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1

Recapturing Quantitative Biology.  

ERIC Educational Resources Information Center

Presents a classroom activity on estimating animal populations. Uses shoe boxes and candies to emphasize the importance of mathematics in biology while introducing the methods of quantitative ecology. (JRH)

Pernezny, Ken; And Others

1996-01-01

2

Quantitative spectroscopy of Deneb  

NASA Astrophysics Data System (ADS)

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 rely on quantitative studies of this class of stars as a whole depends on the quality of the analyses for benchmark objects. We constrain the basic atmospheric parameters and fundamental stellar parameters, as well as chemical abundances of the prototype A-type supergiant Deneb to unprecedented accuracy by applying a sophisticated analysis methodology, which has recently been developed and tested. Methods: The analysis is based on high-S/N and high-resolution spectra in the visual and near-IR. Stellar parameters and abundances for numerous astrophysically interesting elements are derived from synthesis of the photospheric spectrum using a hybrid non-LTE technique, i.e. line-blanketed LTE model atmospheres and non-LTE line formation. Multiple metal ionisation equilibria and numerous hydrogen lines from the Balmer, Paschen, Brackett, and Pfund series are utilised simultaneously for the stellar parameter determination. The stellar wind properties are derived from H? line-profile fitting using line-blanketed hydrodynamic non-LTE models. Further constraints come from matching the photospheric spectral energy distribution from the UV to the near-IR L band. Results: The atmospheric parameters of Deneb are tightly constrained: effective temperature T_eff = 8525±75 K, surface gravity log g = 1.10±0.05, microturbulence ? = 8±1 km s-1, macroturbulence, and projected rotational velocity v sin i are both 20 ± 2 km s-1. The abundance analysis gives helium enrichment by 0.10 dex relative to solar and an N/C ratio of 4.44 ± 0.84 (mass fraction), implying strong mixing with CN-processed matter. The heavier elements are consistently underabundant by 0.20 dex compared to solar. Peculiar abundance patterns, which were suggested in previous analyses cannot be confirmed. Accounting for non-LTE effects is essential for removing systematic trends in the abundance determination, for minimising statistical 1?-uncertainties to ?10-20% and for establishing all ionisation equilibria at the same time. Conclusions: A luminosity of (1.96 ± 0.32)×105 L?, a radius of 203 ± 17 R_?, and a current mass of 19 ± 4 M? are derived. Comparison with stellar evolution predictions suggests that Deneb started as a fast-rotating late O-type star with M^ZAMS? 23 M_? on the main sequence and is currently evolving to the red supergiant stage. Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofisica de Andalucia (CSIC). Appendix A is only available in electronic form at http://www.aanda.org

Schiller, F.; Przybilla, N.

2008-03-01

3

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

4

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

5

[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

2006-06-01

6

Mössbauer Spectroscopy of Biological Systems  

NASA Astrophysics Data System (ADS)

57Fe Mössbauer spectroscopy had an exceptional impact on the development of iron-based metallobiochemistry (we might call it 57Fe-based metallobiochemistry) and its offspring, bioinorganic chemistry. Right from the outset, the new technique has shed considerable light on the nature of various biological problems. In particular, the application of Mössbauer spectroscopy has led to the discovery of previously unknown clusters as well as cluster assemblies that has stimulated research into new biochemical avenues. Moreover, the application of Mössbauer spectroscopy has made possible the characterization of many intermediates in the catalytic cycle of enzymes that sustain life. Some of the intermediates studied have life times of only a few milliseconds and had to be trapped by rapid quench techniques. For these endeavors, the researchers could draw on parallel developments in biological electron paramagnetic resonance (EPR) spectroscopy and, as we shall see, EPR has been a productive complement to biological Mössbauer spectroscopy all the way.

Münck, Eckard; Bominaar, Emile L.

7

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

8

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...

9

Quantitative cell biology with the Virtual Cell  

Microsoft Academic Search

Cell biological processes are controlled by an interacting set of biochemical and electrophysiological events that are distributed within complex cellular structures. Computational models, comprising quantitative data on the interacting molecular participants in these events, provide a means for applying the scientific method to these complex systems. The Virtual Cell is a computational environment designed for cell biologists, to facilitate the

Boris M. Slepchenko; James C. Schaff; Ian Macara; Leslie M. Loew

2003-01-01

10

Informatics and Quantitative Analysis in Biological Imaging  

NSDL National Science Digital Library

Biological imaging is now a quantitative technique for probing cellular structure and dynamics and is increasingly used for cell-based screens. However, the bioinformatics tools required for hypothesis-driven analysis of digital images are still immature. We are developing the Open Microscopy Environment (OME) as an informatics solution for the storage and analysis of optical microscope image data. OME aims to automate image analysis, modeling, and mining of large sets of images and specifies a flexible data model, a relational database, and an XML-encoded file standard that is usable by potentially any software tool. With this design, OME provides a first step toward biological image informatics.

Jason Swedlow (University of Dundee;); Ilya Goldberg (National Institutes of Health;Laboratory of Genetics, National Institute on Aging); Erik Brauner (Harvard Medical School;Institute of Chemistry and Cell Biology); Peter K. Sorger (Harvard Medical School/Massachusetts Institute of Technology;)

2003-04-04

11

Probing biological systems with terahertz spectroscopy  

NASA Astrophysics Data System (ADS)

Terahertz spectroscopy is able to probe several aspects of biological systems. Most well known is its sensitivity to water due to the strong water absorptions at terahertz frequencies. However an increasing number of studies have shown that it is not just water content that terahertz is sensitive to and that other factors such as tissue structure, molecular arrangement or even temperature can also affect the signal. Examples ranging from breast cancer spectroscopy to antibody protein spectroscopy will be presented and discussed.

Pickwell-MacPherson, Emma; Sun, Yiwen; Parrott, Edward P. J.

2012-10-01

12

Unraveling pancreatic islet biology by quantitative proteomics  

PubMed Central

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, Jian-Ying; Dann, Geoffrey P; Liew, Chong Wee; Smith, Richard D; Kulkarni, Rohit N; Qian, Wei-Jun

2011-01-01

13

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

14

Quantitative thermal gradient imaging of biological surfaces  

NASA Astrophysics Data System (ADS)

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 thermal gradients particularly at normal or experimental exchange surfaces. Considering the relatively high specific heat of water and the low level of heat generation, the magnitude of such gradients are small and this require methods with sensitivity < 0.1 degree(s)C, with reasonable time response, and ones adaptable to quantitative spatial mapping. To that end, we have developed a calibration procedure and protocols employing a variety of thermotropic liquid crystal (TLC) formats which can quantitatively map both cellular and tissue surface gradients in a reproducible manner. TLC's used in a quantitative mode have the extreme temperature resolution required for basic biological studies, as well as application where altered cellular metabolism and/or vascular flow patterns are manifested as thermal changes in the spatial thermogram. This paper provides preliminary data on the application of the above protocols for the assessment of the dynamic changes in the thermal gradient pattern on the left-ventricular surface of supported, experimental heart preparations. Accordingly, after initial capture of the calibrated TLC images onto videotape using a multichannel plate intensifier (together with A/D conversion of physiological signals), single frame digitization allows for exact quantitative correlations of changes in the thermogram with hemodynamic parameters throughout the cardiac cycles with a time resolution of approximately equals 33 msec. The type of information obtained has potential value in clinical cardiac diagnosis (ie. coronary artery disease, by-pass assessment, etc.) and other biological applications where altered flow and/or heat production leads to changing surface gradients (ie thrombosis, embolism, tumor cell heat production, etc.) which can now be accurately and quantitatively mapped by the use of TLC's.

Swanson, Curtis J.; Wingard, Christopher J.

1991-03-01

15

Modeling the Effect of Polychromatic Light in Quantitative Absorbance Spectroscopy  

ERIC Educational Resources Information Center

Laboratory experiment is conducted to give the students practical experience with the principles of electronic absorbance spectroscopy. This straightforward approach creates a powerful tool for exploring many of the aspects of quantitative absorbance spectroscopy.

Smith, Rachel; Cantrell, Kevin

2007-01-01

16

Quantitative investigation of two metallohydrolases by X-ray absorption spectroscopy near-edge spectroscopy  

NASA Astrophysics Data System (ADS)

The last several years have witnessed a tremendous increase in biological applications using X-ray absorption spectroscopy (BioXAS), thanks to continuous advancements in synchrotron radiation (SR) sources and detector technology. However, XAS applications in many biological systems have been limited by the intrinsic limitations of the Extended X-ray Absorption Fine Structure (EXAFS) technique e.g., the lack of sensitivity to bond angles. As a consequence, the application of the X-ray absorption near-edge structure (XANES) spectroscopy changed this scenario that is now continuously changing with the introduction of the first quantitative XANES packages such as Minut XANES (MXAN). Here we present and discuss the XANES code MXAN, a novel XANES-fitting package that allows a quantitative analysis of experimental data applied to Zn K-edge spectra of two metalloproteins: Leptospira interrogans Peptide deformylase ( LiPDF) and acutolysin-C, a representative of snake venom metalloproteinases (SVMPs) from Agkistrodon acutus venom. The analysis on these two metallohydrolases reveals that proteolytic activities are correlated to subtle conformation changes around the zinc ion. In particular, this quantitative study clarifies the occurrence of the LiPDF catalytic mechanism via a two-water-molecules model, whereas in the acutolysin-C we have observed a different proteolytic activity correlated to structural changes around the zinc ion induced by pH variations.

Zhao, W.; Chu, W. S.; Yang, F. F.; Yu, M. J.; Chen, D. L.; Guo, X. Y.; Zhou, D. W.; Shi, N.; Marcelli, A.; Niu, L. W.; Teng, M. K.; Gong, W. M.; Benfatto, M.; Wu, Z. Y.

2007-09-01

17

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

18

Quantitative spectroscopy of BA-type supergiants  

NASA Astrophysics Data System (ADS)

Luminous BA-type supergiants have enormous potential for modern astrophysics. They allow topics ranging from non-LTE physics and the evolution of massive stars to the chemical evolution of galaxies and cosmology to be addressed. A hybrid non-LTE technique for the quantitative spectroscopy of these stars is discussed. Thorough tests and first applications of the spectrum synthesis method are presented for the bright Galactic objects ? Leo (A0 Ib), HD 111613 (A2 Iabe), HD 92207 (A0 Iae) and ? Ori (B8 Iae), based on high-resolution and high-S/N Echelle spectra. Stellar parameters are derived from spectroscopic indicators, consistently from multiple non-LTE ionization equilibria and Stark-broadened hydrogen line profiles, and they are verified by spectrophotometry. The internal accuracy of the method allows the 1?-uncertainties to be reduced to ?1-2% in T_eff and to 0.05-0.10 dex in log g. Elemental abundances are determined for over 20 chemical species, with many of the astrophysically most interesting in non-LTE (H, He, C, N, O, Mg, S, Ti, Fe). The non-LTE computations reduce random errors and remove systematic trends in the analysis. Inappropriate LTE analyses tend to systematically underestimate iron group abundances and overestimate the light and ?-process element abundances by up to factors of two to three on the mean. This is because of the different responses of these species to radiative and collisional processes in the microscopic picture, which is explained by fundamental differences of their detailed atomic structure, and not taken into account in LTE. Contrary to common assumptions, significant non-LTE abundance corrections of ~0.3 dex can be found even for the weakest lines (W?? 10 mÅ). Non-LTE abundance uncertainties amount to typically 0.05-0.10 dex (random) and ~0.10 dex (systematic 1?-errors). Near-solar abundances are derived for the heavier elements in the sample stars, and patterns indicative of mixing with nuclear-processed matter for the light elements. These imply a blue-loop scenario for ? Leo because of first dredge-up abundance ratios, while the other three objects appear to have evolved directly from the main sequence. In the most ambitious computations several ten-thousand spectral lines are accounted for in the spectrum synthesis, permitting the accurate reproduction of the entire observed spectra from the visual to near-IR. This prerequisite for the quantitative interpretation of intermediate-resolution spectra opens up BA-type supergiants as versatile tools for extragalactic stellar astronomy beyond the Local Group. The technique presented here is also well suited to improve quantitative analyses of less extreme stars of similar spectral types.

Przybilla, N.; Butler, K.; Becker, S. R.; Kudritzki, R. P.

2006-01-01

19

Photon-tissue interaction model for quantitative assessment of biological tissues  

NASA Astrophysics Data System (ADS)

In this study, we describe a direct fit photon-tissue interaction model to quantitatively analyze reflectance spectra of biological tissue samples. The model rapidly extracts biologically-relevant parameters associated with tissue optical scattering and absorption. This model was employed to analyze reflectance spectra acquired from freshly excised human pancreatic pre-cancerous tissues (intraductal papillary mucinous neoplasm (IPMN), a common precursor lesion to pancreatic cancer). Compared to previously reported models, the direct fit model improved fit accuracy and speed. Thus, these results suggest that such models could serve as real-time, quantitative tools to characterize biological tissues assessed with reflectance spectroscopy.

Lee, Seung Yup; Lloyd, William R.; Wilson, Robert H.; Chandra, Malavika; McKenna, Barbara; Simeone, Diane; Scheiman, James; Mycek, Mary-Ann

2014-02-01

20

CONFOCAL MICROSCOPY SYSTEM PERFORMANCE: QA TESTS, QUANTITATION AND SPECTROSCOPY  

EPA Science Inventory

Confocal Microscopy System Performance: QA tests, Quantitation and Spectroscopy. Robert M. Zucker 1 and Jeremy M. Lerner 2, 1Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research Development, U.S. Environmen...

21

Quantitative applications of photoacoustic spectroscopy in the infrared  

Microsoft Academic Search

Quantitative photoacoustic and transmission infrared spectroscopy have been compared for a highly overlapped three component mixture with concentrations varying from 0 to 60%. A partial leastsquares model has been employed for the quantitative analysis. High correlation coefficients were obtained for both the transmission and photoacoustic model.

Robert J. Rosenthal; Richard T. Carl; John P. Beauchaine; Michael P. Fuller

1988-01-01

22

Quantitative NMR spectroscopy--applications in drug analysis.  

PubMed

NMR spectroscopy being a primary ratio method of measurement is highly suitable to evaluate the quality of drugs. NMR spectroscopy can be used for the identification of a drug substance, the identification and quantification of impurities arising from the synthesis pathway and degradation, or residual solvents as well as the determination of the content in the assay. This review gives an overview of the application of quantitative NMR spectroscopy in International Pharmacopoeias and for licensing purposes. PMID:15893899

Holzgrabe, U; Deubner, R; Schollmayer, C; Waibel, B

2005-08-10

23

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 the…

Feser, Jason; Vasaly, Helen; Herrera, Jose

2013-01-01

24

Quantitative diffusive wave spectroscopy in tissues  

Microsoft Academic Search

High frequency, intensity-modulated light waves are attenuated and phase-shifted by the absorption and scattering properties of highly scattering media, such as tissue. The simultaneous measurement of the average light intensity, modulation amplitude, and phase- shift at a fixed distance from a sinusoidally modulated light source, permits a quantitative determination of the absolute values of the absorption and scattering coefficients from

William W. Mantulin; Joshua B. Fishkin; Peter T. So; Enrico Gratton; John S. Maier

1993-01-01

25

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

26

Quantitative ATR spectroscopy: some basic considerations.  

PubMed

A comprehensive treatment of ATR spectra on the basis of the Lorentz-Lorenz law and Fresnel equations is given. The standard equation for the effective thickness is redefined showing how the lossy case deviates from the lossless case. A matrix effect due to the influence of the real part of the refractive index within an absorption band is demonstrated theoretically as well as experimentally. The concentration of a nonab-sorbing solute sample, i.e., glucose, is determined by ATR spectroscopy near the critical angle. PMID:20309283

Müller, G; Abraham, K; Schaldach, M

1981-04-01

27

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

28

A transformative model for undergraduate quantitative biology education.  

PubMed

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. PMID:20810949

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

2010-01-01

29

Characterizing human pancreatic cancer precursor using quantitative tissue optical spectroscopy  

PubMed Central

In a pilot study, multimodal optical spectroscopy coupled with quantitative tissue-optics models distinguished intraductal papillary mucinous neoplasm (IPMN), a common precursor to pancreatic cancer, from normal tissues in freshly excised human pancreas. A photon-tissue interaction (PTI) model extracted parameters associated with cellular nuclear size and refractive index (from reflectance spectra) and extracellular collagen content (from fluorescence spectra). The results suggest that tissue optical spectroscopy has the potential to characterize pre-cancerous neoplasms in human pancreatic tissues.

Lee, Seung Yup; Lloyd, William R.; Chandra, Malavika; Wilson, Robert H.; McKenna, Barbara; Simeone, Diane; Scheiman, James; Mycek, Mary-Ann

2013-01-01

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

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

32

Quantitative analysis using remote laser-induced breakdown spectroscopy (LIBS)  

Microsoft Academic Search

A measurement system for quantitative, remote materials analysis has been realised. It is based on the method of laser-induced breakdown spectroscopy (LIBS), utilising an optical fibre system, both to deliver the laser radiation to the sample specimen and to collect the light emission from the luminous plasma plume. Distances of up to 100 m between the remote location and the

C. M. Davies; H. H. Telle; D. J. Montgomery; R. E. Corbett

1995-01-01

33

Quantitative Raman spectroscopy in turbid media  

NASA Astrophysics Data System (ADS)

Intrinsic Raman spectra of biological tissue are distorted by the influences of tissue absorption and scattering, which significantly challenge signal quantification. A combined Raman and spatially resolved reflectance setup is introduced to measure the absorption coefficient ?a and the reduced scattering coefficient ?s' of the tissue, together with the Raman signals. The influence of ?a and ?s' on the resonance Raman signal of ?-carotene is measured at 1524 cm-1 by tissue phantom measurements and Monte Carlo simulations for ?a=0.01 to 10 mm-1 and ?s'=0.1 to 10 mm-1. Both methods show that the Raman signal drops roughly proportional to 1/?a for ?a>0.2 mm-1 in the measurement geometry and that the influence of ?s' is weaker, but not negligible. Possible correction functions dependent on the elastic diffuse reflectance are investigated to correct the Raman signal for the influence of ?a and ?s', provided that ?a and ?s' are measured as well. A correction function based on the Monte Carlo simulation of Raman signals is suggested as an alternative. Both approaches strongly reduce the turbidity-induced variation of the Raman signals and allow absolute Raman scattering coefficients to be determined.

Reble, Carina; Gersonde, Ingo; Andree, Stefan; Eichler, Hans Joachim; Helfmann, Jürgen

2010-05-01

34

Quantitative biological microscopy by digital holography  

NASA Astrophysics Data System (ADS)

In this dissertation, improved techniques in digital holography, that have produced high-resolution, high-fidelity images, are discussed. In particular, the angular spectrum method of calculating holographic optical field is noted to have several advantages over the more commonly used Fresnel transformation or Huygens convolution method. It is observed that spurious noise and interference components can be tightly controlled through the analysis and filtering of the angular spectrum. In the angular spectrum method, the reconstruction distance does not have a lower limit, and the off-axis angle between the object and reference waves can be lower than that of the Fresnel requirement, while still allowing the zero-order background to be cleanly separated. Holographic phase images are largely immune from the coherent noise commonly found in amplitude images. With the use of a miniature pulsed laser, the resulting images have 0.5im diffraction-limited lateral resolution and the phase profile is accurate to about several nanometers of optical path length. Samples such as ovarian cancer cells (SKOV-3) and mouse-embryo fibroblast cells have been imaged. These images display intra-cellular and intra-nuclear organelles with clarity and quantitative accuracy. This technique clearly exceeds currently available methods in phase-contrast optical microscopy in both resolution and detail and provides a new modality for imaging morphology of cellular and intracellular structures that is not currently available. Furthermore, we also demonstrate that phase imaging digital holographic movies provide a novel method of non-invasive quantitative viewing of living cells and other objects. This technique is shown to have significant advantages over conventional microscopy.

Mann, Christopher J.

35

Data acquisition and processing modes for quantitative Auger electron spectroscopy  

SciTech Connect

Auger electron spectroscopy has been applied to the quantitative surface analysis of a series of metals (Ag, Cd, In, Sn), indium-tin alloys, indium and tin oxides, and indium-tin oxide (ITO) films. Spectra were obtained by two methods: the conventional modulation technique, which results in the derivative spectrum, and a direct current measurement, which gives an undifferentiated spectrum. For data collected in the latter mode, an instrumental approach and secondary electron background correction are discussed. Quantitative results obtained by using this approach are shown to be more accurate than the traditional measurement method. 7 figures, 3 tables.

Burrell, M.C.; Kaller, R.S.; Armstrong, N.R.

1982-12-01

36

Quantitation and detection of vanadium in biologic and pollution materials  

NASA Technical Reports Server (NTRS)

A review is presented of special considerations and methodology for determining vanadium in biological and air pollution materials. In addition to descriptions of specific analysis procedures, general sections are included on quantitation of analysis procedures, sample preparation, blanks, and methods of detection of vanadium. Most of the information presented is applicable to the determination of other trace elements in addition to vanadium.

Gordon, W. A.

1974-01-01

37

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

38

Infusing Quantitative Approaches throughout the Biological Sciences Curriculum  

ERIC Educational Resources Information Center

A major curriculum redesign effort at the University of Maryland is infusing all levels of our undergraduate biological sciences curriculum with increased emphasis on interdisciplinary connections and quantitative approaches. The curriculum development efforts have largely been guided by recommendations in the National Research Council's…

Thompson, Katerina V.; Cooke, Todd J.; Fagan, William F.; Gulick, Denny; Levy, Doron; Nelson, Kären C.; Redish, Edward F.; Smith, Robert F.; Presson, Joelle

2013-01-01

39

Quantitative Stellar Classification with Low-Resolution Spectroscopy  

NASA Astrophysics Data System (ADS)

Low-resolution spectroscopy (R ~ 1000) is used to efficiently characterize faint stars suspected to host planets. Stellar parameters, i.e. effective temperature, surface gravity, and metallicity can be assessed from these spectra by methods of quantitative classification. For this purpose, more than 130 template stars have been observed with the faint object spectrograph at the Tautenburg 2m telescope, Germany. A large number of lines are measured and the dependence of line depths on stellar parameters is studied.

Eiff, Matthias Ammler-von; Sebastian, Daniel; Guenther, Eike W.

2014-04-01

40

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

41

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

42

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

43

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

44

Validation of biological markers for quantitative risk assessment.  

PubMed Central

The evaluation of biological markers is recognized as necessary to the future of toxicology, epidemiology, and quantitative risk assessment. For biological markers to become widely accepted, their validity must be ascertained. This paper explores the range of considerations that compose the concept of validity as it applies to the evaluation of biological markers. Three broad categories of validity (measurement, internal study, and external) are discussed in the context of evaluating data for use in quantitative risk assessment. Particular attention is given to the importance of measurement validity in the consideration of whether to use biological markers in epidemiologic studies. The concepts developed in this presentation are applied to examples derived from the occupational environment. In the first example, measurement of bromine release as a marker of ethylene dibromide toxicity is shown to be of limited use in constructing an accurate quantitative assessment of the risk of developing cancer as a result of long-term, low-level exposure. This example is compared to data obtained from studies of ethylene oxide, in which hemoglobin alkylation is shown to be a valid marker of both exposure and effect.

Schulte, P; Mazzuckelli, L F

1991-01-01

45

Validation of biological markers for quantitative risk assessment.  

PubMed

The evaluation of biological markers is recognized as necessary to the future of toxicology, epidemiology, and quantitative risk assessment. For biological markers to become widely accepted, their validity must be ascertained. This paper explores the range of considerations that compose the concept of validity as it applies to the evaluation of biological markers. Three broad categories of validity (measurement, internal study, and external) are discussed in the context of evaluating data for use in quantitative risk assessment. Particular attention is given to the importance of measurement validity in the consideration of whether to use biological markers in epidemiologic studies. The concepts developed in this presentation are applied to examples derived from the occupational environment. In the first example, measurement of bromine release as a marker of ethylene dibromide toxicity is shown to be of limited use in constructing an accurate quantitative assessment of the risk of developing cancer as a result of long-term, low-level exposure. This example is compared to data obtained from studies of ethylene oxide, in which hemoglobin alkylation is shown to be a valid marker of both exposure and effect. PMID:2050067

Schulte, P; Mazzuckelli, L F

1991-01-01

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

Integrating Quantitative Thinking into an Introductory Biology Course Improves Students' Mathematical Reasoning in Biological Contexts  

ERIC Educational Resources Information Center

Recent calls for improving undergraduate biology education have emphasized the importance of students learning to apply quantitative skills to biological problems. Motivated by students' apparent inability to transfer their existing quantitative skills to biological contexts, we designed and taught an introductory molecular and cell biology

Hester, Susan; Buxner, Sanlyn; Elfring, Lisa; Nagy, Lisa

2014-01-01

48

Quantitative polarized Raman spectroscopy in highly turbid bone tissue  

PubMed Central

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.

2010-01-01

49

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

50

Quantitative fiber-optic Raman spectroscopy for tissue Raman measurements  

NASA Astrophysics Data System (ADS)

Molecular profiling of tissue using near-infrared (NIR) Raman spectroscopy has shown great promise for in vivo detection and prognostication of cancer. The Raman spectra measured from the tissue generally contain fundamental information about the absolute biomolecular concentrations in tissue and its changes associated with disease transformation. However, producing analogues tissue Raman spectra present a great technical challenge. In this preliminary study, we propose a method to ensure the reproducible tissue Raman measurements and validated with the in vivo Raman spectra (n=150) of inner lip acquired using different laser powers (i.e., 30 and 60 mW). A rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe was utilized for tissue Raman measurements. The investigational results showed that the variations between the spectra measured with different laser powers are almost negligible, facilitating the quantitative analysis of tissue Raman measurements in vivo.

Duraipandian, Shiyamala; Bergholt, Mads; Zheng, Wei; Huang, Zhiwei

2014-03-01

51

Laser bandwidth effects in quantitative cavity ring-down spectroscopy  

NASA Astrophysics Data System (ADS)

We have investigated the effects of laser bandwidth on quantitative cavity ring-down spectroscopy using the rR transitions of the b(v = 0) left arrow X(v = 0) band of molecular oxygen. It is found that failure to account properly for the laser bandwidth leads to systematic errors in the number densities determined from measured ring-down signals. When the frequency-integrated expression for the ring-down signal is fitted and measured laser line shapes are used, excellent agreement between measured and predicted number densities is found.

Hodges, Joseph T.; Looney, J. Patrick; van Zee, Roger D.

1996-07-01

52

Toward Integration: From Quantitative Biology to Mathbio-Biomath?  

PubMed Central

In response to the call of BIO2010 for integrating quantitative skills into undergraduate biology education, 30 Howard Hughes Medical Institute (HHMI) Program Directors at the 2006 HHMI Program Directors Meeting established a consortium to investigate, implement, develop, and disseminate best practices resulting from the integration of math and biology. With the assistance of an HHMI-funded mini-grant, led by Karl Joplin of East Tennessee State University, and support in institutional HHMI grants at Emory and University of Delaware, these institutions held a series of summer institutes and workshops to document progress toward and address the challenges of implementing a more quantitative approach to undergraduate biology education. This report summarizes the results of the four summer institutes (2007–2010). The group developed four draft white papers, a wiki site, and a listserv. One major outcome of these meetings is this issue of CBE—Life Sciences Education, which resulted from proposals at our 2008 meeting and a January 2009 planning session. Many of the papers in this issue emerged from or were influenced by these meetings.

de Pillis, Lisette; Findley, Ann; Joplin, Karl; Pelesko, John; Nelson, Karen; Thompson, Katerina; Usher, David; Watkins, Joseph

2010-01-01

53

Terahertz time-domain spectroscopy of biological tissues  

SciTech Connect

Terahertz absorption spectra and dispersion of biologically important substances such as sugar, water, hemoglobin, lipids and tissues are studied. The characteristic absorption lines in the frequency range of a terahertz spectrometer (0.1-3.5 THz) are found. The refraction indices and absorption coefficients of human tooth enamel and dentine are measured. The method of terahertz phase reflection spectroscopy is developed for strongly absorbing substances. Simple and reliable methods of time-resolved terahertz spectroscopy are developed. (biophotonics)

Nazarov, M M; Shkurinov, A P; Kuleshov, E A [M. V. Lomonosov Moscow State University, Faculty of Physics, Moscow (Russian Federation); Tuchin, V V [N. G. Chernyshevskii Saratov State University, Saratov (Russian Federation)

2008-07-31

54

Nanomechanical spectroscopy of synthetic and biological membranes.  

PubMed

We report that atomic force microscopy based high-speed nanomechanical analysis can identify components of complex heterogeneous synthetic and biological membranes from the measured spectrum of nanomechanical properties. We have investigated phase separated ternary lipid bilayers and purple membranes of Halobacterium salinarum. The nanomechanical spectra recorded on these samples identify all membrane components, some of which are difficult to resolve in conventional phase images. This non-destructive approach can aid the design of synthetic lipid bilayers and studies lateral organization of complex heterogeneous cellular membranes. PMID:24895687

Lü, Junhong; Yang, Ju; Dong, Mingdong; Sahin, Ozgur

2014-06-12

55

Computational laser spectroscopy in a biological tissue.  

PubMed

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. PMID:20396377

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

2010-01-01

56

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

57

Nanomechanical spectroscopy of synthetic and biological membranes  

NASA Astrophysics Data System (ADS)

We report that atomic force microscopy based high-speed nanomechanical analysis can identify components of complex heterogeneous synthetic and biological membranes from the measured spectrum of nanomechanical properties. We have investigated phase separated ternary lipid bilayers and purple membranes of Halobacterium salinarum. The nanomechanical spectra recorded on these samples identify all membrane components, some of which are difficult to resolve in conventional phase images. This non-destructive approach can aid the design of synthetic lipid bilayers and studies lateral organization of complex heterogeneous cellular membranes.We report that atomic force microscopy based high-speed nanomechanical analysis can identify components of complex heterogeneous synthetic and biological membranes from the measured spectrum of nanomechanical properties. We have investigated phase separated ternary lipid bilayers and purple membranes of Halobacterium salinarum. The nanomechanical spectra recorded on these samples identify all membrane components, some of which are difficult to resolve in conventional phase images. This non-destructive approach can aid the design of synthetic lipid bilayers and studies lateral organization of complex heterogeneous cellular membranes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr02643d

Lü, Junhong; Yang, Ju; Dong, Mingdong; Sahin, Ozgur

2014-06-01

58

Quantitative Cherenkov emission spectroscopy for tissue oxygenation assessment  

PubMed Central

Measurements of Cherenkov emission in tissue during radiation therapy are shown to enable estimation of hemoglobin oxygen saturation non-invasively, through spectral fitting of the spontaneous emissions from the treated tissue. Tissue oxygenation plays a critical role in the efficacy of radiation therapy to kill tumor tissue. Yet in-vivo measurement of this has remained elusive in routine use because of the complexity of oxygen measurement techniques. There is a spectrally broad emission of Cherenkov light that is induced during the time of irradiation, and as this travels through tissue from the point of the radiation deposition, the tissue absorption and scatter impart spectral changes. These changes can be quantified by diffuse spectral fitting of the signal. Thus Cherenkov emission spectroscopy is demonstrated for the first time quantitatively in vitro and qualitatively in vivo, and has potential for real-time online tracking of tissue oxygen during radiation therapy when fully characterized and developed.

Axelsson, Johan; Glaser, Adam K.; Gladstone, David J.; Pogue, Brian W.

2012-01-01

59

Quantitative In Vivo Magnetic Resonance Spectroscopy Using Synthetic Signal Injection  

PubMed Central

Accurate conversion of magnetic resonance spectra to quantitative units of concentration generally requires compensation for differences in coil loading conditions, the gains of the various receiver amplifiers, and rescaling that occurs during post-processing manipulations. This can be efficiently achieved by injecting a precalibrated, artificial reference signal, or pseudo-signal into the data. We have previously demonstrated, using in vitro measurements, that robust pseudo-signal injection can be accomplished using a second coil, called the injector coil, properly designed and oriented so that it couples inductively with the receive coil used to acquire the data. In this work, we acquired nonlocalized phosphorous magnetic resonance spectroscopy measurements from resting human tibialis anterior muscles and used pseudo-signal injection to calculate the Pi, PCr, and ATP concentrations. We compared these results to parallel estimates of concentrations obtained using the more established phantom replacement method. Our results demonstrate that pseudo-signal injection using inductive coupling provides a robust calibration factor that is immune to coil loading conditions and suitable for use in human measurements. Having benefits in terms of ease of use and quantitative accuracy, this method is feasible for clinical use. The protocol we describe could be readily translated for use in patients with mitochondrial disease, where sensitive assessment of metabolite content could improve diagnosis and treatment.

Marro, Kenneth I.; Lee, Donghoon; Shankland, Eric G.; Mathis, C. Mark; Hayes, Cecil E.; Friedman, Seth D.; Kushmerick, Martin J.

2010-01-01

60

Determination of glyphosate in biological fluids by 1H and 31P NMR spectroscopy.  

PubMed

Identification of glyphosate in four cases of poisoning, using nuclear magnetic resonance spectroscopy of biological fluids is reported. It has been performed by using a combination of 1H and 31P NMR analyses. Characterization of the N-(phosphonomethyl) glycine herbicide was achieved by chemical shift considerations and coupling constant patterns: CH2-(P) presents specific resonance at 3.12 ppm and appears as a doublet with a H-P characteristic coupling constant of 12.3 Hz. Moreover, resonances due to isopropylamine were present, confirming the ingestion of the considered trade formulation. After a calibration step, quantitation was performed by 1H and 31P NMR spectroscopy. The benefit and reliability of NMR investigations of biological fluids are discussed, particularly when the clinical picture is quite confusing. PMID:15240034

Cartigny, B; Azaroual, N; Imbenotte, M; Mathieu, D; Vermeersch, G; Goullé, J P; Lhermitte, M

2004-07-16

61

Effect of photobleaching on calibration model development in biological Raman spectroscopy  

PubMed Central

A major challenge in performing quantitative biological studies using Raman spectroscopy lies in overcoming the influence of the dominant sample fluorescence background. Moreover, the prediction accuracy of a calibration model can be severely compromised by the quenching of the endogenous fluorophores due to the introduction of spurious correlations between analyte concentrations and fluorescence levels. Apparently, functional models can be obtained from such correlated samples, which cannot be used successfully for prospective prediction. This work investigates the deleterious effects of photobleaching on prediction accuracy of implicit calibration algorithms, particularly for transcutaneous glucose detection using Raman spectroscopy. Using numerical simulations and experiments on physical tissue models, we show that the prospective prediction error can be substantially larger when the calibration model is developed on a photobleaching correlated dataset compared to an uncorrelated one. Furthermore, we demonstrate that the application of shifted subtracted Raman spectroscopy (SSRS) reduces the prediction errors obtained with photobleaching correlated calibration datasets compared to those obtained with uncorrelated ones.

Barman, Ishan; Kong, Chae-Ryon; Singh, Gajendra P.; Dasari, Ramachandra R.

2011-01-01

62

Quantitative Prediction of Synthetic Food Colors by Fluorescence Spectroscopy and Radial Basis Function Neural Networks  

Microsoft Academic Search

In this paper, quantitative prediction of synthetic food colors by fluorescence spectroscopy and radial basis function neural networks is introduced. Taking Amaranth as an example, for sample solution of Amaranth with different concentrations, the fluorescence spectroscopy excited by the light with the wavelength of 400 nm is measured. The peak wavelength of Amaranth solution fluorescence spectroscopy is about 640 nm,

Chen Guo-qing; Su Zhou-ping; Wu Ya-min; Wang Jun; Wei Bai-lin; Zhu Tuo

2009-01-01

63

High-Resolution Waveguide THz Spectroscopy of Biological Molecules?  

PubMed Central

Abstract Low-frequency vibrational modes of biological molecules consist of intramolecular modes, which are dependent on the molecule as a whole, as well as intermolecular modes, which arise from hydrogen-bonding interactions and van der Waals forces. Vibrational modes thus contain important information about conformation dynamics of biological molecules, and can also be used for identification purposes. However, conventional Fourier transform infrared spectroscopy and terahertz time-domain spectroscopy (THz-TDS) often result in broad, overlapping features that are difficult to distinguish. The technique of waveguide THz-TDS has been recently developed, resulting in sharper features. For this technique, an ordered polycrystalline film of the molecule is formed on a metal sample plate. This plate is incorporated into a metal parallel-plate waveguide and probed via waveguide THz-TDS. The planar order of the film reduces the inhomogeneous broadening, and cooling of the samples to 77K reduces the homogenous broadening. This combination results in the line-narrowing of THz vibrational modes, in some cases to an unprecedented degree. Here, this technique has been demonstrated with seven small biological molecules, thymine, deoxycytidine, adenosine, D-glucose, tryptophan, glycine, and L-alanine. The successful demonstration of this technique shows the possibilities and promise for future studies of internal vibrational modes of large biological molecules.

Laman, N.; Harsha, S. Sree; Grischkowsky, D.; Melinger, Joseph S.

2008-01-01

64

Quantitative biological imaging by ptychographic x-ray diffraction microscopy  

PubMed Central

Recent advances in coherent x-ray diffractive imaging have paved the way to reliable and quantitative imaging of noncompact specimens at the nanometer scale. Introduced a year ago, an advanced implementation of ptychographic coherent diffractive imaging has removed much of the previous limitations regarding sample preparation and illumination conditions. Here, we apply this recent approach toward structure determination at the nanoscale to biological microscopy. We show that the projected electron density of unstained and unsliced freeze-dried cells of the bacterium Deinococcus radiodurans can be derived from the reconstructed phase in a straightforward and reproducible way, with quantified and small errors. Thus, the approach may contribute in the future to the understanding of the highly disputed nucleoid structure of bacterial cells. In the present study, the estimated resolution for the cells was 85 nm (half-period length), whereas 50-nm resolution was demonstrated for lithographic test structures. With respect to the diameter of the pinhole used to illuminate the samples, a superresolution of about 15 was achieved for the cells and 30 for the test structures, respectively. These values should be assessed in view of the low dose applied on the order of ?1.3·105 Gy, and were shown to scale with photon fluence.

Giewekemeyer, Klaus; Thibault, Pierre; Kalbfleisch, Sebastian; Beerlink, Andre; Kewish, Cameron M.; Dierolf, Martin; Pfeiffer, Franz; Salditt, Tim

2010-01-01

65

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

2009-05-01

66

THz-Raman spectroscopy for explosives, chemical, and biological detection  

NASA Astrophysics Data System (ADS)

Raman and Terahertz spectroscopy are both widely used for their ability to safely and remotely identify unknown materials. Each approach has its advantages and disadvantages. Traditional Raman spectroscopy typically measures molecular energy transitions in the 200-5000cm-1 region corresponding to sub-molecular stretching or bending transitions, while Terahertz spectroscopy measures molecular energy transitions in the 1-200cm-1 region (30GHz - 6THz) that correspond to low energy rotational modes or vibrational modes of the entire molecule. Many difficult to detect explosives and other hazardous chemicals are known to have multiple relatively strong transitions in this "Terahertz" (<200cm-1, <6THz) regime, suggesting this method as a powerful complementary approach for identification. However, THz signal generation is often expensive, many THz spectroscopy systems are limited to just a few THz range, and strong water absorption bands in this region can act to mask certain transitions if great care isn't taken during sample preparation. Alternatively, low-frequency or "THz-Raman" spectroscopy, which covers the ~5cm-1 to 200cm-1 (150GHz - 6 THz) regions and beyond, offers a powerful, compact and economical alternative to probe these low energy transitions. We present results from a new approach for extending the range of Raman spectroscopy into the Terahertz regime using an ultra-narrow-band volume holographic grating (VHG) based notch filter system. An integrated, compact Raman system is demonstrated utilizing a single stage spectrometer to show both Stokes and anti-Stokes measurements down to <10cm-1 on traditionally difficult to detect explosives, as well as other chemical and biological samples.

Carriere, James T. A.; Havermeyer, Frank; Heyler, Randy A.

2013-05-01

67

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

68

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

69

Spatially resolved NEXAFS spectroscopy of siderophores in biological matrices  

NASA Astrophysics Data System (ADS)

Iron is an essential nutrient for almost all forms of life. In the presence of oxygen iron is present in its ferric form which precipitates under formation of rather insoluble oxide-hydroxide polymers. Hence the bioavailability of iron is extremely low (< 10-17 M at pH 7 for Fe3+). Under such conditions almost all microorganisms synthesize siderophores as iron chelating agents, thus solubilizing ferric iron from rather insoluble iron sources. Siderophores form soluble complexes with Fe3+. The present study aims at developing a methodology that would allow for the specific detection and localization of such iron chelators in their natural environment. The applicability of spatially resolved NEXAFS spectroscopy in the soft X-ray energy (E < 1 keV) range was evaluated for localization of typical fungal hydroxamate siderophores like ferrichrome or coprogen, which can be present in various biological materials. Results obtained with the scanning transmission X-ray microscopes at beamlines 11.0.2 and 5.3.2 of the ALS have shown characteristic signatures for siderophores. Thus NEXAFS spectroscopy at the carbon K-edge, nitrogen K-edge and iron L-edge with high spatial resolution has proven to be extremely useful for their identification in their natural environment. Spectra of different siderophores as well as spectra and images of biological material containing siderophores are presented.

Thieme, J.; Kilcoyne, D.; Tyliszczak, T.; Haselwandter, K.

2013-10-01

70

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

71

Sub-terahertz resonance spectroscopy of biological macromolecules and cells  

NASA Astrophysics Data System (ADS)

Recently we introduced a Sub-THz spectroscopic system for characterizing vibrational resonance features from biological materials. This new, continuous-wave, frequency-domain spectroscopic sensor operates at room temperature between 315 and 480 GHz with spectral resolution of at least 1 GHz and utilizes the source and detector components from Virginia Diode, Inc. In this work we present experimental results and interpretation of spectroscopic signatures from bacterial cells and their biological macromolecule structural components. Transmission and absorption spectra of the bacterial protein thioredoxin, DNA and lyophilized cells of Escherichia coli (E. coli), as well as spores of Bacillus subtillis and B. atrophaeus have been characterized. Experimental results for biomolecules are compared with absorption spectra calculated using molecular dynamics simulation, and confirm the underlying physics for resonance spectroscopy based on interactions between THz radiation and vibrational modes or groups of modes of atomic motions. Such interactions result in multiple intense and narrow specific resonances in transmission/absorption spectra from nano-gram samples with spectral line widths as small as 3 GHz. The results of this study indicate diverse relaxation dynamic mechanisms relevant to sub-THz vibrational spectroscopy, including long-lasting processes. We demonstrate that high sensitivity in resolved specific absorption fingerprints provides conditions for reliable detection, identification and discrimination capability, to the level of strains of the same bacteria, and for monitoring interactions between biomaterials and reagents in near real-time. Additionally, it creates the basis for the development of new types of advanced biological sensors through integrating the developed system with a microfluidic platform for biomaterial samples.

Globus, Tatiana; Moyer, Aaron; Gelmont, Boris; Khromova, Tatyana; Sizov, Igor; Ferrance, Jerome

2013-05-01

72

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

73

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

74

Quantitative UV-Visible Diffuse Reflectance Spectroscopy of Solid Powders  

Microsoft Academic Search

In spite of difficulties in attaining high resolution, the determination of UV-VIS-NIR spectra via diffuse reflectance spectro-scopic measurements on solid powders; provides several advantages. Compounds which are difficult to obtain as suitable single crystals, or are found to be unstable or insoluble in liquid solution, can only be studied by diffuse reflectance spectroscopy. Also, since no solvents are required, any

T. H. Flint; E. A. Boudreaux

1982-01-01

75

CONFOCAL MICROSCOPY SYSTEM PERFORMANCE: FOUNDATIONS FOR MEASUREMENTS, QUANTITATION AND SPECTROSCOPY  

EPA Science Inventory

The confocal laser-scanning microscopy (CLSM) has enormous potential in many biological fields. The goal of a CLSM is to acquire and quantify fluorescence and in some instruments acquire spectral characterization of the emitted signal. The accuracy of these measurements demands t...

76

CONFOCAL MICROSCOPY SYSTEM PERFORMANCE: FOUNDATIONS FOR CALIBRATION, QUANTITATION AND SPECTROSCOPY  

EPA Science Inventory

The confocal laser-scanning microscope (CLSM) has enormous potential in many biological fields. The goal of a CLSM is to acquire and quantify fluorescence and in some instruments acquire spectral characterization of emitted signals. The accuracy of these measurements demands that...

77

CONFOCAL MICROSCOPY SYSTEM PERFORMANCE: SPECTROSCOPY AND FOUNDATIONS FOR QUANTITATION  

EPA Science Inventory

The confocal laser-scanning microscope (CLSM) has enormous potential in many biological fields. The reliability of the CLSM to obtain specific measurements and quantify fluorescence data is dependent on using a correctly aligned machine that contains a stable laser power. For man...

78

Direct and quantitative photothermal absorption spectroscopy of individual particulates  

NASA Astrophysics Data System (ADS)

Photonic structures can exhibit significant absorption enhancement when an object's length scale is comparable to or smaller than the wavelength of light. This property has enabled photonic structures to be an integral component in many applications such as solar cells, light emitting diodes, and photothermal therapy. To characterize this enhancement at the single particulate level, conventional methods have consisted of indirect or qualitative approaches which are often limited to certain sample types. To overcome these limitations, we used a bilayer cantilever to directly and quantitatively measure the spectral absorption efficiency of a single silicon microwire in the visible wavelength range. We demonstrate an absorption enhancement on a per unit volume basis compared to a thin film, which shows good agreement with Mie theory calculations. This approach offers a quantitative approach for broadband absorption measurements on a wide range of photonic structures of different geometric and material compositions.

Tong, Jonathan K.; Hsu, Wei-Chun; Eon Han, Sang; Burg, Brian R.; Zheng, Ruiting; Shen, Sheng; Chen, Gang

2013-12-01

79

Quantitative assessment of the ion-beam irradiation induced direct damage of nucleic acid bases through FTIR spectroscopy  

NASA Astrophysics Data System (ADS)

Energetic particles exist ubiquitously in nature, and when they hit DNA molecules in organisms, they may induce critical biological effects such as mutation. It is however still a challenge to measure directly and quantitatively the damage imposed by the energetic ions on target DNA molecules. In this work we attempted to employ Fourier transformation infrared (FTIR) spectroscopy to assess the ion-induced direct damage of four nucleic acid bases, namely, thymine (T), cytosine (C), guanine (G), and adenine (A), which are the building blocks of DNA molecules. The samples were prepared as thin films, irradiated by argon ion-beams at raised ion fluences, and in the meantime measured by FTIR spectroscopy for the damage in a quasi-in-situ manner. It was found that the low-energy ion-beam induced radiosensitivity of the four bases shows the sequence G > T > C > A, wherein the possible mechanism was also discussed.

Huang, Qing; Su, Xi; Yao, Guohua; Lu, Yilin; Ke, Zhigang; Liu, Jinghua; Wu, Yuejin; Yu, Zengliang

2014-07-01

80

Using Fourier transform IR spectroscopy to analyze biological materials.  

PubMed

IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing. PMID:24992094

Baker, Matthew J; Trevisan, Júlio; Bassan, Paul; Bhargava, Rohit; Butler, Holly J; Dorling, Konrad M; Fielden, Peter R; Fogarty, Simon W; Fullwood, Nigel J; Heys, Kelly A; Hughes, Caryn; Lasch, Peter; Martin-Hirsch, Pierre L; Obinaju, Blessing; Sockalingum, Ganesh D; Sulé-Suso, Josep; Strong, Rebecca J; Walsh, Michael J; Wood, Bayden R; Gardner, Peter; Martin, Francis L

2014-08-01

81

Invited Review Article: Combining scanning probe microscopy with optical spectroscopy for applications in biology and materials science  

NASA Astrophysics Data System (ADS)

This is a comprehensive review of the combination of scanning probe microscopy (SPM) with various optical spectroscopies, with a particular focus on Raman spectroscopy. Efforts to combine SPM with optical spectroscopy will be described, and the technical difficulties encountered will be examined. These efforts have so far focused mainly on the development of tip-enhanced Raman spectroscopy, a powerful technique to detect and image chemical signatures with single molecule sensitivity, which will be reviewed. Beyond tip-enhanced Raman spectroscopy and/or topography measurements, combinations of SPM with optical spectroscopy have a great potential in the characterization of structure and quantitative measurements of physical properties, such as mechanical, optical, or electrical properties, in delicate biological samples and nanomaterials. The different approaches to improve the spatial resolution, the chemical sensitivity, and the accuracy of physical properties measurements will be discussed. Applications of such combinations for the characterization of structure, defects, and physical properties in biology and materials science will be reviewed. Due to the versatility of SPM probes for the manipulation and characterization of small and/or delicate samples, this review will mainly focus on the apertureless techniques based on SPM probes.

Lucas, Marcel; Riedo, Elisa

2012-06-01

82

Quantitative effect of the neonatal fontanel on synthetic near infrared spectroscopy measurements.  

PubMed

Near infrared spectroscopy (NIRS) is a functional imaging technique allowing measurement of local cerebral oxygenation. This modality is particularly adapted to critically ill neonates, as it can be used at the bedside and is a suitable and noninvasive tool for carrying out longitudinal studies. However, NIRS is sensitive to the imaged medium and consequently to the optical properties of biological tissues in which photons propagate. In this study, the effect of the neonatal fontanel was investigated by predicting photon propagation using a probabilistic Monte Carlo approach. Two anatomical newborn head models were created from computed tomography and magnetic resonance images: (1) a realistic model including the fontanel tissue and (2) a model in which the fontanel was replaced by skull tissue. Quantitative change in absorption due to simulated activation was compared for the two models for specific regions of activation and optical arrays simulated in the temporal area. A correction factor was computed to quantify the effect of the fontanel and defined by the ratio between the true and recovered change. The results show that recovered changes in absorption were more precise when determined with the anatomical model including the fontanel. The results suggest that the fontanel should be taken into account in quantification of NIRS responses to avoid misinterpretation in experiments involving temporal areas, such as language or auditory studies. PMID:22109808

Dehaes, Mathieu; Kazemi, Kamran; Pélégrini-Issac, Mélanie; Grebe, Reinhard; Benali, Habib; Wallois, Fabrice

2013-04-01

83

Quantitating metabolites in protein precipitated serum using NMR spectroscopy.  

PubMed

Quantitative NMR-based metabolite profiling is challenged by the deleterious effects of abundant proteins in the intact blood plasma/serum, which underscores the need for alternative approaches. Protein removal by ultrafiltration using low molecular weight cutoff filters thus represents an important step. However, protein precipitation, an alternative and simple approach for protein removal, lacks detailed quantitative assessment for use in NMR based metabolomics. In this study, we have comprehensively evaluated the performance of protein precipitation using methanol, acetonitrile, perchloric acid, and trichloroacetic acid and ultrafiltration approaches using 1D and 2D NMR, based on the identification and absolute quantitation of 44 human blood metabolites, including a few identified for the first time in the NMR spectra of human serum. We also investigated the use of a "smart isotope tag," (15)N-cholamine for further resolution enhancement, which resulted in the detection of a number of additional metabolites. (1)H NMR of both protein precipitated and ultrafiltered serum detected all 44 metabolites with comparable reproducibility (average CV, 3.7% for precipitation; 3.6% for filtration). However, nearly half of the quantified metabolites in ultrafiltered serum exhibited 10-74% lower concentrations; specifically, tryptophan, benzoate, and 2-oxoisocaproate showed much lower concentrations compared to protein precipitated serum. These results indicate that protein precipitation using methanol offers a reliable approach for routine NMR-based metabolomics of human blood serum/plasma and should be considered as an alternative to ultrafiltration. Importantly, protein precipitation, which is commonly used by mass spectrometry (MS), promises avenues for direct comparison and correlation of metabolite data obtained from the two analytical platforms to exploit their combined strength in the metabolomics of blood. PMID:24796490

Nagana Gowda, G A; Raftery, Daniel

2014-06-01

84

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

85

Quantitative Remote Laser-Induced Breakdown Spectroscopy by Multivariate Analysis  

NASA Astrophysics Data System (ADS)

The ChemCam instrument selected for the Mars Science Laboratory (MSL) rover includes a remote Laser- Induced Breakdown Spectrometer (LIBS) that will quantitatively probe samples up to 9m from the rover mast. LIBS is fundamentally an elemental analysis technique. LIBS involves focusing a Nd:YAG laser operating at 1064 nm onto the surface of the sample. The laser ablates material from the surface, generating an expanding plasma containing electronically excited ions, atoms, and small molecules. As these electronically excited species relax back to the ground state, they emit light at wavelengths characteristic of the species present in the sample. Some of this emission is directed into one of three dispersive spectrometers. In this paper, we studied a suite of 18 igneous and highly-metamorphosed samples from a wide variety of parageneses for which chemical analyses by XRF were already available. Rocks were chosen to represent a range of chemical composition from basalt to rhyolite, thus providing significant variations in all of the major element contents (Si, Fe, Al, Ca, Na, K, O, Ti, Mg, and Mn). These samples were probed at a 9m standoff distance under experimental conditions that are similar to ChemCam. Extracting quantitative elemental concentrations from LIBS spectra is complicated by the chemical matrix effects. Conventional methods for obtaining quantitative chemical data from LIBS analyses are compared with new multivariate analysis (MVA) techniques that appear to compensate for these chemical matrix effects. The traditional analyses use specific elemental peak heights or areas, which compared with calibration curves for each element at one or more emission lines for a series of standard samples. Because of matrix effects, the calibration standards generally must have similar chemistries to the unknown samples, and thus this conventional approach imposes severe limitations on application of the technique to remote analyses. In this suite of samples, the use of traditional methods results in chemical analyses with significant uncertainties. Alternatively, greatly-improved quantitative elemental analysis was accomplished by using a Partial Least Squares (PLS) calibration model for all of the major elements of interest. Principal Components Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA) are then employed to predict the rock-type of the sample. These MVA techniques appear to compensate for these matrix effects because the analysis finds correlations between the spectra (independent variables), the individual elements of interest (dependent variables such as Si) as well as the other elements in the matrix.

Clegg, S. M.; Sklute, E. C.; Dyar, M. D.; Barefield, J. E.; Wiens, R. C.

2007-12-01

86

Machine learning methods for quantitative analysis of Raman spectroscopy data  

NASA Astrophysics Data System (ADS)

The automated identification and quantification of illicit materials using Raman spectroscopy is of significant importance for law enforcement agencies. This paper explores the use of Machine Learning (ML) methods in comparison with standard statistical regression techniques for developing automated identification methods. In this work, the ML task is broken into two sub-tasks, data reduction and prediction. In well-conditioned data, the number of samples should be much larger than the number of attributes per sample, to limit the degrees of freedom in predictive models. In this spectroscopy data, the opposite is normally true. Predictive models based on such data have a high number of degrees of freedom, which increases the risk of models over-fitting to the sample data and having poor predictive power. In the work described here, an approach to data reduction based on Genetic Algorithms is described. For the prediction sub-task, the objective is to estimate the concentration of a component in a mixture, based on its Raman spectrum and the known concentrations of previously seen mixtures. Here, Neural Networks and k-Nearest Neighbours are used for prediction. Preliminary results are presented for the problem of estimating the concentration of cocaine in solid mixtures, and compared with previously published results in which statistical analysis of the same dataset was performed. Finally, this paper demonstrates how more accurate results may be achieved by using an ensemble of prediction techniques.

Madden, Michael G.; Ryder, Alan G.

2003-03-01

87

Quantitative monitoring of yeast fermentation using Raman spectroscopy.  

PubMed

Compared to traditional IR methods, Raman spectroscopy has the advantage of only minimal interference from water when measuring aqueous samples, which makes this method potentially useful for in situ monitoring of important industrial bioprocesses. This study demonstrates real-time monitoring of a Saccharomyces cerevisiae fermentation process using a Raman spectroscopy instrument equipped with a robust sapphire ball probe. A method was developed to correct the Raman signal for the attenuation caused by light scattering cell particulate, hence enabling quantification of reaction components and possibly measurement of yeast cell concentrations. Extinction of Raman intensities to more than 50 % during fermentation was normalized with approximated extinction expressions using Raman signal of water around 1,627 cm(-1) as internal standard to correct for the effect of scattering. Complicated standard multi-variant chemometric techniques, such as PLS, were avoided in the quantification model, as an attempt to keep the monitoring method as simple as possible and still get satisfactory estimations. Instead, estimations were made with a two-step approach, where initial scattering correction of attenuated signals was followed by linear regression. In situ quantification measurements of the fermentation resulted in root mean square errors of prediction (RMSEP) of 2.357, 1.611, and 0.633 g/L for glucose, ethanol, and yeast concentrations, respectively. PMID:24996999

Iversen, Jens A; Berg, Rolf W; Ahring, Birgitte K

2014-08-01

88

Functional and pathological analysis of biological systems using vibrational spectroscopy with chemometric and heuristic approaches  

Microsoft Academic Search

Vibrational spectroscopy (Raman and FTIR microspectroscopy) is an attractive modality for the analysis of biological samples since it provides a complete non-invasive acquisition of the biochemical fingerprint of the sample. Studies in our laboratory have applied vibrational spectroscopy to the analysis of biological function in response to external agents (chemotherapeutic drugs, ionising radiation, nanoparticles), together with studies of the pathology

Aidan Meade; Franck Bonnier; Peter Knief; Lorenzo Salford; Haq Nawaz; Fiona Lyng; Hugh Byrne

2009-01-01

89

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

90

Characterization of CdTe Detectors for Quantitative X-ray Spectroscopy  

Microsoft Academic Search

Silicon diodes have traditionally been the detectors of choice for quantitative X-ray spectroscopy. Their response has been very well characterized and existing software algorithms process the spectra for accurate, quantitative analysis. But Si diodes have limited sensitivity at energies above 30 keV, while recent regulations require measurement of heavy metals such as lead and mercury, with K X-ray emissions well

Robert H. Redus; John A. Pantazis; Thanos J. Pantazis; Alan C. Huber; Brian J. Cross

2009-01-01

91

Quantitative analysis of hydrogen peroxide by 1H NMR spectroscopy.  

PubMed

A technique utilizing 1H NMR spectroscopy has been developed to measure the concentration of hydrogen peroxide from 10(-3) to 10 M. Hydrogen peroxide produces a peak at around 10-11 ppm, depending upon the interaction between solvent molecules and hydrogen peroxide molecules. The intensity of this peak can be monitored once every 30 s, enabling the measurement of changes in hydrogen peroxide concentration as a function of time. 1H NMR has several advantages over other techniques: (1) applicability to a broad range of solvents, (2) ability to quantify hydrogen peroxide rapidly, and (3) ability to follow reactions forming and/or consuming hydrogen peroxide as a function of time. As an example, this analytical technique has been used to measure the concentration of hydrogen peroxide as a function of time in a study of hydrogen peroxide decomposition catalyzed by iron(III) tetrakispentafluorophenyl porphyrin. PMID:15756600

Stephenson, Ned A; Bell, Alexis T

2005-03-01

92

Quantitative Surface Atomic Structure Analysis by Low-Energy Ion Scattering Spectroscopy (ISS)  

NASA Astrophysics Data System (ADS)

Surface atomic structure analysis by low-energy ion scattering spectroscopy (ISS) is reviewed, with particular emphasis on quantitative surface atomic structure analysis by ISS. The important differences between ISS and Rutherford backscattering spectroscopy (RBS), some basic characteristics of ISS, a special type of ISS called impact-collision ion scattering spectroscopy (ICISS), and the general features of the shadow cone in the energy range of ISS are discussed as a basis for the description of particular examples of ISS studies which follow. The examples are mainly concerned with the analysis of the atomic arrangement, defect structure, thermal vibration, and electron spatial distribution of the (001) and (111) surfaces of TiC.

Aono, Masakazu; Souda, Ryutaro

1985-10-01

93

Nonlinear Dielectric Spectroscopy of Biological Systems: Principles ans Applications  

NASA Astrophysics Data System (ADS)

Biological cells can be seen, electrically, as consisting of conducting internal and external media separated by a more-or-less non-conducting cell membrane. The classical, linear, ?-dielectric dispersion results from the charging up of this nominally `static' membrane capacitance according to a Maxwell-Wagner type of mechanism, and typically occurs in the radio frequency range. However, because practically all of the external macroscopic field is dropped across the 5 nm thick cell membrane, there is an effective and substantial amplification of the field across this membrane. This is predicted, and is found, to produce substantial nonlinearities when attempts are made to measure harmonics of the single-frequency exciting field. The nature (odd vs even) and magnitude of these harmonics changes substantially with cell status and environment, providing opportunities for using the cells themselves as sensing elements to describe their surroundings. Electrode polarisation effects producing nonlinear dielectricity can confound these measurements and must be bypassed or taken into account. Nonlinear dielectric spectroscopy (NLDS) provides a wholly non-invasive approach to cellular characterisation and diagnosis.

Kell, Douglas B.; Woodward, Andrew M.; Davies, Elizabeth A.; Todd, Robert W.; Evans, Michael F.; Rowland, Jem J.

94

Quantitative Analysis of Panax ginseng by FT-NIR Spectroscopy  

PubMed Central

Near-infrared spectroscopy (NIRS), a rapid and efficient tool, was used to determine the total amount of nine ginsenosides in Panax ginseng. In the study, the regression models were established using multivariate regression methods with the results from conventional chemical analytical methods as reference values. The multivariate regression methods, partial least squares regression (PLSR) and principal component regression (PCR), were discussed and the PLSR was more suitable. Multiplicative scatter correction (MSC), second derivative, and Savitzky-Golay smoothing were utilized together for the spectral preprocessing. When evaluating the final model, factors such as correlation coefficient (R2) and the root mean square error of prediction (RMSEP) were considered. The final optimal results of PLSR model showed that root mean square error of prediction (RMSEP) and correlation coefficients (R2) in the calibration set were 0.159 and 0.963, respectively. The results demonstrated that the NIRS as a new method can be applied to the quality control of Ginseng Radix et Rhizoma.

Xu, Xin-fang; Nie, Li-xing; Pan, Li-li; Hao, Bian; Yuan, Shao-xiong; Lin, Rui-chao; Bu, Hai-bo; Wang, Dan; Dong, Ling; Li, Xiang-ri

2014-01-01

95

Intramyocardial oxygen transport by quantitative diffuse reflectance spectroscopy in calves  

NASA Astrophysics Data System (ADS)

Intramyocardial oxygen transport was assessed during open-chest surgery in calves by diffuse reflectance spectroscopy using a small intramuscular fiber-optic probe. The sum of hemo- and myoglobin tissue fraction and oxygen saturation, the tissue fraction and oxidation of cytochrome aa3, and the tissue fraction of methemoglobin were estimated using a calibrated empirical light transport model. Increasing the oxygen content in the inhaled gas, 21%-50%-100%, in five calves (group A) gave an increasing oxygen saturation of 19+/-4%, 24+/-5%, and 28+/-8% (p<0.001, ANOVA repeated measures design) and mean tissue fractions of 1.6% (cytochrome aa3) and 1.1% (hemo- and myoglobin). Cardiac arrest in two calves gave an oxygen saturation lower than 5%. In two calves (group B), a left ventricular assistive device (LVAD pump) was implanted. Oxygen saturation in group B animals increased with LVAD pump speed (p<0.001, ANOVA) and with oxygen content in inhaled gas (p<0.001, ANOVA). The cytochrome aa3 oxidation level was above 96% in both group A and group B calves, including the two cases involving cardiac arrest. In conclusion, the estimated tissue fractions and oxygenation/oxidation levels of the myocardial chromophores during respiratory and hemodynamic provocations were in agreement with previously presented results, demonstrating the potential of the method.

Lindbergh, Tobias; Larsson, Marcus; Szabó, Zoltán; Casimir-Ahn, Henrik; Strömberg, Tomas

2010-03-01

96

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

97

A comprehensive approach for quantitative lignin characterization by NMR spectroscopy.  

PubMed

A detailed approach for the quantification of different lignin structures in milled wood lignin (MWL) has been suggested using a combination of NMR techniques. 1H-13C heteronuclear multiple quantum coherence and quantitative 13C NMR of nonacetylated and acetylated spruce MWL have been found to have a synergetic effect, resulting in significant progress in the characterization of lignin moieties by NMR. About 80% of side chain moieties, such as different beta-O-4, dibenzodioxocin, phenylcoumaran, pinoresinol, and others, have been identified on the structural level. The presence of appreciable amounts of alpha-O-alkyl and gamma-O-alkyl ethers has been suggested. Although the quantification of various condensed moieties was less precise than for side chain structures, reliable information can be obtained. Comparison of the calculated results with known databases on spruce MWL structure shows that the suggested approach is rather informative and comparable with the information obtained from the combination of various wet chemistry methods. Discrepancies between the results obtained in this study and those previously published are discussed. PMID:15053520

Capanema, Ewellyn A; Balakshin, Mikhail Y; Kadla, John F

2004-04-01

98

Quantitative analysis of potential adulterants of extra virgin olive oil using infrared spectroscopy  

Microsoft Academic Search

The determination of food authenticity and the detection of adulteration are problems of increasing importance in the food industry. This is especially so for ‘value-added’ products, where the potential financial rewards for substitution with a cheaper ingredient are high. In this paper, the potential of infrared spectroscopy as a rapid analytical technique for the quantitative determination of adulterants in extra

Y. W. Lai; E. K. Kemsley; R. H. Wilson

1995-01-01

99

Real-time Quantitative X-Ray Spectroscopy with a von Hamos Spectrometer  

NASA Astrophysics Data System (ADS)

The real-time quantitative spectroscopy of laser-produced plasmas is explored using a compact von Hamos spectrometer and linear CCD array. This system provides excellent spectral resolution and high dynamic range for compact x-ray sources. Possible uses of this spectrometer include applications in x-ray lithography and laser produced plasma diagnostics.

Weeks, Tyler; Johnson, Michael; Raymond, Scott; Johnson, Jon Paul; Knight, Larry; Shevelko, Alexander

2004-10-01

100

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 laboratory…

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

2008-01-01

101

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

102

Online Interactive Teaching Modules Enhance Quantitative Proficiency of Introductory Biology Students  

PubMed Central

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. MathBench Biology Modules were designed to address these needs through a series of interactive, Web-based modules that can be used to supplement existing course content across the biological sciences curriculum. The effect of the modules was assessed in an introductory biology course at the University of Maryland. Over the course of the semester, students showed significant increases in quantitative skills that were independent of previous math course work. Students also showed increased comfort with solving quantitative problems, whether or not they ultimately arrived at the correct answer. A survey of spring 2009 graduates indicated that those who had experienced MathBench in their course work had a greater appreciation for the role of mathematics in modern biology than those who had not used MathBench. MathBench modules allow students from diverse educational backgrounds to hone their quantitative skills, preparing them for more complex mathematical approaches in upper-division courses.

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

2010-01-01

103

Advances in quantitative UV-visible spectroscopy for clinical and pre-clinical application in cancer.  

PubMed

Methods of optical spectroscopy that provide quantitative, physically or physiologically meaningful measures of tissue properties are an attractive tool for the study, diagnosis, prognosis, and treatment of various cancers. Recent development of methodologies to convert measured reflectance and fluorescence spectra from tissue to cancer-relevant parameters such as vascular volume, oxygenation, extracellular matrix extent, metabolic redox states, and cellular proliferation have significantly advanced the field of tissue optical spectroscopy. The number of publications reporting quantitative tissue spectroscopy results in the UV-visible wavelength range has increased sharply in the past three years, and includes new and emerging studies that correlate optically measured parameters with independent measures such as immunohistochemistry, which should aid in increased clinical acceptance of these technologies. PMID:19268567

Brown, J Quincy; Vishwanath, Karthik; Palmer, Gregory M; Ramanujam, Nirmala

2009-02-01

104

Fluidic and microfluidic tools for quantitative systems biology.  

PubMed

Understanding genes and their functions is a daunting task due to the level of complexity in biological organisms. For discovering how genotype and phenotype are linked to each other, it is essential to carry out systematic studies with maximum sensitivity and high-throughput. Recent developments in fluid-handling technologies, both at the macro and micro scale, are now allowing us to apply engineering approaches to achieve this goal. With these newly developed tools, it is now possible to identify genetic factors that are responsible for particular phenotypes, perturb and monitor cells at the single-cell level, evaluate cell-to-cell variability, detect very rare phenotypes, and construct faithful in vitro disease models. PMID:24484878

Okumus, Burak; Yildiz, Sadik; Toprak, Erdal

2014-02-01

105

The genotype-phenotype maps of systems biology and quantitative genetics: distinct and complementary.  

PubMed

The processes by which genetic variation in complex traits is generated and maintained in populations has for a long time been treated in abstract and statistical terms. As a consequence, quantitative genetics has provided limited insights into our understanding of the molecular bases of quantitative trait variation. With the developing technological and conceptual tools of systems biology, cellular and molecular processes are being described in greater detail. While we have a good description of how signaling and other molecular networks are organized in the cell, we still do not know how genetic variation affects these pathways, because systems and molecular biology usually ignore the type and extent of genetic variation found in natural populations. Here we discuss the quantitative genetics and systems biology approaches for the study of complex trait architecture and discuss why these two disciplines would synergize with each other to answer questions that neither of the two could answer alone. PMID:22821467

Landry, Christian R; Rifkin, Scott A

2012-01-01

106

Biological electron energy loss spectroscopy in the field-emission scanning transmission electron microscope.  

PubMed

The dedicated scanning transmission electron microscope (STEM) combined with parallel electron energy loss spectroscopy (EELS) provides a very sensitive means of detecting specific elements in small structures. EELS is more sensitive than optimized energy-dispersive X-ray spectroscopy by a factor of about three for calcium. Measurement of such low concentrations requires special processing methods such as difference-acquisition techniques and multiple least squares procedures for fitting reference spectra. By analyzing data recorded at each pixel in a spectrum-image it is possible to map quantitatively the elemental distributions in a specimen. It is possible to prepare cryosections that are sufficiently thin to avoid excessive plural inelastic scattering so analysis can be performed at 100 keV beam energy. Under optimal conditions, a resolution of 10 nm and detection limits of a few atoms are achievable for elements such as calcium, phosphorus and iron. In the field emission STEM certain types of chemical information can be extracted from biological specimens. Valence EELS has been exploited to measure water distributions in frozen hydrated cryosections. PMID:7638490

Leapman, R D; Sun, S Q; Hunt, J A; Andrews, S B

1994-01-01

107

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

108

Single molecule fluorescence spectroscopy: approaches toward quantitative investigations of structure and dynamics in living cells  

Microsoft Academic Search

The investigation of the structure and dynamics of biomolecules and biomolecular assemblies in living cells is of current interest in molecular biology. Recent developments in single molecule fluorescence spectroscopy (SMFS) have opened ways for investigating the dynamics and stoichiometry of individual biomolecular complexes e.g., by application of single pair fluorescence resonance energy transfer (spFRET) with alternating laser excitation (ALEX), and

Daniel Siegberg; Christian Michael Roth; Dirk-Peter Herten

2006-01-01

109

Identification, quantitation and biological activity of phytoestrogens in a dietary supplement for breast enhancement  

Microsoft Academic Search

A hop-based dietary supplement, marketed for natural breast enhancement, was analysed to determine the identity and biological activity of active constituents and potential biological effects in man. Extracts of the dietary supplement were analysed by LC–MSn and phytoestrogens identified and quantitated by reference to appropriate standards. Only hop-associated phytoestrogens were found in the dietary supplement at significant concentrations as follows

N. G Coldham; M. J Sauer

2001-01-01

110

[Quantitative analysis model of multi-component complex oil spill source based on near infrared spectroscopy].  

PubMed

Near infrared spectroscopy technology was used for quantitative analysis of the simulation of complex oil spill source. Three light petroleum products, i. e. gasoline, diesel fuel and kerosene oil, were selected and configured as simulated mixture of oil spill samples in accordance with different concentrations proportion, and their near infrared spectroscopy in the range of 8 000 -12 000 cm(-1) was collected by Fourier transform near infrared spectrometer. After processing the NIR spectra with different pretreatment methods, partial least squares method was used to establish quantitative analysis model for the mixture of oil spill samples. For gasoline, diesel fuel and kerosene oil, the second derivative method is the optimal pretreatment method, and for these three oil components in the ranges of 8 501.3-7 999.8 and 6 102.1-4 597.8 cm(-1); 6 549.5-4 597.8; 7 999.8-7 498.4 and 102.1-4 597.8 cm(-1), the correlation coefficients R2 of the prediction model are 0.998 2, 0.990 2 and 0.993 6 respectively, while the forecast RMSEP indicators are 0.474 7, 0.936 1 and 1.013 1 respectively; The experimental results show that using near infrared spectroscopy can quantitatively determine the content of each component in the simulated mixed oil spill samples, thus this method can provide effective means for the quantitative detection and analysis of complex marine oil spill source. PMID:23427535

Tan, Ai-Ling; Bi, Wei-Hong

2012-12-01

111

Quantitation of membrane receptor distributions by image correlation spectroscopy: concept and application.  

PubMed Central

Measurement of receptor distributions on cell surfaces is one important aspect of understanding the mechanism whereby receptors function. In recent years, scanning fluorescence correlation spectroscopy has emerged as an excellent tool for making quantitative measurements of cluster sizes and densities. However, the measurements are slow and usually require fixed preparations. Moreover, while the precision is good, the accuracy is limited by the relatively small amount of information in each measurement, such that many are required. Here we present a novel extension of the scanning correlation spectroscopy that solves a number of the present problems. The new technique, which we call image correlation spectroscopy, is based on quantitative analysis of confocal scanning laser microscopy images. Since these can be generated in a matter of a second or so, the measurements become more rapid. The image is collected over a large cell area so that more sampling is done, improving the accuracy. The sacrifice is a lower resolution in the sampling, which leads to a lower precision. This compromise of precision in favor of speed and accuracy still provides an enormous advantage for image correlation spectroscopy over scanning correlation spectroscopy. The present work demonstrates the underlying theory, showing how the principles can be applied to measurements on standard fluorescent beads and changes in distribution of receptors for platelet-derived growth factor on human foreskin fibroblasts. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 6 FIGURE 7

Petersen, N O; Hoddelius, P L; Wiseman, P W; Seger, O; Magnusson, K E

1993-01-01

112

Identification and quantitation of gamma-hydroxybutyrate (NaGHB) by nuclear magnetic resonance spectroscopy.  

PubMed

The most common means of identification of gamma-hydroxybutyrate (NaGHB) involves using Fourier transform infrared spectroscopy (FTIR) or gas chromatography-mass spectrometry (GC-MS) of a suitable derivative. However, these methods may be complicated by possible shifts in chemical equilibrium between gamma-hydroxybutyric acid (GHB), GHB salts and the precursor lactone, gamma-butyrolactone (GBL). This paper addresses the technique of proton and carbon nuclear magnetic resonance spectroscopy (1H and 13C NMR) for the direct and accurate identification of GHB and GBL. The application of 1H NMR for GHB quantitation is also discussed. PMID:12664985

Chew, Shirley L; Meyers, John A

2003-03-01

113

Quantitative EFTEM mapping of near physiological calcium concentrations in biological specimens.  

PubMed

Although electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) provides high sensitivity for measuring the important element, calcium, in biological specimens, the technique has been difficult to apply routinely, because of long acquisition times required. Here we describe a refinement of the complementary analytical technique of energy-filtered transmission electron microscopy (EFTEM), which enables rapid imaging of large cellular regions and measurement of calcium concentrations approaching physiological levels. Extraction of precise quantitative information is possible by averaging large numbers of pixels that are contained in organelles of interest. We employ a modified two-window approach in which the behavior of the background signal in the EELS spectrum can be modeled as a function of specimen thickness t expressed in terms of the inelastic mean free path lambda. By acquiring pairs of images, one above and one below the Ca L(2,3) edge, together with zero-loss and unfiltered images, which are used to determine a relative thickness (t/lambda) map, it is possible to correct the Ca L(2,3) signal for plural scattering. We have evaluated the detection limits of this technique by considering several sources of systematic errors and applied this method to determine mitochondrial total calcium concentrations in freeze-dried cryosections of rapidly frozen stimulated neurons. By analyzing 0.1 microm2 areas of specimen regions that do not contain calcium, it was found that the standard deviation in the measurement of Ca concentrations was about 20 mmol/kg dry weight, corresponding to a Ca:C atomic fraction of approximately 2 x 10(-4). Calcium concentrations in peripheral mitochondria of recently depolarized, and therefore stimulated and Ca loaded, frog sympathetic neurons were in reasonable agreement with previous data. PMID:19118952

Aronova, M A; Kim, Y C; Pivovarova, N B; Andrews, S B; Leapman, R D

2009-02-01

114

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

115

Quantitative influence of cholesterol on non-invasive blood glucose sensing studied with NIR spectroscopy  

NASA Astrophysics Data System (ADS)

Previous study results indicated that there is a certain influence of cholesterol on non-invasive blood glucose sensing studied with NIR spectroscopy. So, this talk aims to investigate quantitative influence of cholesterol through Partial Least Squares (PLS) modeling and Unary Linear Regression (ULR) analysis respectively. PLS modeling results indicate that glucose concentration increase with the increase of cholesterol concentration. ULR analysis results indicate that there is a positive correlation between the increment of glucose and the cholesterol concentration. And the quantitative relationship has been obtained.

Jiang, Jingying; Zhang, Lingling; Zhang, Kai; Xu, Kexin

2012-02-01

116

Quantitative Modeling of Stochastic Systems in Molecular Biology by Using Stochastic Petri Nets  

Microsoft Academic Search

An integrated understanding of molecular and developmental biology must consider the large number of molecular species involved and the low concentrations of many species in vivo. Quantitative stochastic models of molecular interaction networks can be expressed as stochastic Petri nets (SPNs), a mathematical formalism developed in computer science. Existing software can be used to define molecular interaction networks as SPNs

Peter J. E. Goss; Jean Peccoud

1998-01-01

117

Quantitative Elemental Mapping at Atomic Resolution Using X-Ray Spectroscopy  

NASA Astrophysics Data System (ADS)

Elemental mapping using energy-dispersive x-ray spectroscopy in scanning transmission electron microscopy, a well-established technique for precision elemental concentration analysis at submicron resolution, was first demonstrated at atomic resolution in 2010. However, to date atomic resolution elemental maps have only been interpreted qualitatively because the elastic and thermal scattering of the electron probe confounds quantitative analysis. Accounting for this scattering, we present absolute scale quantitative comparisons between experiment and quantum mechanical calculations for both energy dispersive x-ray and electron energy-loss spectroscopy using off-axis reference measurements. The relative merits of removing the scattering effects from the experimental data against comparison with direct simulations are explored.

Kothleitner, G.; Neish, M. J.; Lugg, N. R.; Findlay, S. D.; Grogger, W.; Hofer, F.; Allen, L. J.

2014-02-01

118

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

119

Quantitative scanning capacitance spectroscopy on GaAs and InAs quantum dots  

NASA Astrophysics Data System (ADS)

In this work, quantitative scanning capacitance spectroscopy studies on bulk GaAs samples and InAs quantum dots are carried out in an ambient atmosphere. The experimental results are described by a simple spherical capacitor model, and the corresponding barrier heights and sample dopings are determined. We further find a strong dependence of the C(V) data on the applied tip force. The barrier height decreases significantly with increasing pressure.

Brezna, W.; Roch, T.; Strasser, G.; Smoliner, J.

2005-09-01

120

Quantitative estimation of polysaccharides in molasses using Near Infra Red spectroscopy  

Microsoft Academic Search

Non-invasive near infrared spectroscopy (NIR) in transmittance mode between 1100–2500 nm was employed for the quantitative\\u000a estimation of dextran, starch, gum and pectin in final molasses one at a time. Partial least square regression analyses was\\u000a used to develop a calibration model with 40 samples each in 0th, 1st and 2nd derivatives which gave low SEC values. This method was

Satindar Kaur; R. S. S. Kaler

2008-01-01

121

Quantitative analysis of water distribution in human articular cartilage using terahertz time-domain spectroscopy  

PubMed Central

The water distribution in human osteoarthritic articular cartilage has been quantitatively characterized using terahertz time-domain spectroscopy (THz TDS). We measured the refractive index and absorption coefficient of cartilage tissue in the THz frequency range. Based on our measurements, the estimated water content was observed to decrease with increasing depth cartilage tissue, showing good agreement with a previous report based on destructive biochemical methods.

Jung, Euna; Choi, Hyuck Jae; Lim, Meehyun; Kang, Hyeona; Park, Hongkyu; Han, Haewook; Min, Byung-hyun; Kim, Sangin; Park, Ikmo; Lim, Hanjo

2012-01-01

122

Quantitative analysis of malic and citric acids in fruit juices using proton nuclear magnetic resonance spectroscopy  

Microsoft Academic Search

1H NMR spectroscopy was applied to the quantitative determination of malic and citric acids in apple, apricot, pear, kiwi, orange, strawberry and pineapple juices. Aspartic acid was studied as a potential interference. The effect of the sample pH on the chemical shifts of signals from malic, citric and aspartic acids was examined and a value of 1.0 was selected to

Gloria del Campo; Iñaki Berregi; Raúl Caracena; J. Ignacio Santos

2006-01-01

123

Quantitative determination of glyphosate in human serum by 1H NMR spectroscopy  

Microsoft Academic Search

The determination and quantification of glyphosate in serum using 1H NMR spectroscopy is reported. This method permitted serum samples to be analysed without derivatization or any other sample pre-treatment, using 3-trimethylsilyl 2,2?,3,3?-tetradeuteropropionic acid (TSP-d4) as a qualitative and quantitative standard. Characterization of the herbicide N-(phosphonomethyl)glycine was performed by analysing chemical shifts and coupling constant patterns. Quantification was performed by relative

Bernard Cartigny; Nathalie Azaroual; Michel Imbenotte; Daniel Mathieu; Erika Parmentier; Gaston Vermeersch; Michel Lhermitte

2008-01-01

124

Application of Optical Imaging and Spectroscopy to Radiation Biology  

PubMed Central

Optical imaging and spectroscopy is a diverse field that has been of critical importance in a wide range of areas in radiation research. It is capable of spanning a wide range of spatial and temporal scales, and has the sensitivity and specificity needed for molecular and functional imaging. This review will describe the basic principles of optical imaging and spectroscopy, highlighting a few relevant applications to radiation research.

Palmer, Gregory M.; Vishwanath, Karthik; Dewhirst, Mark W.

2013-01-01

125

Application of optical imaging and spectroscopy to radiation biology.  

PubMed

Optical imaging and spectroscopy is a diverse field that has been of critical importance in a wide range of areas in radiation research. It is capable of spanning a wide range of spatial and temporal scales, and has the sensitivity and specificity needed for molecular and functional imaging. This review will describe the basic principles of optical imaging and spectroscopy, highlighting a few relevant applications to radiation research. PMID:22360397

Palmer, Gregory M; Vishwanath, Karthik; Dewhirst, Mark W

2012-04-01

126

Quantitative Determination of Carthamin in Carthamus Red by 1H-NMR Spectroscopy.  

PubMed

Carthamus Red is a food colorant prepared from the petals of Carthamus tinctorius (Asteraceae) whose major pigment is carthamin. Since an authentic carthamin standard is difficult to obtain commercially for the preparation of calibration curves in HPLC assays, we applied (1)H-NMR spectroscopy to the quantitative determination of carthamin in commercial preparations of Carthamus Red. Carthamus Red was repeatedly extracted in methanol and the extract was dissolved in pyridine-d(5) containing hexamethyldisilane (HMD) prior to (1)H-NMR spectroscopic analysis. The carthamin contents were calculated from the ratios of singlet signal intensities at approximately ?: 9.3 derived from H-16 of carthamin to those of the HMD signal at ?: 0. The integral ratios exhibited good repeatability among NMR spectroscopic analyses. Both the intra-day and inter-day assay variations had coefficients of variation of <5%. Based on the coefficient of absorption, the carthamin contents of commercial preparations determined by (1)H-NMR spectroscopy correlated well with those determined by colorimetry, although the latter were always approximately 1.3-fold higher than the former, irrespective of the Carthamus Red preparations. In conclusion, the quantitative (1)H-NMR spectroscopy used in the present study is simple and rapid, requiring no carthamin standard for calibration. After HMD concentration has been corrected using certified reference materials, the carthamin contents determined by (1)H-NMR spectroscopy are System of Units (SI)-traceable. PMID:24436958

Yoshida, Takamitsu; Terasaka, Kazuyoshi; Kato, Setsuko; Bai, Fan; Sugimoto, Naoki; Akiyama, Hiroshi; Yamazaki, Takeshi; Mizukami, Hajime

2013-01-01

127

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

2013-09-01

128

Quantitative Detection of Purines in Biologically-Relevant Films with TOF-Secondary Ion Mass Spectrometry  

PubMed Central

In purine-depleted environments, the de novo purine biosynthetic pathway is catalyzed to ultimately produce inosine monophosphate (IMP), a purine invisible using current optical microscopy methodology. These enzymes form a complex, termed the “purinosome,” to replenish IMP levels. Before cellular chemical imaging may be applied to monitor the distributions and fluctuations in purine levels, it is necessary to develop a scheme to quantitatively detect purines. Here, IMP and other purines in biologically-relevant matrices have been detected quantitatively. These methods provide a TOF-SIMS protocol using C60+ primary ions to determine the concentration of biomolecules in a cell such as HeLa at the nanomolar level.

Hue, Jonathan J.; Winograd, Nicholas

2014-01-01

129

Quantitative Analysis of the Detection Limits for Heavy-Metal-Contaminated Soils by Laser-Induced Breakdown Spectroscopy.  

National Technical Information Service (NTIS)

Laser-induced breakdown spectroscopy (LIBS) is a rapid remote measurement method for detection of metals in the environment. A major factor in the quantitative use of this technique involves the minimum detection limits under laboratory and field operatio...

D. R. Alexander D. E. Poulain

1996-01-01

130

Quantitative frequency-domain fluorescence spectroscopy in tissues and tissue-like media  

NASA Astrophysics Data System (ADS)

In the never-ending quest for improved medical technology at lower cost, modern near-infrared optical spectroscopy offers the possibility of inexpensive technology for quantitative and non-invasive diagnoses. Hemoglobin is the dominant chromophore in the 700-900 nm spectral region and as such it allows for the optical assessment of hemoglobin concentration and tissue oxygenation by absorption spectroscopy. However, there are many other important physiologically relevant compounds or physiological states that cannot be effectively sensed via optical methods because of poor optical contrast. In such cases, contrast enhancements are required. Fluorescence spectroscopy is an attractive component of optical tissue spectroscopy. Exogenous fluorophores, as well as some endogenous ones, may furnish the desperately needed sensitivity and specificity that is lacking in near-infrared optical tissue spectroscopy. The main focus of this thesis was to investigate the generation and propagation of fluorescence photons inside tissues and tissue-like media (i.e., scattering dominated media). The standard concepts of fluorescence spectroscopy have been incorporated into a diffusion-based picture that is sometimes referred to as photon migration. The novelty of this work lies in the successful quantitative recovery of fluorescence lifetimes, absolute fluorescence quantum yields, fluorophore concentrations, emission spectra, and both scattering and absorption coefficients at the emission wavelength from a tissue-like medium. All of these parameters are sensitive to the fluorophore local environment and hence are indicators of the tissue's physiological state. One application demonstrating the capabilities of frequency-domain lifetime spectroscopy in tissue-like media is a study of the binding of ethidium bromide to bovine leukocytes in fresh milk. Ethidium bromide is a fluorescent dye that is commonly used to label DNA, and hence visualize chromosomes in cells. The lifetime of ethidium bromide increases by an order of magnitude upon binding to DNA. In this thesis, I demonstrated that the fluorescence photon migration model is capable of accurately determining the somatic cell count (SCC) in a milk sample. Although meant as a demonstration of fluorescence tissue spectroscopy, this specific problem has important implications for the dairy industry's warfare against subclinical mastitis (i.e., mammary gland inflammation), since the SCC is often used as an indication of bovine infection.

Cerussi, Albert Edward

1999-09-01

131

NIR Raman spectroscopy in medicine and biology: results and aspects  

Microsoft Academic Search

Analyses of biomaterial by ‘classical’ Raman spectroscopy with excitation in the visible range has not been possible since the fluorescence of many essential constituents of all animal and plant cells and tissues overlays the Raman spectra completely. Fluorescence, however, is virtually avoided, when Raman spectra are excited with the Nd:YAG laser line at 1064nm. Within seven dissertations we explored different

B. Schrader; B Dippel; I Erb; S Keller; T Löchte; H Schulz; E Tatsch; S Wessel

1999-01-01

132

Quantitative monitoring of radiation induced skin toxicities in nude mice using optical biomarkers measured from diffuse optical reflectance spectroscopy.  

PubMed

Monitoring the onset of erythema following external beam radiation therapy has the potential to offer a means of managing skin toxicities via biological targeted agents - prior to full progression. However, current skin toxicity scoring systems are subjective and provide at best a qualitative evaluation. Here, we investigate the potential of diffuse optical spectroscopy (DOS) to provide quantitative metrics for scoring skin toxicity. A DOS fiberoptic reflectance probe was used to collect white light spectra at two probing depths using two short fixed source-collector pairs with optical probing depths sensitive to the skin surface. The acquired spectra were fit to a diffusion theory model of light transport in tissue to extract optical biomarkers (hemoglobin concentration, oxygen saturation, scattering power and slope) from superficial skin layers of nude mice, which were subjected to erythema inducing doses of ionizing radiation. A statistically significant increase in oxygenated hemoglobin (p < 0.0016) was found in the skin post-irradiation - confirming previous reports. More interesting, we observed for the first time that the spectral scattering parameters, A (p = 0.026) and k (p = 0.011), were an indicator of erythema at day 6 and could potentially serve as an early detection optical biomarker of skin toxicity. Our data suggests that reflectance DOS may be employed to provide quantitative assessment of skin toxicities following curative doses of external beam radiation. PMID:24876997

Yohan, Darren; Kim, Anthony; Korpela, Elina; Liu, Stanley; Niu, Carolyn; Wilson, Brian C; Chin, Lee Cl

2014-05-01

133

Quantitative monitoring of radiation induced skin toxicities in nude mice using optical biomarkers measured from diffuse optical reflectance spectroscopy  

PubMed Central

Monitoring the onset of erythema following external beam radiation therapy has the potential to offer a means of managing skin toxicities via biological targeted agents – prior to full progression. However, current skin toxicity scoring systems are subjective and provide at best a qualitative evaluation. Here, we investigate the potential of diffuse optical spectroscopy (DOS) to provide quantitative metrics for scoring skin toxicity. A DOS fiberoptic reflectance probe was used to collect white light spectra at two probing depths using two short fixed source-collector pairs with optical probing depths sensitive to the skin surface. The acquired spectra were fit to a diffusion theory model of light transport in tissue to extract optical biomarkers (hemoglobin concentration, oxygen saturation, scattering power and slope) from superficial skin layers of nude mice, which were subjected to erythema inducing doses of ionizing radiation. A statistically significant increase in oxygenated hemoglobin (p < 0.0016) was found in the skin post-irradiation – confirming previous reports. More interesting, we observed for the first time that the spectral scattering parameters, A (p = 0.026) and k (p = 0.011), were an indicator of erythema at day 6 and could potentially serve as an early detection optical biomarker of skin toxicity. Our data suggests that reflectance DOS may be employed to provide quantitative assessment of skin toxicities following curative doses of external beam radiation.

Yohan, Darren; Kim, Anthony; Korpela, Elina; Liu, Stanley; Niu, Carolyn; Wilson, Brian C; Chin, Lee CL

2014-01-01

134

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

135

Probing the sulfur content in gasoline quantitatively with terahertz time-domain spectroscopy  

NASA Astrophysics Data System (ADS)

Terahertz time-domain spectroscopy (THz-TDS) was used for the quantitative detection of sulfur content in gasoline. Models of chemo metrics methods and partial least squares (PLS) were built to measure THz-TDS and the sulfur content. All of the samples were divided into two parts. One part was used for calibration and the other one for validation. In order to evaluate the quality of the models, the correlation coefficient ( R) and root-mean-square errors (RMSE) of calibration and validation models were calculated. The value of R and RMSE were close to 1 and 0 within acceptable levels, respectively, indicating that the combination of THz-TDS and PLS is a potential method for further quantitative detection.

Qin, FangLi; Li, Qian; Zhan, HongLei; Jin, WuJun; Liu, HongLan; Zhao, Kun

2014-07-01

136

Probing the sulfur content in gasoline quantitatively with terahertz time-domain spectroscopy  

NASA Astrophysics Data System (ADS)

Terahertz time-domain spectroscopy (THz-TDS) was used for the quantitative detection of sulfur content in gasoline. Models of chemo metrics methods and partial least squares (PLS) were built to measure THz-TDS and the sulfur content. All of the samples were divided into two parts. One part was used for calibration and the other one for validation. In order to evaluate the quality of the models, the correlation coefficient (R) and root-mean-square errors (RMSE) of calibration and validation models were calculated. The value of R and RMSE were close to 1 and 0 within acceptable levels, respectively, indicating that the combination of THz-TDS and PLS is a potential method for further quantitative detection.

Qin, FangLi; Li, Qian; Zhan, HongLei; Jin, WuJun; Liu, HongLan; Zhao, Kun

2014-04-01

137

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

138

Accuracy improvement of quantitative analysis in laser-induced breakdown spectroscopy using modified wavelet transform.  

PubMed

A modified algorithm of background removal based on wavelet transform was developed for spectrum correction in laser-induced breakdown spectroscopy (LIBS). The optimal type of wavelet function, decomposition level and scaling factor ? were determined by the root-mean-square error of calibration (RMSEC) of the univariate regression model of the analysis element, which is considered as the optimization criteria. After background removal by this modified algorithm with RMSEC, the root-mean-square error of cross-validation (RMSECV) and the average relative error (ARE) criteria, the accuracy of quantitative analysis on chromium (Cr), vanadium (V), cuprum (Cu), and manganese (Mn) in the low alloy steel was all improved significantly. The results demonstrated that the algorithm developed is an effective pretreatment method in LIBS to significantly improve the accuracy in the quantitative analysis. PMID:24921726

Zou, X H; Guo, L B; Shen, M; Li, X Y; Hao, Z Q; Zeng, Q D; Lu, Y F; Wang, Z M; Zeng, X Y

2014-05-01

139

13C NMR spectroscopy for the quantitative determination of compound ratios and polymer end groups.  

PubMed

(13)C NMR spectroscopic integration employing short relaxation delays was evaluated as a quantitative tool to obtain ratios of diastereomers, regioisomers, constitutional isomers, mixtures of unrelated compounds, peptoids, and sugars. The results were compared to established quantitative methods such as (1)H NMR spectroscopic integration, gas chromatography, and high-performance liquid chromatography and were found to be within <3.4% of (1)H NMR spectroscopic values (most examples give results within <2%). Acquisition of the spectra took 2-30 min on as little as 10 mg of sample, proving the general utility of the technique. The simple protocol was extended to include end group analysis of low molecular weight polymers, which afforded results in accordance with (1)H NMR spectroscopy and matrix-assisted laser desorption-ionization time-of-flight spectrometry. PMID:24601654

Otte, Douglas A L; Borchmann, Dorothee E; Lin, Chin; Weck, Marcus; Woerpel, K A

2014-03-21

140

Chemometrics applied to quantitative analysis of ternary mixtures by terahertz spectroscopy.  

PubMed

Chemometrics was applied to qualitative and quantitative analyses of terahertz spectra obtained in transmission mode. A series of mixtures of three pure analytes, namely, citric acid, d-(-)fructose, and ?-lactose monohydrate under various concentrations, was prepared as pressed pellets with polyethylene as binder. Then, terahertz absorbance spectra were recorded by terahertz time domain spectroscopy and analyzed. First, principal component analysis allowed one to correctly locate the samples into a ternary diagram. Second, quantitative analysis was achieved by partial least-squares (PLS) regression and artificial neural networks (ANN). The concentrations were predicted with values of relative mean square error lower than 0.9% for the three constituents. As a conclusion, chemometrics was demonstrated to be very efficient for the analysis of the ternary mixtures prepared for this study. PMID:24738647

El Haddad, Josette; de Miollis, Frederick; Bou Sleiman, Joyce; Canioni, Lionel; Mounaix, Patrick; Bousquet, Bruno

2014-05-20

141

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

142

Quantitative analysis of annealed scanning probe tips using energy dispersive x-ray spectroscopy  

NASA Astrophysics Data System (ADS)

A quantitative method to measure the reduction in oxide species on the surface of electrochemically etched tungsten tips during direct current annealing is developed using energy dispersive x-ray spectroscopy. Oxide species are found to decrease with annealing current, with the trend repeatable over many tips and along the length of the tip apex. A linear resistivity approximation finds significant oxide sublimation occurs at 1714 K, but surface melting and tip broadening at 2215 K. This method can be applied to calibrate any similar annealing stage, and to identify the tradeoff regime between required morphological and chemical properties.

Cobley, R. J.; Brown, R. A.; Barnett, C. J.; Maffeis, T. G. G.; Penny, M. W.

2013-01-01

143

Quantitative analysis of iobitridol in an injectable preparation by 1H NMR spectroscopy.  

PubMed

Nuclear magnetic resonance spectroscopy was used for direct quantitative determination of iobitridol in an injectable formulation. The method was developed on a medium field strength magnet (400MHz) and validation was performed by assessing specificity, accuracy, precision, linearity, stability of samples and robustness. Validation data confirm that the method is highly appropriate for direct quantification of iobitridol in the final formulation. Moreover the method has a good potential for rapid screening analyses due to straightforward experimental setup and lack of any sample pretreatment. PMID:24531005

Borioni, Anna; Gostoli, Gianluca; Bossù, Elena; Sestili, Isabella

2014-06-01

144

Laser-induced breakdown spectroscopy for quantitative analysis of copper in algae  

NASA Astrophysics Data System (ADS)

Laser-induced breakdown spectroscopy (LIBS) has been applied for quantitative analysis of Cu in algae plants, an issue of paramount importance for environmental monitoring. For the analysis with LIBS, algae were compacted into solid pellets with powdered calcium hydroxide addition as binder and a pulsed Nd:YAG laser was employed to produce the plasmas in air at atmospheric pressure. In this approach, atomic lines from traces of Cu were detected, as well as other major and minor elements. The plasma was characterized and a calibration curve was constructed with reference samples prepared with calcium hydroxide. The results obtained demonstrated the usefulness of the method for Cu monitoring in algae plants.

Garcimuño, M.; Díaz Pace, D. M.; Bertuccelli, G.

2013-04-01

145

Improving the Quantitative Skills of Future Benthologists: Better Integration of Mathematics into Undergraduate Biology Curricula  

NASA Astrophysics Data System (ADS)

Some of the assumptions biology faculty make about the mathematical background of their students are unwarranted. Through assessment, we have found that students know far less about subjects such as graphing, logarithms etc. than we think. This obviously affects how we teach our classes, how much time we devote to covering topics such as statistical analysis and the degree of quantitative analysis we expect. At ASU we have taken several steps to improve the mathematical background of our students. The Math Department now offers statistics and calculus courses designed for biology majors. These courses are taught in computerized classrooms and are focused on biological data and modeling. By requiring these courses as prerequisites, we hope to reduce the review of basic mathematics in our classes and focus on the "important" topics. In Biology we have expanded on the level of quantitative rigor expected in our classes. In addition, we are increasing the use of modeling and computational exercises in these classes. We will present the results of our ongoing assessment approach and discuss how we are implementing some of our initiatives. This work is based on the recommendations outlined in the NRC's Bio2010 and the MAA's Math and Bio 2010.

Creed, R. P.; Marland, E. S.; Venable, M. E.; Arnholt, A. T.; Searcy, M. E.

2005-05-01

146

Quantitative analysis of urinary stone composition with micro-Raman spectroscopy  

NASA Astrophysics Data System (ADS)

Urolithiasis is a common, disturbing disease with high recurrent rate (60% in five years). Accurate identification of urinary stone composition is important for treatment and prevention purpose. Our previous studies have demonstrated that micro-Raman spectroscopy (MRS)-based approach successfully detects the composition of tiny stone powders after minimal invasive urological surgery. But quantitative analysis of urinary stones was not established yet. In this study, human urinary stone mixed with two compositions of COM, HAP, COD, and uric acid, were analyzed quantitatively by using a 632.98 nm Raman spectrometric system. This quantitative analysis was based on the construction of calibration curves of known mixtures of synthetically prepared pure COM, HAP, COD and uric acid. First, the various concentration (mole fraction) ratio of binary mixtures including COM and HAP, COM and COD, or COM and uric acid, were produced. Second, the intensities of the characteristic bands at 1462cm -1(IRCOM), 1477cm-1(IRCOD), 961cm-1(IRHAP) and 1402cm-1(IRuric acid), for COD, COM, HAP and uric acid were used respectively for intensity calculation. Various binary mixtures of known concentration ratio were recorded as the basis for the quantitative analysis. The ratios of the relative intensities of the Raman bands corresponding to binary mixtures of known composition on the inverse of the COM concentration yielded a linear dependence. Third, urinary stone fragments collected from patients after management were analyzed with the use of the calibration curve and the quantitative analysis of unknown samples was made by the interpolation analysis. We successfully developed a MRS-based quantitative analytical method for measuring two composition.

Huang, Yi-Yu; Chiu, Yi-Chun; Chiang, Huihua Kenny; Chou, Y. H. Jet; Lu, Shing-Hwa; Chiu, Allen W.

2010-02-01

147

Quantitation of vitamin B6 in biological samples by isotope dilution mass spectrometry  

SciTech Connect

Methods have been developed for the simultaneous quantitative analysis of vitamin B6 forms in biological samples by isotope dilution mass spectrometry using deuterated forms of pyridoxine, pyridoxal, pyridoxamine, and pyridoxic acid. The biological fluid or tissue sample was homogenized and then treated with a cocktail containing appropriate amounts of each deuterated vitamer, as well as the deuterated, phosphorylated vitamer forms. The individual vitamers were isolated from the homogenate by a complex high-performance liquid chromatographic procedure that provided separate fractions for each of the six vitamers found in biological samples. Aldehydic B6 vitamers were reduced to the alcohol form prior to acetylation and analysis by gas chromatography/mass spectrometry (GC/MS). The three resulting vitamers were analyzed by electron ionization GC/MS using a silicone capillary column. The methods have been applied to analysis of vitamin B6 in liver, milk, urine, and feces at levels as low as 0.02 nmol/ml.

Hachey, D.L.; Coburn, S.P.; Brown, L.T.; Erbelding, W.F.; DeMark, B.; Klein, P.D.

1985-11-15

148

Quantitation of vitamin B6 in biological samples by isotope dilution mass spectrometry.  

PubMed

Methods have been developed for the simultaneous quantitative analysis of vitamin B6 forms in biological samples by isotope dilution mass spectrometry using deuterated forms of pyridoxine, pyridoxal, pyridoxamine, and pyridoxic acid. The biological fluid or tissue sample was homogenized and then treated with a cocktail containing appropriate amounts of each deuterated vitamer, as well as the deuterated, phosphorylated vitamer forms. The individual vitamers were isolated from the homogenate by a complex high-performance liquid chromatographic procedure that provided separate fractions for each of the six vitamers found in biological samples. Aldehydic B6 vitamers were reduced to the alcohol form prior to acetylation and analysis by gas chromatography/mass spectrometry (GC/MS). The three resulting vitamers were analyzed by electron ionization GC/MS using a silicone capillary column. The methods have been applied to analysis of vitamin B6 in liver, milk, urine, and feces at levels as low as 0.02 nmol/ml. PMID:4091275

Hachey, D L; Coburn, S P; Brown, L T; Erbelding, W F; DeMark, B; Klein, P D

1985-11-15

149

[Quantitative analysis of Mn, Cr in steel based on laser-induced breakdown spectroscopy].  

PubMed

Quantitative analysis of trace elements such as manganese and chromium in steel was performed employing laser-induced breakdown spectroscopy (LIBS) technique in the present paper. The experimental measurements indicate that the optimal delay, focal plane and detecting position from the sample surface are 2 micros, -3.5 mm and 1.5 mm,respectively. Mn I: 403.07 nm and Cr I : 427.48 nm were selected as the analytical lines and their contents in the target steel sample were analyzed with traditional quantitative analysis and internal standard methods. Comparison of the results with two kinds of quantitatively analytical methods show that the coefficients of determination gained by internal standard method are 0.998 and 0.979 which are much better than the results obtained by traditional quantitative analysis method. According to the established calibration curve by internal standard method the detection limits of manganese and chromium calculated are 0.005% and 0.040 6%, respectively. PMID:22097868

Wang, Qi; Chen, Xing-Long; Yu, Rong-Hua; Xu, Ming-Ming; Yang, Yang; Wu, Bian; Ni, Zhi-Bo; Dong, Feng-Zhong

2011-09-01

150

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

151

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

152

Nonlinear Dielectric Spectroscopy of Biological Systems: Principles ans Applications  

Microsoft Academic Search

Biological cells can be seen, electrically, as consisting of conducting internal and external media separated by a more-or-less\\u000a non-conducting cell membrane. The classical, linear, ?-dielectric dispersion results from the charging up of this nominally\\u000a ‘static’ membrane capacitance according to a Maxwell-Wagner type of mechanism, and typically occurs in the radio frequency\\u000a range. However, because practically all of the external macroscopic

Douglas B. Kell; Andrew M. Woodward; Elizabeth A. Davies; Robert W. Todd; Michael F. Evans; Jem J. Rowland

153

Detection of Taurine in Biological Tissues by 33S NMR Spectroscopy  

NASA Astrophysics Data System (ADS)

The potential of 33S NMR spectroscopy for biochemical investigations on taurine (2-aminoethanesulfonic acid) is explored. It is demonstrated that 33S NMR spectroscopy allows the selective and unequivocal identification of taurine in biological samples. 33S NMR spectra of homogenated and intact tissues are reported for the first time, together with the spectrum of a living mollusc. Emphasis is placed on the importance of choosing appropriate signal processing methods to improve the quality of the 33S NMR spectra of biological tissues.

Musio, Roberta; Sciacovelli, Oronzo

2001-12-01

154

Broadband Plasmon Waveguide Resonance Spectroscopy for Probing Biological Thin Films  

PubMed Central

A commercially available spectrometer has been modified to perform plasmon waveguide resonance (PWR) spectroscopy over a broad spectral bandwidth. When compared to surface plasmon resonance (SPR), PWR has the advantage of allowing measurements in both s- and p-polarizations on a waveguide surface that is silica or glass rather than a noble metal. Here the waveguide is a BK7 glass slide coated with silver and silica layers. The resonance wavelength is sensitive to the optical thickness of the medium adjacent to the silica layer. The sensitivity of this technique is characterized and compared with broadband SPR both experimentally and theoretically. The sensitivity of spectral PWR is comparable to that of spectral SPR for samples with refractive indices close to that of water. The hydrophilic surface of the waveguide allows supported lipid bilayers to be formed spontaneously by vesicle fusion; in contrast, the surface of an SPR chip requires chemical modification to create a supported lipid membrane. Broadband PWR spectroscopy should be a useful technique to study biointerfaces, including ligand binding to transmembrane receptors and adsorption of peripheral proteins on ligand-bearing membranes.

ZHANG, HAN; OROSZ, KRISTINA S.; TAKAHASHI, HIROMI; SAAVEDRA, S. SCOTT

2010-01-01

155

A reusable electrochemical proximity assay for highly selective, real-time protein quantitation in biological matrices.  

PubMed

Rapid and specific quantitation of a variety of proteins over a wide concentration range is highly desirable for biosensing at the point-of-care, in clinical laboratories, and in research settings. Our recently developed electrochemical proximity assay (ECPA) is a target-flexible, DNA-directed, direct-readout protein quantitation method with detection limits in the low femtomolar range, making it particularly amenable to point-of-care detection. However, consistent quantitation in more complex matrices is required at the point-of-care, and improvements in measurement speed are needed for clinical and research settings. Here, we address these concerns with a reusable ECPA, where a gentle regeneration of the surface DNA monolayer (used to capture the proximity complex) is achieved enzymatically through a novel combination of molecular biology and electrochemistry. Strategically placed uracils in the DNA sequence trigger selective cleavage of the backbone, releasing the assembled proximity complex. This allows repeated protein quantitation by square-wave voltammetry (SWV)-as quickly as 3 min between runs. The process can be repeated up to 19 times on a single electrode without loss of assay sensitivity, and currents are shown to be highly repeatable with similar calibrations using seven different electrodes. The utility of reusable ECPA is demonstrated through two important applications in complex matrices: (1) direct, quantitative monitoring of hormone secretion in real time from as few as five murine pancreatic islets and (2) standard addition experiments in unspiked serum for direct quantitation of insulin at clinically relevant levels. Results from both applications distinguish ECPA as an exceptional tool in protein quantitation. PMID:24827871

Hu, Jiaming; Yu, Yajiao; Brooks, Jessica C; Godwin, Leah A; Somasundaram, Subramaniam; Torabinejad, Ferdous; Kim, Joonyul; Shannon, Curtis; Easley, Christopher J

2014-06-11

156

Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy  

NASA Astrophysics Data System (ADS)

Terahertz wave is the electromagnetic spectrum situated between microwave and infrared wave. Quantitative analysis based on terahertz spectroscopy is very important for the application of terahertz techniques. But how to realize it is still under study. L-tartaric acid is widely used as acidulant in beverage, and other food, such as soft drinks, wine, candy, bread and some colloidal sweetmeats. In this paper, terahertz time-domain spectroscopy is applied to quantify the tartaric acid. Two methods are employed to process the terahertz spectra of different samples with different content of tartaric acid. The first one is linear regression combining correlation analysis. The second is partial least square (PLS), in which the absorption spectra in the 0.8-1.4THz region are used to quantify the tartaric acid. To compare the performance of these two principles, the relative error of the two methods is analyzed. For this experiment, the first method does better than the second one. But the first method is suitable for the quantitative analysis of materials which has obvious terahertz absorption peaks, while for material which has no obvious terahertz absorption peaks, the second one is more appropriate.

Cao, Binghua; Fan, Mengbao

2010-05-01

157

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

158

Spectroscopy of Multilayered Biological Tissues for Diabetes Care  

NASA Astrophysics Data System (ADS)

Neurological and vascular complications of diabetes mellitus are known to cause foot ulceration in diabetic patients. Present clinical screening techniques enable the diabetes care provider to triage treatment by identifying diabetic patients at risk of foot ulceration. However, these techniques cannot effectively identify specific areas of the foot at risk of ulceration. This study aims to develop non-invasive optical techniques for accurate assessment of tissue health and viability with spatial resolution on the order of 1 mm². The thesis can be divided into three parts: (1) the use of hyperspectral tissue oximetry to detect microcirculatory changes prior to ulcer formation, (2) development of a two-layer tissue spectroscopy algorithm and its application to detection of callus formation or epidermal degradation prior to ulceration, and (3) multi-layered tissue fluorescence modeling for identification of bacterial growth in existing diabetic foot wounds. The first part of the dissertation describes a clinical study in which hyperspectral tissue oximetry was performed on multiple diabetic subjects at risk of ulceration. Tissue oxyhemoglobin and deoxyhemoglobin concentrations were estimated using the Modified Beer-Lambert law. Then, an ulcer prediction algorithm was developed based on retrospective analysis of oxyhemoglobin and deoxyhemoglobin concentrations in sites that were known to ulcerate. The ulcer prediction algorithm exhibited a large sensitivity but low specificity of 95 and 80%, respectively. The second part of the dissertation revisited the hyperspectral data presented in part one with a new and novel two-layer tissue spectroscopy algorithm. This algorithm was able to detect not only oxyhemoglobin and deoxyhemoglobin concentrations, but also the thickness of the epidermis, and the tissue's scattering coefficient. Specifically, change in epidermal thickness provided insight into the formation of diabetic foot ulcers over time. Indeed, callus formation or the thickening of the epidermis which preempts ulcer formation was detectable prior to ulceration. This added dimension of information increased the specificity of the ulcer prediction algorithm by 7% without reducing the sensitivity. Finally, the third part of the dissertation describes the feasibility of detecting bacteria in open ulcers. First, a semi-empirical model of multi-layered tissue fluorescence was developed. Then, an inverse method was developed and applied to simulated fluorescence emission spectra of diabetic foot wounds infected with Staphylococcus aureus and stained with indocyanine green dye (ICG). The inverse method was able to detect the blood volume fraction, oxygen saturation, and the intrinsic fluorescence spectrum of the ICG dye from simulated fluorescence emission spectra.

Yudovsky, Dmitry

159

Accuracy improvement of quantitative analysis by spatial confinement in laser-induced breakdown spectroscopy.  

PubMed

To improve the accuracy of quantitative analysis in laser-induced breakdown spectroscopy, the plasma produced by a Nd:YAG laser from steel targets was confined by a cavity. A number of elements with low concentrations, such as vanadium (V), chromium (Cr), and manganese (Mn), in the steel samples were investigated. After the optimization of the cavity dimension and laser fluence, significant enhancement factors of 4.2, 3.1, and 2.87 in the emission intensity of V, Cr, and Mn lines, respectively, were achieved at a laser fluence of 42.9 J/cm(2) using a hemispherical cavity (diameter: 5 mm). More importantly, the correlation coefficient of the V I 440.85/Fe I 438.35 nm was increased from 0.946 (without the cavity) to 0.981 (with the cavity); and similar results for Cr I 425.43/Fe I 425.08 nm and Mn I 476.64/Fe I 492.05 nm were also obtained. Therefore, it was demonstrated that the accuracy of quantitative analysis with low concentration elements in steel samples was improved, because the plasma became uniform with spatial confinement. The results of this study provide a new pathway for improving the accuracy of quantitative analysis of LIBS. PMID:23938689

Guo, L B; Hao, Z Q; Shen, M; Xiong, W; He, X N; Xie, Z Q; Gao, M; Li, X Y; Zeng, X Y; Lu, Y F

2013-07-29

160

Attenuated Total Internal Reflectance Infrared Spectroscopy (ATR-FTIR): A Quantitative Approach for Kidney Stone Analysis  

PubMed Central

The impact of kidney stone disease is significant worldwide, yet methods for quantifying stone components remain limited. A new approach requiring minimal sample preparation for the quantitative analysis of kidney stone components has been investigated utilizing attenuated total internal reflectance infrared spectroscopy (ATR-FTIR). Calcium oxalate monohydrate (COM) and hydroxylapatite (HAP), two of the most common constituents of urinary stones, were used for quantitative analysis. Calibration curves were constructed using integrated band intensities of four infrared absorptions versus concentration (weight %). The correlation coefficients of the calibration curves range from 0.997 to 0.93. The limits of detection range from 0.07 ± 0.02% COM/HAP where COM is the analyte and HAP the matrix to 0.26 ± 0.07% HAP/COM where HAP is the analyte and COM the matrix. This study shows that linear calibration curves can be generated for the quantitative analysis of stone mixtures provided the system is well understood especially with respect to particle size.

Gulley-Stahl, Heather J.; Haas, Jennifer A.; Schmidt, Katherine A.; Evan, Andrew P.; Sommer, Andre J.

2011-01-01

161

Shifted-excitation Raman difference spectroscopy for in vitro and in vivo biological samples analysis  

PubMed Central

The contamination of the Raman scattering signal with luminescence is a well-known problem when dealing with biological media excited by visible light. The viability of the shifted-excitation Raman difference spectroscopy (SERDS) technique for luminescence suppression on Raman spectra of biological samples was studied in this work. A tunable Lithrow-configuration diode laser (? = 785 and 830 nm) coupled (directly or by optical fiber) to a dispersive Raman spectrometer was employed to study two sets of human tissues (tooth and skin) in order to determine the set of experimental parameters suitable for luminescence rejection. It was concluded that systematic and reproducible spectra of biological interest can be acquired by SERDS.

da Silva Martins, Mario Augusto; Ribeiro, Dayana Goncalves; Pereira dos Santos, Edson Aparecido; Martin, Airton Abrahao; Fontes, Adriana; da Silva Martinho, Herculano

2010-01-01

162

NIR Raman spectroscopy in medicine and biology: results and aspects  

NASA Astrophysics Data System (ADS)

Analyses of biomaterial by 'classical' Raman spectroscopy with excitation in the visible range has not been possible since the fluorescence of many essential constituents of all animal and plant cells and tissues overlays the Raman spectra completely. Fluorescence, however, is virtually avoided, when Raman spectra are excited with the Nd : YAG laser line at 1064 nm. Within seven dissertations we explored different fields of potential applications to medical diagnostics. Identification and qualification of tissues and cells is possible. Tumors show small but significant differences to normal tissues; in order to develop a reliable tool for tumor diagnostics more research is necessary, especially a collection of reference spectra in a data bank is needed. Raman spectra of biomineralization structures in teeth and bones show pathological tissues as well as the development of new mineralized structures. NIR Raman spectra of flowers, leaves, and fruit show, without special preparation, their constituents: alkaloids, the essential oils, natural dyes, flavors, spices and drugs. They allow application to taxonomy, optimizing plant breeding and control of food.

Schrader, B.; Dippel, B.; Erb, I.; Keller, S.; Löchte, T.; Schulz, H.; Tatsch, E.; Wessel, S.

1999-05-01

163

Accurate single-shot quantitative phase imaging of biological specimens with telecentric digital holographic microscopy.  

PubMed

The advantages of using a telecentric imaging system in digital holographic microscopy (DHM) to study biological specimens are highlighted. To this end, the performances of nontelecentric DHM and telecentric DHM are evaluated from the quantitative phase imaging (QPI) point of view. The evaluated stability of the microscope allows single-shot QPI in DHM by using telecentric imaging systems. Quantitative phase maps of a section of the head of the drosophila melanogaster fly and of red blood cells are obtained via single-shot DHM with no numerical postprocessing. With these maps we show that the use of telecentric DHM provides larger field of view for a given magnification and permits more accurate QPI measurements with less number of computational operations. PMID:24781590

Doblas, Ana; Sánchez-Ortiga, Emilio; Martínez-Corral, Manuel; Saavedra, Genaro; Garcia-Sucerquia, Jorge

2014-04-01

164

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

165

Dynamic quantitative phase imaging for biological objects using a pixelated phase mask  

PubMed Central

This paper describes research in developing a dynamic quantitative phase imaging microscope providing instantaneous measurements of dynamic motions within and among live cells without labels or contrast agents. It utilizes a pixelated phase mask enabling simultaneous measurement of multiple interference patterns derived using the polarization properties of light to track dynamic motions and morphological changes. Optical path difference (OPD) and optical thickness (OT) data are obtained from phase images. Two different processing routines are presented to remove background surface shape to enable quantification of changes in cell position and volume over time. Data from a number of different moving biological organisms and cell cultures are presented.

Creath, Katherine; Goldstein, Goldie

2012-01-01

166

Quantitative analysis of tropane alkaloids in biological materials by gas chromatography-mass spectrometry.  

PubMed

A simple and rapid method for quantitation of tropane alkaloids in biological materials has been developed using an Extrelut column with gas chromatography-mass spectrometry (GC-MS). Biological materials (serum and urine) were mixed with a borate buffer and then applied to an Extrelut column. The adsorbed tropane alkaloids were eluted with dichloromethane before a GC-MS analysis. Atropine-d(3) was used as an internal standard. The extracted tropane alkaloids were converted to trimethylsilyl derivatives prior to GC analysis, to improve the instability of tropane alkaloids from heating and the property of them for a GC column. The recoveries of the compounds, which had been spiked to biological materials, were more than 80%. The GC separation of the derivatives from endogenous impurities was generally satisfactory with the use of a semi-polar capillary column. Tropane alkaloids showed excellent linearity in the range of 10-5000 ng/ml and the limit of detection was 5.0 ng/ml for biological materials. The present method is simple and more rapid than those previously reported, and was applied to a poisoning case. It is useful for the routine analysis of tropane alkaloids in cases of suspected tropane alkaloids poisoning. PMID:12427448

Namera, Akira; Yashiki, Mikio; Hirose, Yasuo; Yamaji, Seiichi; Tani, Tadato; Kojima, Tohru

2002-11-01

167

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

NASA Technical Reports Server (NTRS)

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 a 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 sciences by the challenge of mounting a well-constrained yet sufficiently adaptive and inclusive search for life beyond Earth. Our understanding of the life-planet interaction is still, however, largely empirical. A variety of approaches seek to move from empirical to mechanistic descriptions. One approach focuses on the relationship between biology and energy, which is at once universal (all life requires energy), unique (life manages energy flow in a fashion not seen in abiotic systems), and amenable to characterization and quantification in thermodynamic terms. Simultaneously, a focus on energy flow addresses a critical point of interface between life and its geological, chemical, and physical environment. Characterizing and quantifying this relationship for life on Earth will support the development of integrative and predictive models for biology-environment dynamics. Understanding this relationship at its most fundamental level holds potential for developing concepts of habitability and biosignatures that can optimize astrobiological exploration strategies and are extensible to all life.

Hoehler, Tori M.

2010-01-01

168

Artificial neural network for Cu quantitative determination in soil using a portable Laser Induced Breakdown Spectroscopy system  

NASA Astrophysics Data System (ADS)

Laser Induced Breakdown Spectroscopy (LIBS) is an advanced analytical technique for elemental determination based on direct measurement of optical emission of excited species on a laser induced plasma. In the realm of elemental analysis, LIBS has great potential to accomplish direct analysis independently of physical sample state (solid, liquid or gas). Presently, LIBS has been easily employed for qualitative analysis, nevertheless, in order to perform quantitative analysis, some effort is still required since calibration represents a difficult issue. Artificial neural network (ANN) is a machine learning paradigm inspired on biological nervous systems. Recently, ANNs have been used in many applications and its classification and prediction capabilities are especially useful for spectral analysis. In this paper an ANN was used as calibration strategy for LIBS, aiming Cu determination in soil samples. Spectra of 59 samples from a heterogenic set of reference soil samples and their respective Cu concentration were used for calibration and validation. Simple linear regression (SLR) and wrapper approach were the two strategies employed to select a set of wavelengths for ANN learning. Cross validation was applied, following ANN training, for verification of prediction accuracy. The ANN showed good efficiency for Cu predictions although the features of portable instrumentation employed. The proposed method presented a limit of detection (LOD) of 2.3 mg dm - 3 of Cu and a mean squared error (MSE) of 0.5 for the predictions.

Ferreira, Edilene C.; Milori, Débora M. B. P.; Ferreira, Ednaldo J.; Da Silva, Robson M.; Martin-Neto, Ladislau

2008-10-01

169

Surface-Enhanced Raman Spectroscopy Based Quantitative Bioassay on Aptamer-Functionalized Nanopillars Using Large-Area Raman Mapping  

PubMed Central

Surface-enhanced Raman spectroscopy (SERS) has been used in a variety of biological applications due to its high sensitivity and specificity. Here, we report a SERS-based biosensing approach for quantitative detection of biomolecules. A SERS substrate bearing gold-decorated silicon nanopillars is functionalized with aptamers for sensitive and specific detection of target molecules. In this study, TAMRA-labeled vasopressin molecules in the picomolar regime (1 pM to 1 nM) are specifically captured by aptamers on the nanostructured SERS substrate and monitored by using an automated SERS signal mapping technique. From the experimental results, we show concentration-dependent SERS responses in the picomolar range by integrating SERS signal intensities over a scanning area. It is also noted that our signal mapping approach significantly improves statistical reproducibility and accounts for spot-to-spot variation in conventional SERS quantification. Furthermore, we have developed an analytical model capable of predicting experimental intensity distributions on the substrates for reliable quantification of biomolecules. Lastly, we have calculated the minimum needed area of Raman mapping for efficient and reliable analysis of each measurement. Combining our SERS mapping analysis with an aptamer-functionalized nanopillar substrate is found to be extremely efficient for detection of low-abundance biomolecules.

Yang, Jaeyoung; Palla, Mirko; Bosco, Filippo Giacomo; Rindzevicius, Tomas; Alstr?m, Tommy Sonne; Schmidt, Michael Stenbaek; Boisen, Anja; Ju, Jingyue; Lin, Qiao

2013-01-01

170

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

171

Monitoring iron carbide production from iron ore by quantitative Mössbauer spectroscopy  

NASA Astrophysics Data System (ADS)

The process of converting iron ore (principally Fe 2O 3 or Fe 3O 4) into iron carbide (Fe 3C) to be used as feedstock for steel-making yields complex mixtures of several iron containing compounds as a function of processing conditions. In addition to the above compounds (hematite, magnetite and cementite), the mixtures typically contain wustite (FeO) and metallic iron (Fe). Mössbauer spectroscopy has been developed into a quantitative analytical method for monitoring the degree of conversion to carbide from samples periodically extracted from a fluidized bed reactor type of pilot plant. Emphasis has been placed on standardizing and simplifying the analysis procedure for routine use in an industrial environment.

Stephens, Frank A.; Williamson, D. L.; Hager, John P.

1993-04-01

172

Quantitative laser-induced breakdown spectroscopy of standard reference materials of various categories  

NASA Astrophysics Data System (ADS)

The quantitative laser-induced breakdown spectroscopy analysis was carried out with standard reference materials (SRM). In order to minimize errors due to the matrix effect, we used 21 SRM samples that belong to different categories of food, clay, sludge, steelmaking alloy, and geochemical and agricultural materials. The principal component analysis was used for rapid identification and discrimination of the samples. Nine elements (Al, Ca, Mg, Ti, Si, Fe, K, Na, and Mn) in each sample were analyzed. While each category of samples shows a specific tendency in the calibration curves of Na, Ti, Si, Al, Fe, and Mn, other elements (K, Ca, and Mg) do not pose any noticeable similarity. The present results establish benchmark calibration curves for characterizing various SRMs.

Choi, Soo-Jin; Lee, Kang-Jae; Yoh, Jack J.

2013-12-01

173

Sample thickness and quantitative concentration measurements in Br K-edge XANES spectroscopy of organic materials.  

PubMed

While XANES spectroscopy is an established tool for quantitative information on chemical structure and speciation, elemental concentrations are generally quantified by other methods. The edge step in XANES spectra represents the absolute amount of the measured element in the sample, but matrix effects and sample thickness complicate the extraction of accurate concentrations from XANES measurements, particularly at hard X-ray energies where the X-ray beam penetrates deeply into the sample. The present study demonstrates a method of quantifying concentration with a detection limit approaching 1 mg kg(-1) using information routinely collected in the course of a hard X-ray XANES experiment. The XANES normalization procedure unambiguously separates the signal of the absorber from any source of background. The effects of sample thickness on edge steps at the bromine K-edge were assessed and an empirical correction factor for use with samples of variable mass developed. PMID:24763653

Leri, Alessandra C; Ravel, Bruce

2014-05-01

174

Quantitative determination of glyphosate in human serum by 1H NMR spectroscopy.  

PubMed

The determination and quantification of glyphosate in serum using (1)H NMR spectroscopy is reported. This method permitted serum samples to be analysed without derivatization or any other sample pre-treatment, using 3-trimethylsilyl 2,2',3,3'-tetradeuteropropionic acid (TSP-d(4)) as a qualitative and quantitative standard. Characterization of the herbicide N-(phosphonomethyl)glycine was performed by analysing chemical shifts and coupling constant patterns. Quantification was performed by relative integration of CH(2)-P protons to the TSP-d(4) resonance peak. The method was tested for repeatability (n=5) and yielded coefficients of variation of 1% and 3%, respectively: detection and quantification limits were also determined and were 0.03 and 0.1mmol/L, respectively. The method was applied to the quantification of glyphosate in a case of acute poisoning. PMID:18371753

Cartigny, Bernard; Azaroual, Nathalie; Imbenotte, Michel; Mathieu, Daniel; Parmentier, Erika; Vermeersch, Gaston; Lhermitte, Michel

2008-01-15

175

Qualitative and quantitative assessment of water sorption in natural fibres using ATR-FTIR spectroscopy.  

PubMed

In the field of composite materials, natural fibres appear to be a viable replacement for glass fibres. However, in humid conditions, strong hydrophilic behaviour of such materials can lead to their structural modification. Then, understanding moisture sorption mechanisms in these materials is an important issue for their efficient use. In this work, the water sorption on three natural fibres (flax, hemp and sisal) was studied using Fourier transformed infrared spectroscopy. The spectral information allowed both qualitative and quantitative analyses of the moisture absorption mechanisms. The main chemical functions involved in the water sorption phenomenon were identified. The absolute water content of the fibres was also determined by using a partial least square regression (PLS-R) approach. Moreover, typical sorption isotherm curves described by Park model were fitted as well as water diffusion kinetics. These last applications confirmed the validity of the FTIR spectra based predictive models. PMID:24299761

Célino, Amandine; Gonçalves, Olivier; Jacquemin, Frédéric; Fréour, Sylvain

2014-01-30

176

AFM probes with integrated electrostatic actuators for fast, quantitative imaging and force spectroscopy  

NASA Astrophysics Data System (ADS)

In this talk, we summarize our efforts in developing novel AFM probes (FIRAT) with integrated sensing and actuation. These probes exploit recent advances in microscale sensor technology and open up the design space for AFM applications including fast imaging, quantitative material characterization and single molecular mechanics measurements. For fast imaging applications in air, probes with aluminum force sensing structures are surface micromachined on quartz substrates. Using 0.7-0.8?m thick, 40?mx60?m clamped-clamped beams over 2.8?m of air gap, probes with resonance frequencies in the order of 1MHz and Q in the 5-15 range are obtained. These probes are actuated directly by electrostatic forces applied to the mechanical structure by rigid electrodes on the substrate shaped as optical diffraction gratings, enabling imaging bandwidths in the order of 100kHz. The integrated grating interferometer provides 10fm/Hz level displacement sensitivity down to 3Hz. The surface micromachining approach used for probe fabrication lets one to precisely control the probe dynamics and overcome the difficulties associated with regular AFM cantilevers for applications such as time resolved interaction force (TRIF) measurements. Using FIRAT probes with over damped dynamics, clean TRIF signals are obtained while imaging the surface at regular speeds. This enables us to use a simple model to invert quantitative mechanical properties of a variety of polymers. For measurements on single molecules, membrane type FIRAT probes suitable for in liquid operation have been developed. These probes are made of dielectric materials with embedded actuation electrodes. Used only as actuators or both actuators and force sensors, these devices are shown to enable parallel force spectroscopy measurements. We also show that the spring constant of these probes can be electrically reduced to achieve higher force sensitivity while not affecting its noise performance and discuss the effect of hydrodynamic forces in these membrane type probes as compared to cantilever type probes for fast force spectroscopy measurements.

Degertekin, Levent

2008-03-01

177

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)] [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)] [Sandia National Laboratories, Albuquerque, New Mexico 87185-0342 (United States)

1997-02-01

178

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

179

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

PubMed

Calibration-free laser-induced breakdown spectroscopy (CF-LIBS) method is employed for quantitative determination of oxide concentrations in multi-component materials. Industrial oxide materials from steel industry are laser ablated in air, and the optical plasma emission is collected by spectrometers and gated detectors. The temperature and electron number density of laser-induced plasma are determined from measured LIBS spectra. Emission lines of aluminium (Al), calcium (Ca), iron (Fe), manganese (Mn), magnesium (Mg), silicon (Si), titanium (Ti), and chromium (Cr) of low self-absorption are selected, and the concentration of oxides CaO, Al(2)O(3), MgO, SiO(2), FeO, MnO, TiO(2), and Cr(2)O(3) is calculated by CF-LIBS analysis. For all sample materials investigated, we find good match of calculated concentration values (C(CF)) with nominal concentration values (C(N)). The relative error in oxide concentration, e(r)?=?|C(CF)?-?C(N)|/C(N), decreases with increasing concentration and it is e(r)???100% for concentration C(N)???1 wt.%. The CF-LIBS results are stable against fluctuations of experimental parameters. The variation of laser pulse energy over a large range changes the error by less than 10% for major oxides (C(N)???10 wt.%). The results indicate that CF-LIBS method can be employed for fast and stable quantitative compositional analysis of multi-component materials. PMID:21523330

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

2011-07-01

180

Quantitative characterization of a hardwood milled wood lignin by nuclear magnetic resonance spectroscopy.  

PubMed

The structure of Eucalyptus grandis milled wood lignin (MWL) was investigated by 2D 1H-13C HSQC, HMQC, and 1H-1H TOCSY correlation NMR techniques and by quantitative 13C NMR as well as by the permanganate oxidation degradation technique. The combination of 2D NMR and quantitative 13C NMR spectroscopy of nonacetylated and acetylated lignin preparations allowed reliable identification and calculation of the amount of different lignin structures. About 85% of side-chain moieties were estimated on the structural level. This information was substantiated by data on the quantity of various functional groups and interunit linkages as a whole. A modified method for calculation of the h:g:s ratio has been suggested and compared with previously suggested approaches. E. grandis MWL has been determined to have an h:g:s ratio of 2:36:62. The amounts of various phenolic/etherified noncondensed/condensed guaiacyl and syringyl moieties were approximately estimated. E. grandis MWL contained approximately 0.60/Ar of beta-O-4 moieties along with small amounts of other structural units such as pino/syringyresinol (0.03/Ar), phenylcoumaran (0.03/Ar), and spirodienone (0.05/Ar). The degree of condensation was estimated at approximately 21%; the main condensed structures are 4-O-5 moieties (approximately 0.09/Ar). The structure of E. grandis MWL was compared with those of other lignin preparations isolated from various hardwoods. PMID:16332110

Capanema, Ewellyn A; Balakshin, Mikhail Yu; Kadla, John F

2005-12-14

181

[Simultaneous quantitative analysis of multielements in Al alloy samples by laser-induced breakdown spectroscopy].  

PubMed

The multielement components of some aluminium alloy samples were quantified by using laser-induced breakdown spectroscopy (LIBS). The Nd : YAG pulsed laser was used to produce plasma in ambient air. The spectral range of 200-980 nm was simultaneously obtained through a multichannel grating spectrometer and CCD detectors. The authors studied the influences of time delays, energy of the laser, and depth profile of elements in samples on spectral intensity, and optimized the experimental parameters based on the influence analysis. With the optimal experimental parameters, the authors made the calibration curves by four certified aluminum alloy samples for eight elements, Si, Fe, Cu, Mn, Mg, Zn, Sn, and Ni, and quantified the composition of an aluminum sample. The obtained maximum relative standard deviation (RSD) was 5.89%, and relative errors were--20.99%-15%. Experimental results show that LIBS is an effective technique for quantitative analysis of aluminum alloy samples, though the improved accuracy of the quantitative analysis is necessary. PMID:20210173

Sun, Lan-Xiang; Yu, Hai-Bin

2009-12-01

182

A quantitative analysis of elements in soil using laser-induced breakdown spectroscopy technique  

NASA Astrophysics Data System (ADS)

Laser-induced breakdown spectroscopy (LIBS) was applied to the quantitative analysis of elemental composition of soil. The experiment was performed in air at atmospheric pressure and at room temperature. A Nd:YAG laser with the fundamental wavelength of 1064 nm was employed to generate the soil plasma. The emission spectra from the plasma were collected by the Cerny-Turner type of spectrometer, which was equipped with an intensified charge-coupled device (ICCD). The plasma temperature and electron density were evaluated by the Boltzmann plot method and the Saha-Boltzmann equation respectively. Then the concentrations of elements in soil were further obtained by the internal standard of iron element and some selected atomic/ionic lines. In order to prove the credibility and reliability of the present LIBS results, a comparison between the LIBS results and the nominal concentrations was performed. It was found that the LIBS results agree with the nominal concentrations. Therefore the LIBS technique promises to fast and in simultaneous multi-element quantitative analysis of soil.

He, G.-C.; Sun, D.-X.; Su, M.-G.; Dong, C.-Z.

2011-09-01

183

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

184

Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.  

DOEpatents

A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. A low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic transaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively.

Alfano, Robert R. (Bronx, NY); Wang, Wubao (Flushing, NY)

2003-05-06

185

High-throughput screening of optimal solution conditions for structural biological studies by fluorescence correlation spectroscopy  

PubMed Central

Protein aggregation is an essential molecular event in a wide variety of biological situations, and is a causal factor in several degenerative diseases. The aggregation of proteins also frequently hampers structural biological analyses, such as solution NMR studies. Therefore, precise detection and characterization of protein aggregation are of crucial importance for various research fields. In this study, we demonstrate that fluorescence correlation spectroscopy (FCS) using a single-molecule fluorescence detection system enables the detection of otherwise invisible aggregation of proteins at higher protein concentrations, which are suitable for structural biological experiments, and consumes relatively small amounts of protein over a short measurement time. Furthermore, utilizing FCS, we established a method for high-throughput screening of protein aggregation and optimal solution conditions for structural biological experiments.

Sugiki, Toshihiko; Yoshiura, Chie; Kofuku, Yutaka; Ueda, Takumi; Shimada, Ichio; Takahashi, Hideo

2009-01-01

186

Quantitative assay of element mass inventories in single cell biological systems with micro-PIXE  

NASA Astrophysics Data System (ADS)

Elemental concentrations in micro-PIXE (Particle Induced X-ray Emission) maps of elements in biological tissue slices have been determined using auxiliary information on the sample matrix composition from EBS (Elastic Backscattering Spectroscopy) and STIM (Scanning Transmission Ion Microscopy). The thin sample approximation may be used for evaluating micro-PIXE data in cases, where X-ray absorption in the sample can be neglected and the mass of elements in a selected area can be estimated. The resulting sensitivity amounts to an impressive 10-12 g of the selected elements. Two cases are presented as examples. In the first, we determined the total mass of gold nanoparticles internalized by human monocyte-derived dendritic cells (MDDC). In the second, an inventory of the mass of elements in the micro-particulate material adsorbed at the wall of the lorica of the microzooplankton species Tintinnopsis radix has been created.

Ogrinc, Nina; Pelicon, Primož; Vavpeti?, Primož; Kelemen, Mitja; Grlj, Nataša; Jeromel, Luka; Tomi?, Sergej; ?oli?, Miodrag; Beran, Alfred

2013-07-01

187

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

188

Quantitative laser-induced breakdown spectroscopy for aerosols via internal calibration: Application to the oxidative coating of aluminum nanoparticles  

Microsoft Academic Search

We present a methodology for the quantitative use of laser-induced breakdown spectroscopy (LIBS) for the compositional characterization of nanoaerosols, using an internal standard. The approach involves finding the optimal laser delay time to collect spectra for each of the elemental species of interest, and measuring the plasma temperature, and background gas density under the same conditions. This enabled us to

D. Mukherjee; A. Rai; M. R. Zachariah

2006-01-01

189

An uncertainty budget for the determination of the purity of glyphosate by quantitative nuclear magnetic resonance (QNMR) spectroscopy  

Microsoft Academic Search

An uncertainty budget is presented for the results of measurements of purity of the agrochemical glyphosate using 1H and 31P quantitative nuclear magnetic resonance (QNMR) spectroscopy. The budget combines intralaboratory precision from repeated independent measurements of a batch, and other Type A and Type B effects. Consideration of correlation of uncertainties in ratios of mass determinations has been included. Expanded

TareqSaed Al-Deen; D. Brynn Hibbert; James M. Hook; Robert J. Wells

2004-01-01

190

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

191

Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets  

PubMed Central

An integrated understanding of molecular and developmental biology must consider the large number of molecular species involved and the low concentrations of many species in vivo. Quantitative stochastic models of molecular interaction networks can be expressed as stochastic Petri nets (SPNs), a mathematical formalism developed in computer science. Existing software can be used to define molecular interaction networks as SPNs and solve such models for the probability distributions of molecular species. This approach allows biologists to focus on the content of models and their interpretation, rather than their implementation. The standardized format of SPNs also facilitates the replication, extension, and transfer of models between researchers. A simple chemical system is presented to demonstrate the link between stochastic models of molecular interactions and SPNs. The approach is illustrated with examples of models of genetic and biochemical phenomena where the UltraSAN package is used to present results from numerical analysis and the outcome of simulations.

Goss, Peter J. E.; Peccoud, Jean

1998-01-01

192

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

PubMed Central

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.

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

2013-01-01

193

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

194

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

195

Quantitative measurement of AMS and orange mixtures by terahertz time-domain spectroscopy  

NASA Astrophysics Data System (ADS)

Terahertz time domain spectroscopy (THz-TDS) is a new kind of nondestructive detection method, frequency of terahertz wave spans from a few tens of GHz to several THz, which is used to detect material because of its strong identification, it can supply rich vibration information caused by intermolecular and large intra-molecular. Ammonium sulfamate (AMS) is a kind of herbicide, it has special value for many woody plants, which can prevent annual weeds. The excess use of pesticide is a huge threaten for human health in recent years, thus the research on detection of pesticide has absolutely important meaning, in this paper, pure AMS and mixture samples of AMS and orange are measured using THz-TDS, and their absorption coefficient are calculated by the model, which is put forward based on Fresnel equation. We qualitatively analyze the absorption coefficient spectra of pure AMS, which is useful for us to identify the pesticide in agriculture products. Meanwhile, we measured 14 mixture samples of AMS and orange, the weight ratio of mixtures are from 0% to 59.9%. Nine samples are considered as calibration set and the other five samples are regarded as prediction set, to quantitatively analyze the concentration of AMS by the partial least squares (PLS), the result shows that the prediction error is less then 4.5%, in addition, the relationship of the average absorption and weight ratio are absolutely linear. The experiment demonstrates that THz-TDS is promising and efficient to quantitatively detect the component of mixtures, and it has important reference value for the detection of pesticide in agriculture food.

Wang, Qiang; Ma, Yehao; Wang, Xiaowei

2012-05-01

196

Characterization and quantitation of aprepitant drug substance polymorphs by attenuated total reflectance fourier transform infrared spectroscopy.  

PubMed

In this study, we report the use of attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR) for the identification and quantitation of two polymorphs of Aprepitant, a substance P antagonist for chemotherapy-induced emesis. Mixtures of the polymorph pair were prepared by weight and ATR-FT-IR spectra of the powdered samples were obtained over the wavelength range of 700-1500 cm(-1). Significant spectral differences between the two polymorphs at 1140 cm(-1) show that ATR-FT-IR can provide definitive identification of the polymorphs. To investigate the feasibility of ATR-FT-IR for quantitation of polymorphic forms of Aprepitant, a calibration plot was constructed with known mixtures of the two polymorphs by plotting the peak ratio of the second derivative of absorbance spectra against the weight percent of form II in the polymorphic mixture. Using this novel approach, 3 wt % of one crystal form could be detected in mixtures of the two polymorphs. The accuracy of ATR-FT-IR in determining polymorph purity of the drug substance was tested by comparing the results with those obtained by X-ray powder diffractometry (XRPD). Indeed, polymorphic purity results obtained by ATR-FT-IR were found to be in good agreement with the predictions made by XRPD and compared favorably with actual values in the known mixtures. The present study clearly demonstrates the potential of ATR-FT-IR as a quick, easy, and inexpensive alternative to XRPD for the determination of polymorphic identity and purity of solid drug substances. The technique is ideally suited for polymorph analysis, because it is precise, accurate, and requires minimal sample preparation. PMID:12585491

Helmy, Roy; Zhou, George X; Chen, Yadan W; Crocker, Louis; Wang, Tao; Wenslow, Robert M; Vailaya, Anant

2003-02-01

197

In Vivo Quantitative Studies of Dynamic Intracellular Processes Using Fluorescence Correlation Spectroscopy  

PubMed Central

It has been a significant challenge to quantitatively study the dynamic intracellular processes in live cells. These studies are essential for a thorough understanding of the underlying mechanisms regulating the signaling pathways and the transitions between cell cycle stages. Our studies of Cdc20, an important mitotic checkpoint protein, throughout the cell cycle demonstrate that fluorescence correlation spectroscopy is a powerful tool for in vivo quantitative studies of dynamic intracellular processes. In this study, Cdc20 is found to be present primarily in a large complex (>1 Mda) during interphase with a diffusion constant of 1.8 ± 0.1 ?m2/s and a concentration of 76 ± 24 nM, consistent with its association with the APC/C. During mitosis, however, a proportion of Cdc20 dissociates from APC/C at a rate of 12 pM/s into a soluble pool with a diffusion constant of 19.5 ± 5.0 ?m2/s, whose size is most consistent with free Cdc20. This free pool accumulates to 50% of total Cdc20 (?40 nM) during chronic activation of the mitotic checkpoint but disappears during mitotic exit at a rate of 31 pM/s. The observed changes in the biochemical assembly states of Cdc20 closely correlate to the known temporal pattern of the activity of APC/CCdc20 in mitosis. Photon counting histograms reveal that both complexes contain only a single molecule of Cdc20. The underlying mechanisms of the activities of APC/CCdc20 throughout the cell cycle are discussed in light of our experimental observations.

Wang, Zifu; Shah, Jagesh V.; Berns, Michael W.; Cleveland, Don W.

2006-01-01

198

Quantitative FT-IR spectroscopy of gypsum raw material for industry  

NASA Astrophysics Data System (ADS)

Today quality control (QC) is a big issue for being competitive in the gypsum industry. Knowledge and understanding of the raw material help to enhance the quality and permanence of products. Therefore a rapid, precise and user-friendly FT-IR spectroscopic method for quantitative analysis of gypsum, anhydrite, magnesite and dolomite from the gypsum deposit of Puchberg, Austria is being developed. There are decisive advantages of FT-IR spectroscopy compared to thermogravimetric methods (TG, DTA, DSC) or XRD, which are commonly used for QC, e.g. it is frequently available in industry labs and a spectrum can be obtained in a few minutes, with a minimum of sample preparation. The effects of particle size and ratio of dilution with KBr were investigated in transmission mode, using KBr pellets, as well as in diffuse reflexion mode. Little differences in particle size lead to enormous differences in peak height in transmission mode, but show only little effects in diffuse reflexion. The small amounts of sample used in KBr pellets (e.g. 2 mg sample : 500 mg KBr) also turned out to be disadvantageous, just like the time consuming sample preparation. Measurements in diffuse reflexion with a sample to KBr ratio of 1:10 show promising results for use in standardization, whereas higher dilutions hardly improve the quality, and ratios of 1:5 still show components of specular reflection. The calibration model for quantitative analysis is being constructed measuring various defined mixtures of >98% pure natural minerals (gypsum, magnesite, dolomite), and synthetic materials (anhydrite). The latter was obtained by heating gypsum at 350^oC for 10 h. The synthetic material was chosen, because natural material was not available in sufficient amounts with high purity. The IR method is compared with results achieved with XRD-Rietveld and thermogravimetric methods. Advantages of chemometrical software based on multivariate statistical techniques will be investigated and compared with standard techniques using simple peak fitting methods.

Schwendtner, K.; Libowitzky, E.; Götzinger, M. A.; Koss, S.

2003-04-01

199

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

200

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

201

A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples  

NASA Astrophysics Data System (ADS)

The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans - a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

Beasley, D. G.; Alves, L. C.; Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C.; Le Trequesser, Q.; Marques, A. C.; Seznec, H.; da Silva, R. C.

2014-07-01

202

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

203

ATR-FTIR spectroscopy and quantitative multivariate analysis of paints and coating materials.  

PubMed

The applicability of ATR-FTIR spectroscopy with partial least squares (PLS) data analysis was evaluated for quantifying the components of mixtures of paint binding media and pigments, and alkyd resins. PLS methods were created using a number of standard mixtures. Validation and measurement uncertainty estimation was carried out. Binary, ternary and quaternary mixtures of several common binding media and pigments were quantified, with standard measurement uncertainties in most cases below 3g/100g. Classes of components - aromatic anhydrides and alcohols - used in alkyd resin synthesis were also successfully quantified, with standard uncertainties in the range of 2-3g/100g. This is a more demanding application because in alkyd resins aromatic anhydrides and alcohols have reacted to form a polyester, and are not present in their original forms. Once a PLS method has been calibrated, analysis time and cost are significantly reduced from typical quantitative methods such as GC/MS. This is beneficial in the case of routine analysis where the components are known. PMID:24945861

Hayes, Philippa Alice; Vahur, Signe; Leito, Ivo

2014-12-10

204

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

PubMed

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 28.3 mm2) for Raman data collection proved to be more reliable for the compositional determination of these pharmaceutical suspensions, especially when the samples were turbid. The reproducibility of measurement using the WAI scheme was compared to that of using a conventional small-spot scheme which employed a much smaller illumination area (about 100 microm spot size). A layer of isobutyric anhydride was placed in front of the sample vials to correct the variation in the Raman intensity due to the fluctuation of laser power. Corrections were accomplished using the isolated carbonyl band of isobutyric anhydride. The acetaminophen concentrations of prediction samples were accurately estimated using a partial least squares (PLS) calibration model. The prediction accuracy was maintained even with changes in laser power. It was noted that the prediction performance was somewhat degraded for turbid suspensions with high acetaminophen contents. When comparing the results of reproducibility obtained with the WAI scheme and those obtained using the conventional scheme, it was concluded that the quantitative determination of the active pharmaceutical ingredient (API) in turbid suspensions is much improved when employing a larger laser coverage area. This is presumably due to the improvement in representative sampling. PMID:17531823

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

2007-06-12

205

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

206

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

207

Quantitative analysis of synthetic calcium carbonate polymorphs using FT-IR spectroscopy.  

PubMed

Fourier Transform Infrared Spectroscopy (FT-IR) was used successfully for the simultaneous quantitative analysis of calcium carbonate phases (calcite, aragonite, vaterite) in ternary mixtures. From the FT-IR spectra of pure calcite, aragonite and vaterite powders with KBr, the absorptivities, alpha, of the absorption bands at 713 cm(-1) for calcite, 745 cm(-1) for vaterite, 713 and 700 cm(-1) for aragonite, were determined. In order to overcome the absorption band overlapping a set of equations based on Beer's law was developed. The detection limits were also established and found to be 1.1 x 10(-4) mg calcite per mm(2) of pellet at 713 cm(-1), 3.6 x 10(-4) mg aragonite per mm(2) of pellet at 700 cm(-1), 1.8 x 10(-4) mg aragonite per mm(2) of pellet at 713 cm(-1) and 3.1 x 10(-4) mg vaterite per mm(2) of pellet at 745 cm(-1). Analysis of a known ternary mixture of calcium carbonate polymorphs tested the validity of the method. PMID:18968970

Vagenas, N V; Gatsouli, A; Kontoyannis, C G

2003-03-10

208

Quantitative orientation measurements in thin lipid films by attenuated total reflection infrared spectroscopy.  

PubMed Central

Quantitative orientation measurements by attenuated total reflectance (ATR) infrared spectroscopy require the accurate knowledge of the dichroic ratio and of the mean-square electric fields along the three axes of the ATR crystal. In this paper, polarized ATR spectra of single supported bilayers of the phospholipid dimyristoylphosphatidic acid covered by either air or water have been recorded and the dichroic ratio of the bands due to the methylene stretching vibrations has been calculated. The mean-square electric field amplitudes were calculated using three formalisms, namely the Harrick thin film approximation, the two-phase approximation, and the thickness- and absorption-dependent one. The results show that for dry bilayers, the acyl chain tilt angle varies with the formalism used, while no significant variations are observed for the hydrated bilayers. To test the validity of the different formalisms, s- and p-polarized ATR spectra of a 40-A lipid layer were simulated for different acyl chain tilt angles. The results show that the thickness- and absorption-dependent formalism using the mean values of the electric fields over the film thickness gives the most accurate values of acyl chain tilt angle in dry lipid films. However, for lipid monolayers or bilayers, the tilt angle can be determined with an acceptable accuracy using the Harrick thin film approximation. Finally, this study shows clearly that the uncertainty on the determination of the tilt angle comes mostly from the experimental error on the dichroic ratio and from the knowledge of the refractive index.

Picard, F; Buffeteau, T; Desbat, B; Auger, M; Pezolet, M

1999-01-01

209

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

PubMed Central

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, SH; Cerussi, AE; Merritt, SI; Ruth, J; Tromberg, BJ

2012-01-01

210

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

211

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

NASA Astrophysics Data System (ADS)

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° by using a Monte Carlo simulation method. The calculation employs a general definition of backscattering factor, Casnati's ionization cross section, up-to-date Monte Carlo model of electron scattering, and a large number of electron trajectories to ensure less statistical error. Both the configuration geometry of concentric hemispherical analyzer and the cylindrical mirror analyzer for Auger electron detection are considered in the calculation. The calculated backscattering factors are found to describe very well an experimental dependence of Auger electron intensity on primary energy and on incident angle for Si, Cu, Ag, and W in literature. The calculated numerical values of backscattering factor are stored in an open and online database at http://micro.ustc.edu.cn/BSFDataBase/BFAES.htm.

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

2008-12-01

212

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

SciTech Connect

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 deg. - 89 deg. and for principal Auger transition and Auger electrons emitted from over 28 pure elements at an emission angle of 0 deg. - 89 deg. by using a Monte Carlo simulation method. The calculation employs a general definition of backscattering factor, Casnati's ionization cross section, up-to-date Monte Carlo model of electron scattering, and a large number of electron trajectories to ensure less statistical error. Both the configuration geometry of concentric hemispherical analyzer and the cylindrical mirror analyzer for Auger electron detection are considered in the calculation. The calculated backscattering factors are found to describe very well an experimental dependence of Auger electron intensity on primary energy and on incident angle for Si, Cu, Ag, and W in literature. The calculated numerical values of backscattering factor are stored in an open and online database at http://micro.ustc.edu.cn/BSFDataBase/BFAES.htm.

Zeng, R. G.; Ding, Z. J.; Li, Y. G.; Mao, S. F. [Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

2008-12-01

213

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

SciTech Connect

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 number of electron trajectories to ensure less statistical error. The results reveal several noticeable properties of backscattering factor, i.e., its slow variation with primary energy at higher overvoltage ratios, and dependence on the geometrical configuration of a detector. However, only for large emission angles of Auger signals a considerable angular dependence of backscattering factor is found. Specifically a calculation is carried out for detection in the solid angles of a cylindrical mirror analyzer. This backscattering factor can be less than unity for very low primary energies closing to ionization energy and/or for large incident angles. The physical cause has been detailed and analyzed.

Ding, Z. J.; Tan, W. S.; Li, Y. G. [Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, 230026 Anhui (China) and Department of Physics, University of Science and Technology of China, Hefei, 230026 Anhui (China)

2006-04-15

214

Quantitative analysis and detection of adulteration in crab meat using visible and near-infrared spectroscopy.  

PubMed

Visible and near-infrared spectroscopy (VIS/NIR) has been used to detect economic adulteration of crab meat samples. Atlantic blue and blue swimmer crab meat samples were adulterated with surimi-based imitation crab meat in 10% increments. Waveform evaluation revealed that the main features seen in the spectral data arise from water absorptions with a decrease in sample absorbance with increasing adulteration level. Prediction and quantitative analysis was done using raw data, a 15-point smoothing average, a first derivative, a second derivative, and 150 wavelength spectral data gathered from a correlogram. Regression analysis included partial least squares (PLS) and principal component analysis (PCR). Both models were able to perform similarly in predicting crab meat adulteration. The best model for both PLS and PCR used the first derivative spectral data gathered from the correlogram, with a standard error of prediction (SEP) of 0.252 and 0.244, respectively. The results suggest that VIS/NIR technology can be successfully used to detect adulteration in crab meat samples adulterated with surimi-based imitation crab meat. PMID:16478227

Gayo, Javier; Hale, Scott A; Blanchard, Susan M

2006-02-22

215

Quantitative estimation of concentrations of dissolved rare earth elements using reflectance spectroscopy  

NASA Astrophysics Data System (ADS)

Characteristic spectral parameters such as the wavelength and depth of absorption bands are widely used to quantitatively estimate the composition of samples from hyperspectral reflectance data in soil science, mineralogy as well as vegetation study. However, little research has been conducted on the spectral characteristic of rare earth elements (REE) and their relationship with chemical composition of aqueous solutions. Reflectance spectra of ore leachate solutions and contaminated stream water from a few REE mines in the Jiangxi Province, China, are studied for the first time in this work. The results demonstrate that the six diagnostic absorption features of the rare earths are recognized in visible and near-infrared wavelengths at 574, 790, 736, 520, 861, and 443 nm. The intensity of each of these six absorption bands is linearly correlated with the abundance of total REE, with the r2 value >0.95 and the detection limit at ?75,000 ?g/L. It is suggested that reflectance spectroscopy provides an ideal routine analytical tool for characterizing leachate samples. The outcome of this study also has implications for monitoring the environmental effect of REE mining, in particular in stream water systems by hyperspectral remote sensing.

Dai, Jingjing; Wang, Denghong; Wang, Runsheng; Chen, Zhenghui

2013-01-01

216

Evaluation of green coffee beans quality using near infrared spectroscopy: a quantitative approach.  

PubMed

Characterisation of coffee quality based on bean quality assessment is associated with the relative amount of defective beans among non-defective beans. It is therefore important to develop a methodology capable of identifying the presence of defective beans that enables a fast assessment of coffee grade and that can become an analytical tool to standardise coffee quality. In this work, a methodology for quality assessment of green coffee based on near infrared spectroscopy (NIRS) is proposed. NIRS is a green chemistry, low cost, fast response technique without the need of sample processing. The applicability of NIRS was evaluated for Arabica and Robusta varieties from different geographical locations. Partial least squares regression was used to relate the NIR spectrum to the mass fraction of defective and non-defective beans. Relative errors around 5% show that NIRS can be a valuable analytical tool to be used by coffee roasters, enabling a simple and quantitative evaluation of green coffee quality in a fast way. PMID:22953929

Santos, João Rodrigo; Sarraguça, Mafalda C; Rangel, António O S S; Lopes, João A

2012-12-01

217

Quantitative hydrogen analysis of zircaloy-4 in laser-induced breakdown spectroscopy with ambient helium gas  

SciTech Connect

This experiment was carried out to address the need for overcoming the difficulties encountered in hydrogen analysis by means of plasma emission spectroscopy in atmospheric ambient gas. The result of this study on zircaloy-4 samples from a nuclear power plant demonstrates the possibility of attaining a very sharp emission line from impure hydrogen with a very low background and practical elimination of spectral contamination of hydrogen emission arising from surface water and water vapor in atmospheric ambient gas. This was achieved by employing ultrapure ambient helium gas as well as the proper defocusing of the laser irradiation and a large number of repeated precleaning laser shots at the same spot of the sample surface. Further adjustment of the gating time has led to significant reduction of spectral width and improvement of detection sensitivity to {approx}50 ppm. Finally, a linear calibration curve was also obtained for the zircaloy-4 samples with zero intercept. These results demonstrate the feasibility of this technique for practical in situ and quantitative analysis of hydrogen impurity in zircaloy-4 tubes used in a light water nuclear power plant.

Ramli, Muliadi; Fukumoto, Ken-ichi; Niki, Hideaki; Abdulmadjid, Syahrun Nur; Idris, Nasrullah; Maruyama, Tadashi; Kagawa, Kiichiro; Tjia, May On; Pardede, Marincan; Kurniawan, Koo Hendrik; Hedwig, Rinda; Lie, Zener Sukra; Lie, Tjung Jie; Kurniawan, Davy Putra

2007-12-01

218

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

PubMed

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 show that the damage caused by high-dose data acquisition affects the accuracy of a multiple-least-squares (MLS) compositional analysis because of inaccuracies in the reference spectrum used to represent the protein. Higher spatial resolution combined with more accurate compositional analysis can be achieved if a reference spectrum is used that better represents the electron-beam-damaged protein component under frozen-hydrated conditions rather than one separately collected from dry protein under low-dose conditions. We thus introduce a method to extract the best-fitting protein reference spectrum from an experimental spectrum dataset. This method can be used when the MLS-fitting problem is sufficiently constrained so that the only unknown is the reference spectrum for the protein component. We apply this approach to map the distribution of water in cryo-sections obtained from frozen-hydrated tissue of porcine skin. The raw spectral data were collected at doses up to 10(5)e/nm(2) despite the fact that observable damage begins at doses as low as 10(3)e/nm(2). The resulting spatial resolution of 10nm is 5-10 times better than that in previous studies of frozen-hydrated tissue and is sufficient to resolve sub-cellular water fluctuations as well as the inter-cellular lipid-rich regions of skin where water-mediated processes are believed to play a significant role in the phenotype of keratinocytes in the stratum corneum. PMID:20447768

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

2010-06-01

219

Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.  

DOEpatents

A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. In accordance with the teachings of the invention, a low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic tansaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively. For example, it may also be used to diagnose diseases associated with the concentration of Raman-active constituents in urine, lymph and saliva It may be used to identify cancer in the breast, cervix, uterus, ovaries and the like by measuring the fingerprint excitation Raman spectra of these tissues. It may also be used to reveal the growing of tumors or cancers by measuring the levels of nitric oxide in tissue.

Alfano, Robert R. (Bronx, NY); Wang, Wubao (Flushing, NY)

2000-11-21

220

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

221

Heterogeneous nanostructures for plasmonic interaction with luminescence and quantitative surface-enhanced Raman spectroscopy  

NASA Astrophysics Data System (ADS)

NIR-to-visible up-conversion nanomaterials have been investigated in many promising applications including nextgeneration displays, solar cells, and biological labels. When doped with different trivalent lanthanide ions, NaYF4 nanoparticles can produce up-converted emission from visible to infra-red wavelengths. However, the quantum yield of this class of materials is low. Noble metals in the vicinity of the phosphor can increase the phosphorescence by local field enhancement due to plasmonic resonances, and by modification of the radiative rate of the phosphor. Most previous studies have investigated the phenomenon by placing nanophosphors onto a metal substrate, or by fabrication of nano structures with spacers such as polymers, dielectric materials (silica). By contrast, we have studied the interaction between the luminescence and the surface plasmon using a core-shell type nanostructure where a uniform shell of silver is shown to grown on doped-NaYF4 nanophosphors by Ostwald ripening. We further demonstrate the proximity effect of metal-enhanced luminescence by exciting an undoped NaYF4 shell. The result shows a significant synergistic enhancement of up-conversion luminescence due to the active shell as spacer layer. In addition, we have shown this novel nanostructure may be useful in surface-enhanced Raman spectroscopy (SERS).

Das, Gautom K.; Sudheendra, L.; Kennedy, Ian M.

2014-03-01

222

Center for Synchrotron Biosciences' U2B beamline: an international resource for biological infrared spectroscopy.  

PubMed

A synchrotron infrared (IR) beamline, U2B, dedicated to the biomedical and biological sciences has been constructed and is in operation at the National Synchrotron Light Source (NSLS) of Brookhaven National Laboratory. The facility is operated by the Center for Synchrotron Biosciences of the Albert Einstein College of Medicine in cooperation with the NSLS. Owing to the broadband nature of the synchrotron beam with brightness 1000 times that of conventional sources, Fourier transform IR spectroscopy experiments are feasible on diffraction-limited sample areas at high signal-to-noise ratios and with relatively short data-acquisition times. A number of synchrotron IR microscopy experiments that have been performed in the mid-IR spectral range (500-5000 cm(-1)) are summarized, including time-resolved protein-folding studies in the microsecond time regime, IR imaging of neurons, bone and other biological tissues, as well as imaging of samples of interest in the chemical and environmental sciences. Owing to the high flux output of this beamline in the far-IR region (50-500 cm(-1)), investigations of hydrogen bonding and dynamic molecular motions of biomolecules have been carried out from 10 to 300 K using a custom-made cryostat and an evacuated box. This facility is intended as an international resource for biological IR spectroscopy fully available to outside users based on competitive proposal. PMID:12091724

Marinkovic, N S; Huang, R; Bromberg, P; Sullivan, M; Toomey, J; Miller, L M; Sperber, E; Moshe, S; Jones, K W; Chouparova, E; Lappi, S; Franzen, S; Chance, M R

2002-07-01

223

Spectroscopy of scattered light for the characterization of micro and nanoscale objects in biology and medicine.  

PubMed

The biomedical uses for the spectroscopy of scattered light by micro and nanoscale objects can broadly be classified into two areas. The first, often called light scattering spectroscopy (LSS), deals with light scattered by dielectric particles, such as cellular and sub-cellular organelles, and is employed to measure their size or other physical characteristics. Examples include the use of LSS to measure the size distributions of nuclei or mitochondria. The native contrast that is achieved with LSS can serve as a non-invasive diagnostic and scientific tool. The other area for the use of the spectroscopy of scattered light in biology and medicine involves using conducting metal nanoparticles to obtain either contrast or electric field enhancement through the effect of the surface plasmon resonance (SPR). Gold and silver metal nanoparticles are non-toxic, they do not photobleach, are relatively inexpensive, are wavelength-tunable, and can be labeled with antibodies. This makes them very promising candidates for spectrally encoded molecular imaging. Metal nanoparticles can also serve as electric field enhancers of Raman signals. Surface enhanced Raman spectroscopy (SERS) is a powerful method for detecting and identifying molecules down to single molecule concentrations. In this review, we will concentrate on the common physical principles, which allow one to understand these apparently different areas using similar physical and mathematical approaches. We will also describe the major advancements in each of these areas, as well as some of the exciting recent developments. PMID:24480270

Turzhitsky, Vladimir; Qiu, Le; Itzkan, Irving; Novikov, Andrei A; Kotelev, Mikhail S; Getmanskiy, Michael; Vinokurov, Vladimir A; Muradov, Alexander V; Perelman, Lev T

2014-02-01

224

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

225

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

226

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

227

Cancer therapy prognosis using quantitative ultrasound spectroscopy and a kernel-based metric  

NASA Astrophysics Data System (ADS)

In this study, a kernel-based metric based on the Hilbert-Schmidt independence criterion (HSIC) is proposed in a computer-aided-prognosis system to monitor cancer therapy effects. In order to induce tumour cell death, sarcoma xenograft tumour-bearing mice were injected with microbubbles followed by ultrasound and X-ray radiation therapy successively as a new anti-vascular treatment. High frequency (central frequency 30 MHz) ultrasound imaging was performed before and at different times after treatment and using spectroscopy, quantitative ultrasound (QUS) parametric maps were derived from the radiofrequency (RF) signals. The intensity histogram of midband fit parametric maps was computed to represent the pre- and post-treatment images. Subsequently, the HSIC-based metric between preand post-treatment samples were computed for each animal as a measure of distance between the two distributions. The HSIC-based metrics computes the distance between two distributions in a reproducing kernel Hilbert space (RKHS), meaning that by using a kernel, the input vectors are non-linearly mapped into a different, possibly high dimensional feature space. Computing the population means in this new space, enhanced group separability (compared to, e.g., Euclidean distance in the original feature space) is ideally obtained. The pre- and post-treatment parametric maps for each animal were thus represented by a dissimilarity measure, in which a high value of this metric indicated more treatment effect on the animal. It was shown in this research that this metric has a high correlation with cell death and if it was used in supervised learning, a high accuracy classification was obtained using a k-nearest-neighbor (k-NN) classifier.

Gangeh, Mehrdad J.; Hashim, Amr; Giles, Anoja; Czarnota, Gregory J.

2014-03-01

228

Quantitative treatment of coarsely binned low-resolution recordings in molecular absorption spectroscopy  

NASA Astrophysics Data System (ADS)

Optical multichannel detectors like photodiode arrays or CCD cameras combined with grating spectrometers are commonly used as detection systems in quantitative absorption spectroscopy. As a trade-off to broad spectral coverage, banded spectral features are sometimes recorded with insufficient spectral resolution and/or insufficiently fine detector binning. This renders the true physical spectrum of recorded intensities changed by instrumental and spectrum specific artefacts thus impeding comparability between results from different set-ups. In this work, it is demonstrated that in the case of a "well-behaved" - i.e. free of ro-vibronic structure - absorption band like the iodine monoxide IO(4 ? 0) transition, these effects can easily change the apparent peak absorption by up to 50%. Also deviations from the strict linearity (Beer-Lambert's law) between absorber concentration and apparent, i.e. pixelwise optical density occur. This can be critical in studies of chemical kinetics. It is shown that the observed non-linearity can cause errors of up to 50% in the determination of a second order rate coefficient for the IO self reaction. To overcome the problem, a consistent and rigorous integral approach for the treatment of intensity recordings is developed. Linearity between optical density and absorber concentration thereby is re-established. The method is validated using artificial test data as well as experimental data of the IO(4 ? 0) absorption transition, obtained in the context of I 2/O 3 photochemistry studies. The agreement is accurate to within ±2% (test data) and ±3% (experimental data) supporting the validity of the approach. Possible consequences for other spectroscopic work are indicated.

Spietz, Peter; Martín, Juan Carlos Gómez; Burrows, John P.

2006-06-01

229

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

230

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

2012-11-01

231

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

232

Quantitative analysis of three-dimensional biological cells using interferometric microscopy  

NASA Astrophysics Data System (ADS)

Live biological cells are three-dimensional microscopic objects that constantly adjust their sizes, shapes and other biophysical features. Wide-field digital interferometry (WFDI) is a holographic technique that is able to record the complex wavefront of the light which has interacted with in-vitro cells in a single camera exposure, where no exogenous contrast agents are required. However, simple quasi-three-dimensional holographic visualization of the cell phase profiles need not be the end of the process. Quantitative analysis should permit extraction of numerical parameters which are useful for cytology or medical diagnosis. Using a transmission-mode setup, the phase profile represents the multiplication between the integral refractive index and the thickness of the sample. These coupled variables may not be distinct when acquiring the phase profiles of dynamic cells. Many morphological parameters which are useful for cell biologists are based on the cell thickness profile rather than on its phase profile. We first overview methods to decouple the cell thickness and its refractive index using the WFDI-based phase profile. Then, we present a whole-cell-imaging approach which is able to extract useful numerical parameters on the cells even in cases where decoupling of cell thickness and refractive index is not possible or desired.

Shaked, Natan T.; Wax, Adam

2011-05-01

233

Monitoring intracellular polyphosphate accumulation in enhanced biological phosphorus removal systems by quantitative image analysis.  

PubMed

A rapid methodology for intracellular storage polyphosphate (poly-P) identification and monitoring in enhanced biological phosphorus removal (EBPR) systems is proposed based on quantitative image analysis (QIA). In EBPR systems, 4',6-diamidino-2-phenylindole (DAPI) is usually combined with fluorescence in situ hybridization to evaluate the microbial community. The proposed monitoring technique is based on a QIA procedure specifically developed for determining poly-P inclusions within a biomass suspension using solely DAPI by epifluorescence microscopy. Due to contradictory literature regarding DAPI concentrations used for poly-P detection, the present work assessed the optimal DAPI concentration for samples acquired at the end of the EBPR aerobic stage when the accumulation occurred. Digital images were then acquired and processed by means of image processing and analysis. A correlation was found between average poly-P intensity values and the analytical determination. The proposed methodology can be seen as a promising alternative procedure for quantifying intracellular poly-P accumulation in a faster and less labour-intensive way. PMID:24901627

Mesquita, Daniela P; Amaral, A Luís; Leal, Cristiano; Carvalheira, Mónica; Cunha, Jorge R; Oehmen, Adrian; Reis, Maria A M; Ferreira, Eugénio C

2014-01-01

234

Quantitative elemental X-ray imaging of frozen-hydrated biological samples.  

PubMed

It is shown that quantitative X-ray imaging of planed, frozen-hydrated, biological bulk samples that have not been etched is possible. X-ray imaging represents a better alternative to static beam (selected area) analysis of fractured frozen-hydrated samples. This procedure avoids the undesirable necessity of etching planed frozen-hydrated samples to provide an interpretable electron image. Qualitative oxygen and carbon X-ray images, which can be acquired in a short time, can be used for distinguishing morphological features and remove the requirement for electron images. In test samples of frozen-hydrated albumin, containing salts, analyses by X-ray images compared well with static beam (selected area) analyses from the same samples. An example of an analysis of frozen-hydrated insect Malpighian tubules is given in which the response to ouabain treatment was analysed. In this example X-ray imaging showed that ouabain resulted in a significant increase in cytoplasmic and luminal Na and a significant decrease in cytoplasmic and luminal K. X-ray imaging also showed that there was a significant increase in cellular water content. The presence of a potassium gradient in soybean root nodules was also demonstrated. The use of standard deviation images for processing low count images increases analytical precision but results in underestimates of the true concentrations. PMID:9674156

Marshall, A T; Xu, W

1998-06-01

235

Using Softer X-ray Absorption Spectroscopy to Probe Biological Systems  

SciTech Connect

Many inorganic species are now recognized as being essential for life, including many forms of sulfur, phosphate and numerous classes of metal ions. For example, recent progress in the fields of biochemistry and biology has pointed out the critical importance of sulfur in the biosynthesis of vital cofactors and active sites in proteins, and in the complex reaction mechanisms often involved. Special attention has also been drawn to the diverse roles of alkaline (Na{sup +}, K{sup +}) and alkaline earth (Mg{sup 2+}, Ca{sup 2+}) metal ions in mediating the activity of RNA, proteins and many processes in living cells. While the general effect of these ions in biology is mostly understood, information on their detailed role is deficient. Here the application of softer X-ray absorption spectroscopy (XAS) to probe the local structural and electronic environment of such ions within their biological complexes and during physiological reactions is discussed. In addition, the required experimental set-up and the difficulties associated with conducting softer XAS experiments on biological samples are presented.

Akabayov,B.; Doonan, C.; Pickering, I.; George, G.; Sagi, I.

2005-01-01

236

High-resolution two-dimensional j-resolved NMR spectroscopy for biological systems.  

PubMed

NMR spectroscopy is a principal tool in metabolomic studies and can, in theory, yield atom-level information critical for understanding biological systems. Nevertheless, NMR investigations on biological tissues generally have to contend with field inhomogeneities originating from variations in macroscopic magnetic susceptibility; these field inhomogeneities broaden spectral lines and thereby obscure metabolite signals. The congestion in one-dimensional NMR spectra of biological tissues often leads to ambiguities in metabolite identification and quantification. We propose an NMR approach based on intermolecular double-quantum coherences to recover high-resolution two-dimensional (2D) J-resolved spectra from inhomogeneous magnetic fields, such as those created by susceptibility variations in intact biological tissues. The proposed method makes it possible to acquire high-resolution 2D J-resolved spectra on intact biological samples without recourse to time-consuming shimming procedures or the use of specialized hardware, such as magic-angle-spinning probes. Separation of chemical shifts and J couplings along two distinct dimensions is achieved, which reduces spectral crowding and increases metabolite specificity. Moreover, the apparent J coupling constants observed are magnified by a factor of 3, facilitating the accurate measurement of small J couplings, which is useful in metabolic analyses. Dramatically improved spectral resolution is demonstrated in our applications of the technique on pig brain tissues. The resulting spectra contain a wealth of chemical shift and J-coupling information that is invaluable for metabolite analyses. A spatially localized experiment applied on an intact fish (Crossocheilus siamensis) reveals the promise of the proposed method in in vivo metabolite studies. Moreover, the proposed method makes few demands on spectrometer hardware and therefore constitutes a convenient and effective manner for metabonomics study of biological systems. PMID:24806938

Huang, Yuqing; Cai, Shuhui; Zhang, Zhiyong; Chen, Zhong

2014-05-01

237

Tip-enhanced Raman spectroscopy and related techniques in studies of biological materials  

NASA Astrophysics Data System (ADS)

Biological materials can be highly heterogeneous at the nanometer scale. The investigation of nanostructures is often hampered by the low spatial resolution (e.g. spectroscopic techniques) or very little chemical information (e.g. atomic force microscopy (AFM), scanning tunneling microscopy (STM)) provided by analytical techniques. Our research focuses on combined instruments, which allow the analysis of the exactly same area of a sample by complementary techniques, such as AFM and Raman spectroscopy. Tip-enhanced Raman spectroscopy (TERS) combines the high spatial resolution of AFM or STM with the chemical information provided by Raman spectroscopy. The technique is based on enhancement effects known from surface-enhanced Raman scattering (SERS). In TERS the enhancing metallic nanostructure is brought to the sample by an AFM or STM tip. With a TERS-active tip, enhanced Raman signals can be generated from a sample area as small as 10-50 nm in diameter. AFM analysis of bacterial biofilms has demonstrated their heterogeneity at the nanometer scale, revealing a variety of nanostructures such as pili, flagella, and extracelullar polymers. TERS measurements of the biopolymers alginate and cytochrome c have yielded spectroscopic fingerprints even of such weak Raman scatterers, which in future can allow their localization in complex matrices. Furthermore, biofilms of the bacterium Halomonas meridiana were studied, which was found to be involved in the generation of the mineral dolomite. Only combined AFM-Raman analysis was able to identify the nanoglobules found in laboratory cultures of H. meridiana as dolomite nanoparticles. Our combined setups are and will be applied to the investigation of biofilms, fish spermatozoa as well as biological membranes.

Schmid, Thomas; Sebesta, Aleksandar; Stadler, Johannes; Opilik, Lothar; Balabin, Roman M.; Zenobi, Renato

2010-02-01

238

Multivariate processing strategies for enhancing qualitative and quantitative analysis based on infrared spectroscopy  

NASA Astrophysics Data System (ADS)

Airborne passive Fourier transform infrared spectrometry is gaining increased attention in environmental applications because of its great flexibility. Usually, pattern recognition techniques are used for automatic analysis of large amount of collected data. However, challenging problems are the constantly changing background and high calibration cost. As aircraft is flying, background is always changing. Also, considering the great variety of backgrounds and high expense of data collection from aircraft, cost of collecting representative training data is formidable. Instead of using airborne data, data generated from simulation strategies can be used for training purposes. Training data collected under controlled conditions on the ground or synthesized from real backgrounds can be both options. With both strategies, classifiers may be developed with much lower cost. For both strategies, signal processing techniques need to be used to extract analyte features. In this dissertation, signal processing methods are applied either in interferogram or spectral domain for features extraction. Then, pattern recognition methods are applied to develop binary classifiers for automated detection of air-collected methanol and ethanol vapors. The results demonstrate, with optimized signal processing methods and training set composition, classifiers trained from ground-collected or synthetic data can give good classification on real air-collected data. Near-infrared (NIR) spectrometry is emerging as a promising tool for noninvasive blood glucose detection. In combination with multivariate calibration techniques, NIR spectroscopy can give quick quantitative determinations of many species with minimal sample preparation. However, one main problem with NIR calibrations is degradation of calibration model over time. The varying background information will worsen the prediction precision and complicate the multivariate models. To mitigate the needs for frequent recalibration and improve robustness of calibration models, signal processing methods can be used to decrease the influence of such non-constant background variation. In this dissertation, signal processing methods are also applied to NIR single-beam spectra collected during short-term and long-term studies. The prediction performance of the calibration models demonstrates, with suppression of non-constant background information by optimal wavelet processing procedures, robustness of calibration models with time can be significantly improved.

Wan, Boyong

239

Impact of pellet thickness on quantitative terahertz spectroscopy of solid samples in a polyethylene matrix.  

PubMed

Pellets composed of different weight-percent (wt-%) of lactose within a polyethylene (PE) matrix are used to examine how the physical thickness of solid samples impact analytical measurements performed over terahertz (THz) frequencies when using time-domain THz spectroscopy. Results indicate that the thickness of each pellet depends on the mass and physical properties of the individual components that comprise the pellet. Thickness of mixture pellets depends on the porosity of the individual pellet components. Porosity measurements presented here for PE and lactose give values of 25.6 ± 0.3 and 14.5 ± 0.1, respectively, which indicate that more air is trapped within the compressed PE matrix compared to that for lactose. This difference in porosity creates different pellet thicknesses for pellets of the same nominal mass but with different relative amounts of PE and lactose. For this binary matrix, the thickness of each pellet is found to be a linear combination of the compressed densities of the individual components. Analysis of the time-domain THz spectra reveals that thinner samples are confounded by a fringe pattern observed in the frequency-domain spectra. This fringe pattern is created by an etalon corresponding to the air/pellet interfaces for the sample in the optical path. Spectra collected from thicker pellets are confounded by a sloping baseline caused by scattering effects within the pellet matrix. The quantitative impact of pellet thickness is determined by comparing the mean standard error of calibration (MSEC) and mean standard error of prediction (MSEP) for a set of leave-three-out cross validation multivariate calibration models based on the partial least-squares (PLS) algorithm. Results indicate that PLS models are capable of analytical measurements with MSEC and MSEP values between 0.04 and 0.20 wt-%. Analysis of spectral variance captured within the corresponding spectral loadings for each model indicates that spectral variance is lowest for the 300 mg samples where the impact of scattering is minimal under conditions when the sample etalon is nonexistent. PMID:23438763

Namkung, Hankyu; Kim, Jaejin; Chung, Hoeil; Arnold, Mark A

2013-04-01

240

Determination of a Quantitative Algorithm for the Measurement of Muscle Oxygenation Using CW Near-Infrared Spectroscopy Mean Optical Pathlength Without the Influence of Adipose Tissue.  

National Technical Information Service (NTIS)

Near-infrared spectroscopy (NIRS) is a useful technique for noninvasive measurement of oxygenation of the brain and muscle. However, no accurate, quantitative algorithms for continuous wave NIRS (CW-NIRS) have yet been presented dute to the following two ...

J. Shao K. Yamamoto L. Lin M. Niwayama N. Kudo

2000-01-01

241

Quantitative determination of glufosinate in biological samples by liquid chromatography with ultraviolet detection after p-nitrobenzoyl derivatization  

Microsoft Academic Search

We have established a new HPLC method for derivatizing and quantifying glufosinate (GLUF) in human serum and urine using p-nitrobenzoyl chloride (PNBC). The p-nitrobenzoyl derivative of GLUF (PNB-GLUF) was produced quantitatively over 10 min at room temperature. PNB-GLUF possesses the property of ultraviolet (UV) light absorption with a ?max of 272.8 nm, and was isolated from biological specimens by reversed-phase

Yasushi Hori; Manami Fujisawa; Kenji Shimada; Mitsuru Sato; Michio Kikuchi; Masao Honda; Yasuo Hirose

2002-01-01

242

Quantitative correlation of the in vitro biological effect with parameters of molecular complexation in mutagen-interceptor systems.  

PubMed

According to the theory of interceptor-protector action a quantitative link between the physico-chemical parameters of molecular complexation and in vitro biological effect in aromatic drug-interceptor systems must exist. In the present communication such link between relative change in mutagenicity of IQ-type aromatic mutagens on addition of aromatic interceptor molecules with equilibrium hetero-association constants of mutagen-interceptor complexation has been found using the published in vitro data in bacteria cell systems. PMID:24972156

Buchelnikov, Anatoly S; Evstigneev, Maxim P

2014-09-21

243

Quantitative analysis of surface amine groups on plasma-polymerized ethylenediamine films using UV–visible spectroscopy compared to chemical derivatization with FT-IR spectroscopy, XPS and TOF-SIMS  

Microsoft Academic Search

A quantitative analysis of the surface density of amine groups on a plasma-polymerized ethylenediamine thin film deposited on a platinum surface using inductively coupled plasma chemical vapor deposition method is described. UV–visible spectroscopy together with a chemical derivatization technique using Fourier transform infrared (FT-IR) spectroscopy was used to obtain the quantitative information. Chemical tags of pentafluorobenzaldehyde were hybridized with the

Jinmo Kim; Donggeun Jung; Yongki Kim; Dae Won Moon; Tae Geol Lee

2007-01-01

244

Quantitative Infrared Spectroscopy of Glucose in Blood Using Partial Least-Squares Analyses.  

National Technical Information Service (NTIS)

The concentration of glucose in drawn samples of human blood has been determined using attenuated total reflectance (ATR) Fourier transform infrared (FT-IR) spectroscopy and partial least-squares (PLS) multivariate calibration. A twelve sample calibration...

K. J. Ward D. M. Haaland M. R. Robinson R. P. Eaton

1989-01-01

245

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

National Technical Information Service (NTIS)

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), hydroxyethylenediaminetetraac...

C. K. Mann T. J. Vickers

1994-01-01

246

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

PubMed

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. PMID:22734784

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

2012-06-01

247

Raman spectroscopy: A tool for the quantitative analysis of mineral components of solid mixtures. The case of calcium oxalate monohydrate and hydroxyapatite  

Microsoft Academic Search

A quantitative analytical methodology based on Raman spectroscopy (RS) was developed for the compositional analysis of binary solid mixtures consisting of calcium oxalate monohydrate (COM) and hydroxyapatite (HAP). The ratios of the relative intensities of the Raman bands corresponding to HAP and COM were used for the construction of calibration curves used for the quantitative analysis. The intensities at 960

Christos G. Kontoyannis; Nikolaos C. Bouropoulos; Petros G. Koutsoukos

1997-01-01

248

Quantitative Raman Spectroscopy to monitor microbial metabolism in situ under pressure  

NASA Astrophysics Data System (ADS)

Although high hydrostatic pressure (HHP) biotopes are ubiquitous on Earth, little is known about the metabolism of piezophile organisms. Cell culture under HHP can be technically challenging, and equipment- dependent. In addition, the depressurization step required for analysis can lead to erroneous data. Therefore, to understand how piezophile organisms react to pressure, it is crucial to be able to monitor their activity in situ under HHP. We developed the use of Quantitative Raman Spectroscopy (QRS, 1) to monitor in situ the metabolism of organic molecules. This technique is based on the specific spectral signature of an analyte from which its concentration can be deduced. An application of this technique to the monitoring of alcoholic fermentation by the piezotolerant micro-eucaryote Saccharomyces cerevisiae is presented. Ethanol fermentation from glucose was monitored during 24h from ambient P up to 100 MPa in the low- pressure Diamond Anvil Cell (lpDAC, 2). The experimental compression chamber consisted in a 300 ?m-thick Ni gasket in which a 500 ?m-diameter hole was drilled. Early-stationnary yeast cells were inoculated into fresh low-fluorescence medium containing 0.15 M of glucose. Ethanol concentration was determined in situ by QRS using the symmetric C-C stretching mode of ethanol at 878 cm-1 normalizing the data to the intensity of the sulfate S-O stretching mode at 980 cm-1. In our setup, the detection limit of ethanol is lower than 0.05 mM with a precision below 1%. At ambient P, ethanol production in the lpDAC and in control experiments proceeds with the same kinetics. Thus, yeast is not affected by its confinement. This is further confirmed by its ability to bud with a generation time similar to control experiments performed in glass tubes at ambient pressure inside the lpDAC. Ethanol production by yeast occurs to at least 65 MPa (3). At 10 MPa, fermentation proceeds 3 times faster than at ambient P. Fermentation rates decrease linearly from 20 to at least 65 MPa. No ethanol was detected at 100 MPa. From these data, the pressure at which ethanol fermentation stops in yeast was 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. At higher pressure, they become progressively repressed, and are completely inhibited above 87 MPa. Our in situ monitoring constitutes a direct demonstration of yeast metabolism in situ under pressure up to 100 MPa. Our data agree with previous ex-situ data by Abe and Horikoshi (4). However, we observed that ethanol production is not completely inhibited around 50 MPa as predicted, but could be detected at significantly higher pressures (up to 87 MPa). QSR is a powerful method to monitor microbial activities, since almost any organic molecule with a carbon chain ranging from 1 to 6 carbon can be detected and quantified. The only limitation of QSR is that the Raman spectrum of the molecule exhibits at least one peak not masked by the spectrum of the growth medium. 1 Pelletier M J Appl Spectr 57:20A-42A, 2003 2 Daniel I, Oger P, Picard A, Cardon H and Chervin J-C (submitted to Rev Sci Instr) 3 Picard A, Daniel I, Montagnac G and Oger P (submitted to Extremophiles) 4 Abe F and Horikoshi K Extremophiles 1: 89-93, 1997

Picard, A.; Daniel, I.; Oger, P.

2006-12-01

249

Magnetic induction spectroscopy: non-contact measurement of the electrical conductivity spectra of biological samples  

NASA Astrophysics Data System (ADS)

Measurement of the electrical conductivity of biological tissues as a function of frequency, often termed ‘bioelectrical impedance spectroscopy (BIS)’, provides valuable information on tissue structure and composition. In implementing BIS though, there can be significant practical difficulties arising from the electrode-sample interface which have likely limited its deployment in industrial applications. In magnetic induction spectroscopy (MIS) these difficulties are eliminated through the use of fully non-contacting inductive coupling between the sensors and sample. However, inductive coupling introduces its own set of technical difficulties, primarily related to the small magnitudes of the induced currents and their proportionality with frequency. This paper describes the design of a practical MIS system incorporating new, highly-phase-stable electronics and compares its performance with that of electrode-based BIS in measurements on biological samples including yeast suspensions in saline (concentration 50-400 g l-1) and solid samples of potato, cucumber, tomato, banana and porcine liver. The shapes of the MIS spectra were in good agreement with those for electrode-based BIS, with a residual maximum discrepancy of 28%. The measurement precision of the MIS was 0.05 S m-1 at 200 kHz, improving to 0.01 S m-1 at a frequency of 20 MHz, for a sample volume of 80 ml. The data-acquisition time for each MIS measurement was 52 s. Given the value of spectroscopic conductivity information and the many advantages of obtaining these data in a non-contacting manner, even through electrically-insulating packaging materials if necessary, it is concluded that MIS is a technique with considerable potential for monitoring bio-industrial processes and product quality.

Barai, A.; Watson, S.; Griffiths, H.; Patz, R.

2012-08-01

250

Quantitative Low-Energy X-Ray Spectroscopy (50-100-A Region).  

National Technical Information Service (NTIS)

The quantitative analysis of emission spectra in the 10-100-A region has become of considerable importance for high-temperature plasma diagnostics (region) and for molecular orbital and solid-state-band analysis. Because measurement intensities are typica...

B. L. Henke K. Taniguchi

1975-01-01

251

[Research on the analytical line auto-selection for quantitative analysis of materials with laser-induced breakdown spectroscopy].  

PubMed

To realize auto-selection of analytical lines for quantitative analysis of materials with laser-induced breakdown spectroscopy, two parameters, i. e. the relative detected-to-theory intensity ratio (RDTIR) and wavelength difference of detected and theory (WDDT) were defined. The spectral lines seriously disturbed by self-absorption and spectral interference were excluded automatically by setting reasonable thresholds of RDTIR and WDDT. By analyzing the experimental data of high-alloy steel (GBW01605), the analytical lines of iron (Fe), chromium (Cr), nickel (Ni), manganese (Mn) and copper (Cu) were selected, and the results were in line with the principle of lines selection. PMID:22715743

Du, Zhen-hui; Meng, Fan-li; Li, Jin-yi; Ma, Yi-wen; Sun, Lan-xiang; Cong, Zhi-bo; Xin, Yong

2012-04-01

252

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

253

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.

254

Quantitative local equivalence ratio determination in laminar premixed methane-air flames by laser induced breakdown spectroscopy (LIBS)  

NASA Astrophysics Data System (ADS)

Laser induced breakdown spectroscopy has been used in order to obtain quantitative local equivalence ratio measurements in laminar premixed methane-air Bunsen flames. The total emission intensities of the 656.3 nm H ? and the 777 nm O(I) atomic spectral lines were simultaneously measured and a linear relation of the H/O intensity ratio with the flame equivalence ratio ? was established. Axial and radial profiles of local equivalence ratio were thus obtained for both lean and rich flames and were used to provide information regarding flame structure and dynamics.

Stavropoulos, P.; Michalakou, A.; Skevis, G.; Couris, S.

2005-03-01

255

Combining surface sensitive vibrational spectroscopy and fluorescence microscopy to study biological interfaces  

NASA Astrophysics Data System (ADS)

A multimodal system combining surface sensitive sum frequency generation (SFG) vibrational spectroscopy and total-internal reflection fluorescence (TIRF) microscopy for surface and interface study was developed. Interfacial molecular structural information can be detected using SFG spectroscopy while interfacial fluorescence signal can be visualized using TIRF microscopy from the same sample. As a proof of concept experiment, SFG spectra of fluorescent polystyrene (PS) beads with different surface coverage were correlated with TIRF signal observed. Results showed that SFG signals from the ordered surfactant methyl groups were detected from the substrate surface, while signals from PS phenyl groups on the beads were not seen. Additionally, a lipid monolayer labeled using lipid-associated dye was deposited on a silica substrate and studied in different environments. The contact with water of this lipid monolayer caused SFG signal to disappear, indicating a possible lipid molecular disorder and the formation of lipid bilayers or liposomes in water. TIRF was able to visualize the presence of lipid molecules on the substrate, showing that the lipids were not removed from the substrate surface by water. The integration of the two surface sensitive techniques can simultaneously visualize interfacial molecular dynamics and characterize interfacial molecular structures in situ, which is important and is expected to find extensive applications in biological interface related research.

Zhang, Chi; Jasensky, Joshua; Wu, Jing; Chen, Zhan

2014-03-01

256

Quantitative analysis of routine chemical constituents in tobacco by near-infrared spectroscopy and support vector machine  

NASA Astrophysics Data System (ADS)

It is important to monitor quality of tobacco during the production of cigarette. Therefore, in order to scientifically control the tobacco raw material and guarantee the cigarette quality, fast and accurate determination routine chemical of constituents of tobacco, including the total sugar, reducing sugar, Nicotine, the total nitrogen and so on, is needed. In this study, 50 samples of tobacco from different cultivation areas were surveyed by near-infrared (NIR) spectroscopy, and the spectral differences provided enough quantitative analysis information for the tobacco. Partial least squares regression (PLSR), artificial neural network (ANN), and support vector machine (SVM), were applied. The quantitative analysis models of 50 tobacco samples were studied comparatively in this experiment using PLSR, ANN, radial basis function (RBF) SVM regression, and the parameters of the models were also discussed. The spectrum variables of 50 samples had been compressed through the wavelet transformation technology before the models were established. The best experimental results were obtained using the (RBF) SVM regression with ? = 1.5, 1.3, 0.9, and 0.1, separately corresponds to total sugar, reducing sugar, Nicotine, and total nitrogen, respectively. Finally, compared with the back propagation (BP-ANN) and PLSR approach, SVM algorithm showed its excellent generalization for quantitative analysis results, while the number of samples for establishing the model is smaller. The overall results show that NIR spectroscopy combined with SVM can be efficiently utilized for rapid and accurate analysis of routine chemical compositions in tobacco. Simultaneously, the research can serve as the technical support and the foundation of quantitative analysis of other NIR applications.

Zhang, Yong; Cong, Qian; Xie, Yunfei; Yang, Jingxiu; Zhao, Bing

2008-12-01

257

Vibrational spectroscopy as a routine tool for the quantitative analysis of serum?  

NASA Astrophysics Data System (ADS)

Mid-infrared and Raman spectroscopy together with multivariate data analysis offers the potential to be applied to clinical laboratory analysis due to their reagent-free nature, the speed of analysis and the possibility of obtaining a variety of information from a single measurement. In what we believe to be among the largest studies on mid-infrared and Raman spectroscopy for the analysis of multiple analytes in serum, samples from 247 donors have been analyzed with the emphasis on reproducibility. In an independent validation, root-mean-square errors of prediction (RMSEP) ranged from 328 mg/dL for the quantification of protein (mean concentration: 7008 mg/dL) using mid-infrared spectroscopy to 1.1 mg/dL for uric acid (mean concentration: 5.3 mg/dL) in the case of Raman spectroscopy. Both techniques deliver similar performances. We also performed first steps towards determining system precision and accuracy. In a fivefold measurement of 5 randomly chosen samples from this study, precision and accuracy range from 4% to 16% and from 4% to 29%, respectively. However, when considering the physiological and pathological range of concentrations of analytes, vibrational spectroscopy might open the path towards less expensive and more rapid multiparameter analysis of small sample volumes in those cases, in which moderate accuracy is permissible.

Rohleder, D.; Kocherscheidt, G.; Gerber, K.; Kiefer, W.; Köhler, W.; Möcks, J.; Petrich, W.

2006-03-01

258

Confocal micro-Raman spectroscopy of single biological cells using optical trapping and shifted excitation difference techniques  

Microsoft Academic Search

We report on the study of single biological cells with a confocal micro-Raman spectroscopy system that uses optical trapping and shifted excitation Raman difference technique. A tunable diode laser was used to capture a living cell in solution, confine it in the confocal excitation volume, and then excite the Raman scattering. The optical trapping allows us to lift the cell

Changan Xie; Yong-Qing Li

2003-01-01

259

Direct determination and speciation of mercury compounds in environmental and biological samples by carbon bed atomic absorption spectroscopy  

Microsoft Academic Search

A method was developed for the direct determination of mercury in water and biological samples using a unique carbon bed atomizer for atomic absorption spectroscopy. The method avoided sources of error such as loss of volatile mercury during sample digestion and contamination of samples through added reagents by eliminating sample pretreatment steps. The design of the atomizer allowed use of

Skelly

1982-01-01

260

High Sensitivity Quantitative Lipidomics Analysis of Fatty Acids in Biological Samples by Gas Chromatography-Mass Spectrometry  

PubMed Central

Historically considered to be simple membrane components serving as structural elements and energy storing entities, fatty acids are now increasingly recognized as potent signaling molecules involved in many metabolic processes. Quantitative determination of fatty acids and exploration of fatty acid profiles have become common place in lipid analysis. We present here a reliable and sensitive method for comprehensive analysis of free fatty acids and fatty acid composition of complex lipids in biological material. The separation and quantitation of fatty acids is achieved by capillary gas chromatography. The analytical method uses pentafluorobenzyl bromide derivatization and negative chemical ionization gas chromatography-mass spectrometry. The chromatographic procedure provides base line separation between saturated and unsaturated fatty acids of different chain lengths as well as between most positional isomers. Fatty acids are extracted in the presence of isotope-labeled internal standards for high quantitation accuracy. Mass spectrometer conditions are optimized for broad detection capacity and sensitivity capable of measuring trace amounts of fatty acids in complex biological samples.

Quehenberger, Oswald; Armando, Aaron M.; Dennis, Edward A.

2011-01-01

261

Quantitative thermal emission spectroscopy of minerals: A laboratory technique for measurement and calibration  

Microsoft Academic Search

Previous descriptions of thermal emission spectroscopy have presented techniques that vary in accuracy and reproducibility. Contributions of thermal energy from the instrument and environment are major calibration factors that limit accuracy in emissivity determination. Reproducibility is related to the stability of these quantities. Sample temperature determination is also a significant factor in arriving at accurate emissivity. All of the factors

Steven W. Ruff; Philip R. Christensen; Paul W. Barbera; Donald L. Anderson

1997-01-01

262

Quantitative analysis of pork dry-cured sausages to quality control by NIR spectroscopy  

Microsoft Academic Search

Near infrared spectroscopy technology (diode array instrument) was used to study the feasibility of applying quality controls to typical Spanish sausages by performing a proximate analysis (fat, moisture and protein) on the finished product (intact and homogenized). This could be used to provide quality controls at various stages once the finished product was obtained: finished product, storage, distribution and marketing.

A. J. Gaitán-Jurado; V. Ortiz-Somovilla; F. España-España; J. Pérez-Aparicio; E. J. De Pedro-Sanz

2008-01-01

263

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

264

Methane detection using Wavelength Modulation Spectroscopy and a multiline quantitation method  

Microsoft Academic Search

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

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

2005-01-01

265

Remote gas detection and quantitative analysis from infrared emission spectra obtained by Fourier transform infrared spectroscopy  

Microsoft Academic Search

Techniques for obtaining quantitative values of the temperatures and concentrations of remote hot gaseous effluents from their measured passive emission spectra have been examined in laboratory experiments. The high sensitivity of the spectrometer in the vicinity of the 2397 cm-1 band head region of CO2 has allowed the gas temperature to be calculated from the relative intensity of the observed

Moira Hilton; Alan H. Lettington; Ian M. Mills

1994-01-01

266

Quantitative FT-IR spectroscopy of gypsum raw material for industry  

Microsoft Academic Search

Today quality control (QC) is a big issue for being competitive in the gypsum industry. Knowledge and understanding of the raw material help to enhance the quality and permanence of products. Therefore a rapid, precise and user-friendly FT-IR spectroscopic method for quantitative analysis of gypsum, anhydrite, magnesite and dolomite from the gypsum deposit of Puchberg, Austria is being developed. There

K. Schwendtner; E. Libowitzky; M. A. Götzinger; S. Koss

2003-01-01

267

[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

268

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

269

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

270

Absorption spectroscopy.  

PubMed

Absorption spectroscopy is one of the most widely used techniques employed for determining the concentrations of absorbing species (chromophores) in solutions. It is a nondestructive technique which biologists and biochemists and now systems biologists use to quantify the cellular components and characteristic parameters of functional molecules. This quantification is most relevant in the context of systems biology. For creating a quantitative depiction of a metabolic pathway, a number of parameters and variables are important and these need to be determined experimentally. This chapter describes the UV-visible absorption spectroscopy used to produce experimental data for bottom-up modeling approaches of systems biology which uses concentrations and kinetic parameters (K(m) and V(max)) of enzymes of metabolic/signaling pathways, intracellular concentrations of metabolites and fluxes. It also briefly describes the application of this technique for quantification of biomolecules and investigating biomolecular interactions. PMID:21943892

Nilapwar, Sanjay M; Nardelli, Maria; Westerhoff, Hans V; Verma, Malkhey

2011-01-01

271

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

272

Multispectral diode laser based shifted excitation Raman difference spectroscopy for biological sample identification  

NASA Astrophysics Data System (ADS)

Raman spectroscopy is a well established analytical method with applications in many areas, e.g. analysis of biological samples. To overcome the problem of an undesired fluorescence background masking the Raman signals we present a multi-spectral approach using shifted excitation Raman difference spectroscopy (SERDS). For our investigations we applied microsystem diode lasers which realize two slightly shifted excitation wavelengths required to perform SERDS at 488 nm, 671 nm, and 785 nm. The emission at 488 nm with an optical power of up to 30 mW and a spectral shift of 0.3 nm (12 cm-1) is realized by frequency doubling of a 976 nm distributed feedback (DFB) diode laser. The 671 nm laser diode contains two separate laser cavities (spectral shift: 0.7 nm (13 cm-1)) each incorporating a volume Bragg grating as frequency selective element. In that case, optical powers up to 50 mW can be obtained. For investigations at 785 nm we used a DFB laser with a maximum optical power of 110 mW and a spectral shift of 0.5 nm (7 cm-1). Meat, fat tissue, connective tissue and bones from pork and beef were used as test samples to demonstrate the effective background removal using SERDS. For all three wavelengths integration times of only 5 - 10 seconds were necessary showing the possibility of SERDS for rapid sample identification. A comparison with conventional Raman spectra is given pointing out the improvement of spectral quality. The applicability of SERDS for other analytical applications, e.g. medical diagnosis will be discussed.

Sowoidnich, Kay; Kronfeldt, Heinz-Detlef

2012-05-01

273

Quantitative Colocalization Analysis of Multicolor Confocal Immunofluorescence Microscopy Images: Pushing Pixels to Explore Biological Phenomena  

PubMed Central

Quantitative colocalization analysis is an advanced digital imaging tool to examine antigens of interest in immunofluorescence images obtained using confocal microscopes. It employs specialized algorithms to estimate the degree of overlap of fluorescence signals and thus enables acquiring important new information not otherwise obtainable using qualitative approaches alone. As raw confocal images have high levels of background, they should be prepared to become suitable for reliable calculation of colocalization coefficients by correcting it. We provide concise theoretical basis of quantitative colocalization analysis, discuss its limitations, and describe proper use of the technique. The use of quantitative colocalization analysis is demonstrated by studying bile salt export pump and multidrug resistance associated protein 2 in the liver and major basic protein and platelet activating factor receptor antigens in conjunctiva. The review is focused on the applicability and correct interpretation of the results of colocalization coefficients calculations.

Zinchuk, Vadim; Zinchuk, Olga; Okada, Teruhiko

2007-01-01

274

Quantitative analysis of hydrogenated diamondlike carbon films by visible Raman spectroscopy  

NASA Astrophysics Data System (ADS)

The correlations between properties of hydrogenated diamondlike carbon films and their Raman spectra have been investigated. The films are prepared by plasma deposition technique, keeping different hydrogen to methane ratios during the growth process. The hydrogen concentration, sp3 content, hardness, and optical Tauc gap of the materials have been estimated from a detailed analysis of their Raman spectra. We have also measured the same parameters of the films by using other commonly used techniques, such as sp3 content in films by x-ray photoelectron spectroscopy, their Tauc gap by ellipsometric measurements, and hardness by microhardness testing. The reasons for the mismatch between the characteristics of the films, as obtained by Raman measurements and by the above mentioned techniques, have been discussed. We emphasize on the importance of the visible Raman spectroscopy in reliably predicting the above key properties of diamondlike carbon films.

Singha, Achintya; Ghosh, Aditi; Roy, Anushree; Ray, Nihar Ranjan

2006-08-01

275

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

276

Resolution of fluorophore mixtures in biological media using fluorescence spectroscopy and monte carlo simulation.  

PubMed

In excitation-emission fluorescence spectroscopy, the simultaneous quantitative prediction and qualitative resolution of mixtures of fluorophores using chemometrics is a major challenge because of the scattering and reabsorption effects (turbidity) presented mainly in biomaterials. The measured fluorescence spectra are distorted by multiple scattering and reabsorption events in the surrounding medium, thereby diminishing the performance of the commonly used three-way resolution methods such as parallel factor (PARAFAC) analysis or multivariate curve resolution-alternating least squares (MCR-ALS). In this work we show that spectral loadings and concentration profiles from model mixtures provided using PARAFAC and MCR-ALS are severely distorted by reabsorption and scattering phenomena, although both models fit rather well the experimental data in terms of percentage of the explained variance. The method to correct the fluorescence excitation-emission matrix (EEM) consisted in measuring the optical properties (absorption parameter ?a , scattering parameter ?s, and anisotropy factor g) of samples and calculating the corresponding transfer function by means of the Monte Carlo simulation method. By applying this transfer function to the measured EEM, it was possible to compensate for reabsorption and scattering effects and to restore the ideal EEM, i.e., the EEM that is due only to fluorophores, without distortions from the absorbers and scatterers that are present. The PARAFAC and MCR-ALS decomposition of the resulting ideal EEMs provided spectral loadings and concentration profiles that matched the true profiles. PMID:25014836

Lakhal, Lyes; Acha, Victor; Aussenac, Thierry

2014-07-01

277

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

278

Validation of Reflectance Infrared Spectroscopy as a Quantitative Method to Measure Percutaneous Absorption In Vivo  

Microsoft Academic Search

Attenuated total-reflectance infrared (ATR-IR) spectroscopy has been used to follow the penetration of a model compound (4-cyanophenol; CP) across human stratum corneum (SC) in vivo, in man. CP was administered for periods of 1, 2, or 3 hr, either (a) as a 10% (w\\/v) solution in propylene glycol or (b) in an identical vehicle which also contained 5% (v\\/v) oleic

Naruhito Higo; Aarti Naik; D. Bommi Bommannan; Russell O. Potts; Richard H. Guy

1993-01-01

279

Quantitative determinations of levofloxacin and rifampicin in pharmaceutical and urine samples using nuclear magnetic resonance spectroscopy  

Microsoft Academic Search

Rapid, specific and simple methods for determining levofloxacin and rifampicin antibiotic drugs in pharmaceutical and human urine samples were developed. The methods are based on 1H NMR spectroscopy using maleic acid as an internal standard and DMSO-d6 as NMR solvent. Integration of NMR signals at 8.9 and 8.2ppm were, respectively, used for calculating the concentration of levofloxacin and rifampicin drugs

A. A. Salem; H. A. Mossa; B. N. Barsoum

2005-01-01

280

Quantitative analysis of palm carotene using fourier transform infrared and near infrared spectroscopy  

Microsoft Academic Search

?-Carotene content is usually determined by using ultraviolet (UV)-visible spectrophotometry at 446 nm. In this study, two\\u000a spectroscopic techniques, namely, Fourier transform infrared (FTIR) and near infrared (NIR) spectroscopy, have been investigated\\u000a and compared to UV-visible spectrophotometry to measure the ?-carotene content of crude palm oil (CPO). Calibration curves\\u000a ranging from 200 to 800 ppm were prepared by extracting ?-carotene

M. H. Moh; Y. B. Che Man; B. S. Badlishah; S. Jinap; M. S. Saad; W. J. W. Abdullah

1999-01-01

281

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

282

Quantitative analysis of bayberry juice acidity based on visible and near-infrared spectroscopy  

NASA Astrophysics Data System (ADS)

Visible and near-infrared (Vis/NIR) reflectance spectroscopy has been investigated for its ability to nondestructively detect acidity in bayberry juice. What we believe to be a new, better mathematic model is put forward, which we have named principal component analysis-stepwise regression analysis-backpropagation neural network (PCA-SRA-BPNN), to build a correlation between the spectral reflectivity data and the acidity of bayberry juice. In this model, the optimum network parameters, such as the number of input nodes, hidden nodes, learning rate, and momentum, are chosen by the value of root-mean-square (rms) error. The results show that its prediction statistical parameters are correlation coefficient (r) of 0.9451 and root-mean-square error of prediction (RMSEP) of 0.1168. Partial least-squares (PLS) regression is also established to compare with this model. Before doing this, the influences of various spectral pretreatments (standard normal variate, multiplicative scatter correction, S. Golay first derivative, and wavelet package transform) are compared. The PLS approach with wavelet package transform preprocessing spectra is found to provide the best results, and its prediction statistical parameters are correlation coefficient (r) of 0.9061 and RMSEP of 0.1564. Hence, these two models are both desirable to analyze the data from Vis/NIR spectroscopy and to solve the problem of the acidity prediction of bayberry juice. This supplies basal research to ultimately realize the online measurements of the juice's internal quality through this Vis/NIR spectroscopy technique.

Shao, Yongni; He, Yong; Mao, Jingyuan

2007-09-01

283

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

284

Tracking Biological Organic Compounds In Atmospheric Deposition In Alpine Environments With Fluorescence Spectroscopy  

NASA Astrophysics Data System (ADS)

Alpine environments, such as those of the Colorado Rocky Mountains, USA and the Sierra Nevada Mountains, Spain, contain undeveloped, barren soils that are carbon-limited. Atmospheric wet and dry deposition of organic carbon (OC) represents a substantial fraction of the OC load available to alpine soils, and includes contributions from atmospheric pollutants, dust, and biological aerosols, such as bacteria, algae, fungi, and plant debris. To evaluate the seasonal variability and sources of atmospheric deposition at these alpine sites, we measured the chemical characteristics of weekly wet and dry deposition and snowpack samples, including characterization of dissolved organic matter (DOM) and water soluble organic matter (WSOM) with fluorescence spectroscopy. The excitation-emission matrix (EEM) spectra we acquired show the presence of recurring peaks at low excitation and emission wavelengths typically associated with highly biodegradable organic carbon, presumably derived from the aromatic amino acids, tyrosine and tryptophan. Solar simulation experiments demonstrated that amino acid-like fluorescent components were more resistant to photo-degradation than humic- and fulvic-like fluorescent components. Our results also reveal the presence of a unique fluorophore, not previously described, that is found in both Rocky Mountains and the Sierra Nevada snowpack, wet deposition, and dry deposition and may be attributed to fluorescent pigments in bacteria. Biological aerosols may represent a labile source of carbon for alpine soil microbes, and consequently their deposition has important consequences for biogeochemical processes occurring in barren, alpine soils. Excitation emission matrix image of 24 Aug 2010 wet deposition sample from the Soddie site at Niwot Ridge, Colorado showing a unique fluorescent component with dual excitation peaks (285 nm and 340 nm) at 410 nm emission.

Mladenov, N.; Oldani, K. M.; Williams, M. W.; Schmidt, S. K.; Darcy, J.; Lemons, S.; Reche, I.

2013-12-01

285

Quantitative determination of dimethylaminoethanol in cosmetic formulations by nuclear magnetic resonance spectroscopy.  

PubMed

A nuclear magnetic resonance (NMR) spectroscopic method was validated for the quantitative determination of dimethylaminoethanol (DMAE) in cosmetic formulations. The linearity in the range from 0.5000 to 1.5000 g (DMAE salt/mass maleic acid) presents a correlation coefficient > 0.99 for all DMAE salts. The repeatability (intraday), expressed as relative standard deviation, ranged from 1.08 to 1.44% for samples and 1.31 to 1.88% for raw materials. The detection limit and quantitation limit were 0.0017 and 0.0051 g for DMAE, 0.0018 and 0.0054 g for DMAE bitartrate, and 0.0023 and 0.0071 g for DMAE acetamidobenzoate, respectively. The proposed method is simple, precise, and accurate and can be used in the quality control of raw materials and cosmetic gels containing these compounds as active substances. PMID:19202790

Batista, Ivani Aparecida Soares de Andrade; Gonçalves, Maria Inês de Almeida; Singh, Anil Kumar; Hackmann, Erika Rosa Maria Kedor; Santoro, Maria Inês Rocha Miritello

2008-01-01

286

Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology  

Microsoft Academic Search

Gregor Mendel was either clever or lucky enough to study traits of simple inheritance in his pea plants; however, many plant characters of interest to modern geneticists are decidedly complex. Understanding the genetic basis of such complex, or quantitative, traits requires a combination of modern molecular genetic techniques and powerful statistical methods. These approaches have begun to give us insight

Rodney Mauricio

2001-01-01

287

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

288

Analytical and biological variables influencing quantitative hepatitis C virus (HCV) measurement in HIV-HCV coinfection  

PubMed Central

The present review considers issues pertaining to the precision and variability of quantitative hepatitis C virus (HCV) measurement in general, outlines the characteristics of HCV RNA in HIV-HCV coinfection and evaluates those factors which may affect this measure. The clinical relevance of accurate HCV measurement in HIV-HCV coinfection is discussed.

Cooper, Curtis; MacPherson, Paul; Cameron, William

2006-01-01

289

Electrical pulse induced biological effects using dielectric spectroscopy and mathematical models  

NASA Astrophysics Data System (ADS)

This dissertation studies the effects of pulsed electric fields (PEFs) on biological cells by measuring the changes in the electrical properties of the pulsed cells and mathematically modeling avascular tumor growth, cell population dynamics, and Ohmic heating. These issues are critical because of the recent use of intense ultrashort PEFs for various biological and medical applications. Recent research using PEFs for tumor treatment motivated an investigation of a simple model for the growth of an avascular tumor. We modeled tumor growth before and after necrotic core formation by incorporating spatial dependence into a one dimensional scaling law. This model emphasized the importance of cell metabolic rate in determining the final steady state size of the tumor. Experimental results showing changes in cell survival and cell cycle due to PEFs led to an investigation of a simple mathematical model for cell population dynamics that considered the cells to be proliferating (dividing) or quiescent (resting). Although some cell populations apparently reached steady state quickly, the proliferating cell population fell below one, meaning that the overall cell population would eventually decay away. This result, which was unaltered by including a transition from the quiescent to proliferating state, emphasized the importance of targeting proliferating cells for successful cancer treatments. Time domain dielectric spectroscopy was used to measure the electrical properties of a biological cell suspension over a wide frequency range with a single pulse following multiple PEFs. Fitting the dielectric properties of a cancer cell (Jurkat) suspension to a double shell model yielded the dielectric parameters of the cell membrane, cytoplasm, nuclear envelope, and nucleoplasm. Decreased cytoplasm and nucleoplasm conductivity and increased suspension conductivity suggestion transport from the cell interior to the exterior consistent with electroporation. Reduced cell membrane conductivity suggests possible changes in ion channel structure or function. PEF-induced heating is a concern because of the desire to distinguish between electrical and thermal effects. A model for cellular Ohmic heating showed that a typical ultrawideband electrochemotherapy pulse heated the cell by 0.05 C. The heat dissipated rapidly, indicating that Ohmic heating from multiple pulses is not cumulative.

Garner, Allen Lawrence

290

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

291

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

292

Diffuse reflectance spectroscopy and optical polarization imaging of in-vivo biological tissue  

NASA Astrophysics Data System (ADS)

A number of optical techniques have been reported in the scientific literature as accomplishable methodologies to diagnose diseases in biological tissue, for instance, diffuse reflectance spectroscopy (DRS) and optical polarization imaging (OPI). The skin is the largest organ in the body and consists of three primary layers, namely, the epidermis (the outermost layer exposed to the world), the dermis, and the hypodermis. The epidermis changes from to site to site, mainly because of difference in hydration. A lower water content increase light scattering and reduce the penetration depth of radiation. In this work, two hairless mice have been selected to evaluate their skin features by using DRS and OPI. Four areas of the specimen body were chosen to realize the comparison: back, abdomen, tail, and head. From DRS, it was possible to distinguish the skin nature because of different blood irrigation at dermis. In the other hand, OPI shows pseudo-depolarizing regions in the measured Mueller images related to a spatially varying propagation of the scattered light. This provides information about the cell size in the irradiated skin.

Mora-Núñez, A.; Castillejos, Y.; García-Torales, G.; Martínez-Ponce, G.

2013-11-01

293

Quantitative analysis of bayberry juice acidity based on visible and near-infrared spectroscopy  

SciTech Connect

Visible and near-infrared (Vis/NIR) reflectance spectroscopy has been investigated for its ability to nondestructively detect acidity in bayberry juice. What we believe to be a new, better mathematic model is put forward, which we have named principal component analysis-stepwise regression analysis-backpropagation neural network (PCA-SRA-BPNN), to build a correlation between the spectral reflectivity data and the acidity of bayberry juice. In this model, the optimum network parameters,such as the number of input nodes, hidden nodes, learning rate, and momentum, are chosen by the value of root-mean-square (rms) error. The results show that its prediction statistical parameters are correlation coefficient (r) of 0.9451 and root-mean-square error of prediction(RMSEP) of 0.1168. Partial least-squares (PLS) regression is also established to compare with this model. Before doing this, the influences of various spectral pretreatments (standard normal variate, multiplicative scatter correction, S. Golay first derivative, and wavelet package transform) are compared. The PLS approach with wavelet package transform preprocessing spectra is found to provide the best results, and its prediction statistical parameters are correlation coefficient (r) of 0.9061 and RMSEP of 0.1564. Hence, these two models are both desirable to analyze the data from Vis/NIR spectroscopy and to solve the problem of the acidity prediction of bayberry juice. This supplies basal research to ultimately realize the online measurements of the juice's internal quality through this Vis/NIR spectroscopy technique.

Shao Yongni; He Yong; Mao Jingyuan

2007-09-01

294

Quantitative analysis of bayberry juice acidity based on visible and near-infrared spectroscopy.  

PubMed

Visible and near-infrared (Vis/NIR) reflectance spectroscopy has been investigated for its ability to nondestructively detect acidity in bayberry juice. What we believe to be a new, better mathematic model is put forward, which we have named principal component analysis-stepwise regression analysis-backpropagation neural network (PCA-SRA-BPNN), to build a correlation between the spectral reflectivity data and the acidity of bayberry juice. In this model, the optimum network parameters, such as the number of input nodes, hidden nodes, learning rate, and momentum, are chosen by the value of root-mean-square (rms) error. The results show that its prediction statistical parameters are correlation coefficient (r) of 0.9451 and root-mean-square error of prediction (RMSEP) of 0.1168. Partial least-squares (PLS) regression is also established to compare with this model. Before doing this, the influences of various spectral pretreatments (standard normal variate, multiplicative scatter correction, S. Golay first derivative, and wavelet package transform) are compared. The PLS approach with wavelet package transform preprocessing spectra is found to provide the best results, and its prediction statistical parameters are correlation coefficient (r) of 0.9061 and RMSEP of 0.1564. Hence, these two models are both desirable to analyze the data from Vis/NIR spectroscopy and to solve the problem of the acidity prediction of bayberry juice. This supplies basal research to ultimately realize the online measurements of the juice's internal quality through this Vis/NIR spectroscopy technique. PMID:17805379

Shao, Yongni; He, Yong; Mao, Jingyuan

2007-09-01

295

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

296

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. T.

1994-01-01

297

Comparison of electron energy-loss and quantitative optical spectroscopy on individual optical gold antennas  

NASA Astrophysics Data System (ADS)

Using a rather large set of different individual metallic optical antennas, we compare directly measured electron energy-loss spectra with measured quantitative optical extinction and scattering cross-section spectra on the identical antennas. All antenna resonances lie near 1.4 µm wavelength. In contrast to other reports, we find identical resonance positions for electrons and photons to within the experimental errors. We discuss possible artifacts which can lead to seemingly different resonance positions in experiments. Our experimental results agree well with complete numerical calculations of both sorts of spectra.

Husnik, Martin; von Cube, Felix; Irsen, Stephan; Linden, Stefan; Niegemann, Jens; Busch, Kurt; Wegener, Martin

2013-10-01

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 >http://bioeda1.polito.it:8080/medSearchServlet/. PMID:24091396

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

2013-01-01

299

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

300

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

301

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

302

Quantitative determination of pulegone in pennyroyal oil by FT-IR spectroscopy.  

PubMed

Pulegone constitutes a monoterpene occurring in Mentha species and primarily in Mentha pulegium L. (pennyroyal). A major source of human exposure to pulegone is the use of pennyroyal essential oil in flavorings, confectionery and cosmetics. The rapid quantification of pulegone in hydrodistilled pennyroyal oils (which were also "spiked" to increase the validation range) by Fourier transform infrared spectroscopy (FT-IR) combined with partial least-squares (PLS) regression was evaluated, using the spectral region 1650-1260 cm(-1). Gas chromatography was applied as the reference method for pennyroyal oil samples, which ranged in pulegone content from 157 to 860 mg/mL. The two methods were subjected to statistical tests and proved equivalent in terms of accuracy and reproducibility (99% confidence level). The use of FT-IR spectroscopy could offer a viable alternative to the standard analysis procedures presently applied for quantification of valuable plant substances and could also provide the processing industry with a simple and high-throughput technique for the fast quality check of incoming raw materials such as pennyroyal oils. PMID:19817373

Petrakis, Eleftherios A; Kimbaris, Athanasios C; Pappas, Christos S; Tarantilis, Petros A; Polissiou, Moschos G

2009-11-11

303

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

304

Quantitative comparison of chemical, biological and mechanical induction of secondary compounds in Pinus pinaster seedlings  

Microsoft Academic Search

Chemical elicitors and mechanical treatments simulating real insect herbivory have been increasingly used to study induced\\u000a defensive responses in woody plants. However, simultaneous quantitative comparisons of plant chemical defences elicited by\\u000a real and simulated herbivory have received little attention. In this paper we compared the effects of real herbivory, simulated\\u000a herbivory using two chemical elicitors, and mechanical damage treatments on

Xoaquín Moreira; Rafael Zas; Luis Sampedro

305

Quantitative Detection and Biological Propagation of Scrapie Seeding Activity In Vitro Facilitate Use of Prions as Model Pathogens for Disinfection  

PubMed Central

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 ?101- to ?105.5-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.

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

2011-01-01

306

Quantitative HRMAS proton total correlation spectroscopy applied to cultured melanoma cells treated by chloroethyl nitrosourea: demonstration of phospholipid metabolism alterations.  

PubMed

Recent NMR spectroscopy developments, such as high-resolution magic angle spinning (HRMAS) probes and correlation-enhanced 2D sequences, now allow improved investigations of phospholipid (Plp) metabolism. Using these modalities we previously demonstrated that a mouse-bearing melanoma tumor responded to chloroethyl nitrosourea (CENU) treatment in vivo by altering its Plp metabolism. The aims of the present study were to investigate whether HRMAS proton total correlation spectroscopy (TOCSY) could be used as a quantitative technique to probe Plp metabolism, and to determine the Plp metabolism response of cultured B16 melanoma cells to CENU treatment in vitro. The exploited TOCSY signals of Plp derivatives arose from scalar coupling among the protons of neighbor methylene groups within base headgroups (choline and ethanolamine). For strongly expressed Plp derivatives, TOCSY signals were compared to saturation recovery signals and demonstrated a linear relationship. HRMAS proton TOCSY was thus used to provide concentrations of Plp derivatives during long-term follow-up of CENU-treated cell cultures. Strong Plp metabolism alteration was observed in treated cultured cells in vitro involving a down-regulation of phosphocholine, and a dramatic and irreversible increase of phosphoethanolamine. These findings are discussed in relation to previous in vivo data, and to Plp metabolism enzymatic involvement. PMID:12541243

Morvan, Daniel; Demidem, Aicha; Papon, Janine; Madelmont, Jean Claude

2003-02-01

307

Characterization and quantitation of a tertiary mixture of salts by Raman spectroscopy in simulated hydrothermal vent fluid.  

PubMed

This article will demonstrate that Raman spectroscopy can be a useful tool for monitoring the chemical composition of hydrothermal vent fluids in the deep ocean. Hydrothermal vent systems are difficult to study because they are commonly found at depths greater than 1000 m under high pressure (200-300 bar) and venting fluid temperatures are up to 400 degrees C. Our goal in this study was to investigate the use of Raman spectroscopy to characterize and quantitate three Raman-active salts that are among the many chemical building blocks of deep ocean vent chemistry. This paper presents initial sampling and calibration studies as part of a multiphase project to design, develop, and deploy a submersible deep sea Raman instrument for in situ analysis of hydrothermal vent systems. Raman spectra were collected from designed sets of seawater solutions of carbonate, sulfate, and nitrate under different physical conditions of temperature and pressure. The role of multivariate analysis techniques to preprocess the spectral signals and to develop optimal calibration models to accurately estimate the concentrations of a set of mixtures of simulated seawater are discussed. The effects that the high-pressure and high-temperature environment have upon the Raman spectra of the analytes were also systematically studied. Information gained from these lab experiments is being used to determine design criteria and performance attributes for a deployable deep sea Raman instrument to study hydrothermal vent systems in situ. PMID:16854265

Dable, Brian K; Love, Brooke A; Battaglia, Tina M; Booksh, Karl S; Lilley, Marvin D; Marquardt, Brian J

2006-07-01

308

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

NASA Astrophysics Data System (ADS)

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 forms of mannitol in a drug product was carried out using a partial least-squares method. In drug products containing meprobamate, sorbitol, and carbamazepine, the thermodynamically stable form was found exclusively, whereas metastable polymorphs were found in solid dosage forms of acemetacin, phenylbutazone, famotidine and mannitol. A mixture of two polymorphic forms of mannitol in Lipobay tablets was determined to consist of 30.8±3.8% of the metastable modification I. The simple sample preparation, the occurrence of sharp bands in the spectra as well as the high reproducibility and accuracy qualifies FT-Raman spectroscopy for the identification and quantification of crystal forms in drug products. The method is perfectly suited to meet the regulatory requirements of monitoring crystal forms during processing and storage and often succeeds in detecting the present crystal form in drug products even when the used excipients are not known.

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

2003-12-01

309

Quantitative analysis of entacapone isomers using surface-enhanced Raman spectroscopy and partial least squares regression.  

PubMed

Surface-enhanced Raman spectroscopy (SERS) and partial least squares (PLS) regression have been applied for the quantification of entacapone isomers E and Z in solution. Nine mixtures of isomers Z and E in ethanol ranging from 0% to 100% w/w were analyzed, for a total entacapone concentration of 1 × 10(-3) mol L(-1). Upon deposition onto commercially available Klarite® gold plates, highly intense and reproducible SERS spectra were obtained from the entacapone isomers. Based on the spectral measurements, a two-component PLS model for correlation of predicted and real content of the isomers mixtures was developed. Root-mean-square error of the predicted composition was found to be 8% of isomer Z in the isomers mixture, corresponding to the absolute concentration of 8 × 10(-5) mol L(-1) of isomer Z in solution. PMID:23231910

Ratkaj, Marina; Biljan, Tomislav; Miljani?, Snežana

2012-12-01

310

Quantitative analysis of minerals in oil shales by fourier transform in frared spectroscopy  

SciTech Connect

Infrared spectroscopy provides several advantages for mineral analyses of oil shales. The technique can be applied to samples of minimal size, masses of 100 micrograms generally being sufficient to obtain useful spectra. The spectral measurement times can range from seconds to a few minutes depending on application. Detection of mineral phases by infrared does not require crystallinity, and the sensitivity of the technique to amorphous, microcrystalline and crystalline phases is often comparable. In addition, infrared can generally distinguish structural isomeric and isomorphic materials. Infrared can generally detect and differentiate the mineral phases commonly found in oil shales including the clays, feldspars and carbonates, which are often more difficult to determine by other methods. While the utility of infrared for mineral analyses has led to a variety of qualitative applications of the technique, few attempts have been reported where the technique is applied for complete quantification of mineral phases.

Brown, J.M.; Elliott, J.J.

1987-04-01

311

[Quantitative analysis of contents in compound fertilizer and application research using near infrared reflectance spectroscopy].  

PubMed

In the present study, a new approach to fast determining the content of urea, biuret and moisture in compound fertilizer composed of urea, ammonium dihydrogenphosphate and potassium chloride was proposed by using near infrared diffuse reflectance spectroscopy. After preprocessing the original spectrum, partial least squares (PLS) models of urea, biuret and moisture were built with the R2 values of 0.9861, 0.9770 and 0.9713 respectively, the root mean square errors of cross validation were 2.59, 0.38, 0.132 respectively. And the prediction correlation factors were 0.9733, 0.9215 and 0.9679 respectively. The authors detected six kinds of compound fertilizer in market for the model verification, the correlation factors were 0.9237, 0.9786 and 0.9874 respectively. The data implied that the new method can be used for situ quality control in the production process of compound fertilizer. PMID:24783536

Song, Le; Zhang, Hong; Ni, Xiao-Yu; Wu, Lin; Liu, Bin-Mei; Yu, Li-Xiang; Wang, Qi; Wu, Yue-Jin

2014-01-01

312

Quantitative analysis of microbicide concentrations in fluids, gels and tissues using confocal Raman spectroscopy.  

PubMed

Topical vaginal anti-HIV microbicides are an important focus in female-based strategies to prevent the sexual transmission of HIV. Understanding microbicide pharmacokinetics is essential to development, characterization and implementation of efficacious microbicide drug delivery formulations. Current methods to measure drug concentrations in tissue (e.g., LC-MS/MS, liquid chromatography coupled with tandem mass spectrometry) are highly sensitive, but destructive and complex. This project explored the use of confocal Raman spectroscopy to detect microbicide drugs and to measure their local concentrations in fluids, drug delivery gels, and tissues. We evaluated three candidate microbicide drugs: tenofovir, Dapivirine and IQP-0528. Measurements were performed in freshly excised porcine buccal tissue specimens, gel vehicles and fluids using two Horiba Raman microscopes, one of which is confocal. Characteristic spectral peak calibrations for each drug were obtained using serial dilutions in the three matrices. These specific Raman bands demonstrated strong linear concentration dependences in the matrices and were characterized with respect to their unique vibrational signatures. At least one specific Raman feature was identified for each drug as a marker band for detection in tissue. Sensitivity of detection was evaluated in the three matrices. A specific peak was also identified for tenofovir diphosphate, the anti-HIV bioactive product of tenofovir after phosphorylation in host cells. Z-scans of drug concentrations vs. depth in excised tissue specimens, incubated under layers of tenofovir solution in a Transwell assay, showed decreasing concentration with depth from the surface into the tissue. Time-dependent concentration profiles were obtained from tissue samples incubated in the Transwell assay, for times ranging 30 minutes - 6 hours. Calibrations and measurements from tissue permeation studies for tenofovir showed good correlation with gold standard LC-MS/MS data. These results demonstrate that confocal Raman spectroscopy holds promise as a tool for practical, minimally invasive, label-free measurement of microbicide drug concentrations in fluids, gels and tissues. PMID:24386455

Chuchuen, Oranat; Henderson, Marcus H; Sykes, Craig; Kim, Min Sung; Kashuba, Angela D M; Katz, David F

2013-01-01

313

Quantitative Analysis of Microbicide Concentrations in Fluids, Gels and Tissues Using Confocal Raman Spectroscopy  

PubMed Central

Topical vaginal anti-HIV microbicides are an important focus in female-based strategies to prevent the sexual transmission of HIV. Understanding microbicide pharmacokinetics is essential to development, characterization and implementation of efficacious microbicide drug delivery formulations. Current methods to measure drug concentrations in tissue (e.g., LC-MS/MS, liquid chromatography coupled with tandem mass spectrometry) are highly sensitive, but destructive and complex. This project explored the use of confocal Raman spectroscopy to detect microbicide drugs and to measure their local concentrations in fluids, drug delivery gels, and tissues. We evaluated three candidate microbicide drugs: tenofovir, Dapivirine and IQP-0528. Measurements were performed in freshly excised porcine buccal tissue specimens, gel vehicles and fluids using two Horiba Raman microscopes, one of which is confocal. Characteristic spectral peak calibrations for each drug were obtained using serial dilutions in the three matrices. These specific Raman bands demonstrated strong linear concentration dependences in the matrices and were characterized with respect to their unique vibrational signatures. At least one specific Raman feature was identified for each drug as a marker band for detection in tissue. Sensitivity of detection was evaluated in the three matrices. A specific peak was also identified for tenofovir diphosphate, the anti-HIV bioactive product of tenofovir after phosphorylation in host cells. Z-scans of drug concentrations vs. depth in excised tissue specimens, incubated under layers of tenofovir solution in a Transwell assay, showed decreasing concentration with depth from the surface into the tissue. Time-dependent concentration profiles were obtained from tissue samples incubated in the Transwell assay, for times ranging 30 minutes - 6 hours. Calibrations and measurements from tissue permeation studies for tenofovir showed good correlation with gold standard LC-MS/MS data. These results demonstrate that confocal Raman spectroscopy holds promise as a tool for practical, minimally invasive, label-free measurement of microbicide drug concentrations in fluids, gels and tissues.

Chuchuen, Oranat; Henderson, Marcus H.; Sykes, Craig; Kim, Min Sung; Kashuba, Angela D. M.; Katz, David F.

2013-01-01

314

Development of capillary electrophoresis methods for quantitative determination of taurine in vehicle system and biological media.  

PubMed

CE methods have been developed for the determination of taurine in pharmaceutical formulation (microemulsion) and in biological media such as sweat. The CE system with end-column pulsed amperometric detection has been found to be an interesting method in comparison with UV and fluorescence detection for its simplicity and rapidity. A gold-disk electrode of 100 mm diameter was used as the working electrode. The effects of a field decoupler at the end of the capillary, separation voltage, injection and pressure times were investigated. A detection limit of 4 x 10(-5) mol/L was reached using integrated pulsed amperometric detection, a method successfully applied to taurine analysis of the biological samples such as sweat. For taurine analysis of oil-in-water microemulsion, fluorescence detector was the favored method, the detection limit of which was 4 x 10(-11) mol/L. PMID:16856126

da Silva, Dayse L P; Rüttinger, Hans H; Mrestani, Yahia; Baum, Walter F; Neubert, Reinhard H H

2006-06-01

315

A Comparison of Multivariate and Pre-Processing Methods for Quantitative Laser-Induced Breakdown Spectroscopy of Geologic Samples  

NASA Technical Reports Server (NTRS)

The ChemCam instrument selected for the Curiosity rover is capable of remote laser-induced breakdown spectroscopy (LIBS).[1] We used a remote LIBS instrument similar to ChemCam to analyze 197 geologic slab samples and 32 pressed-powder geostandards. The slab samples are well-characterized and have been used to validate the calibration of previous instruments on Mars missions, including CRISM [2], OMEGA [3], the MER Pancam [4], Mini-TES [5], and Moessbauer [6] instruments and the Phoenix SSI [7]. The resulting dataset was used to compare multivariate methods for quantitative LIBS and to determine the effect of grain size on calculations. Three multivariate methods - partial least squares (PLS), multilayer perceptron artificial neural networks (MLP ANNs) and cascade correlation (CC) ANNs - were used to generate models and extract the quantitative composition of unknown samples. PLS can be used to predict one element (PLS1) or multiple elements (PLS2) at a time, as can the neural network methods. Although MLP and CC ANNs were successful in some cases, PLS generally produced the most accurate and precise results.

Anderson, R. B.; Morris, R. V.; Clegg, S. M.; Bell, J. F., III; Humphries, S. D.; Wiens, R. C.

2011-01-01

316

Partial Least Squares and Neural Networks for Quantitative Calibration of Laser-induced Breakdown Spectroscopy (LIBs) of Geologic Samples  

NASA Technical Reports Server (NTRS)

The ChemCam instrument [1] on the Mars Science Laboratory (MSL) rover will be used to obtain the chemical composition of surface targets within 7 m of the rover using Laser Induced Breakdown Spectroscopy (LIBS). ChemCam analyzes atomic emission spectra (240-800 nm) from a plasma created by a pulsed Nd:KGW 1067 nm laser. The LIBS spectra can be used in a semiquantitative way to rapidly classify targets (e.g., basalt, andesite, carbonate, sulfate, etc.) and in a quantitative way to estimate their major and minor element chemical compositions. Quantitative chemical analysis from LIBS spectra is complicated by a number of factors, including chemical matrix effects [2]. Recent work has shown promising results using multivariate techniques such as partial least squares (PLS) regression and artificial neural networks (ANN) to predict elemental abundances in samples [e.g. 2-6]. To develop, refine, and evaluate analysis schemes for LIBS spectra of geologic materials, we collected spectra of a diverse set of well-characterized natural geologic samples and are comparing the predictive abilities of PLS, cascade correlation ANN (CC-ANN) and multilayer perceptron ANN (MLP-ANN) analysis procedures.

Anderson, R. B.; Morris, Richard V.; Clegg, S. M.; Humphries, S. D.; Wiens, R. C.; Bell, J. F., III; Mertzman, S. A.

2010-01-01

317

Quantitative X-ray Absorption and Emission Spectroscopies: Electronic Structure Elucidation of Cu2S and CuS  

PubMed Central

The electronic structures of Cu2S and CuS have been under intense scrutiny, with the aim of understanding the relationship between their electronic structures and commercially important physical properties. Here, X-ray absorption and emission spectroscopic data have been analyzed using a quantitative, molecular orbital (MO) based approach to understand the electronic structure of these two complex systems. Cu2S is shown to have a significant amount of Cu2+ sites and therefore Cu0 centers. The presence of low-valent Cu is correlated with the electrical conductivity of Cu2S, especially at high temperatures. CuS is shown to have tetrahedral Cu2+ and trigonal Cu1+ sites, with crystal planes that have alternating high and low charge on the Cu centers. These alternating charges may contribute to internal energy transitions required for photoluminescence properties. The in-depth electronic structure solutions presented here not only solve a complicated much-debated problem, but also demonstrate the strength of quantitative MO based approach to X-ray spectroscopies

Kumar, Prashant; Nagarajan, Rajamani

2013-01-01

318

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

319

Evaluation of the ERETIC Method as an Improved Quantitative Reference for 1H HR-MAS Spectroscopy of Prostate Tissue  

PubMed Central

The Electronic REference To access In vivo Concentrations (ERETIC) method was applied to 1H HR-MAS spectroscopy. The accuracy, precision, and stability of ERETIC as a quantitative reference were evaluated in solution and human prostate tissue samples. For comparison, the reliability of 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid (TSP) as a quantitation reference was also evaluated. The ERETIC and TSP peak areas were found to be stable in solution over the short-term and long-term, with long-term relative standard deviations (RSDs) of 4.10% and 2.60%, respectively. Quantification of TSP in solution using the ERETIC peak as a reference and a calibrated, rotor-dependent conversion factor yielded results with a precision ?2.9% and an accuracy error ?4.2% when compared with the expected values. The ERETIC peak area reproducibility was superior to TSP’s reproducibility, corrected for mass, in both prostate surgical and biopsy samples (4.53% vs. 21.2% and 3.34% vs. 31.8%, respectively). Furthermore, the tissue TSP peaks exhibited only 27.5% of the expected area, which would cause an overestimation of metabolite concentrations if used as a reference. The improved quantification accuracy and precision provided by ERETIC may enable the detection of smaller metabolic differences that may exist between individual tissue samples and disease states.

Albers, Mark J.; Butler, Thomas N.; Rahwa, Iman; Bao, Nguyen; Keshari, Kayvan R.; Swanson, Mark G.; Kurhanewicz, John

2010-01-01

320

Evaluation of the ERETIC method as an improved quantitative reference for 1H HR-MAS spectroscopy of prostate tissue.  

PubMed

The Electronic REference To access In vivo Concentrations (ERETIC) method was applied to (1)H HR-MAS spectroscopy. The accuracy, precision, and stability of ERETIC as a quantitative reference were evaluated in solution and human prostate tissue samples. For comparison, the reliability of 3-(trimethylsilyl)propionic-2,2,3,3-d(4) acid (TSP) as a quantitation reference was also evaluated. The ERETIC and TSP peak areas were found to be stable in solution over the short-term and long-term, with long-term relative standard deviations (RSDs) of 4.10% and 2.60%, respectively. Quantification of TSP in solution using the ERETIC peak as a reference and a calibrated, rotor-dependent conversion factor yielded results with a precision < or =2.9% and an accuracy error < or =4.2% when compared with the expected values. The ERETIC peak area reproducibility was superior to TSP's reproducibility, corrected for mass, in both prostate surgical and biopsy samples (4.53% vs. 21.2% and 3.34% vs. 31.8%, respectively). Furthermore, the tissue TSP peaks exhibited only 27.5% of the expected area, which would cause an overestimation of metabolite concentrations if used as a reference. The improved quantification accuracy and precision provided by ERETIC may enable the detection of smaller metabolic differences that may exist between individual tissue samples and disease states. PMID:19235261

Albers, Mark J; Butler, Thomas N; Rahwa, Iman; Bao, Nguyen; Keshari, Kayvan R; Swanson, Mark G; Kurhanewicz, John

2009-03-01

321

Quantitative study of spin noise spectroscopy in a classical gas of {sup 41}K atoms  

SciTech Connect

We present a general derivation of the electron spin noise power spectrum in alkali gases as measured by optical Faraday rotation, which applies to both classical gases at high temperatures as well as ultracold quantum gases. We show that the spin-noise power spectrum is determined by an electron spin-spin correlation function, and we find that measurements of the spin-noise power spectra for a classical gas of {sup 41}K atoms are in good agreement with the predicted values. Experimental and theoretical spin noise spectra are directly and quantitatively compared in both longitudinal and transverse magnetic fields up to the high magnetic-field regime (where Zeeman energies exceed the intrinsic hyperfine energy splitting of the {sup 41}K ground state)

Mihaila, Bogdan [Materials Science and Technology Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Crooker, Scott A.; Rickel, Dwight G. [National High Magnetic Field Laboratory, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Blagoev, Krastan B.; Smith, Darryl L. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Littlewood, Peter B. [Cavendish Laboratory, Madingley Road, Cambridge CB3 0HE (United Kingdom)

2006-10-15

322

Remote gas detection and quantitative analysis from infrared emission spectra obtained by Fourier transform infrared spectroscopy  

NASA Astrophysics Data System (ADS)

Techniques for obtaining quantitative values of the temperatures and concentrations of remote hot gaseous effluents from their measured passive emission spectra have been examined in laboratory experiments. The high sensitivity of the spectrometer in the vicinity of the 2397 cm-1 band head region of CO2 has allowed the gas temperature to be calculated from the relative intensity of the observed rotational lines. The spatial distribution of the CO2 in a methane flame has been reconstructed tomographically using a matrix inversion technique. The spectrometer has been calibrated against a black body source at different temperatures and a self absorption correction has been applied to the data avoiding the need to measure the transmission directly. Reconstruction artifacts have been reduced by applying a smoothing routine to the inversion matrix.

Hilton, Moira; Lettington, Alan H.; Mills, Ian M.

1994-06-01

323

Quantitative spectroscopy on individual wire, slot, bow-tie, rectangular, and square-shaped optical antennas.  

PubMed

By using a recently introduced approach combining a focus-modulation technique with a common-path interferometer, we measure quantitatively the extinction, scattering, and absorption cross-section spectra of individual optical antennas. The experimental results on thin-wire antennas, slot antennas, bow-tie antennas, rectangular antennas, and square-shaped antennas resonating at around 1.4 ?m wavelength are discussed. We find increased resonant scattering cross sections for the latter four antennas compared to the thin-wire antenna, both in absolute terms and relative to the absorption cross section. The square-shaped antenna's resonant extinction cross section approaches the limit of a coherent point dipole. However, the ratio of the resonant extinction cross section to the geometrical cross section of 38 is largest for the simple thin-wire antenna. PMID:24322083

Husnik, Martin; Niegemann, Jens; Busch, Kurt; Wegener, Martin

2013-11-15

324

Quantitative analysis of carbonaceous aerosols using Laser-Induced Breakdown Spectroscopy: A study on mass loading induced plasma matrix effects.  

SciTech Connect

We present results indicating mass loading induced plasma matrix effects on the application of quantitative laser-induced breakdown spectroscopy (LIBS) for estimation of carbon contents in aerosols. An in-house flow-controlled powder-dispersion system generated carbonaceous aerosols with varying bi-modal particle size distributions ({approx} 1 {micro}m and 10 {micro}m median diameters), thereby resulting in a wide mass loading range. For ease of chemical handling and to eliminate toxic effects, common talcum powder was used as our standard aerosol. Normalized atomic species concentrations of C, i.e., (C)/(Si) ratios, were calculated from atomic emission lines of C I (248 nm), Si I (252 nm), and plasma temperatures estimated from a series of Mg I lines. The results show a decrease in (C)/(Si) ratio to about 65% of the initial value as relative mass loadings increased (5.5-100%) due to the increase in number concentrations of larger sized particles ({approx}10 {micro}m median diameter). As a comparison, normalized ratio of (Mg)/(Si) did not exhibit any marked change with increased mass loading. The normalized total absorption of photon flux across the C I (248 nm) spectral line indicated a strong correlation to the percentage decrease in (C)/(Si) ratio. We used an impactor with a cut-off size of around 10 {micro}m diameter to generate mono-modal aerosolized powders ({approx}1 {micro}m median diameter) that had lower relative mass loadings (0.32-0.16%). Similar LIBS analysis on these did not indicate any of the matrix effects. We conclude that for aerosol systems with widely varying mass loadings, quantitative LIBS analysis can be significantly affected by plasma matrix effects, specifically for the C I (248 nm) emission line as noticed in this study. This bears significance for the application of quantitative LIBS in the chemical characterization of all forms of carbonaceous aerosols.

Mukherjee, Dibyendu [ORNL; Cheng, Mengdawn [ORNL

2008-01-01

325

Determining Enzyme Kinetics for Systems Biology with Nuclear Magnetic Resonance Spectroscopy  

PubMed Central

Enzyme kinetics for systems biology should ideally yield information about the enzyme’s activity under in vivo conditions, including such reaction features as substrate cooperativity, reversibility and allostery, and be applicable to enzymatic reactions with multiple substrates. A large body of enzyme-kinetic data in the literature is based on the uni-substrate Michaelis-Menten equation, which makes unnatural assumptions about enzymatic reactions (e.g., irreversibility), and its application in systems biology models is therefore limited. To overcome this limitation, we have utilised NMR time-course data in a combined theoretical and experimental approach to parameterize the generic reversible Hill equation, which is capable of describing enzymatic reactions in terms of all the properties mentioned above and has fewer parameters than detailed mechanistic kinetic equations; these parameters are moreover defined operationally. Traditionally, enzyme kinetic data have been obtained from initial-rate studies, often using assays coupled to NAD(P)H-producing or NAD(P)H-consuming reactions. However, these assays are very labour-intensive, especially for detailed characterisation of multi-substrate reactions. We here present a cost-effective and relatively rapid method for obtaining enzyme-kinetic parameters from metabolite time-course data generated using NMR spectroscopy. The method requires fewer runs than traditional initial-rate studies and yields more information per experiment, as whole time-courses are analyzed and used for parameter fitting. Additionally, this approach allows real-time simultaneous quantification of all metabolites present in the assay system (including products and allosteric modifiers), which demonstrates the superiority of NMR over traditional spectrophotometric coupled enzyme assays. The methodology presented is applied to the elucidation of kinetic parameters for two coupled glycolytic enzymes from Escherichia coli (phosphoglucose isomerase and phosphofructokinase). 31P-NMR time-course data were collected by incubating cell extracts with substrates, products and modifiers at different initial concentrations. NMR kinetic data were subsequently processed using a custom software module written in the Python programming language, and globally fitted to appropriately modified Hill equations.

Eicher, Johann J.; Snoep, Jacky L.; Rohwer, Johann M.

2012-01-01

326

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

327

Fourier transform infrared spectroscopy in the study of lipid phase transitions in model and biological membranes: practical considerations.  

PubMed

Fourier transform infrared (FTIR) spectroscopy is a powerful, nonperturbing technique that has been used to good effect for the detection and characterization of lipid phase transitions in model and natural membranes. The technique is also quite versatile, covering a wide range of sophisticated applications, from which fairly detailed information about the structure and organization of membranes and other lipid assemblies can be obtained. In this chapter, an introduction to this particular application of FTIR spectroscopy is presented. Special emphasis is put on how the technique can be used to study lipid phase transitions under biologically relevant conditions. The chapter is intended to give an overview of the capabilities of FTIR spectroscopy in the field of lipid and biomembrane research, and provide the reader with some practical guidelines for the design and execution of simple FTIR spectroscopic experiments suitable for the detection and characterization of lipid phase transitions in hydrated lipid bilayers. PMID:17951736

Lewis, Ruthven N A H; McElhaney, Ronald N

2007-01-01

328

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

329

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

PubMed Central

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 hr or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples.

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

2013-01-01

330

Development of a biologically relevant calcium phosphate substrate for sum frequency generation vibrational spectroscopy.  

PubMed

A novel biologically relevant composite substrate has been prepared consisting of a calcium phosphate (CaP) layer formed by magnetron sputter-coating from a hydroxyapatite (HA) target onto a gold-coated silicon substrate. The CaP layer is intended to mimic tooth and bone surfaces and allows polymers used in oral care to be deposited in a procedure analogous to that used for dental surfaces. The polymer cetyl dimethicone copolyol (CDC) was deposited onto the CaP surface of the substrate by Langmuir Blodgett deposition, and the structure of the adsorbed layer was investigated by the surface specific technique of sum frequency generation (SFG) vibrational spectroscopy. The gold sublayer provides enhancement of the SFG signal arising from the polymer but plays no part in the adsorption of the polymer. The surface morphology of the substrate was investigated using SEM and AFM. The surface roughness was commensurate with that of the thermally evaporated gold sublayer and uniform over areas of at least 36 mum(2). The chemical composition of the CaP-coated surface was determined by FTIR and TOF-SIMS. It was concluded that the surface is primarily calcium phosphate present as a mixture of amorphous, non-hydroxylated phases rather than solely stoichiometric hydroxyapatite. The SFG spectra from CDC on CaP were closely similar, both in resonance wavenumbers and in their relative intensities, with spectra of thin films of CDC recorded directly on gold. Application of previous analysis of the spectra of CDC on gold therefore enabled interpretation of the polymer orientation and conformation on the CaP substrate. PMID:16834276

McGall, Sarah J; Davies, Paul B; Neivandt, David J

2005-10-01

331

Quantitative Sulfur Analysis using Stand-off Laser-Induced Breakdown Spectroscopy  

NASA Astrophysics Data System (ADS)

The laser-induced breakdown spectrometer (LIBS) in the ChemCam instrument on Mars Science Laboratory has the capability to produce robust, quantitative analyses not only for major elements, but also for a large range of light elements and trace elements that are of great interest to geochemists. However, sulfur presents a particular challenge because it reacts easily with oxygen in the plasma and because the brightest S emission lines lie outside ChemCam's spectral range. This work was undertaken within the context of our larger effort to identify and compensate for matrix effects, which are chemical properties of the material that influence the ratio of a given emission line to the abundance of the element producing that line. Samples for this study include two suites of rocks: a suite of 12 samples that are mixtures of sulfate minerals and host rocks, generally with high S contents (0.1-26.0 wt% S), and a large suite of 118 igneous rocks from varying parageneses with S contents in the 0-2 wt% range. These compositions provide several different types of matrices to challenge our calibration procedures. Samples were analyzed under ChemCam-like conditions: a Nd:YAG laser producing 17 mJ per 10ns pulse was directed onto samples positioned 5-9 m away from the laser and tele­scope. The samples were placed in a vacuum chamber filled with 7 Torr CO2 to replicate the Martian surface pressure as the atmospheric pressure influences the LIBS plasma. Some of the LIBS plasma emission is collected with a telescope and transmitted through a 1 m, 300 um, 0.22NA optical fiber connected to a commercial Ocean Optics spectrometer. We are testing and comparing three different strategies to evaluate sulfur contents. 1) We have calculated regression lines comparing the intensity at each channel to the S content. This analysis shows that there are dozens of S emission lines in the ChemCam wavelength range that are suitable for use in quantitative analysis, even in the presence of Fe. 2) Partial least-squares analyses of these data show that S can be predicted with better than 10% accuracy, even when present at levels <0.15 wt%. 3) When peaks in the spectra are fit, the resultant peak areas can be regressed against concentration using step-wise multiple regression analysis to determine which subset of S lines gives the most accurate concentrations. All three methods of calibration show that excellent S analyses can be produced under Mars conditions at stand-off distances of up to 9 m.

Dyar, M. D.; Tucker, J. M.; Clegg, S. M.; Barefield, J. E.; Wiens, R. C.

2008-12-01

332

Quantitative measurement of intracellular transport of nanocarriers by spatio-temporal image correlation spectroscopy  

PubMed Central

Spatio-temporal image correlation spectroscopy (STICS) is a powerful technique for assessing the nature of particle motion in complex systems although it has been rarely used to investigate the intracellular dynamics of nanocarriers so far. Here we introduce a method to characterize the mode of motion of nanocarriers and to quantify their transport parameters on different length scales from single-cell to subcellular level. Using this strategy we were able to study the mechanisms responsible for the intracellular transport of DOTAP-DOPC/DNA and DC-Chol-DOPE/DNA lipoplexes in CHO-K1 live cells. Measurement of both diffusion coefficients and velocity vectors (magnitude and direction) averaged over regions of the cell revealed the presence of distinct modes of motion. Lipoplexes diffused slowly on the cell surface (diffusion coefficient, D ? 0.003 µm2/s). In the cytosol, the lipoplexes’ motion was characterized by active transport with average velocity ? ? 0.03 µm/s and random motion. The method permitted us to generate intracellular transport map showing several regions of concerted motion of lipoplexes.

Coppola, S; Pozzi, D; De Sanctis, S Candeloro; Digman, M A; Gratton, E; Caracciolo, G

2013-01-01

333

Quantitative evaluation of noncovalent interactions between glyphosate and dissolved humic substances by NMR spectroscopy.  

PubMed

Interactions of glyphosate (N-phosphonomethylglycine) herbicide (GLY) with soluble fulvic acids (FAs) and humic acids (HAs) at pH 5.2 and 7 were studied by (1)H and (31)P NMR spectroscopy. Increasing concentrations of soluble humic matter determined broadening and chemical shift drifts of proton and phosphorus GLY signals, thereby indicating the occurrence of weak interactions between GLY and humic superstructures. Binding was larger for FAs and pH 5.2 than for HAs and pH 7, thus suggesting formation of hydrogen bonds between GLY carboxyl and phosphonate groups and protonated oxygen functions in humic matter. Changes in relaxation and correlation times of (1)H and (31)P signals and saturation transfer difference NMR experiments confirmed the noncovalent nature of GLY-humic interactions. Diffusion-ordered NMR spectra allowed calculation of the glyphosate fraction bound to humic superstructures and association constants (K(a)) and Gibbs free energies of transfer for GLY-humic complex formation at both pH values. These values showed that noncovalent interactions occurred most effectively with FAs and at pH 5.2. Our findings indicated that glyphosate may spontaneously and significantly bind to soluble humic matter by noncovalent interactions at slightly acidic pH and, thus, potentially pollute natural water bodies by moving through soil profiles in complexes with dissolved humus. PMID:22591574

Mazzei, Pierluigi; Piccolo, Alessandro

2012-06-01

334

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 1 x 10(-6) to 5 x 10(-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 different PCA 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

2013-12-01

335

Quantitative analysis of adhesive resin in the hybrid layer using Raman spectroscopy  

PubMed Central

The objective was to determine absolute molar concentration of adhesive resin components in the hybrid layer by establishing methods based on Raman spectroscopy fundamentals. The hybrid layer was treated as a three-component system consisting of collagen and an adhesive resin containing two monomers. Adhesive standard specimens and Raman peak area ratios obtained with a 785 nm excitation wavelength were used to construct separate calibration curves for comonomer relative molar concentration and Bis-GMA absolute molar concentration. Since collagen and water had no measurable peaks in the fingerprint region, a dilution coefficient Kj was defined to describe their impact on Raman peak area and to calculate HEMA absolute molar concentration. Methodology was validated using an analogous system containing acetone/ethanol/water. The absolute molar concentration of Bis-GMA and HEMA decreased 87% and 83%, respectively, from the top quarter to the middle of the hybrid layer. Additionally, less Bis-GMA penetrated the hybrid layer than HEMA, as indicated by the ?20% decrease in comonomer molar concentration ratio between the adhesive resin layer and the top half of the hybrid layer. Lack of complete monomer infiltration will further challenge dentin-adhesive bond longevity.

Zou, Yuan; Armstrong, Steven R.; Jessop, Julie L. P.

2009-01-01

336

[Quantitative analysis of goose and duck mixed down using visible/NIR spectroscopy].  

PubMed

Goose down and duck down have very similar appearance but the quality of goose down is better than that of duck down in general. There is a highest allowable limit as specified by the various national standards of feather and down for the percentage of duck feather or down mixed in goose feather or down. Traditional detection method, manual inspection with a high-scale microscope, is labor intensive and not suitable for large-volume samples analysis and on-site rapid testing. In the present paper, visible/near-infrared (NIR) spectroscopy combined with successive projection algorithm (SPA) for characteristic wavelengths selection was used to determinate the content of duck down mixed in goose down. In the range of 450-930 nm, the multiple linear regression (MLR) model established with the 8 characteristic wavelengths selected by SPA achieved good prediction, the correlation coefficient of 0.983, root mean square error of calibration (RMSEC) of 5.44%, and root mean square error of prediction (RMSEP) of 5.75%. Therefore, it is expected to be used for rapid detection of feather and down quality in future. PMID:22715765

Xu, Hui-rong; Song, Bao-guo; Wan, Wang-jun; Zhou, Ying; Ying, Yi-bin

2012-04-01

337

Compact focusing von Hamos spectrometer for quantitative x-ray spectroscopy  

NASA Astrophysics Data System (ADS)

A compact focusing crystal spectrometer based on the von Hamos scheme is described. Cylindrically curved mica and graphite crystals with a radius of curvature of R=20 mm are used in the spectrometer. A front illuminated charge-coupled device (CCD) linear array detector makes this spectrometer useful for real-time spectroscopy of laser-produced plasma x-ray sources within the wavelength range of ?=1.8-10 Å. Calibration of crystals and the CCD linear array makes it possible to measure absolute photon fluxes. X-ray spectra in an absolute intensity scale were obtained from Mg, Ti, and Fe laser-produced plasmas, with a spectral resolution ?/??=800-2000 for the mica and ?/??=200-300 for graphite crystal spectrometers. The spectrometer has high efficiency in a wide spectral range, it is compact (40 mm diam, 150 mm length), easy to align, and flexible. The spectrometer is promising for absolute spectral measurements of x-ray radiation of low-intensity sources (femtosecond laser-produced plasmas, micropinches, electron-beam-ion-trap sources, etc.).

Shevelko, A. P.; Kasyanov, Yu. S.; Yakushev, O. F.; Knight, L. V.

2002-10-01

338

Metabolic profiles of human brain tumors using quantitative in vivo 1H magnetic resonance spectroscopy.  

PubMed

Proton spectroscopy can noninvasively provide useful information on brain tumor type and grade. Short- (30 ms) and long- (136 ms) echo time (TE) (1)H spectra were acquired from normal white matter (NWM), meningiomas, grade II astrocytomas, anaplastic astrocytomas, glioblastomas, and metastases. Very low myo-Inositol ([mI]) and creatine ([Cr]) were characteristic of meningiomas, and high [mI] characteristic of grade II astrocytomas. Tumor choline ([Cho]) was greater than NWM and increased with grade for grade II and anaplastic astrocytomas, but was highly variable for glioblastomas. Higher [Cho] and [Cr] correlated with low lipid and lactate (P < 0.05), indicating a dilution of metabolite concentrations due to necrosis in high-grade tumors. Metabolite peak area ratios showed no correlation with lipids and mI/Cho (at TE = 30 ms), and Cr/Cho (at TE = 136 ms) best correlated with tumor grade. The quantified lipid, macromolecule, and lactate levels increased with grade of tumor, consistent with progression from hypoxia to necrosis. Quantification of lipids and macromolecules at short TE provided a good marker for tumor grade, and a scatter plot of the sum of alanine, lactate, and delta 1.3 lipid signals vs. mI/Cho provided a simple way to separate most tumors by type and grade. PMID:12541241

Howe, F A; Barton, S J; Cudlip, S A; Stubbs, M; Saunders, D E; Murphy, M; Wilkins, P; Opstad, K S; Doyle, V L; McLean, M A; Bell, B A; Griffiths, J R

2003-02-01

339

Quantitative determinations of levofloxacin and rifampicin in pharmaceutical and urine samples using nuclear magnetic resonance spectroscopy  

NASA Astrophysics Data System (ADS)

Rapid, specific and simple methods for determining levofloxacin and rifampicin antibiotic drugs in pharmaceutical and human urine samples were developed. The methods are based on 1H NMR spectroscopy using maleic acid as an internal standard and DMSO-d6 as NMR solvent. Integration of NMR signals at 8.9 and 8.2 ppm were, respectively, used for calculating the concentration of levofloxacin and rifampicin drugs per unit dose. Maleic acid signal at 6.2 ppm was used as the reference signal. Recoveries of (97.0-99.4) ± 0.5 and (98.3-99.7) ± 1.08% were obtained for pure levofloxacin and rifampicin, respectively. Corresponding recoveries of 98.5-100.3 and 96.8-100.0 were, respectively, obtained in pharmaceutical capsules and urine samples. Relative standard deviations (R.S.D.) values ?2.7 were obtained for analyzed drugs in pure, pharmaceutical and urine samples. Statistical Student's t-test gave t-values ?2.87 indicating insignificant difference between the real and the experimental values at the 95% confidence level. F-test revealed insignificant difference in precisions between the developed NMR methods and each of fluorimetric and HPLC methods for analyzing levofloxacin and rifampicin.

Salem, A. A.; Mossa, H. A.; Barsoum, B. N.

2005-11-01

340

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

NASA Astrophysics Data System (ADS)

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 chlorinated solvents. Raman spectra of an extensive collection of solvent mixtures (200+) were collected using a JY-Horiba LabRam, infinity with a 488 nm excitation source. The solvent mixtures comprised of several chlorinated solvents: dichloromethane, chloroform, and 1,1,1-trichloroethane, mixed with solvents such as toluene, cyclohexane and/or acetone. The spectra were then analysed using a variety of chemometric techniques (Principal Component Analysis and Principal Component Regression) and machine learning (Neural Networks and Genetic Programming). In each case models were developed to identify the presence of chlorinated solvents in mixtures at levels of ~5%, to identify the type of chlorinated solvent and then to accurately quantify the amount of chlorinated solvent.

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

2005-06-01

341

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

NASA Astrophysics Data System (ADS)

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 (Al3+, Sb2+, As2+, Cd2+ and Pb2+) by surface-enhanced Raman spectroscopy. Calibration curves were established for all metal ions between the concentration ranges of 1 x 10-6 to 5 x 10-4 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.

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

2013-12-01

342

Electrons, Photons, and Force: Quantitative Single-Molecule Measurements from Physics to Biology  

PubMed Central

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution.

2011-01-01

343

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

344

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)] [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)] [Sandia National Laboratories, Albuquerque, New Mexico 87185-0343 (United States); Radigan, K.J. [National Semiconductor Corporation, Santa Clara, California 95052 (United States)] [National Semiconductor Corporation, Santa Clara, California 95052 (United States)

1995-07-01

345

Open Slit Spectroscopy for Quantitative Analysis and Uv-Resonance Raman  

NASA Astrophysics Data System (ADS)

In emission spectral measurement with a dispersive spectrometer, if the entrance slit is widely opened, more light from a relatively large sample area can be collected, thus both energy throughput and spatial averaging advantages can be achieved in the measurement. With the entrance slit widely opened, the spectral bandpass becomes large. Radiations of different wavelengths likely fall on the same area of the detector. This can lead to a multiplex advantage and also extend the accessible wavelength range for a given spectral window. The problem for opening the entrance slit is the decrease of spectral resolution. This project aimed to overcome this problem so that all the advantages associated with opening entrance slit are retained without loss of spectral resolution. The research we have done to solve this problem is to apply Hadamard transform and deconvolution in spectral measurements. The way we implement Hadamard transform in emission spectroscopy is to take spectra with a Hadamard mask in place of the conventional entrance slit, then inversely transform the measured data to recover the well-resolved spectra with improved signal-to-noise ratio. A spectrum can also be taken simply with the entrance slit widely opened. By deconvolving the slit function with such a wide-slit spectrum a best resolved spectrum can be recovered. Major difficulties involving in deconvolution have been discussed in Chapter 5 of this dissertation, and a novel algorithm is proposed there as well. Another important aspect involved in this project is the incorporation of fiber optics with Hadamard transform and deconvolution in spectral measurements. This greatly improved the flexibility and collection efficiency in our measurement system.

Zhu, Jianxiong

346

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

347

X-ray absorption spectroscopy of a quantitatively Mo(V) dimethyl sulfoxide reductase species.  

PubMed

Molybdenum K-edge X-ray absorption spectroscopy (XAS) has been used to probe the structure of a Mo(V) species that has been suggested to be a catalytic intermediate in the reaction of dimethyl sulfoxide (DMSO) reductase with the alternative substrate trimethylamine N-oxide (Bennet et al. Eur. J. Biochem. 1994, 255, 321-331; Cobb et al. J. Biol. Chem. 2005, 280, 11007-11017; Mtei, et al. J. Am. Chem. Soc. 2011, 133, 9672-9774). The oxidized Mo(VI) state of DMSO reductase has previously been structurally characterized as being six coordinate, with four sulfurs from pyranopterin dithiolene molybdenum cofactors, a terminal oxygen ligand, and an additional oxygen coordination from a serine residue. We find the most plausible structure for the Mo(V) active site is a five-coordinate species with four sulfur donors from the two pyranopterin dithiolene ligands, with an average Mo-S bond-length of 2.35 Å, plus a single oxygen donor at 1.99 Å, very likely from an Mo-OH ligand. Our results thus suggest that the oxygen of the serine residue has dissociated from the metal ion, suggesting hitherto unsuspected flexibility of the active site, and calling into question whether this putative intermediate is catalytically relevant. The relevance to previous Mo(V) electron paramagnetic resonance and other spectroscopic studies on DMSO reductase is discussed. XAS of an extensively studied Mo(V) form of Rhodobacter sphaeroides DMSO reductase (the high-g split species) shows that previously suggested structures for the active site are likely incorrect. PMID:23445435

Pushie, M Jake; Cotelesage, Julien J H; Lyashenko, Ganna; Hille, Russ; George, Graham N

2013-03-18

348

Non-invasive quantitative assessment of oxidative metabolism in quadriceps muscles by near infrared spectroscopy  

PubMed Central

Background—Near infrared spectroscopy can be used in non-invasive monitoring of changes in skeletal muscle oxygenation in exercising subjects. Objective—To evaluate whether this method can be used to assess metabolic capacity of muscles. Two distinctive variables abstracted from a curve of changes in muscle oxygenation were assessed. Methods—Exercise on a cycle ergometer was performed by 18 elite male athletes and eight healthy young men. A measuring probe was placed on the skin of the quadriceps muscle to measure reflected light at two wavelengths (760 and 850 nm), so that the relative index of muscle oxygenation could be calculated. Exercise intensity was increased from 50 W in 50 W increments until the subject was exhausted. During exercise, changes in muscle oxygenation and blood lactate concentration were recorded. The following two variables for assessment of muscle oxygenation were then abstracted and analysed by plotting curves of changes in muscle oxygenation: the rate of recovery of muscle oxygen saturation (RR) and the relative value of the effective decrease in muscle oxygenation (Deff). Results—Data analysis showed a correlation between muscle oxygenation and blood lactate concentration at the various exercise intensities and verified the feasibility of the experiment. Data for the athletes were compared with those for the controls using the Aspin-Welch test of significance; t = 2.3 and 2.86 for RR and Deff respectively. There were significant differences (p = 0.05) between the athletes and the control group with respect to these two variables. Conclusion—RR and Deff may be distinctive variables that can be used to characterise muscle oxidative metabolism during human body movement. Key Words: recovery; muscle; oxygen saturation; exercise; elite athletes

Ding, H; Wang, G; Lei, W; Wang, R; Huang, L; Xia, Q; Wu, J

2001-01-01

349

Quantitative Spectroscopy of Blue Supergiants in Metal-poor Dwarf Galaxy NGC 3109  

NASA Astrophysics Data System (ADS)

We present a quantitative analysis of the low-resolution (~4.5 Å) spectra of 12 late-B and early-A blue supergiants (BSGs) in the metal-poor dwarf galaxy NGC 3109. A modified method of analysis is presented which does not require use of the Balmer jump as an independent T eff indicator, as used in previous studies. We determine stellar effective temperatures, gravities, metallicities, reddening, and luminosities, and combine our sample with the early-B-type BSGs analyzed by Evans et al. to derive the distance to NGC 3109 using the flux-weighted gravity-luminosity relation (FGLR). Using primarily Fe-group elements, we find an average metallicity of [\\bar{Z}] = –0.67 ± 0.13, and no evidence of a metallicity gradient in the galaxy. Our metallicities are higher than those found by Evans et al. based on the oxygen abundances of early-B supergiants ([\\bar{Z}] = –0.93 ± 0.07), suggesting a low ?/Fe ratio for the galaxy. We adjust the position of NGC 3109 on the BSG-determined galaxy mass-metallicity relation accordingly and compare it to metallicity studies of H II regions in star-forming galaxies. We derive an FGLR distance modulus of 25.55 ± 0.09 (1.27 Mpc) that compares well with Cepheid and tip of the red giant branch distances. The FGLR itself is consistent with those found in other galaxies, demonstrating the reliability of this method as a measure of extragalactic distances.

Hosek, Matthew W., Jr.; Kudritzki, Rolf-Peter; Bresolin, Fabio; Urbaneja, Miguel A.; Evans, Christopher J.; Pietrzy?ski, Grzegorz; Gieren, Wolfgang; Przybilla, Norbert; Carraro, Giovanni

2014-04-01

350

A method of online quantitative interpretation of diffuse reflection profiles of biological tissues  

NASA Astrophysics Data System (ADS)

We have developed a method of combined interpretation of spectral and spatial characteristics of diffuse reflection of biological tissues, which makes it possible to determine biophysical parameters of the tissue with a high accuracy in real time under conditions of their general variability. Using the Monte Carlo method, we have modeled a statistical ensemble of profiles of diffuse reflection coefficients of skin, which corresponds to a wave variation of its biophysical parameters. On its basis, we have estimated the retrieval accuracy of biophysical parameters using the developed method and investigated the stability of the method to errors of optical measurements. We have showed that it is possible to determine online the concentrations of melanin, hemoglobin, bilirubin, oxygen saturation of blood, and structural parameters of skin from measurements of its diffuse reflection in the spectral range 450-800 nm at three distances between the radiation source and detector.

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

2013-02-01

351

Quantitative Assessment of Liver Fat with Magnetic Resonance Imaging and Spectroscopy  

PubMed Central

Hepatic steatosis is characterized by abnormal and excessive accumulation of lipids within hepatocytes. It is an important feature of diffuse liver disease, and the histological hallmark of non-alcoholic fatty liver disease (NAFLD). Other conditions associated with steatosis include alcoholic liver disease, viral hepatitis, HIV and genetic lipodystrophies, cystic fibrosis liver disease, and hepatotoxicity from various therapeutic agents. Liver biopsy, the current clinical gold standard for assessment of liver fat, is invasive and has sampling errors, and is not optimal for screening, monitoring, clinical decision making, or well-suited for many types of research studies. Non-invasive methods that accurately and objectively quantify liver fat are needed. Ultrasound (US) and computed tomography (CT) can be used to assess liver fat but have limited accuracy as well as other limitations. Magnetic resonance (MR) techniques can decompose the liver signal into its fat and water signal components and therefore assess liver fat more directly than CT or US. Most magnetic resonance (MR) techniques measure the signal fat-fraction (the fraction of the liver MR signal attributable to liver fat), which may be confounded by numerous technical and biological factors and may not reliably reflect fat content. By addressing the factors that confound the signal fat-fraction, advanced MR techniques measure the proton density fat-fraction (the fraction of the liver proton density attributable to liver fat), which is a fundamental tissue property and a direct measure of liver fat content. These advanced techniques show promise for accurate fat quantification and are likely to be commercially available soon.

Reeder, Scott B.; Cruite, Irene; Hamilton, Gavin; Sirlin, Claude B.

2011-01-01

352

Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy  

NASA Astrophysics Data System (ADS)

Two new approaches to quantify sulfur functionalities in natural organic matter from S K-edge XANES spectroscopy are presented. In the first, the K-edge spectrum is decomposed into Gaussian and two arctangent functions, as in the usual Gaussian curve fitting (GCF) method, but the applicability of the model is improved by a rigorous simulation procedure that constrains the model-fit to converge toward chemically and physically realistic values. Fractions of each type of functionality are obtained after spectral decomposition by correcting Gaussian areas for the change in X-ray absorption cross-section with increasing oxidation state. This correction is made using published calibration curves and a new curve obtained in this study. Calibration-induced errors, inherent to the choice of a particular curve, are typically lower than 5% of total sulfur for oxidized species (e.g., sulfate), may reach 10% for organic reduced sulfur, and may be as high as 30-40% for inorganic reduced sulfur. A generic curve, which reduces the calibration-induced uncertainty by a factor of two on data collected to avoid X-ray overabsorption, is derived. In the second analytical scheme, the K-edge spectrum is partitioned into a weighted sum of component species, as in the usual linear combination fitting (LCF) method, but is fit to an extended database of reference spectra under the constraint of non-negativity in the loadings (Combo fit). The fraction of each sulfur functionality is taken as the sum of all positive fractions of references with similar oxidation state of sulfur. The two proposed methods are applied to eight humic and fulvic acids from the International Humic Substances Society (IHSS). The nature and fractions of sulfur functionalities obtained by the two analytical approaches are consistent with each other. The accuracy of the derived values, expressed as the difference in values of a fraction obtained on the same material by the two independent methods, is on average 4.5 ± 3.0% of total sulfur for exocyclic reduced sulfur, 4.1 ± 2.1% for heterocyclic reduced sulfur, and 1.6 ± 1.4% for sulfate. Total reduced sulfur has a better accuracy of estimation (2.4 ± 1.6%) than either exocyclic and heterocyclic sulfur, because the errors on the two reduced pools have opposite sign. Experimental difficulties and uncertainties of the results associated with the analysis of concentrated and heterogeneous samples are discussed. The spectra of the IHSS materials and the reference compounds are made available as an open source for interlaboratory testing.

Manceau, Alain; Nagy, Kathryn L.

2012-12-01

353

Quantitative determination of glufosinate in biological samples by liquid chromatography with ultraviolet detection after p-nitrobenzoyl derivatization.  

PubMed

We have established a new HPLC method for derivatizing and quantifying glufosinate (GLUF) in human serum and urine using p-nitrobenzoyl chloride (PNBC). The p-nitrobenzoyl derivative of GLUF (PNB-GLUF) was produced quantitatively over 10 min at room temperature. PNB-GLUF possesses the property of ultraviolet (UV) light absorption with a lambda(max) of 272.8 nm, and was isolated from biological specimens by reversed-phase chromatography using Inertsil Ph-3. In experiments at a UV wavelength of 273 nm, GLUF has a quantitative detection limit of 0.005 microg/ml, and when it was added to both serum and urine to yield concentrations of 0.1-1000 microg/ml, its recovery rate was quite satisfactory: at least 93.8% in all cases. Further, the measured amounts of GLUF in 23 serum samples from patients intoxicated by ingestion of GLUF compared favorably with those obtained by fluorescence derivatization-HPLC using 9-fluorenylmethyl chloroformate (R=0.998). This technique of analysis is, in addition, applicable for Glyphosat, which possesses a chemical structure resembling that of GLUF, and it will be of great use in the determination of these two compounds. PMID:11885854

Hori, Yasushi; Fujisawa, Manami; Shimada, Kenji; Sato, Mitsuru; Kikuchi, Michio; Honda, Masao; Hirose, Yasuo

2002-02-15

354

Quantitative high-performance liquid chromatography of nucleosides in biological materials.  

PubMed

A rigorous, comprehensive, and reliable reversed-phase high-performance liquid chromatographic (HPLC) method has been developed for the analysis of ribonucleosides in urine (psi, m1A, m1I, m2G, A, m2(2)G). An initial isolation of ribonucleosides with an affinity gel containing an immobilized phenylboronic acid was used to improve selectivity and sensitivity. Response for all nucleosides was linear from 0.1 to 50 nmoles injected and good quantitation was obtained for 25 microliter or less of sample placed on the HPLC column. Excellent precision of analysis for urinary nucleosides was achieved on matrix dependent and independent samples, and the high resolution of the reversed-phase column allowed the complete separation of 9 nucleosides from other unidentified UV absorbing components at the 1-ng level. Supporting experimental data are presented on precision, recovery, chromatographic methods, minimum detection limit, retention time, relative molar response, sample clean-up, stability of nucleosides, boronate gel capacity, and application to analysis of urine from patients with leukemia and breast cancer. This method is now being used routinely for the determination of the concentration and ratios of nucleosides in urine from patients with different types of cancer and in chemotherapy response studies. PMID:632336

Gehrke, C W; Kuo, K C; Davis, G E; Suits, R D; Waalkes, T P; Borek, E

1978-03-21

355

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

356

A method for quantitative mapping of thick oil spills using imaging spectroscopy  

USGS Publications Warehouse

In response to the Deepwater Horizon oil spill in the Gulf of Mexico, a method of near-infrared imaging spectroscopic analysis was developed to map the locations of thick oil floating on water. Specifically, this method can be used to derive, in each image pixel, the oil-to-water ratio in oil emulsions, the sub-pixel areal fraction, and its thicknesses and volume within the limits of light penetration into the oil (up to a few millimeters). The method uses the shape of near-infrared (NIR) absorption features and the variations in the spectral continuum due to organic compounds found in oil to identify different oil chemistries, including its weathering state and thickness. The method is insensitive to complicating conditions such as moderate aerosol scattering and reflectance level changes from other conditions, including moderate sun glint. Data for this analysis were collected by the NASA Airborne Visual Infrared Imaging Spectrometer (AVIRIS) instrument, which was flown over the oil spill on May 17, 2010. Because of the large extent of the spill, AVIRIS flight lines could cover only a portion of the spill on this relatively calm, nearly cloud-free day. Derived lower limits for oil volumes within the top few millimeters of the ocean surface directly probed with the near-infrared light detected in the AVIRIS scenes were 19,000 (conservative assumptions) to 34,000 (aggressive assumptions) barrels of oil. AVIRIS covered about 30 percent of the core spill area, which consisted of emulsion plumes and oil sheens. Areas of oil sheen but lacking oil emulsion plumes outside of the core spill were not evaluated for oil volume in this study. If the core spill areas not covered by flight lines contained similar amounts of oil and oil-water emulsions, then extrapolation to the entire core spill area defined by a MODIS (Terra) image collected on the same day indicates a minimum of 66,000 to 120,000 barrels of oil was floating on the surface. These estimates are preliminary and subject to revision pending further analysis. Based on laboratory measurements, near-infrared (NIR) photons penetrate only a few millimeters into oil-water emulsions. As such, the oil volumes derived with this method are lower limits. Further, the detection is only of thick surface oil and does not include sheens, underwater oil, or oil that had already washed onto beaches and wetlands, oil that had been burned or evaporated as of May 17. Because NIR light penetration within emulsions is limited, and having made field observations that oil emulsions sometimes exceeded 20 millimeters in thickness, we estimate that the volume of oil, including oil thicker than can be probed in the AVIRIS imagery, is possibly as high as 150,000 barrels in the AVIRIS scenes. When this value is projected to the entire spill, it gives a volume of about 500,000 barrels for thick oil remaining on the sea surface as of May 17. AVIRIS data cannot be used to confirm this higher volume, and additional field work including more in-situ measurements of oil thickness would be required to confirm this higher oil volume. Both the directly detected minimum range of oil volume, and the higher possible volume projection for oil thicker than can be probed with NIR spectroscopy imply a significantly higher total volume of oil relative to that implied by the early NOAA (National Oceanic and Atmospheric Administration) estimate of 5,000 barrels per day reported on their Web site.

Clark, Roger N.; Swayze, Gregg A.; Leifer, Ira; Livo, K. Eric; Kokaly, Raymond; Hoefen, Todd; Lundeen, Sarah; Eastwood, Michael; Green, Robert O.; Pearson, Neil; Sarture, Charles; McCubbin, Ian; Roberts, Dar; Bradley, Eliza; Steele, Denis; Ryan, Thomas; Dominguez, Roseanne; the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) Team

2010-01-01

357

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

358

Ba and Bb fragments of factor B activation: fragment production, biological activities, neoepitope expression and quantitation in clinical samples.  

PubMed

Factor B is a centrally important component of the alternative complement pathway. Alternative pathway activation results in factor B cleavage and production of the amino-terminal Ba and the carboxyl-terminal Bb fragments which have molecular weights of approximately 30,000 and 63,000 daltons, respectively. Both Ba and Bb fragments have been reported to express a variety of biological activities in vitro. Thus, binding of Ba and Bb fragments to specific B lymphocyte surface receptors modulates proliferation of prestimulated B cells. In addition, the enzymatically active Bb fragment induces activation and spreading of human and murine macrophages and monocytes as well as regulates C5a des Arg chemotactic activity. The fractional catabolic rate and metabolism of factor B in vivo is similar to that of C3, C4 and C5 complement proteins, which are among the most metabolically active plasma proteins in the circulatory system. Factor B hyperconsumption and increased catabolism, concomitant with factor B fragment production, occurs in a wide variety of diseases, including gram-negative sepsis, autoimmune diseases and burns. Measurement of alternative pathway activation in vivo has been attempted utilized a number of different techniques to quantitate factor B fragments in biological fluids. However, the recent development of enzyme immunoassays (EIA) employing monoclonal antibodies (MoAbs) reactive with factor B fragment neoepitopes provides the best approach currently available for the quantitation of factor B activation fragments. Results obtained using these new MoAb-based EIAs have indicated that factor B fragment concentrations were elevated, as compared with normal donor levels, in EDTA plasma samples obtained from patients with rheumatoid arthritis and systemic lupus erythematosus (SLE). Plasma concentrations of factor B fragments, especially Ba fragment levels, in these patients showed a positive correlation with disease activity scores. One of the highest disease activity correlations was obtained with Ba fragment measurements in SLE plasma samples. In fact, the results strongly suggested that quantitation of Ba fragment levels in SLE plasma samples more accurately reflected disease activity and was a more sensitive predictor of impending flare in these patients than any other test(s) currently available. PMID:2472921

Kolb, W P; Morrow, P R; Tamerius, J D

1989-01-01

359

3-Dimensional quantitative detection of nanoparticle content in biological tissue samples after local cancer treatment  

NASA Astrophysics Data System (ADS)

X-ray computed tomography is nowadays used for a wide range of applications in medicine, science and technology. X-ray microcomputed tomography (XµCT) follows the same principles used for conventional medical CT scanners, but improves the spatial resolution to a few micrometers. We present an example of an application of X-ray microtomography, a study of 3-dimensional biodistribution, as along with the quantification of nanoparticle content in tumoral tissue after minimally invasive cancer therapy. One of these minimal invasive cancer treatments is magnetic drug targeting, where the magnetic nanoparticles are used as controllable drug carriers. The quantification is based on a calibration of the XµCT-equipment. The developed calibration procedure of the X-ray-µCT-equipment is based on a phantom system which allows the discrimination between the various gray values of the data set. These phantoms consist of a biological tissue substitute and magnetic nanoparticles. The phantoms have been studied with XµCT and have been examined magnetically. The obtained gray values and nanoparticle concentration lead to a calibration curve. This curve can be applied to tomographic data sets. Accordingly, this calibration enables a voxel-wise assignment of gray values in the digital tomographic data set to nanoparticle content. Thus, the calibration procedure enables a 3-dimensional study of nanoparticle distribution as well as concentration.

Rahn, Helene; Alexiou, Christoph; Trahms, Lutz; Odenbach, Stefan

2014-06-01

360

Quantitative assessment of collagen fibre orientations from two-dimensional images of soft biological tissues  

PubMed Central

In this work, we outline an automated method for the extraction and quantification of material parameters characterizing collagen fibre orientations from two-dimensional images. Morphological collagen data among different length scales were obtained by combining the established methods of Fourier power spectrum analysis, wedge filtering and progressive regions of interest splitting. Our proposed method yields data from which we can determine parameters for computational modelling of soft biological tissues using fibre-reinforced constitutive models and gauge the length scales most appropriate for obtaining a physically meaningful measure of fibre orientations, which is representative of the true tissue morphology of the two-dimensional image. Specifically, we focus on three parameters quantifying different aspects of the collagen morphology: first, using maximum-likelihood estimation, we extract location parameters that accurately determine the angle of the principal directions of the fibre reinforcement (i.e. the preferred fibre directions); second, using a dispersion model, we obtain dispersion parameters quantifying the collagen fibre dispersion about these principal directions; third, we calculate the weighted error entropy as a measure of changes in the entire fibre distributions at different length scales, as opposed to their average behaviour. With fully automated imaging techniques (such as multiphoton microscopy) becoming increasingly popular (which often yield large numbers of images to analyse), our method provides an ideal tool for quickly extracting mechanically relevant tissue parameters which have implications for computational modelling (e.g. on the mesh density) and can also be used for the inhomogeneous modelling of tissues.

Schriefl, Andreas J.; Reinisch, Andreas J.; Sankaran, Sethuraman; Pierce, David M.; Holzapfel, Gerhard A.

2012-01-01

361

Comparison of various assays to quantitate macrophage activation by biological response modifiers  

SciTech Connect

Macrophages treated with various compounds that enhance host antitumor resistance exhibit measurable changes in metabolism, function, and surface antigens. In this study, murine peptone-induced peritoneal macrophages were stimulated in vitro by bacterial lipopolysaccharide (LPS), muramyl dipeptide (MDP), and poly I.poly C. They were subsequently compared in their ability to release superoxide and act as tumoristatic and tumoricidal effector cells. Superoxide generation was assayed by the reduction of ferricytochrome C. All three compounds failed to induce significant O/sub 2/- release, unless the cells were also treated with phorbol myristate acetate (PMA). MDP was most active in potentiating the PMA response. In the tumor growth inhibition assay, cytostatic activity was comparable for all three compounds and did not exceed 32 percent. The combination of subthreshold levels of these compounds and hybridoma-derived MAF acted synergistically to induce potent cytostatic activity. In the chromium release assay, LPS and poly I.poly C rendered macrophages cytolytic for P815 target cells at concentrations greater than or equal to 1 microgram/ml. In contrast, significant cytolysis was observed with MDP only at 100 micrograms/ml. Defining precisely the effect of various biological response modifiers on several parameters of macrophage function may facilitate use of these agents in cancer therapy.

Schultz, R.M.; Nanda, S.; Altom, M.G.

1984-01-01

362

Quantitative estimation of global patterns of surface ocean biological productivity and its seasonal variation on timescales from centuries to millennia  

NASA Astrophysics Data System (ADS)

We present a quantitative method, based on the relative abundances of benthic foraminifera in deep-sea sediments, for estimating surface ocean biological productivity over the timescale of centuries to millennia. We calibrate the method using a global data set composed of 207 samples from the Atlantic, Pacific, and Indian Oceans from a water depth range between 2300 and 3600 m. The sample set was developed so that other, potentially significant, environmental variables would be uncorrelated to overlying surface ocean productivity. A regression of assemblages against productivity yielded an r2 = 0.89 demonstrating a strong productivity signal in the faunal data. In addition, we examined assemblage response to annual variability in biological productivity (seasonality). Our data set included a range of seasonalities which we quantified into a seasonality index using the pigment color bands from the coastal zone color scanner (CZCS). The response of benthic foraminiferal assemblage composition to our seasonality index was tested with regression analysis. We obtained a statistically highly significant r2 = 0.75. Further, discriminant function analysis revealed a clear separation among sample groups based on surface ocean productivity and our seasonality index. Finally, we tested the response of benthic foraminiferal assemblages to three different modes of seasonality. We observed a distinct separation of our samples into groups representing low seasonal variability, strong seasonality with a single main productivity event in the year, and strong seasonality with multiple productivity events in the year. Reconstructing surface ocean biological productivity with benthic foraminifera will aid in modeling marine biogeochemical cycles. Also, estimating mode and range of annual seasonality will provide insight to changing oceanic processes, allowing the examination of the mechanisms causing changes in the marine biotic system over time. This article contains supplementary material.

Loubere, Paul; Fariduddin, Mohammad

1999-03-01

363

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

364

Studying flow close to an interface by total internal reflection fluorescence cross-correlation spectroscopy: quantitative data analysis.  

PubMed

Total internal reflection fluorescence cross-correlation spectroscopy (TIR-FCCS) has recently [S. Yordanov et al., Optics Express 17, 21149 (2009)] been established as an experimental method to probe hydrodynamic flows near surfaces, on length scales of tens of nanometers. Its main advantage is that fluorescence occurs only for tracer particles close to the surface, thus resulting in high sensitivity. However, the measured correlation functions provide only rather indirect information about the flow parameters of interest, such as the shear rate and the slip length. In the present paper, we show how to combine detailed and fairly realistic theoretical modeling of the phenomena by Brownian dynamics simulations with accurate measurements of the correlation functions, in order to establish a quantitative method to retrieve the flow properties from the experiments. First, Brownian dynamics is used to sample highly accurate correlation functions for a fixed set of model parameters. Second, these parameters are varied systematically by means of an importance-sampling Monte Carlo procedure in order to fit the experiments. This provides the optimum parameter values together with their statistical error bars. The approach is well suited for massively parallel computers, which allows us to do the data analysis within moderate computing times. The method is applied to flow near a hydrophilic surface, where the slip length is observed to be smaller than 10nm, and, within the limitations of the experiments and the model, indistinguishable from zero. PMID:22304189

Schmitz, R; Yordanov, S; Butt, H J; Koynov, K; Dünweg, B

2011-12-01

365

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

366

Studying flow close to an interface by total internal reflection fluorescence cross-correlation spectroscopy: Quantitative data analysis  

NASA Astrophysics Data System (ADS)

Total internal reflection fluorescence cross-correlation spectroscopy (TIR-FCCS) has recently [S. Yordanov , Optics ExpressOPEXFF1094-408710.1364/OE.17.021149 17, 21149 (2009)] been established as an experimental method to probe hydrodynamic flows near surfaces, on length scales of tens of nanometers. Its main advantage is that fluorescence occurs only for tracer particles close to the surface, thus resulting in high sensitivity. However, the measured correlation functions provide only rather indirect information about the flow parameters of interest, such as the shear rate and the slip length. In the present paper, we show how to combine detailed and fairly realistic theoretical modeling of the phenomena by Brownian dynamics simulations with accurate measurements of the correlation functions, in order to establish a quantitative method to retrieve the flow properties from the experiments. First, Brownian dynamics is used to sample highly accurate correlation functions for a fixed set of model parameters. Second, these parameters are varied systematically by means of an importance-sampling Monte Carlo procedure in order to fit the experiments. This provides the optimum parameter values together with their statistical error bars. The approach is well suited for massively parallel computers, which allows us to do the data analysis within moderate computing times. The method is applied to flow near a hydrophilic surface, where the slip length is observed to be smaller than 10nm, and, within the limitations of the experiments and the model, indistinguishable from zero.

Schmitz, R.; Yordanov, S.; Butt, H. J.; Koynov, K.; Dünweg, B.

2011-12-01

367

Relative sensitivity of magnetic resonance spectroscopy and quantitative magnetic resonance imaging to cognitive function among nondemented individuals infected with HIV.  

PubMed

In the present study, we examined the relationships among cognitive function, magnetic resonance spectroscopy (MRS) brain metabolite indices measured in the basal ganglia, and quantitative magnetic resonance imaging (MRI) of the caudate nucleus and the putamen in the earliest stages of HIV-related cognitive involvement. Participants included 22 HIV-positive individuals and 20 HIV-negative individuals. HIV-positive individuals performed significantly more poorly than the HIV-negative individuals on several cognitive measures. In addition, the choline/creatine ratio was significantly higher and the N-acetyl aspartate/choline ratio was significantly lower among HIV patients. The caudate and putamen sizes were smaller among HIV-positive patients compared with controls; however, the differences did not reach statistical significance. Correlation analyses revealed associations between cognitive function and select MRS indices. In addition, caudate size was significantly correlated with performances on higher-order thinking tests whereas putamen size was significantly correlated with performances on motor tests. The results suggest that MRS differences are more pronounced than area size differences between seropositive and seronegative individuals in mild stages of HIV-related cognitive impairment. However, basal ganglia size remains an important contributor to cognitive status in this population. Longitudinal studies are needed to determine the evolution of these imaging correlates of HIV-cognitive impairment in HIV. PMID:18764968

Paul, Robert H; Ernst, Thomas; Brickman, Adam M; Yiannoutsos, Constantin T; Tate, David F; Cohen, Ronald A; Navia, Bradford A

2008-09-01

368

The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization.  

PubMed

Life is the most complex physical phenomenon in the Universe, manifesting an extraordinary diversity of form and function over an enormous scale from the largest animals and plants to the smallest microbes and subcellular units. Despite this many of its most fundamental and complex phenomena scale with size in a surprisingly simple fashion. For example, metabolic rate scales as the 3/4-power of mass over 27 orders of magnitude, from molecular and intracellular levels up to the largest organisms. Similarly, time-scales (such as lifespans and growth rates) and sizes (such as bacterial genome lengths, tree heights and mitochondrial densities) scale with exponents that are typically simple powers of 1/4. The universality and simplicity of these relationships suggest that fundamental universal principles underly much of the coarse-grained generic structure and organisation of living systems. We have proposed a set of principles based on the observation that almost all life is sustained by hierarchical branching networks, which we assume have invariant terminal units, are space-filling and are optimised by the process of natural selection. We show how these general constraints explain quarter power scaling and lead to a quantitative, predictive theory that captures many of the essential features of diverse biological systems. Examples considered include animal circulatory systems, plant vascular systems, growth, mitochondrial densities, and the concept of a universal molecular clock. Temperature considerations, dimensionality and the role of invariants are discussed. Criticisms and controversies associated with this approach are also addressed. PMID:15855389

West, Geoffrey B; Brown, James H

2005-05-01

369

Trace elemental analysis by laser-induced breakdown spectroscopy—Biological applications  

NASA Astrophysics Data System (ADS)

Laser-Induced Breakdown Spectroscopy (LIBS) is a sensitive optical technique capable of fast multi-elemental analysis of solid, gaseous and liquid samples. Since the late 1980s LIBS became visible in the analytical atomic spectroscopy scene; its applications having been developed continuously since then. In this paper, the use of LIBS for trace element determination in different matrices is reviewed. The main emphasis is on spatially resolved analysis of microbiological, plant and animal samples.

Kaiser, Jozef; Novotný, Karel; Martin, Madhavi Z.; Hrdli?ka, Aleš; Malina, Radomír; Hartl, Martin; Adam, Vojt?ch; Kizek, René

2012-12-01

370

Anomalous Diffusion in Polymer Solution as Probed by Fluorescence Correlation Spectroscopy and Its Universal Importance in Biological Systems  

NASA Astrophysics Data System (ADS)

Experimental evidence of anomalous diffusion occurring in an inhomogeneous media (hyaluronan aquous solution) was obtained by use of fluorescence correlation spectroscopy (FCS) combined with other techniques (PFG-NMR and Photochemical reactions). The diffusion coefficient was obtained as a function of diffusion time or diffusion distance. Since this polymer solution can be regarded as a model system of extracellular matrices (ECMs), intercellular communication, which takes part in ECM, is greatly influenced by this anomalous diffusion mode. Therefore universal importance of anomalous diffusion in biological activity is identified in this series of independent experiments to measure diffusion coefficients.

Ushida, Kiminori

2008-02-01

371

Synchrotron radiation circular dichroism (SRCD) spectroscopy: An emerging method in structural biology for examining protein conformations and protein interactions  

NASA Astrophysics Data System (ADS)

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.; Gekko, Kunihiko; Vrønning Hoffmann, Søren; Lin, Yi-Hung; Sutherland, John C.; Tao, Ye; Wien, Frank; Janes, Robert W.

2011-09-01

372

Real sample temperature: a critical issue in the experiments of nuclear resonant vibrational spectroscopy on biological samples  

PubMed Central

There are several practical and intertangled issues which make the experiments of nuclear resonant vibrational spectroscopy (NRVS) on biological samples difficult to perform. The sample temperature is one of the most important issues. In NRVS the real sample temperatures can be very different from the readings on the temperature sensors. In this study the following have been performed: (i) citing and analyzing various existing NRVS data to assess the real sample temperatures during the NRVS measurements and to understand their trends with the samples’ loading conditions; (ii) designing several NRVS measurements with (Et4N)[FeCl4] to verify these trends; and (iii) proposing a new sample-loading procedure to achieve significantly lower real sample temperatures and to balance among the intertangled experimental issues in biological NRVS measurements.

Wang, Hongxin; Yoda, Yoshitaka; Kamali, Saeed; Zhou, Zhao-Hui; Cramer, Stephen P.

2012-01-01

373

Spectroscopy  

NSDL National Science Digital Library

This site describes the theory and practice of IR and NMR spectroscopy for classroom and laboratory instruction. Although it is written for a course at the University of Colorado, Boulder, this site is appropriate for anyone doing analytical measurements with infrared or NMR.

2011-08-05

374

Nuclear Magnetic Resonance Spectroscopy Applications: Proton NMR In Biological Objects Subjected To Magic Angle Spinning  

SciTech Connect

Proton NMR in Biological Objects Submitted to Magic Angle Spinning, In Encyclopedia of Analytical Science, Second Edition (Paul J. Worsfold, Alan Townshend and Colin F. Poole, eds.), Elsevier, Oxford 6:333-342. Published January 1, 2005. Proposal Number 10896.

Wind, Robert A.; Hu, Jian Zhi

2005-01-01

375

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

376

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

377

Development and validation of a direct, non-destructive quantitative method for medroxyprogesterone acetate in a pharmaceutical suspension using FT-Raman spectroscopy  

Microsoft Academic Search

A simple linear regression method was developed and statistically validated for the direct and non-destructive quantitative analysis—without sample preparation—of the active pharmaceutical ingredient (API) medroxyprogesterone acetate (MPA) in an aqueous pharmaceutical suspension (150mg in 1.0ml) using FT-Raman spectroscopy. The linear regression was modelled by plotting the highest peak intensity of the vector normalized spectral band between 1630 and 1590cm?1 against

T. R. M. De Beer; G. J. Vergote; W. R. G. Baeyens; J. P. Remon; C. Vervaet; F. Verpoort

2004-01-01

378

Quantitative analysis of CN\\/TiCN\\/TiN multilayers and their thermal stability by Auger electron spectroscopy and Rutherford backscattering spectrometry depth profiles  

Microsoft Academic Search

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

P. Prieto; C. Morant; A. Munoz; E. Elizalde; J. M. Sanz

2006-01-01

379

Spectroscopy  

Microsoft Academic Search

The hyperfine splittings of the nuclear energy levels in rare-earth (R) isotopes are sen- sitive measures of the complex interplay between magnetic exchange and electrostatic crystal-field interactions operating at the atomic level. Mössbauer spectroscopy has been used to great effect in the on-going investigation of these fundamental interactions in R compounds and in this paper we present an overview of

J. M. CADOGAN; D. H. RYAN

380

Quantitative monitoring of an activated sludge reactor using on-line UV-visible and near-infrared spectroscopy.  

PubMed

The performance of an activated sludge reactor can be significantly enhanced through use of continuous and real-time process-state monitoring, which avoids the need to sample for off-line analysis and to use chemicals. Despite the complexity associated with wastewater treatment systems, spectroscopic methods coupled with chemometric tools have been shown to be powerful tools for bioprocess monitoring and control. Once implemented and optimized, these methods are fast, nondestructive, user friendly, and most importantly, they can be implemented in situ, permitting rapid inference of the process state at any moment. In this work, UV-visible and NIR spectroscopy were used to monitor an activated sludge reactor using in situ immersion probes connected to the respective analyzers by optical fibers. During the monitoring period, disturbances to the biological system were induced to test the ability of each spectroscopic method to detect the changes in the system. Calibration models based on partial least squares (PLS) regression were developed for three key process parameters, namely chemical oxygen demand (COD), nitrate concentration (N-NO(3)(-)), and total suspended solids (TSS). For NIR, the best results were achieved for TSS, with a relative error of 14.1% and a correlation coefficient of 0.91. The UV-visible technique gave similar results for the three parameters: an error of approximately 25% and correlation coefficients of approximately 0.82 for COD and TSS and 0.87 for N-NO(3)(-) . The results obtained demonstrate that both techniques are suitable for consideration as alternative methods for monitoring and controlling wastewater treatment processes, presenting clear advantages when compared with the reference methods for wastewater treatment process qualification. PMID:19701801

Sarraguça, Mafalda C; Paulo, Ana; Alves, Madalena M; Dias, Ana M A; Lopes, João A; Ferreira, Eugénio C

2009-10-01

381

Quantitative analysis of surface amine groups on plasma-polymerized ethylenediamine films using UV visible spectroscopy compared to chemical derivatization with FT-IR spectroscopy, XPS and TOF-SIMS  

NASA Astrophysics Data System (ADS)

A quantitative analysis of the surface density of amine groups on a plasma-polymerized ethylenediamine thin film deposited on a platinum surface using inductively coupled plasma chemical vapor deposition method is described. UV-visible spectroscopy together with a chemical derivatization technique using Fourier transform infrared (FT-IR) spectroscopy was used to obtain the quantitative information. Chemical tags of pentafluorobenzaldehyde were hybridized with the surface amine groups and were easily detected due to the characteristic absorption bands of C-F stretching, aromatic ring and C dbnd N stretching vibrations in the reflection-absorption FT-IR spectra. The surface amine density was reproducibly controlled as a function of deposition plasma power and quantified using UV-visible spectroscopy. A good linear correlation was observed between the FT-IR intensities of the characteristic absorption bands and the surface amine densities, suggesting the possibility of using this chemical derivatization technique to quantify the surface densities of specific functional groups on an organic surface. Chemical derivatization was also used with X-ray photoelectron spectroscopy on the same samples, and the results were compared with those obtained from FT-IR and time-of-flight secondary ion mass spectrometry. Although each analysis technique has different probing depths from the surface, the three different data sets obtained from the chemical tags correlated well with each other since each analysis technique measured the chemical tags on the sample surface.

Kim, Jinmo; Jung, Donggeun; Park, Yongsup; Kim, Yongki; Moon, Dae Won; Lee, Tae Geol

2007-02-01

382

Retrieving the optical parameters of biological tissues using diffuse reflectance spectroscopy and Fourier series expansions. I. theory and application.  

PubMed

The determination of optical parameters of biological tissues is essential for the application of optical techniques in the diagnosis and treatment of diseases. Diffuse Reflection Spectroscopy is a widely used technique to analyze the optical characteristics of biological tissues. In this paper we show that by using diffuse reflectance spectra and a new mathematical model we can retrieve the optical parameters by applying an adjustment of the data with nonlinear least squares. In our model we represent the spectra using a Fourier series expansion finding mathematical relations between the polynomial coefficients and the optical parameters. In this first paper we use spectra generated by the Monte Carlo Multilayered Technique to simulate the propagation of photons in turbid media. Using these spectra we determine the behavior of Fourier series coefficients when varying the optical parameters of the medium under study. With this procedure we find mathematical relations between Fourier series coefficients and optical parameters. Finally, the results show that our method can retrieve the optical parameters of biological tissues with accuracy that is adequate for medical applications. PMID:23082281

Muñoz Morales, Aarón A; Vázquez Y Montiel, Sergio

2012-10-01

383

Gross boron determination in biological samples by inductively coupled plasma-atomic emission spectroscopy  

SciTech Connect

This paper describes a method for the analysis of boron in biological samples including urine, blood plasma, and tissues with subsequent boron determinations by ICP-AES. A comparison will be made between results obtained by this method and by the prompt-gamma technique on the same samples. 4 refs., 2 figs., 2 tabs.

Bauer, W.F.; Johnson, D.A.; Steele, S.M.; Messick, K.; Miller, D.L.; Propp, W.A.

1988-01-01

384

Micron surface-enhanced Raman spectroscopy of intact biological organisms and model systems  

SciTech Connect

Surface-enhanced Raman spectra have been obtained within intact zebrafish embryos and inside the 500-fL pores of a Nucleopore filter membrane with the use of coated microelectrodes with 1-3 {mu}m active silver tip diameters. The spectra obtained demonstrate the microelectrode`s ability to penetrate biological membranes as well as restricted volumes. 8 refs., 5 figs.

Todd, E.A.; Morris, M.D. [Univ. of Michigan, Ann Arbor, MI (United States)

1994-05-01

385

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

386

Elucidation of molecular structures at buried polymer interfaces and biological interfaces using sum frequency generation vibrational spectroscopy  

PubMed Central

Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques.

Zhang, Chi; Myers, John; Chen, Zhan

2013-01-01

387

State of the art Raman techniques for biological applications.  

PubMed

Raman spectroscopy is a powerful tool for the elucidation of qualitative and quantitative information from biological systems and has huge potential in areas such as biotechnologies, drug discovery, agro-chemical research and clinical diagnostics. This report summarises the principal Raman techniques applied to biomedical systems and discusses the challenges that exist to the wide spread adoption of Raman spectroscopy. PMID:24662479

Rae, Alasdair; Stosch, Rainer; Klapetek, Petr; Hight Walker, Angela R; Roy, Debdulal

2014-07-01

388

Roles of biologic breast tissue composition and quantitative image analysis of mammographic images in breast tumor characterization  

NASA Astrophysics Data System (ADS)

Purpose. Investigate whether knowledge of the biologic image composition of mammographic lesions provides imagebased biomarkers above and beyond those obtainable from quantitative image analysis (QIA) of X-ray mammography. Methods. The dataset consisted of 45 in vivo breast lesions imaged with the novel 3-component breast (3CB) imaging technique based on dual-energy mammography (15 malignant, 30 benign diagnoses). The 3CB composition measures of water, lipid, and protein thicknesses were assessed and mathematical descriptors, `3CB features', were obtained for the lesions and their periphery. The raw low-energy mammographic images were analyzed with an established in-house QIA method obtaining `QIA features' describing morphology and texture. We investigated the correlation within the `3CB features', within the `QIA features', and between the two. In addition, the merit of individual features in the distinction between malignant and benign lesions was assessed. Results. Whereas many descriptors within the `3CB features' and `QIA features' were, often by design, highly correlated, correlation between descriptors of the two feature groups was much weaker (maximum absolute correlation coefficient 0.58, p<0.001) indicating that 3CB and QIA-based biomarkers provided potentially complementary information. Single descriptors from 3CB and QIA appeared equally well-suited for the distinction between malignant and benign lesions, with maximum area under the ROC curve 0.71 for a protein feature (3CB) and 0.71 for a texture feature (QIA). Conclusions. In this pilot study analyzing the new 3CB imaging modality, knowledge of breast tissue composition appeared additive in combination with existing mammographic QIA methods for the distinction between benign and malignant lesions.

Drukker, Karen; Giger, Maryellen L.; Duewer, Fred; Malkov, Serghei; Flowers, Christopher I.; Joe, Bonnie; Kerlikowske, Karla; Drukteinis, Jennifer S.; Shepherd, John

2014-03-01

389

Ultrasensitive detection of individual gold nanoparticles: spectroscopy and applications to biology  

Microsoft Academic Search

Gold nanoparticles are now widely used in different fields of chemistry, physics and biology. For many applications, it became\\u000a crucial to use the smallest ones and at the same time to be able to detect them at the single particle level with versatile\\u000a optical methods. Such methods should also allow the study of their intimate optical properties. Here we review

Laurent Cognet; Brahim Lounis

2008-01-01

390

Diffuse reflectance UV–Visible spectroscopy for the qualitative and quantitative study of chromophores adsorbed or grafted on silica  

Microsoft Academic Search

Diffuse reflectance UV–Visible spectroscopy (DRUV) is used to study the adsorption and grafting of the pyrene derivative 1 on different types of silicas. For the adsorbed silicas, the formation of dimeric aggregates is evidenced both by DRUV and by fluorescence spectroscopy. The processing of the UV spectrophotometric data allows, as in solution, the determination of apparent equilibrium constants and of

S. Lacombe; H. Cardy; N. Soggiu; S. Blanc; J. L. Habib-Jiwan; J. Ph. Soumillion

2001-01-01

391

BIOLOG  

EPA Science Inventory

BIOLOG contains more than 43,000 citations to literature on microbial degradation and toxicity of more than 6,000 chemicals. Records are organized by CAS Registry Number and by 6 categories (i.e., biodegradation/toxicity; oxygen condition (anaerobic/aerobic); culture type (pure e...

392

Reverse micelles in integral membrane protein structural biology by solution NMR spectroscopy  

PubMed Central

SUMMARY Integral membrane proteins remain a significant challenge to structural studies by solution NMR spectroscopy. This is due not only to spectral complexity but also because the effects of slow molecular reorientation are exacerbated by the need to solublize the protein in aqueous detergent micelles. These assemblies can be quite large and require deuteration for use of the TROSY effect. In principle, another approach is to employ reverse micelle encapsulation to solublize the protein in a low viscosity solvent where the rapid tumbling of the resulting particle allows use of standard triple resonance methods. The preparation of such samples of membrane proteins is difficult. Using a 54 kDa construct of the homotetrameric potassium channel KcsA we demonstrate a strategy that employs a hybrid surfactant to transfer the protein to the reverse micelle system.

Kielec, Joseph M.; Valentine, Kathleen G.; Babu, Charles R.; Wand, A. Joshua

2009-01-01

393

Surface-enhanced Raman spectroscopy-active substrates: adapting the shape of plasmonic nanoparticles for different biological applications.  

PubMed

We discuss the relationship between the shape of plasmonic nanoparticles and the biological surface-enhanced Raman spectroscopy (SERS) applications which they can enable. As a step forward in developing SERS-active substrates adapted to a particular application, we demonstrate that a modification of the widely used protocol for the sodium citrate mediated reduction of chloroauric acid, which is typically employed only for obtaining spherical gold nanoparticles, can yield flat polygonal nanoparticles at room temperature and a decreased amount of the reducing agent. The significant advantage of the described approach is that it allows for synthesis of nanoparticles with different geometries using a well-established synthesis protocol without the need for any additional chemicals or special synthesis apparatus. By contrasting spherical and anisotropically shaped nanoparticles, we demonstrate that multifaceted nanoparticles with sharp edges are better suitable for SERS analysis of low concentration analytes requiring strong SERS enhancement. On the other hand, gold nanoparticles with isotropic shapes, while giving a smaller enhancement, can provide a more reproducible SERS signal. This is important for analytical applications of complex biological systems where large SERS enhancement may not always be required, whereas data reproducibility and minimal false positive rate are imperative. Using a SERS-active substrate comprising isotropically shaped gold nanoparticles, we demonstrate the differences between Gram-negative (E. coli) and Gram-positive (S. aureus) bacteria, attributable to the outer membrane and peptidoglycan layer, with the level of detail which has not been previously reported with optical spectroscopic techniques. PMID:24734732

Vitol, Elina A; Friedman, Gary; Gogotsi, Yury

2014-04-01

394

Direct determination and speciation of mercury compounds in environmental and biological samples by carbon bed atomic absorption spectroscopy  

SciTech Connect

A method was developed for the direct determination of mercury in water and biological samples using a unique carbon bed atomizer for atomic absorption spectroscopy. The method avoided sources of error such as loss of volatile mercury during sample digestion and contamination of samples through added reagents by eliminating sample pretreatment steps. The design of the atomizer allowed use of the 184.9 nm mercury resonance line in the vacuum ultraviolet region, which increased sensitivity over the commonly used spin-forbidden 253.7 nm line. The carbon bed atomizer method was applied to a study of mercury concentrations in water, hair, sweat, urine, blood, breath and saliva samples from a non-occupationally exposed population. Data were collected on the average concentration, the range and distribution of mercury in the samples. Data were also collected illustrating individual variations in mercury concentrations with time. Concentrations of mercury found were significantly higher than values reported in the literature for a ''normal'' population. This is attributed to the increased accuracy gained by eliminating pretreatment steps and increasing atomization efficiency. Absorption traces were obtained for various solutions of pure and complexed mercury compounds. Absorption traces of biological fluids were also obtained. Differences were observed in the absorption-temperatures traces of various compounds. The utility of this technique for studying complexation was demonstrated.

Skelly, E.M.

1982-01-01

395

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

2011-12-20

396

[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

397

Fast and accurate quantitative metabolic profiling of body fluids by nonlinear sampling of 1H–13C two-dimensional nuclear magnetic resonance spectroscopy.  

PubMed

Two-dimensional (2D) nuclear magnetic resonance (NMR) methods have shown to be an excellent analytical tool for the identification and characterization of statistically relevant changes in low-abundance metabolites in body fluid. The advantage of 2D NMR in terms of minimized ambiguities in peak assignment, aided in metabolite identifications and comprehensive metabolic profiling comes with the cost of increased NMR data collection time; making it inconvenient choice for routine metabolic profiling. We present here a method for the reduction in NMR data collection time of 2D (1)H-(13)C NMR spectroscopy for the purpose of quantitative metabolic profiling. Our method combines three techniques; which are nonlinear sampling (NLS), forward maximum (FM) entropy reconstruction, and J-compensated quantitative heteronuclear single quantum (HSQC) (1)H-(13)C NMR spectra. We report here that approximately 22-fold reduction in 2D NMR data collection time for the body fluid samples can be achieved by this method, without any compromise in quantitative information recovery of various low abundance metabolites. The method has been demonstrated in standard mixture solution, native, and lyophilized human urine samples. Our proposed method has potential to make quantitative metabolic profiling by 2D NMR as a routine method for various metabonomic studies. PMID:23061661

Rai, Ratan Kumar; Sinha, Neeraj

2012-11-20

398

ENVIRONMENTAL AND BIOLOGICAL APPLICATIONS OF EXTENDED X-RAY ABSORPTION FINE STRUCTURE (EXAFS) AND X-RAY ABSORPTION NEAR EDGE STRUCTURE (XANES) SPECTROSCOPIES  

Microsoft Academic Search

XAS (X-ray absorption spectroscopy) has proven to be a powerful technique in several fields including the biological and environmental sciences. It has enabled scientists to analyze samples that could not be analyzed using classical techniques such as XRD (X-ray diffraction). In addition, it allows for the direct determination of elemental oxidation states, where the use of other methods is time

J. G. Parsons; M. V. Aldrich; J. L. Gardea-Torresdey

2002-01-01

399

Study on the synthesis, biological activity and spectroscopy of naphthalimide-diamine conjugates.  

PubMed

Eleven novel naphthalimide-diamine conjugates were synthesized and their structures were confirmed by elemental analysis, 1H-NMR, 13C-NMR and MS. Their in vitro antitumor activities were assessed using MTT assays on two cancerous cell lines K562, HCT116, and one normal hepatoma cell line QSG 7701. Compound 7f exhibited potent antitumor activity on HCT116 cells and favorable cell selectivity toward QSG 7701 compared with the positive control, amonafide. Moreover, 7f could block HeG2 cells in the G2/M phase and induce HeG2 cells apoptosis. The interaction of compound 7f with herring sperm DNA was studied by UV/vis absorption and fluorescence spectroscopy under physiological conditions (pH = 7.4). The observed spectral quenching of compound 7f by DNA and the displacement of EB from DNA-EB complex by compound 7f indicated that compound 7f could intercalate into DNA base pairs, which was also corroborated by the effect of KI on compound-DNA interaction. Further caloric fluorescent tests revealed that the quenching mechanism was a static type. Meanwhile, the binding constants, thermodynamic parameters and the effect of NaCl on compound-DNA interaction showed that the type of interaction force was mainly hydrogen bonds and the binding process was driven by hydrogen and van der Waals bonding. PMID:24918538

Tian, Zhi-Yong; Li, Jing-Hua; Li, Qian; Zang, Feng-Lei; Zhao, Zhong-Hua; Wang, Chao-Jie

2014-01-01

400

Sensing Lanthanide Metal Content in Biological Tissues with Magnetic Resonance Spectroscopy  

PubMed Central

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 ?10 mM for Tm(III) Eu(III), and Yb(III), and ?3 mM for Gd(III), gadodiamide, and Dy(III). Improved sample handling methods are needed to improve measurement accuracy for samples with lower concentrations.

Hingorani, Dina V.; Gonzalez, Sandra I.; Li, Jessica F.; Pagel, Mark D.

2013-01-01

401

Quantitative nonlinear spectroscopy: a direct comparison of degenerate four-wave mixing with cavity ring-down spectroscopy applied to NaH  

Microsoft Academic Search

Cavity ring-down spectroscopy and degenerate four-wave mixing have been applied for spectroscopic studies, temperature determination, and measurement of relative dipole transition moments of photochemically produced sodium hydride. In our experiment, NaH was formed within a heat-pipe oven after 3p excitation of sodium in a hydrogen atmosphere with a second dye laser. The reaction product NaH was probed in the near

Leo Lehr; Peter Hering

1997-01-01

402

Characterization of biological macromolecules by combined mass mapping and electron energy-loss spectroscopy.  

PubMed

The combination of scanning transmission electron microscopy (STEM) and parallel-detection energy-loss spectroscopy (EELS) was used to detect specific bound elements within macr