy reveals both qualitative and quantitative differences in equine subchondral bone during maturation  

NASA Astrophysics Data System (ADS)

The collagen phase in bone is known to undergo major changes during growth and maturation. The objective of this study is to clarify whether Fourier transform infrared (FTIR) microspectroscopy, coupled with cluster analysis, can detect quantitative and qualitative changes in the collagen matrix of subchondral bone in horses during maturation and growth. Equine subchondral bone samples (n = 29) from the proximal joint surface of the first phalanx are prepared from two sites subjected to different loading conditions. Three age groups are studied: newborn (0 days old), immature (5 to 11 months old), and adult (6 to 10 years old) horses. Spatial collagen content and collagen cross-link ratio are quantified from the spectra. Additionally, normalized second derivative spectra of samples are clustered using the k-means clustering algorithm. In quantitative analysis, collagen content in the subchondral bone increases rapidly between the newborn and immature horses. The collagen cross-link ratio increases significantly with age. In qualitative analysis, clustering is able to separate newborn and adult samples into two different groups. The immature samples display some nonhomogeneity. In conclusion, this is the first study showing that FTIR spectral imaging combined with clustering techniques can detect quantitative and qualitative changes in the collagen matrix of subchondral bone during growth and maturation.

Kobrina, Yevgeniya; Isaksson, Hanna; Sinisaari, Miikka; Rieppo, Lassi; Brama, Pieter A.; van Weeren, René; Helminen, Heikki J.; Jurvelin, Jukka S.; Saarakkala, Simo

2010-11-01

243

Spectral simulation methods for enhancing qualitative and quantitative analyses based on infrared spectroscopy and quantitative calibration methods for passive infrared remote sensing of volatile organic compounds  

NASA Astrophysics Data System (ADS)

Infrared spectroscopy (IR) has over the years found a myriad of applications including passive environmental remote sensing of toxic pollutants and the development of a blood glucose sensor. In this dissertation, capabilities of both these applications are further enhanced with data analysis strategies employing digital signal processing and novel simulation approaches. Both quantitative and qualitative determinations of volatile organic compounds are investigated in the passive IR remote sensing research described in this dissertation. In the quantitative work, partial least-squares (PLS) regression analysis is used to generate multivariate calibration models for passive Fourier transform IR remote sensing measurements of open-air generated vapors of ethanol in the presence methanol as an interfering species. A step-wise co-addition scheme coupled with a digital filtering approach is used to attenuate the effects of variation in optical path length or plume width. For the qualitative study, an IR imaging line scanner is used to acquire remote sensing data in both spatial and spectral domains. This technology is capable of not only identifying but also specifying the location of the sample under investigation. Successful implementation of this methodology is hampered by the huge costs incurred to conduct these experiments and the impracticality of acquiring large amounts of representative training data. To address this problem, a novel simulation approach is developed that generates training data based on synthetic analyte-active and measured analyte-inactive data. Subsequently, automated pattern classifiers are generated using piecewise linear discriminant analysis to predict the presence of the analyte signature in measured imaging data acquired in remote sensing applications. Near infrared glucose determinations based on the region of 5000--4000 cm-1 is the focus of the research in the latter part of this dissertation. A six-component aqueous matrix of glucose in the presence of five other interferent species, all spanning physiological levels, is analyzed quantitatively. Multivariate PLS regression analysis in conjunction with samples designated into a calibration set is used to formulate models for predicting glucose concentrations. Variations in the instrumental response caused by drift and environmental factors are observed to degrade the performance of these models. As a remedy, a model updating approach based on spectral simulation is developed that is highly successful in eliminating the adverse effects of non-chemical variations.

Sulub, Yusuf Ismail

244

Quantitative and evolutionary biology of alternative splicing: how changing the mix of alternative transcripts affects phenotypic plasticity and reaction norms.  

PubMed

Alternative splicing (AS) of pre-messenger RNA is a common phenomenon that creates different transcripts from a single gene, and these alternative transcripts affect phenotypes. The majority of AS research has examined tissue and developmental specificity of expression of particular AS transcripts, how this specificity affects cell function, and how aberrant AS is related to disease. Few studies have examined quantitative between-individual variation in AS within a cell or tissue type, or in relation to phenotypes, but the results are compelling: quantitative variation in AS affects plastic traits such as stress, anxiety, fear, egg production, muscle performance, energetics and plant growth. Genomic analyses of AS are also at a nascent stage, but have revealed a number of significant evolutionary patterns. Growing knowledge of upstream genes and kinases that regulate AS provides the as-yet little explored potential to examine how these genes and pathways respond to environmental and genotype variables. Research in this area can provide glimpses of a labyrinth of genetic architectures that have rarely been considered in evolutionary and organismal biology, or in quantitative genetics. The scarcity of contribution to knowledge about AS from these fields is illustrated by the fact that heritability of quantitative variation in AS has not yet been determined for any gene in any organism. New research tactics that incorporate quantitative analyses of AS will allow organismal and evolutionary biologists to attain a fuller mechanistic understanding of many of the traits they study, and may lead to more rapid discovery of functionally important polymorphisms. PMID:17006532

Marden, J H

2006-09-27

245

Quantitative evaluation of pigment particles in organic layers by fibre-optics diffuse-reflectance spectroscopy  

NASA Astrophysics Data System (ADS)

Fibre-optics diffuse-reflectance spectroscopy was used to evaluate pigment quantity in art glazes. Measurements are non-invasive, without any contact, and can be performed in situ, without moving the work of art under investigation from its conservation place. Reflectance spectra are processed using Kubelka Munk theory in order to obtain scattering and absorption parameters of the samples. Assuming a linear dependance of these optical properties with the pigment volume concentration of the paint layers, we were able to evaluate pigment quantities in the samples from reflectance measurements. Results are in excellent agreement with those obtained by X-ray diffraction and micro-X-ray fluorescence.

Dupuis, G.; Menu, M.

2005-02-01

246

Multivariate calibration applied to near-infrared spectroscopy for the quantitative analysis of dilute aqueous solutions  

NASA Astrophysics Data System (ADS)

The penetration depths possible with near-infrared spectroscopy make it well suited for reagentless monitoring of analytes in body fluids or noninvasive monitoring of human tissue. As an initial step in achieving these goals, we have conducted near-infrared in-vitro experiments of dilute aqueous solutions containing analytes of physiological importance. By combining partial least squares (PLS) multivariate calibration methods with Latin Hypercube statistical designs, we have obtained precise near-infrared spectral determinations of urea, creatinine, and NaCl in dilute aqueous solutions. Cross-validated PLS calibrations for the three analytes and temperature were very precise and resulted in R2 values greater than 0.997.

Haaland, David M.; Jones, Howland D.

1994-01-01

247

Domain Dynamics in Piezoresponse Force Spectroscopy: Quantitative Deconvolution and Hysteresis Loop Fine Structure  

SciTech Connect

Domain dynamics in the Piezoresponse Force Spectroscopy (PFS) experiment is studied using the combination of local hysteresis loop acquisition with simultaneous domain imaging. The analytical theory for PFS signal from domain of arbitrary cross-section and length is developed for the analysis of experimental data on Pb(Zr,Ti)O3 polycrystalline films. The results suggest formation of oblate domain at early stage of the nucleation and growth, consistent with efficient screening of depolarization field. The fine structure of the hysteresis loop is shown to be related to the observed jumps in the domain geometry during domain wall propagation (nanoscale Barkhausen jumps), indicative of strong domain-defect interactions.

Bdikin, Igor [University of Aveiro, Portugal; Kholkin, Andrei [University of Aveiro, Portugal; Morozovska, A. N. [National Academy of Science of Ukraine, Kiev, Ukraine; Svechnikov, S. V. [National Academy of Science of Ukraine, Kiev, Ukraine; Kim, S.-H. [INOSTEK Inc., Gyeonggi, Korea; Kalinin, Sergei V [ORNL

2008-01-01

248

High-Field EPR Spectroscopy on Transfer Proteins in Biological Action  

NASA Astrophysics Data System (ADS)

In the last decade joint efforts of biologists, chemists, and physicists were made to understand the dominant factors determining specificity and directionality of transmembrane transfer processes in proteins. Characteristic examples of such factors are time varying specific H-bonding patterns and/or polarity effects of the microenvironment. In this overview, a few large paradigm biosystems are surveyed which have been explored lately in our laboratory. Taking advantage of the improved spectral and temporal resolution of high-frequency/high-field EPR at 95 GHz/3.4 T and 360 GHz/12.9 T, as compared to conventional X-band EPR (9.5 GHz/0.34 T), three transfer proteins in action are characterized with respect to structure and dynamics: (1) light-induced electron-transfer intermediates in wild-type and mutant reaction-centre proteins from photosynthetic bacteria Rhodobacter sphaeroides, (2) light-driven proton-transfer intermediates of site-specifically nitroxide spin-labelled mutants of bacteriorhodopsin proteins from Halobacterium salinarium, (3) refolding intermediates of site-specifically nitroxide spin-labelled mutants of the channel-forming protein domain of Colicin A bacterial toxin produced in Escherichia coli. The information obtained is complementary to that of protein crystallography, solid-state NMR, infrared and optical spectroscopy techniques. A unique strength of high-field EPR is particularly noteworthy: it can provide detailed information on transient intermediates of proteins in biological action. They can be observed and characterized while staying in their working states on biologically relevant time scales.

Möbius, K.; Schnegg, A.; Plato, M.; Fuchs, M. R.; Savitsky, A.

2006-08-01

249

IRMPD spectroscopy of protonated S-nitrosocaptopril, a biologically active, synthetic amino acid.  

PubMed

S-Nitrosocaptopril, a biologically active S-nitrosothiol, is generated as protonated species and isolated in the gas phase by electrospray ionization coupled to Fourier Transform Ion Cyclotron Resonance (FT-ICR) or ion-trap mass spectrometry. The structural and IR spectroscopic characterization of protonated S-nitrosocaptopril (SNOcapH(+)) is aided by the comparative study of the parent species lacking the NO feature, namely protonated captopril. The study is accomplished by methodologies based on tandem mass spectrometry, namely by energy resolved collision-induced dissociation and infrared multiple-photon dissociation (IRMPD) spectroscopy, backed by density functional theory calculations. IRMPD spectra have been obtained both in the 1000-1900 cm(-1) fingerprint range, using a beamline of the infrared free electron laser (IR-FEL) at the Centre Laser Infrarouge d'Orsay (CLIO), and in the O-H and N-H stretching region (2900-3700 cm(-1)) using the tunable IR radiation of a tabletop parametric oscillator/amplifier (OPO/OPA) laser source. The structural features of the ion have been ascertained by comparison of the experimental IRMPD spectra with the IR transitions calculated for the lowest energy isomers. Evidence is obtained that protonation occurs at the amide carbonyl oxygen which is found to be the thermodynamically most basic site. However, SNOcapH(+) is present as a thermally equilibrated mixture of low-energy structures, with a major contribution of the most stable isomer characterized by a trans relationship of the positively charged OH group with respect to the carboxylic acid functionality on the adjacent proline ring and by an anti conformation at the S-N (partial) double bond, though the energy difference with the analogous trans-syn isomer is less than 1 kJ mol(-1). The highly diagnostic N-O stretching mode has been unambiguously identified, which may be regarded as an informative probe for S-nitrosation features in more complex, biologically active molecules. PMID:20852770

Coletti, Cecilia; Re, Nazzareno; Scuderi, Debora; Maître, Philippe; Chiavarino, Barbara; Fornarini, Simonetta; Lanucara, Francesco; Sinha, Rajeev K; Crestoni, Maria Elisa

2010-09-17

250

Quantitative comparison of the hemodynamic activation elicited by cardinal and oblique gratings with functional near-infrared spectroscopy.  

PubMed

Evidence has been accumulated for over a century indicating that the visual system of humans and many animals is more sensitive to contour stimulation at vertical or horizontal orientations than oblique orientations. However, the neural basis for this orientation anisotropy is still a subject of debate. In the present study, we recorded brain activity over the parietal-occipital and frontal lobes with functional near-infrared spectroscopy (fNIRS) when human participants were presented with gratings in different orientations. The oblique gratings induced a much larger change in the oxygenated hemoglobin concentration than vertical and horizontal gratings in the left occipital lobe. However, we did not find any significant orientation anisotropy in the frontal lobe. Our study showed that different quantitative changes in the hemoglobin concentrations occurred in response to differently oriented stimuli in the visual cortex and that fNIRS could potentially be a valuable tool in the assessment of the hemodynamic responses of the visual system. PMID:23528283

Sun, Meirong; Huang, Jing; Wang, Fang; An, An; Tian, Fenghua; Liu, Hanli; Niu, Haijing; Song, Yan

2013-05-01

251

Quantitative determination of the cubic-to-monoclinic phase transformation in fully stabilized zirconias by Raman spectroscopy  

SciTech Connect

Vibrational Raman spectroscopy was used successfully for the quantitative determination of the cubic and monoclinic phases of zirconia. Pressed pellets with known composition were prepared using monoclinic and cubic powders from different manufacturers and were used as standard mixtures. An intensity ratio plot of the 617-cm[sup [minus]1] band, which is attributed to the presence of both phases, to either the 177-cm[sup [minus]1] or 476-cm[sup [minus]1] monoclinic band against the inverse monoclinic molar fraction ([chi]) yielded a straight line which was described by ratio = 0.11[chi][sup [minus]1] + 0.26 and ratio = 0.12 [chi][sup [minus]1] + 0.29, respectively. The method was found to be independent of the origin of the powders.

Kontoyannis, C.G.; Carountzos, G. (Univ. of Patras (Greece))

1994-08-01

252

Quantitative detection of nitrate in water and wastewater by surface-enhanced Raman spectroscopy.  

PubMed

The presence of inorganic nitrogen species in water can be unsuitable for drinking and detrimental to the environment. In this study, a surface-enhanced Raman spectroscopy (SERS) method coupled with a commercially available gold nanosubstrate (a gold-coated silicon material) was evaluated for the detection of nitrate and nitrite in water and wastewater. Applications of SERS coupled with gold nanosubstrates resulted in an enhancement of Raman signals by a factor of ?10(4) compared to that from Raman spectroscopy. The new method was able to detect nitrate with linear ranges of 1-10,000 mg NO3(-)/L (R(2)=?0.978) and 1-100 mg NO3(-)/L (R(2)=?0.919) for water and wastewater samples, respectively. Among the common anions, phosphate appeared to be the major interfering anion affecting nitrate measurement. Nevertheless, the percentage error of nitrate measurement in wastewater by the proposed SERS method was comparable to that by ion chromatography. The nitrate detection limits in water and wastewater samples were about 0.5 mg/L. The SERS method could simultaneously detect sulfate, which may serve as a reference standard in water. These results suggested that the SERS coupled with nanosubstrates is a promising method to determine nitrate concentrations in water and wastewater. PMID:23108715

Gajaraj, Shashikanth; Fan, Cui; Lin, Mengshi; Hu, Zhiqiang

2012-10-30

253

Quantitative mapping of alluvial fan evolution using ground-based reflectance spectroscopy  

NASA Astrophysics Data System (ADS)

The ability of field-based reflectance spectroscopy to resolve the relative proportions of Fe-oxides and clays in soils was used to map the composition, relative age and distribution of segments within late Quaternary fan systems in Sfakia, southwest Crete. The spectrometric results demonstrate that luvisols that have formed on the surfaces of fan segments are characterized by distinctive Fe-oxides (types) and clay minerals (species). Furthermore, Fe-oxide and clay concentrations display a clear and consistent trend whereby for each study fan luvisols formed on increasingly proximal fan segments are characterized by a progressive build-up of spectrally distinct secondary iron oxides and clay minerals, which suggests that proximal segments formed first. The relative ages and hence order of formation of segments suggested by the spectral data are strongly supported by an optically stimulated luminescence (OSL)-based geochronology which provides a tentative maximum age of 144 ka for the oldest (stage 1) surface and 11.2 ka for the youngest (stage 2C) surface. Moreover, the chronometric data indicate that time intervals of the order 20 to 25,000 years are necessary to generate sufficient differences in pedogenic Fe-oxides and clay concentrations to enable differentiation of fan segments by field spectroscopy.

Ferrier, Graham; Pope, Richard J. J.

2012-11-01

254

In vitro quantitation of human femoral artery atherosclerosis using near-infrared Raman spectroscopy  

NASA Astrophysics Data System (ADS)

Near-infrared Raman spectroscopy has been used in vitro to identify calcified atherosclerotic plaques in human femoral arteries. Raman techniques allow for the identification of these plaques in a nondestructive manner, which may allow for the diagnosis of coronary artery disease in cardiac patients in the future. As Raman spectroscopy also reveals chemical information about the composition of the arteries, it can also be used as a prognostic tool. The in vivo detection of atherosclerotic plaques at risk for rupture in cardiac patients will enhance treatment methods while improving clinical outcomes for these procedures. Raman spectra were excited by an Invictus 785-nm NIR laser and measured with a fiber-coupled micro-Raman RXN system (Kaiser Optical Systems, Inc., Ann Arbor, MI) equipped with a 785 nm CW laser and CCD detector. Chemical mapping of arteries obtained post mortem allowed for the discrete location of atherosclerotic plaques. Raman peaks at 961 and 1073 cm-1 reveal the presence of calcium hydroxyapatite and carbonate apatite, which are known to be present in calcified plaques. By mapping the locations of these peaks the boundaries of the plaques can be precisely determined. Areas of varying degrees of calcification were also identified. Because this can be useful in determining the degree of plaque calcification and vessel stenosis, this may have a significant impact on the clinical treatment of atherosclerotic plaques in the future.

Dykes, Ava C.; Anastasiadis, Pavlos; Allen, John S., III; Sharma, Shiv K.

2012-05-01

255

In situ monitoring by quantitative Raman spectroscopy of alcoholic fermentation by Saccharomyces cerevisiae under high pressure.  

PubMed

We monitored alcoholic fermentation in Saccharomyces cerevisiae as a function of high hydrostatic pressure. Ethanol production from 0.15 M glucose was measured by Raman spectroscopy in situ in a diamond-anvil cell. At 10 MPa, fermentation proceeds three times faster than at ambient pressure and the fermentation yield is enhanced by 5% after 24 h. Above 20 MPa, the reaction kinetics slows down with increasing pressure. The pressure above which no more ethanol is produced is calculated to be 87 +/- 7 MPa. These results indicate that the activity of one or several enzymes of the glycolytic pathway is enhanced at low pressure up to 10 MPa. At higher pressures, they become progressively repressed, and they are completely inhibited above 87 MPa. Although fermentation was predicted to stop at ca. 50 MPa, due to the loss of activity of phosphofructokinase, the present study demonstrates that there is still an activity of ca. 30% of that measured at ambient pressure at 65 MPa. This study also validates the use of Raman spectroscopy for monitoring the metabolism of living microorganisms. PMID:17186315

Picard, A; Daniel, I; Montagnac, G; Oger, P

2006-12-22

256

Methane detection using Wavelength Modulation Spectroscopy and a multiline quantitation method  

NASA Astrophysics Data System (ADS)

In this paper the application of the Inverse Least Squares algorithm (ILS) to the detection of methane using its behaviour in the near-infrared band is presented. In order to test the effectiveness of this method, different methane concentrations were measured. Wavelength Modulation Spectroscopy (WMS) was employed to obtain the first and second harmonics of the modulation signal. The use of both harmonics in spectroscopy eliminates the dependence of the measured absorbance on parameters such as: fiber misalignments, optical power fluctuations, etc. This property greatly increases the accuracy of the concentration readings. The benefits of analysing multiple lines in gas detection are discussed together with the capabilities of the ILS algorithm. The ILS algorithm is based on the Beer-Lambert law. This law is extended to include multiple wavelengths and rearranged in such a way that the concentration of the chemical species depends on the measured absorbances. In order to apply the previous algorithm, three absorption lines centered at 1665.961 nm, 1666.201 nm and 1666.483 nm were used. The obtained results are compared with the most usual single-line calibration method based on linear regression. This comparison shows that ILS gives a superior performance. Specifically, results indicate that the ILS multiline algorithm is less noise dependent and has a higher reliability than single-line calibration methods.

Cubillas, Ana M.; Conde, Olga M.; Quintela, María Ángeles; Cobo, Adolfo; López-Higuera, José Miguel

2005-09-01

257

Quantitative performance measurements of bent crystal Laue analyzers for X-ray fluorescence spectroscopy  

PubMed Central

Third-generation synchrotron radiation sources pose difficult challenges for energy-dispersive detectors for XAFS because of their count rate limitations. One solution to this problem is the bent crystal Laue analyzer (BCLA), which removes most of the undesired scatter and fluorescence before it reaches the detector, effectively eliminating detector saturation due to background. In this paper experimental measurements of BCLA performance in conjunction with a 13-element germanium detector, and a quantitative analysis of the signal-to-noise improvement of BCLAs are presented. The performance of BCLAs are compared with filters and slits.

Karanfil, C.; Bunker, G.; Newville, M.; Segre, C. U.; Chapman, D.

2012-01-01

258

Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology  

Microsoft Academic Search

Summary Phylogenetics has inherent utility in evolutionary devel- opmental biology (EDB) as it is an established method- ology for estimating evolutionary relationships and for making comparisons between levels of biological orga- nization. However, explicit phylogenetic methods gen- erally have been limited to two levels of organization in EDB—the species and the gene. We demonstrate that phylogenetic methods can be applied

Jeanne M. Serb; Todd H. Oakley

2005-01-01

259

Electron Momentum Spectroscopy and Its Applications to Molecules of Biological Interest  

NASA Astrophysics Data System (ADS)

Energy and wave function are the heart and soul of Schrödinger quantum mechanics. Electron momentum spectroscopy (EMS) so far provides the most stringent test for quantum mechanical models (theory, basis sets and the combination of both) through observables such as binding energy spectra and Dyson orbital momentum distributions. The capability of EMS to measure Dyson orbitals of a molecule as momentum distributions provides a unique opportunity to assess the models of quantum mechanics based on orbitals, rather than on energy dominated (mostly isotropic) properties. Recently, the author introduced a technique called dual space analysis (DSA), which is based on EMS and quantum mechanics to analyze orbital based information in the more familiar position space as well as the less familiar momentum space. In this article, the development of EMS and DSA is reviewed through the applications to molecules of biological interest such as amino acids, nucleic acid bases and recently nucleosides. The emphasis is the applications of DSA to study isomerization processes and chemical bonding mechanisms of these molecules.

Wang, Feng

2007-11-01

260

Biological effects and physical safety aspects of NMR imaging and in vivo spectroscopy  

SciTech Connect

An assessment is made of the biological effects and physical hazards of static and time-varying fields associated with the NMR devices that are being used for clinical imaging and in vivo spectroscopy. A summary is given of the current state of knowledge concerning the mechanisms of interaction and the bioeffects of these fields. Additional topics that are discussed include: (1) physical effects on pacemakers and metallic implants such as aneurysm clips, (2) human health studies related to the effects of exposure to nonionizing electromagnetic radiation, and (3) extant guidelines for limiting exposure of patients and medical personnel to the fields produced by NMR devices. On the basis of information available at the present time, it is concluded that the fields associated with the current generation of NMR devices do not pose a significant health risk in themselves. However, rigorous guidelines must be followed to avoid the physical interaction of these fields with metallic implants and medical electronic devices. 476 refs., 5 figs., 2 tabs.

Tenforde, T.S.; Budinger, T.F.

1985-08-01

261

Quantitative analysis of chromate (CrVI) by normal Raman spectroscopy and surface-enhanced Raman spectroscopy using poly(diallyldimethylammonium) chloride-capped gold nanoparticles  

NASA Astrophysics Data System (ADS)

Chromate (CrVI) has emerged as a widespread environmental contaminant found in groundwater and surface water, and there is a great need for rapid detection and monitoring of this contaminant. Normal Raman scattering (NRS) spectroscopy with a detection limit of CrVI at concentrations of 0.2 g/L was attached. And surface-enhanced Raman scattering (SERS) spectroscopy technique was found to be capable of detecting CrVI at concentrations as low as 2.5 mg/L using poly(diallyldimethylammonium) chloride modified gold nanoparticles (PDDA-AuNPs) as a substrate. The SERS substrate was successfully fabricated by combining the selfassembly technique with a heat-treatment-based strategy using poly(diallyldimethylammonium) chloride (PDDA) as the reducing and stabilizing agents. With the 520 cm-1 band of silicon as internal standard, band intensity ratios of CrVI to silicon, that is I 902/ I 520, were found to have a quantitative relationship with a large concentration range of CrVI from 0.2 to 20.0 g/L for NRS ( R 2 = 0.994) and from 2.5 to 25.0 mg/L for SERS ( R 2 = 0.980), respectively. Besides, the SERS methodology was reproducible, and susceptible to the interference of pH value. The optimum pH for CrVI detection by SERS was 3.38. The application of NRS and SERS showed high practical potential for rapid screening and routine analysis of CrVI in environmental samples.

Xiao, J.; Meng, Y. Y.; Zhang, P. L.; Wen, W.; Liu, Z. M.; Zhang, T.

2012-10-01

262

Quantitative optical spectroscopy can identify long-term local tumor control in irradiated murine head and neck xenografts  

NASA Astrophysics Data System (ADS)

Noninvasive and longitudinal monitoring of tumor oxygenation status using quantitative diffuse reflectance spectroscopy is used to test whether a final treatment outcome could be estimated from early optical signatures in a murine model of head and neck cancer when treated with radiation. Implanted tumors in the flank of 23 nude mice are exposed to 39 Gy of radiation, while 11 animals exposed to sham irradiation serve as controls. Diffuse optical reflectance is measured from the tumors at baseline (prior to irradiation) and then serially until 17 days posttreatment. The fastest and greatest increase in baseline-corrected blood oxygen saturation levels are observed from the animals that show complete tumor regression with no recurrence 90 days postirradiation, relative to both untreated and treated animals with local recurrences. These increases in saturation are observed starting 5 days posttreatment and last up to 17 days posttreatment. This preclinical study demonstrates that diffuse reflectance spectroscopy could provide a practical method far more effective than the growth delay assay to prognosticate treatment outcome in solid tumors and may hold significant translational promise.

Vishwanath, Karthik; Klein, Daniel; Chang, Kevin; Schroeder, Thies; Dewhirst, Mark W.; Ramanujam, Nimmi

2009-09-01

263

Quantitative analysis of corroded copper patina by step scan and rapid scan photoacoustic Fourier transform infrared spectroscopy  

NASA Astrophysics Data System (ADS)

Atmospheric corrosion enhanced by increasing air pollution causes increasing damage at valuable metallic monuments worthy of protection, e.g., the roof of the Stockholm City Hall. To explore the potential use of Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) in quantitative corrosion product analysis, the determination of the chemical composition of copper patina samples formed under atmospheric conditions was studied. As an experimental technique, we used a FTIR spectrometer in combination with sample-gas-microphone PAS using helium as the transfer gas at room temperature. The main components of the different samples-brochantite Cu4SO4(OH)6 and antlerite Cu3SO4(OH)4-were identified by their characteristic vibrational absorption bands. A quantitative analysis of these two components has been performed with rapid- and step-scan FTIR/PAS by using artificially corroded copper samples with differing ratios of composition. From these data, calibration curves were obtained allowing a nondestructive determination of the brochantite/antlerite ratio for quality control within an accuracy of about 10%.

Faubel, Werner; Heissler, Stefan; Palmer, Richard A.

2003-01-01

264

Compartment syndrome: A quantitative study of high-energy phosphorus compounds using sup 31 P-magnetic resonance spectroscopy  

SciTech Connect

The purpose of this study was to quantitate the intracellular high-energy phosphate compounds during 6 hours of tissue ischemia in the anterior tibial compartment of beagles subjected to an induced traumatized compartment syndrome. The goal of this work was to provide clinicians with objective criteria to augment clinical judgment regarding surgical intervention in the impending compartment syndrome. A beagle model was utilized in which the Delta pressure (difference between the mean arterial pressure and compartment pressure) could be controlled. The model, in conjunction with {sup 31}P-magnetic resonance spectroscopy (MRS), allowed a measure of high-energy phosphate compounds and pH in the compartment at various Delta pressures. The extent of ischemic metabolic insult in the compartment was then quantitated. Our data suggest the following: (1) lower Delta pressures result in a proportionally greater drop in the intracellular phosphocreatine ratio and pH; (2) at lower Delta pressures, there is proportionally greater decline in the percentage recovery post-fasciotomy; (3) blood pressure is extremely important and periods of hypotension may result in increased muscle damage at lower compartment pressures.

Heppenstall, R.B.; Sapega, A.A.; Izant, T.; Fallon, R.; Shenton, D.; Park, Y.S.; Chance, B. (Veterans Administration Medical Center, Philadelphia, PA (USA))

1989-08-01

265

Quantitative infrared spectroscopy of formalin-fixed, paraffin-embedded tissue specimens: paraffin wax removal with organic solvents.  

PubMed

Formalin-fixed, paraffin-embedded tissue specimens form the basis for diagnostic histopathology. Although adequate for morphologic visualization, clinical variability in preparation of formalin-fixed, paraffin-embedded clinical specimens represents an obstacle to quantitative molecular genetic analysis in areas such as genomics and proteomics. A quantitative reexamination of classical histopathology tissue preparation methods was initiated to determine which protocol steps might improve molecular analysis, beginning with deparaffinization. Infrared spectroscopy in the spectral region above 2000/cm of fixed sectioned model cell cultures through glass microscope slides showed all solvents remove over 97% of paraffin. To further compare extractions among solvents xylene, hexane and limonene, the correlation coefficients between the spectrum of paraffin and the spectra of the mounted extracted model tissue sections across the spectral interval containing the prominent CH stretching bands of paraffin were calculated. The correlation coefficients allow different extraction methods to be ranked in terms of how much paraffin remains. The results indicate that among 3 model tissue sample types, xylene extraction removes more paraffin than hexane or limonene. More importantly, these results establish a starting point from which further analysis of preanalytical processing methods can proceed. PMID:19786865

Meuse, Curtis W; Barker, Peter E

2009-12-01

266

Influence of particle size on the quantitative determination of salicylic acid in a pharmaceutical ointment using FT-Raman spectroscopy.  

PubMed

A second order polynomial calibration model was developed and statistically validated for the direct and non-destructive quantitative analysis - without sample preparation - of the active pharmaceutical ingredient (API) salicylic acid in a pharmaceutical ointment using FT-Raman spectroscopy. The calibration curve was modeled by plotting the peak intensity of the vector normalized spectral band between 757 and 784cm(-1) against the known salicylic acid concentrations in standards. At this band, no spectral interferences from the ointment vehiculum (white vaseline) are observed. For the validation of the polynomial model, its fit and its predictive properties were evaluated. The validated model was used for the quantification of 25 ointments, compounded by different retail pharmacists. The same standards and samples were used, both for development and validation of a regression model and for quantitative determination by HPLC - with sample preparation - as described for the related substances of salicylic acid in the Ph. Eur. IV. The quantification results obtained by the FT-Raman method corresponded with the HPLC results (p=0.22), provided that the particle size of salicylic acid in the standards is the same as in the analyzed samples. The non-destructive FT-Raman method is a reliable alternative for the destructive HPLC method, as it is faster and does not require sample pre-treatment procedures. PMID:17161940

De Beer, T R M; Baeyens, W R G; Heyden, Y Vander; Remon, J P; Vervaet, C; Verpoort, F

2006-11-18

267

Final Report: Investigation of Saturated Degenerate Four-Wave Mixing Spectroscopy For Quantitative Concentration Measurements  

SciTech Connect

Our research efforts over the last few years have focused on the development of strategies for the quantitative application of DFWM and PS in flame environments. We have developed, validated, and applied a theoretical methodology based on direct numerical integration (DNI) of the time-dependent density matrix equations for analysis of the physics of the DFWM and PS processes. The incorporation of the Zeeman state structure of the energy levels of the radiative transitions has allowed us to investigate the physics of the PS process and polarization effects in DFWM. Our research effort has focused mainly on the moderate saturation regime, with laser pulse lengths significantly greater than characteristic collisional times, and with the assumption of monochromatic lasers. Recently, we have completed a study of multi-axial-mode laser effects of homogeneously broadened PS.

Lucht, R. P.

2001-03-20

268

Purity analysis of hydrogen cyanide, cyanogen chloride and phosgene by quantitative (13)C NMR spectroscopy.  

PubMed

Hydrogen cyanide, cyanogen chloride and phosgene are produced in tremendously large quantities today by the chemical industry. The compounds are also particularly attractive to foreign states and terrorists seeking an inexpensive mass-destruction capability. Along with contemporary warfare agents, therefore, the US Army evaluates protective equipment used by warfighters and domestic emergency responders against the compounds, and requires their certification at > or = 95 carbon atom % before use. We have investigated the (13)C spin-lattice relaxation behavior of the compounds to develop a quantitative NMR method for characterizing chemical lots supplied to the Army. Behavior was assessed at 75 and 126 MHz for temperatures between 5 and 15 degrees C to hold the compounds in their liquid states, dramatically improving detection sensitivity. T(1) values for cyanogen chloride and phosgene were somewhat comparable, ranging between 20 and 31 s. Hydrogen cyanide values were significantly shorter at 10-18 s, most likely because of a (1)H--(13)C dipolar contribution to relaxation not possible for the other compounds. The T(1) measurements were used to derive relaxation delays for collecting the quantitative (13)C data sets. At 126 MHz, only a single data acquisition with a cryogenic probehead gave a signal-to-noise ratio exceeding that necessary for certifying the compounds at > or = 95 carbon atom % and 99% confidence. Data acquired at 75 MHz with a conventional probehead, however, required > or = 5 acquisitions to reach this certifying signal-to-noise ratio for phosgene, and >/= 12 acquisitions were required for the other compounds under these same conditions. In terms of accuracy and execution time, the NMR method rivals typical chromatographic methods. PMID:17924355

Henderson, Terry J; Cullinan, David B

2007-11-01

269

Quantitative compositional analysis using thermal emission spectroscopy: Application to igneous and metamorphic rocks  

NASA Astrophysics Data System (ADS)

The mineral composition of a suite of igneous and metamorphic rocks was determined using the thermal infrared emission spectra of these rocks in a linear spectral deconvolution algorithm. This algorithm assumes that the infrared spectrum of each rock is a linear mixture of the component mineral spectra weighted by volume abundance. A diverse suite of 36 common rock-forming and accessory minerals was used in the deconvolution. The model was tested by comparing the mineralogy derived from the infrared spectrum with petrographically estimated abundances for 45 igneous and 51 metamorphic rock samples. The mineral abundances derived from these two techniques agree to within +/-7-15% for the primary minerals feldspar, pyroxene, quartz, and calcite/dolomite and +/-9-17% for secondary minerals such as micas and amphiboles. These differences are comparable to the error for traditional thin section mode estimates, which are +/-5-15% for major minerals and <=5% for minor minerals. The detection limit for the primary and secondary minerals found in the rocks analyzed ranged from 5 to 10%. Each major rock type studied here was easily distinguished by its spectral characteristics. The best results, in both the qualitative determination of the rock type and dominant minerals and the quantitative reproduction of absorption features and mineral composition, were obtained for igneous rock samples. For metamorphic rocks, pelite and quartzo-feldspathic samples gave slightly better results than calcareous or mafic samples. A controlled analysis, in which the end-member suite was reduced based on an initial estimate of the rock type, only improved the results by several percent for most primary and secondary minerals. The quality of the obtained results demonstrates that a linear deconvolution of infrared emission spectra provides an accurate, rapid technique for determining the quantitative mineral composition of rock samples in a laboratory and has application to future in situ measurements.

Feely, Kimberly C.; Christensen, Philip R.

1999-10-01

270

Spectroscopy  

NSDL National Science Digital Library

This page is a set of concept test questions about organic chemistry spectroscopy. There are ten questions about topics including trans isomer and NMR spectra, C-X vibration, wavenumber absorption, and carbon signals.

2008-03-11

271

Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery  

Microsoft Academic Search

As biology is becoming a data-driven discipline, ontologies become increasingly important for systematically capturing the existing knowledge. This essay discusses current trends and how ontologies can also be used for discovery.

Lars J. Jensen; Peer Bork

2010-01-01

272

Use of 5-(4-dimethylaminobenzylidene)rhodanine in quantitating silver grains eluted from autoradiograms of biological material  

SciTech Connect

5-(4-Dimethylaminobenzylidene)rhodanine, a silver-specific dye, was used in a colorimetric assay to quantitate the autoradiographic deposition of silver onto X-ray film after exposure to sodium dodecyl sulfate-polyacrylamide gels of radiolabeled biological material. Silver grains were eluted from autoradiograms with 5 N potassium hydroxide, dissolved in nitric acid, and neutralized with 1 M Trizma Base. The concentration of silver was measured spectrophotometrically owing to the chelation properties of the dye. After corrections for background exposure were made, the silver contents of excised bands were then determined by comparison to a standard curve generated with silver nitrate. We have used this silver assay to quantitate the relative amount of each polypeptide band comprising the polyomavirus structural protein VP2 doublet. The method reported here has proven useful when densitometry is inconvenient (i.e., short distance between bands, irregular shape of bands, very faint bands) in addition to being inexpensive and simple to perform.

Ludlow, J.W.; Guikema, J.A.; Consigli, R.A.

1986-04-01

273

Quantitative determination of polyphosphate in sediments using Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy and partial least squares regression.  

PubMed

Phosphorus (P) is a major cause of eutrophication and subsequent loss of water quality in freshwater ecosystems. A major part of the flux of P to eutrophic lake sediments is organically bound or of biogenic origin. Despite the broad relevance of polyphosphate (Poly-P) in bioremediation and P release processes in the environment, its quantification is not yet well developed for sediment samples. Current methods possess significant disadvantages because of the difficulties associated with using a single extractant to extract a specific P compound without altering others. A fast and reliable method to estimate the quantitative contribution of microorganisms to sediment P release processes is needed, especially when an excessive P accumulation in the form of polyphosphate (Poly-P) occurs. Development of novel approaches for application of emerging spectroscopic techniques to complex environmental matrices such as sediments significantly contributes to the speciation models of P mobilization, biogeochemical nutrient cycling and development of nutrient models. In this study, for the first time Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy in combination with partial least squares (PLS) was used to quantify Poly-P in sediments. To reduce the high absorption matrix components in sediments such as silica, a physical extraction method was developed to separate sediment biological materials from abiotic particles. The aim was to achieve optimal separation of the biological materials from sediment abiotic particles with minimum chemical change in the sample matrix prior to ATR-FTIR analysis. Using a calibration set of 60 samples for the PLS prediction models in the Poly-P concentration range of 0-1 mg g(-1) d.w. (dry weight of sediment) (R(2) = 0.984 and root mean square error of prediction RMSEP = 0.041 at Factor-1) Poly-P could be detected at less than 50 ?g g(-l) d.w. Using this technique, there is no solvent extraction or chemical treatment required, sample preparation is minimal and simple, and the analysis time is greatly reduced. The results from this study demonstrated the potential of ATR FT-IR spectroscopy as an alternative method to study Poly-P in sediments. PMID:22801463

Khoshmanesh, Aazam; Cook, Perran L M; Wood, Bayden R

2012-08-21

274

Biological indicators of wetland health: Comparing qualitative and quantitative vegetation measures with anuran measures  

Microsoft Academic Search

Understanding wetland responses to human perturbations is essential to the effective management of Florida's surface and ground water resources. Southwest Florida Water Management District (SWFWMD) Rules (Chapter 40D-2.301(c) FAC) prohibit adverse environmental effects to wetlands, fish and wildlife caused by groundwater withdrawal. Numerous studies have documented the responses of biological attributes across taxa and regions to human disturbance. Biological assessment

Shannon M Gonzalez

2004-01-01

275

A slit grating spectrograph for quantitative soft x-ray spectroscopy  

NASA Astrophysics Data System (ADS)

In this article we describe a new slit grating spectrograph which is based on an e-beam written 10 000 linepairs/mm freestanding transmission diffraction grating. In combination with a thinned, back-illuminated charge coupled device (CCD), the spectrograph allows for real-time spectroscopy of laser-produced plasma x-ray sources within the wavelength region ?=1-20 nm. Calibration of grating and CCD allow for the possibility to measure absolute photon fluxes, currently within the wavelength region ?=1-6 nm. The compact spectrograph is easy to align and flexible in its use. Absolutely calibrated spectra were obtained from a liquid-jet laser-plasma source in the water window, with a spectral resolution ?/??>=330 at ?=3.37 nm. A simple change in experimental geometry allowed single-shot spectra to be recorded with ?/??>=60 at the same wavelength. In addition, spectra from this laser-plasma source were measured within the range ?=9-20 nm.

Wilhein, T.; Rehbein, S.; Hambach, D.; Berglund, M.; Rymell, L.; Hertz, H. M.

1999-03-01

276

On quantitative measurements in phase-shift off-axis cavity-enhanced absorption spectroscopy  

NASA Astrophysics Data System (ADS)

The contribution of amplified spontaneous emission (ASE) from a fibre-coupled DFB near-infrared diode laser has been analysed for phase-shift off-axis cavity-enhanced absorption spectroscopy (PS-OA-CEAS). A new phasor representation of the laser coherent component and the ASE components, with both long and short ring-down times, has been proposed for calculating absorption spectra from the phase and amplitude of the cavity output intensity. The line strength of the R(4) CO 2 line at 1604.7 nm has been estimated for the case when the intensity of the ASE component, passing through the cavity without long-term ringing, contributes up to ˜60% of the total light intensity observed at the cavity output. It has been shown that neglecting the ASE contribution can lead to an overestimation of the line strength by a factor of ˜4.8, whereas the line strength, calculated in accordance with the phasor model introduced here, is close to the actual line strength from Hitran.

Kasyutich, Vasili L.; Martin, Philip A.

2007-09-01

277

Surface enhanced Raman spectroscopy as a new spectral technique for quantitative detection of metal ions.  

PubMed

Four newly synthesized poly (propylene amine) dendrimers from first and second generation modified with 1,8-naphthalimide units in the dendrimer periphery have been investigated as ligands for the detection of heavy metal ions (Al(3+), Sb(2+), As(2+), Cd(2+) and Pb(2+)) by surface-enhanced Raman spectroscopy. Calibration curves were established for all metal ions between the concentration ranges of  1x10(-6) to 5x10(-4) M. It has been shown that these dendrimers can be coordinated, especially with different metal ions. Using dendrimer molecules and silver colloids at the same time allowed us to obtain an SERS signal from the abovementioned metal ions at very low concentrations. Principle component analysis (PCA) analysis was also applied to the collected SERS data. Four differentPCA models were developed to accomplish the discrimination of five metal ions, which interacted with each of the four dendrimer molecules, separately. A detailed investigation was performed in the present study to provide the basis of a new approach for heavy metal detection. PMID:23973576

Temiz, Havva Tumay; Boyaci, Ismail Hakki; Grabchev, Ivo; Tamer, Ugur

2013-08-03

278

Quantitative analysis of cotton (Gossypium hirsutum) lint trash by fluorescence spectroscopy.  

PubMed

The presence of cotton plant botanical components, or trash, embedded in lint subsequent to harvesting and ginning is an important criterion in the classification of baled cotton by the U.S. Department of Agriculture Agricultural Marketing Service. The trash particles may be reduced in size to the point that specific trash types are not identifiable by image or gravimetric analysis, and it is desirable to quantify different trash types so that processing lines may be optimized for removal of the most problematic trash to enhance processing performance and cotton lint quality. Currently, there are no methods available to adequately quantify cotton lint trash based on botanical origin. The present work attempts to address this issue through the analysis by fluorescence spectroscopy of dimethyl sulfoxide extracts of mixtures of six botanical trash types. The fluorescence data are subsequently subjected to chemometric analysis. The resulting 6 partial least-squares calibration models obtained from 128 mixtures are demonstrated in the case of leaf and hull to be capable of predicting individual trash component concentrations with a high degree of confidence. PMID:17536818

Gamble, Gary R; Foulk, Jonn A

2007-05-31

279

Use of polymer-coated AgClBr fibers for fiber optic evanascent wave spectroscopy (FEWS) of biological fluids  

Microsoft Academic Search

Silver halide IR-transmitting fibers were coated with polymer films in order to protect them from deterioration caused by interaction with biological fluids. Such coated fibers can be used for human blood serum analysis carried out the fiberoptic evanescent wave spectroscopy (FEWS) using a Fourier transform infrared spectrometer. A dip-coating procedure was worked out for coating fibers with polystyrene or silicone-elastomer

Edward Bormashenko; Roman Pogreb; Semion Sutovski; Irena Vaserman; Abraham Katzir

1999-01-01

280

The road not taken: Applications of fluorescence spectroscopy and electronic structure theory to systems of materials and biological relevance  

NASA Astrophysics Data System (ADS)

Applications of Fluorescence Spectroscopy and Electronic Structure Theory to Systems of Materials and Biological Relevance. The photophysics of curcumin was studied in micelles and the solvation dynamics were probed. The high-energy ionic liquid HEATN was also studied using the fragment molecular orbital method. The solvation dynamics of the HEATN system were determined. This marks the first study of the solvation dynamics in a triazolium ionic liquid system.

Carlson, Philip Joseph

281

Identification and quantitation assays for intact tablets of two related pharmaceutical preparations by reflectance near-infrared spectroscopy: validation of the procedure  

Microsoft Academic Search

Quantitative analysis based on near-infrared (NIR) spectroscopy uses individual calibration equations for each sample studied because of the need to model all possible chemical and physical variability sources. A NIR method, using a fibre optical probe, for the analysis of two different and related pharmaceuticals from two different production steps (cores and tablets) is studied. Both pharmaceuticals have the same

M. Blanco; A. Eustaquio; J. M. González; D. Serrano

2000-01-01

282

Quantitative analysis of mephedrone using liquid chromatography tandem mass spectroscopy: application to human hair.  

PubMed

Recent abuse of designer drugs such as mephedrone has presented a requirement for sensitive, reliable and reproducible methods for the detection of these controlled drugs in different matrices. This study focuses on a fully developed validated method for the quantitative analysis of mephedrone and its two metabolites 4-methylephedrine and 4-methylnorephedrine in human hair. The calibration curve was found to be linear in the range 5-100 pg/mg for mephedrone and 10-150 pg/mg for 4-methylephedrine and 4-methylnorephedrine. The method was successfully validated for the intraday precision, interday precision, limit of detection, accuracy and extraction recovery. Five out of 154 hair samples were confirmed to be positive for mephedrone. Due to the structural similarities to other methcathinones and amphetamines, one can propose the metabolism for mephedrone based on a similar pathway that has been previously used for these psychoactive drugs. The outlined method can be valuable for the future detection of mephedrone and its two metabolites in hair. PMID:22209483

Shah, Syeda A B; Deshmukh, Nawed I K; Barker, James; Petróczi, Andrea; Cross, Paul; Archer, Roland; Naughton, Declan P

2011-12-03

283

Fiber optic based multiparametric spectroscopy in vivo: toward a new quantitative tissue vitality index  

NASA Astrophysics Data System (ADS)

In our previous publication (Mayevsky et al SPIE 5326: 98-105, 2004) we described a multiparametric fiber optic system enabling the evaluation of 4 physiological parameters as indicators of tissue vitality. Since the correlation between the various parameters may differ in various pathophysiological conditions there is a need for an objective quantitative index that will integrate the relative changes measured in real time by the multiparametric monitoring system into a single number-vitality index. Such an approach to calculate tissue vitality index is critical for the possibility to use such an instrument in clinical environments. In the current presentation we are reporting our preliminary results indicating that calculation of an objective tissue vitality index is feasible. We used an intuitive empirical approach based on the comparison between the calculated index by the computer and the subjective evaluation made by an expert in the field of physiological monitoring. We used the in vivo brain of rats as an animal model in our current studies. The rats were exposed to anoxia, ischemia and cortical spreading depression and the responses were recorded in real time. At the end of the monitoring session the results were analyzed and the tissue vitality index was calculated offline. Mitochondrial NADH, tissue blood flow and oxy-hemoglobin were used to calculate the vitality index of the brain in vivo, where each parameter received a different weight, in each experiment type based on their significance. It was found that the mitochondrial NADH response was the main factor affected the calculated vitality index.

Kutai-Asis, Hofit; Barbiro-Michaely, Efrat; Deutsch, Assaf; Mayevsky, Avraham

2006-03-01

284

Quantitative analysis of biological tissues using Fourier transform-second-harmonic generation imaging  

NASA Astrophysics Data System (ADS)

We demonstrate the use of Fourier transform-second-harmonic generation (FT-SHG) imaging of collagen fibers as a means of performing quantitative analysis of obtained images of selected spatial regions in porcine trachea, ear, and cornea. Two quantitative markers, preferred orientation and maximum spatial frequency are proposed for differentiating structural information between various spatial regions of interest in the specimens. The ear shows consistent maximum spatial frequency and orientation as also observed in its real-space image. However, there are observable changes in the orientation and minimum feature size of fibers in the trachea indicating a more random organization. Finally, the analysis is applied to a 3D image stack of the cornea. It is shown that the standard deviation of the orientation is sensitive to the randomness in fiber orientation. Regions with variations in the maximum spatial frequency, but with relatively constant orientation, suggest that maximum spatial frequency is useful as an independent quantitative marker. We emphasize that FT-SHG is a simple, yet powerful, tool for extracting information from images that is not obvious in real space. This technique can be used as a quantitative biomarker to assess the structure of collagen fibers that may change due to damage from disease or physical injury.

Ambekar Ramachandra Rao, Raghu; Mehta, Monal R.; Toussaint, Kimani C., Jr.

2010-02-01

285

Qualitative and quantitative determination of human biomarkers by laser photoacoustic spectroscopy methods  

NASA Astrophysics Data System (ADS)

The hypothesis that blood, urine and other body fluids and tissues can be sampled and analyzed to produce clinical information for disease diagnosis or therapy monitoring is the basis of modern clinical diagnosis and medical practice. The analysis of breath air has major advantages because it is a non-invasive method, represents minimal risk to personnel collecting the samples and can be often sampled. Breath air samples from the human subjects were collected using aluminized bags from QuinTron and analyzed using the laser photoacoustic spectroscopy (LPAS) technique. LPAS is used to detect traces of ethylene in breath air resulting from lipid peroxidation in lung epithelium following the radiotherapy and also traces of ammonia from patients subjected to hemodialysis for treatment of renal failure. In the case of patients affected by cancer and treated by external radiotherapy, all measurements were done at 10P(14) CO2 laser line, where the ethylene absorption coefficient has the largest value (30.4 cm-1 atm-1), whereas for patients affected by renal failure and treated by standard dialysis, all measurements were performed at 9R(30) CO2 laser line, where the ammonia absorption coefficient has the maximum value of 57 cm-1 atm-1. The levels of ethylene and ammonia in exhaled air, from patients with cancer and renal failure, respectively, were measured and compared with breath air contents from healthy humans. Human gas biomarkers were measured at sub-ppb (parts per billion) concentration sensitivities. It has been demonstrated that LPAS technique will play an important role in the future of exhaled breath air analysis. The key attributes of this technique are sensitivity, selectivity, fast and real time response, as well as its simplicity.

Popa, C.; Bratu, A. M.; Matei, C.; Cernat, R.; Popescu, A.; Dumitras, D. C.

2011-07-01

286

Quantitative determination of prednisone in tablets by infrared attenuated total reflection and Raman spectroscopy.  

PubMed

The quantification of prednisone in tablets was performed using partial least squares (PLS) models based on FTIR-attenuated total reflection (ATR) and FT-Raman spectra. To compare the predictive ability of these models, the relative standard error of prediction (RSEP) values were calculated. In the case of prednisone determination from the FT-Raman data, RSEP values of 3.1 and 3.2% for the calibration and validation data sets were obtained. For FTIR-ATR models, which were constructed using five spectra for each sample, these errors amounted to 2.6 and 2.9%, respectively. Four commercial products containing 1, 5, 10, and 20 mg prednisone/tablet were quantified. Concentrations derived from the elaborated models correlated strongly with the results of reference analyses and with the declared values (in parentheses). The analyses gave recoveries of 100.0-101.6% (100.1-103.0%) and 98.1-103.2% (100.4-102.9%) for FTIR-ATR and FT-Raman data, respectively. A successful quantification of prednisolone in tablets containing 5 mg active ingredient/tablet was also performed using the PLS model, which was based on FTIR-ATR spectra, with a recovery of 99.8 (98.8%). Both reported spectroscopic techniques can be used as fast and convenient alternatives to the standard pharmacopeial methods of prednisone and prednisolone quantification in solid dosage forms. However, in the case of FTIR-ATR spectroscopy, it is necessary to repeat measurements several times to obtain sufficiently low quantification errors. PMID:22816265

Mazurek, Sylwester; Szostak, Roman

287

Quantitation of ten 30S ribosomal assembly intermediates using fluorescence triple correlation spectroscopy.  

PubMed

The self-assembly of bacterial 30S ribosomes involves a large number of RNA folding and RNA-protein binding steps. The sequence of steps determines the overall assembly mechanism and the structure of the mechanism has ramifications for the robustness of biogenesis and resilience against kinetic traps. Thermodynamic interdependencies of protein binding inferred from omission-reconstitution experiments are thought to preclude certain assembly pathways and thus enforce ordered assembly, but this concept is at odds with kinetic data suggesting a more parallel assembly landscape. A major challenge is deconvolution of the statistical distribution of intermediates that are populated during assembly at high concentrations approaching in vivo assembly conditions. To specifically resolve the intermediates formed by binding of three ribosomal proteins to the full length 16S rRNA, we introduce Fluorescence Triple-Correlation Spectroscopy (F3CS). F3CS identifies specific ternary complexes by detecting coincident fluctuations in three-color fluorescence data. Triple correlation integrals quantify concentrations and diffusion kinetics of triply labeled species, and F3CS data can be fit alongside auto-correlation and cross-correlation data to quantify the populations of 10 specific ribosome assembly intermediates. The distribution of intermediates generated by binding three ribosomal proteins to the entire native 16S rRNA included significant populations of species that were not previously thought to be thermodynamically accessible, questioning the current interpretation of the classic omission-reconstitution experiments. F3CS is a general approach for analyzing assembly and function of macromolecular complexes, especially those too large for traditional biophysical methods. PMID:22869699

Ridgeway, William K; Millar, David P; Williamson, James R

2012-08-06

288

Quantitation of ten 30S ribosomal assembly intermediates using fluorescence triple correlation spectroscopy  

PubMed Central

The self-assembly of bacterial 30S ribosomes involves a large number of RNA folding and RNA-protein binding steps. The sequence of steps determines the overall assembly mechanism and the structure of the mechanism has ramifications for the robustness of biogenesis and resilience against kinetic traps. Thermodynamic interdependencies of protein binding inferred from omission-reconstitution experiments are thought to preclude certain assembly pathways and thus enforce ordered assembly, but this concept is at odds with kinetic data suggesting a more parallel assembly landscape. A major challenge is deconvolution of the statistical distribution of intermediates that are populated during assembly at high concentrations approaching in vivo assembly conditions. To specifically resolve the intermediates formed by binding of three ribosomal proteins to the full length 16S rRNA, we introduce Fluorescence Triple-Correlation Spectroscopy (F3CS). F3CS identifies specific ternary complexes by detecting coincident fluctuations in three-color fluorescence data. Triple correlation integrals quantify concentrations and diffusion kinetics of triply labeled species, and F3CS data can be fit alongside auto-correlation and cross-correlation data to quantify the populations of 10 specific ribosome assembly intermediates. The distribution of intermediates generated by binding three ribosomal proteins to the entire native 16S rRNA included significant populations of species that were not previously thought to be thermodynamically accessible, questioning the current interpretation of the classic omission-reconstitution experiments. F3CS is a general approach for analyzing assembly and function of macromolecular complexes, especially those too large for traditional biophysical methods.

Ridgeway, William K.; Millar, David P.; Williamson, James R.

2012-01-01

289

Quantitative analysis of borophosphosilicate glass films on silicon using infrared external reflection--absorption spectroscopy  

SciTech Connect

Borophosphosilicate glass (BPSG) dielectric thin films deposited on both bare and oxide-coated undoped silicon wafers have been analyzed using infrared external reflection--absorption spectroscopy (IRRAS). The partial least-squares (PLS1) algorithm was used to simultaneously determine boron content, phosphorous content, and film thickness, with standard errors of prediction of 0.08 wt %, 0.11 wt %, and 24 A, respectively, in the BPSG films on oxide-coated wafers (similar results were obtained with the bare wafer BPSG sample set). These results were statistically equivalent to the precisions of the reference methods used to determine each BPSG property, indicating that the precisions of the PLS1 models were limited by the precisions of the reference methods. IRRAS reproducibility and repeatability results verified that the method can be more precise than the reference methods. The reproducibility results were derived from the standard deviation of ten PLS1 predictions of ten IRRAS spectra that were obtained from a single BPSG sample that was moved in and out of the sample chamber between each spectral measurement. The repeatability results were obtained similarly, but the sample was not moved between acquiring the ten spectra. The precision of the IRRAS method from the repeatability data was found to be {plus_minus}0.006 wt % B, {plus_minus}0.011 wt % P, and {plus_minus}4 A film thickness. The reproducibility results were generally less precise than the repeatability results. Studies done as a function of spectral resolution and signal averaging showed that very rapid IRRAS measurements could be made (up to 2 Hz) with high PLS1 prediction precision for the three calibrated BPSG properties. The results show that the IRRAS technique has great potential for rapid, at-line quality control monitoring of BPSG thin films on undoped silicon wafers. {copyright} {ital 1995} {ital American} {ital Vacuum} {ital Society}

Franke, J.E.; Zhang, L.; Niemczyk, T.M. [Chemistry Department, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Haaland, D.M. [Sandia National Laboratories, Albuquerque, New Mexico 87185-0343 (United States); Radigan, K.J. [National Semiconductor Corporation, Santa Clara, California 95052 (United States)

1995-07-01

290

Dynamic nuclear polarization-enhanced 13C NMR spectroscopy of static biological solids  

NASA Astrophysics Data System (ADS)

We explore the possibility of using dynamic nuclear polarization (DNP) to enhance signals in structural studies of biological solids by solid state NMR without sample spinning. Specifically, we use 2D 13C–13C exchange spectroscopy to probe the peptide backbone torsion angles (?, ?) in a series of selectively 13C-labeled 40-residue ?-amyloid (A?1–40) samples, in both fibrillar and non-fibrillar states. Experiments are carried out at 9.39 T and 8 K, using a static double-resonance NMR probe and low-power microwave irradiation at 264 GHz. In frozen solutions of A?1–40 fibrils doped with DOTOPA-TEMPO, we observe DNP signal enhancement factors of 16–21. We show that the orientation- and frequency-dependent spin polarization exchange between sequential backbone carbonyl 13C labels can be simulated accurately using a simple expression for the exchange rate, after experimentally determined homogeneous 13C lineshapes are incorporated in the simulations. The experimental 2D 13C–13C exchange spectra place constraints on the ? and ? angles between the two carbonyl labels. Although the data are not sufficient to determine ? and ? uniquely, the data do provide non-trivial constraints that could be included in structure calculations. With DNP at low temperatures, 2D 13C–13C exchange spectra can be obtained from a 3.5 mg sample of A?1–40 fibrils in 4 h or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples.

Potapov, Alexey; Yau, Wai-Ming; Tycko, Robert

2013-06-01

291

Rapid Quantitation of a Large Scope of Eicosanoids in Two Models of Inflammation: Development of an Electrospray and Tandem Mass Spectrometry Method and Application to Biological Studies  

Microsoft Academic Search

Assessment of eicosanoid levels in biological systems is important for understanding their role in cell function and pathophysiological events. Current methods of eicosanoid quantitation are limited by sensitivity, scope, or throughput. The development of a new method for eicosanoid assessment in biological samples by electrospray and tandem mass spectrometry (MS\\/MS) in the multiple reaction monitoring mode is described here. In

Alon Margalit; Kevin L. Duffin; Peter C. Isakson

1996-01-01

292

Quantitative Zn speciation in a contaminated dredged sediment by ?-PIXE, ?-SXRF, EXAFS spectroscopy and principal component analysis  

NASA Astrophysics Data System (ADS)

Dredging and disposal of sediments onto agricultural soils is a common practice in industrial and urban areas that can be hazardous to the environment when the sediments contain heavy metals. This chemical hazard can be assessed by evaluating the mobility and speciation of metals after sediment deposition. In this study, the speciation of Zn in the coarse (500 to 2000 ?m) and fine (<2 ?m) fractions of a contaminated sediment dredged from a ship canal in northern France and deposited on an agricultural soil was determined by physical analytical techniques on raw and chemically treated samples. Zn partitioning between coexisting mineral phases and its chemical associations were first determined by micro-particle-induced X-ray emission and micro-synchrotron-based X-ray radiation fluorescence. Zn-containing mineral species were then identified by X-ray diffraction and powder and polarized extended X-ray absorption fine structure spectroscopy (EXAFS). The number, nature, and proportion of Zn species were obtained by a coupled principal component analysis (PCA) and least squares fitting (LSF) procedure, applied herein for the first time to qualitatively (number and nature of species) and quantitatively (relative proportion of species) speciate a metal in a natural system. The coarse fraction consists of slag grains originating from nearby Zn smelters. In this fraction, Zn is primarily present as sphalerite (ZnS) and to a lesser extent as willemite (Zn 2SiO 4), Zn-containing ferric (oxyhydr)oxides, and zincite (ZnO). In the fine fraction, ZnS and Zn-containing Fe (oxyhydr)oxides are the major forms, and Zn-containing phyllosilicate is the minor species. Weathering of ZnS, Zn 2SiO 4, and ZnO under oxidizing conditions after the sediment disposal accounts for the uptake of Zn by Fe (oxyhydr)oxides and phyllosilicates. Two geochemical processes can explain the retention of Zn by secondary minerals: uptake on preexisting minerals and precipitation with dissolved Fe and Si. The second process likely occurs because dissolved Zn and Si are supersaturated with respect to Zn phyllosilicate. EXAFS spectroscopy, in combination with PCA and LSF, is shown to be a meaningful approach to quantitatively determining the speciation of trace elements in sediments and soils.

Isaure, Marie-Pierre; Laboudigue, Agnès; Manceau, Alain; Sarret, Géraldine; Tiffreau, Christophe; Trocellier, Patrick; Lamble, Géraldine; Hazemann, Jean-Louis; Chateigner, Daniel

2002-05-01

293

An Assessment of the Quantitative Skills of Students Taking Introductory College Biology Courses.  

ERIC Educational Resources Information Center

|The mathematical skills possessed by students taking introductory biology courses were investigated. A list of 23 mathematical competencies was identified as part of the development of a 46-item multiple-choice test to measure the extent to which students possessed these competencies. The Biomathematics Skills Test (BST) was administered to…

Marsh, Jeffrey Flake; Anderson, Norman D.

294

Illustrating Key Problems that Can Lead Towards a Quantitative Physical Biology  

Microsoft Academic Search

Waddington has questioned whether a theoretical biology can be formulated, analogous to theoretical physics. This paper proposes two problems that physicists might tackle. One is to account for the relation between weight specific blood flow and weight specific oxygen consumption that is found with changing activity level in mammals. An essentially unique correlation is shown to exist for all sizes

A. S. Iberall

1972-01-01

295

QUANTITATIVE DETERMINATION BY 14C ANALYSIS OF THE BIOLOGICAL COMPONENT IN FUELS  

Microsoft Academic Search

Radiocarbon analysis was performed by liquid scintillation counting (LSC) and accelerator mass spectrometry (AMS) to assess whether the content of biological components in hydrocarbon fuels could be derived. Different fuel mixtures were prepared containing bioethanol, fossil ethanol, and fossil gasoline. The specific 14C activity of these mixtures was obtained from LSC measurements and directly related to the concentration of carbon

Ivo J Dijs; Eric van der Windt; Lauri Kaihola; Klaas van der Borg

2006-01-01

296

ON THE BIOLOGICAL INFORMATION CONTENT OF COMMON NAMES: A QUANTITATIVE CASE STUDY OF PHILIPPINE FISHES  

Microsoft Academic Search

An analysis was perfomled on the common names of fishes in the Philippines, based on the COMMON NAMES table of rlShBase, a large biological database with key information on fishes. The existence of common names for fish species in 10 Philippine languages was found to depend on the commercial importance, depth range and habitat of these species in the Philippines.

Maria Lourdes; D. PALOMAR; Cristina V. GARILAO; Daniel PAULY

1999-01-01

297

Teacher knowledge and discourse control: Quantitative evidence from novice biology teachers' classrooms  

Microsoft Academic Search

This article describes the effects of science teacher subject-matter knowledge on classroom discourse at the level of individual utterances. It details one of three parallel analyses conducted in a year-long study of language in the classrooms of four new biology teachers. The conceptual framework of the study predicts that when teaching unfamiliar subject matter, teachers use a variety of discourse

William S. Carlsen

1993-01-01

298

Gelsius: A Literature-Based Workflow for Determining Quantitative Associations Between Genes and Biological Processes.  

PubMed

An effective knowledge extraction and quantification methodology from biomedical literature would allow the researcher to organize and analyze the results of high throughput experiments on microarrays and next generation sequencing technologies. Despite the large amount of raw information available on the Web, a tool able to extract a measure of the correlation between a list of genes and biological processes is not yet available. In this paper we present Gelsius, a workflow that incorporates biomedical literature to quantify the correlation between genes and terms describing biological processes. To achieve this target, we build different modules focusing on query expansion and document cononicalization. In this way we reached to improve the measurement of correlation, performed using a latent semantic analysis approach. To the best of our knowledge, this is the first complete tool able to extract a measure of genes-biological processes correlation from literature. We demonstrate the effectiveness of the proposed workflow on six biological processes and a set of genes, by showing that correlation results for known relationships are in accordance with definitions of gene functions provided by NCI Thesaurus. On the other side, the tool is able to propose new candidate relationships for later experimental validation. The tool is available at the following web site: http://bioeda1.polito.it:8080/medSearchServlet/ PMID:23439219

Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; Piva, Roberto; Macii, Enrico

2013-02-20

299

Developments in cell biology for quantitative immunoelectron microscopy based on thin sections: a review  

Microsoft Academic Search

Quantitative immunoelectron microscopy uses ultrathin sections and gold particle labelling to determine distributions of molecules\\u000a across cell compartments. Here, we review a portfolio of new methods for comparing labelling distributions between different\\u000a compartments in one study group (method 1) and between the same compartments in two or more groups (method 2). Specimen samples\\u000a are selected unbiasedly and then observed and

Terry M. Mayhew; John M. Lucocq

2008-01-01

300

Raman Spectroscopy Techniques for the Detection of Biological Samples in Suspensions and as Aerosol Particles: A Review  

NASA Astrophysics Data System (ADS)

This article reviews current scientific literature focusing on Raman spectroscopy modalities that have been successfully applied to the detection of biological samples in aqueous suspensions and in aerosols. Normal Raman, surface enhanced Raman scattering, coherent anti-stokes Raman scattering, resonance Raman and UV-Raman spectropies, allow the detection of biological samples in situ in the near field and as well as in the far field at standoff distances. Applications span from fundamental studies to applied research in areas of defense and security and in monitoring of environmental pollution. A primary focus has been placed on biological samples including bacteria, pollen, virus, and biological contents in these specimens, in suspensions, and in aerosols. Several Raman spectroscopy studies have been reviewed to show how various modalities can achieve detection in these biosystems. Current data generated by our group is also included. Necessary parameters used to accomplish the detection and data analysis, which could also be used to interpret the results and to render the methodologies robust and reliable, are discussed.

Félix-Rivera, Hilsamar; Hernández-Rivera, Samuel P.

2012-03-01

301

Quantitative detection and biological propagation of scrapie seeding activity in vitro facilitate use of prions as model pathogens for disinfection.  

PubMed

Prions are pathogens with an unusually high tolerance to inactivation and constitute a complex challenge to the re-processing of surgical instruments. On the other hand, however, they provide an informative paradigm which has been exploited successfully for the development of novel broad-range disinfectants simultaneously active also against bacteria, viruses and fungi. Here we report on the development of a methodological platform that further facilitates the use of scrapie prions as model pathogens for disinfection. We used specifically adapted serial protein misfolding cyclic amplification (PMCA) for the quantitative detection, on steel wires providing model carriers for decontamination, of 263K scrapie seeding activity converting normal protease-sensitive into abnormal protease-resistant prion protein. Reference steel wires carrying defined amounts of scrapie infectivity were used for assay calibration, while scrapie-contaminated test steel wires were subjected to fifteen different procedures for disinfection that yielded scrapie titre reductions of ?10(1)- to ?10(5.5)-fold. As confirmed by titration in hamsters the residual scrapie infectivity on test wires could be reliably deduced for all examined disinfection procedures, from our quantitative seeding activity assay. Furthermore, we found that scrapie seeding activity present in 263K hamster brain homogenate or multiplied by PMCA of scrapie-contaminated steel wires both triggered accumulation of protease-resistant prion protein and was further propagated in a novel cell assay for 263K scrapie prions, i.e., cerebral glial cell cultures from hamsters. The findings from our PMCA- and glial cell culture assays revealed scrapie seeding activity as a biochemically and biologically replicative principle in vitro, with the former being quantitatively linked to prion infectivity detected on steel wires in vivo. When combined, our in vitro assays provide an alternative to titrations of biological scrapie infectivity in animals that substantially facilitates the use of prions as potentially highly indicative test agents in the search for novel broad-range disinfectants. PMID:21647368

Pritzkow, Sandra; Wagenführ, Katja; Daus, Martin L; Boerner, Susann; Lemmer, Karin; Thomzig, Achim; Mielke, Martin; Beekes, Michael

2011-05-27

302

Calibrated real-time PCR assay for quantitation of human herpesvirus 8 DNA in biological fluids.  

PubMed

Accurate laboratory tests for the diagnosis of active human herpesvirus 8 (HHV-8) infection are becoming essential to study the pathogenesis of HHV-8-associated tumors and for the clinical management of HHV-8-infected individuals. We have developed a highly sensitive, calibrated quantitative real-time PCR assay for the measurement of cell-free HHV-8 DNA in body fluids, based on the addition of a synthetic DNA calibrator prior to DNA extraction. The calibrator controls each sample for the presence of PCR inhibitors, determines a cutoff value of sensitivity for negative samples, and normalizes positive samples for the efficiency of DNA recovery. The assay shows a wide dynamic range of detection (between 1 and 10(6) viral genome equivalents/reaction) and a high degree of accuracy even in the presence of high amounts (up to 1 micro g) of human genomic DNA. Moreover, the assay has a very high sensitivity (lower detection limit, 10 genome equivalents/ml) and a high degree of reproducibility and repeatability with a coefficient of variation (CV) of <15 and 23%, respectively. Furthermore, the use of the calibrator improves the accuracy of quantitation and decreases the intersample variability (CV, 9 and 6%, respectively). The sensitivity and specificity of the assay were tested with a series of clinical specimens obtained from patients affected by various HHV-8-related diseases, as well as from a wide number of controls. In conclusion, our calibrated real-time PCR assay provides a reliable high-throughput method for quantitation of HHV-8 DNA in clinical and laboratory specimens. PMID:12454167

Broccolo, Francesco; Locatelli, Giuseppe; Sarmati, Loredana; Piergiovanni, Sara; Veglia, Fabrizio; Andreoni, Massimo; Buttò, Stefano; Ensoli, Barbara; Lusso, Paolo; Malnati, Mauro S

2002-12-01

303

Calibrated Real-Time PCR Assay for Quantitation of Human Herpesvirus 8 DNA in Biological Fluids  

PubMed Central

Accurate laboratory tests for the diagnosis of active human herpesvirus 8 (HHV-8) infection are becoming essential to study the pathogenesis of HHV-8-associated tumors and for the clinical management of HHV-8-infected individuals. We have developed a highly sensitive, calibrated quantitative real-time PCR assay for the measurement of cell-free HHV-8 DNA in body fluids, based on the addition of a synthetic DNA calibrator prior to DNA extraction. The calibrator controls each sample for the presence of PCR inhibitors, determines a cutoff value of sensitivity for negative samples, and normalizes positive samples for the efficiency of DNA recovery. The assay shows a wide dynamic range of detection (between 1 and 106 viral genome equivalents/reaction) and a high degree of accuracy even in the presence of high amounts (up to 1 ?g) of human genomic DNA. Moreover, the assay has a very high sensitivity (lower detection limit, 10 genome equivalents/ml) and a high degree of reproducibility and repeatability with a coefficient of variation (CV) of <15 and 23%, respectively. Furthermore, the use of the calibrator improves the accuracy of quantitation and decreases the intersample variability (CV, 9 and 6%, respectively). The sensitivity and specificity of the assay were tested with a series of clinical specimens obtained from patients affected by various HHV-8-related diseases, as well as from a wide number of controls. In conclusion, our calibrated real-time PCR assay provides a reliable high-throughput method for quantitation of HHV-8 DNA in clinical and laboratory specimens.

Broccolo, Francesco; Locatelli, Giuseppe; Sarmati, Loredana; Piergiovanni, Sara; Veglia, Fabrizio; Andreoni, Massimo; Butto, Stefano; Ensoli, Barbara; Lusso, Paolo; Malnati, Mauro S.

2002-01-01

304

Brain metabolite composition during early human brain development as measured by quantitative in vivo 1H magnetic resonance spectroscopy.  

PubMed

Biochemical maturation of the brain can be studied noninvasively by (1)H magnetic resonance spectroscopy (MRS) in human infants. Detailed time courses of cerebral tissue contents are known for the most abundant metabolites only, and whether or not premature birth affects biochemical maturation of the brain is disputed. Hence, the last trimester of gestation was observed in infants born prematurely, and their cerebral metabolite contents at birth and at expected term were compared with those of fullterm infants. Successful quantitative short-TE (1)H MRS was performed in three cerebral locations in 21 infants in 28 sessions (gestational age 32-43 weeks). The spectra were analyzed with linear combination model fitting, considerably extending the range of observable metabolites to include acetate, alanine, aspartate, cholines, creatines, gamma-aminobutyrate, glucose, glutamine, glutamate, glutathione, glycine, lactate, myo-inositol, macromolecular contributions, N-acetylaspartate, N-acetylaspartylglutamate, o-phosphoethanolamine, scyllo-inositol, taurine, and threonine. Significant effects of age and location were found for many metabolites, including the previously observed neuronal maturation reflected by an increase in N-acetylaspartate. Absolute brain metabolite content in premature infants at term was not considerably different from that in fullterm infants, indicating that prematurity did not affect biochemical brain maturation substantially in the studied population, which did not include infants of extremely low birthweight. PMID:12465103

Kreis, R; Hofmann, L; Kuhlmann, B; Boesch, C; Bossi, E; Hüppi, P S

2002-12-01

305

Proton HR-MAS spectroscopy and quantitative pathologic analysis of MRI/3D-MRSI-targeted postsurgical prostate tissues.  

PubMed

Proton high-resolution magic angle spinning ((1)H HR-MAS) NMR spectroscopy and quantitative histopathology were performed on the same 54 MRI/3D-MRSI-targeted postsurgical prostate tissue samples. Presurgical MRI/3D-MRSI targeted healthy and malignant prostate tissues with an accuracy of 81%. Even in the presence of substantial tissue heterogeneity, distinct (1)H HR-MAS spectral patterns were observed for different benign tissue types and prostate cancer. Specifically, healthy glandular tissue was discriminated from prostate cancer based on significantly higher levels of citrate (P = 0.04) and polyamines (P = 0.01), and lower (P = 0.02) levels of the choline-containing compounds choline, phosphocholine (PC), and glycerophosphocholine (GPC). Predominantly stromal tissue lacked both citrate and polyamines, but demonstrated significantly (P = 0.01) lower levels of choline compounds than cancer. In addition, taurine, myo-inositol, and scyllo-inositol were all higher in prostate cancer vs. healthy glandular and stromal tissues. Among cancer samples, larger increases in choline, and decreases in citrate and polyamines (P = 0.05) were observed with more aggressive cancers, and a MIB-1 labeling index correlated (r = 0.62, P = 0.01) with elevated choline. The elucidation of spectral patterns associated with mixtures of different prostate tissue types and cancer grades, and the inclusion of new metabolic markers for prostate cancer may significantly improve the clinical interpretation of in vivo prostate MRSI data. PMID:14587005

Swanson, Mark G; Vigneron, Daniel B; Tabatabai, Z Laura; Males, Ryan G; Schmitt, Lars; Carroll, Peter R; James, Joyce K; Hurd, Ralph E; Kurhanewicz, John

2003-11-01

306

Rate-equation model for quantitative concentration measurements in flames with picosecond pump-probe absorption spectroscopy  

NASA Astrophysics Data System (ADS)

Measurement of radical concentrations is important in understanding the chemical kinetics involved in combustion. Application of optical techniques allows for the nonintrusive determination of specific radical concentrations. One of the most challenging problems for investigators is to obtain flame data that are independent of the collisional environment. We seek to obviate this difficulty by the use of picosecond pump-probe absorption spectroscopy. A picosecond pump-probe absorption model is developed by rate-equation analysis. Implications are discussed for a laser-pulse width that is much smaller than the excited-state lifetime of the absorbing atom or molecule. The possibility of quantitative, quenching-independent concentration measurements is discussed, and detection limits for atomic sodium and the hydroxyl radical are estimated. For a three-level absorber-emitter, the model leads to a novel pump-probe strategy, called dual-beam asynchronous optical sampling, that can be used to obtain both the electronic quenching-rate coefficient and the doublet mixing-rate coefficient during a single measurement. We discuss the successful demonstration of the

King, Galen B.; Laurendeau, Normand M.; Fiechtner, Gregory J.

1995-02-01

307

Noninvasive, quantitative analysis of drug mixtures in containers using spatially offset Raman spectroscopy (SORS) and multivariate statistical analysis.  

PubMed

In this paper, spatially offset Raman spectroscopy (SORS) is demonstrated for noninvasively investigating the composition of drug mixtures inside an opaque plastic container. The mixtures consisted of three components including a target drug (acetaminophen or phenylephrine hydrochloride) and two diluents (glucose and caffeine). The target drug concentrations ranged from 5% to 100%. After conducting SORS analysis to ascertain the Raman spectra of the concealed mixtures, principal component analysis (PCA) was performed on the SORS spectra to reveal trends within the data. Partial least squares (PLS) regression was used to construct models that predicted the concentration of each target drug, in the presence of the other two diluents. The PLS models were able to predict the concentration of acetaminophen in the validation samples with a root-mean-square error of prediction (RMSEP) of 3.8% and the concentration of phenylephrine hydrochloride with an RMSEP of 4.6%. This work demonstrates the potential of SORS, used in conjunction with multivariate statistical techniques, to perform noninvasive, quantitative analysis on mixtures inside opaque containers. This has applications for pharmaceutical analysis, such as monitoring the degradation of pharmaceutical products on the shelf, in forensic investigations of counterfeit drugs, and for the analysis of illicit drug mixtures which may contain multiple components. PMID:22524958

Olds, William J; Sundarajoo, Shankaran; Selby, Mark; Cletus, Biju; Fredericks, Peter M; Izake, Emad L

2012-05-01

308

Quantitative measurement of cerebral blood flow in a juvenile porcine model by depth-resolved near-infrared spectroscopy  

NASA Astrophysics Data System (ADS)

Nearly half a million children and young adults are affected by traumatic brain injury each year in the United States. Although adequate cerebral blood flow (CBF) is essential to recovery, complications that disrupt blood flow to the brain and exacerbate neurological injury often go undetected because no adequate bedside measure of CBF exists. In this study we validate a depth-resolved, near-infrared spectroscopy (NIRS) technique that provides quantitative CBF measurement despite significant signal contamination from skull and scalp tissue. The respiration rates of eight anesthetized pigs (weight: 16.2+/-0.5 kg, age: 1 to 2 months old) are modulated to achieve a range of CBF levels. Concomitant CBF measurements are performed with NIRS and CT perfusion. A significant correlation between CBF measurements from the two techniques is demonstrated (r2=0.714, slope=0.92, p<0.001), and the bias between the two techniques is -2.83 mL.min-1.100 g-1 (CI0.95: -19.63 mL.min-1.100 g-1-13.9 mL.min-1.100 g-1). This study demonstrates that accurate measurements of CBF can be achieved with depth-resolved NIRS despite significant signal contamination from scalp and skull. The ability to measure CBF at the bedside provides a means of detecting, and thereby preventing, secondary ischemia during neurointensive care.

Elliott, Jonathan T.; Diop, Mamadou; Tichauer, Kenneth M.; Lee, Ting-Yim; Lawrence, Keith St.

2010-05-01

309

Quantitative study of protein-protein interactions in live cell by dual-color fluorescence correlation spectroscopy.  

PubMed

Dual-color FCS is a powerful method to monitor protein-protein interactions in living cells. The main idea is based on the cross-correlation analysis of temporal fluorescence intensity fluctuations of two fluorescent proteins to obtain their co-diffusion and relative concentration. But, when performing these experiments, the spectral overlap in the emission of the two colors produces an artifact that corrupts the cross-correlation data: spectral bleed-through. We have shown that problems with cross talk are overcome with Fluorescence Lifetime Correlation Spectroscopy (FLCS). FLCS applied to dual-color cross-correlation, utilizing for example eGFP and mCherry fluorescent proteins, allows the determination of protein-protein interactions in living cells without the need of spectral bleed-through calibration. Here, we present in detail how this methodology can be implemented using a commercial setup (Microtime from PicoQuant, SP8 SMD from Leica or any conventional confocal with PicoQuant TCSPC module, and also with a Becker and Hickl TCSPC module). The dual-color FLCS experimental procedure where the different laser intensities do not have to be controlled during the experiment constitutes a very powerful technique to quantitatively study protein interactions in live samples. PMID:24108650

Padilla-Parra, Sergi; Audugé, Nicolas; Coppey-Moisan, Maïté; Tramier, Marc

2014-01-01

310

A quantitative method to detect explosives and other selected semivolatiles in soil samples by Fourier transform infrared spectroscopy  

SciTech Connect

The current methods for hazardous waste site characterization are time consuming, cumbersome, and expensive. Typically, characterization requires a preliminary site assessment and subsequent sampling of potentially contaminated soils and waters. The samples are sent to laboratories for analysis using EPA-certified methods. It is often necessary to repeat the entire sampling-analysis cycle to characterize a site completely and accurately. For these reasons, new methods of site assessment and characterization are continually being researched. TWs paper describes a Fourier transform infrared (FTIR) spectroscopy method that rapidly screens soil samples from potentially hazardous waste sites. Analysis of a soil sample by FTIR takes approximately 10 minutes. The method has been developed to identify and quantify explosives in the field and is directly applicable to selected volatile organics, semivolatile organics, and pesticides. The soil samples are desorbed in a CDS 122 thermal desorption unit under vacuum into a variable pathlength, long-path cell heated to 180{degrees}C. The spectral data, 128 co-added scans at I cm{sup {minus}l} resolution, are collected and stored using a Nicolet 60SX FTIR spectrometer. Classical least squares (CLS) analysis has been used to obtain quantitative results.

Clapper-Gowdy, M.; Demirgian, J. (Argonne National Lab., IL (United States)); Lang, K.; Robaittaille, G. (Army Toxic and Hazardous Materials Agency, Aberdeen Proving Ground, MD (United States))

1992-01-01

311

Quantitative Conformationally Sampled Pharmacophore (CSP) for ? Opioid Ligands: Reevaluation of hydrophobic moieties essential for biological activity  

PubMed Central

Recent studies have indicated several therapeutic applications for ? opioid agonists and antagonists. To exploit the therapeutic potential of ? opioids developing a structural basis for the activity of ligands at the ? opioid receptor is essential. The conformationally sampled pharmacophore (CSP) method (Bernard et al., JACS, 125: 3103–3107, 2003) is extended here to obtain quantitative models of ? opioid ligand efficacy and affinity. Quantification is performed via overlap integrals of the conformational space sampled by ligands with respect to a reference compound. Iterative refinement of the CSP model identified hydrophobic groups other than the traditional phenylalanine residues as important for efficacy and affinity in DSLET and ICI 174,864. The obtained models for a structurally diverse set of peptidic and non-peptidic ? opioid ligands offer good predictions with R2 values > 0.9 and the predicted efficacy for a set of test compounds was consistent with the experimental value.

Bernard, Denzil; Coop, Andrew; MacKerell, Alexander D.

2008-01-01

312

Mapping of thermal injury in biologic tissues using quantitative pathologic techniques  

NASA Astrophysics Data System (ADS)

Qualitative and quantitative pathologic techniques can be used for (1) mapping of thermal injury, (2) comparisons lesion sizes and configurations for different instruments or heating sources and (3) comparisons of treatment effects. Concentric zones of thermal damage form around a single volume heat source. The boundaries between some of these zones are distinct and measurable. Depending on the energy deposition, heating times and tissue type, the zones can include the following beginning at the hotter center and progressing to the cooler periphery: (1) tissue ablation, (2) carbonization, (3) tissue water vaporization, (4) structural protein denaturation (thermal coagulation), (5) vital enzyme protein denaturation, (6) cell membrane disruption, (7) hemorrhage, hemostasis and hyperhemia, (8) tissue necrosis and (9) wound organization and healing.

Thomsen, Sharon L.

1999-05-01

313

Quantitative determination of clopidogrel and its metabolites in biological samples: a mini-review.  

PubMed

Clopidogrel has been applied in antiplatelet therapy since 1998 and is the thienopyridine with the largest clinical experience. By 2011, clopidogrel (Plavix(®)) was the second top-selling drug in the world. Following complete patent expiry in 2012/2013 its use is expected to grow even further from generics entering the market. Prefaced by a brief description of clopidogrel metabolism, this review analyzes analytical methods addressing the quantification of clopidogrel and its metabolites in biological samples. Techniques that have been applied to analyze human plasma or serum are predominantly LC-MS and LC-MS/MS. The lowest level of clopidogrel quantification that has been achieved is 5pg/mL, the shortest runtime is 1.5min and almost 100% recovery has been reported using solid-phase extraction for sample preparation. PMID:23369880

Elsinghorst, Paul W

2013-01-10

314

Chromatography-mass spectrometry methods for the quantitation of statins in biological samples.  

PubMed

The 3-hydroxy-3-methyl glutaryl coenzyme A (HMG-CoA) reductase inhibitors, more commonly known as 'statins', are a novel class of drugs widely used for the treatment of hypercholesterolaemia in patients with established cardiovascular disease as well as those at high risk of developing atherosclerosis. Published chromatographic-mass spectrometric methods for the quantification of presently available seven statins, atorvastatin, simvastatin, lovastatin, pravastatin, fluvastatin, rosuvastatin and pitavastatin are reviewed. High performance liquid chromatography (HPLC) in combination with tandem mass spectrometry (MS/MS) is the analytical technique of choice for the quantification of statins in biological samples. This review envisages that most of the methods used for quantification of statins are in plasma and they are suitable for therapeutic drug monitoring of these drugs. PMID:17433599

Nirogi, Ramakrishna; Mudigonda, Koteshwara; Kandikere, Vishwottam

2007-02-13

315

Development of Cellular Absorptive Tracers (CATs) for a Quantitative Characterization of the Complexity of Nanoscale Biological Systems  

NASA Astrophysics Data System (ADS)

A new method is proposed in this study, which is entitled Cellular Absorptive Tracers (CATs; PNNL Invention Disclosure; Saripalli, P. 2001), to characterize the extent, location, and morphology of cell mass in microelectromechanical systems (MEMS), by preferentially absorbing into the living or lysed cells or adsorbing at the cell surfaces. The CATs were used to demonstrate their utility to quantitatively characterize the biomass, its location, and morphology in MEMS. A series of experiments had conducted, using different number/types of cells and morphologic distributions (e.g., concentrated vs. disperse) within the microenvironmental chamber. The experiments were conducted such that, simultaneously with CATs characterization, a number of metabolic parameters (such as oxygen, CO2, glucose, pH, methanol, formate and small molecule metabolites, etc.) also were measured by fluorescence microscopy (Lidstrom and Meldrum, Nature, 2003). Results of partition and transport experiments show that adsorption of a CAT molecule into the cellular mass results in its retardation during flow, which is a good measure of the biomass quantity and distribution. The molecules chosen were used to demonstrate their utility to quantitatively characterize the biomass, its location and morphology in MEMS. The results yield first-of-their-kind data sets relating metabolic parameters to location, heterogeneity, and morphology of cells. The data were used to obtain quantitative information needed for the characterization of biomass in MEMS, and to develop the theory relating the cellular phenomena of interest to cellular heterogeneity and morphology. The proposed research contributes a new set of tools for a rapid, noninvasive characterization of nano-scale biological systems.

Choi, J.; Saripalli, P.; Meldrum, D.; Lee, S.

2005-12-01

316

Rapid and Quantitative Detection of the Microbial Spoilage of Meat by Fourier Transform Infrared Spectroscopy and Machine Learning  

PubMed Central

Fourier transform infrared (FT-IR) spectroscopy is a rapid, noninvasive technique with considerable potential for application in the food and related industries. We show here that this technique can be used directly on the surface of food to produce biochemically interpretable “fingerprints.” Spoilage in meat is the result of decomposition and the formation of metabolites caused by the growth and enzymatic activity of microorganisms. FT-IR was exploited to measure biochemical changes within the meat substrate, enhancing and accelerating the detection of microbial spoilage. Chicken breasts were purchased from a national retailer, comminuted for 10 s, and left to spoil at room temperature for 24 h. Every hour, FT-IR measurements were taken directly from the meat surface using attenuated total reflectance, and the total viable counts were obtained by classical plating methods. Quantitative interpretation of FT-IR spectra was possible using partial least-squares regression and allowed accurate estimates of bacterial loads to be calculated directly from the meat surface in 60 s. Genetic programming was used to derive rules showing that at levels of 107 bacteria·g?1 the main biochemical indicator of spoilage was the onset of proteolysis. Thus, using FT-IR we were able to acquire a metabolic snapshot and quantify, noninvasively, the microbial loads of food samples accurately and rapidly in 60 s, directly from the sample surface. We believe this approach will aid in the Hazard Analysis Critical Control Point process for the assessment of the microbiological safety of food at the production, processing, manufacturing, packaging, and storage levels.

Ellis, David I.; Broadhurst, David; Kell, Douglas B.; Rowland, Jem J.; Goodacre, Royston

2002-01-01

317

Use of FT-NIR transmission spectroscopy for the quantitative analysis of an active ingredient in a translucent pharmaceutical topical gel formulation  

Microsoft Academic Search

The objective of this study was to demonstrate the use of transmission Fourier transform near-infrared (FT-NIR) spectroscopy\\u000a for quantitative analysis of an active ingredient in a translucent gel formulation. Gels were prepared using Carbopol 980\\u000a with 0%, 1%, 2%, 4%, 6%, and 8% ketoprofen and analyzed with an FT-NIR spectrophotometer operated in the transmission mode.\\u000a The correlation coefficient of the

Mark S. Kemper; Edgar J. Magnuson; Stephen R. Lowry; William J. McCarthy; Napasinee Aksornkoae; D. Christopher Watts; James R. Johnson; Atul J. Shukla

2001-01-01

318

The influence of multivariate analysis methods and target grain size on the accuracy of remote quantitative chemical analysis of rocks using laser induced breakdown spectroscopy  

Microsoft Academic Search

Laser-induced breakdown spectroscopy (LIBS) was used to quantitatively analyze 195 rock slab samples with known bulk chemical compositions, 90 pressed-powder samples derived from a subset of those rocks, and 31 pressed-powder geostandards under conditions that simulate the ChemCam instrument on the Mars Science Laboratory Rover (MSL), Curiosity. The low-volatile (<2 wt.%) silicate samples (90 rock slabs, corresponding powders, and 22

Ryan B. Anderson; Richard V. Morris; Samuel M. Clegg; James F. Bell; Roger C. Wiens; Seth D. Humphries; Trevor G. Graff; Rhonda McInroy

2011-01-01

319

The influence of multivariate analysis methods and target grain size on the accuracy of remote quantitative chemical analysis of rocks using laser induced breakdown spectroscopy  

Microsoft Academic Search

Laser-induced breakdown spectroscopy (LIBS) was used to quantitatively analyze 195 rock slab samples with known bulk chemical compositions, 90 pressed-powder samples derived from a subset of those rocks, and 31 pressed-powder geostandards under conditions that simulate the ChemCam instrument on the Mars Science Laboratory Rover (MSL), Curiosity. The low-volatile (<2wt.%) silicate samples (90 rock slabs, corresponding powders, and 22 geostandards)

Ryan B. Anderson; Richard V. Morris; Samuel M. Clegg; James F. Bell; Roger C. Wiens; Seth D. Humphries; Trevor G. Graff; Rhonda McInroy

2011-01-01

320

Influence of Laser Wavelength on Laser-induced Breakdown Spectroscopy Applied to Semi-Quantitative Analysis of Trace-Elements in a Plant Sample  

Microsoft Academic Search

Laser-induced breakdown spectroscopy (LIBS) as a powerful analytical technique is applied to analyze trace-elements in fresh plant samples. We investigate the LIBS spectra of fresh holly leaves and observe more than 430 lines emitted from 25 elements and molecules in the region 230-438 nm. The influence of laser wavelength on LIBS applied to semi-quantitative analysis of trace-element contents in plant

Da-Cheng Zhang; Xin-Wen Ma; Wei-Qiang Wen; Peng-Ju Zhang; Xiao-Long Zhu; Bin Li; Hui-Ping Liu

2010-01-01

321

Quantitative determination of unsaturation in photocured halogenated acrylates and methacrylates by FT-IR and Raman-spectroscopy and by thermal analysis  

Microsoft Academic Search

The photo-polymerization of tetrachloroethylacrylate (TeCEA), pentafluorophenylacrylate (PFPA) and pentafluorophenylmethacrylate (PFPMA) was examined by quantitative FT-IR and FT-Raman spectroscopy and by thermal analysis. The agreement between the FT-Raman results and thermal analysis was good for all monomers. The FT-IR measurement yielded higher percentages of unsaturation than the two other techniques in the slowly reacting PFPMA polymer, which can be attributed to

M. Jöhnck; L. Müller; A. Neyer; J. W. Hofstraat

1999-01-01

322

Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy: An Emerging Method in Structural Biology for Examining Protein Conformations and Protein Interactions  

SciTech Connect

Circular dichroism (CD) spectroscopy is a well-established technique in structural biology. The use of synchrotron radiation as an intense light source for these measurements extends the applications possible using lab-based instruments. In recent years, there has been a major growth in synchrotron radiation circular dichroism (SRCD) beamlines worldwide, including ones at the NSLS, ISA, SRS, HiSOR, BSRF, NSRRC, SOLEIL, Diamond, TERAS, BESSYII, and ANKA synchrotrons. Through the coordinated efforts of beamline scientists and users at these sites, important proof-of-principle studies have been done enabling the method to be developed for novel and productive studies on biological systems. This paper describes the characteristics of SRCD beamlines and some of the new types of applications that have been undertaken using these beamlines.

Wallace, B.A.; Sutherland, J.; Gekko, K.; Hoffmann, S. V.; Lin, Y.-H.; Tao, Y.; Wien, F.; Janes, R. W.

2011-09-01

323

Polarized Enhanced Backscattering Spectroscopy for Characterization of Biological Tissues at Subdiffusion Length-scales  

PubMed Central

Since the early 1980’s, the enhanced backscattering (EBS) phenomenon has been well-studied in a large variety of non-biological materials. Yet, until recently the use of conventional EBS for the characterization of biological tissue has been fairly limited. In this work we detail the unique ability of EBS to provide spectroscopic, polarimetric, and depth-resolved characterization of biological tissue using a simple backscattering instrument. We first explain the experimental and numerical procedures used to accurately measure and model the full azimuthal EBS peak shape in biological tissue. Next we explore the peak shape and height dependencies for different polarization channels and spatial coherence of illumination. We then illustrate the extraordinary sensitivity of EBS to the shape of the scattering phase function using suspensions of latex microspheres. Finally, we apply EBS to biological tissue samples in order to measure optical properties and observe the spatial length-scales at which backscattering is altered in early colon carcinogenesis.

Radosevich, Andrew J.; Rogers, Jeremy D.; Turzhitsky, Vladimir; Mutyal, Nikhil N.; Yi, Ji; Roy, Hemant K.; Backman, Vadim

2013-01-01

324

Applications of X-ray absorption spectroscopy to biologically relevant metal-based chemistry  

NASA Astrophysics Data System (ADS)

Recent developments in the understanding of the biosynthesis of the active site of the nitrogenase enzyme, the structure of the iron centre of [Fe]-hydrogenase and the structure and biomimetic chemistry of the [FeFe] hydrogenase H-cluster as deduced by application of X-ray spectroscopy are reviewed. The techniques central to this work include X-ray absorption spectroscopy either in the form of extended X-ray absorption fine structure (EXAFS), X-ray absorption near-edge structure (XANES) and nuclear resonant vibrational spectroscopy (NRVS). Examples of the advances in the understanding of the chemistry of the system through integration of a range of spectroscopic and computational techniques with X-ray spectroscopy are highlighted. The critical role played by ab initio calculation of structural and spectroscopic properties of transition-metal compounds using density functional theory (DFT) is illustrated both by the calculation of nuclear resonance vibrational spectroscopy (NRVS) spectra and the structures and spectra of intermediates through the catalytic reactions of hydrogenase model compounds.

Best, Stephen P.; Cheah, Mun Hon

2010-02-01

325

Teacher knowledge and discourse control: Quantitative evidence from novice biology teachers' classrooms  

NASA Astrophysics Data System (ADS)

This article describes the effects of science teacher subject-matter knowledge on classroom discourse at the level of individual utterances. It details one of three parallel analyses conducted in a year-long study of language in the classrooms of four new biology teachers. The conceptual framework of the study predicts that when teaching unfamiliar subject matter, teachers use a variety of discourse strategies to constrain student talk to a narrowly circumscribed topic domain. This article includes the results of an utterance-by-utterance analysis of teacher and student talk in a 30-lesson sample of science instruction. Data are broken down by classroom activity (e.g., lecture, laboratory, group work) for several measures, including mean duration of utterances, domination of the speaking floor by the teacher, frequency of teacher questioning, cognitive level of teacher questions, and student verbal participation. When teaching unfamiliar topics, the four teachers in this study tended to talk more often and for longer periods of time, ask questions frequently, and rely heavily on low cognitive level questions. The rate of student questions to the teacher varied with classroom activity. In common classroom communicative settings, student questions were less common when the teacher was teaching unfamiliar subject matter. The implications of these findings include a suggestion that teacher knowledge may be an important unconsidered variable in research on the cognitive level of questions and teacher wait-time.

Carlsen, William S.

326

Quantitative global and gene-specific promoter methylation in relation to biological properties of neuroblastomas  

PubMed Central

Background In this study we aimed to quantify tumor suppressor gene (TSG) promoter methylation densities levels in primary neuroblastoma tumors and cell lines. A subset of these TSGs is associated with a CpG island methylator phenotype (CIMP) in other tumor types. Methods The study panel consisted of 38 primary tumors, 7 established cell lines and 4 healthy references. Promoter methylation was determined by bisulphate Pyrosequencing for 14 TSGs; and LINE-1 repeat element methylation was used as an indicator of global methylation levels. Results Overall mean TSG Z-scores were significantly increased in cases with adverse outcome, but were unrelated to global LINE-1 methylation. CIMP with hypermethylation of three or more gene promoters was observed in 6/38 tumors and 7/7 cell lines. Hypermethylation of one or more TSG (comprising TSGs BLU, CASP8, DCR2, CDH1, RASSF1A and RASSF2) was evident in 30/38 tumors. By contrast only very low levels of promoter methylation were recorded for APC, DAPK1, NORE1A, P14, P16, TP73, PTEN and RARB. Similar involvements of methylation instability were revealed between cell line models and neuroblastoma tumors. Separate analysis of two proposed CASP8 regulatory regions revealed frequent and significant involvement of CpG sites between exon 4 and 5, but modest involvement of the exon 1 region. Conclusions/significance The results highlight the involvement of TSG methylation instability in neuroblastoma tumors and cell lines using quantitative methods, support the use of DNA methylation analyses as a prognostic tool for this tumor type, and underscore the relevance of developing demethylating therapies for its treatment.

2012-01-01

327

Developments in cell biology for quantitative immunoelectron microscopy based on thin sections: a review.  

PubMed

Quantitative immunoelectron microscopy uses ultrathin sections and gold particle labelling to determine distributions of molecules across cell compartments. Here, we review a portfolio of new methods for comparing labelling distributions between different compartments in one study group (method 1) and between the same compartments in two or more groups (method 2). Specimen samples are selected unbiasedly and then observed and expected distributions of gold particles are estimated and compared by appropriate statistical procedures. The methods can be used to analyse gold label distributed between volume-occupying (organelle) and surface-occupying (membrane) compartments, but in method 1, membranes must be treated as organelles. With method 1, gold counts are combined with stereological estimators of compartment size to determine labelling density (LD). For volume-occupiers, LD can be expressed simply as golds per test point and, for surface-occupiers, as golds per test line intersection. Expected distributions are generated by randomly assigning gold particles to compartments and expressing observed/expected counts as a relative labelling index (RLI). Preferentially-labelled compartments are identified from their RLI values and by Chi-squared analysis of observed and expected distributions. For method 2, the raw gold particle counts distributed between compartments are simply compared across groups by contingency table and Chi-squared analysis. This identifies the main compartments responsible for the differences between group distributions. Finally, we discuss labelling efficiency (the number of gold particles per target molecule) and describe how it can be estimated for volume- or surface-occupiers by combining stereological data with biochemical determinations. PMID:18553098

Mayhew, Terry M; Lucocq, John M

2008-06-14

328

Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries  

PubMed Central

High-throughput screening (HTS) of chemical compounds to identify modulators of molecular targets is a mainstay of pharmaceutical development. Increasingly, HTS is being used to identify chemical probes of gene, pathway, and cell functions, with the ultimate goal of comprehensively delineating relationships between chemical structures and biological activities. Achieving this goal will require methodologies that efficiently generate pharmacological data from the primary screen and reliably profile the range of biological activities associated with large chemical libraries. Traditional HTS, which tests compounds at a single concentration, is not suited to this task, because HTS is burdened by frequent false positives and false negatives and requires extensive follow-up testing. We have developed a paradigm, quantitative HTS (qHTS), tested with the enzyme pyruvate kinase, to generate concentration–response curves for >60,000 compounds in a single experiment. We show that this method is precise, refractory to variations in sample preparation, and identifies compounds with a wide range of activities. Concentration–response curves were classified to rapidly identify pyruvate kinase activators and inhibitors with a variety of potencies and efficacies and elucidate structure–activity relationships directly from the primary screen. Comparison of qHTS with traditional single-concentration HTS revealed a high prevalence of false negatives in the single-point screen. This study demonstrates the feasibility of qHTS for accurately profiling every compound in large chemical libraries (>105 compounds). qHTS produces rich data sets that can be immediately mined for reliable biological activities, thereby providing a platform for chemical genomics and accelerating the identification of leads for drug discovery.

Inglese, James; Auld, Douglas S.; Jadhav, Ajit; Johnson, Ronald L.; Simeonov, Anton; Yasgar, Adam; Zheng, Wei; Austin, Christopher P.

2006-01-01

329

Development of a radioimmunoassay for the quantitative determination of 8-prenylnaringenin in biological matrices.  

PubMed

Seven carboxylic acid haptens of 8-prenylnaringenin (8-PN) were synthesized, coupled to cationized bovine serum albumin, and employed to raise specific antisera in rabbits. Two linkers of different lengths (C3H6COOH and C6H12COOH) were coupled to the C7-OH group and separated into their respective enantiomers yielding the first four haptens. Racemic derivatives with C4'-OH coupled linkers C5H10COOH and C9H18COOH were synthesized carrying a methylated C7-OH. Another racemic C4'-OH hapten (CH2COOH) was prepared starting from naringenin. The haptens elicited variable antibody titers dependent on linker lengths, with short linkers giving the best results. Three antisera were characterized in detail: anti-C7-carboxy-propyloxy-2S-(-)-8-PN (anti-H-11), anti-C7-carboxy-propyloxy-2R-(+)-8-PN (anti-H-10), and anti-C4'-carboxy-methoxy-rac-8-PN (anti-H-25). anti-H-10 and anti-H-11 showed about 9% enantiomeric cross-reactivity, and anti-H-11 did not discriminate between isoxanthohumol (IX) and 8-PN (84% cross-reactivity). For anti-H-10, cross-reactivities in the range of 2-5% were found for xanthohumol, IX, and 6-prenylnaringenin. Respective numbers for anti-H-25 were 0.02, 0.1, and 0.2%. Tritiated 8-PN was synthesized yielding a 3H-tracer of high specific radioactivity (2.22 GBq/mg). A radioimmunoassay using anti-H-25 and 3H-8-PN was established and used for the quantitative determination of 8-PN in various beer brands and in the urine of six men after the consumption of three different brands of beer. Furthermore, the dose-dependent excretion of 8-PN was tested after the consumption of a higher volume of a single beer brand with and without spiking with 8-PN and a small oral dose of authentic 8-PN, respectively. Conflicting results led to a pilot test on the in vivo conversion (demethylation) of IX into 8-PN in two men. Conversion rates of 1.9 and 4.4% were estimated. Thus, the total 8-PN dose in beer brands spiced with natural hop or hop products seems to be the sum of the 8-PN amount in a consumed volume and the amount arising from the conversion of IX. PMID:15826034

Schaefer, Olaf; Bohlmann, Rolf; Schleuning, Wolf-Dieter; Schulze-Forster, Kai; Hümpel, Michael

2005-04-20

330

Influence of Laser Wavelength on Laser-induced Breakdown Spectroscopy Applied to Semi-Quantitative Analysis of Trace-Elements in a Plant Sample  

NASA Astrophysics Data System (ADS)

Laser-induced breakdown spectroscopy (LIBS) as a powerful analytical technique is applied to analyze trace-elements in fresh plant samples. We investigate the LIBS spectra of fresh holly leaves and observe more than 430 lines emitted from 25 elements and molecules in the region 230-438 nm. The influence of laser wavelength on LIBS applied to semi-quantitative analysis of trace-element contents in plant samples is studied. The results show that the UV laser has lower relative standard deviations and better repeatability for semi-quantitative analysis of trace-element contents in plant samples. This work may be helpful for improving the quantitative analysis power of LIBS applied to plant samples.

Zhang, Da-Cheng; Ma, Xin-Wen; Wen, Wei-Qiang; Zhang, Peng-Ju; Zhu, Xiao-Long; Li, Bin; Liu, Hui-Ping

2010-06-01

331

Spectroscopic characterization of biological agents using FTIR, normal Raman and surface-enhanced Raman spectroscopies  

Microsoft Academic Search

FTIR, Raman spectroscopy and Surface Enhanced Raman Scattering (SERS) requires a minimum of sample allows fast identification of microorganisms. The use of this technique for characterizing the spectroscopic signatures of these agents and their stimulants has recently gained considerable attention due to the fact that these techniques can be easily adapted for standoff detection from considerable distances. The techniques also

Tatiana Luna-Pineda; Kristina Soto-Feliciano; Edwin De La Cruz-Montoya; Leonardo C. Pacheco Londoño; Carlos Ríos-Velázquez; Samuel P. Hernández-Rivera

2007-01-01

332

Quantitation of Absorbers in Turbid Media Using Time-Integrated Spectroscopy Based on Microscopic Beer-Lambert Law  

Microsoft Academic Search

Based on the microscopic Beer-Lambert law, two practical time-integrated spectroscopy (TIS) methods, called dual-wavelength spectroscopy method, and dual-wavelength and dual-site spectroscopy method, are described to determine the absolute concentration of an absorber in variously shaped turbid media. We demonstrate, for the first time, the validity of the TIS methods by means of experiments in which the absolute concentrations of an

Hedong Zhang; Mitsuharu Miwa; Yutaka Yamashita; Yutaka Tsuchiya

1998-01-01

333

Raman Micro-spectroscopy Study of Healthy and Burned Biological Tissue  

NASA Astrophysics Data System (ADS)

Burn injuries are a significant medical problem, and need to be treated quickly and precisely. Burned skin needs to be removed early, within hours (less than 24 hrs) of injury, when the margins of the burn are still hard to define. Studies show that treating and excising burn wounds soon after the injury prevents the wound from becoming deeper, reduces the release of proinflammatory mediators, and reduces or prevents the systemic inflammatory reaction syndrome. Also, removing burned skin prepares the affected region for skin grafting. Raman micro-spectroscopy could be used as an objective diagnostic method that will assist burn surgeons in distinguishing unburned from burned areas. As a first step in developing a diagnostic tool, we present Raman micro-spectroscopy information from normal and burned ex vivo rat skin.

Zarnani, Faranak; Glosser, Robert; Idris, Ahamed

2011-10-01

334

Short communication Sensing minute changes in biological cell monolayers with THz differential time-domain spectroscopy  

Microsoft Academic Search

We used terahertz differential time-domain spectroscopy (THz-DTDS) to measure minute changes of bovine lung microvessel endothelial cells (BLMVEC) in response to vascular endothelial growth factor (VEGF). These changes were reflected by alterations in THz wave attenuations and THz dielectric properties of the treated cells. The VEGF-induced THz attenuations of cell monolayers correlated well with changes in transendothelial resistance, as measured

Hai-Bo Liu; George Plopper; Sarah Earley; Yunqing Chen; Bradley Ferguson; X.-C. Zhang

335

Sensing minute changes in biological cell monolayers with THz differential time-domain spectroscopy  

Microsoft Academic Search

We used terahertz differential time-domain spectroscopy (THz-DTDS) to measure minute changes of bovine lung microvessel endothelial cells (BLMVEC) in response to vascular endothelial growth factor (VEGF). These changes were reflected by alterations in THz wave attenuations and THz dielectric properties of the treated cells. The VEGF-induced THz attenuations of cell monolayers correlated well with changes in transendothelial resistance, as measured

Hai-Bo Liu; George Plopper; Sarah Earley; Yunqing Chen; Bradley Ferguson; X.-C. Zhang

2007-01-01

336

Quantitative fractography  

Microsoft Academic Search

In many disciplines, such as biology, botany, geology, materials science and medicine, quantitative image analysis is being used to an increasing extent. In materials science this technique makes it possible to relate the microsctructure to the mechanical properties. In this review we shall show that image analysis can be applied in a fractographic study to characterize quantitatively the morphology of

J. L. Chermant; M. Coster

1979-01-01

337

Fiber optic evanescent wave spectroscopy (FEWS) and its applications for multicomponent analysis of blood and biological fluids  

NASA Astrophysics Data System (ADS)

In numerous cases the technique of Fiberoptic Evanescent Wave Spectroscopy (FEWS) offers great advantages over regular IR spectroscopic methods. It provides an easy way for measuring the absorption spectra of highly absorbing or highly scattering samples. With FEWS one can perform measurements in situ and in real time and this is potentially useful for measurements on biological samples or for the monitoring of chemical reactions. In the present work, the FEWS technique was used to analyze human blood serum using a Fourier Transform Infrared Spectrometer. A special cell based on IR transmitting non-toxic silver halide fibers was designed. Further improvements in the analysis were obtained by adopting some multivariate calibration techniques that have already been used in clinical chemistry. The blood constituents analyzed were: urea, total protein, cholesterol, uric acid and calcium. Good agreement between our results and the ordinary chemical and enzymatic methods was obtained.

Simhi, Ronit; Bunimovich, D.; Sela, Ben-Ami; Katzir, Abraham

1995-05-01

338

Simultaneous AFM force spectroscopy and FRET measurements on single biological molecules  

NASA Astrophysics Data System (ADS)

Single Molecule Fluorescence Resonance Energy Transfer (FRET) and single molecule force measurements with the Atomic Force Microscope (AFM) are two powerful techniques that have facilitated much progress in the biological sciences. However each of these techniques suffers from limitations that can be overcome by the use of a combined single molecule AFM-FRET approach. Here, we describe an instrument that successfully combines single molecule AFM with FRET to apply forces on individual biological molecules and simultaneously monitor their conformational dynamics. To validate this technique, we measured the force induced shearing of dye-labeled, double stranded DNA. Single DNA molecules were sheared and mechanical transitions corresponding to DNA rupture were correlated with changes in FRET.

Li, Hui; Yan, Chi-Fu; Sivasankar, Sanjeevi

2011-03-01

339

Infrared fiber optic evanescent wave spectroscopy: applications in biology and medicine  

NASA Astrophysics Data System (ADS)

A new powerful and highly sensitive technique for non-invasive biomedical diagnostics in vivo has been developed using Infrared Fiberoptic Evanescent Wave Fourier Transform Spectroscopy (FEW-FTIR). This compact and portable method allows to detect functional chemical groups and bonds via vibrational spectroscopy directly from surfaces including living tissue. Such differences and similarities in molecular structure of tissue and materials can be evaluated online. Operating in the attenuated total reflection (ATR) regime in the middle-infrared (MIR) range, the FEW-FTIR technique provides direct contact between the fiber probe and tissue for non-destructive, non-invasive, fast and remote (few meters) diagnostics and quality control of materials. This method utilizes highly flexible and extremely low loss unclad fibers, for example silver halide fibers. Applications of this method include investigations of normal skin, precancerous and cancerous conditions, monitoring of the process of aging, allergic reactions and radiation damage to the skin. This setup is suitable as well for the detection of the influence of environmental factors (sun, water, pollution, and weather) on skin surfaces. The FEW-FTIR technique is very promising also for fast histological examinations in vitro. In this review, we present recent investigations of skin, breast, lung, stomach, kidney tissues in vivo and ex vivo (during surgery) to define the areas of tumor localization. The main advantages of the FEW-FTIR technique for biomedical, clinical, and environmental applications are discussed.

Afanasyeva, Natalia I.; Bruch, Reinhard F.; Katzir, Abraham

1999-04-01

340

Testing biological liquid samples using modified m-line spectroscopy method  

NASA Astrophysics Data System (ADS)

Non-chemical method of detection of sugar concentration in biological (animal and plant source) liquids has been investigated. Simplified set was build to show the easy way of carrying out the survey and to make easy to gather multiple measurements for error detecting and statistics. Method is suggested as easy and cheap alternative for chemical methods of measuring sugar concentration, but needing a lot effort to be made precise.

Augusciuk, Elzbieta; Rybi?ski, Grzegorz

2005-09-01

341

Assessment of the maturity and biological parameters of compost produced from dairy manure and rice chaff by excitation-emission matrix fluorescence spectroscopy.  

PubMed

The assessment of maturity and biological parameters is important in the composting process. In this study, excitation-emission matrix (EEM) fluorescence spectroscopy was applied to evaluate the maturity and biological parameters of compost produced from the co-composting of dairy and rice chaff. The results from a Pearson correlation analysis between traditional physico-chemical maturity indices and fluorescence regional integration (FRI) parameters showed that among the FRI parameters, P(V,n)/P(III,n) and P(V,n) were suitable for the assessment of compost maturity. Moreover, the FRI parameters could be used to evaluate biological parameters including the germination index (GI) and ribotype evolution which indicate the bacterial community structure and dynamics. P(IV,n) was the most suitable indicator for revealing the community structure and dynamics during the composting process. Fluorescence spectroscopy combined with the FRI analysis could be used as a sensitive and efficient tool for assessing compost maturity and biological parameters. PMID:22342088

Tian, Wei; Li, Lingzhi; Liu, Fang; Zhang, Zhenhua; Yu, Guanghui; Shen, Qirong; Shen, Biao

2012-01-26

342

Mapping nanoparticles injected into a biological tissue using laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

We describe a setup for LIBS mapping of nanoparticles and trace metallic elements in biological organ as well as the followed experimental procedure. Mapping was performed for metallic elements such as Gd, Si, Ca and Fe, with a resolution of 100 ?m on kidney slices sampled from a mouse 24 h after intravenous injection of a solution of gadolinium-based nanoparticles. An approach for quantifying Gd in the tissue is also presented with a good agreement with measurement performed by ICP-OES. We demonstrate that LIBS offers a simple and robust method to study the distribution of gadolinium-based nanoparticles in biological samples, without any labeling of the nanoparticles. The used bench-top instrumentation is fully compatible with the standard optical microscopy, which shows its large potential use in Biology and Medicine as a tool for complementary observation of trace metallic elements with respect to the classical optical observations which are generally based on the responses of biomolecules or cells.

Motto-Ros, V.; Sancey, L.; Wang, X. C.; Ma, Q. L.; Lux, F.; Bai, X. S.; Panczer, G.; Tillement, O.; Yu, J.

2013-09-01

343

Quantitative Determination of the Biodegradable Polymer Poly(?-hydroxybutyrate) in a Recombinant Escherichia coli Strain by Use of Mid-Infrared Spectroscopy and Multivariative Statistics  

PubMed Central

Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS) multivariative statistical technique was used for quantitative analysis of the poly(?-hydroxybutyrate) (PHB) contents of bacterial cells. A total of 237 replicate spectra from 34 samples were obtained together with gas chromatography-determined reference PHB contents. Using the PLS regression, we were able to relate the infrared spectra to the reference PHB contents, and the correlation coefficient between the measured and predicted values for the optimal model with a standard error of prediction of 1.49% PHB was 0.988. With this technique, there are no solvent requirements, sample preparation is minimal and simple, and analysis time is greatly reduced; our results demonstrate the potential of FTIR spectroscopy as an alternative to the conventional methods used for analysis of PHB in bacterial cells.

Kansiz, Mustafa; Billman-Jacobe, Helen; McNaughton, Don

2000-01-01

344

In vitro quantitative ((1))H and ((19))F nuclear magnetic resonance spectroscopy and imaging studies of fluvastatin™ in Lescol® XL tablets in a USP-IV dissolution cell.  

PubMed

Swellable polymeric matrices are key systems in the controlled drug release area. Currently, the vast majority of research is still focused on polymer swelling dynamics. This study represents the first quantitative multi-nuclear (((1))H and ((19))F) fast magnetic resonance imaging study of the complete dissolution process of a commercial (Lescol® XL) tablet, whose formulation is based on the hydroxypropyl methylcellulose (HPMC) polymer under in vitro conditions in a standard USP-IV (United States Pharmacopeia apparatus IV) flow-through cell that is incorporated into high field superconducting magnetic resonance spectrometer. Quantitative RARE ((1))H magnetic resonance imaging (MRI) and ((19))F nuclear magnetic resonance (NMR) spectroscopy and imaging methods have been used to give information on: (i) dissolution media uptake and hydrodynamics; (ii) active pharmaceutical ingredient (API) mobilisation and dissolution; (iii) matrix swelling and dissolution and (iv) media activity within the swelling matrix. In order to better reflect the in vivo conditions, the bio-relevant media Simulated Gastric Fluid (SGF) and Fasted State Simulated Intestinal Fluid (FaSSIF) were used. A newly developed quantitative ultra-fast MRI technique was applied and the results clearly show the transport dynamics of media penetration and hydrodynamics along with the polymer swelling processes. The drug dissolution and mobility inside the gel matrix was characterised, in parallel to the ((1))H measurements, by ((19))F NMR spectroscopy and MRI, and the drug release profile in the bulk solution was recorded offline by UV spectrometer. We found that NMR spectroscopy and 1D-MRI can be uniquely used to monitor the drug dissolution/mobilisation process within the gel layer, and the results from ((19))F NMR spectra indicate that in the gel layer, the physical mobility of the drug changes from "dissolved immobilised drug" to "dissolved mobilised drug". PMID:21911016

Zhang, Qilei; Gladden, Lynn; Avalle, Paolo; Mantle, Michael

2011-09-03

345

Estimation of regional hemoglobin concentration in biological tissues using diffuse reflectance spectroscopy with a novel spectral interpretation algorithm  

NASA Astrophysics Data System (ADS)

Both in medical research and clinical settings, regional hemoglobin concentrations ([Hb]) in the microcirculation of biological tissues are highly sought. Diffuse reflectance spectroscopy has been proven to be a favorable method by which to detect regional [Hb]. This paper introduces a new algorithm to retrieve [Hb] information from diffuse reflectance spectra. The proposed algorithm utilizes the natural logarithmic operation and the differential wavelet transform to effectively quench the scattering effects, and then employs the concept of isosbestic wavelength in the transformed spectra to reduce the effects of hemoglobin oxygenation. As a result, the intensity at the defined isosbestic wavelength of the transformed spectra is a good indicator of [Hb] estimation. The algorithm was derived and validated using theoretical spectra produced by Monte Carlo simulation of photon migration. Its accuracy was further evaluated using liquid tissue phantoms, and its clinical utility with an in vivo clinical study of brain tumors. The results demonstrate the applicability of the algorithm for real-time [Hb] estimations from diffuse reflectance spectra, acquired by means of a fiber-optic spectroscopy system.

Chen, P.; Fernald, B.; Lin, W.

2011-07-01

346

Spectroscopic-tomography of biological membrane with high-spatial resolution by the imaging-type 2D Fourier spectroscopy  

NASA Astrophysics Data System (ADS)

We proposed the imaging-type 2-dimensional Fourier spectroscopy that is the phase-shift interferometry between the objective lights. The proposed method can measure the 2D spectral image at the limited depth. Because of the imaging optical system, the 2D spectral images can be measured in high spatial resolution. And in the depth direction, we can get the spectral distribution only in the focal plane. In this report, we mention about the principle of the proposed wide field imaging-type 2D Fourier spectroscopy. And, we obtained the spectroscopic tomography of biological tissue of mouse's ear. In the visible region, we confirmed the difference of spectral characteristics between blood vessel region and other region. In the near infrared region (?=900nm~1700nm), we can obtain the high-contrast blood vessel image of mouse's ear in the deeper part by InGaAs camera. Furthermore, in the middle infrared region(?=8?~14?m), we have successfully measured the radiation spectroscopic-imaging with wild field of view by the infrared module, such as the house plants. Additionally, we propose correction geometrical model that can convert the mechanical phase-shift value into the substantial phase difference in each oblique optical axes. We successfully verified the effectiveness of the proposed correction geometrical model and can reduce the spectral error into the error range into +/-3nm using the He-Ne laser whose wavelength 632.8nm.

Inui, Asuka; Tsutsumi, Ryosuke; Qi, Wei; Takuma, Takashi; Ishimaru, Ichiro

2011-06-01

347

[Study on rapid quantitative analysis of the active ingredient in ABC extinguishing agent and type identification of extinguishing agent powders using near infrared spectroscopy].  

PubMed

A new quantitative method to determine the NH4H2PO4 in ABC powder extinguishing agent and to distinguish between ABC and BC powder extinguishing agents using near infrared diffuse reflectance spectroscopy is proposed. A PLS calibration model for the NH4H2PO4 content in extinguishing agent powder was established, with RMSECV = 2.1, RMSEP = 2.4. An identification model for ABC and BC powder extinguishing agents was built by SIMCA and the identification accuracy rate is 100%. This method, compared to the present standard method, has the characteristics of rapidness and easy operation, whichis fit for the quantitative analysis and type distinguishing of the fire products on site. PMID:23156767

Hu, Ai-qin; Yuan, Hong-fu; Xue, Gang; Song, Chun-feng; Li, Xiao-yu; Xie, Jin-chun

2012-08-01

348

Quantitation of In Vitro ?-1 Adrenergic Receptor Antagonist Binding Capacity to Biologic Melanin Using Tandem Mass Spectrometry.  

PubMed

Abstract Purpose: The purpose of this study was to develop methods to allow evaluation of the binding characteristics for a series of ?-1 antagonists to biologically-derived melanin. Methods: Fresh bovine globes were used to obtain iridal and choroid/retinal pigment epithelial (CRPE) derived melanin. Binding characteristics of chloroquine, tamsulosin and doxazosin were then evaluated in vitro using tandem mass spectroscopy. Results: Tandem mass spectrometry-based assays were developed for three ?-1 antagonists that provided linear assay ranges which spanned (minimally) 0.01-10?µg/mL, while exhibiting excellent inter-assay precision and accuracy. When applied to the evaluation of binding characteristics for iridal melanin, mean chloroquine and tamsulosin fractions were found to be 41.9?±?14.2 pmoles?mg(-1) and 25.34?±?6.186?pmoles?mg(-1), respectively. Mean iridal doxazosin binding was found to be 6.36?±?2.19 pmoles?mg(-1). Interestingly, mean levels of tamsulosin, but not doxazosin found bound to choroid/CRPE derived melanin approached that of chloroquine (27.91?µg/mL, 25.68?µg/mL and 5.94?µg/mL for chloroquine, tamsulosin and doxazosin, respectively). One way ANOVA for binding affinity for chloroquine, tamsulosin and doxazosin was statistically significant for both iridal and CRPE-derived melanin (p?=?0.0012 and 0.0023), respectively. A Bonferroni post-hoc analysis demonstrated a statistically significant difference in the amount of binding between tamsulosin, doxazosin and chloroquine to iridal but not CRPE derived melanin (p?

Gaynes, Jeffrey S; Micic, Cedomir; Gaynes, Bruce I; Borgia, Jeffrey A

2013-09-18

349

Recent applications of /sup 13/C NMR spectroscopy to biological systems  

SciTech Connect

Carbon-13 nuclear magnetic resonance (NMR) spectroscopy, in conjunction with carbon-13 labelling, is a powerful new analytical technique for the study of metabolic pathways and structural components in intact organelles, cells, and tissues. The technique can provide, rapidly and non-destructively, unique information about: the architecture and dynamics of structural components; the nature of the intracellular environment; and metabolic pathways and relative fluxes of individual carbon atoms. With the aid of results recently obtained by us and those reported by a number of other laboratories, the problems and potentialities of the technique will be reviewed with emphasis on: the viscosities of intracellular fluids; the structure and dynamics of the components of membranes; and the primary and secondary metabolic pathways of carbon in microorganisms, plants, and mammalian cells in culture.

Matwiyoff, N.A.

1981-01-01

350

Sensing minute changes in biological cell monolayers with THz differential time-domain spectroscopy.  

PubMed

We used terahertz differential time-domain spectroscopy (THz-DTDS) to measure minute changes of bovine lung microvessel endothelial cells (BLMVEC) in response to vascular endothelial growth factor (VEGF). These changes were reflected by alterations in THz wave attenuations and THz dielectric properties of the treated cells. The VEGF-induced THz attenuations of cell monolayers correlated well with changes in transendothelial resistance, as measured using electric cell-substrate impedance sensing (ECIS). However, the morphological differences that gave rise to these changes were not observed with standard optical phase contrast microscopy. We conclude that THz-DTDS is a highly sensitive, non-invasive, powerful new tool to measure minute changes in the morphology of live, cultured cell monolayers. This method enables spectroscopic investigations of cells in the THz band, providing information unavailable through other conventional methods such as optical phase contrast microscopy and ECIS. PMID:16621500

Liu, Hai-Bo; Plopper, George; Earley, Sarah; Chen, Yunqing; Ferguson, Bradley; Zhang, X-C

2006-04-18

351

Detection of trace Al in model biological tissue with laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

Laser-induced breakdown spectroscopy (LIBS), which is an excellent tool for trace elemental analysis, was studied as a method of detecting sub-part-per-106 (ppm) concentrations of aluminum in surrogates of human tissue. Tissue was modeled using a 2% agarose gelatin doped with an Al2O3 nanoparticle suspension. A calibration curve created with standard reference samples of known Al concentrations was used to determine the limit of detection, which was less than 1 ppm. Rates of false negative and false positive detection results for a much more realistic sampling methodology were also studied, suggesting that LIBS could be a candidate for the real-time in vivo detection of metal contamination in human soft tissue.

Adamson, Marian D.; Rehse, Steven J.

2007-08-01

352

Detection and Quantitative Analysis of Chemical Species in Hanford Tank Materials Using Raman Spectroscopy Technology: FY94Florida State University Raman Spectroscopy Report  

SciTech Connect

This report provides a summary of work completed in FY-94 by FSU to develop and investigate the feasibility of using Raman spectroscopy with Hanford tank waste materials. Raman performance impacts from sample morphology, including the effects of absorption, particle size, density, color and refractive index, are discussed. An algorithm for relative species concentration measurement from Raman data is presented. An Algorithm for applying Raman to tank waste core screening is presented and discussed. A library of absorption and Raman spectra are presented that support this work.

Reich, F.R.

1997-08-11

353

High-resolution NMR spectroscopy of biological tissues usingprojected Magic Angle Spinning  

SciTech Connect

High-resolution NMR spectra of materials subject toanisotropic broadening are usually obtained by rotating the sample aboutthe magic angle, which is 54.7 degrees to the static magnetic field. Inprojected Magic Angle Spinning (p-MAS), the sample is spun about twoangles, neither of which is the magic angle. This provides a method ofobtaining isotropic spectra while spinning at shallow angles. The p-MASexperiment may be used in situations where spinning the sample at themagic angle is not possible due to geometric or other constraints,allowing the choice of spinning angle to be determined by factors such asthe shape of the sample, rather than by the spin physics. The applicationof this technique to bovine tissue samples is demonstrated as a proof ofprinciple for future biological or medical applications.

Martin, Rachel W.; Jachmann, Rebecca C.; Sakellariou, Dimitris; Nielsen, Ulla Gro; Pines, Alexander

2005-01-27

354

Cellular Phone-Based Image Acquisition and Quantitative Ratiometric Method for Detecting Cocaine and Benzoylecgonine for Biological and Forensic Applications  

PubMed Central

Here we describe the first report of using low-cost cellular or web-based digital cameras to image and quantify standardized rapid immunoassay strips as a new point-of-care diagnostic and forensics tool with health applications. Quantitative ratiometric pixel density analysis (QRPDA) is an automated method requiring end-users to utilize inexpensive (? $1 USD/each) immunotest strips, a commonly available web or mobile phone camera or scanner, and internet or cellular service. A model is described whereby a central computer server and freely available IMAGEJ image analysis software records and analyzes the incoming image data with time-stamp and geo-tag information and performs the QRPDA using custom JAVA based macros (http://www.neurocloud.org). To demonstrate QRPDA we developed a standardized method using rapid immunotest strips directed against cocaine and its major metabolite, benzoylecgonine. Images from standardized samples were acquired using several devices, including a mobile phone camera, web cam, and scanner. We performed image analysis of three brands of commercially available dye-conjugated anti-cocaine/benzoylecgonine (COC/BE) antibody test strips in response to three different series of cocaine concentrations ranging from 0.1 to 300 ng/ml and BE concentrations ranging from 0.003 to 0.1 ng/ml. This data was then used to create standard curves to allow quantification of COC/BE in biological samples. Across all devices, QRPDA quantification of COC and BE proved to be a sensitive, economical, and faster alternative to more costly methods, such as gas chromatography-mass spectrometry, tandem mass spectrometry, or high pressure liquid chromatography. The limit of detection was determined to be between 0.1 and 5 ng/ml. To simulate conditions in the field, QRPDA was found to be robust under a variety of image acquisition and testing conditions that varied temperature, lighting, resolution, magnification and concentrations of biological fluid in a sample. To determine the effectiveness of the QRPDA method for quantifying cocaine in biological samples, mice were injected with a sub-locomotor activating dose of cocaine (5 mg/kg; i.p.) and were found to have detectable levels of COC/BE in their urine (160.6 ng/ml) and blood plasma (8.1 ng/ml) after 15–30 minutes. By comparison rats self-administering cocaine in a 4 hour session obtained a final BE blood plasma level of 910 ng/ml with an average of 62.5 infusions. It is concluded that automated QRPDA is a low-cost, rapid and highly sensitive method for the detection of COC/BE with health, forensics, and bioinformatics application and the potential to be used with other rapid immunotest strips directed at several other targets. Thus, this report serves as a general reference and method describing the use of image analysis of lateral flow rapid test strips.

Cadle, Brian A.; Rasmus, Kristin C.; Varela, Juan A.; Leverich, Leah S.; O'Neill, Casey E.; Bachtell, Ryan K.; Cooper, Donald C.

2010-01-01

355

Electronic Spectroscopy of Biological Molecules in Supersonic Jets: The Amino Acid Tryptophane  

NASA Astrophysics Data System (ADS)

The jet-cooled ultraviolet absorption spectrum of the amino acid tryptophan has been measured by cavity ringdown laser absorption spectroscopy covering the region where the origin bands of the S1<--S0 transition of the six conformers A to F are located. Tryptophan was transferred to the gas phase employing two different methods, thermal heating and laser vaporization. The latter technique has been proved to be more efficient in the sense that it allowed us to obtain higher densities of tryptophan in the jet for short times and that thermal decomposition of the sample, which occurred upon thermal heating, could be avoided. On the other hand, a better signal-to-noise ratio was obtained with conventional heating. For comparison, we have also carried out laser-induced fluorescence (LIF) measurements. It was found that the bands belonging to conformer A were stronger in the LIF spectra than in the absorption spectra. This is explained with a higher fluorescence yield for conformer A compared to the other conformers. It follows that LIF is not suited to properly describe the absorption behavior of tryptophan for the electronic transition under study.

Huisken, F.; Rouillé, G.; Arold, M.; Staicu, A.; Henning, Th.

2008-12-01

356

Subwavelength Raman imaging of biological samples using near-field spectroscopy  

NASA Astrophysics Data System (ADS)

Scanning near-field optical microscopy and Raman scattering were combined to obtain subwavelength molecular resolution. Near-field microscopy allows to overcome the diffraction limit valid for all lens or mirror based optical instruments and lateral resolutions well below 100 nm have been claimed. Raman spectroscopy yields information on the vibrational states of a molecule and therefore allows to distinguish between different chemical compounds easily. This is an advantage to the more widely used near-field fluorescence microscopy. To enhance the notoriously weak near-field Raman signal the sample was brought onto a Raman enhancing surface (silver coated Teflon nanospheres). Additionally brilliant cresyl blue acted as a Raman label for our DNA samples. On such samples Raman images with a resolution better than 100 nm have been obtained. A single near-field SERS spectrum was measured in approximately 60 seconds. The acquisition time currently depends critically on the transmission of the near-field probes. Nevertheless, it is possible to measure whole near-field Raman images in a reasonable time. From these Raman images a preliminary distinction of different constitutions of adsorbed molecules can be done.

Deckert, Volker; Zeisel, Dieter; Zenobi, Renato; Vo-Dinh, Tuan

1999-06-01

357

Sensing lanthanide metal content in biological tissues with magnetic resonance spectroscopy.  

PubMed

The development and validation of MRI contrast agents consisting of a lanthanide chelate often requires a determination of the concentration of the agent in ex vivo tissue. We have developed a protocol that uses 70% nitric acid to completely digest tissue samples that contain Gd(III), Dy(III), Tm(III), Eu(III), or Yb(III) ions, or the MRI contrast agent gadodiamide. NMR spectroscopy of coaxial tubes containing a digested sample and a separate control solution of nitric acid was used to rapidly and easily measure the bulk magnetic susceptibility (BMS) shift caused by each lanthanide ion and gadodiamide. Each BMS shift was shown to be linearly correlated with the concentration of each lanthanide ion and gadodiamide in the 70% nitric acid solution and in digested rat kidney and liver tissues. These concentration measurements had outstanding precision, and also had good accuracy for concentrations ³10 mM for Tm(III) Eu(III), and Yb(III), and ³3 mM for Gd(III), gadodiamide, and Dy(III). Improved sample handling methods are needed to improve measurement accuracy for samples with lower concentrations. PMID:24152931

Hingorani, Dina V; Gonzalez, Sandra I; Li, Jessica F; Pagel, Mark D

2013-10-11

358

Electron paramagnetic resonance spectroscopy studies of oxidative degradation of an active pharmaceutical ingredient and quantitative analysis of the organic radical intermediates using partial least-squares regression.  

PubMed

Electron paramagnetic resonance (EPR) spectroscopy was used to study the radical species formed during the oxidation of an active pharmaceutical ingredient in the solid state. It was found that the extent of radical generation correlated to the formation of an oxidative degradation product. Multifrequency EPR and electron nuclear double resonance spectroscopy gave additional information on the identity of the organic radical species involved in the oxidation process, and a mechanism was proposed for the degradation, involving the formation of both carbon-centered and peroxy radicals. The multivariate analysis technique of partial least-squares (PLS) regression was then used to determine the extent of oxidation of the active pharmaceutical ingredient from the EPR spectra. The suitability of this approach was demonstrated from its application to a series of standards. The conventional approach for the quantitative analysis of EPR spectra is to measure the peak height or to perform double integration of the spectral region containing the signal of interest. Both of these methods have intrinsic errors associated with them, particularly for weak EPR signals with a poor signal-to-noise ratio or a sloping background response. The results obtained showed that greatly improved quantitation was obtained using the PLS regression approach. PMID:16408946

Williams, Helen Elizabeth; Loades, Victoria Catherine; Claybourn, Mike; Murphy, Damien Martin

2006-01-15

359

Analytical Application of Laser Excited Shpol'Skii Spectroscopy: Direct Identification and Quantitation of Polynuclear Aromatic Compounds.  

National Technical Information Service (NTIS)

The object of the present work is to develop a broader application base for laser exicted Shpol'skii spectroscopy. Potential problems that may emerge are identified and solutions are provided. An atlas of reference spectra useful for the selective identif...

A. E. Elsaid

1986-01-01

360

Analytical application of laser excited shpol'skii spectroscopy: direct identification and quantitation of polynuclear aromatic compounds  

SciTech Connect

The object of the present work is to develop a broader application base for laser exicted Shpol'skii spectroscopy. Potential problems that may emerge are identified and solutions are provided. An atlas of reference spectra useful for the selective identification of individual polycyclic aromatic hydrocarbons (PAHs) has been completed. 210 refs., 83 figs., 5 tabs. (PLG)

Elsaid, A.E.

1986-01-01

361

Quantitative Differential Effects of Rhodamine 123 on Normal Cells and Human Colon Cancer Cells by Magnetic Resonance Spectroscopy  

Microsoft Academic Search

Rhodamine 123 is a lipophilic cationic compound that is selectively taken up by cancer cell mitochondria. This compound is toxic to epithelial cancer cells in vitro and displays significant anticancer activity in vivo. However, the mechanism of action of rhodamine 123 in intact, actively metabolizing cell preparations is unknown. We have used 3~p. and laC- nuclear magnetic resonance spectroscopy to

Samuel Singer; Leo J. Neuringer; William G. Thiily; Lan Bo Chen

1993-01-01

362

Direct, non-destructive quantitative measurement of an active pharmaceutical ingredient in an intact capsule formulation using Raman spectroscopy  

Microsoft Academic Search

The active pharmaceutical ingredient (ambroxol) in an intact capsule formulation has been non-destructively quantified using Raman spectroscopy. To improve the problem of insufficient representive sampling inherent in Raman measurements, we have employed a wide area illumination (WAI) scheme that enables much improved sample coverage through a circular excitation laser spot with a 6mm diameter. One of the anticipated sources of

Jaejin Kim; Jaegeun Noh; Hoeil Chung; Young-Ah Woo; Mark S. Kemper; Youngil Lee

2007-01-01

363

Singlet Delta Oxygen: A Quantitative Analysis Using Off-Axis Integrated-Cavity- Output-Spectroscopy (ICOS).  

National Technical Information Service (NTIS)

A new spectroscopic technique applicable to the detection of ultra- weak and for- bidden molecular transitions is presented. The method is based on off-axis integrated-cavity-output spectroscopy (ICOS). The primary goal for this research effort is to util...

J. E. Gallagher

2006-01-01

364

Near-infrared spectroscopy quantitative determination of pefloxacin mesylate concentration in pharmaceuticals by using partial least squares and principal component regression multivariate calibration.  

PubMed

Pefloxacin mesylate, a broad-spectrum antibacterial fluoroquinolone, has been widely used in clinical practice. Therefore, it is very important to detect the concentration of Pefloxacin mesylate. In this research, the near-infrared spectroscopy (NIRS) has been applied to quantitatively analyze on 108 injection samples, which was divided into a calibration set containing 89 samples and a prediction set containing 19 samples randomly. In order to get a satisfying result, partial least square (PLS) regression and principal components regression (PCR) have been utilized to establish quantitative models. Also, the process of establishing the models, parameters of the models, and prediction results were discussed in detail. In the PLS regression, the values of the coefficient of determination (R(2)) and root mean square error of cross-validation (RMSECV) of PLS regression are 0.9263 and 0.00119, respectively. For comparison, though applying PCR method to get the values of R(2) and RMSECV we obtained are 0.9685 and 0.00108, respectively. And the values of the standard error of prediction set (SEP) of PLS and PCR models are 0.001480 and 0.001140. The result of the prediction set suggests that these two quantitative analysis models have excellent generalization ability and prediction precision. However, for this PFLX injection samples, the PCR quantitative analysis model achieved more accurate results than the PLS model. The experimental results showed that NIRS together with PCR method provide rapid and accurate quantitative analysis of PFLX injection samples. Moreover, this study supplied technical support for the further analysis of other injection samples in pharmaceuticals. PMID:20299275

Xie, Yunfei; Song, Yan; Zhang, Yong; Zhao, Bing

2010-02-21

365

A Rapid and High-Throughput Quantitation Assay of the Nuclear Factor ?B Activity Using Fluorescence Correlation Spectroscopy in the Setting of Clinical Laboratories  

PubMed Central

Background Transcription factor nuclear factor-?B (NF-?B) plays a key role in the regulation of immune responses to inflammation. However, convenient assay systems to quantitate the NF-?B activity level in a timely manner are not available in the setting of clinical laboratories. Therefore, we developed a novel and high-throughput quantitative assay based on fluorescence correlation spectroscopy (FCS) to detect the NF-?B activity level in cellular nuclear extracts and evaluated the performance of this method. The basic principle of this assay is to calculate the binding fraction of NF-?B to fluorescent-labeled DNA probes, which contain NF-?B binding sites. Methods Non-fluorescent competitive probes are employed to normalize the influence of the viscosity of the nuclear extracts between samples and to eliminate the influence of nonspecific binding of the fluorescent probes. To confirm accurate quantitation, human recombinant NF-?B p50 was mixed into U937 cell nuclear extracts, and the binding fraction of the fluorescent probes to NF-?B in the mixture was calculated for quantitation. To evaluate whether this method can be applied to measure the NF-?B activity in human lymphocytes, the NF-?B activity levels of systemic inflammatory response syndrome patients during perioperative periods were measured. Results The percentage recovery was 88.9%. The coefficients of variation of the intra-assay were approximately 10%. NF-?B activity levels during the perioperative period can were successfully measured. The assay time for the FCS measurement was within 20 minutes. Conclusions This assay system can be used to quantitate NF-?B activity levels in a timely manner in the setting of hospital laboratories.

Harada, Kenu; Mikuni, Shintaro; Beppu, Hideyuki; Niimi, Hideki; Abe, Shigeki; Hano, Nobuko; Yamagata, Koichi; Kinjo, Masataka; Kitajima, Isao

2013-01-01

366

Direct Quantitation and Detection of Salmonellae in Biological Samples without Enrichment, Using Two-Step Filtration and Real-Time PCR  

Microsoft Academic Search

A new two-step filtration protocol followed by a real-time PCR assay based on SYBR green I detection was developed to directly quantitate salmonellae in two types of biological samples: i.e., chicken rinse and spent irrigation water. Four prefiltration filters, one type of final filter, and six protocols for recovery of salmonellae from the final filter were evaluated to identify an

Petra F. G Wolffs; Kari Glencross; Romain Thibaudeau; Mansel W. Griffiths

2006-01-01

367

Ordered silicon nanocones arrays for label-free DNA quantitative analysis by surface-enhanced Raman spectroscopy  

NASA Astrophysics Data System (ADS)

Ordered vertical silicon nanocones arrays coated with silver nanoparticles (AgNPs@SiNCs) are developed as surface-enhanced Raman scattering (SERS)-active substrate, which features good uniformity and reliable reproducibility of SERS signals. Label-free DNA at low concentrations (10-8 M) could be quantitatively analyzed via SERS using the AgNPs@SiNCs. The Raman peak at 732 cm-1 due to adenine breathing mode was selected as an endogenous Raman marker for quantitative detection of label-free DNA. The AgNPs@SiNCs as high-performance SERS-active substrates are attractive for surface enhancement mechanism investigation and biochemical sensing applications.

Xu, Ting-Ting; Huang, Jian-An; He, Li-Fang; He, Yao; Su, Shao; Lee, Shuit-Tong

2011-10-01

368

High-field EPR spectroscopy applied to biological systems: characterization of molecular switches for electron and ion transfer.  

PubMed

The last decade witnessed a tremendous growth in combined efforts of biologists, chemists and physicists to understand the dominant factors determining the specificity and directionality of transmembrane transfer processes in proteins. A large variety of experimental techniques is being used including X-ray and neutron diffraction, but also time-resolved optical, infrared and magnetic resonance spectroscopy. This is done in conjunction with genetic engineering strategies to construct site-specific mutants for controlled modification of the proteins. As a general perception of these efforts, the substantial influence of weak interactions within the protein and its membrane interfaces is recognized. The weak interactions are subject to subtle changes during the reaction cycle owing to the inherent flexibility of the protein-membrane complex. Specific conformational changes accomplish molecular-switch functions for the transfer process to proceed with optimum efficiency. Characteristic examples of time varying non-bonded interactions are specific H-patterns and/or polarity effects of the microenvironment. The present perception has emerged from the coupling of newly developed spectroscopic techniques - and advanced EPR certainly deserves credit in this respect - with newly developed computational strategies to interpret the experimental data in terms of protein structure and dynamics. By now, the partners of this coupling, particularly high-field EPR spectroscopy and DFT-based quantum theory, have reached a level of sophistication that applications to large biocomplexes are within reach. In this review, a few large paradigm biosystems are surveyed which were explored lately in our laboratory. Taking advantage of the improved spectral and temporal resolution of high-frequency/high-field EPR at 95 GHz/3.4 T and 360 GHz/12.9 T, as compared to conventional X-band EPR (9.5 GHz/0.34 T), three biosystems are characterized with respect to structure and dynamics: (1) Light-induced electron-transfer intermediates in wild-type and mutant reaction-centre proteins from the photosynthetic bacterium Rhodobacter sphaeroides, (2) light-driven proton-transfer intermediates of site-specifically nitroxide spin-labelled mutants of bacteriorhodopsin proteins from Halobacterium salinarium, (3) refolding intermediates of site-specifically nitroxide spin-labelled mutants of the channel-forming protein domain of Colicin A bacterial toxin produced in Escherichia coli. The detailed information obtained is complementary to that of protein crystallography, solid-state NMR, infrared and optical spectroscopy techniques. A unique strength of high-field EPR is particularly noteworthy: it can provide highly desired detailed information on transient intermediates of proteins in biological action. They can be observed and characterized while staying in their working states on biologically relevant time scales. The review introduces the audience to origins and basic experiments of EPR in relation to NMR, describes the underlying strategies for extending conventional EPR to high-field/high-frequency EPR, and highlights those details of molecular information that are obtained from high-field EPR in conjunction with genetic engineering and that are not accessible by "classical" spectroscopy. The importance of quantum-chemical interpretation of the experimental data by DFT and advanced semiempirical molecular-orbital theory is emphasized. A short description of the laboratory-built 95 GHz and 360 GHz EPR/ENDOR spectrometers at FU Berlin is also presented. The review concludes with an outlook to future opportunities and challenges of advanced bio-EPR in interdisciplinary research. PMID:19785170

Möbius, K; Savitsky, A; Schnegg, A; Plato, M; Fuchst, M

2005-01-01

369

Determination of phytic acid by gas chromatography-mass spectroscopy: application to biological samples.  

PubMed

A GC-MS method is reported for the determination of phytic acid based on purification by anion-exchange chromatography, enzymatic hydrolysis of phytic acid to myo-inositol and derivation to trimethylsilyl derivative, with scyllo-inositol as an internal standard. Analytical features of the method are: limit of detection 9 microg l(-1) phytic acid, linear working range 18-500 microg l(-1) phytic acid, and coefficient of variation 1.9%. The method has been successfully applied to a variety of biological samples: various rat organs (kidney, liver, brain and bone), human plasma and urine and kidney stones. A comparative study of sample treatments, including deproteization, lipid extraction and the presence of a chelator, is also reported. Phytic acid amounts found in rat organs ranged from 1.07 g kg(-1) for bone to 32.0 g kg(-1) for brain. Phytic acid in human plasma was of the order of 0.14 mg l(-1). In kidney stones, phytic acid was found in calcium containing stones. PMID:11417869

March, J G; Simonet, B M; Grases, F

2001-06-15

370

Applications of High Resolution Laser Induced Breakdown Spectroscopy for Environmental and Biological Samples  

SciTech Connect

This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

Martin, Madhavi Z [ORNL; Labbe, Nicole [ORNL; Wagner, Rebekah J. [Pennsylvania State University, University Park, PA

2013-01-01

371

Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics  

NASA Astrophysics Data System (ADS)

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.

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

372

Salicylate Detection by Complexation with Iron(III) and Optical Absorbance Spectroscopy: An Undergraduate Quantitative Analysis Experiment  

ERIC Educational Resources Information Center

|An experiment for the undergraduate quantitative analysis laboratory involving applications of visible spectrophotometry is described. Salicylate, a component found in several medications, as well as the active by-product of aspirin decomposition, is quantified. The addition of excess iron(III) to a solution of salicylate generates a deeply…

Mitchell-Koch, Jeremy T.; Reid, Kendra R.; Meyerhoff, Mark E.

2008-01-01

373

Near infrared spectroscopy in combination with chemometrics as a process analytical technology (PAT) tool for on-line quantitative monitoring of alcohol precipitation.  

PubMed

The application of near infrared (NIR) spectroscopy for on-line quantitative monitoring of alcohol precipitation of the Danhong injection was investigated. For the NIR measurements, two fiber optic probes designed to transmit NIR radiation through a 2mm path length flow cell were applied to collect spectra in real-time. Particle swarm optimization- (PSO-) based least square support vector machines (LS-SVM) and partial least squares (PLS) models were developed for quantitative analysis of the critical intermediate quality attributes: the soluble solid content (SSC) and concentrations of danshensu (DSS), protocatechuic aldehyde (PA), hydroxysafflor yellow A (HSYA) and salvianolic acid B (SAB). The optimal models were then used for on-line quantitative monitoring of alcohol precipitation. The results showed that the PSO-based LS-SVM with a radial basis function (RBF) kernel was slightly better than the conventional PLS method, even though both methods exhibited satisfactory fitting results and predictive abilities. In this study, successful models were built and applied on-line; these models proffer real-time data and instant feedback about alcohol precipitation. PMID:23357639

Jin, Ye; Wu, Zengzeng; Liu, Xuesong; Wu, Yongjiang

2013-01-11

374

In Situ Adsorption Studies at the Solid/Liquid Interface:Characterization of Biological Surfaces and Interfaces Using SumFrequency Generation Vibrational Spectroscopy, Atomic Force Microscopy,and Quartz Crystal Microbalance  

SciTech Connect

Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and quartz crystal microbalance (QCM) have been used to study the molecular surface structure, surface topography and mechanical properties, and quantitative adsorbed amount of biological molecules at the solid-liquid interface. The molecular-level behavior of designed peptides adsorbed on hydrophobic polystyrene and hydrophilic silica substrates has been examined as a model of protein adsorption on polymeric biomaterial surfaces. Proteins are such large and complex molecules that it is difficult to identify the features in their structure that lead to adsorption and interaction with solid surfaces. Designed peptides which possess secondary structure provide simple model systems for understanding protein adsorption. Depending on the amino acid sequence of a peptide, different secondary structures ({alpha}-helix and {beta}-sheet) can be induced at apolar (air/liquid or air/solid) interfaces. Having a well-defined secondary structure allows experiments to be carried out under controlled conditions, where it is possible to investigate the affects of peptide amino acid sequence and chain length, concentration, buffering effects, etc. on adsorbed peptide structure. The experiments presented in this dissertation demonstrate that SFG vibrational spectroscopy can be used to directly probe the interaction of adsorbing biomolecules with a surface or interface. The use of well designed model systems aided in isolation of the SFG signal of the adsorbing species, and showed that surface functional groups of the substrate are sensitive to surface adsorbates. The complementary techniques of AFM and QCM allowed for deconvolution of the effects of surface topography and coverage from the observed SFG spectra. Initial studies of biologically relevant surfaces are also presented: SFG spectroscopy was used to study the surface composition of common soil bacteria for use in bioremediation of nuclear waste.

Phillips, D.C.

2006-05-16

375

The use of Fourier-transform infrared spectroscopy for the quantitative determination of glucose concentration in whole blood  

NASA Astrophysics Data System (ADS)

Fourier-transform infrared transmission spectroscopy has been used for the determination of glucose concentration in whole blood samples from 28 patients. A 4-vector partial least-squares calibration model, using the spectral range 950-1200 cm-1, yielded a standard-error-of-prediction of 0.59 mM for an independent test set. For blood samples from a single patient, we found that the glucose concentration was proportional to the difference between the values of the second derivative spectrum at 1082 cm-1 and 1093 cm-1. This indicates that spectroscopy at these two specific wavenumbers alone could be used to determine the glucose concentration in blood plasma samples from a single patient, with a prediction error of 0.95 mM.

Shen, Y. C.; Davies, A. G.; Linfield, E. H.; Elsey, T. S.; Taday, P. F.; Arnone, D. D.

2003-07-01

376

Establishing the gas phase dimerization of niobium(V) fluoride and tantalum(V) fluoride by quantitative Raman spectroscopy  

Microsoft Academic Search

The vapors of NbF5 and TaF5 have been investigated by Raman spectroscopy in the temperature range 475–675K and at total pressures from ?0.1 to ?4.0atm. The temperature and pressure dependence of the spectra is indicative of equilibrium shifts between monomer and associated (polymer) gaseous species. The intensities of Raman bands, which were characteristic of the various species present, were exploited

S. Boghosian; E. A. Pavlatou; G. N. Papatheodorou

2005-01-01

377

High-Resolution NMR Spectroscopy: An Alternative Fast Tool for Qualitative and Quantitative Analysis of Diacylglycerol (DAG) Oil  

Microsoft Academic Search

Multinuclear (1H, 13C, 31P) and multidimensional NMR spectroscopy was employed for the analysis of diacylglycerol (DAG) oil and the quantification\\u000a of its acylglycerols and acyl chains composition. A number of gradient selected two dimensional NMR techniques (TOCSY, HSQC-DEPT,\\u000a HSQC-TOCSY, and HMBC) facilitated the assignment of the complex one dimensional 1H- and 13C-NMR spectra. In several cases, the aforementioned 2D-NMR techniques

Emmanuel Hatzakis; Alexia Agiomyrgianaki; Sarantos Kostidis; Photis Dais

378

Rapid evaluation and quantitative analysis of thyme, origano and chamomile essential oils by ATR-IR and NIR spectroscopy  

Microsoft Academic Search

The essential oils obtained from various chemotypes of thyme, origano and chamomile species were studied by ATR\\/FT-IR as well as NIR spectroscopy. Application of multivariate statistics (PCA, PLS) in conjunction with analytical reference data leads to very good IR and NIR calibration results. For the main essential oil components (e.g. carvacrol, thymol, ?-terpinene, ?-bisabolol and ?-farnesene) standard errors are in

Hartwig Schulz; Rolf Quilitzsch; Hans Krüger

2003-01-01

379

Identification of antibody isotypes in biological fluids by means of micro-Raman spectroscopy and chemometric methods  

NASA Astrophysics Data System (ADS)

Clinical diagnosis of infections, generally are realized by serological methods, which identifies the antibodies presents in serum or tissue fluids of the patient. Antibodies are proteins present in our bodies that aid in the elimination of pathogens or antigens. Identification of antibodies isotypes is important because can help to predict when and whether patients will recover from infections and are commonly diagnosed by means of indirect methods such as serological test. In the other hand, the majority of these methods requires specific kits for the analysis, special sample preparation, chemical reagents, expensive equipment and require long time for getting results. In this work we show the feasibility to discriminate antibody isotypes in biological fluids like human colostrum by means of Raman spectroscopy and chemometrics. Spectra were obtained using an excitation wavelength of 514 nm over dried samples of human colostrum labeled previously as positives to specific IgG and IgM antibodies against Toxoplasma Gondii by means of ELISA test. Partial least square-discriminant analysis (PLS-DA) was used to discriminate among antibody isotypes by use second derivative of Raman spectra of colostrum samples.

Araujo-Andrade, C.; Pichardo-Molina, J. L.; Barbosa-Sabanero, G.; Frausto-Reyes, C.

2008-03-01

380

Quantitative Applications of Deep-Sea Raman Spectroscopy: Geochemistry of 1,4- thioxane in sea water  

Microsoft Academic Search

We have developed quantitative Raman spectroscopic techniques for the novel detection of dissolved species in sea water to determine their fundamental properties. In this example we use a field-deployable Raman system to determine the solubility of 1,4-thioxane (TO) in sea water as 0.65 to 0.63 mol\\/kg H2O between 4.5°C and 25.0°C (which varies greatly from an earlier report of 2.75

X. Zhang; K. C. Hester; P. M. Walz; E. T. Peltzer; P. G. Brewer

2008-01-01

381

Quantitative analysis of retinol and retinol palmitate in vitamin tablets using 1 H -nuclear magnetic resonance spectroscopy  

Microsoft Academic Search

1H-NMR spectrometry was applied to the quantitative analysis of Vitamin A in four different types of vitamin tablets without any chromatographic purification or saponification. The experiment was performed analysing the H-15 resonance, which appears at ? 4.32 for retinol and ? 4.69 for retinol palmitate, well separated from other resonances in the 1H-NMR spectrum. Compounds were quantified using the relative

Young Hae Choi; Hye Kyong Kim; Erica G Wilson; Cornelis Erkelens; Ben Trijzelaar; Robert Verpoorte

2004-01-01

382

Quantitative analysis of natural rubber, polybutadiene rubber and styrene\\/butadiene rubber blends by infra-red spectroscopy  

Microsoft Academic Search

Infra-red spectra of natural rubber (NR), polybutadiene rubber (PBR) and styrene butadiene rubber (SBR) have been studied for the estimation of these polymers in ternary rubber blends. A study of different infra-red active bands suggests that the bands at 1316 Cm-1, 1379 Cm-1 and 1493 Cm-1 are most appropriate for quantitative purpose. A detailed analysis of observed data has been

V. K. Kaushik; Y. N. Sharma

1985-01-01

383

Rapid separation and quantitation of curcuminoids combining pseudo two-dimensional liquid flash chromatography and NMR spectroscopy.  

PubMed

Rapid separation, characterization and quantitation of curcuminoids are important owing to their numerous pharmacological properties including antimicrobial, antiviral, antifungal, anticancer, and anti-inflammatory activities. In the present study, pseudo two-dimensional liquid flash chromatography was used for the separation of four curcuminoids (curcumin, demethoxy curcumin, bisdemethoxy curcumin and dihydro bisdemethoxy curcumin) for the first time. Silica and diol columns were used for separation of curcuminoids using gradient mobile phase. The separated peaks were monitored at 244, 360nm to obtain four compounds. The purity of compounds were determined by rapid quantitative (1)H NMR (qNMR) using 3-(trimethylsilyl) propionic-(2,2,3,3-d4) acid sodium salt (TSP-d4) (0.012%) in D2O. These results were compared with those obtained by HPLC method. The purity of isolated curcuminoids using pseudo 2D chromatography was found to be in the range of 92.4-95.45%. The structures of these compounds were characterized unambiguously using (13)C (APT) NMR spectra. The developed pseudo 2D separation technique has the advantage of simplified automation with shorter run time compared to conventional separation techniques. The method that combines rapid pseudo 2D separation and simple quantitation using qNMR reported herein can be of wide utility for routine analysis of curcuminoids in complex mixtures. PMID:24013126

Jayaprakasha, G K; Nagana Gowda, G A; Marquez, Sixto; Patil, Bhimanagouda S

2013-08-16

384

Research in quantitative microscopic X-ray fluorescence analysis  

Microsoft Academic Search

A feasibility study of quantitative elemental microanalysis of biological materials and glass samples by microbeam X-ray fluorescence spectroscopy was completed. The research included testing the homogeneity of existing standards for X-ray fluorescence calibration and verification of a fundamental parameters method for quantitative analysis. The goal was to evaluate the X-ray fluorescence spectrometer as a tool for elemental analysis at the

M. Lankosz; M. Szczerbowska-Boruchowska; J. Chwiej; J. Ostachowicz; A. Simionovici; S. Bohic

2004-01-01

385

The Use of Confocal Raman Spectroscopy to Quantitatively Study the Interactions Between Immersive Water and Graphene/Graphene Oxide Surfaces  

NASA Astrophysics Data System (ADS)

The unique mechanical, chemical, optical, and electrical properties of graphene allow for many potential applications in biomaterials. Understanding and quantifying the surface interactions between graphene/graphene oxide and aqueous liquid is essential for the design of such graphene-based nanocomposites. Graphene sheets were produced by the mechanical exfoliation of graphite. We have used depth Confocal Raman Spectroscopy (CRM) profiles to measure graphene wettability using a water immersive objective lens, and demonstrated how surface energy between graphene/graphene oxide and immersive aqueous liquid can be affected to simultaneously measure the depth image profiles. Contact angles were also measured to further investigate the compatibility between graphene/graphene oxide and its environment.

Narcross, Hannah; Jeon, Byung Ho; Lee, Jong-Won; Ryu, Chang Yeol

2012-02-01

386

Identification and quantitative determination of carbohydrates in ethanolic extracts of two conifers using 13C NMR spectroscopy.  

PubMed

We developed a method for the direct identification and quantification of carbohydrates in raw vegetable extracts using (13)C NMR spectroscopy without any preliminary step of precipitation or reduction of the components. This method has been validated (accuracy, precision and response linearity) using pure compounds and artificial mixtures before being applied to authentic ethanolic extracts of pine needles, pine wood and pine cones and fir twigs. We determined that carbohydrates represented from 15% to 35% of the crude extracts in which pinitol was the principal constituent accompanied by arabinitol, mannitol, glucose and fructose. PMID:18299126

Duquesnoy, Emilie; Castola, Vincent; Casanova, Joseph

2008-01-12

387

Use of FT-NIR transmission spectroscopy for the quantitative analysis of an active ingredient in a translucent pharmaceutical topical gel formulation.  

PubMed

The objective of this study was to demonstrate the use of transmission Fourier transform near-infrared (FT-NIR) spectroscopy for quantitative analysis of an active ingredient in a translucent gel formulation. Gels were prepared using Carbopol 980 with 0%, 1%, 2%, 4%, 6%, and 8% ketoprofen and analyzed with an FT-NIR spectrophotometer operated in the transmission mode. The correlation coefficient of the calibration was 0.9996, and the root mean squared error of calibration was 0.0775%. The percent relative standard deviation for multiple measurements was 0.10%. The results prove that FT-NIR can be a good alternative to other, more time-consuming means of analysis for these types of formulations. PMID:11741274

Kemper, M S; Magnuson, E J; Lowry, S R; McCarthy, W J; Aksornkoae, N; Watts, D C; Johnson, J R; Shukla, A J

2001-01-01

388

Quantitative determination of wear metals in engine oils using laser-induced breakdown spectroscopy: A comparison between liquid jets and static liquids  

NASA Astrophysics Data System (ADS)

A comparison of laser-induced breakdown spectroscopy (LIBS) sensitivity in laminar liquid jets and at the surface of a static liquid has been performed. Limits of detection (LODs) have been estimated for Na, Mg, Al, Ca, Ti, V, Cr, Mn, Ni, Fe, Cu, Zn, Mo, Ag, Cd, and Ba under similar conditions using both experimental arrangements. LODs in liquid jets are found to be four times lower on average compared to measurements at static surfaces. Data acquisition rates in jet experiments are also generally higher than for static liquids due to reduced problems with splashing effects. The use of LIBS in jets has also been investigated for quantitative analysis of used lubricants. A number of contaminants have been measured in a set of used engine oils and the results compared to analysis via ICP-AES, where a good correlation is obtained.

Yaroshchyk, Pavel; Morrison, Richard J. S.; Body, Doug; Chadwick, Bruce L.

2005-08-01

389

Nanometer-scale, quantitative composition mappings of InGaN layers from a combination of scanning transmission electron microscopy and energy dispersive x-ray spectroscopy.  

PubMed

Using elastic scattering theory we show that a small set of energy dispersive x-ray spectroscopy (EDX) measurements is sufficient to experimentally evaluate the scattering function of electrons in high-angle annular dark field scanning transmission microscopy (HAADF-STEM). We then demonstrate how to use this function to transform qualitative HAADF-STEM images of InGaN layers into precise, quantitative chemical maps of the indium composition. The maps obtained in this way combine the resolution of HAADF-STEM and the chemical precision of EDX. We illustrate the potential of such chemical maps by using them to investigate nanometer-scale fluctuations in the indium composition and their impact on the growth of epitaxial InGaN layers. PMID:23089619

Pantzas, K; Patriarche, G; Troadec, D; Gautier, S; Moudakir, T; Suresh, S; Largeau, L; Mauguin, O; Voss, P L; Ougazzaden, A

2012-10-22

390

Quantitative determination of the oxidation state of iron in biotite using x-ray photoelectron spectroscopy: II. In situ analyses  

SciTech Connect

X-ray photoelectron spectroscopy (XPS) was used to determine Fe(III)/{Sigma}Fe in individual biotite crystals in thin sections of ten metapelites and one syenite. The in situ XPS analyses of Fe(III)/{Sigma}Fe in biotite crystals in the metapelites were compared with published Fe(III)/{Sigma}Fe values determined by Moessbauer spectroscopy (MS) for mineral separates from the same hand samples. The difference between Fe(III)/{Sigma}Fe by the two techniques was greatest for samples with the lowest Fe(III)/{Sigma}Fe (by MS). For eight metamorphic biotites with Fe(III)/{Sigma}Fe = 9-27% comparison of the two techniques yielded a linear correlation of r = 0.94 and a statistically acceptable fit of [Fe(III)/{Sigma}Fe]{sub xps} = [Fe(III)/{Sigma}Fe]{sub ms}. The difference between Fe(III)/{Sigma}Fe by the two techniques was greater for two samples with Fe(III)/{Sigma}Fe {le} 6% (by MS). For biotite in the syenite sample, Fe(III)/{Sigma}Fe determined by both in situ XPS and bulk wet chemistry/electron probe microanalysis were similar. This contribution demonstrates that XPS can be used to analyze bulk Fe(III)/{Sigma}Fe in minerals in thin sections when appropriate precautions taken to avoid oxidation of the near-surface during preparation of samples. 25 refs., 3 figs., 4 tabs.

Raeburn, S.P. [Pennsylvania State Univ., University Park, PA (United States)]|[Lehigh Univ., Bethlehem, PA (United States); Ilton, E.S. [Lehigh Univ., Bethlehem, PA (United States); Veblen, D.R. [Johns Hopkins Univ., Baltimore, MD (United States)

1997-11-01

391

Quantitative determination of nutrient content in poultry manure by near infrared spectroscopy based on artificial neural networks.  

PubMed

Excessively applied manure contains a considerable amount of nutrient content such as nitrogen and phosphorus that could potentially pollute groundwater and soil. The present paper evaluated the use of nonlinear regression methods, such as artificial neural networks (ANN), for developing near infrared reflectance spectroscopy calibration models to predict nutrient content in poultry manure. Four representative nutrient ingredients (ammonia nitrogen, AN; total potassium, TK; total nitrogen, TN; total phosphorus, TP) in poultry manure were selected for evaluating ANN feasibility using 91 diverse samples in which three-fourths of the samples were used as a training set and one-fourth as a validation set. The performance of the ANN models was compared with the partial least squares (PLS) models. We found that the ANN models for all 4 nutrient contents consistently gave better predictions than PLS models. The ratios of prediction to deviation of 2.62 (AN), 1.51 (TK), 2.75 (TN), and 2.01 (TP) with the PLS models were improved to 3.02 (AN), 1.74 (TK), 3.41 (TN), and 2.71 (TP) with the corresponding ANN models. These findings demonstrated that the near infrared reflectance spectroscopy model based on the ANN method may be an appropriate tool to predict nutrient content in poultry manure. PMID:19903946

Chen, L J; Xing, L; Han, L J

2009-12-01

392

Quantitative speciation of Mn-bearing particulates emitted from autos burning (methylcyclopentadienyl)manganese tricarbonyl-added gasolines using XANES spectroscopy  

SciTech Connect

The chemical nature of Mn-containing particulates emitted from (methylcyclopentadienyl)manganese tricarbonyl-added gasoline engines has been elucidated using Mn K-edge X-ray absorption fine structure (XAFS) spectroscopy. Edge shift data from the X-ray absorption near-edge structure (SANES) spectra showed that the average Mn valence in these particulates is {approximately}2.2. Using a principal component analysis (PCA) algorithm, the number and type of probable species contained in these particulates were determined to be three, consisting of Mn{sub 3}O{sub 4}, MnSO{sub 4}{sm_bullet}H{sub 2}O, and a divalent manganese phosphate, Mn{sub 5}(PO{sub 4})[PO{sub 3}(OH)]{sub 2}{sm_bullet}4H{sub 2}O. The proportions of these Mn phases in each particulate sample were evaluated quantitatively using least-squares fitting (LSF) of the experimental XANES spectra with linear combinations of these principal component (model compound) spectra. Two groups of Mn-bearing particulates may be distinguished: group I having 4--9 wt % of Mn{sub 3}O{sub 4} and exhibiting a single intense first major absorption maximum at the Mn K-edge and group II containing 15--22 wt % of Mn{sub 3}O{sub 4} and exhibiting a doublet absorption maximum at lower intensity. Fourier transforms of the EXAFS signals were found to corroborate the XANES results. This study clearly establishes XANES spectroscopy, in combination with PCA and LSF, as a quantitative analytical tool for speciation of dilute and/or amorphous multicomponent environmental materials not easily attainable with conventional methods.

Ressler, T.; Wong, J.; Roos, J.; Smith, I.L.

2000-03-15

393

Quantitative data on blood flow during tumor PDT obtained by laser Doppler spectroscopy in the hen's egg test system  

NASA Astrophysics Data System (ADS)

Oxygen supply is the most important requirement of type II photodynamic reactions. Prerequisite in photodynamic tumor therapy is an intact tumor blood flow during irradiation. Most photosensitizers destroy tumor vessels due to accumulation in endothelial cells. As a prerequisite to develop novel photosensitizing drugs an in-vivo test system is required to quantitatively assess for inertness of those sensitizers to the blood supply. We adapted and further developed a system capable of measuring the relative oxygen supply to heterotransplanted tumors on the yolk sac membrane (YSM) of fertilized chicken eggs.

Vervoorts, Anja; Rood, H. A.; Klotz, Marcus; Moser, Joerg G.; Rosenbruch, Martin

1995-01-01

394

Quantitative 3.0T MR Spectroscopy Reveals Decreased Creatine Concentration in the Dorsolateral Prefrontal Cortex of Patients with Social Anxiety Disorder  

PubMed Central

Background The brain biochemical changes of social anxiety have not been clarified although there have been a limited number of MR spectroscopic studies which utilized metabolite/creatine ratios. Present study aimed to explore the alteration of absolute metabolite concentration in social anxiety disorder using quantitative MR spectroscopy. Materials and Methods With a 3.0T MR scanner, single voxel MR spectroscopy (stimulated echo acquisition mode, TR/TE/TM?=?2000/20/16 ms) was performed in the left dorsolateral prefrontal cortex and related regions of nine medication-free patients with social anxiety disorder and nine controls. Absolute metabolite concentration was calculated using tissue water as the internal reference and corrected for the partial volume of cerebrospinal fluid. Results In the left dorsolateral prefrontal cortex, the N-acetyl aspartate/creatine ratio of patients was significantly higher than that of controls, and this was due to the decrease of creatine concentration instead of the increase of N-acetyl aspartate concentration. Furthermore, the creatine concentration of the left dorsolateral prefrontal cortex was negatively correlated with the scores of Liebowitz social anxiety scale. Conclusions The alteration of creatine level in the left dorsolateral prefrontal cortex suggests abnormal energy metabolism and correlates with symptom severity in social anxiety disorder. And metabolite concentration is preferable to metabolite/creatine ratio for the investigation of individual, absolute metabolite changes in this region of social anxiety disorder.

Nie, Xiaojing; Wu, Qizhu; Li, Jun; Zhang, Wei; Huang, Xiaoqi; Gong, Qiyong

2012-01-01

395

Raman Spectroscopy.  

ERIC Educational Resources Information Center

Reviews literature on Raman spectroscopy from late 1981 to late 1983. Topic areas include: instrumentation and sampling; liquids and solutions; gases and matrix isolation; biological molecules; polymers; high-temperature and high-pressure studies; Raman microscopy; thin films and surfaces; resonance-enhanced and surface-enhanced spectroscopy; and…

Gerrard, Donald L.

1984-01-01

396

Raman Spectroscopy.  

ERIC Educational Resources Information Center

|Reviews literature on Raman spectroscopy from late 1981 to late 1983. Topic areas include: instrumentation and sampling; liquids and solutions; gases and matrix isolation; biological molecules; polymers; high-temperature and high-pressure studies; Raman microscopy; thin films and surfaces; resonance-enhanced and surface-enhanced spectroscopy; and…

Gerrard, Donald L.

1984-01-01

397

Quantitative assessment of the hepatic pharmacokinetics of the antimicrobial sitafloxacin in humans using in vivo 19F magnetic resonance spectroscopy  

PubMed Central

Aims To measure hepatic concentrations of the fluorine-containing antimicrobial, sitafloxacin, using in vivo 19F magnetic resonance spectroscopy (MRS). Methods Data were acquired from eight healthy subjects at 2, 5, 8 and 24 h following doses of 500 mg day?1 for 5 days using a 1H/19F surface coil in a 1.5T clinical MR system. Tissue water was used as a reference. Results Estimated liver concentrations at 2 h were 15.0 ± 4.0 µg ml?1 (mean ± 95% CI), compared with 3.54 ± 0.58 µg ml?1 in plasma (n = 6), and fell below threshold concentrations (2 µg ml?1) by 24 h. Conclusions 19F MRS is able to detect and quantify sitafloxacin in the liver. There was no evidence for the hepatic retention of the drug.

Payne, Geoffrey S; Collins, David J; Loynds, Peter; Mould, Graham; Murphy, Philip S; Dzik-Jurasz, Andrzej S K; Kessar, Preminda; Haque, Nazneen; Yamaguchi, Masayuki; Atarashi, Shogo; Leach, Martin O

2005-01-01

398

Quantitative evaluation of multiple adulterants in roasted coffee by Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) and chemometrics.  

PubMed

The current study presents an application of Diffuse Reflectance Infrared Fourier Transform Spectroscopy for detection and quantification of fraudulent addition of commonly employed adulterants (spent coffee grounds, coffee husks, roasted corn and roasted barley) to roasted and ground coffee. Roasted coffee samples were intentionally blended with the adulterants (pure and mixed), with total adulteration levels ranging from 1% to 66% w/w. Partial Least Squares Regression (PLS) was used to relate the processed spectra to the mass fraction of adulterants and the model obtained provided reliable predictions of adulterations at levels as low as 1% w/w. A robust methodology was implemented that included the detection of outliers. High correlation coefficients (0.99 for calibration; 0.98 for validation) coupled with low degrees of error (1.23% for calibration; 2.67% for validation) confirmed that DRIFTS can be a valuable analytical tool for detection and quantification of adulteration in ground, roasted coffee. PMID:24054633

Reis, Nádia; Franca, Adriana S; Oliveira, Leandro S

2013-06-14

399

The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source.  

PubMed

The 18ID undulator beamline of the Biophysics Collaborative Access Team at the Advanced Photon Source, Argonne, IL, USA, is a high-performance instrument designed for, and dedicated to, the study of partially ordered and disordered biological materials using the techniques of small-angle X-ray scattering, fiber diffraction, and X-ray absorption spectroscopy. The beamline and associated instrumentation are described in detail and examples of the representative experimental results are presented. PMID:15310956

Fischetti, R; Stepanov, S; Rosenbaum, G; Barrea, R; Black, E; Gore, D; Heurich, R; Kondrashkina, E; Kropf, A J; Wang, S; Zhang, Ke; Irving, T C; Bunker, G B

2004-08-17

400

Quantitative NMR spectroscopy of complex technical mixtures using a virtual reference: chemical equilibria and reaction kinetics of formaldehyde-water-1,3,5-trioxane.  

PubMed

Quantitative 1H NMR spectroscopy was used to study chemical equilibria and reaction kinetics of both the formation and decomposition of 1,3,5-trioxane in aqueous formaldehyde solutions. The reaction was homogeneously catalyzed with up to 0.10 g g(-1) sulfuric acid at temperatures between 360 and 383 K so that most of the experiments had to be carried out pressurized. The studied mixtures were complex due to the formation of methylene glycol and poly(oxymethylene) glycols in aqueous formaldehyde and the presence of considerable amounts of ionized species. Most common internal standards are decomposed by the hot sulfuric acid and external standards were not applicable using the flow NMR probe or pressurizable NMR sample tubes. Therefore, for the quantification of the small trioxane signals, a novel procedure was applied, in which electronically generated NMR signals were used as highly stable Virtual References (VR). The NMR decoupler channel with wave-form generator was used as the source of the reference signal, which was irradiated into the probe using the lock coil. Details on the experimental procedure are presented. It is shown that the presented method yields reliable quantitative reaction data for the complex studied mixtures. PMID:16773212

Maiwald, Michael; Grützner, Thomas; Ströfer, Eckhard; Hasse, Hans

2006-05-12

401

Principles, performance, and applications of spectral reconstitution (SR) in quantitative analysis of oils by Fourier transform infrared spectroscopy (FT-IR).  

PubMed

Spectral reconstitution (SR) is a dilution technique developed to facilitate the rapid, automated, and quantitative analysis of viscous oil samples by Fourier transform infrared spectroscopy (FT-IR). This technique involves determining the dilution factor through measurement of an absorption band of a suitable spectral marker added to the diluent, and then spectrally removing the diluent from the sample and multiplying the resulting spectrum to compensate for the effect of dilution on the band intensities. The facsimile spectrum of the neat oil thus obtained can then be qualitatively or quantitatively analyzed for the parameter(s) of interest. The quantitative performance of the SR technique was examined with two transition-metal carbonyl complexes as spectral markers, chromium hexacarbonyl and methylcyclopentadienyl manganese tricarbonyl. The estimation of the volume fraction (VF) of the diluent in a model system, consisting of canola oil diluted to various extents with odorless mineral spirits, served as the basis for assessment of these markers. The relationship between the VF estimates and the true volume fraction (VF(t)) was found to be strongly dependent on the dilution ratio and also depended, to a lesser extent, on the spectral resolution. These dependences are attributable to the effect of changes in matrix polarity on the bandwidth of the ?(CO) marker bands. Excellent VF(t) estimates were obtained by making a polarity correction devised with a variance-spectrum-delineated correction equation. In the absence of such a correction, SR was shown to introduce only a minor and constant bias, provided that polarity differences among all the diluted samples analyzed were minimal. This bias can be built into the calibration of a quantitative FT-IR analytical method by subjecting appropriate calibration standards to the same SR procedure as the samples to be analyzed. The primary purpose of the SR technique is to simplify preparation of diluted samples such that only approximate proportions need to be adhered to, rather than using exact weights or volumes, the marker accounting for minor variations. Additional applications discussed include the use of the SR technique in extraction-based, quantitative, automated FT-IR methods for the determination of moisture, acid number, and base number in lubricating oils, as well as of moisture content in edible oils. PMID:23601545

García-González, Diego L; Sedman, Jacqueline; van de Voort, Frederik R

2013-04-01

402

A Novel HPLC Method for the Concurrent Analysis and Quantitation of Seven Water-Soluble Vitamins in Biological Fluids (Plasma and Urine): A Validation Study and Application  

PubMed Central

An HPLC method was developed and validated for the concurrent detection and quantitation of seven water-soluble vitamins (C, B1, B2, B5, B6, B9, B12) in biological matrices (plasma and urine). Separation was achieved at 30°C on a reversed-phase C18-A column using combined isocratic and linear gradient elution with a mobile phase consisting of 0.01% TFA aqueous and 100% methanol. Total run time was 35 minutes. Detection was performed with diode array set at 280 nm. Each vitamin was quantitatively determined at its maximum wavelength. Spectral comparison was used for peak identification in real samples (24 plasma and urine samples from abstinent alcohol-dependent males). Interday and intraday precision were <4% and <7%, respectively, for all vitamins. Recovery percentages ranged from 93% to 100%.

Grotzkyj Giorgi, Margherita; Howland, Kevin; Martin, Colin; Bonner, Adrian B.

2012-01-01

403

Beyond Pandora’s Box: quantitatively evaluating non-target effects of parasitoids in classical biological control  

Microsoft Academic Search

A seminal paper by Howarth (Proc Hawaii Entomol Soc 24:239–244, 1983) entitled “Classical biological control: Panacea or Pandora’s\\u000a Box” ignited a sometimes acrimonious debate over the relative safety of introductions for classical biological control. Extolled\\u000a for years as environmentally benign, the litany of negative non-target effects profiled by Howarth heightened awareness of\\u000a this issue. Several factors have muddied this debate

Dylan Parry

2009-01-01

404

Quantitative analysis of CN/TiCN/TiN multilayers and their thermal stability by Auger electron spectroscopy and Rutherford backscattering spectrometry depth profiles  

SciTech Connect

CN/TiCN/TiN multilayers and the respective single layers have been deposited on Si(100) substrates using a dual ion-beam sputtering system. Both the multilayers and the respective single layers have been chemically characterized by Auger electron spectroscopy (AES) depth profiling combined with factor analysis and by Rutherford backscattering spectrometry (RBS). The combination of AES and RBS allows a quantitative chemical characterization of the multilayer and the respective single layers. Whereas RBS has some difficulties to determine the in-depth distribution of the light elements along the multilayer, AES depth profiling enables their quantitative analysis and even their chemical state along the multilayer. On the contrary, RBS shows its advantages to determine the heavy elements, including the contaminants incorporated during the deposition process (e.g., W). Under special experimental conditions it is shown that RBS is able to determine the composition of the single layers (i.e., CN/Si, TiCN/Si, and TiN/Si) in good agreement with AES depth profiling. As a result of this complementary use we obtain a complete quantitative chemical characterization of the single layers and multilayers. In addition, the thermal stability of the multilayers upon heating for 1 h in vacuum and ambient atmospheres at 500 deg. C has been studied by AES depth profiling. The results show that whereas the multilayer is stable in vacuum it undergoes significant changes when it is heated in air. In fact, it is shown that annealing in air for 1 h causes the disappearance of the CN top layer and the oxidation of the TiCN layer that leads to the formation of TiO{sub 2} on its surface.

Prieto, P.; Morant, C.; Climent-Font, A.; Munoz, A.; Elizalde, E.; Sanz, J.M. [Departamento de Fisica Aplicada C-XII, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Departamento de Fisica Aplicada C-XII, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid, Spain and Centro de Micro-Analisis de Materiales, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Centro de Micro-Analisis de Materiales, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Departamento de Fisica Aplicada C-XII, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid (Spain)

2006-03-15

405

Quantitative Three-Dimensional Microscopy Approaches With Applications in Breast Cancer Biology Including Measurement of Genomic Instability  

Microsoft Academic Search

Understanding tissue development, tissue homeostasis and what goes wrong in these processes during tumorigenesis, requires knowledge of the kinetics of multiple, molecular pathways in individual cells while cells are in their tissue context. This review outlines progress and future directions necessary in quantitative microscopy for gaining this knowledge, using the mammary gland as a model system.

Stephen Lockett; Carlos Ortiz de Solorzano; Daniel Baggett; Koei Chin

2004-01-01

406

Quantitative and evolutionary biology of alternative splicing: how changing the mix of alternative transcripts affects phenotypic plasticity and reaction norms  

Microsoft Academic Search

Alternative splicing (AS) of pre-messenger RNA is a common phenomenon that creates different transcripts from a single gene, and these alternative transcripts affect phenotypes. The majority of AS research has examined tissue and developmental specificity of expression of particular AS transcripts, how this specificity affects cell function, and how aberrant AS is related to disease. Few studies have examined quantitative

J H Marden

2008-01-01

407

Quantitative NMR spectroscopy of supramolecular complexes: Dynamic side pores in ClpP are important for product release  

PubMed Central

The highly conserved, 300-kDa cylindrical protease ClpP is an important component of the cellular protein quality machinery. It consists of 14 subunits arranged into two heptameric rings that enclose a large chamber containing the protease active sites. ClpP associates with ClpX and ClpA ATPases that unfold and translocate substrates into the protease catalytic chamber through axial pores located at both ends of the ClpP cylinder. Although the pathway of substrate delivery is well established, the pathway of product release is unknown. Here, we use recently developed transverse relaxation optimized spectroscopy (TROSY) of methyl groups to show that the interface between the heptameric rings exchanges between two structurally distinct conformations. The conformational exchange process has been quantified by magnetization exchange and methyl TROSY relaxation dispersion experiments recorded between 0.5°C and 40°C, so that the thermodynamic properties for the transition could be obtained. Restriction of the observed motional freedom in ClpP through the introduction of a cysteine linkage results in a protease where substrate release becomes significantly slowed relative to the rate observed in the reduced enzyme, suggesting that the observed motions lead to the formation of transient side pores that may play an important role in product release.

Sprangers, Remco; Gribun, Anna; Hwang, Peter M.; Houry, Walid A.; Kay, Lewis E.

2005-01-01

408

Quantitative determination of the oxidation state of iron in biotite using x-ray photoelectron spectroscopy: I. Calibration  

SciTech Connect

X-ray photoelectron spectroscopy (XPS) analyses of Fe(III)/{Sigma}Fe were calibrated with nine single crystals of biotite of known Fe(III)/{Sigma}Fe content. Peak shape parameters for the component Fe{sup 2+} and Fe{sup 3+} Fe 3p peaks were obtained by a constrained lease squares fitting method that minimized the difference between Fe(III)/{Sigma}Fe determined by XPS and wet chemistry/electron microprobe (WCEM) analyses. Fe{sup 2+} and Fe{sup 3+} peak separation was estimated from the separation of minima in the second derivative of Fe 3p spectra. The single set of derived peak parameters yielded a good linear correlation (r = 0.87) between XPS and WCEM values over the sample displaying progressive oxidation during XPS analysis resulted in Fe{sup 2} and Fe{sup 3+} component peak shapes largely consistent with the constrained least squares fitting methods. Beam damage, which appeared to be restricted to three single crystals with low {Sigma}Fe, low Fe/Mg, and high Fe(II)/{Sigma}Fe, caused increases in Fe(III)/{Sigma}Fe that were proportional to the duration of sample exposure. 60 refs., 6 figs., 7 tabs.

Raeburn, S.P. [Pennsylvania State Univ., University Park, PA (United States); Ilton, E.S. [Lehigh Univ., Bethlehem, PA (United States); Veblen, D.R. [Johns Hopkins Univ., Baltimore, MD (United States)

1997-11-01

409

Quantitative one-dimensional imaging using picosecond dual-broadband pure-rotational coherent anti-Stokes Raman spectroscopy.  

PubMed

We employ picosecond dual-broadband pure-rotational coherent anti-Stokes Raman spectroscopy (CARS) in a one-dimensional (1D) imaging configuration. Temperature and O(2):N(2) concentration ratios are measured along a 1D line of up to 12 mm in length. The images consist of up to 330 individual rotational CARS (RCARS) spectra, corresponding to 330 spatially resolved volume elements in the probe volume. Signal levels are sufficient for the collection of single-laser-pulse images at temperatures of up to approximately 1200 K and shot-averaged images at flame temperatures, demonstrated at 2100 K. The precision of picosecond pure-rotational 1D imaging CARS is assessed by acquiring a series of 100 single-laser-pulse images in a heated flow of N(2) from 410 K-1200 K and evaluating a single volume element for temperature in each image. Accuracy is demonstrated by comparing temperatures from the evaluated averaged spectra to thermocouple readings in the heated flow. Deviations from the thermocouple of <30 K in the evaluated temperature were found at up to 1205 K. Accuracy and single-shot precision are compared to those reported for single-point nanosecond dual-broadband pure-RCARS and nanosecond 1D vibrational CARS. PMID:21509070

Kliewer, Christopher J; Gao, Yi; Seeger, Thomas; Patterson, Brian D; Farrow, Roger L; Settersten, Thomas B

2011-04-20

410

Quantitative analysis of toxic metals lead and cadmium in water jet by laser-induced breakdown spectroscopy  

SciTech Connect

Laser-induced breakdown spectroscopy (LIBS) has been applied to the analysis of toxic metals Pb and Cd in Pb(NO{sub 3}){sub 2} and Cd(NO{sub 3}){sub 2}.4H{sub 2}O aqueous solutions, respectively. The plasma is generated by focusing a nanosecond Nd:YAG ({lambda}=1064 nm) laser on the surface of liquid in the homemade liquid jet configuration. With an assumption of local thermodynamic equilibrium (LTE), calibration curves of Pb and Cd were obtained at different delay times between 1 to 5 {mu}s. The temporal behavior of limit of detections (LOD) was investigated and it is shown that the minimum LODs for Pb and Cd are 4 and 68 parts in 10{sup 6} (ppm), respectively. In order to demonstrate the correctness of the LTE assumption, plasma parameters including plasma temperature and electron density are evaluated, and it is shown that the LTE condition is satisfied at all delay times.

Cheri, M. Sadegh; Tavassoli, S. H.

2011-03-20

411

Application of LCModel for quality control and quantitative in vivo 1H MR spectroscopy by short echo time STEAM sequence.  

PubMed

The linear combination of model spectra (LCModel) calculation of a parameter for long-term quality control, kT, was introduced, representing the ratio of the temporal and nominal intensities of CH3 groups of lactate and acetate in a quality control phantom. This procedure is a part of the quality assurance of the scanner using fully automatic measurement and calculation of kT parameters, and utilizing Shewhart regulation control charts for continuous evaluation of the magnetic resonance (MR) scanner setting. The application of the kT parameter for the correction of in vivo data increases the precision of molar concentration determination by about 4%. This was tested by the quantitative in vivo MR determination of the molar concentrations of 13 prominent metabolites (N-acetylaspartate (NAA), N-acetylaspartylglutamate, creatine and phosphocreatine (Cr), choline-containing compounds (Cho), myo-inositol, scyllo-inositol, gamma-aminobutyric acid, glutamine, glutamate, glucose, lactate, alanine, taurine) in the white matter and hippocampus of the brain in groups of volunteers, using a short echo time stimulated echo acquisition mode sequence (echo time = 10 ms) and the LCModel technique. The repeatability of the measurement of prominent metabolites such as NAA, Cr and Cho was found to be around 10% (relative standard deviation, n = 6); precision in a group of volunteers (n = 20 and 28, respectively) was in the range of approximately 13-20%. For other metabolites, which are measured with a lower signal-to-noise ratio, the precision can be much lower. PMID:10697221

Hájek, M; Burian, M; Dezortová, M

2000-02-01

412

A comparison of single particle tracking and temporal image correlation spectroscopy for quantitative analysis of endosome motility.  

PubMed

Single particle tracking (SPT) is becoming a standard method to extract transport parameters from time-lapse image sequences of fluorescent vesicles in living cells. Another method to obtain these data is temporal image correlation spectroscopy (TICS), but this method is less often used for measurement of intracellular vesicle transport. Here, we present an extensive comparison of SPT and TICS. First we examine the effect of photobleaching, shading and noise on SPT and TICS analysis using simulated image sequences. To this end, we developed a simple photophysical model, which relates spatially varying illumination intensity to the bleaching propensity and fluorescence intensity of the moving particles. We found that neither SPT nor TICS are affected by photobleaching per se, but the transport parameters obtained by both methods are sensitive to the signal-to-noise ratio. In addition, the number of obtained trajectories in SPT is affected by noise. Diffusion constants determined by TICS are significantly overestimated when large immobile fluorescent structures are present in the image sequences, while the opposite is true for SPT. To improve the performance of both techniques, we compare three different methods for image denoising. Appropriate denoising significantly reduced the effect of noise and of immobile structures on both methods. Shape fluctuations of simulated particles had a more pronounced effect on TICS than on SPT analysis. In denoised images of fluorescent beads or cytosolic vesicles containing fluorescent protein NPC2 in human skin fibroblast cells, the transport parameters acquired by SPT and TICS were comparable emphasizing the value of both analysis methods. PMID:24102535

Lund, F W; Wüstner, D

2013-09-19

413

Quantitative determination of dielectric thin-film properties on product wafers using infrared reflection-absorption spectroscopy  

SciTech Connect

Process monitoring of borophosphosilicate glass (BPSG) dielectric thin films used in the manufacture of microelectronic devices is currently performed using multivariate calibration models developed from transmission infrared (IR) spectra of the films deposited on undoped monitor Si wafers. It would more be desirable to monitor the BPSG deposition on the actual product or device wafers. Because product wafers are opaque in the IR, reflection rather than transmission spectroscopy must be used to monitor the BPSG films deposited on product wafers. In this article, we demonstrate, for the first time, that IR reflection spectra of product wafers can be used to monitor the boron and phosphorus contents of the film and the film thickness to a precision that is comparable to that found for IR analysis of BPSG deposited on monitor wafers. The cross-validated standard errors of prediction of 0.11 wtthinsp{percent}, 0.11 wtthinsp{percent}, and 3 nm for B, P, and thickness, respectively, were achieved using multivariate partial least squares (PLS) models applied to the IR reflectance spectra obtained from reference product wafers. The prediction abilities were found to be independent of the position of the infrared spectrum on a given device and independent of which devices of the same structure were examined. The multivariate calibration models could be used to predict the B and P contents and film thickness of BPSG on device structures of different types and even for devices of different feature sizes if the PLS models were adjusted for slope and intercept differences. Therefore, the time and expense of generating calibrations for new device structures can be greatly reduced by the use of a small number of reference samples of the new devices to estimate the required slope and intercept adjustments for the models. {copyright} {ital 1998 American Vacuum Society.}

Niemczyk, T.M.; Zhang, L. [Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Haaland, D.M. [Sandia National Laboratories, Albuquerque, New Mexico 87185-0342 (United States); Radigan, K.J. [National Semiconductor Corporation, Santa Clara, California 95052 (United States)

1998-11-01

414

Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries  

Microsoft Academic Search

High-throughput screening (HTS) of chemical compounds to identify modulators of molecular targets is a mainstay of pharmaceutical development. Increasingly, HTS is being used to identify chemical probes of gene, pathway, and cell functions, with the ultimate goal of comprehensively delineating relationships between chemical structures and biological activities. Achieving this goal will require methodologies that efficiently generate pharmacological data from the

James Inglese; Douglas S. Auld; Ajit Jadhav; Ronald L. Johnson; Anton Simeonov; Adam Yasgar; Wei Zheng; Christopher P. Austin

2006-01-01

415

Stir Bar Sorptive Extraction: A New Quantitative and Comprehensive Sampling Technique for Determination of Chemical Signal Profiles from Biological Media  

Microsoft Academic Search

Various applications of a novel sampling procedure in chemical ecology are outlined. The stir bar extraction method features the analytical reproducibility needed in recording the analytical profiles of volatile and semivolatile components of biological mixtures. This methodology has been demonstrated here through the examples of small volume urine samples, glandular tissue volatiles, and the air blown through animal cages. Its

Helena A. Soini; Kevin E. Bruce; Donald Wiesler; Frank David; Pat Sandra; Milos V. Novotny

2005-01-01