Science.gov

Sample records for quantitative biological spectroscopy

  1. 2D-Cosy NMR Spectroscopy as a Quantitative Tool in Biological Matrix: Application to Cyclodextrins.

    PubMed

    Dufour, Gilles; Evrard, Brigitte; de Tullio, Pascal

    2015-11-01

    Classical analytical quantifications in biological matrices require time-consuming sample pre-treatments and extractions. Nuclear magnetic resonance (NMR) analysis does not require heavy sample treatments or extractions which therefore increases its accuracy in quantification. In this study, even if quantitative (q)NMR could not be applied to 2D spectra, we demonstrated that cross-correlations and diagonal peak intensities have a linear relationship with the analyzed pharmaceutical compound concentration. This work presents the validation process of a 2D-correlation spectroscopy (COSY) NMR quantification of 2-hydroxypropyl-β-cyclodextrin in plasma. Specificity, linearity, precision (repeatability and intermediate precision), trueness, limits of quantification (LOQs), and accuracy were used as validation criteria. 2D-NMR could therefore be used as a valuable and accurate analytical technique for the quantification of pharmaceutical compounds, including hardly detectable compounds such as cyclodextrins or poloxamers, in complex biological matrices based on a calibration curve approach.

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

    PubMed

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

    2016-05-19

    PEBBLE (probe encapsulated by biologically localized embedding) nanosensor encapsulating an intensity-based fluorescence indicator and an inert reference fluorescence dye inside the pores of stable matrix can be used as a generalized wavelength-ratiometric probe. However, the lack of an efficient quantitative model render the choices of inert reference dyes and intensity-based fluorescence indicators used in PEBBLEs based generalized wavelength-ratiometric probes rather limited. In this contribution, an extended quantitative fluorescence model was derived specifically for generalized wavelength-ratiometric probes based on PEBBLE technique (QFMGRP) with a view to simplify the design of PEBBLEs and hence further extend their application potentials. The effectiveness of QFMGRP has been tested on the quantitative determination of free Ca(2+) in both simulated and real turbid media using a Ca(2+) sensitive PEBBLE nanosensor encapsulating Rhod-2 and eosin B inside the micropores of stable polyacrylamide matrix. Experimental results demonstrated that QFMGRP could realize precise and accurate quantification of free Ca(2+) in turbid samples, even though there is serious overlapping between the fluorescence excitation peaks of eosin B and Ca(2+) bound Rhod-2. The average relative predictive error value of QFMGRP for the test simulated turbid samples was 5.9%, about 2-4 times lower than the corresponding values of partial least squares calibration model and the empirical ratiometric model based on the ratio of fluorescence intensities at the excitation peaks of Ca(2+) bound Rhod-2 and eosin B. The recovery rates of QFMGRP for the real and spiked turbid samples varied from 93.1% to 101%, comparable to the corresponding results of atomic absorption spectrometry. PMID:27126788

  3. Recapturing Quantitative Biology.

    ERIC Educational Resources Information Center

    Pernezny, Ken; And Others

    1996-01-01

    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)

  4. Quantitative velocity modulation spectroscopy

    NASA Astrophysics Data System (ADS)

    Hodges, James N.; McCall, Benjamin J.

    2016-05-01

    Velocity Modulation Spectroscopy (VMS) is arguably the most important development in the 20th century for spectroscopic study of molecular ions. For decades, interpretation of VMS lineshapes has presented challenges due to the intrinsic covariance of fit parameters including velocity modulation amplitude, linewidth, and intensity. This limitation has stifled the growth of this technique into the quantitative realm. In this work, we show that subtle changes in the lineshape can be used to help address this complexity. This allows for determination of the linewidth, intensity relative to other transitions, velocity modulation amplitude, and electric field strength in the positive column of a glow discharge. Additionally, we explain the large homogeneous component of the linewidth that has been previously described. Using this component, the ion mobility can be determined.

  5. Quantitative Spectroscopy of Deneb

    NASA Astrophysics Data System (ADS)

    Schiller, Florian; Przybilla, N.

    We use the visually brightest A-type supergiant Deneb (A2 Ia) as benchmark for testing a spectro- scopic analysis technique developed for quantitative studies of BA-type supergiants. Our NLTE spectrum synthesis technique allows us to derive stellar parameters and elemental abundances with unprecedented accuracy. The study is based on a high-resolution and high-S/N spectrum obtained with the Echelle spectrograph FOCES on the Calar Alto 2.2 m telescope. Practically all inconsistencies reported in earlier studies are resolved. A self-consistent view of Deneb is thus obtained, allowing us to discuss its evolutionary state in detail by comparison with the most recent generation of evolution models for massive stars. The basic atmospheric parameters Teff = 8525 ± 75 K and log g = 1.10 ± 0.05 dex (cgs) and the distance imply the following fundamental parameters for Deneb: M spec = 17 ± 3 M⊙ , L = 1.77 ± 0.29 · 105 L⊙ and R = 192 ± 16 R⊙ . The derived He and CNO abundances indicate mixing with nuclear processed matter. The high N/C ratio of 4.64 ± 1.39 and a N/O ratio of 0.88 ± 0.07 (mass fractions) could in principle be explained by evolutionary models with initially very rapid rotation. A mass of ˜ 22 M⊙ is implied for the progenitor on the zero-age main se- quence, i.e. it was a late O-type star. Significant mass-loss has occurred, probably enhanced by pronounced centrifugal forces. The observational constraints favour a scenario for the evolu- tion of Deneb where the effects of rotational mixing may be amplified by an interaction with a magnetic field. Analogous analyses of such highly luminous BA-type supergiants will allow for precision studies of different galaxies in the Local Group and beyond.

  6. A Quantitative Infrared Spectroscopy Experiment.

    ERIC Educational Resources Information Center

    Krahling, Mark D.; Eliason, Robert

    1985-01-01

    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)

  7. Quantitative spectroscopy of hot stars

    NASA Technical Reports Server (NTRS)

    Kudritzki, R. P.; Hummer, D. G.

    1990-01-01

    A review on the quantitative spectroscopy (QS) of hot stars is presented, with particular attention given to the study of photospheres, optically thin winds, unified model atmospheres, and stars with optically thick winds. It is concluded that the results presented here demonstrate the reliability of Qs as a unique source of accurate values of the global parameters (effective temperature, surface gravity, and elemental abundances) of hot stars.

  8. Quantitative biology of single neurons

    PubMed Central

    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

    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. PMID:22915636

  9. Quantitative tunneling spectroscopy of nanocrystals

    SciTech Connect

    First, Phillip N; Whetten, Robert L; Schaaff, T Gregory

    2007-05-25

    The proposed goals of this collaborative work were to systematically characterize the electronic structure and dynamics of 3-dimensional metal and semiconducting nanocrystals using scanning tunneling microscopy/spectroscopy (STM/STS) and ballistic electron emission spectroscopy (BEES). This report describes progress in the spectroscopic work and in the development of methods for creating and characterizing gold nanocrystals. During the grant period, substantial effort also was devoted to the development of epitaxial graphene (EG), a very promising materials system with outstanding potential for nanometer-scale ballistic and coherent devices ("graphene" refers to one atomic layer of graphitic, sp2 -bonded carbon atoms [or more loosely, few layers]). Funding from this DOE grant was critical for the initial development of epitaxial graphene for nanoelectronics

  10. Biomolecular Plasmonics for Quantitative Biology and Nanomedicine

    PubMed Central

    Lee, Somin Eunice; Lee, Luke P.

    2012-01-01

    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. PMID:20801636

  11. Quantitative biology: where modern biology meets physical sciences

    PubMed Central

    Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E.; Fai, Thomas G.; Podolski, Marija

    2014-01-01

    Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines. PMID:25368426

  12. Quantitative biology: where modern biology meets physical sciences.

    PubMed

    Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E; Fai, Thomas G; Podolski, Marija

    2014-11-01

    Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines.

  13. Probing biological systems with terahertz spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

    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.

  14. Modeling the Effect of Polychromatic Light in Quantitative Absorbance Spectroscopy

    ERIC Educational Resources Information Center

    Smith, Rachel; Cantrell, Kevin

    2007-01-01

    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.

  15. Quantitative atomic spectroscopy for primary thermometry

    SciTech Connect

    Truong, Gar-Wing; Luiten, Andre N.; May, Eric F.; Stace, Thomas M.

    2011-03-15

    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.

  16. Unraveling pancreatic islet biology by quantitative proteomics

    SciTech Connect

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

    2011-08-01

    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.

  17. Submillimeter wave spectroscopy of biological macromolecules

    NASA Astrophysics Data System (ADS)

    Globus, Tatiana

    2005-03-01

    The recently emergence of submillimeter-wave or terahertz (THz) spectroscopy of biological molecules has demonstrated the capability to detect low-frequency internal molecular vibrations involving the weakest hydrogen bonds of the DNA base pairs and/or non-bonded interactions. These multiple bonds, although having only ˜ 5% of the strength of covalent bonds, stabilize the structure of bio-polymers, by holding the two strands of the DNA double helix together, or polypeptides together in different secondary structure conformations. There will be a review of THz-frequency transmission (absorption) results for biological materials obtained from Fourier Transform Infrared (FTIR) spectroscopy during the last few years^1,2. Multiple resonances, due to low frequency vibrational modes within biological macromolecules, have been unambiguously demonstrated in qualitative agreement with theoretical prediction, thereby confirming the fundamental physical nature of observed resonance features. The discovery of resonance character of interaction between THz radiation and biological materials opens many possible applications for THz spectroscopy technique in biological sensing and biomedicine using multiple resonances as distinctive spectral fingerprints. However, many issues still require investigation. Kinetics of interactions with radiation at THz has not been studied and vibrational lifetimes have not been measured directly as a function of frequency. The strength of resonant modes of bio-molecules in aqueous environment and strong dependence of spectra on molecular orientation need explanation. Vibrational modes have not been assigned to specific motions within molecules. THz spectroscopy of bio-polymers makes it only in first steps. 1. T. Globus, D. Woolard, M. Bykhovskaia, B. Gelmont, L. Werbos, A. Samuels. International Journal of High Speed Electronics and Systems (IJHSES), 13, No. 4, 903-936 (2003). 2. T. Globus, T. Khromova, D. Woolard and B. Gelmont. Proceedings of

  18. Biologically based, quantitative risk assessment of neurotoxicants.

    PubMed

    Slikker, W; Crump, K S; Andersen, M E; Bellinger, D

    1996-01-01

    The need for biologically based, quantitative risk assessment procedures for noncancer endpoints such as neurotoxicity has been discussed in reports by the United States Congress (Office of Technology Assessment, OTA), National Research Council (NRC), and a federal coordinating council. According to OTA, current attention and resources allocated to health risk assessment research are inadequate and not commensurate with its impact on public health and the economy. Methods to include continuous rather than dichotomous data for neurotoxicity endpoints, biomarkers of exposure and effects, and pharmacokinetic and mechanistic data have been proposed for neurotoxicity risk assessment but require further review and validation before acceptance. The purpose of this symposium was to examine procedures to enhance the risk assessment process for neurotoxicants and to discuss techniques to make the process more quantitative. Accordingly, a review of the currently used safety factor risk assessment approach for neurotoxicants is provided along with specific examples of how this process may be enhanced with the use of the benchmark dose approach. The importance of including physiologically based pharmacokinetic data in the risk assessment process and specific examples of this approach is presented for neurotoxicants. The role of biomarkers of exposure and effect and mechanistic information in the risk assessment process are also addressed. Finally, quantitative approaches with the use of continuous neurotoxicity data are demonstrated and the outcomes compared to those generated by currently used risk assessment procedures. PMID:8838636

  19. Histochemical analysis of biological tissues using Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Manoharan, Ramasamy; Wang, Yang; Feld, Michael S.

    1996-02-01

    This paper reviews the application of the Raman spectroscopic technique for analysis of biological tissue. The advantages and disadvantages of visible, near-IR and UV excitations are described, and the problems and prospects of using these methodologies for disease diagnosis are addressed. In situ analysis of tissue proteins, lens, cornea, blood constituents, biological stones and several hard tissues is reviewed, and the potentials for diagnosing arterial disease, and cancer in gynecological tissues, soft tissues, breast, colon, bladder and brain are also presented. Recent technological advances in instrumentation allow the use of Raman spectroscopy for real time histochemical analysis of tissues. The capability of Raman microspectroscopy for providing spatial information about the distribution of biochemical constituents in tissues has been demonstrated. The work reviewed indicates the promise of Raman spectroscopy for endoscopic imaging and real-time quantitation of biochemical constituents in clinical situations.

  20. Quantitative cell biology: the essential role of theory.

    PubMed

    Howard, Jonathon

    2014-11-01

    Quantitative biology is a hot area, as evidenced by the recent establishment of institutes, graduate programs, and conferences with that name. But what is quantitative biology? What should it be? And how can it contribute to solving the big questions in biology? The past decade has seen very rapid development of quantitative experimental techniques, especially at the single-molecule and single-cell levels. In this essay, I argue that quantitative biology is much more than just the quantitation of these experimental results. Instead, it should be the application of the scientific method by which measurement is directed toward testing theories. In this view, quantitative biology is the recognition that theory and models play critical roles in biology, as they do in physics and engineering. By tying together experiment and theory, quantitative biology promises a deeper understanding of underlying mechanisms, when the theory works, or to new discoveries, when it does not.

  1. Quantitative Characterization of Tissue Microstructure with Temporal Diffusion Spectroscopy

    PubMed Central

    Xu, Junzhong; Does, Mark D.; Gore, John C.

    2009-01-01

    The signals recorded by diffusion-weighted magnetic resonance imaging (DWI) are dependent on the micro-structural properties of biological tissues, so it is possible to obtain quantitative structural information non-invasively from such measurements. Oscillating gradient spin echo (OGSE) methods have the ability to probe the behavior of water diffusion over different time scales and the potential to detect variations in intracellular structure. To assist in the interpretation of OGSE data, analytical expressions have been derived for diffusion-weighted signals with OGSE methods for restricted diffusion in some typical structures, including parallel planes, cylinders and spheres, using the theory of temporal diffusion spectroscopy. These analytical predictions have been confirmed with computer simulations. These expressions suggest how OGSE signals from biological tissues should be analyzed to characterize tissue microstructure, including how to estimate cell nuclear sizes. This approach provides a model to interpret diffusion data obtained from OGSE measurements that can be used for applications such as monitoring tumor response to treatment in vivo. PMID:19616979

  2. Quantitative Spectroscopy of Distant Type Ia Supernovae

    NASA Astrophysics Data System (ADS)

    Bronder, T. J.; Hook, I.; Howell, D. A.; Sullivan, M.; Perrett, K.; Conley, A.; Astier, P.; Basa, S.; Carlberg, R. G.; Guy, J.; Pain, R.; Pritchet, C. J.; Neill, James D.

    2007-08-01

    Quantitative analysis of 24 high-z (zmed = 0.81) Type Ia supernovae (SNe Ia) spectra observed at the Gemini Telescopes for the Supernova Legacy Survey (SNLS) is presented. This analysis includes equivalent width measurements of SNe Ia-specific absorption features with methods tailored to the reduced signal-to-noise and host galaxy contamination present in these distant spectra. The results from this analysis are compared to corresponding measurements of a large set of low-z SNe Ia from the literature. This comparison showed no significant difference (less than 2σ) between the spectroscopic features of the distant and nearby SNe; a result that supports the assumption that SNe Ia are not evolving with redshift. Additionally, a new correlation between SiII absorption (observed near peak luminosity) and SNe Ia peak magnitudes is presented.

  3. An introduction to biological NMR spectroscopy.

    PubMed

    Marion, Dominique

    2013-11-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP).

  4. An Introduction to Biological NMR Spectroscopy*

    PubMed Central

    Marion, Dominique

    2013-01-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). PMID:23831612

  5. Quantitative Raman spectroscopy in turbid media

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    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 μa and the reduced scattering coefficient μs' of the tissue, together with the Raman signals. The influence of μa and μs' on the resonance Raman signal of β-carotene is measured at 1524 cm-1 by tissue phantom measurements and Monte Carlo simulations for μa=0.01 to 10 mm-1 and μs'=0.1 to 10 mm-1. Both methods show that the Raman signal drops roughly proportional to 1/μa for μa>0.2 mm-1 in the measurement geometry and that the influence of μs' 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 μa and μs', provided that μa and μs' 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.

  6. 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...

  7. 1, 2, 3, 4: infusing quantitative literacy into introductory biology.

    PubMed

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

    2010-01-01

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

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

    ERIC Educational Resources Information Center

    Feser, Jason; Vasaly, Helen; Herrera, Jose

    2013-01-01

    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…

  9. Development of Electron Energy Loss Spectroscopy in the Biological Sciences

    PubMed Central

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

    2012-01-01

    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. PMID:23049161

  10. APD detectors for biological fluorescence spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2006-11-01

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

  11. Ultrafast spectroscopy in biological and organic materials

    NASA Astrophysics Data System (ADS)

    Bai, Guang

    This thesis consists of an experimental investigation of the dynamics of the biological material, visual pigment rhodopsin, and the persistent hole burning material, octaethylpophine-doped polystyrene (OEP/PS), utilizing femtosecond laser spectroscopy. The cis-trans isomerization of the retinal chromophore in rhodopsin at ambient temperature has been studied by employing a novel three beam femtosecond transient absorption method, and a new model is proposed. Two- thirds of the excited rhodopsin molecules isomerize promptly via curve-crossing to form bathorhodopsin in ~200 femtoseconds. The remaining third will miss curve-crossing and stay in the excited state, which never isomerizes and decays to the ground state rhodopsin in ~3 picoseconds. These results are consistent with recent two-beam femtosecond transient experiments[1-6] and agree well with molecular dynamics calculations[7-8]. The three-beam pump-probe measurement is an important technical advance in the characterization of transient species in the initial step of vision, which directly measures the formation dynamics of the ground state species. Using this technique, we could drive the bathorhodopsin back into rhodopsin. This is the first experimental evidence of trans to cis formation of rhodopsin at ambient temperature. The characteristic parameters and phototransformation pathway of OEP/PS have been studied for optical storage applications. Femtosecond accumulated photon echo and time-resolved absorption spectroscopy were used. The optical dephasing time T2 for a laser bandwidth covering the whole inhomogeneous zero-phonon absorption band is 200 ± 50 ps at 1.4 K. T2 reduces significantly to 100 ps when the temperature increases to 4.2 K. This temperature dependence indicates that OEP/PS must operate at very low temperatures. The saturation dose is 6 J/cm2. The maximum number of readings is equivalent to the same amount of energy of writing. 150 fs single-shot detection of a 4-bit packet stored in an

  12. Quantitative analysis of bisphosphonates in biological samples.

    PubMed

    Lapko, Veniamin N; Miller, Patrick S; Sheldon, Curtis E; Nachi, Ridha; Kafonek, Chris J

    2014-01-01

    Bisphosphonate drugs pose significant challenges for bioanalysis due to various complicating factors. In 2006, a novel approach, utilizing 'on-column' derivatization with diazomethane, was reported that revolutionized the application of liquid-chromatography-tandem mass spectrometry to bisphosphonates bioanalysis. The methodology enables superior biological sample clean-up while transforming bisphosphonates into species amenable to liquid-chromatography-tandem mass spectrometry detection. Since then, the approach has been successfully applied to numerous bisphosphonates. The use of an alternative methylation reagent - trimethylsilyl diazomethane - for on-column derivatization has been reported recently. This review focuses on published methods utilizing on-column derivatization for bioanalysis of major bisphosphonate drugs in biological matrices. Critical points required for successful application of on-column derivatization to the bioanalysis of bisphosphonates will be discussed.

  13. A transformative model for undergraduate quantitative biology education.

    PubMed

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

    2010-01-01

    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.

  14. Quantitative Phase Microscopy of Live Biological Cell Dynamics

    NASA Astrophysics Data System (ADS)

    Shaked, Natan T.; Wax, Adam

    2010-04-01

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

  15. Optical spectroscopy for quantitative sensing in human pancreatic tissues

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

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

  16. Quantitative analysis of gallstones using laser-induced breakdown spectroscopy.

    PubMed

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

    2008-11-01

    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.

  17. Quantitative analysis of gallstones using laser-induced breakdown spectroscopy

    SciTech Connect

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

    2008-11-01

    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.

  18. Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

    SciTech Connect

    Perras, Frederic A.

    2015-12-15

    Here, nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities.

  19. Reproducible quantitative proteotype data matrices for systems biology

    PubMed Central

    Röst, Hannes L.; Malmström, Lars; Aebersold, Ruedi

    2015-01-01

    Historically, many mass spectrometry–based proteomic studies have aimed at compiling an inventory of protein compounds present in a biological sample, with the long-term objective of creating a proteome map of a species. However, to answer fundamental questions about the behavior of biological systems at the protein level, accurate and unbiased quantitative data are required in addition to a list of all protein components. Fueled by advances in mass spectrometry, the proteomics field has thus recently shifted focus toward the reproducible quantification of proteins across a large number of biological samples. This provides the foundation to move away from pure enumeration of identified proteins toward quantitative matrices of many proteins measured across multiple samples. It is argued here that data matrices consisting of highly reproducible, quantitative, and unbiased proteomic measurements across a high number of conditions, referred to here as quantitative proteotype maps, will become the fundamental currency in the field and provide the starting point for downstream biological analysis. Such proteotype data matrices, for example, are generated by the measurement of large patient cohorts, time series, or multiple experimental perturbations. They are expected to have a large effect on systems biology and personalized medicine approaches that investigate the dynamic behavior of biological systems across multiple perturbations, time points, and individuals. PMID:26543201

  20. Reproducible quantitative proteotype data matrices for systems biology.

    PubMed

    Röst, Hannes L; Malmström, Lars; Aebersold, Ruedi

    2015-11-01

    Historically, many mass spectrometry-based proteomic studies have aimed at compiling an inventory of protein compounds present in a biological sample, with the long-term objective of creating a proteome map of a species. However, to answer fundamental questions about the behavior of biological systems at the protein level, accurate and unbiased quantitative data are required in addition to a list of all protein components. Fueled by advances in mass spectrometry, the proteomics field has thus recently shifted focus toward the reproducible quantification of proteins across a large number of biological samples. This provides the foundation to move away from pure enumeration of identified proteins toward quantitative matrices of many proteins measured across multiple samples. It is argued here that data matrices consisting of highly reproducible, quantitative, and unbiased proteomic measurements across a high number of conditions, referred to here as quantitative proteotype maps, will become the fundamental currency in the field and provide the starting point for downstream biological analysis. Such proteotype data matrices, for example, are generated by the measurement of large patient cohorts, time series, or multiple experimental perturbations. They are expected to have a large effect on systems biology and personalized medicine approaches that investigate the dynamic behavior of biological systems across multiple perturbations, time points, and individuals.

  1. Spectroscopy, colorimetry, and biological chemistry in the nineteenth century.

    PubMed Central

    Rinsler, M G

    1981-01-01

    The development of colorimetry and spectroscopy in the nineteenth century is described. An account is given of the application of their techniques to biological chemistry during that period. PMID:7014652

  2. Quantitative Genetic Interactions Reveal Layers of Biological Modularity

    PubMed Central

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

    2010-01-01

    In the past, biomedical research has embraced a reductionist approach, primarily focused on characterizing the individual components that comprise a system of interest. Recent technical developments have significantly increased the size and scope of data describing biological systems. At the same time, advances in the field of systems biology have evoked a broader view of how the underlying components are interconnected. In this essay, we discuss how quantitative genetic interaction mapping has enhanced our view of biological systems, allowing a deeper functional interrogation at different biological scales. PMID:20510918

  3. Integrating quantitative thinking into an introductory biology course improves students' mathematical reasoning in biological contexts.

    PubMed

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

    2014-01-01

    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 course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students' understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students' inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students' biology learning.

  4. Integrating quantitative thinking into an introductory biology course improves students' mathematical reasoning in biological contexts.

    PubMed

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

    2014-01-01

    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 course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students' understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students' inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students' biology learning. PMID:24591504

  5. Integrating Quantitative Thinking into an Introductory Biology Course Improves Students’ Mathematical Reasoning in Biological Contexts

    PubMed Central

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

    2014-01-01

    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 course in which we integrated application of prerequisite mathematical skills with biology content and reasoning throughout all aspects of the course. In this paper, we describe the principles of our course design and present illustrative examples of course materials integrating mathematics and biology. We also designed an outcome assessment made up of items testing students’ understanding of biology concepts and their ability to apply mathematical skills in biological contexts and administered it as a pre/postcourse test to students in the experimental section and other sections of the same course. Precourse results confirmed students’ inability to spontaneously transfer their prerequisite mathematics skills to biological problems. Pre/postcourse outcome assessment comparisons showed that, compared with students in other sections, students in the experimental section made greater gains on integrated math/biology items. They also made comparable gains on biology items, indicating that integrating quantitative skills into an introductory biology course does not have a deleterious effect on students’ biology learning. PMID:24591504

  6. Raman Spectroscopy of Optically Trapped Single Biological Micro-Particles

    PubMed Central

    Redding, Brandon; Schwab, Mark J.; Pan, Yong-le

    2015-01-01

    The combination of optical trapping with Raman spectroscopy provides a powerful method for the study, characterization, and identification of biological micro-particles. In essence, optical trapping helps to overcome the limitation imposed by the relative inefficiency of the Raman scattering process. This allows Raman spectroscopy to be applied to individual biological particles in air and in liquid, providing the potential for particle identification with high specificity, longitudinal studies of changes in particle composition, and characterization of the heterogeneity of individual particles in a population. In this review, we introduce the techniques used to integrate Raman spectroscopy with optical trapping in order to study individual biological particles in liquid and air. We then provide an overview of some of the most promising applications of this technique, highlighting the unique types of measurements enabled by the combination of Raman spectroscopy with optical trapping. Finally, we present a brief discussion of future research directions in the field. PMID:26247952

  7. Infusing Quantitative Approaches throughout the Biological Sciences Curriculum

    ERIC Educational Resources Information Center

    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

    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…

  8. A Transformative Model for Undergraduate Quantitative Biology Education

    ERIC Educational Resources Information Center

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

    2010-01-01

    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…

  9. Quantitation and detection of vanadium in biologic and pollution materials

    NASA Technical Reports Server (NTRS)

    Gordon, W. A.

    1974-01-01

    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.

  10. Toward Integration: From Quantitative Biology to Mathbio-Biomath?

    ERIC Educational Resources Information Center

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

    2010-01-01

    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…

  11. Label-Free Technologies for Quantitative Multiparameter Biological Analysis

    PubMed Central

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

    2009-01-01

    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. PMID:19221722

  12. High-Content Screening for Quantitative Cell Biology.

    PubMed

    Mattiazzi Usaj, Mojca; Styles, Erin B; Verster, Adrian J; Friesen, Helena; Boone, Charles; Andrews, Brenda J

    2016-08-01

    High-content screening (HCS), which combines automated fluorescence microscopy with quantitative image analysis, allows the acquisition of unbiased multiparametric data at the single cell level. This approach has been used to address diverse biological questions and identify a plethora of quantitative phenotypes of varying complexity in numerous different model systems. Here, we describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions. We review the steps involved in the design of useful biological assays and automated image analysis, and describe major challenges associated with each. Additionally, we highlight emerging technologies and future challenges, and discuss how the field of HCS might be enhanced in the future.

  13. Quantitative analysis of virgin coconut oil in cream cosmetics preparations using fourier transform infrared (FTIR) spectroscopy.

    PubMed

    Rohman, A; Man, Yb Che; Sismindari

    2009-10-01

    Today, virgin coconut oil (VCO) is becoming valuable oil and is receiving an attractive topic for researchers because of its several biological activities. In cosmetics industry, VCO is excellent material which functions as a skin moisturizer and softener. Therefore, it is important to develop a quantitative analytical method offering a fast and reliable technique. Fourier transform infrared (FTIR) spectroscopy with sample handling technique of attenuated total reflectance (ATR) can be successfully used to analyze VCO quantitatively in cream cosmetic preparations. A multivariate analysis using calibration of partial least square (PLS) model revealed the good relationship between actual value and FTIR-predicted value of VCO with coefficient of determination (R2) of 0.998.

  14. Terahertz time-domain spectroscopy of biological tissues

    SciTech Connect

    Nazarov, M M; Shkurinov, A P; Kuleshov, E A; Tuchin, V V

    2008-07-31

    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)

  15. Computational Laser Spectroscopy in a Biological Tissue

    PubMed Central

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

    2010-01-01

    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

  16. Localized phosphorus spectroscopy in vivo: Quantitation of metabolite concentrations

    NASA Astrophysics Data System (ADS)

    Wylezinska-Arridge, Marzena Malgorzata

    This project was dedicated to the investigation of the factors that may affect absolute quantitation in localized 31P MRS and if possible to the improvement of the accuracy of both localization and quantification. Three aspects have been looked at: 1) the acquisition /localization technique used; 2) the strategy used for conversion of signal amplitude/peak areas into concentrations; and 3) methods for MRS signal processing and analysis. With respect to the first aspect, image selected in vivo spectroscopy (ISIS) and point resolved spectroscopy (PRESS), were considered. Aspects of ISIS localization, including relaxation effects during inversion and excitation adiabatic pulses, and uniformity of spin excitation across the "in vivo" 31P spectral range, were investigated using simulation. In order to reduce the chemical shift displacement error in ISIS, a new adiabatic pulse for spin inversion, has been designed and experimentally verified. For PRESS, the performance of the selective 90[degrees] and 180[degrees] pulses was investigated experimentally and using simulations. The consequences of nonideal flip angles on T1 measurements based on two PRESS experiments were analyzed. Effects of amplitude and phase modulation of the ATP signal during the PRESS sequence were analyzed using product-operator formalism for an AMX system. A tissue substitute material, with known metabolite concentrations and simulating the 31P spectrum obtained from neonatal brain, has been developed for testing quantitation accuracy. The manufacture, physical properties and chemical stability of a material has been presented. The following calibration protocols have been experimentally verified: use of water as an internal concentration reference (ICR), and use of a standard phantom as an external concentration reference (ECR). A modified ECR protocol using the tissue substitute material as a reference, has been suggested to deal with problems related to off-resonance effects. This protocol has

  17. Quantitative Tissue Spectroscopy of Near Infrared Fluorescent Nanosensor Implants.

    PubMed

    Iverson, Nicole M; Bisker, Gili; Farias, Edgardo; Ivanov, Vsevolod; Ahn, Jiyoung; Wogan, Gerald N; Strano, Michael S

    2016-05-01

    Implantable, near infrared (nIR) fluorescent nanosensors are advantageous for in vivo monitoring of biological analytes since they can be rendered selective for a particular target molecule while utilizing their unique optical properties and the nIR tissue transparency window for information transfer without an internal power source or telemetry. However, basic questions remain regarding the optimal encapsulation platform, geometrical properties, and concentration ranges required for high signal to noise ratio and effective detection through biological tissue. In this work, we systematically explore these variables quantitatively to optimize the performance of such optical nanosensors for biomedical applications. We investigate both alginate and polyethylene glycol (PEG) as model hydrogel systems, encapsulating d(GT)15 ssDNA-wrapped single-walled carbon nanotubes (SWNT) as model fluorescent nanoparticle sensors, responsive to riboflavin. Hydrogel sensors implanted 0.5 mm into thick tissue samples exhibit 50% reduction of initial fluorescence intensity, allowing an optical detection limit of 5.4 mm and 5.1 mm depth in tissue for alginate and PEG gels, respectively, at a SWNT concentration of 10 mg L(-1), and 785 nm laser excitation of 80 mW and 30 s exposure. These findings are supported with in vivo nIR fluorescent imaging of SWNT hydrogels implanted subcutaneously in mice. For the case of SWNT, we find that the alginate system is preferable in terms of emission intensity, sensor response, rheological properties, and shelf life. PMID:27305824

  18. Quantitative analysis of polyethylene blends by Fourier transform infrared spectroscopy.

    PubMed

    Cran, Marlene J; Bigger, Stephen W

    2003-08-01

    The quantitative analysis of binary polyethylene (PE) blends by Fourier transform infrared (FT-IR) spectroscopy has been achieved based on the ratio of two absorbance peaks in an FT-IR spectrum. The frequencies for the absorbance ratio are selected based on structural entities of the PE components in the blend. A linear relationship between the absorbance ratio and the blend composition was found to exist if one of the absorbance peaks is distinct to one of the components and the other peak is common to both components. It was also found that any peak resulting from short-chain branching in copolymers (such as linear low-density polyethylene (LLDPE) or metallocene-catalyzed LLDPE (mLLDPE)), is suitable for use as the peak that is designated as being distinct to that component. In order to optimize the linearity of the equation, however, the selection of the second common peak is the most important and depends on the blend system studied. Indeed, under certain circumstances peaks that are not spectrally distinct can be used successfully to apply the method. The method exhibits potential for the routine analysis of PE blends that have been calibrated prior to its application.

  19. Quantitative Assessment of Amino Acid Damage upon keV Ion Beam Irradiation Through FTIR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Huang, Qing; Ke, Zhigang; Su, Xi; Yuan, Hang; Zhang, Shuqing; Yu, Zengliang

    2010-06-01

    Ion beam irradiation induces important biological effects and it is a long-standing task to acquire both qualitative and quantitative assessment of these effects. One effective way in the investigation is to utilize Fourier transformation infrared (FTIR) spectroscopy because it can offer sensitive and non-invasive measurements. In this paper a novel protocol was employed to prepare biomolecular samples in the form of thin and transversely uniform solid films that were suitable for both infrared and low-energy ion beam irradiation experiments. Under the irradiation of N+ and Ar+ ion beams of 25 keV with fluence ranging from 5×1015 ions/cm2 to 2.5×10 ions/cm2, the ion radio-sensitivity of four amino acids, namely, glycine, tyrosine, methionine and phenylalanine, were evaluated and compared. The ion beam irradiation caused biomolecular decomposition accompanied by molecular desorption of volatile species and the damage was dependent on ion type, fluence, energy and types of amino acids. The effectiveness of application of FTIR spectroscopy to the quantitative assessment of biomolecular damage dose effect induced by low-energy ion radiation was thus demonstrated.

  20. Quantitative laser-induced breakdown spectroscopy analysis of calcified tissue samples

    NASA Astrophysics Data System (ADS)

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

    2001-06-01

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

  1. Biological characteristics of crucian by quantitative inspection method

    NASA Astrophysics Data System (ADS)

    Chu, Mengqi

    2015-04-01

    Biological characteristics of crucian by quantitative inspection method Through quantitative inspection method , the biological characteristics of crucian was preliminary researched. Crucian , Belongs to Cypriniformes, Cyprinidae, Carassius auratus, is a kind of main plant-eating omnivorous fish,like Gregarious, selection and ranking. Crucian are widely distributed, perennial water all over the country all have production. Determine the indicators of crucian in the experiment, to understand the growth, reproduction situation of crucian in this area . Using the measured data (such as the scale length ,scale size and wheel diameter and so on) and related functional to calculate growth of crucian in any one year.According to the egg shape, color, weight ,etc to determine its maturity, with the mean egg diameter per 20 eggs and the number of eggs per 0.5 grams, to calculate the relative and absolute fecundity of the fish .Measured crucian were female puberty. Based on the relation between the scale diameter and length and the information, linear relationship between crucian scale diameter and length: y=1.530+3.0649. From the data, the fertility and is closely relative to the increase of age. The older, the more mature gonad development. The more amount of eggs. In addition, absolute fecundity increases with the pituitary gland.Through quantitative check crucian bait food intake by the object, reveals the main food, secondary foods, and chance food of crucian ,and understand that crucian degree of be fond of of all kinds of bait organisms.Fish fertility with weight gain, it has the characteristics of species and populations, and at the same tmes influenced by the age of the individual, body length, body weight, environmental conditions (especially the nutrition conditions), and breeding habits, spawning times factors and the size of the egg. After a series of studies of crucian biological character, provide the ecological basis for local crucian's feeding, breeding

  2. Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

    PubMed Central

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

    2013-01-01

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

  3. Quantitative nano-mechanics of biological cells with AFM

    NASA Astrophysics Data System (ADS)

    Sokolov, Igor

    2013-03-01

    The importance of study of living cells is hard to overestimate. Cell mechanics is a relatively young, yet not a well-developed area. Besides just a fundamental interest, large practical need has emerged to measure cell mechanics quantitatively. Recent studies revealed a significant correlation between stiffness of biological cells and various human diseases, such as cancer, malaria, arthritis, and even aging. However, really quantitative studies of mechanics of biological cells are virtually absent. It is not even clear if the cell, being a complex and heterogeneous object, can be described by the elastic modulus at all. Atomic force microscopy (AFM) is a natural instrument to study properties of cells in their native environments. Here we will demonstrate that quantitative measurements of elastic modulus of cells with AFM are possible. Specifically, we will show that the ``cell body'' (cell without ``brush'' surface layer, a non-elastic layer surrounding cells) typically demonstrates the response of a homogeneous elastic medium up to the deformation of 10-20%, but if and only if a) the cellular brush layer is taken into account, b) rather dull AFM probes are used. This will be justified with the help of the strong condition of elastic behavior of material: the elastic modulus is shown to be independent on the indentation depth. We will also demonstrate that an attempt either to ignore the brush layer or to use sharp AFM probes will result in the violation of the strong condition, which implies impossibility to use the concept of the elastic modulus to describe cell mechanics in such experiments. Examples of quantitative measurements of the Young's modulus of the cell body and the cell brush parameters will be given for various cells. Address when submitting: Clarkson University, Potsdam, NY 13699

  4. Lessons learned from quantitative dynamical modeling in systems biology.

    PubMed

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

    2013-01-01

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

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

    ERIC Educational Resources Information Center

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

    2014-01-01

    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…

  6. Nanosecond and femtosecond laser spectroscopy of molecules of biological interest

    NASA Astrophysics Data System (ADS)

    Villani, P.; Orlando, S.; Santagata, A.; De Bonis, A.; Veronesi, S.; Giardini, A.

    2007-07-01

    This paper mainly concerns on nanosecond and femtosecond laser spectroscopy of aromatic organic compounds as neurotransmitters, and plume diagnostics of the ablated species, in order to characterize the plasma dynamics, i.e. the temporal and spatial evolution of the plume. Optical emission spectroscopy has been applied to characterize the transient species produced in the femtosecond (fs) and nanosecond (ns) regimes. The laser sources employed for optical emission spectroscopy are a frequency-doubled Nd:YAG Handy ( λ = 532 nm, τ = 5 ns) and a frequency-doubled Nd:glass ( λ = 527 nm, τ = 250 fs). These studies aim to detect and give information on the photoexcitation and photodissociation of these biological molecules and to compare the plasma characteristics in the two ablation regimes.

  7. Quantitative measures of healthy aging and biological age

    PubMed Central

    Kim, Sangkyu; Jazwinski, S. Michal

    2015-01-01

    Numerous genetic and non-genetic factors contribute to aging. To facilitate the study of these factors, various descriptors of biological aging, including ‘successful aging’ and ‘frailty’, have been put forth as integrative functional measures of aging. A separate but related quantitative approach is the ‘frailty index’, which has been operationalized and frequently used. Various frailty indices have been constructed. Although based on different numbers and types of health variables, frailty indices possess several common properties that make them useful across different studies. We have been using a frailty index termed FI34 based on 34 health variables. Like other frailty indices, FI34 increases non-linearly with advancing age and is a better indicator of biological aging than chronological age. FI34 has a substantial genetic basis. Using FI34, we found elevated levels of resting metabolic rate linked to declining health in nonagenarians. Using FI34 as a quantitative phenotype, we have also found a genomic region on chromosome 12 that is associated with healthy aging and longevity. PMID:26005669

  8. Quantitative mass spectrometry of unconventional human biological matrices.

    PubMed

    Dutkiewicz, Ewelina P; Urban, Pawel L

    2016-10-28

    The development of sensitive and versatile mass spectrometric methodology has fuelled interest in the analysis of metabolites and drugs in unconventional biological specimens. Here, we discuss the analysis of eight human matrices-hair, nail, breath, saliva, tears, meibum, nasal mucus and skin excretions (including sweat)-by mass spectrometry (MS). The use of such specimens brings a number of advantages, the most important being non-invasive sampling, the limited risk of adulteration and the ability to obtain information that complements blood and urine tests. The most often studied matrices are hair, breath and saliva. This review primarily focuses on endogenous (e.g. potential biomarkers, hormones) and exogenous (e.g. drugs, environmental contaminants) small molecules. The majority of analytical methods used chromatographic separation prior to MS; however, such a hyphenated methodology greatly limits analytical throughput. On the other hand, the mass spectrometric methods that exclude chromatographic separation are fast but suffer from matrix interferences. To enable development of quantitative assays for unconventional matrices, it is desirable to standardize the protocols for the analysis of each specimen and create appropriate certified reference materials. Overcoming these challenges will make analysis of unconventional human biological matrices more common in a clinical setting.This article is part of the themed issue 'Quantitative mass spectrometry'. PMID:27644966

  9. Quantitative mass spectrometry of unconventional human biological matrices

    NASA Astrophysics Data System (ADS)

    Dutkiewicz, Ewelina P.; Urban, Pawel L.

    2016-10-01

    The development of sensitive and versatile mass spectrometric methodology has fuelled interest in the analysis of metabolites and drugs in unconventional biological specimens. Here, we discuss the analysis of eight human matrices-hair, nail, breath, saliva, tears, meibum, nasal mucus and skin excretions (including sweat)-by mass spectrometry (MS). The use of such specimens brings a number of advantages, the most important being non-invasive sampling, the limited risk of adulteration and the ability to obtain information that complements blood and urine tests. The most often studied matrices are hair, breath and saliva. This review primarily focuses on endogenous (e.g. potential biomarkers, hormones) and exogenous (e.g. drugs, environmental contaminants) small molecules. The majority of analytical methods used chromatographic separation prior to MS; however, such a hyphenated methodology greatly limits analytical throughput. On the other hand, the mass spectrometric methods that exclude chromatographic separation are fast but suffer from matrix interferences. To enable development of quantitative assays for unconventional matrices, it is desirable to standardize the protocols for the analysis of each specimen and create appropriate certified reference materials. Overcoming these challenges will make analysis of unconventional human biological matrices more common in a clinical setting. This article is part of the themed issue 'Quantitative mass spectrometry'.

  10. High-Resolution Waveguide THz Spectroscopy of Biological Molecules☆

    PubMed Central

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

    2008-01-01

    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. PMID:17933879

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

    ERIC Educational Resources Information Center

    Hill, Devon W.; And Others

    1988-01-01

    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)

  12. Quantitative Determination of DNA-Ligand Binding Using Fluorescence Spectroscopy

    ERIC Educational Resources Information Center

    Healy, Eamonn F.

    2007-01-01

    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.

  13. Biological X-ray absorption spectroscopy and metalloproteomics.

    PubMed

    Ascone, Isabella; Strange, Richard

    2009-05-01

    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

  14. Raman spectroscopy of human skin: looking for a quantitative algorithm to reliably estimate human age

    NASA Astrophysics Data System (ADS)

    Pezzotti, Giuseppe; Boffelli, Marco; Miyamori, Daisuke; Uemura, Takeshi; Marunaka, Yoshinori; Zhu, Wenliang; Ikegaya, Hiroshi

    2015-06-01

    The possibility of examining soft tissues by Raman spectroscopy is challenged in an attempt to probe human age for the changes in biochemical composition of skin that accompany aging. We present a proof-of-concept report for explicating the biophysical links between vibrational characteristics and the specific compositional and chemical changes associated with aging. The actual existence of such links is then phenomenologically proved. In an attempt to foster the basics for a quantitative use of Raman spectroscopy in assessing aging from human skin samples, a precise spectral deconvolution is performed as a function of donors' ages on five cadaveric samples, which emphasizes the physical significance and the morphological modifications of the Raman bands. The outputs suggest the presence of spectral markers for age identification from skin samples. Some of them appeared as authentic "biological clocks" for the apparent exactness with which they are related to age. Our spectroscopic approach yields clear compositional information of protein folding and crystallization of lipid structures, which can lead to a precise identification of age from infants to adults. Once statistically validated, these parameters might be used to link vibrational aspects at the molecular scale for practical forensic purposes.

  15. Raman spectroscopy of human skin: looking for a quantitative algorithm to reliably estimate human age.

    PubMed

    Pezzotti, Giuseppe; Boffelli, Marco; Miyamori, Daisuke; Uemura, Takeshi; Marunaka, Yoshinori; Zhu, Wenliang; Ikegaya, Hiroshi

    2015-06-01

    The possibility of examining soft tissues by Raman spectroscopy is challenged in an attempt to probe human age for the changes in biochemical composition of skin that accompany aging. We present a proof-of-concept report for explicating the biophysical links between vibrational characteristics and the specific compositional and chemical changes associated with aging. The actual existence of such links is then phenomenologically proved. In an attempt to foster the basics for a quantitative use of Raman spectroscopy in assessing aging from human skin samples, a precise spectral deconvolution is performed as a function of donors' ages on five cadaveric samples, which emphasizes the physical significance and the morphological modifications of the Raman bands. The outputs suggest the presence of spectral markers for age identification from skin samples. Some of them appeared as authentic "biological clocks" for the apparent exactness with which they are related to age. Our spectroscopic approach yields clear compositional information of protein folding and crystallization of lipid structures, which can lead to a precise identification of age from infants to adults. Once statistically validated, these parameters might be used to link vibrational aspects at the molecular scale for practical forensic purposes.

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

    PubMed

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

    2011-03-01

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

  17. Quantitative Measurement of Trans-Fats by Infrared Spectroscopy

    ERIC Educational Resources Information Center

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

    2007-01-01

    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.

  18. [Quantitative Detection of Chinese Cabbage Clubroot Based on FTIR Spectroscopy].

    PubMed

    Wang, Wei-ping; Chai, A-li; Shi, Yan-xia; Xie, Xue-wen; Li, Bao-ju

    2015-05-01

    Clubroot, caused by Plasmodiophora brassicae, is considered the most devastating soilborne disease in Brassica crops. It has emerged as a serious disease threatening the cruciferous crop production industry in China. Nowadays, the detection techniques for P. brassicae are laborious, time-consuming and low sensitivity. Rapid and effective detection methods are needed. The objective of this study is to develop a Fourier transform infrared spectrometer (FTIR) technique for detection of P. brassicae effectively and accurately. FTIR and Real-time PCR techniques were applied in quantitative detection of P. brassicae. Chinese cabbages were inoculated with P. brassicae. By analyzing the FTIR spectra of P. brassicae, infected clubroots and healthy roots, three specific bands 1 105, 1 145 and 1 228 cm-1 were selected. According to the correlation between the peak areas at these sensitive bands and Real-time PCR Ct value, quantitative evaluation model of P. brassicae was established based on FTIR y=34. 17 +12. 24x - 9. 81x2 - 6. 05x3, r=0. 98 (p<0. 05). To validate accuracy of the model, 10 clubroot samples were selected randomly from field, and detected by FTIR spectrum model, the results showed that the average error is 1. 60%. This demonstrated that the FTIR technology is an available one for the quantitative detection of P. brassicae in clubroot, and it provides a new method for quantitative and quickly detection of Chinese cabbage clubroot.

  19. Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

    PubMed Central

    Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

    2015-01-01

    Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

  20. Quantitative distinction between bound and free NADH in biological systems

    NASA Astrophysics Data System (ADS)

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

    2004-07-01

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

  1. Quantitatively Resolving Multivalent Interactions on Macroscopic Scale Using Force Spectroscopy

    PubMed Central

    Hu, Qiongzheng; Yang, Haopeng; Wang, Yuhong; Xu, Shoujun

    2016-01-01

    Multivalent interactions remain difficult to be characterized and consequently controlled, particularly on a macroscopic scale. Using force-induced remnant magnetization spectroscopy (FIRMS), we have resolved the single-, double-, and triple- biotin—streptavidin interactions, multivalent DNA interactions and CXCL12-CXCR4 interactions, on millimetre-scale surfaces. Our results establish FIRMS as a viable method for systematic resolution and controlled formation of multivalent interactions. PMID:26864087

  2. Direct and quantitative photothermal absorption spectroscopy of individual particulates

    SciTech Connect

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

    2013-12-23

    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.

  3. Biological evolution of replicator systems: towards a quantitative approach.

    PubMed

    Martin, Osmel; Horvath, J E

    2013-04-01

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

  4. Sub-terahertz resonance spectroscopy of biological macromolecules and cells

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

    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.

  5. Fourier transform Raman spectroscopy of synthetic and biological calcium phosphates.

    PubMed

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

    1994-05-01

    Fourier-transform (FT) Raman spectroscopy was used to characterize the organic and mineral components of biological and synthetic calcium phosphate minerals. Raman spectroscopy provides information on biological minerals that is complimentary to more widely used infrared methodologies as some infrared-inactive vibrational modes are Raman-active. The application of FT-Raman technology has, for the first time, enabled the problems of high sample fluorescence and low signal-to-noise that are inherent in calcified tissues to be overcome. Raman spectra of calcium phosphates are dominated by a very strong band near 960 cm-1 that arises from the symmetric stretching mode (v1) of the phosphate group. Other Raman-active phosphate vibrational bands are seen at approximately 1075 (v3), 590 (v4), and 435 cm-1 (v2). Minerals containing acidic phosphate groups show additional vibrational modes. The different calcium phosphate mineral phases can be distinguished from one another by the relative positions and shapes of these bands in the Raman spectra. FT-Raman spectra of nascent, nonmineralized matrix vesicles (MV) show a distinct absence of the phosphate v1 band even though these structures are rich in calcium and phosphate. Similar results were seen with milk casein and synthetic Ca-phosphatidyl-serine-PO4 complexes. Hence, the phosphate and/or acidic phosphate ions in these noncrystalline biological calcium phosphates is in a molecular environment that differs from that in synthetic amorphous calcium phosphate. In MV, the first distinct mineral phase to form contained acidic phosphate bands similar to those seen in octacalcium phosphate. The mineral phase present in fully mineralized MV was much more apatitic, resembling that found in bones and teeth.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. 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...

  7. 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...

  8. 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...

  9. Nanoscale devices for online dielectric spectroscopy of biological cells.

    PubMed

    Debuisson, Damien; Treizebré, Anthony; Houssin, Timothée; Leclerc, Eric; Bartès-Biesel, Dominique; Legrand, Dominique; Mazurier, Joel; Arscott, Steve; Bocquet, Bertrand; Senez, Vincent

    2008-06-01

    Nanoscale probes have been developed for the online characterization of the electrical properties of biological cells by dielectric spectroscopy. Two types of sensors have been designed and fabricated. The first one is devoted to low (<10 MHz) frequency range analysis and consists of gold nanoelectrodes. The second one works for high (>40 Hz) frequency range analysis and consists of a gold nanowire. The patterning of the sensors is performed by electron beam lithography. These devices are integrated in a microfluidic channel network for the manipulation of the cells and for the improvement of the performances of the sensors. These devices are used for the analysis of a well-characterized biological model in the area of the ligand-receptor interaction. The purpose is to monitor the interaction between the lactoferrin (the ligand) and the nucleolin and sulfated proteoglycans (the receptors) present or not on a set of mutant Chinese hamster ovary cell lines and their following internalization into the cytoplasm. Initial measurements have been performed with this microsystem and they demonstrate its capability for label-free, real-time, analysis of a dynamic mechanism involving biological cells.

  10. Machine learning methods for quantitative analysis of Raman spectroscopy data

    NASA Astrophysics Data System (ADS)

    Madden, Michael G.; Ryder, Alan G.

    2003-03-01

    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.

  11. Quantitative Determination of Lineshape Parameters from Velocity Modulation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hodges, James N.; McCall, Benjamin J.

    2016-06-01

    Velocity Modulation Spectroscopy (VMS) has stood as the gold standard in molecular ion spectroscopy for 30 years. Whether in a traditional uni-directional experiment or more complicated cavity-enhanced layouts with additional layers of modulation, VMS remains the preferred ion detection scheme and is responsible for the detection and transition frequency determination of around 50 molecules. Despite its success, VMS still has a great deal of untapped potential. There have only been two other published studies of VMS lineshapes and both struggle with the highly correlated parameters: linewidth, intensity, and velocity modulation amplitude, i.e. the maximum Doppler shift during a period of the discharge. Due to this difficulty, both Gao and Civis made concessions to achieve a good fit. Careful analysis of the contour of the transition profile allows us to properly disentangle those parameters in order to probe the environment of the positive column. We can extract the precise values for the translational temperature of the ion, the relative transition intensity, the ion mobility, and the electric field strength just from the lineshape of a single transition. A firm understanding of the lineshape will facilitate chemical and physical investigations of positive columns and allow for a better understanding of more complicated detection schemes. H. Gao et al., Acta Phys. Sin. 50, 1463 (2001) S. Civis, Chem. Phys. 186, 63 (1994)

  12. Quantitative Sum-Frequency Generation Vibrational Spectroscopy of Molecular Surfaces and Interfaces: Lineshape, Polarization and Orientation

    SciTech Connect

    Wang, Hongfei; Velarde, Luis; Gan, Wei; Fu, Li

    2015-04-01

    Sum-frequency generation vibrational spectroscopy (SFG) can provide detailed information and understanding of molecular vibrational spectroscopy, orientational and conformational structure, and interactions of molecular surfaces and interfaces, through quantitative measurement and analysis. In this review, we present the current status and discuss the main developments on the measurement of intrinsic SFG spectral lineshape, formulations for polarization measurement and orientation analysis of the SFG-VS spectra. The main focus is to present a coherent formulation and discuss the main concepts or issues that can help to make SFG-VS a quantitative analytical and research tool in revealing the chemistry and physics of complex molecular surface and interface.

  13. Experimental investigation of saturated polarization spectroscopy for quantitative concentration measurements.

    PubMed

    Reichardt, T A; Giancola, W C; Lucht, R P

    2000-04-20

    Polarization-spectroscopy (PS) line shapes and signal intensities are measured in well-characterized hydrogen-air flames operated over a wide range of equivalence ratios. We use both low (perturbative) and high (saturating) pump beam intensities in the counterpropagating pump-probe geometry. The effects of saturation on the line-center signal intensity and the resonance linewidth are investigated. The PS signal intensities are used to measure relative OH number densities in a series of near-adiabatic flames at equivalence ratios (phi) ranging from 0.5 to 1.5. The use of saturating pump intensities minimizes the effect of pump beam absorption, providing more accurate number density measurements. When calibrated to the calculated OH concentration in the phi = 0.6 flame, the saturated PS number density measurements probing the P(1)(2) transition are in excellent agreement with OH absorption measurements, equilibrium calculations of OH number density, and previous saturated degenerate four-wave mixing OH number density measurements. PMID:18345100

  14. Intramyocardial oxygen transport by quantitative diffuse reflectance spectroscopy in calves

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

    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.

  15. Gas-Phase Database for Quantitative Infrared Spectroscopy

    SciTech Connect

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

    2004-12-10

    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.

  16. Using Fourier transform IR spectroscopy to analyze biological materials

    PubMed Central

    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

    2015-01-01

    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

  17. Phosphorene: Synthesis, Scale-Up, and Quantitative Optical Spectroscopy.

    PubMed

    Woomer, Adam H; Farnsworth, Tyler W; Hu, Jun; Wells, Rebekah A; Donley, Carrie L; Warren, Scott C

    2015-09-22

    Phosphorene, a two-dimensional (2D) monolayer of black phosphorus, has attracted considerable theoretical interest, although the experimental realization of monolayer, bilayer, and few-layer flakes has been a significant challenge. Here, we systematically survey conditions for liquid exfoliation to achieve the first large-scale production of monolayer, bilayer, and few-layer phosphorus, with exfoliation demonstrated at the 10 g scale. We describe a rapid approach for quantifying the thickness of 2D phosphorus and show that monolayer and few-layer flakes produced by our approach are crystalline and unoxidized, while air exposure leads to rapid oxidation and the production of acid. With large quantities of 2D phosphorus now available, we perform the first quantitative measurements of the material's absorption edge-which is nearly identical to the material's band gap under our experimental conditions-as a function of flake thickness. Our interpretation of the absorbance spectrum relies on an analytical method introduced in this work, allowing the accurate determination of the absorption edge in polydisperse samples of quantum-confined semiconductors. Using this method, we found that the band gap of black phosphorus increased from 0.33 ± 0.02 eV in bulk to 1.88 ± 0.24 eV in bilayers, a range that is larger than that of any other 2D material. In addition, we quantified a higher-energy optical transition (VB-1 to CB), which changes from 2.0 eV in bulk to 3.23 eV in bilayers. This work describes several methods for producing and analyzing 2D phosphorus while also yielding a class of 2D materials with unprecedented optoelectronic properties.

  18. Branching out of single-molecule fluorescence spectroscopy: challenges for chemistry and influence on biology.

    PubMed

    Tinnefeld, Philip; Sauer, Markus

    2005-04-29

    In the last decade emerging single-molecule fluorescence-spectroscopy tools have been developed and adapted to analyze individual molecules under various conditions. Single-molecule-sensitive optical techniques are now well established and help to increase our understanding of complex problems in different disciplines ranging from materials science to cell biology. Previous dreams, such as the monitoring of the motility and structural changes of single motor proteins in living cells or the detection of single-copy genes and the determination of their distance from polymerase molecules in transcription factories in the nucleus of a living cell, no longer constitute unsolvable problems. In this Review we demonstrate that single-molecule fluorescence spectroscopy has become an independent discipline capable of solving problems in molecular biology. We outline the challenges and future prospects for optical single-molecule techniques which can be used in combination with smart labeling strategies to yield quantitative three-dimensional information about the dynamic organization of living cells. PMID:15849689

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

    ERIC Educational Resources Information Center

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

    2008-01-01

    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…

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

    SciTech Connect

    Watson, J.D.; Siniscalco, M.

    1986-01-01

    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)

  1. Cold Spring Harbor symposia on quantitative biology: Volume 51, Molecular biology of Homo sapiens

    SciTech Connect

    Not Available

    1986-01-01

    Thirteen years marked the time between the discovery of the double helix in 1953 and the elucidation of the genetic code in 1966. A similar interval has now passed since the development by Cohen and Boyer of a simple procedure for the cloning of selective DNA fragments. The scientific advances made possible by the subsequent modification and elaboration of these original cloning procedures now amaze, stimulate, and increasingly often overwhelm us. Facts that until recently were virtually unobtainable now flow forth almost effortlessly. Most excitingly, the frenetic pace of these new discoveries, instead of marking the impending end of a glorious moment of learning, give every indication of opening up scientific frontiers that will take hundreds if not thousands of years to explore thoroughly. This new era of enlightenment is nowhere more apparent than in our newfound ability to study ourselves at the molecular level. This volume is the first of two collections of papers submitted by the contributors to the Cold Spring Harbor symposia on quantitative biology for 1986 - molecular biology of Homo sapiens. Contained in this collection are 80 papers grouped into sessions entitled Human Gene Map, Genetic Diagnosis, Human Evolution, and Drugs Made Off Human Genes.

  2. Invited review article: combining scanning probe microscopy with optical spectroscopy for applications in biology and materials science.

    PubMed

    Lucas, Marcel; Riedo, Elisa

    2012-06-01

    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.

  3. 3D Imaging of Nanoparticle Distribution in Biological Tissue by Laser-Induced Breakdown Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gimenez, Y.; Busser, B.; Trichard, F.; Kulesza, A.; Laurent, J. M.; Zaun, V.; Lux, F.; Benoit, J. M.; Panczer, G.; Dugourd, P.; Tillement, O.; Pelascini, F.; Sancey, L.; Motto-Ros, V.

    2016-07-01

    Nanomaterials represent a rapidly expanding area of research with huge potential for future medical applications. Nanotechnology indeed promises to revolutionize diagnostics, drug delivery, gene therapy, and many other areas of research. For any biological investigation involving nanomaterials, it is crucial to study the behavior of such nano-objects within tissues to evaluate both their efficacy and their toxicity. Here, we provide the first account of 3D label-free nanoparticle imaging at the entire-organ scale. The technology used is known as laser-induced breakdown spectroscopy (LIBS) and possesses several advantages such as speed of operation, ease of use and full compatibility with optical microscopy. We then used two different but complementary approaches to achieve 3D elemental imaging with LIBS: a volume reconstruction of a sliced organ and in-depth analysis. This proof-of-concept study demonstrates the quantitative imaging of both endogenous and exogenous elements within entire organs and paves the way for innumerable applications.

  4. Using Active Learning to Teach Concepts and Methods in Quantitative Biology.

    PubMed

    Waldrop, Lindsay D; Adolph, Stephen C; Diniz Behn, Cecilia G; Braley, Emily; Drew, Joshua A; Full, Robert J; Gross, Louis J; Jungck, John A; Kohler, Brynja; Prairie, Jennifer C; Shtylla, Blerta; Miller, Laura A

    2015-11-01

    This article provides a summary of the ideas discussed at the 2015 Annual Meeting of the Society for Integrative and Comparative Biology society-wide symposium on Leading Students and Faculty to Quantitative Biology through Active Learning. It also includes a brief review of the recent advancements in incorporating active learning approaches into quantitative biology classrooms. We begin with an overview of recent literature that shows that active learning can improve students' outcomes in Science, Technology, Engineering and Math Education disciplines. We then discuss how this approach can be particularly useful when teaching topics in quantitative biology. Next, we describe some of the recent initiatives to develop hands-on activities in quantitative biology at both the graduate and the undergraduate levels. Throughout the article we provide resources for educators who wish to integrate active learning and technology into their classrooms.

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

    NASA Astrophysics Data System (ADS)

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

    2004-02-01

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

  6. P-31 magnetic resonance spectroscopy and near-infrared spectroscopy provide unique quantitative data for evaluation of exercising muscles

    NASA Astrophysics Data System (ADS)

    Park, Jane H.; Golwyn, Daniel; Olsen, Nancy J.; Newman, John H.; Powers, Alvin C.; Davis, Beverly C.; Rader, Kara; Chance, Britton

    1994-09-01

    P-31 magnetic resonance spectroscopy (MRS) and near-infra spectroscopy (NIRS) have been used to characterize the dynamic aspects of human muscle contraction. P-31 MRS is a non- invasive method for measuring ATP, phosphocreatine (PCr), and pH in exercising muscles and thereby provides information regarding oxidative and glycolytic capacities for generating high energy phosphate compounds. NIRS evaluates kinetic changes in oxygen levels in muscles during exercise and recovery. These two methods provide unique quantitative data for studies of normal muscle contraction and for more complex investigations of muscle diseases. Non-invasive MRS and NIRS examinations are readily repeatable and yield important data for longitudinal patient evaluation and therapeutic management.

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

    SciTech Connect

    Felzer, B.; Hauff, P.; Goetz, A.F.H.

    1994-02-01

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

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

    PubMed

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

    2005-01-01

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

  9. Quantitative water mapping of cryosectioned cells by electron energy-loss spectroscopy.

    PubMed

    Sun, S Q; Shi, S L; Hunt, J A; Leapman, R D

    1995-01-01

    A direct technique based on electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) has been developed to map subcellular distributions of water in frozen-hydrated biological cryosections. Previously, methods for water determination have been indirect in that they have required the cryosections to be dehydrated first. The new approach makes use of spectrum-imaging, where EELS data are collected in parallel at each pixel. Several operations are required to process the spectra including: subtraction of the detector dark current, deconvolution by the detector point-spread function, removal of plural inelastic scattering and correction for the support film. The resulting single scattering distributions are fitted to standard reference spectra at each pixel, and water content can be determined from the fitting coefficients. Although the darkfield or brightfield image from a hydrated cryosection shows minimal structure, the processed EELS image reveals strong contrast due to variations in water content. Reference spectra have been recorded from the major biomolecules (protein, lipid, carbohydrate, nucleic acid) as well as from vitrified water and crystalline ice. It has been found that quantitative results can be obtained for the majority of subcellular compartments by fitting only water and protein reference spectra, and the accuracy of the method for these compartments has been estimated as +/- 3.5%. With the present instrumentation the maximum allowed dose of 2 x 10(3) e/nm2 limits the useful spatial resolution to around 80 nm for +/- 5% precision at a single pixel. By averaging pixel intensities a value of 56.8% with a precision of +/- 2.0% has been determined for the water content of liver mitochondria. The water mapping technique may prove useful for applications to cell physiology and pathophysiology. PMID:7897645

  10. Qualitative and quantitative laser-induced breakdown spectroscopy of bronze objects

    NASA Astrophysics Data System (ADS)

    Tankova, V.; Blagoev, K.; Grozeva, M.; Malcheva, G.; Penkova, P.

    2016-03-01

    Laser-induced breakdown spectroscopy (LIBS) is an analytical technique for qualitative and quantitative elemental analysis of solids, liquids and gases. In this work, the method was applied for investigation of archaeological bronze objects. The analytical information obtained by LIBS was used for qualitative determination of the elements in the material used for manufacturing of the objects under study. Quantitative chemical analysis was also performed after generating calibration curves with standard samples of similar matrix composition. Quantitative estimation of the elemental concentration of the bulk of the samples was performed, together with investigation of the surface layer of the objects. The results of the quantitative analyses gave indications about the manufacturing process of the investigated objects.

  11. Detection of Biological Materials Using Ion Mobility Spectroscopy

    SciTech Connect

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

    1999-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Jiang, Dejun; Zhao, Shusen; Shen, Jingling

    2008-03-01

    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.

  13. Improvement in Quantitative X-ray Microanalysis of Biological Cryosections

    NASA Astrophysics Data System (ADS)

    Schultz, Michael; Rudolf, Frank; Gallitelli, Maria-Fiora

    1999-05-01

    The accuracy of Na measurements in biological cryosections has been improved through replacement of the 8 [mu]m Be window of the Si(Li) detector with a Super Atmospheric Thin Window (SuperATW) window mounted on a germanium electron microscope (GEM) detector. Greater accuracy of Ca measurements was also attained when a GEM detector instead of an Si(Li) detector was used for analysis of total Ca concentrations in cardiac muscle. Although the advantage of improved sensitivity for Na and Ca is lost in spot mode analysis because of the overriding contribution of biological variability, this advantage becomes important in X-ray mapping. We compared the two systems by analyzing cryosections of identical biological material under comparable conditions. We found that Si contamination in thin biological cryosections is unpredictable; it may be widespread and differ in degree in various cell compartments of the same cell. Hence, a correction for Si contamination should be included in the calculations of elemental concentrations. We suggest here a procedure for measuring and subtracting Si contamination from elemental spectra.

  14. Light Scattering and Absorption Spectroscopy in Three Dimensions Using Quantitative Low Coherence Interferometry for Biomedical Applications

    NASA Astrophysics Data System (ADS)

    Robles, Francisco E.

    The behavior of light after interacting with a biological medium reveals a wealth of information that may be used to distinguish between normal and disease states. This may be achieved by simply imaging the morphology of tissues or individual cells, and/or by more sophisticated methods that quantify specific surrogate biomarkers of disease. To this end, the work presented in this dissertation demonstrates novel tools derived from low coherence interferometry (LCI) that quantitatively measure wavelength-dependent scattering and absorption properties of biological samples, with high spectral resolution and micrometer spatial resolution, to provide insight into disease states. The presented work first describes a dual window (DW) method, which decomposes a signal sampled in a single domain (in this case the frequency domain) to a distribution that simultaneously contains information from both the original domain and the conjugate domain (here, the temporal or spatial domain). As the name suggests, the DW method utilizes two independently adjustable windows, each with different spatial and spectral properties to overcome limitations found in other processing methods that seek to obtain the same information. A theoretical treatment is provided, and the method is validated through simulations and experiments. With this tool, the spatially dependent spectral behavior of light after interacting with a biological medium may be analyzed to extract parameters of interest, such as the scattering and absorption properties. The DW method is employed to investigate scattering properties of samples using Fourier domain LCI (fLCI). In this method, induced temporal coherence effects provide insight into structural changes in dominant scatterers, such as cell nuclei within tissue, which can reveal the early stages of cancerous development. fLCI is demonstrated in complex, three-dimensional samples using a scattering phantom and an ex-vivo animal model. The results from the latter

  15. Molecular Orientation Analysis of Alkyl Methylene Groups from Quantitative Coherent Anti-Stokes Raman Scattering Spectroscopy.

    PubMed

    Zhang, Chi; Wang, Jie; Jasensky, Joshua; Chen, Zhan

    2015-04-16

    Quantitative data analysis in coherent anti-Stokes Raman scattering (CARS) spectroscopy is important for extracting molecular structural information. We developed a method to derive molecular tilt angle with respect to the surface normal based on quantitative CARS spectral analysis. We showed that the tilt angle of methylene alkyl chains on a surface can be directly obtained from the CH2 symmetric/asymmetric peak ratio in a CARS spectrum. The lipid alkyl chain tilt angle from a lipid monolayer was measured to be ∼0° and was verified by sum frequency generation spectroscopy, which probes the orientations of the lipid methyl end groups. The tilt angle of a silane monolayer alkyl chain was derived to be ∼35°, which agrees with the theoretical prediction. This method is submonolayer sensitive and can also be used to interpret polarization-dependent signals in CARS microscopy. It can be applied to elucidate detailed molecular structure from CARS spectroscopic and microscopic measurements.

  16. [Study of infrared spectroscopy quantitative analysis method for methane gas based on data mining].

    PubMed

    Zhang, Ai-Ju

    2013-10-01

    Monitoring of methane gas is one of the important factors affecting the coal mine safety. The online real-time monitoring of the methane gas is used for the mine safety protection. To improve the accuracy of model analysis, in the present paper, the author uses the technology of infrared spectroscopy to study the gas infrared quantitative analysis algorithm. By data mining technology application in multi-component infrared spectroscopy quantitative analysis algorithm, it was found that cluster analysis partial least squares algorithm is obviously superior to simply using partial least squares algorithm in terms of accuracy. In addition, to reduce the influence of the error on the accuracy of model individual calibration samples, the clustering analysis was used for the data preprocessing, and such denoising method was found to improve the analysis accuracy.

  17. [Quantitative Approach to Melamine Detection in Egg White with Surface-Enhanced Raman Spectroscopy].

    PubMed

    Wang, Qiao-hua; Liu, Ya-li; Ma, Mei-hu; Wang, Hong

    2015-04-01

    Due to the harmfulness of melamine to human, the quantitative detection of melamine in egg is very necessary. In the present study, the surface enhanced Raman spectra technology combined with chemometric analysis method was used to conduct melamine quantitative detection in egg white. Firstly, the melamine egg sample could be got by the method of artificial feeding hens usingdifferent feeding formulation. Then the surface enhanced Raman spectra of egg white was determined using portable Raman spectroscopy (Opto Trace RamTracer-200) and Raman enhancement reagents, and the melamine content within the white eggs was measured with gas chromatography mass spectrometry technology. The software of Raman Analyzer was used for baseline correction of Raman spectra. The correlation coefficient method was used to choose 320 spectral variables from the surface enhanced Raman spectroscopy as input variables to establish partial least squares quantitative calibration model . And the peaks-decomposition method was used to establish peaks-decomposition quantitative calibration model. Both models selected 90 and 44 samples respectively as calibration sets and validation sets during model establishment, and both models achieved good prediction effect. The determination coefficient between predicted values of partial least squares quantitative calibration model and measured values of gas chromatography mass spectrometry was 0.856, and root mean square error of prediction was 1.547. The determination coefficient was 0.947 and RMSEP was 0.893 for the peaks-decomposition quantitative calibration model. This study demonstrated that the method can effectively quantitatively detect melamine in eggs. Testing a sample only takes 15 minutes, which can provide a new way for the melamine egg detection. PMID:26197575

  18. Quantitative Imaging of Single Upconversion Nanoparticles in Biological Tissue

    PubMed Central

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

    2013-01-01

    The unique luminescent properties of new-generation synthetic nanomaterials, upconversion nanoparticles (UCNPs), enabled high-contrast optical biomedical imaging by suppressing the crowded background of biological tissue autofluorescence and evading high tissue absorption. This raised high expectations on the UCNP utilities for intracellular and deep tissue imaging, such as whole animal imaging. At the same time, the critical nonlinear dependence of the UCNP luminescence on the excitation intensity results in dramatic signal reduction at (∼1 cm) depth in biological tissue. Here, we report on the experimental and theoretical investigation of this trade-off aiming at the identification of optimal application niches of UCNPs e.g. biological liquids and subsurface tissue layers. As an example of such applications, we report on single UCNP imaging through a layer of hemolyzed blood. To extend this result towards in vivo applications, we quantified the optical properties of single UCNPs and theoretically analyzed the prospects of single-particle detectability in live scattering and absorbing bio-tissue using a human skin model. The model predicts that a single 70-nm UCNP would be detectable at skin depths up to 400 µm, unlike a hardly detectable single fluorescent (fluorescein) dye molecule. UCNP-assisted imaging in the ballistic regime thus allows for excellent applications niches, where high sensitivity is the key requirement. PMID:23691012

  19. Quantitative Detection of Pharmaceuticals Using a Combination of Paper Microfluidics and Wavelength Modulated Raman Spectroscopy

    PubMed Central

    Craig, Derek; Mazilu, Michael; Dholakia, Kishan

    2015-01-01

    Raman spectroscopy has proven to be an indispensable technique for the identification of various types of analytes due to the fingerprint vibration spectrum obtained. Paper microfluidics has also emerged as a low cost, easy to fabricate and portable approach for point of care testing. However, due to inherent background fluorescence, combining Raman spectroscopy with paper microfluidics is to date an unmet challenge in the absence of using surface enhanced mechanisms. We describe the first use of wavelength modulated Raman spectroscopy (WMRS) for analysis on a paper microfluidics platform. This study demonstrates the ability to suppress the background fluorescence of the paper using WMRS and the subsequent implementation of this technique for pharmaceutical analysis. The results of this study demonstrate that it is possible to discriminate between both paracetamol and ibuprofen, whilst, also being able to detect the presence of each analyte quantitatively at nanomolar concentrations. PMID:25938464

  20. Quantitative detection of pharmaceuticals using a combination of paper microfluidics and wavelength modulated Raman spectroscopy.

    PubMed

    Craig, Derek; Mazilu, Michael; Dholakia, Kishan

    2015-01-01

    Raman spectroscopy has proven to be an indispensable technique for the identification of various types of analytes due to the fingerprint vibration spectrum obtained. Paper microfluidics has also emerged as a low cost, easy to fabricate and portable approach for point of care testing. However, due to inherent background fluorescence, combining Raman spectroscopy with paper microfluidics is to date an unmet challenge in the absence of using surface enhanced mechanisms. We describe the first use of wavelength modulated Raman spectroscopy (WMRS) for analysis on a paper microfluidics platform. This study demonstrates the ability to suppress the background fluorescence of the paper using WMRS and the subsequent implementation of this technique for pharmaceutical analysis. The results of this study demonstrate that it is possible to discriminate between both paracetamol and ibuprofen, whilst, also being able to detect the presence of each analyte quantitatively at nanomolar concentrations.

  1. Online Interactive Teaching Modules Enhance Quantitative Proficiency of Introductory Biology Students

    ERIC Educational Resources Information Center

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

    2010-01-01

    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.…

  2. Spatial modulation spectroscopy for imaging and quantitative analysis of single dye-doped organic nanoparticles inside cells.

    PubMed

    Devadas, Mary Sajini; Devkota, Tuphan; Guha, Samit; Shaw, Scott K; Smith, Bradley D; Hartland, Gregory V

    2015-06-01

    Imaging of non-fluorescent nanoparticles in complex biological environments, such as the cell cytosol, is a challenging problem. For metal nanoparticles, Rayleigh scattering methods can be used, but for organic nanoparticles, such as dye-doped polymer beads or lipid nanoparticles, light scattering does not provide good contrast. In this paper, spatial modulation spectroscopy (SMS) is used to image single organic nanoparticles doped with non-fluorescent, near-IR croconaine dye. SMS is a quantitative imaging technique that yields the absolute extinction cross-section of the nanoparticles, which can be used to determine the number of dye molecules per particle. SMS images were recorded for particles within EMT-6 breast cancer cells. The measurements allowed mapping of the nanoparticle location and the amount of dye in a single cell. The results demonstrate how SMS can facilitate efforts to optimize dye-doped nanoparticles for effective photothermal therapy of cancer.

  3. [A multivariate nonlinear model for quantitative analysis in laser-induced breakdown spectroscopy].

    PubMed

    Chen, Xing-Long; Fu, Hong-Bo; Wang, Jing-Ge; Ni, Zhi-Bo; He, Wen-Gan; Xu, Jun; Rao Rui-zhong; Dong, Rui-Zhong

    2014-11-01

    Most quantitative models used in laser-induced breakdown spectroscopy (LIBS) are based on the hypothesis that laser-induced plasma approaches the state of local thermal equilibrium (LTE). However, the local equilibrium is possible only at a specific time segment during the evolution. As the populations of each energy level does not follow Boltzmann distribution in non-LTE condition, those quantitative models using single spectral line would be inaccurate. A multivariate nonlinear model, in which the LTE is not required, was proposed in this article to reduce the signal fluctuation and improve the accuracy of quantitative analysis. This multivariate nonlinear model was compared with the internal calibration model which is based on the LTE condition. The content of Mn in steel samples was determined by using the two models, respectively. A minor error and a minor relative standard deviation (RSD) were observed in multivariate nonlinear model. This result demonstrates that multivariate nonlinear model can improve measurement accuracy and repeatability.

  4. Quantitative determination and validation of avermectin B1a in commercial products using quantitative nuclear magnetic resonance spectroscopy.

    PubMed

    Hou, Zhuoni; Liang, Xianrui; Du, Liping; Su, Feng; Su, Weike

    2014-09-01

    Nuclear magnetic resonance is defined as a quantitative spectroscopic tool that enables a precise determination of the number of substances in liquids as well as in solids. There is few report demonstrating the application of NMR in the quantification of avermectin B1a (AVB1a ); here, a proton nuclear magnetic resonance spectroscopy ((1) H NMR) using benzene [1-methoxy-4-(2-nitroethyl) (PMN)] as an internal standard and deuterochloroform as an NMR solvent was tested for the quantitative determination of AVB1a . The integrated signal of AVB1a at 5.56 ppm and the signal of PMN at 8.14 ppm in the (1) H NMR spectrum were used for quantification purposes. Parameters of specificity, linearity, accuracy, precision, intermediate precision, range, limit of detection (LOD), limit of quantification (LOQ), stability and robustness were validated. The established method was accurate and precise with good recovery (98.86%) and relative standard deviation (RSD) of assay (0.34%) within the linearity of the calibration curve ranging from 5.08 to 13.58 mg/ml (R(2)  = 0.9999). The LOD and LOQ were 0.009 and 0.029 mg/ml, which indicated the excellent sensitivity of the method. The stability of the method was testified by a calculated RSD of 0.11%. The robustness was testified by modification of four different parameters, and the differences among each parameter were all less than 0.1%. Comparing with the assay described by the manufacturer of avermectin tablets, there was no significant difference between the assay obtained by HPLC and quantitative NMR (qNMR), which indicated qNMR was a simple and efficient method for the determination of AVB1a in commercial formulation products. PMID:24943110

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

    NASA Astrophysics Data System (ADS)

    Cerussi, Albert Edward

    1999-09-01

    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

  6. Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses

    PubMed Central

    Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

    2016-01-01

    Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning. PMID:27146161

  7. Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses.

    PubMed

    Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

    2016-01-01

    Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning.

  8. Development and Assessment of Modules to Integrate Quantitative Skills in Introductory Biology Courses.

    PubMed

    Hoffman, Kathleen; Leupen, Sarah; Dowell, Kathy; Kephart, Kerrie; Leips, Jeff

    2016-01-01

    Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning. PMID:27146161

  9. Sender-receiver systems and applying information theory for quantitative synthetic biology.

    PubMed

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-02-01

    Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning.

  10. Sender–receiver systems and applying information theory for quantitative synthetic biology

    PubMed Central

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-01-01

    Sender–receiver (S–R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S–R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning. PMID:25282688

  11. Online interactive teaching modules enhance quantitative proficiency of introductory biology students.

    PubMed

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

    2010-01-01

    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. PMID:20810959

  12. Raman Spectroscopy Studies of Normal and Burned Biological Tissue

    NASA Astrophysics Data System (ADS)

    Zarnani, Faranak; Maass, David; Idris, Ahamed; Glosser, Robert

    2011-03-01

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

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

    PubMed

    Landry, Christian R; Rifkin, Scott A

    2012-01-01

    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.

  14. A Novel Systems-Biology Algorithm for the Analysis of Coordinated Protein Responses Using Quantitative Proteomics.

    PubMed

    García-Marqués, Fernando; Trevisan-Herraz, Marco; Martínez-Martínez, Sara; Camafeita, Emilio; Jorge, Inmaculada; Lopez, Juan Antonio; Méndez-Barbero, Nerea; Méndez-Ferrer, Simón; Del Pozo, Miguel Angel; Ibáñez, Borja; Andrés, Vicente; Sánchez-Madrid, Francisco; Redondo, Juan Miguel; Bonzon-Kulichenko, Elena; Vázquez, Jesús

    2016-05-01

    The coordinated behavior of proteins is central to systems biology. However, the underlying mechanisms are poorly known and methods to analyze coordination by conventional quantitative proteomics are still lacking. We present the Systems Biology Triangle (SBT), a new algorithm that allows the study of protein coordination by pairwise quantitative proteomics. The Systems Biology Triangle detected statistically significant coordination in diverse biological models of very different nature and subjected to different kinds of perturbations. The Systems Biology Triangle also revealed with unprecedented molecular detail an array of coordinated, early protein responses in vascular smooth muscle cells treated at different times with angiotensin-II. These responses included activation of protein synthesis, folding, turnover, and muscle contraction - consistent with a differentiated phenotype-as well as the induction of migration and the repression of cell proliferation and secretion. Remarkably, the majority of the altered functional categories were protein complexes, interaction networks, or metabolic pathways. These changes could not be detected by other algorithms widely used by the proteomics community, and the vast majority of proteins involved have not been described before to be regulated by AngII. The unique capabilities of The Systems Biology Triangle to detect functional protein alterations produced by the coordinated action of proteins in pairwise quantitative proteomics experiments make this algorithm an attractive choice for the biological interpretation of results on a routine basis.

  15. Quantitative analysis of peanut oil content in ternary blended edible oil using near infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Chen, Huacai; Liu, Fuli; Wang, Zhilan; Jin, Shangzhong

    2008-03-01

    Calibration models of quantitative analysis of peanut oil content in ternary blended edible oil by near infrared spectroscopy were built using partial least square (PLS) regression. A total of 92 samples blended with three kinds of pure oil in different proportion (V/V) were prepared. Near infrared diffuse reflectance spectra of the samples were collected over 4 000 cm -1-10 000 cm -1 spectral region with a FT-NIR spectrometer. A calibration model of prediction to the peanut oil content was established with PLS using the original spectra and validated with leave-one-out cross validation method. The correlation coefficient and the RMSEC of the model were 0.9926 and 2.91%, respectively. The result showed that near infrared spectroscopy could be an ideal tool for fast determination to the peanut oil content in blended edible oil.

  16. Raman and multichannel Raman spectroscopy of biological systems

    NASA Astrophysics Data System (ADS)

    Bertoluzza, Alessandro; Caramazza, R.; Fagnano, C.

    1991-05-01

    Raman and multichannel Raman spectroscopy are molecular techniques able to monitor the bulk and surface structure of a biomaterial, in a non destructive and non invasive way, giving therefore useful information on physical and chemical aspects of biocompatibility. The same techniques can also be adequately used for the characterization of the biomaterial-host tissue interface, hence providing structural information on the biochemical aspect of biocompatibility. Moreover, multichannel Raman spectroscopy can also determine "in vivo" and "in situ" the bulk and surface structure of a biomaterial and the molecular interactions between biomaterials and tissues. Useful information at a molecular level on the biomaterial-tissue system can so be deduced. In particular, the application of traditional Paman spectroscopy to bioactive glasses (glasses derived from Hench's bioglass and meta and oligophosphates of calcium by themselves and with the addition of sodium and aluminium) useful in orthopedics and the application to hydrophobic (PMMA) and hydrophilic (PHEMA and PVP) organic polymers useful in ophthalmology are shown. Instead the applications of multichannel Paman spectroscopy are elucidated in the case of intraocular lenses (lOLs) based on PMMA and contact lenses (CLs) based on hydrophi I ic polymers.

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

    ERIC Educational Resources Information Center

    Bazzi, Ali; Kreuz, Bette; Fischer, Jeffrey

    2004-01-01

    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…

  18. Quantitative compositional analysis of sedimentary materials using thermal emission spectroscopy: 1. Application to sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Thorpe, Michael T.; Rogers, A. Deanne; Bristow, Thomas F.; Pan, Cong

    2015-11-01

    Thermal emission spectroscopy is used to determine the mineralogy of sandstone and mudstone rocks as part of an investigation of linear spectral mixing between sedimentary constituent phases. With widespread occurrences of sedimentary rocks on the surface of Mars, critical examination of the accuracy associated with quantitative models of mineral abundances derived from thermal emission spectra of sedimentary materials is necessary. Although thermal emission spectroscopy has been previously proven to be a viable technique to obtain quantitative mineralogy from igneous and metamorphic materials, sedimentary rocks, with natural variation of composition, compaction, and grain size, have yet to be examined. In this work, we present an analysis of the thermal emission spectral (~270-1650 cm-1) characteristics of a suite of 13 sandstones and 14 mudstones. X-ray diffraction and traditional point counting procedures were all evaluated in comparison with thermal emission spectroscopy. Results from this work are consistent with previous thermal emission spectroscopy studies and indicate that bulk rock mineral abundances can be estimated within 11.2% for detrital grains (i.e., quartz and feldspars) and 14.8% for all other mineral phases present in both sandstones and mudstones, in comparison to common in situ techniques used for determining bulk rock composition. Clay-sized to fine silt-sized grained phase identification is less accurate, with differences from the known ranging from ~5 to 24% on average. Nevertheless, linear least squares modeling of thermal emission spectra is an advantageous technique for determining abundances of detrital grains and sedimentary matrix and for providing a rapid classification of clastic rocks.

  19. Quantitative analysis of (styrene/acrylonitrile/methyl methacrylate) co-polymer systems by infrared resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Jalbout, Abraham F.; Jiang, Tao; Fengqi, Liu; Ding, C.; Darwish, Abdalla M.

    2002-02-01

    A detailed careful analysis of the infrared resonance (IR) spectra of polystyrene (PSt), polymethyl methacrylate (PMMA), polyacrylonitrile (PAN) and their co-mixtures were performed. Through this study the absorption peak area to weight ratios as well as working curves were obtained to test for their reliability as well as their suitability. Satisfactory results were achieved and these working curves were then used to measure the polymerized components of binary and ternary co-polymers. By investigating the acquired data we conclude that the monomer preferential polymeric sequence is St>MMA>AN. A quantitative method to measure P (St/AN/MMA) concentrations by IR spectroscopy is proposed in this work.

  20. Quantitative analysis of oils and fats by Fourier transform Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Sadeghi-Jorabchi, H.; Wilson, R. H.; Belton, P. S.; Edwards-Webb, J. D.; Coxon, D. T.

    The rapid analysis of fats and oils is of great importance in the food industry. It is shown that Fourier transform Raman spectroscopy may be used for this purpose. Good quality spectra, free of fluorescence, may be obtained and the spectra may be interpreted in terms of changes in total unsaturation, cis/trans isomer ratios and the number of double bonds in the hydrocarbon chains. Quantitative analysis of total unsaturation and cis/trans is possible and offers considerable improvements in speed when compared with conventional methods.

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

    SciTech Connect

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

    2013-01-14

    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.

  2. Optical fibre spectroscopy sensor for the quantitative determination of industrial textile dyes

    NASA Astrophysics Data System (ADS)

    Cubillas, Ana M.; Conde, Olga M.; Anuarbe, Pedro; Gutierrez, Monica; Martinez, Vicente; Lopez-Higuera, Jose M.

    2009-10-01

    In this paper, an extrinsic optical fibre sensor (OFS) for the quantitative determination of dyes used in the textile industry is presented. The system proposed is based on absorption spectroscopy and multivariate calibration methods to infer the concentration of different textile dyes. The performance of the sensor has been successfully assessed using calibrated dyes, with a very good correlation between the multivariate calibration models and the predicted values. The sensor system here demonstrated could be used to predict the colour of dye mixtures during the dyebath and, therefore, reduce the manufacturing costs.

  3. Quantitative mixture fraction measurements in combustion system via laser induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Mansour, Mohy; Imam, Hisham; Elsayed, Khaled A.; Elbaz, A. M.; Abbass, Wafaa

    2015-01-01

    Laser induced breakdown spectroscopy (LIBS) technique has been applied to quantitative mixture fraction measurements in flames. The measured spectra of different mixtures of natural gas and air are used to obtain the calibration parameters for local elemental mass fraction measurements and hence calculate the mixture fraction. The results are compared with the mixture fraction calculations based on the ratios of the spectral lines of H/N elements, H/O elements and C/(N+O) and they show good agreement within the reaction zone of the flames. Some deviations are observed outside the reaction zone. The ability of LIBS technique as a tool for quantitative mixture fraction as well as elemental fraction measurements in reacting and non-reacting of turbulent flames is feasible.

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

    PubMed Central

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

    2014-01-01

    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

  5. Quantitative Analysis of the Trends Exhibited by the Three Interdisciplinary Biological Sciences: Biophysics, Bioinformatics, and Systems Biology.

    PubMed

    Kang, Jonghoon; Park, Seyeon; Venkat, Aarya; Gopinath, Adarsh

    2015-12-01

    New interdisciplinary biological sciences like bioinformatics, biophysics, and systems biology have become increasingly relevant in modern science. Many papers have suggested the importance of adding these subjects, particularly bioinformatics, to an undergraduate curriculum; however, most of their assertions have relied on qualitative arguments. In this paper, we will show our metadata analysis of a scientific literature database (PubMed) that quantitatively describes the importance of the subjects of bioinformatics, systems biology, and biophysics as compared with a well-established interdisciplinary subject, biochemistry. Specifically, we found that the development of each subject assessed by its publication volume was well described by a set of simple nonlinear equations, allowing us to characterize them quantitatively. Bioinformatics, which had the highest ratio of publications produced, was predicted to grow between 77% and 93% by 2025 according to the model. Due to the large number of publications produced in bioinformatics, which nearly matches the number published in biochemistry, it can be inferred that bioinformatics is almost equal in significance to biochemistry. Based on our analysis, we suggest that bioinformatics be added to the standard biology undergraduate curriculum. Adding this course to an undergraduate curriculum will better prepare students for future research in biology.

  6. Prospects and challenges of quantitative phase imaging in tumor cell biology

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Götte, Martin; Greve, Burkhard; Ketelhut, Steffi

    2016-03-01

    Quantitative phase imaging (QPI) techniques provide high resolution label-free quantitative live cell imaging. Here, prospects and challenges of QPI in tumor cell biology are presented, using the example of digital holographic microscopy (DHM). It is shown that the evaluation of quantitative DHM phase images allows the retrieval of different parameter sets for quantification of cellular motion changes in migration and motility assays that are caused by genetic modifications. Furthermore, we demonstrate simultaneously label-free imaging of cell growth and morphology properties.

  7. 3D Imaging of Nanoparticle Distribution in Biological Tissue by Laser-Induced Breakdown Spectroscopy

    PubMed Central

    Gimenez, Y.; Busser, B.; Trichard, F.; Kulesza, A.; Laurent, J. M.; Zaun, V.; Lux, F.; Benoit, J. M.; Panczer, G.; Dugourd, P.; Tillement, O.; Pelascini, F.; Sancey, L.; Motto-Ros, V.

    2016-01-01

    Nanomaterials represent a rapidly expanding area of research with huge potential for future medical applications. Nanotechnology indeed promises to revolutionize diagnostics, drug delivery, gene therapy, and many other areas of research. For any biological investigation involving nanomaterials, it is crucial to study the behavior of such nano-objects within tissues to evaluate both their efficacy and their toxicity. Here, we provide the first account of 3D label-free nanoparticle imaging at the entire-organ scale. The technology used is known as laser-induced breakdown spectroscopy (LIBS) and possesses several advantages such as speed of operation, ease of use and full compatibility with optical microscopy. We then used two different but complementary approaches to achieve 3D elemental imaging with LIBS: a volume reconstruction of a sliced organ and in-depth analysis. This proof-of-concept study demonstrates the quantitative imaging of both endogenous and exogenous elements within entire organs and paves the way for innumerable applications. PMID:27435424

  8. Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Cao, Binghua; Fan, Mengbao

    2010-10-01

    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.

  9. Noninvasive quantitation of phosphorus metabolites in human tissue by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Roth, K.; Hubesch, B.; Meyerhoff, D. J.; Naruse, S.; Gober, J. R.; Lawry, T. J.; Boska, M. D.; Matson, G. B.; Weiner, M. W.

    Quantitation of metabolite concentrations by NMR spectroscopy is complicated by the need to determine the volume from which signals are detected, and by the need to obtain the relative sensitivity of detection within this volume. The use of coils with inhomogeneous B1 fields further complicates these problems. In order to quantify metabolite concentrations using 31P NMR spectroscopy, an external reference of hexamethyl phosphoroustriamide was used. Studies were performed on phantoms, using either a surface coil or a Helmholtz head coil to confirm the accuracy of both the ISIS volume selection technique and the use of an external reference. The limitations of this method are related to contamination and signal loss inherent in the ISIS technique and difficulties with integration of broad overlapping peaks. The method was applied to seven normal human subjects. The integrals for metabolite signals in normal brain and calf muscle were determined by using NMRI software. The T1 values of the signals of all phosphorus metabolites in the selected volume were measured in order to correct for saturation effects. The concentrations for PCr, P i, and ATP were 4.9, 2.0, and 2.5 m M in brain and 36.5, 5.7, and 7.3 m M in muscle. These results are in good agreement with those reported for animals, demonstrating the validity of this quantitation technique.

  10. Studying Biology to Understand Risk: Dosimetry Models and Quantitative Adverse Outcome Pathways

    EPA Science Inventory

    Confidence in the quantitative prediction of risk is increased when the prediction is based to as great an extent as possible on the relevant biological factors that constitute the pathway from exposure to adverse outcome. With the first examples now over 40 years old, physiologi...

  11. Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data.

    PubMed

    Bordon, Jure; Moskon, Miha; Zimic, Nikolaj; Mraz, Miha

    2015-01-01

    Quantitative modelling of biological systems has become an indispensable computational approach in the design of novel and analysis of existing biological systems. However, kinetic data that describe the system's dynamics need to be known in order to obtain relevant results with the conventional modelling techniques. These data are often hard or even impossible to obtain. Here, we present a quantitative fuzzy logic modelling approach that is able to cope with unknown kinetic data and thus produce relevant results even though kinetic data are incomplete or only vaguely defined. Moreover, the approach can be used in the combination with the existing state-of-the-art quantitative modelling techniques only in certain parts of the system, i.e., where kinetic data are missing. The case study of the approach proposed here is performed on the model of three-gene repressilator. PMID:26451831

  12. Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data.

    PubMed

    Bordon, Jure; Moskon, Miha; Zimic, Nikolaj; Mraz, Miha

    2015-01-01

    Quantitative modelling of biological systems has become an indispensable computational approach in the design of novel and analysis of existing biological systems. However, kinetic data that describe the system's dynamics need to be known in order to obtain relevant results with the conventional modelling techniques. These data are often hard or even impossible to obtain. Here, we present a quantitative fuzzy logic modelling approach that is able to cope with unknown kinetic data and thus produce relevant results even though kinetic data are incomplete or only vaguely defined. Moreover, the approach can be used in the combination with the existing state-of-the-art quantitative modelling techniques only in certain parts of the system, i.e., where kinetic data are missing. The case study of the approach proposed here is performed on the model of three-gene repressilator.

  13. Broadband Plasmon Waveguide Resonance Spectroscopy for Probing Biological Thin Films

    PubMed Central

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

    2010-01-01

    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. PMID:19796490

  14. Quantitative Raman Spectroscopy when the Signal-to-Noise is Below the Limit of Quantitation due to Fluorescence Interference: Advantages of a Moving Window Sequentially Shifted Excitation Approach.

    PubMed

    Marshall, Sarah; Cooper, John B

    2016-09-01

    Raman spectroscopy is a useful analytical tool. However, its application is often limited because shot noise from fluorescence obscures the Raman signal. In such cases, quantitative analysis is not possible when the signal-to-noise ratio (SNR) drops below two. A method is described for performing quantitative Raman spectroscopy that not only removes fluorescence backgrounds, but also results in a significant improvement in the SNR. The Raman data is extracted using a moving window sequentially shifted excitation algorithm. To demonstrate the capabilities of the method, a binary mixture of two analytes at varying concentrations is quantified in the presence of a highly fluorescent dye. Linear calibration plots were constructed and validated for the binary model using individual Raman peaks with SNR ranging from 0.073-12.6; r(2) values are greater than 0.96 in all cases, with all but the weakest peaks yielding values greater than 0.997. The presented method demonstrates a universal and autonomous approach for the quantitative analysis of highly fluorescent samples via Raman spectroscopy. The lower limit on the SNR ratio for quantitative Raman analysis with the described method is 0.1. In order to assess the effectiveness of the presented method, the entire set of experiments was also processed using the more common shifted excitation Raman difference spectroscopy (SERDS) approach. The advantages of the proposed method over SERDS are demonstrated for both the detection limit and the SNR of the processed spectra. PMID:27613308

  15. Quantitative confocal fluorescence microscopy of dynamic processes by multifocal fluorescence correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Krmpot, Aleksandar J.; Nikolić, Stanko N.; Vitali, Marco; Papadopoulos, Dimitrios K.; Oasa, Sho; Thyberg, Per; Tisa, Simone; Kinjo, Masataka; Nilsson, Lennart; Gehring, Walter J.; Terenius, Lars; Rigler, Rudolf; Vukojevic, Vladana

    2015-07-01

    Quantitative confocal fluorescence microscopy imaging without scanning is developed for the study of fast dynamical processes. The method relies on the use of massively parallel Fluorescence Correlation Spectroscopy (mpFCS). Simultaneous excitation of fluorescent molecules across the specimen is achieved by passing a single laser beam through a Diffractive Optical Element (DOE) to generate a quadratic illumination matrix of 32×32 light sources. Fluorescence from 1024 illuminated spots is detected in a confocal arrangement by a matching matrix detector consisting of the same number of single-photon avalanche photodiodes (SPADs). Software was developed for data acquisition and fast autoand cross-correlation analysis by parallel signal processing using a Graphic Processing Unit (GPU). Instrumental performance was assessed using a conventional single-beam FCS instrument as a reference. Versatility of the approach for application in biomedical research was evaluated using ex vivo salivary glands from Drosophila third instar larvae expressing a fluorescently-tagged transcription factor Sex Combs Reduced (Scr) and live PC12 cells stably expressing the fluorescently tagged mu-opioid receptor (MOPeGFP). We show that quantitative mapping of local concentration and mobility of transcription factor molecules across the specimen can be achieved using this approach, which paves the way for future quantitative characterization of dynamical reaction-diffusion landscapes across live cells/tissue with a submillisecond temporal resolution (presently 21 μs/frame) and single-molecule sensitivity.

  16. Toward quantitative deuterium analysis with laser-induced breakdown spectroscopy using atmospheric-pressure helium gas

    SciTech Connect

    Hedwig, Rinda; Lie, Zener Sukra; Kurniawan, Koo Hendrik; Kagawa, Kiichiro; Tjia, May On

    2010-01-15

    An experimental study has been carried out for the development of quantitative deuterium analysis using the neodymium doped yttrium aluminum garnet laser-induced breakdown spectroscopy (LIBS) with atmospheric pressure surrounding He gas by exploring the appropriate experimental condition and special sample cleaning technique. The result demonstrates the achievement of a full resolution between the D and H emission lines from zircaloy-4 samples, which is prerequisite for the desired quantitative analysis. Further, a linear calibration line with zero intercept was obtained for the emission intensity of deuterium from a number of zircaloy samples doped with predetermined concentrations of deuterium. The result is obtained by setting a +4 mm defocusing position for the laser beam, 6 {mu}s detection gating time, and 7 mm imaging position of the plasma for the detection, which is combined with a special procedure of repeated laser cleaning of the samples. This study has thus provided the basis for the development of practical quantitative deuterium analysis by LIBS.

  17. A novel rapid quantitative analysis of drug migration on tablets using laser induced breakdown spectroscopy.

    PubMed

    Yokoyama, Makoto; Tourigny, Martine; Moroshima, Kenji; Suzuki, Junsuke; Sakai, Miyako; Iwamoto, Kiyoshi; Takeuchi, Hirofumi

    2010-11-01

    There have been few reports wherein drug migration from the interior to the surface of a tablet has been analyzed quantitatively until now. In this paper, we propose a novel, rapid, quantitative analysis of drug migration in tablets using laser induced breakdown spectroscopy (LIBS). To evaluate drug migration, model tablets containing nicardipine hydrochloride as active pharmaceutical ingredient (API) were prepared by a conventional wet granulation method. Since the color of this API is pale yellow and all excipients are white, we can observe the degree of drug migration by visual inspection in these model tablets. In order to prepare tablets with different degrees of drug migration, the temperature of the drying process after tableting was varied between 50 to 80 °C. Using these manifold tablets, visual inspection, Fourier transform (FT)-IR mapping and LIBS analysis were carried out to evaluate the drug migration in the tablets. While drug migration could be observed using all methods, only LIBS analysis could provide quantitative analysis wherein the average LIBS intensity was correlated with the degree of drug migration obtained from the drying temperature. Moreover, in this work, we compared the sample preparation, data analysis process and measurement time for visual inspection, FT-IR mapping and LIBS analysis. The results of the comparison between these methods demonstrated that LIBS analysis is the simplest and the fastest method for migration monitoring. From the results obtained, we conclude that LIBS analysis is one of most useful process analytical technology (PAT) tools to solve the universal migration problem.

  18. Quantitative Determination of Fluorine Content in Blends of Polylactide (PLA)-Talc Using Near Infrared Spectroscopy.

    PubMed

    Tamburini, Elena; Tagliati, Chiara; Bonato, Tiziano; Costa, Stefania; Scapoli, Chiara; Pedrini, Paola

    2016-08-02

    Near-infrared spectroscopy (NIRS) has been widely used for quantitative and/or qualitative determination of a wide range of matrices. The objective of this study was to develop a NIRS method for the quantitative determination of fluorine content in polylactide (PLA)-talc blends. A blending profile was obtained by mixing different amounts of PLA granules and talc powder. The calibration model was built correlating wet chemical data (alkali digestion method) and NIR spectra. Using FT (Fourier Transform)-NIR technique, a Partial Least Squares (PLS) regression model was set-up, in a concentration interval of 0 ppm of pure PLA to 800 ppm of pure talc. Fluorine content prediction (R²cal = 0.9498; standard error of calibration, SEC = 34.77; standard error of cross-validation, SECV = 46.94) was then externally validated by means of a further 15 independent samples (R²EX.V = 0.8955; root mean standard error of prediction, RMSEP = 61.08). A positive relationship between an inorganic component as fluorine and NIR signal has been evidenced, and used to obtain quantitative analytical information from the spectra.

  19. Quantitative Determination of Fluorine Content in Blends of Polylactide (PLA)-Talc Using Near Infrared Spectroscopy.

    PubMed

    Tamburini, Elena; Tagliati, Chiara; Bonato, Tiziano; Costa, Stefania; Scapoli, Chiara; Pedrini, Paola

    2016-01-01

    Near-infrared spectroscopy (NIRS) has been widely used for quantitative and/or qualitative determination of a wide range of matrices. The objective of this study was to develop a NIRS method for the quantitative determination of fluorine content in polylactide (PLA)-talc blends. A blending profile was obtained by mixing different amounts of PLA granules and talc powder. The calibration model was built correlating wet chemical data (alkali digestion method) and NIR spectra. Using FT (Fourier Transform)-NIR technique, a Partial Least Squares (PLS) regression model was set-up, in a concentration interval of 0 ppm of pure PLA to 800 ppm of pure talc. Fluorine content prediction (R²cal = 0.9498; standard error of calibration, SEC = 34.77; standard error of cross-validation, SECV = 46.94) was then externally validated by means of a further 15 independent samples (R²EX.V = 0.8955; root mean standard error of prediction, RMSEP = 61.08). A positive relationship between an inorganic component as fluorine and NIR signal has been evidenced, and used to obtain quantitative analytical information from the spectra. PMID:27490548

  20. Multiwavelength UV/visible spectroscopy for the quantitative investigation of platelet quality

    NASA Astrophysics Data System (ADS)

    Mattley, Yvette D.; Leparc, German F.; Potter, Robert L.; Garcia-Rubio, Luis H.

    1998-04-01

    The quality of platelets transfused is vital to the effectiveness of the transfusion. Freshly prepared, discoid platelets are the most effective treatment for preventing spontaneous hemorrhage or for stopping an abnormal bleeding event. Current methodology for the routine testing of platelet quality involves random pH testing of platelet rich plasma and visual inspection of platelet rich plasma for a swirling pattern indicative of the discoid shape of the cells. The drawback to these methods is that they do not provide a quantitative and objective assay for platelet functionality that can be used on each platelet unit prior to transfusion. As part of a larger project aimed at characterizing whole blood and blood components with multiwavelength UV/vis spectroscopy, isolated platelets and platelet in platelet rich plasma have been investigated. Models based on Mie theory have been developed which allow for the extraction of quantitative information on platelet size, number and quality from multi-wavelength UV/vis spectra. These models have been used to quantify changes in platelet rich plasma during storage. The overall goal of this work is to develop a simple, rapid quantitative assay for platelet quality that can be used prior to platelet transfusion to ensure the effectiveness of the treatment. As a result of this work, the optical properties for isolated platelets, platelet rich plasma and leukodepleted platelet rich plasma have been determined.

  1. Quantitative analysis of skin chemicals using rapid near-infrared Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhao, Jianhua; Huang, Zhiwei; Zeng, Haishan; McLean, David I.; Lui, Harvey

    2008-02-01

    Raman spectroscopy is a non-invasive optical technique that is very sensitive to the structure and conformation of biochemical constitutes. It has been successfully used to study dysplasia and cancer in a variety of human tissues including skin. Researchers have a strong interest in quantitative analysis of the Raman spectra in the hope to find the quantitative molecule changes associated with cancers. Because skin is the largest organ in humans, it is very important to study the variability of Raman spectra for different body sites. In this presentation we report our quantitative analysis of normal skin Raman spectra of twenty-five body sites. Partial least square (PLS) analysis was used to quantify the skin molecules from the in vivo Raman spectra. We find that the absolute Raman intensity differs from person to person and from body site to body site. However the normalized Raman spectra are identical for the same body site. It is particularly interesting to find that the distribution of skin molecules is clustered for the same body regions.

  2. Quantitative neuropathology by high resolution magic angle spinning proton magnetic resonance spectroscopy

    PubMed Central

    Cheng, L. L.; Ma, M. J.; Becerra, L.; Ptak, T.; Tracey, I.; Lackner, A.; González, R. G.

    1997-01-01

    We describe a method that directly relates tissue neuropathological analysis to medical imaging. Presently, only indirect and often tenuous relationships are made between imaging (such as MRI or x-ray computed tomography) and neuropathology. We present a biochemistry-based, quantitative neuropathological method that can help to precisely quantify information provided by in vivo proton magnetic resonance spectroscopy (1HMRS), an emerging medical imaging technique. This method, high resolution magic angle spinning (HRMAS) 1HMRS, is rapid and requires only small amounts of unprocessed samples. Unlike chemical extraction or other forms of tissue processing, this method analyzes tissue directly, thus minimizing artifacts. We demonstrate the utility of this method by assessing neuronal damage using multiple tissue samples from differently affected brain regions in a case of Pick disease, a human neurodegenerative disorder. Among different regions, we found an excellent correlation between neuronal loss shown by traditional neurohistopathology and decrease of the neuronal marker N-acetylaspartate measured by HRMAS 1HMRS. This result demonstrates for the first time, to our knowledge, a direct, quantitative link between a decrease in N-acetylaspartate and neuronal loss in a human neurodegenerative disease. As a quantitative method, HRMAS 1HMRS has potential applications in experimental and clinical neuropathologic investigations. It should also provide a rational basis for the interpretation of in vivo 1HMRS studies of human neurological disorders. PMID:9177231

  3. Quantitative detection of astaxanthin and cantaxanthin in Atlantic salmon by resonance Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Ermakov, Igor V.; Ermakova, Maia R.; Gellermann, Werner

    2006-02-01

    Two major carotenoids species found in salmonids muscle tissues are astaxanthin and cantaxanthin. They are taken up from fish food and are responsible for the attractive red-orange color of salmon filet. Since carotenoids are powerful antioxidants and biomarkers of nutrient consumption, they are thought to indicate fish health and resistance to diseases in fish farm environments. Therefore, a rapid, accurate, quantitative optical technique for measuring carotenoid content in salmon tissues is of economic interest. We demonstrate the possibility of using fast, selective, quantitative detection of astaxanthin and cantaxanthin in salmon muscle tissues, employing resonance Raman spectroscopy. Analyzing strong Raman signals originating from the carbon-carbon double bond stretch vibrations of the carotenoid molecules under blue laser excitation, we are able to characterize quantitatively the concentrations of carotenoids in salmon muscle tissue. To validate the technique, we compared Raman data with absorption measurements of carotenoid extracts in acetone. A close correspondence was observed in absorption spectra for tissue extract in acetone and a pure astaxanthin solution. Raman results show a linear dependence between Raman and absorption data. The proposed technique holds promise as a method of rapid screening of carotenoid levels in fish muscle tissues and may be attractive for the fish farm industry to assess the dietary status of salmon, risk for infective diseases, and product quality control.

  4. Feasibility of quantitative diffuse reflectance spectroscopy for targeted measurement of renal ischemia during laparoscopic partial nephrectomy

    NASA Astrophysics Data System (ADS)

    Goel, Utsav O.; Maddox, Michael M.; Elfer, Katherine N.; Dorsey, Philip J.; Wang, Mei; McCaslin, Ian Ross; Brown, J. Quincy; Lee, Benjamin R.

    2014-10-01

    Reduction of warm ischemia time during partial nephrectomy (PN) is critical to minimizing ischemic damage and improving postoperative kidney function, while maintaining tumor resection efficacy. Recently, methods for localizing the effects of warm ischemia to the region of the tumor via selective clamping of higher-order segmental artery branches have been shown to have superior outcomes compared with clamping the main renal artery. However, artery identification can prolong operative time and increase the blood loss and reduce the positive effects of selective ischemia. Quantitative diffuse reflectance spectroscopy (DRS) can provide a convenient, real-time means to aid in artery identification during laparoscopic PN. The feasibility of quantitative DRS for real-time longitudinal measurement of tissue perfusion and vascular oxygenation in laparoscopic nephrectomy was investigated in vivo in six Yorkshire swine kidneys (n=three animals). DRS allowed for rapid identification of ischemic areas after selective vessel occlusion. In addition, the rates of ischemia induction and recovery were compared for main renal artery versus tertiary segmental artery occlusion, and it was found that the tertiary segmental artery occlusion trends toward faster recovery after ischemia, which suggests a potential benefit of selective ischemia. Quantitative DRS could provide a convenient and fast tool for artery identification and evaluation of the depth, spatial extent, and duration of selective tissue ischemia in laparoscopic PN.

  5. Characterisation of transmission Raman spectroscopy for rapid quantitative analysis of intact multi-component pharmaceutical capsules.

    PubMed

    Hargreaves, Michael D; Macleod, Neil A; Smith, Mark R; Andrews, Darren; Hammond, Stephen V; Matousek, Pavel

    2011-02-20

    A detailed characterisation of the performance of transmission Raman spectroscopy was performed from the standpoint of rapid quantitative analysis of pharmaceutical capsules using production relevant formulations comprising of active pharmaceutical ingredient (API) and 3 common pharmaceutical excipients. This research builds on our earlier studies that identified the unique benefits of transmission Raman spectroscopy compared to conventional Raman spectroscopy. These include the ability to provide bulk information of the content of capsules, thus avoiding the sub-sampling problem, and the suppression of interference from the capsule shell. This study demonstrates, for the first time, the technique's insensitivity to the amount of material held within the capsules. Different capsules sizes with different overall fill weights (100-400 mg) and capsule shell colours were assayed with a single calibration model developed using only one weight and size sample set (100 mg) to a relative error of typically <3%. The relative root mean square error of prediction of the concentration of API for the main sample set (nominal content 75%, w/w) was 1.5% with a 5s acquisition time. Models built using the same calibration set also predicted the 3 low level excipients with relative errors of 5-15%. The quantity of API was also predicted (with a relative error within ∼3%) using the same model for capsules prepared with different generations of API (i.e. API manufactured via different processes). The study provides further foundation blocks for the establishment of this emerging technique as a routine pharmaceutical analysis tool, capitalising on the inherently high chemical specificity of Raman spectroscopy and the non-invasive nature of the measurement. Ultimately, this technique has significant promise as a Process Analytical Technology (PAT) tool for online production application. PMID:20947277

  6. Spatial modulation spectroscopy for imaging and quantitative analysis of single dye-doped organic nanoparticles inside cells

    NASA Astrophysics Data System (ADS)

    Devadas, Mary Sajini; Devkota, Tuphan; Guha, Samit; Shaw, Scott K.; Smith, Bradley D.; Hartland, Gregory V.

    2015-05-01

    Imaging of non-fluorescent nanoparticles in complex biological environments, such as the cell cytosol, is a challenging problem. For metal nanoparticles, Rayleigh scattering methods can be used, but for organic nanoparticles, such as dye-doped polymer beads or lipid nanoparticles, light scattering does not provide good contrast. In this paper, spatial modulation spectroscopy (SMS) is used to image single organic nanoparticles doped with non-fluorescent, near-IR croconaine dye. SMS is a quantitative imaging technique that yields the absolute extinction cross-section of the nanoparticles, which can be used to determine the number of dye molecules per particle. SMS images were recorded for particles within EMT-6 breast cancer cells. The measurements allowed mapping of the nanoparticle location and the amount of dye in a single cell. The results demonstrate how SMS can facilitate efforts to optimize dye-doped nanoparticles for effective photothermal therapy of cancer.Imaging of non-fluorescent nanoparticles in complex biological environments, such as the cell cytosol, is a challenging problem. For metal nanoparticles, Rayleigh scattering methods can be used, but for organic nanoparticles, such as dye-doped polymer beads or lipid nanoparticles, light scattering does not provide good contrast. In this paper, spatial modulation spectroscopy (SMS) is used to image single organic nanoparticles doped with non-fluorescent, near-IR croconaine dye. SMS is a quantitative imaging technique that yields the absolute extinction cross-section of the nanoparticles, which can be used to determine the number of dye molecules per particle. SMS images were recorded for particles within EMT-6 breast cancer cells. The measurements allowed mapping of the nanoparticle location and the amount of dye in a single cell. The results demonstrate how SMS can facilitate efforts to optimize dye-doped nanoparticles for effective photothermal therapy of cancer. Electronic supplementary information (ESI

  7. Detection of Taurine in Biological Tissues by 33S NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Musio, Roberta; Sciacovelli, Oronzo

    2001-12-01

    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.

  8. Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

    PubMed

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

    2013-12-01

    We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in

  9. Spectroscopy of Multilayered Biological Tissues for Diabetes Care

    NASA Astrophysics Data System (ADS)

    Yudovsky, Dmitry

    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

  10. Quantitative characterization of traumatic bruises by combined pulsed photothermal radiometry and diffuse reflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    Vidovič, Luka; Milanič, Matija; Randeberg, Lise L.; Majaron, Boris

    2015-02-01

    We apply diffuse reflectance spectroscopy (DRS) and pulsed photothermal radiometry (PPTR) for characterization of the bruise evolution process. While DRS provides information in a wide range of visible wavelengths, the PPTR enables extraction of detailed depth distribution and concentration profiles of selected absorbers (e.g. melanin, hemoglobin). In this study, we simulate experimental DRS spectra and PPTR signals using the Monte Carlo technique and focus on characterization of a suitable fitting approach for their analysis. We find inverse Monte Carlo to be superior to the diffusion approximation approach for the inverse analysis of DRS spectra. The analysis is then augmented with information obtainable by the fitting of the PPTR signal. We show that both techniques can be coupled in a combined fitting approach. The combining of two complementary techniques improves the robustness and accuracy of the inverse analysis, enabling a comprehensive quantitative characterization of the bruise evolution dynamics.

  11. Quantitative analysis of Cu and Co adsorbed on fish bones via laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Rezk, R. A.; Galmed, A. H.; Abdelkreem, M.; Ghany, N. A. Abdel; Harith, M. A.

    2016-09-01

    In the present work, laser-induced breakdown spectroscopy (LIBS) has been applied for qualitative and quantitative analysis of heavy metals adsorbed by fish bones. Fish bones were used as a natural and low cost heavy metal sorbent (mainly Cu and Co) from synthetic wastewater. The removal efficiency of the adsorbent was studied as a function of initial metal concentration and pH value. Optimal experimental conditions were evaluated for improving the sensitivity of LIBS technique through parametric dependence studies. Furthermore, calibration curves were constructed based on X-ray fluorescence (XRF) analysis technique, whereas, the limits of detection (LOD) for Cu and Co were calculated. The results were validated by comparing LIBS data with those obtained by XRF spectrometry. The results of the two techniques are strongly correlated which verified the feasibility of using LIBS to detect traces of heavy metals adsorbed from wastewater by fish bones. This study reflects the potential of using LIBS in environmental applications.

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

    PubMed

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

    2008-01-15

    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

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

    SciTech Connect

    Mann, C.K.; Vickers, T.J.

    1994-10-11

    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.

  14. Quantitative analysis of sesquiterpene lactones in extract of Arnica montana L. by 1H NMR spectroscopy.

    PubMed

    Staneva, Jordanka; Denkova, Pavletta; Todorova, Milka; Evstatieva, Ljuba

    2011-01-01

    (1)H NMR spectroscopy was used as a method for quantitative analysis of sesquiterpene lactones present in a crude lactone fraction isolated from Arnica montana. Eight main components - tigloyl-, methacryloyl-, isobutyryl- and 2-methylbutyryl-esters of helenalin (H) and 11α,13-dihydrohelenalin (DH) were identified in the studied sample. The method allows the determination of the total amount of sesquiterpene lactones and the quantity of both type helenalin and 11α,13-dihydrohelenalin esters separately. Furthermore, 6-O-tigloylhelenalin (HT, 1), 6-O-methacryloylhelenalin (HM, 2), 6-O-tigloyl-11α,13-dihydrohelenalin (DHT, 5), and 6-O-methacryloyl-11α,13-dihydrohelenalin (DHM, 6) were quantified as individual components.

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

    PubMed

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

    2012-12-01

    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.

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

    SciTech Connect

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

    2007-10-01

    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

  17. Quantitative LC-MS/MS Glycomic Analysis of Biological Samples Using AminoxyTMT.

    PubMed

    Zhou, Shiyue; Hu, Yunli; Veillon, Lucas; Snovida, Sergei I; Rogers, John C; Saba, Julian; Mechref, Yehia

    2016-08-01

    Protein glycosylation plays an important role in various biological processes, such as modification of protein function, regulation of protein-protein interactions, and control of turnover rates of proteins. Moreover, glycans have been considered as potential biomarkers for many mammalian diseases and development of aberrant glycosylation profiles is an important indicator of the pathology of a disease or cancer. Hence, quantitation is an important aspect of a comprehensive glycomics study. Although numerous MS-based quantitation strategies have been developed in the past several decades, some issues affecting sensitivity and accuracy of quantitation still exist, and the development of more effective quantitation strategies is still required. Aminoxy tandem mass tag (aminoxyTMT) reagents are recently commercialized isobaric tags which enable relative quantitation of up to six different glycan samples simultaneously. In this study, liquid chromatography and mass spectrometry conditions have been optimized to achieve reliable LC-MS/MS quantitative glycomic analysis using aminoxyTMT reagents. Samples were resuspended in 0.2 M sodium chloride solution to promote the formation of sodium adduct precursor ions, which leads to higher MS/MS reporter ion yields. This method was first evaluated with glycans from model glycoproteins and pooled human blood serum samples. The observed variation of reporter ion ratios was generally less than 10% relative to the theoretical ratio. Even for the highly complex minor N-glycans, the variation was still below 15%. This strategy was further applied to the glycomic profiling of N-glycans released from blood serum samples of patients with different esophageal diseases. Our results demonstrate the benefits of utilizing aminoxyTMT reagents for reliable quantitation of biological glycomic samples. PMID:27377957

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

    SciTech Connect

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

    2006-12-01

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

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

    PubMed

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

    2006-12-01

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

  20. Terahertz time-domain spectroscopy and quantitative analysis of metal gluconates.

    PubMed

    Li, Shaoxian; Yang, Jingqi; Zhao, Hongwei; Yang, Na; Jing, Dandan; Zhang, Jianbing; Li, Qingnuan; Han, Jiaguang

    2015-01-01

    A series of metal gluconates (Na(+), K(+), Mg(2+), Ca(2+), Fe(2+), Cu(2+), and Zn(2+)) were investigated by terahertz (THz) time-domain spectroscopy. The absorption coefficients and refractive indices of the samples were obtained in the frequency range of 0.5-2.6 THz. The gluconates showed distinct THz characteristic fingerprints, and the dissimilarities reflect their different structures, hydrogen-bond networks, and molecular interactions. In addition, some common features were observed among these gluconates, and the similarities probably come from the similar carbohydrate anion group. The X-ray powder diffraction measurements of these metal gluconates were performed, and the copper(II) gluconate was found to be amorphous, corresponding to the monotonic increase feature in the THz absorption spectrum. The results suggest that THz spectroscopy is sensitive to molecular structure and physical form. Binary and ternary mixtures of different gluconates were quantitatively analyzed based on the Beer-Lambert law. A chemical map of a tablet containing calcium D-gluconate monohydrate and α-lactose in the polyethylene host was obtained by THz imaging. The study shows that THz technology is a useful tool in pharmaceutical research and quality control applications. PMID:25506686

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

    SciTech Connect

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

    1997-02-01

    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}

  2. Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems.

    PubMed

    Konur, Savas; Gheorghe, Marian; Dragomir, Ciprian; Mierla, Laurentiu; Ipate, Florentin; Krasnogor, Natalio

    2015-01-16

    Computational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations). These models incorporate a set of methods for specifying, modeling, testing, and simulating biological systems. In addition, they can be analyzed using algorithmic techniques (e.g., formal verification). This paper shows how formal verification is utilized in systems and synthetic biology through qualitative vs quantitative analysis. Here, we choose two well-known case studies: quorum sensing in P. aeruginosas and pulse generator. The paper reports verification analysis of two systems carried out using some model checking tools, integrated to the Infobiotics Workbench platform, where system models are based on stochastic P systems.

  3. Quantitative phase imaging of biological cells using spatially low and temporally high coherent light source.

    PubMed

    Ahmad, Azeem; Dubey, Vishesh; Singh, Gyanendra; Singh, Veena; Mehta, Dalip Singh

    2016-04-01

    In this Letter, we demonstrate quantitative phase imaging of biological samples, such as human red blood cells (RBCs) and onion cells using narrow temporal frequency and wide angular frequency spectrum light source. This type of light source was synthesized by the combined effect of spatial, angular, and temporal diversity of speckle reduction technique. The importance of using low spatial and high temporal coherence light source over the broad band and narrow band light source is that it does not require any dispersion compensation mechanism for biological samples. Further, it avoids the formation of speckle or spurious fringes which arises while using narrow band light source. PMID:27192285

  4. Quantitatively Resolving Ligand–Receptor Bonds on Cell Surfaces Using Force-Induced Remnant Magnetization Spectroscopy

    PubMed Central

    2016-01-01

    Molecule-specific noncovalent bonding on cell surfaces is the foundation for cellular recognition and functioning. A major challenge in probing these bonds is to resolve the specific bonds quantitatively and efficiently from the nonspecific interactions in a complex environment. Using force-induced remnant magnetization spectroscopy (FIRMS), we were able to resolve quantitatively three different interactions for magnetic beads bearing anti-CD4 antibodies with CD4+ T cell surfaces based upon their binding forces. The binding force of the CD4 antibody–antigen bonds was determined to be 75 ± 3 pN. For comparison, the same bonds were also studied on a functionalized substrate surface, and the binding force was determined to be 90 ± 6 pN. The 15 pN difference revealed by high-resolution FIRMS illustrates the significant impact of the bonding environment. Because the force difference was unaffected by the cell number or the receptor density on the substrate, we attributed it to the possible conformational or local environmental differences of the CD4 antigens between the cell surface and substrate surface. Our results show that the high force resolution and detection efficiency afforded by FIRMS are valuable for studying protein–protein interactions on cell surfaces. PMID:27163031

  5. Quantitative analysis of boron oxide in borosilicate glasses by infrared spectroscopy

    SciTech Connect

    Haaland, D.M.

    1986-11-01

    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.

  6. Quantitative analysis of lead in aqueous solutions by ultrasonic nebulizer assisted laser induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhong, Shi-Lei; Lu, Yuan; Kong, Wei-Jin; Cheng, Kai; Zheng, Ronger

    2016-08-01

    In this study, an ultrasonic nebulizer unit was established to improve the quantitative analysis ability of laser-induced breakdown spectroscopy (LIBS) for liquid samples detection, using solutions of the heavy metal element Pb as an example. An analytical procedure was designed to guarantee the stability and repeatability of the LIBS signal. A series of experiments were carried out strictly according to the procedure. The experimental parameters were optimized based on studies of the pulse energy influence and temporal evolution of the emission features. The plasma temperature and electron density were calculated to confirm the LTE state of the plasma. Normalizing the intensities by background was demonstrated to be an appropriate method in this work. The linear range of this system for Pb analysis was confirmed over a concentration range of 0-4,150ppm by measuring 12 samples with different concentrations. The correlation coefficient of the fitted calibration curve was as high as 99.94% in the linear range, and the LOD of Pb was confirmed as 2.93ppm. Concentration prediction experiments were performed on a further six samples. The excellent quantitative ability of the system was demonstrated by comparison of the real and predicted concentrations of the samples. The lowest relative error was 0.043% and the highest was no more than 7.1%.

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

    PubMed

    Sun, Lan-Xiang; Yu, Hai-Bin

    2009-12-01

    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.

  8. Quantitative Surface Chirality Detection with Sum Frequency Generation Vibrational Spectroscopy: Twin Polarization Angle Approach

    SciTech Connect

    Wei, Feng; Xu, Yanyan; Guo, Yuan; Liu, Shi-lin; Wang, Hongfei

    2009-12-27

    Here we report a novel twin polarization angle (TPA) approach in the quantitative chirality detection with the surface sum-frequency generation vibrational spectroscopy (SFG-VS). Generally, the achiral contribution dominates the surface SFG-VS signal, and the pure chiral signal is usually two or three orders of magnitude smaller. Therefore, it has been difficult to make quantitative detection and analysis of the chiral contributions to the surface SFG- VS signal. In the TPA method, by varying together the polarization angles of the incoming visible light and the sum frequency signal at fixed s or p polarization of the incoming infrared beam, the polarization dependent SFG signal can give not only direct signature of the chiral contribution in the total SFG-VS signal, but also the accurate measurement of the chiral and achiral components in the surface SFG signal. The general description of the TPA method is presented and the experiment test of the TPA approach is also presented for the SFG-VS from the S- and R-limonene chiral liquid surfaces. The most accurate degree of chiral excess values thus obtained for the 2878 cm⁻¹ spectral peak of the S- and R-limonene liquid surfaces are (23.7±0.4)% and ({25.4±1.3)%, respectively.

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

    PubMed Central

    Yang, Jaeyoung; Palla, Mirko; Bosco, Filippo Giacomo; Rindzevicius, Tomas; Alstrøm, Tommy Sonne; Schmidt, Michael Stenbæk; Boisen, Anja; Ju, Jingyue; Lin, Qiao

    2013-01-01

    Surface-enhanced Raman spectroscopy (SERS) has been used in a variety of biological applications due to its high sensitivity and specificity. Here, we report a SERS-based biosensing approach for quantitative detection of biomolecules. A SERS substrate bearing gold-decorated silicon nanopillars 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. PMID:23713574

  10. [Quantitative Analysis of Dimethoate Pesticide Residues in Honey by Surface-Enhanced Raman Spectroscopy].

    PubMed

    Sun, Xu-dong; Dong, Xiao-ling

    2015-06-01

    The feasibility of a combination method of surface-enhanced Raman spectroscopy (SERS) technology and linear regression algorithm was investigated for rapid quantitative analysis of pesticide residues in honey. The total of 30 samples was applied in the experiment with dimethoate pesticide residues range from 1 ppm to 10 ppm. The samples were divided into calibration set (20) and prediction set (10). The substrate of Klarite with an inverted pyramidal structure was adopted for improvement of the relative intensity of the majority of Raman shift peaks. The comparative analysis was carried out between SERS spectra of dimethoate pesticide residues in honey samples and conventional Raman spectra of dimethoate standard sample. And four characteristic Raman shift peaks at the wavenumbers of 867, 1 065, 1 317 and 1 453 cm(-1) were found, which were related with the vibrational information of dimethoate molecule. The relationship was developed by linear regression algorithm between the intensity of Raman shift and the concentration of dimethoate pesticide residues. The 10 new samples in the prediction set were applied to evaluate the performance of the models. By comparison, the optimal model was obtained with the characteristic Raman shift peak of 867 cm(-1). The higher correlation coefficient of prediction of 0.984 and lower root mean square error of prediction of 0.663 ppm were obtained. The detection limit of this method was 2 ppm, which was close to the maximum levels of pesticide residue detection limits. Experimental results showed that it was feasible to rapidly analyze quantitative of pesticide residues in honey with the combination method of SERS technology and linear regression algorithm. Compared with the conventional method coupled with the suitable pretreatment, the combination method of SERS technology and linear regression method could analyze the dimethoate pesticide residues in honey, and it also provided an optional method for rapid quantitative analysis

  11. [Qualitative-Quantitative Analysis of Rice Bran Oil Adulteration Based on Laser Near Infrared Spectroscopy].

    PubMed

    Tu, Bin; Song, Zhi-qiang; Zheng, Xiao; Zeng, Lu-lu; Yin, Cheng; He, Dong-ping; Qi, Pei-shi

    2015-06-01

    The purpose of this study is mainly to have qualitative-quantitative analysis on the adulteration in rice bran oil by near-infrared spectroscopy analytical technology combined with chemo metrics methods. The author configured 189 adulterated oil samples according to the different mass ratios by selecting rice bran oil as base oil and choosing soybean oil, corn oil, colza oil, and waste oil of catering industry as adulterated oil. Then, the spectral data of samples was collected by using near-infrared spectrometer, and it was pre-processed through the following methods, including without processing, Multiplicative Scatter Correction(MSC), Orthogonal Signal Correction(OSC), Standard Normal Variate and Standard Normal Variate transformation DeTrending(SNV_DT). Furthermore, this article extracted characteristic wavelengths of the spectral datum from the pre-processed date by Successive Projections Algorithm(SPA), established qualitatively classified calibration methods of adulterated oil through classification method of Support Vector Machine(SVM), optimized model parameters(C, g) by Mesh Search Algorithm and determined the optimal process condition. In extracting characteristic wavelengths of the spectral datum from pretreatment by Backward interval Partial Least Squares(BiPLS) and SPA, quantitatively classified calibration models of adulterated oil through Partial Least Squares(PLS) and Support Vector Machine Regression(SVR) was established respectively. In the end, the author optimized the combination of model parameters(C, g) by Mesh Search Algorithm and determined the optimal parameter model. According to the analysis, the accuracy of prediction set and calibration set for SVC model reached 95% and 100% respectively. Compared with the prediction of the adulteration oil content of rice bran oil which was established by the PLS model, the SVR model is the better one, although both of them could implement the content prediction. Furthermore, the correlation

  12. Fast quantitative retardance imaging of biological samples using quadri-wave interferometry (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Aknoun, Sherazade; Bon, Pierre; Savatier, Julien; Monneret, Serge; Wattellier, Benoit F.

    2016-03-01

    We describe the use of polarized spatially coherent illumination to perform linear retardance imaging and measurements of semi-transparent biological samples using a quantitative phase imaging technique [1]. Quantitative phase imaging techniques [2-5] are used in microscopy for the imaging of semi-transparent samples and gives information about the optical path difference (OPD). The strength of those techniques is their non-invasive (the sample is not labelled) and fast approach. However, this high contrast is non-specific and cannot be linked to specific properties of the sample. To overcome this limitation, we propose to use polarized light in combination with QPI. Indeed, anisotropy has been used to reveal ordered fibrous structures in biological samples without any staining or labelling with polarized light microscopy [6-8]. Recent studies have shown polarimetry as a potential diagnostic tool for various dermatological diseases on thick tissue samples [9]. Particularly, specific collagen fibers spatial distribution has been demonstrated to be a signature for the optical diagnosis and prognosis of cancer in tissues [10]. In this paper, we describe a technical improvement of our technique based on high-resolution quadri-wave lateral shearing interferometry (QWLSI) and liquid crystal retarder to perform quantitative linear birefringence measurements on biological samples. The system combines a set of quantitative phase images with different excitation polarizations to create birefringence images. These give information about the local retardance and orientation of biological anisotropic components. We propose using a commercial QWLSI [11] (SID4Bio, Phasics SA, Saint Aubin, France) directly plugged onto a lateral video port of an inverted microscope (TE2000-U, Nikon, Japan). We are able to take retardance images in less than 1 second which allows us to record dynamic phenomena (living cells study) and make high speed acquisitions to reconstruct tissues virtual

  13. Functional genomics bridges the gap between quantitative genetics and molecular biology

    PubMed Central

    Lappalainen, Tuuli

    2015-01-01

    Deep characterization of molecular function of genetic variants in the human genome is becoming increasingly important for understanding genetic associations to disease and for learning to read the regulatory code of the genome. In this paper, I discuss how recent advances in both quantitative genetics and molecular biology have contributed to understanding functional effects of genetic variants, lessons learned from eQTL studies, and future challenges in this field. PMID:26430152

  14. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 1. Structures of DNA

    SciTech Connect

    Not Available

    1983-01-01

    The proceedings for the 47th Annual Cold Spring Harbor Symposia on Quantitative Biology are presented. This symposium focused on the Structure of DNA. Topics presented covered research in the handedness of DNA, conformational analysis, chemically modified DNA, chemical synthesis of DNA, DNA-protein interactions, DNA within nucleosomes, DNA methylation, DNA replication, gyrases and topoisomerases, recombining and mutating DNA, transcription of DNA and its regulation, the organization of genes along DNA, repetitive DNA and pseudogenes, and origins of replication, centromeres, and teleomeres.

  15. Functional genomics bridges the gap between quantitative genetics and molecular biology.

    PubMed

    Lappalainen, Tuuli

    2015-10-01

    Deep characterization of molecular function of genetic variants in the human genome is becoming increasingly important for understanding genetic associations to disease and for learning to read the regulatory code of the genome. In this paper, I discuss how recent advances in both quantitative genetics and molecular biology have contributed to understanding functional effects of genetic variants, lessons learned from eQTL studies, and future challenges in this field.

  16. Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology.

    PubMed

    Theophilou, Georgios; Paraskevaidi, Maria; Lima, Kássio M G; Kyrgiou, Maria; Martin-Hirsch, Pierre L; Martin, Francis L

    2015-05-01

    The complex processes driving cancer have so far impeded the discovery of dichotomous biomarkers associated with its initiation and progression. Reductionist approaches utilizing 'omics' technologies have met some success in identifying molecular alterations associated with carcinogenesis. Systems biology is an emerging science that combines high-throughput investigation techniques to define the dynamic interplay between regulatory biological systems in response to internal and external cues. Vibrational spectroscopy has the potential to play an integral role within systems biology research approaches. It is capable of examining global models of carcinogenesis by scrutinizing chemical bond alterations within molecules. The application of infrared or Raman spectroscopic approaches coupled with computational analysis under the systems biology umbrella can assist the transition of biomarker research from the molecular level to the system level. The comprehensive representation of carcinogenesis as a multilevel biological process will inevitably revolutionize cancer-related healthcare by personalizing risk prediction and prevention.

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  18. 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

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

    2006-01-01

    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…

  19. Graphene-based platform for nano-scale infrared near-field spectroscopy of biological materials

    NASA Astrophysics Data System (ADS)

    Khatib, Omar; Wood, Joshua D.; Doidge, Gregory P.; Damhorst, Gregory L.; Rangarajan, Aniruddh; Bashir, Rashid; Pop, Eric; Lyding, Joseph W.; Basov, Dimitri N.

    2014-03-01

    In biological and life sciences, Fourier Transform Infrared (FTIR) spectroscopy serves as a noninvasive probe of vibrational fingerprints used to identify chemical and molecular species. Near-field spectroscopy, based on the illumination of an atomic force microscope (AFM) tip with an infrared laser, allows for determination of IR properties of a material at nanometer length scales. However, application of near-field IR spectroscopy to most biological systems has thus far been elusive. Physiological conditions required for experimentation are incompatible with typical implementations of nano-FTIR. Recently it became possible to trap water and small biomolecules underneath large-area graphene sheets grown by chemical vapor deposition (CVD). The graphene layer serves as an IR-transparent cover that allows for a near-field interrogation of the underlying layers. We present near-field nano-imaging and spectroscopy data of unencapsulated Tobacco Mosaic Viruses (TMV), compared to those sandwiched between two large-area graphene sheets, and discuss the applicability of near-field IR spectroscopy to trapped biomolecules in aqueous environments.

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

    NASA Astrophysics Data System (ADS)

    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

    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

  1. [Quantitative analysis of thiram by surface-enhanced raman spectroscopy combined with feature extraction Algorithms].

    PubMed

    Zhang, Bao-hua; Jiang, Yong-cheng; Sha, Wen; Zhang, Xian-yi; Cui, Zhi-feng

    2015-02-01

    Three feature extraction algorithms, such as the principal component analysis (PCA), the discrete cosine transform (DCT) and the non-negative factorization (NMF), were used to extract the main information of the spectral data in order to weaken the influence of the spectral fluctuation on the subsequent quantitative analysis results based on the SERS spectra of the pesticide thiram. Then the extracted components were respectively combined with the linear regression algorithm--the partial least square regression (PLSR) and the non-linear regression algorithm--the support vector machine regression (SVR) to develop the quantitative analysis models. Finally, the effect of the different feature extraction algorithms on the different kinds of the regression algorithms was evaluated by using 5-fold cross-validation method. The experiments demonstrate that the analysis results of SVR are better than PLSR for the non-linear relationship between the intensity of the SERS spectrum and the concentration of the analyte. Further, the feature extraction algorithms can significantly improve the analysis results regardless of the regression algorithms which mainly due to extracting the main information of the source spectral data and eliminating the fluctuation. Additionally, PCA performs best on the linear regression model and NMF is best on the non-linear model, and the predictive error can be reduced nearly three times in the best case. The root mean square error of cross-validation of the best regression model (NMF+SVR) is 0.0455 micormol x L(-1) (10(-6) mol x L(-1)), and it attains the national detection limit of thiram, so the method in this study provides a novel method for the fast detection of thiram. In conclusion, the study provides the experimental references the selecting the feature extraction algorithms on the analysis of the SERS spectrum, and some common findings of feature extraction can also help processing of other kinds of spectroscopy.

  2. Quantitative Fluorescence Studies in Living Cells: Extending Fluorescence Fluctuation Spectroscopy to Peripheral Membrane Proteins

    NASA Astrophysics Data System (ADS)

    Smith, Elizabeth Myhra

    The interactions of peripheral membrane proteins with both membrane lipids and proteins are vital for many cellular processes including membrane trafficking, cellular signaling, and cell growth/regulation. Building accurate biophysical models of these processes requires quantitative characterization of the behavior of peripheral membrane proteins, yet methods to quantify their interactions inside living cells are very limited. Because peripheral membrane proteins usually exist both in membrane-bound and cytoplasmic forms, the separation of these two populations is a key challenge. This thesis aims at addressing this challenge by extending fluorescence fluctuation spectroscopy (FFS) to simultaneously measure the oligomeric state of peripheral membrane proteins in the cytoplasm and at the plasma membrane. We developed a new method based on z-scan FFS that accounts for the fluorescence contributions from cytoplasmic and membrane layers by incorporating a fluorescence intensity z-scan through the cell. H-Ras-EGFP served as a model system to demonstrate the feasibility of the technique. The resolvability and stability of z-scanning was determined as well as the oligomeric state of H-Ras-EGFP at the plasma membrane and in the cytoplasm. Further, we successfully characterized the binding affinity of a variety of proteins to the plasma membrane by quantitative analysis of the z-scan fluorescence intensity profile. This analysis method, which we refer to as z-scan fluorescence profile deconvoution, was further used in combination with dual-color competition studies to determine the lipid specificity of protein binding. Finally, we applied z-scan FFS to provide insight into the early assembly steps of the HTLV-1 retrovirus.

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

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Ma, Yehao; Wang, Xiaowei

    2012-06-01

    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.

  4. Semi-quantitative analysis of gentian violet by surface-enhanced Raman spectroscopy using silver colloids.

    PubMed

    Liu, Fangfang; Gu, Huaimin; Yuan, Xiaojuan; Dong, Xiao

    2010-11-01

    The viability of the application of surface-enhanced Raman spectroscopy (SERS) to the semi-quantitative analysis of the triphenylmethane dye gentian violet was examined by using activated borohydride-reduced silver colloids. Raman and SERS spectra of aqueous solutions of gentian violet at different pH values were acquired for the first time and equally intense SERS signals were obtained at both acidic and alkaline pH values. Two maxima intensities observed in the pH profile revealed the presence of different ionization states of the dye. The pH conditions for SERS were optimized over the pH range 1 to 12 and the biggest enhancement for SERS of this charged dye was found to be at pH 2.0; thus, this condition was used for semi-quantitative analysis. A good linear correlation was observed for the dependence of the signal intensities of the SERS bands at 1620 cm(-1) (R = 0.999) and 1370 cm(-1) (R = 0.952) on dye concentration over the range 10(-6) to 10(-4) mol/L, using laser excitation at 514.5 nm. At concentrations of dye above 10(-2) mol/L, the concentration dependence of the SERS signals is nonlinear. This is explained as due to the precipitation of metallic silver as well as due to saturation caused by complete coverage of the SERS substrate. A series of intensities of the band at 1620 cm(-1) measured from dye molecules proved that the single-molecule limit of gentian violet is attained at the concentration of 10(-9) mol/L.

  5. Confocal reflectance quantitative phase microscopy system for cell biology studies (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Singh, Vijay Raj; So, Peter T. C.

    2016-03-01

    Quantitative phase microscopy (QPM), used to measure the refractive index, provides the optical path delay measurement at each point of the specimen under study and becomes an active field in biological science. In this work we present development of confocal reflection phase microscopy system to provide depth resolved quantitative phase information for investigation of intracellular structures and other biological specimen. The system hardware development is mainly divided into two major parts. First, creates a pinhole array for parallel confocal imaging of specimen at multiple locations simultaneously. Here a digital micro mirror device (DMD) is used to generate pinhole array by turning on a subset micro-mirrors arranged on a grid. Second is the detection of phase information of confocal imaging foci by using a common path interferometer. With this novel approach, it is possible to measure the nuclei membrane fluctuations and distinguish them from the plasma membrane fluctuations. Further, depth resolved quantitative phase can be correlated to the intracellular contents and 3D map of refractive index measurements.

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

    SciTech Connect

    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

    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.

  7. Quantitative Proton Magnetic Resonance Spectroscopy and Spectroscopic Imaging of the Brain: A Didactic Review

    PubMed Central

    Alger, Jeffry R.

    2011-01-01

    This article presents background information related to methodology for estimating brain metabolite concentration from Magnetic Resonance Spectroscopy (MRS) and Magnetic Resonance Spectroscopic Imaging (MRSI) measurements of living human brain tissue. It reviews progress related to this methodology with emphasis placed on progress reported during the past ten years. It is written for a target audience composed of radiologists and MRI technologists. It describes in general terms the relationship between MRS signal amplitude and concentration. It then presents an overview of the many practical problems associated with deriving concentration solely from absolute measured signal amplitudes and demonstrates how a various signal calibration approaches can be successfully used. The concept of integrated signal amplitude is presented with examples that are helpful for qualitative reading of MRS data as well as for understanding the methodology used for quantitative measurements. The problems associated with the accurate measurement of individual signal amplitudes in brain spectra having overlapping signals from other metabolites and overlapping nuisance signals from water and lipid is presented. Current approaches to obtaining accurate amplitude estimates with least squares fitting software are summarized. PMID:21613876

  8. Hemoglobin consumption by P. falciparum in individual erythrocytes imaged via quantitative phase spectroscopy

    PubMed Central

    Rinehart, Matthew T.; Park, Han Sang; Walzer, Katelyn A.; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Plasmodium falciparum infection causes structural and biochemical changes in red blood cells (RBCs). To quantify these changes, we apply a novel optical technique, quantitative phase spectroscopy (QPS) to characterize individual red blood cells (RBCs) during the intraerythrocytic life cycle of P. falciparum. QPS captures hyperspectral holograms of individual RBCs to measure spectroscopic changes across the visible wavelength range (475–700 nm), providing complex information, i.e. amplitude and phase, about the light field which has interacted with the cell. The complex field provides complimentary information on hemoglobin content and cell mass, which are both found to dramatically change upon infection by P. falciparum. Hb content progressively decreases with parasite life cycle, with an average 72.2% reduction observed for RBCs infected by schizont-stage P. falciparum compared to uninfected cells. Infection also resulted in a 33.1% reduction in RBC’s optical volume, a measure of the cells’ non-aqueous components. Notably, optical volume is only partially correlated with hemoglobin content, suggesting that changes in other dry mass components such as parasite mass may also be assessed using this technique. The unique ability of QPS to discriminate individual healthy and infected cells using spectroscopic changes indicates that the approach can be used to detect disease. PMID:27087557

  9. Quantitative Kα line spectroscopy for energy transport in ultra-intense laser plasma interaction

    NASA Astrophysics Data System (ADS)

    Zhang, Z.; Nishimura, H.; Fujioka, S.; Arikawa, Y.; Nakai, M.; Chen, H.; Park, J.; Williams, G. J.; Ozaki, T.; Shiraga, H.; Kojima, S.; Johzaki, T.; Sunahara, A.; Miyanaga, N.; Kawanaka, J.; Nakata, Y.; Jitsuno, T.; Azechi, H.

    2016-03-01

    Absolute Ka line spectroscopy is proposed for studying laser-plasma interactions taking place in the cone-guided fast ignition targets. X-ray spectra ranging from 20 to 100 keV were quantitatively measured with a Laue spectrometer. The absolute sensitivities of the Laue spectrometer system were calibrated using pre-characterized laser-produced x-ray sources and radioisotopes. The integrated reflectivity for the crystal is in good agreement with predictions by an open code for x-ray diffraction. The energy transfer efficiency from incident laser beams to hot electrons, as the energy transfer agency, is derived as a consequence of this work. The absolute yield of Au and Ta Ka lines were measured in the fast ignition experimental campaign performed at Institute of Laser Engineering, Osaka University. Applying the hot electron spectrum information from the electron spectrometer, an energy transfer efficiency of the incident LFEX [1], a kJ-class PW laser, to hot electrons was derived for a planar and cone-guided geometry.

  10. Hemoglobin consumption by P. falciparum in individual erythrocytes imaged via quantitative phase spectroscopy

    NASA Astrophysics Data System (ADS)

    Rinehart, Matthew T.; Park, Han Sang; Walzer, Katelyn A.; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-04-01

    Plasmodium falciparum infection causes structural and biochemical changes in red blood cells (RBCs). To quantify these changes, we apply a novel optical technique, quantitative phase spectroscopy (QPS) to characterize individual red blood cells (RBCs) during the intraerythrocytic life cycle of P. falciparum. QPS captures hyperspectral holograms of individual RBCs to measure spectroscopic changes across the visible wavelength range (475–700 nm), providing complex information, i.e. amplitude and phase, about the light field which has interacted with the cell. The complex field provides complimentary information on hemoglobin content and cell mass, which are both found to dramatically change upon infection by P. falciparum. Hb content progressively decreases with parasite life cycle, with an average 72.2% reduction observed for RBCs infected by schizont-stage P. falciparum compared to uninfected cells. Infection also resulted in a 33.1% reduction in RBC’s optical volume, a measure of the cells’ non-aqueous components. Notably, optical volume is only partially correlated with hemoglobin content, suggesting that changes in other dry mass components such as parasite mass may also be assessed using this technique. The unique ability of QPS to discriminate individual healthy and infected cells using spectroscopic changes indicates that the approach can be used to detect disease.

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

    PubMed Central

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

    2012-01-01

    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. PMID:20551502

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

    NASA Astrophysics Data System (ADS)

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

    2005-08-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

    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 μg/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.

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

    PubMed

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

    2012-12-01

    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

  15. Absolute quantitative analysis for sorbic acid in processed foods using proton nuclear magnetic resonance spectroscopy.

    PubMed

    Ohtsuki, Takashi; Sato, Kyoko; Sugimoto, Naoki; Akiyama, Hiroshi; Kawamura, Yoko

    2012-07-13

    An analytical method using solvent extraction and quantitative proton nuclear magnetic resonance (qHNMR) spectroscopy was applied and validated for the absolute quantification of sorbic acid (SA) in processed foods. The proposed method showed good linearity. The recoveries for samples spiked at the maximum usage level specified for food in Japan and at 0.13 g kg(-1) (beverage: 0.013 g kg(-1)) were larger than 80%, whereas those for samples spiked at 0.063 g kg(-1) (beverage: 0.0063 g kg(-1)) were between 56.9 and 83.5%. The limit of quantification was 0.063 g kg(-1) for foods (and 0.0063 g kg(-1) for beverages containing Lactobacillus species). Analysis of the SA content of commercial processed foods revealed quantities equal to or greater than those measured using conventional steam-distillation extraction and high-performance liquid chromatography quantification. The proposed method was rapid, simple, accurate, and precise, and provided International System of Units traceability without the need for authentic analyte standards. It could therefore be used as an alternative to the quantification of SA in processed foods using conventional method. PMID:22704472

  16. Absolute quantification for benzoic acid in processed foods using quantitative proton nuclear magnetic resonance spectroscopy.

    PubMed

    Ohtsuki, Takashi; Sato, Kyoko; Sugimoto, Naoki; Akiyama, Hiroshi; Kawamura, Yoko

    2012-09-15

    The absolute quantification method of benzoic acid (BA) in processed foods using solvent extraction and quantitative proton nuclear magnetic resonance spectroscopy was developed and validated. BA levels were determined using proton signals (δ(H) 7.53 and 7.98) referenced to 2-dimethyl-2-silapentane-5-sulfonate-d(6) sodium salt (DSS-d(6)) after simple solvent extraction from processed foods. All recoveries from several kinds of processed foods, spiked at their specified maximum Japanese usage levels (0.6-2.5 g kg(-1)) and at 0.13 g kg(-1) and 0.063 g kg(-1), were greater than 80%. The limit of quantification was confirmed as 0.063 g kg(-1) in processed foods, which was sufficiently low for the purposes of monitoring BA. The accuracy of the proposed method is equivalent to the conventional method using steam-distillation extraction and high-performance liquid chromatography. The proposed method was both rapid and simple. Moreover, it provided International System of Units traceability without the need for authentic analyte standards. Therefore, the proposed method is a useful and practical tool for determining BA levels in processed foods. PMID:22967562

  17. Hemoglobin consumption by P. falciparum in individual erythrocytes imaged via quantitative phase spectroscopy.

    PubMed

    Rinehart, Matthew T; Park, Han Sang; Walzer, Katelyn A; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Plasmodium falciparum infection causes structural and biochemical changes in red blood cells (RBCs). To quantify these changes, we apply a novel optical technique, quantitative phase spectroscopy (QPS) to characterize individual red blood cells (RBCs) during the intraerythrocytic life cycle of P. falciparum. QPS captures hyperspectral holograms of individual RBCs to measure spectroscopic changes across the visible wavelength range (475-700 nm), providing complex information, i.e. amplitude and phase, about the light field which has interacted with the cell. The complex field provides complimentary information on hemoglobin content and cell mass, which are both found to dramatically change upon infection by P. falciparum. Hb content progressively decreases with parasite life cycle, with an average 72.2% reduction observed for RBCs infected by schizont-stage P. falciparum compared to uninfected cells. Infection also resulted in a 33.1% reduction in RBC's optical volume, a measure of the cells' non-aqueous components. Notably, optical volume is only partially correlated with hemoglobin content, suggesting that changes in other dry mass components such as parasite mass may also be assessed using this technique. The unique ability of QPS to discriminate individual healthy and infected cells using spectroscopic changes indicates that the approach can be used to detect disease. PMID:27087557

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

    NASA Astrophysics Data System (ADS)

    Fan, Yuxia; Cheng, Fang; Xie, Lijuan

    2010-04-01

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

  19. Absolute quantification for benzoic acid in processed foods using quantitative proton nuclear magnetic resonance spectroscopy.

    PubMed

    Ohtsuki, Takashi; Sato, Kyoko; Sugimoto, Naoki; Akiyama, Hiroshi; Kawamura, Yoko

    2012-09-15

    The absolute quantification method of benzoic acid (BA) in processed foods using solvent extraction and quantitative proton nuclear magnetic resonance spectroscopy was developed and validated. BA levels were determined using proton signals (δ(H) 7.53 and 7.98) referenced to 2-dimethyl-2-silapentane-5-sulfonate-d(6) sodium salt (DSS-d(6)) after simple solvent extraction from processed foods. All recoveries from several kinds of processed foods, spiked at their specified maximum Japanese usage levels (0.6-2.5 g kg(-1)) and at 0.13 g kg(-1) and 0.063 g kg(-1), were greater than 80%. The limit of quantification was confirmed as 0.063 g kg(-1) in processed foods, which was sufficiently low for the purposes of monitoring BA. The accuracy of the proposed method is equivalent to the conventional method using steam-distillation extraction and high-performance liquid chromatography. The proposed method was both rapid and simple. Moreover, it provided International System of Units traceability without the need for authentic analyte standards. Therefore, the proposed method is a useful and practical tool for determining BA levels in processed foods.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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 3 g/100 g. Classes of components - aromatic anhydrides and alcohols - used in alkyd resin synthesis were also successfully quantified, with standard uncertainties in the range of 2-3 g/100 g. 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.

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

    PubMed

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

    2014-12-10

    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

  2. Quantitative estimation of carbonation and chloride penetration in reinforced concrete by laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Eto, Shuzo; Matsuo, Toyofumi; Matsumura, Takuro; Fujii, Takashi; Tanaka, Masayoshi Y.

    2014-11-01

    The penetration profile of chlorine in a reinforced concrete (RC) specimen was determined by laser-induced breakdown spectroscopy (LIBS). The concrete core was prepared from RC beams with cracking damage induced by bending load and salt water spraying. LIBS was performed using a specimen that was obtained by splitting the concrete core, and the line scan of laser pulses gave the two-dimensional emission intensity profiles of 100 × 80 mm2 within one hour. The two-dimensional profile of the emission intensity suggests that the presence of the crack had less effect on the emission intensity when the measurement interval was larger than the crack width. The chlorine emission spectrum was measured without using the buffer gas, which is usually used for chlorine measurement, by collinear double-pulse LIBS. The apparent diffusion coefficient, which is one of the most important parameters for chloride penetration in concrete, was estimated using the depth profile of chlorine emission intensity and Fick's law. The carbonation depth was estimated on the basis of the relationship between carbon and calcium emission intensities. When the carbon emission intensity was statistically higher than the calcium emission intensity at the measurement point, we determined that the point was carbonated. The estimation results were consistent with the spraying test results using phenolphthalein solution. These results suggest that the quantitative estimation by LIBS of carbonation depth and chloride penetration can be performed simultaneously.

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

    PubMed Central

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

    1999-01-01

    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. PMID:9876167

  4. Quantitative identification of metastable magnesium carbonate minerals by solid-state 13C NMR spectroscopy.

    PubMed

    Moore, Jeremy K; Surface, J Andrew; Brenner, Allison; Wang, Louis S; Skemer, Philip; Conradi, Mark S; Hayes, Sophia E

    2015-01-01

    In the conversion of CO2 to mineral carbonates for the permanent geosequestration of CO2, there are multiple magnesium carbonate phases that are potential reaction products. Solid-state (13)C NMR is demonstrated as an effective tool for distinguishing magnesium carbonate phases and quantitatively characterizing magnesium carbonate mixtures. Several of these mineral phases include magnesite, hydromagnesite, dypingite, and nesquehonite, which differ in composition by the number of waters of hydration or the number of crystallographic hydroxyl groups. These carbonates often form in mixtures with nearly overlapping (13)C NMR resonances which makes their identification and analysis difficult. In this study, these phases have been investigated with solid-state (13)C NMR spectroscopy, including both static and magic-angle spinning (MAS) experiments. Static spectra yield chemical shift anisotropy (CSA) lineshapes that are indicative of the site-symmetry variations of the carbon environments. MAS spectra yield isotropic chemical shifts for each crystallographically inequivalent carbon and spin-lattice relaxation times, T1, yield characteristic information that assist in species discrimination. These detailed parameters, and the combination of static and MAS analyses, can aid investigations of mixed carbonates by (13)C NMR.

  5. Quantitative analysis of metformin in antidiabetic tablets by laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Contreras, U.; Ornelas-Soto, N.; Meneses-Nava, M. A.; Barbosa-García, O.; López-de-Alba, P. L.; López-Martínez, L.

    2011-09-01

    Nowadays the production of counterfeit and low quality drugs affects human health and generates losses to pharmaceutical industries and tax revenue losses to government. Currently there are several methods for pharmaceutical product analysis; nevertheless, most of them depend on complex and time consuming steps such as sample preparation. In contrast to conventional methods, Laser-induced breakdown spectroscopy (LIBS) is evaluated as a potential analytical technique for the rapid screening and quality control of anti-diabetic solid formulations. In this paper authors propose a simple method to analyze qualitatively and quantitatively Active Pharmaceutical Ingredients (APIs) such as Metformin hydrochloride. The authors used ten nanosecond duration pulses (FWHM) from a Nd:YAG laser produces the induced breakdown for the analysis. Light is collected and focused into a Cerny-Turner spectrograph and dispersed into an ICCD camera for its detection. We used atomic emissions from Chlorine atoms present only in APIs as analyte signal. The analysis was improved using Bromine as internal standard. Linear calibration curves from synthetic samples were prepared achieving linearity higher than 99%. Our results were compared with HPLC results and validation was performed by statistical methods. The validation analysis suggests that both methods have no significant differences i.e., the proposed method can be implemented for monitoring the pharmaceutical production process in-situ in real time or for inspection and recognition of authenticity.

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

    PubMed

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

    2011-02-01

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

  7. Quantitative determination of calcium, magnesium, and zinc in fingernails by laser-induced breakdown spectroscopy.

    PubMed

    Rusak, David A; Zeleniak, Ann E; Obuhosky, Jillian L; Holdren, Scott M; Noldy, Craig A

    2013-12-15

    Quantitative determination of Ca, Mg, and Zn in fingernails was performed with laser-induced breakdown spectroscopy. Two different methods of producing solid standards for calibration were explored - preparation of keratin pellets and deposition of aqueous solutions to filter papers. Measurements of the temperature and electron density of the plasma produced on keratin pellets, filter paper, and nails were performed, and it was determined that the standards prepared on filter paper gave plasma temperatures and electron densities closer to those observed on the nails. The ablation rate of the filter paper was also more similar to that of the nails. Using calibration curves produced using these filter paper standards, Ca, Mg, and Zn were determined in fingernails of 11 subjects. For comparison, the same samples were digested and atomic absorption was used to determine the same three elements. The differences in results are discussed in light of sample homogeneity and instrumental precision; the best agreement was obtained for determination of Zn. The work suggests that the filter paper method of standard preparation may be appropriate for LIBS analysis of other samples that give relatively low temperature, low electron density plasmas (i.e., polymers).

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

    DOEpatents

    Alfano, Robert R.; Wang, Wubao

    2003-05-06

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-06-01

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

  10. Application of multivariate analysis and vibrational spectroscopy in classification of biological systems

    NASA Astrophysics Data System (ADS)

    Salman, A.; Shufan, E.; Lapidot, I.; Tsror, L.; Zeiri, L.; Sahu, R. K.; Moreh, R.; Mordechai, S.; Huleihel, M.

    2015-12-01

    Fourier Transform Infrared (FTIR) and Raman spectroscopies have emerged as powerful tools for chemical analysis. This is due to their ability to provide detailed information about the spatial distribution of chemical composition at the molecular level. A biological sample, i.e. bacteria or fungi, has a typical spectrum. This spectral fingerprint, characterizes the sample and can therefore be used for differentiating between biology samples which belong to different groups, i.e., several different isolates of a given fungi. When the spectral differences between the groups are minute, multivariate analysis should be used to provide a good differentiation. We hereby review several results which demonstrate the differentiation success obtained by combining spectroscopy measurements and multivariate analysis.

  11. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    PubMed Central

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-01-01

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope. PMID:26961578

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

    SciTech Connect

    Not Available

    1993-12-31

    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.

  13. Mapping biological composition through quantitative phase and absorption X-ray ptychography

    NASA Astrophysics Data System (ADS)

    Jones, Michael W. M.; Elgass, Kirstin; Junker, Mark D.; Luu, Mac B.; Ryan, Michael T.; Peele, Andrew G.; van Riessen, Grant A.

    2014-10-01

    Isolating compositional information in biological X-ray imaging can be problematic as such information is conflated with thickness and density variations when viewing in projection through a sample. We demonstrate an effective method for identifying variations in material composition by simultaneously using the quantitative phase and magnitude images provided through soft X-ray ptychography. Using this approach we show significantly increased contrast and improved reliability of the identification of intracellular features from uncharacterised samples. While demonstrated for X-ray ptychography, this method is immediately applicable to electron and optical microscopy methods where the complex transmission function of the sample is recovered.

  14. Near-infrared spectroscopy and hyperspectral imaging: non-destructive analysis of biological materials.

    PubMed

    Manley, Marena

    2014-12-21

    Near-infrared (NIR) spectroscopy has come of age and is now prominent among major analytical technologies after the NIR region was discovered in 1800, revived and developed in the early 1950s and put into practice in the 1970s. Since its first use in the cereal industry, it has become the quality control method of choice for many more applications due to the advancement in instrumentation, computing power and multivariate data analysis. NIR spectroscopy is also increasingly used during basic research performed to better understand complex biological systems, e.g. by means of studying characteristic water absorption bands. The shorter NIR wavelengths (800-2500 nm), compared to those in the mid-infrared (MIR) range (2500-15 000 nm) enable increased penetration depth and subsequent non-destructive, non-invasive, chemical-free, rapid analysis possibilities for a wide range of biological materials. A disadvantage of NIR spectroscopy is its reliance on reference methods and model development using chemometrics. NIR measurements and predictions are, however, considered more reproducible than the usually more accurate and precise reference methods. The advantages of NIR spectroscopy contribute to it now often being favoured over other spectroscopic (colourimetry and MIR) and analytical methods, using chemicals and producing chemical waste, such as gas chromatography (GC) and high performance liquid chromatography (HPLC). This tutorial review intends to provide a brief overview of the basic theoretical principles and most investigated applications of NIR spectroscopy. In addition, it considers the recent development, principles and applications of NIR hyperspectral imaging. NIR hyperspectral imaging provides NIR spectral data as a set of images, each representing a narrow wavelength range or spectral band. The advantage compared to NIR spectroscopy is that, due to the additional spatial dimension provided by this technology, the images can be analysed and visualised as

  15. Near-infrared spectroscopy and hyperspectral imaging: non-destructive analysis of biological materials.

    PubMed

    Manley, Marena

    2014-12-21

    Near-infrared (NIR) spectroscopy has come of age and is now prominent among major analytical technologies after the NIR region was discovered in 1800, revived and developed in the early 1950s and put into practice in the 1970s. Since its first use in the cereal industry, it has become the quality control method of choice for many more applications due to the advancement in instrumentation, computing power and multivariate data analysis. NIR spectroscopy is also increasingly used during basic research performed to better understand complex biological systems, e.g. by means of studying characteristic water absorption bands. The shorter NIR wavelengths (800-2500 nm), compared to those in the mid-infrared (MIR) range (2500-15 000 nm) enable increased penetration depth and subsequent non-destructive, non-invasive, chemical-free, rapid analysis possibilities for a wide range of biological materials. A disadvantage of NIR spectroscopy is its reliance on reference methods and model development using chemometrics. NIR measurements and predictions are, however, considered more reproducible than the usually more accurate and precise reference methods. The advantages of NIR spectroscopy contribute to it now often being favoured over other spectroscopic (colourimetry and MIR) and analytical methods, using chemicals and producing chemical waste, such as gas chromatography (GC) and high performance liquid chromatography (HPLC). This tutorial review intends to provide a brief overview of the basic theoretical principles and most investigated applications of NIR spectroscopy. In addition, it considers the recent development, principles and applications of NIR hyperspectral imaging. NIR hyperspectral imaging provides NIR spectral data as a set of images, each representing a narrow wavelength range or spectral band. The advantage compared to NIR spectroscopy is that, due to the additional spatial dimension provided by this technology, the images can be analysed and visualised as

  16. Introduction to the Symposium "Leading Students and Faculty to Quantitative Biology through Active Learning".

    PubMed

    Waldrop, Lindsay D; Miller, Laura A

    2015-11-01

    The broad aim of this symposium and set of associated papers is to motivate the use of inquiry-based, active-learning teaching techniques in undergraduate quantitative biology courses. Practical information, resources, and ready-to-use classroom exercises relevant to physicists, mathematicians, biologists, and engineers are presented. These resources can be used to address the lack of preparation of college students in STEM fields entering the workforce by providing experience working on interdisciplinary and multidisciplinary problems in mathematical biology in a group setting. Such approaches can also indirectly help attract and retain under-represented students who benefit the most from "non-traditional" learning styles and strategies, including inquiry-based, collaborative, and active learning.

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

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.

    2010-01-01

    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.

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

    PubMed

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

    2013-11-01

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

  19. Infrared Spectroscopy as a Versatile Analytical Tool for the Quantitative Determination of Antioxidants in Agricultural Products, Foods and Plants

    PubMed Central

    Cozzolino, Daniel

    2015-01-01

    Spectroscopic methods provide with very useful qualitative and quantitative information about the biochemistry and chemistry of antioxidants. Near infrared (NIR) and mid infrared (MIR) spectroscopy are considered as powerful, fast, accurate and non-destructive analytical tools that can be considered as a replacement of traditional chemical analysis. In recent years, several reports can be found in the literature demonstrating the usefulness of these methods in the analysis of antioxidants in different organic matrices. This article reviews recent applications of infrared (NIR and MIR) spectroscopy in the analysis of antioxidant compounds in a wide range of samples such as agricultural products, foods and plants. PMID:26783838

  20. Quantitative Analysis of Naturally Colored Cotton and White Cotton Blends by UV-VIS Diffuse Reflectance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hu, X.; Zhang, Q.; Yu, H.; Zhao, D.; Dong, S.; Zhou, W.; Tang, Z.

    2015-01-01

    A new method was discussed to quantitatively analyze the blend ratio of naturally colored cotton (NCC) and white cotton (WC) by UV-vis diffuse reflectance spectroscopy (UV-vis DRS). Three kinds of spectroscopy parameters, diffuse reflectance, reflection absorbance, and the K-M function, were used to correlate them with the blend ratio of NCC/ WC fibers. The results showed that diffuse reflectance and blending ratio had the highest correlation coefficients. Therefore this method can be widely used to quantify the blending ratio of NCC/WC fibers as a result of its greater accuracy and simplicity compared to traditional detection methods.

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

    SciTech Connect

    Robert P. Lucht

    2005-03-09

    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

  2. 59. Cold Spring Harbor symposium on quantitative biology: Molecular genetics of cancer

    SciTech Connect

    1994-12-31

    Investigation of the mechanistic aspects of cancer has its roots in the studies on tumor viruses and their effects on cell proliferation, function, and growth. This outstanding progress was well documented in previous Cold Spring Harbor Symposia on Quantitative Biology. In the early to mid 1980s, progress on the development of chromosome mapping strategies and the accumulation of DNA probes that identified polymorphisms, encouraged by the international Human Genome Project, enabled the identification of other genes that contributed to familial inheritance of high susceptibility to specific cancers. This approach was very successful and led to a degree of optimism that one aspect of cancer, the multistep genetic process from early neoplasia to metastatic tumors, was beginning to be understood. It therefore seemed appropriate that the 59th Symposium on Quantitative Biology focus attention on the Molecular Genetics of Cancer. The concept was to combine the exciting progress on the identification of new genetic alterations in human tumor cells with studies on the function of the cancer gene products and how they go awry in tumor cells.

  3. Influence of drinking water composition on quantitation and biological activity of dissolved microcystin (cyanotoxin).

    PubMed

    Oliveira, Ana C P; Magalhães, Valéria F; Soares, Raquel M; Azevedo, Sandra M F O

    2005-04-01

    Toxic cyanobacteria in aquatic environments have been implicated in many poisoning incidents of livestock, wildlife, and domestic animals. Microcystins (MCYSTs) in water supplies represent a risk to public health. This work investigated the effect of water composition on the quantitation and biological activity of MCYSTs analyzed by different methods (HPLC, ELISA, and protein phosphatase 1 inhibition assay). Different MCYST concentrations were added to deionized water and quantified, confirming the efficiency of these analytical methods. MCYST concentrations diluted in drinking water had reduced detection by all methods tested. The drinking water used contained a free chlorine concentration of 2.5 mg/L and an Fe concentration of 0.45 mg/L, and the conductivity was 69.8 microS cm(-1), whereas in deionized water, free chlorine and Fe were not detectable, and the conductivity was 1.6 microS cm(-1). Drinking water also interfered with the biological activity of MYCSTs, as these toxins showed reduced protein phosphatase-1 inhibition. A free chlorine concentration of 2.5 mg/L in deionized water was completely effective in preventing any detection of 10 microg/L of added MCYSTs. Fe and Al ions also were very effective in reducing MCYST detection. The chemical composition of drinking water thus affected MCYST detection, indicating a significant reduction in quantitation of this molecule either because of its decomposition or through complexation with metal ions.

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

    NASA Astrophysics Data System (ADS)

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

    2005-09-01

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

  5. Quantitative determination and classification of energy drinks using near-infrared spectroscopy.

    PubMed

    Rácz, Anita; Héberger, Károly; Fodor, Marietta

    2016-09-01

    Almost a hundred commercially available energy drink samples from Hungary, Slovakia, and Greece were collected for the quantitative determination of their caffeine and sugar content with FT-NIR spectroscopy and high-performance liquid chromatography (HPLC). Calibration models were built with partial least-squares regression (PLSR). An HPLC-UV method was used to measure the reference values for caffeine content, while sugar contents were measured with the Schoorl method. Both the nominal sugar content (as indicated on the cans) and the measured sugar concentration were used as references. Although the Schoorl method has larger error and bias, appropriate models could be developed using both references. The validation of the models was based on sevenfold cross-validation and external validation. FT-NIR analysis is a good candidate to replace the HPLC-UV method, because it is much cheaper than any chromatographic method, while it is also more time-efficient. The combination of FT-NIR with multidimensional chemometric techniques like PLSR can be a good option for the detection of low caffeine concentrations in energy drinks. Moreover, three types of energy drinks that contain (i) taurine, (ii) arginine, and (iii) none of these two components were classified correctly using principal component analysis and linear discriminant analysis. Such classifications are important for the detection of adulterated samples and for quality control, as well. In this case, more than a hundred samples were used for the evaluation. The classification was validated with cross-validation and several randomization tests (X-scrambling). Graphical Abstract The way of energy drinks from cans to appropriate chemometric models.

  6. Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions

    NASA Astrophysics Data System (ADS)

    Olivieri, Giorgia; Parry, Krista M.; Powell, Cedric J.; Tobias, Douglas J.; Brown, Matthew A.

    2016-04-01

    Over the past decade, energy-dependent ambient pressure X-ray photoelectron spectroscopy (XPS) has emerged as a powerful analytical probe of the ion spatial distributions at the vapor (vacuum)-aqueous electrolyte interface. These experiments are often paired with complementary molecular dynamics (MD) simulations in an attempt to provide a complete description of the liquid interface. There is, however, no systematic protocol that permits a straightforward comparison of the two sets of results. XPS is an integrated technique that averages signals from multiple layers in a solution even at the lowest photoelectron kinetic energies routinely employed, whereas MD simulations provide a microscopic layer-by-layer description of the solution composition near the interface. Here, we use the National Institute of Standards and Technology database for the Simulation of Electron Spectra for Surface Analysis (SESSA) to quantitatively interpret atom-density profiles from MD simulations for XPS signal intensities using sodium and potassium iodide solutions as examples. We show that electron inelastic mean free paths calculated from a semi-empirical formula depend strongly on solution composition, varying by up to 30% between pure water and concentrated NaI. The XPS signal thus arises from different information depths in different solutions for a fixed photoelectron kinetic energy. XPS signal intensities are calculated using SESSA as a function of photoelectron kinetic energy (probe depth) and compared with a widely employed ad hoc method. SESSA simulations illustrate the importance of accounting for elastic-scattering events at low photoelectron kinetic energies (<300 eV) where the ad hoc method systematically underestimates the preferential enhancement of anions over cations. Finally, some technical aspects of applying SESSA to liquid interfaces are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2006-06-01

    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.

  8. Quantitative UV spectroscopy of polyynes and cyanopolyynes and their predicted abundances in CRL 618 and Titan

    NASA Astrophysics Data System (ADS)

    Yves, Benilan

    Polyynes and cyanopolyynes (linear molecules with general formula C2n+2 H2 and HC2n+1 N respectively) are important organic molecules in astrophysical environments since they have been proposed to be the main link between the observed gas phase molecules and the carbon soot. Polyynes and cyanopolyynes are observed outside the solar system in various astrophysical objects as the young proto-planetary nebula CRL 618 where C4 H2 , C6 H2 , HC3 N and HC5 N were quantified. Furthermore, cyanopolyynes as long as HC11 N have been detected in the interstellar medium. Polyynes are probably also present there but the absence of a permanent dipole moment precludes their detection in the radio domain. In Saturn's moon Titan, diacetylene and cyanoacetylene are the only members of the polyyne and cyanopolyyne families which have been detected. Quantitative spectroscopy of polyynes and cyanopolyynes in the ultraviolet domain is essential for photochemical modeling and spectroscopic parameters for C4 H2 , C6 H2 , C8 H2 and HC3 N and HC5 N were lacking to calculate their photolysis rates. Consequently, we have undertaken for those molecules systematic absorption cross section measurements at low temperatures representative of CRL 618 and Titan environments. We will present the low temperature absorption cross sections of the first members of the polyyne and cyanopolyyne families and show their temperature dependencies. Using a simplified photochemical model for polyynes and cyanopolyynes in Titan and CRL 618, we predict their relative abundances and compare them with the observed values. For longer polyynes and cyanopolyynes, we have determined ultraviolet spectra by extrapolation and calculated their photolysis rate in both environments. This leads us to predict their abundances in Titan and CRL618.

  9. Quantitative determination and classification of energy drinks using near-infrared spectroscopy.

    PubMed

    Rácz, Anita; Héberger, Károly; Fodor, Marietta

    2016-09-01

    Almost a hundred commercially available energy drink samples from Hungary, Slovakia, and Greece were collected for the quantitative determination of their caffeine and sugar content with FT-NIR spectroscopy and high-performance liquid chromatography (HPLC). Calibration models were built with partial least-squares regression (PLSR). An HPLC-UV method was used to measure the reference values for caffeine content, while sugar contents were measured with the Schoorl method. Both the nominal sugar content (as indicated on the cans) and the measured sugar concentration were used as references. Although the Schoorl method has larger error and bias, appropriate models could be developed using both references. The validation of the models was based on sevenfold cross-validation and external validation. FT-NIR analysis is a good candidate to replace the HPLC-UV method, because it is much cheaper than any chromatographic method, while it is also more time-efficient. The combination of FT-NIR with multidimensional chemometric techniques like PLSR can be a good option for the detection of low caffeine concentrations in energy drinks. Moreover, three types of energy drinks that contain (i) taurine, (ii) arginine, and (iii) none of these two components were classified correctly using principal component analysis and linear discriminant analysis. Such classifications are important for the detection of adulterated samples and for quality control, as well. In this case, more than a hundred samples were used for the evaluation. The classification was validated with cross-validation and several randomization tests (X-scrambling). Graphical Abstract The way of energy drinks from cans to appropriate chemometric models. PMID:27531031

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    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.

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

    SciTech Connect

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

    1998-10-14

    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.

  12. Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions.

    PubMed

    Olivieri, Giorgia; Parry, Krista M; Powell, Cedric J; Tobias, Douglas J; Brown, Matthew A

    2016-04-21

    Over the past decade, energy-dependent ambient pressure X-ray photoelectron spectroscopy(XPS) has emerged as a powerful analytical probe of the ion spatial distributions at the vapor (vacuum)-aqueous electrolyteinterface. These experiments are often paired with complementary molecular dynamics (MD) simulations in an attempt to provide a complete description of the liquidinterface. There is, however, no systematic protocol that permits a straightforward comparison of the two sets of results. XPS is an integrated technique that averages signals from multiple layers in a solution even at the lowest photoelectron kinetic energies routinely employed, whereas MD simulations provide a microscopic layer-by-layer description of the solution composition near the interface. Here, we use the National Institute of Standards and Technology database for the Simulation of Electron Spectra for Surface Analysis (SESSA) to quantitatively interpret atom-density profiles from MD simulations for XPS signal intensities using sodium and potassium iodide solutions as examples. We show that electron inelastic mean free paths calculated from a semi-empirical formula depend strongly on solution composition, varying by up to 30% between pure water and concentrated NaI. The XPS signal thus arises from different information depths in different solutions for a fixed photoelectron kinetic energy. XPS signal intensities are calculated using SESSA as a function of photoelectron kinetic energy (probe depth) and compared with a widely employed ad hoc method. SESSA simulations illustrate the importance of accounting for elastic-scattering events at low photoelectron kinetic energies (<300 eV) where the ad hoc method systematically underestimates the preferential enhancement of anions over cations. Finally, some technical aspects of applying SESSA to liquidinterfaces are discussed. PMID:27389231

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

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

    SciTech Connect

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

    1986-02-15

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

  15. An integrative strategy for quantitative analysis of the N-glycoproteome in complex biological samples

    PubMed Central

    2014-01-01

    Background The complexity of protein glycosylation makes it difficult to characterize glycosylation patterns on a proteomic scale. In this study, we developed an integrated strategy for comparatively analyzing N-glycosylation/glycoproteins quantitatively from complex biological samples in a high-throughput manner. This strategy entailed separating and enriching glycopeptides/glycoproteins using lectin affinity chromatography, and then tandem labeling them with 18O/16O to generate a mass shift of 6 Da between the paired glycopeptides, and finally analyzing them with liquid chromatography-mass spectrometry (LC-MS) and the automatic quantitative method we developed based on Mascot Distiller. Results The accuracy and repeatability of this strategy were first verified using standard glycoproteins; linearity was maintained within a range of 1:10–10:1. The peptide concentration ratios obtained by the self-build quantitative method were similar to both the manually calculated and theoretical values, with a standard deviation (SD) of 0.023–0.186 for glycopeptides. The feasibility of the strategy was further confirmed with serum from hepatocellular carcinoma (HCC) patients and healthy individuals; the expression of 44 glycopeptides and 30 glycoproteins were significantly different between HCC patient and control serum. Conclusions This strategy is accurate, repeatable, and efficient, and may be a useful tool for identification of disease-related N-glycosylation/glycoprotein changes. PMID:24428921

  16. Quantitative measurement of porphyrins in biological tissues and evaluation of tissue porphyrins during toxicant exposures.

    PubMed

    Woods, J S; Miller, H D

    1993-10-01

    Porphyrins are formed in most eukaryotic tissues as intermediates in the biosynthesis of heme. Assessment of changes in tissue porphyrin levels occurring in response to the actions of various drugs or toxicants is potentially useful in the evaluation of chemical exposures and effects. The present paper describes a rapid and sensitive method for the extraction and quantitation of porphyrins in biological tissues which overcomes difficulties encountered in previously described methods, particularly the loss of porphyrins during extraction and interference of porphyrin quantitation by coeluting fluorescent tissue constituents. In this procedure 8- through 2-carboxyl porphyrins are quantitatively extracted from tissue homogenates using HCl and methanol and are subsequently separated from potentially interfering contaminants by sequential methanol/phosphate elution on a C-18 preparatory column. Porphyrins are then separated and measured by reversed-phase high-performance liquid chromatography and spectrofluorometric techniques. Recovery of tissue porphyrins using this method is close to 100% with an intraassay variability of less than 10%. We have employed this procedure to measure liver and kidney porphyrin concentrations in male Fischer rats and to define the distinctive changes in tissue porphyrin patterns associated with treatment with the hepatic and renal porphyrinogenic chemicals, allylisopropylacetamide, and methyl mercury hydroxide, respectively. This method is applicable to the measurement of tissue porphyrin changes resulting from drug or toxicant exposures in clinical, experimental or environmental assessments.

  17. Combining Raman and FT-IR spectroscopy with quantitative isotopic labeling for differentiation of E. coli cells at community and single cell levels.

    PubMed

    Muhamadali, Howbeer; Chisanga, Malama; Subaihi, Abdu; Goodacre, Royston

    2015-04-21

    There is no doubt that the contribution of microbially mediated bioprocesses toward maintenance of life on earth is vital. However, understanding these microbes in situ is currently a bottleneck, as most methods require culturing these microorganisms to suitable biomass levels so that their phenotype can be measured. The development of new culture-independent strategies such as stable isotope probing (SIP) coupled with molecular biology has been a breakthrough toward linking gene to function, while circumventing in vitro culturing. In this study, for the first time we have combined Raman spectroscopy and Fourier transform infrared (FT-IR) spectroscopy, as metabolic fingerprinting approaches, with SIP to demonstrate the quantitative labeling and differentiation of Escherichia coli cells. E. coli cells were grown in minimal medium with fixed final concentrations of carbon and nitrogen supply, but with different ratios and combinations of (13)C/(12)C glucose and (15)N/(14)N ammonium chloride, as the sole carbon and nitrogen sources, respectively. The cells were collected at stationary phase and examined by Raman and FT-IR spectroscopies. The multivariate analysis investigation of FT-IR and Raman data illustrated unique clustering patterns resulting from specific spectral shifts upon the incorporation of different isotopes, which were directly correlated with the ratio of the isotopically labeled content of the medium. Multivariate analysis results of single-cell Raman spectra followed the same trend, exhibiting a separation between E. coli cells labeled with different isotopes and multiple isotope levels of C and N.

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

    NASA Astrophysics Data System (ADS)

    Ogrinc, Nina; Pelicon, Primož; Vavpetič, Primož; Kelemen, Mitja; Grlj, Nataša; Jeromel, Luka; Tomić, Sergej; Čolić, Miodrag; Beran, Alfred

    2013-07-01

    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.

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

    DOEpatents

    Alfano, Robert R.; Wang, Wubao

    2000-11-21

    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.

  20. Quantitative, comparable coherent anti-Stokes Raman scattering (CARS) spectroscopy: correcting errors in phase retrieval

    NASA Astrophysics Data System (ADS)

    Camp, Charles H., Jr.; Lee, Young Jong; Cicerone, Marcus T.

    2016-04-01

    Coherent anti-Stokes Raman scattering (CARS) microspectroscopy has demonstrated significant potential for biological and materials imaging. To date, however, the primary mechanism of disseminating CARS spectroscopic information is through pseudocolor imagery, which explicitly neglects a vast majority of the hyperspectral data. Furthermore, current paradigms in CARS spectral processing do not lend themselves to quantitative sample-to-sample comparability. The primary limitation stems from the need to accurately measure the so-called nonresonant background (NRB) that is used to extract the chemically-sensitive Raman information from the raw spectra. Measurement of the NRB on a pixel-by-pixel basis is a nontrivial task; thus, reference NRB from glass or water are typically utilized, resulting in error between the actual and estimated amplitude and phase. In this manuscript, we present a new methodology for extracting the Raman spectral features that significantly suppresses these errors through phase detrending and scaling. Classic methods of error-correction, such as baseline detrending, are demonstrated to be inaccurate and to simply mask the underlying errors. The theoretical justification is presented by re-developing the theory of phase retrieval via the Kramers-Kronig relation, and we demonstrate that these results are also applicable to maximum entropy method-based phase retrieval. This new error-correction approach is experimentally applied to glycerol spectra and tissue images, demonstrating marked consistency between spectra obtained using different NRB estimates, and between spectra obtained on different instruments. Additionally, in order to facilitate implementation of these approaches, we have made many of the tools described herein available free for download.

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

    NASA Astrophysics Data System (ADS)

    Wan, Boyong

    2007-12-01

    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

  2. Quantitative Raman spectroscopy of highly fluorescent samples using pseudosecond derivatives and multivariate analysis.

    PubMed

    O'Grady, A; Dennis, A C; Denvir, D; McGarvey, J J; Bell, S E

    2001-05-01

    Intense luminescence backgrounds cause significant problems in quantitative Raman spectroscopy, particularly in multivariate analysis where background suppression is essential. Taking second derivatives reduces the background, but differentiation increases the apparent noise that arises on spectra recorded with CCD detectors due to random, but fixed, variations in the pixel-to-pixel response. We have recently reported a very general method for correcting CCD fixed-pattern response in which spectra are taken at two or more slightly shifted spectrometer positions and are then subtracted to give a derivative-like shifted, subtracted Raman (SSR) spectrum. Here we show that differentiating SSR data (which has inherently higher S/N than the undifferenced data) yields spectra that are similar to those that are obtained from the normal two-step differentiation process and can be characterized as pseudo-second-derivative, PSD, spectra. The backgrounds are suppressed in the PSD spectra, which means they can be used directly in multivariate data analysis, but they have significantly higher S/N ratios than do simple second derivatives. To demonstrate the improvement brought about by using PSD spectra, we have analyzed known samples, consisting of simple binary mixtures of methanol and ethanol doped with laser dye. When the background levels of all samples included in the models were < or =10x greater than the intensity of the strongest Raman bands, partial least-squares calibration of the PSD data gave a standard error of prediction of 3.2%. Calibration using second derivatives gave a prediction error which was approximately twice as large, at 6.5%; however, when data with background levels . approximately 100x larger than the strongest Raman bands were included, the noise on the second-derivative spectra was so large as to prevent a meaningful calibration. Conversely, the PSD treatment of these samples gave a very satisfactory calibration with a standard error of prediction

  3. [Application of NIR Spectroscopy for Nondestructive Qualitative and Quantitative Analysis of Lotus Seeds].

    PubMed

    Zhu, Heng-yin; Fu, Xia-ping; You, Gui-rong; He, Jin-cheng

    2015-10-01

    By extracting the Near Infrared (NIR) diffuse reflectance spectral characteristics from the post-harvest lotus seeds in different storage periods, the quantitative and qualitative analysis were applied to lotus seeds with the Soluble Solids Content (SSC) and dry matter content (DM) as criteria. The results of the Partial Least Squares Regression (PLSR) and distance discrimination (DA) models showed that the absorption spectra of lotus seeds and lotus kernels has clear relations to their SSC and DM. The PLSR models of SSC and DM of lotus seeds had the best performance in 5 941-12 480 cm(-1) spectral region in this study. Their correlation coefficients of prediction were 0.74 and 0.82, and the correlation coefficients of calibration were 0.82 and 0.84, and the correlation coefficients of leave one out cross validation were 0.72 and 0.71. The PLSR model of SSC of lotus kernels was better in 7 891-9 310 cm(-1) spectral region. Its correlation coefficient of prediction was 0.79, and the correlation coefficient of calibration was 0.84, and the correlation coefficient of leave one out cross validation was 0.77. The PLSR model of DM of lotus kernels is better in the full spectral region. Its correlation coefficient of prediction was 0.92, and the correlation coefficient of calibration was 0.89, and the correlation coefficient of leave one out cross validation was 0.82. For lotus seeds, the DA model in 5 400-7 885 cm(-1) spectral region is the best with a correctness of 84.2%. And for lotus kernels, the DA model in 9 226-12 480 cm(-1) spectral region is the best with a correctness of 90.8%. For dry lotus kernels, the discriminant accuracy of the DA model is 98.9% in the optimal spectral region. All kernels with membrane and plumule were correctly discriminated. This research shows that the NIR spectroscopy technique can be used to determine SSC and DM content of lotus seeds and lotus kernels, as well as to discriminate their freshness and also to discriminate dry lotus

  4. Solid-phase extraction and liquid chromatographic quantitation of quinfamide in biological samples.

    PubMed

    Morales, J M; Jung, C H; Alarcón, A; Barreda, A

    2000-09-15

    This paper describes a high-performance liquid chromatographic method for the assay of quinfamide and its main metabolite, 1-(dichloroacetyl)-1,2,3,4,-tetrahydro-6-quinolinol, in plasma, urine and feces. It requires 1 ml of biological fluid, an extraction using Sep-Pack cartridges and acetonitrile for drug elution. Analysis was performed on a CN column (5 microm) using water-acetonitrile-methanol (40:50:10) as a mobile phase at 269 nm. Results showed that the assay was linear in the range between 0.08 and 2.0 microg/ml. The limit of quantitation was 0.08 microg/ml. Maximum assay coefficient of variation was 14%. Recovery obtained in plasma, urine and feces ranged from 82% to 98%.

  5. Prediction of intracellular storage polymers using quantitative image analysis in enhanced biological phosphorus removal systems.

    PubMed

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

    2013-04-01

    The present study focuses on predicting the concentration of intracellular storage polymers in enhanced biological phosphorus removal (EBPR) systems. For that purpose, quantitative image analysis techniques were developed for determining the intracellular concentrations of PHA (PHB and PHV) with Nile blue and glycogen with aniline blue staining. Partial least squares (PLS) were used to predict the standard analytical values of these polymers by the proposed methodology. Identification of the aerobic and anaerobic stages proved to be crucial for improving the assessment of PHA, PHB and PHV intracellular concentrations. Current Nile blue based methodology can be seen as a feasible starting point for further enhancement. Glycogen detection based on the developed aniline blue staining methodology combined with the image analysis data proved to be a promising technique, toward the elimination of the need for analytical off-line measurements.

  6. Biological X-ray spectroscopy on 3rd generation synchrotron radiation sources

    NASA Astrophysics Data System (ADS)

    Ralston, Corie Y.; Chen, Jie; Peng, Gang; George, Simon J.; van Elp, Jan; Cramer, Stephen P.

    1995-02-01

    Third generation synchrotron radiation sources such as the Advanced Light Source (ALS) at Lawrence Berkeley Laboratory deliver 1-2 orders of magnitude more monochromatic flux (and many orders of magnitude higher brightness) than previously available. This paper describes the ring and existing beamlines of the advanced light source, and plans for crystallography and elliptical wiggler stations are discussed. Using nickel metalloprotein spectra recorded at NSLS and SSRL as examples, this paper describes how the higher monochromatic flux available from the ALS will be used for biological soft X-ray spectroscopy.

  7. Application of terahertz time-domain spectroscopy combined with chemometrics to quantitative analysis of imidacloprid in rice samples

    NASA Astrophysics Data System (ADS)

    Chen, Zewei; Zhang, Zhuoyong; Zhu, Ruohua; Xiang, Yuhong; Yang, Yuping; Harrington, Peter B.

    2015-12-01

    Terahertz time-domain spectroscopy (THz-TDS) has been utilized as an effective tool for quantitative analysis of imidacloprid in rice powder samples. Unlike previous studies, our method for sample preparation was mixing imidacloprid with rice powder instead of polyethylene. Then, terahertz time domain transmission spectra of these mixed samples were measured and the absorption coefficient spectra of the samples with frequency range extending from 0.3 to 1.7 THz were obtained. Asymmetric least square (AsLS) method was utilized to correct the slope baselines that are presented in THz absorption coefficient spectra and improve signal-to-noise ratio of THz spectra. Chemometrics methods, including partial least squares (PLS), support vector regression (SVR), interval partial least squares (iPLS), and backward interval partial least squares (biPLS), were used for quantitative model building and prediction. To achieve a reliable and unbiased estimation, bootstrapped Latin partition was chosen as an approach for statistical cross-validation. Results showed that the mean value of root mean square error of prediction (RMSEP) for PLS (0.5%) is smaller than SVR (0.7%), these two methods were based on the whole absorption coefficient spectra. In addition, PLS performed a better performance with a lower RMSEP (0.3%) based on the THz absorption coefficient spectra after AsLS baseline correction. Alternatively, two methods for variable selection, namely iPLS and biPLS, yielded models with improved predictions. Comparing with conventional PLS and SVR, the mean values of RMSEP were 0.4% (iPLS) and 0.3% (biPLS) by selecting the informative frequency ranges. The results demonstrated that an accurate quantitative analysis of imidacloprid in rice powder samples could be achieved by terahertz time-domain transmission spectroscopy combined with chemometrics. Furthermore, these results demonstrate that THz time-domain spectroscopy can be used for quantitative determinations of other

  8. A quantitative study for determination of sugar concentration using attenuated total reflectance terahertz (ATR-THz) spectroscopy

    NASA Astrophysics Data System (ADS)

    Suhandy, Diding; Suzuki, Tetsuhito; Ogawa, Yuichi; Kondo, Naoshi; Ishihara, Takeshi; Takemoto, Yuichiro

    2011-06-01

    The objective of our research was to use ATR-THz spectroscopy together with chemometric for quantitative study in food analysis. Glucose, fructose and sucrose are main component of sugar both in fresh and processed fruits. The use of spectroscopic-based method for sugar determination is well reported especially using visible, near infrared (NIR) and middle infrared (MIR) spectroscopy. However, the use of terahertz spectroscopy for sugar determination in fruits has not yet been reported. In this work, a quantitative study for sugars determination using attenuated total reflectance terahertz (ATR-THz) spectroscopy was conducted. Each samples of glucose, fructose and sucrose solution with different concentrations were prepared respectively and their absorbance spectra between wavenumber 20 and 450 cm-1 (between 0.6 THz and 13.5 THz) were acquired using a terahertz-based Fourier Transform spectrometer (FARIS-1S, JASCO Co., Japan). This spectrometer was equipped with a high pressure of mercury lamp as light source and a pyroelectric sensor made from deuterated L-alanine triglycine sulfate (DLTGS) as detector. Each spectrum was acquired using 16 cm-1 of resolution and 200 scans for averaging. The spectra of water and sugar solutions were compared and discussed. The results showed that increasing sugar concentration caused decreasing absorbance. The correlation between sugar concentration and its spectra was investigated using multivariate analysis. Calibration models for glucose, fructose and sucrose determination were developed using partial least squares (PLS) regression. The calibration model was evaluated using some parameters such as coefficient of determination (R2), standard error of calibration (SEC), standard error of prediction (SEP), bias between actual and predicted sugar concentration value and ratio prediction to deviation (RPD) parameter. The cross validation method was used to validate each calibration model. It is showed that the use of ATR

  9. Classification of the biological material with use of FTIR spectroscopy and statistical analysis

    NASA Astrophysics Data System (ADS)

    Bombalska, Aneta; Mularczyk-Oliwa, Monika; Kwaśny, Mirosław; Włodarski, Maksymilian; Kaliszewski, Miron; Kopczyński, Krzysztof; Szpakowska, Małgorzata; Trafny, Elżbieta A.

    2011-04-01

    Rapid detection and discrimination of dangerous biological materials such as bacteria and their spores has become a security aim of considerable importance. Various analytical methods, including FTIR spectroscopy combined with statistical analysis have been used to identify vegetative bacteria, bacterial spores and background interferants. The present work discusses the application of FTIR technique performed in reflectance mode using Horizontal Attenuated Total Reflectance accessory (HATR) to the discrimination of biological materials. In comparison with transmission technique the HATR is more rapid and do not require the sample destruction, simultaneously giving similar absorbance bands. HATR-FTIR results combined with statistical analysis PCA and HCA demonstrate that this combination provides novel and accurate microbial identification technique.

  10. Detection of biological contaminants on foods and food surfaces using laser-induced breakdown spectroscopy (LIBS).

    PubMed

    Multari, Rosalie A; Cremers, David A; Dupre, Jo Anne M; Gustafson, John E

    2013-09-11

    The rapid detection of biological contaminants, such as Escherichia coli O157:H7 and Salmonella enterica , on foods and food-processing surfaces is important to ensure food safety and streamline the food-monitoring process. Laser-induced breakdown spectroscopy (LIBS) is an ideal candidate technology for this application because sample preparation is minimal and results are available rapidly (seconds to minutes). Here, multivariate regression analysis of LIBS data is used to differentiate the live bacterial pathogens E. coli O157:H7 and S. enterica on various foods (eggshell, milk, bologna, ground beef, chicken, and lettuce) and surfaces (metal drain strainer and cutting board). The type (E. coli or S. enterica) of bacteria could be differentiated in all cases studied along with the metabolic state (viable or heat killed). This study provides data showing the potential of LIBS for the rapid identification of biological contaminants using spectra collected directly from foods and surfaces. PMID:23941554

  11. Quantifying Carbon-14 for Biology Using Cavity Ring-Down Spectroscopy.

    PubMed

    McCartt, A Daniel; Ognibene, Ted J; Bench, Graham; Turteltaub, Kenneth W

    2016-09-01

    A cavity ring-down spectroscopy (CRDS) instrument was developed using mature, robust hardware for the measurement of carbon-14 in biological studies. The system was characterized using carbon-14 elevated glucose samples and returned a linear response up to 387 times contemporary carbon-14 concentrations. Carbon-14 free and contemporary carbon-14 samples with varying carbon-13 concentrations were used to assess the method detection limit of approximately one-third contemporary carbon-14 levels. Sources of inaccuracies are presented and discussed, and the capability to measure carbon-14 in biological samples is demonstrated by comparing pharmacokinetics from carbon-14 dosed guinea pigs analyzed by both CRDS and accelerator mass spectrometry. The CRDS approach presented affords easy access to powerful carbon-14 tracer techniques that can characterize complex biochemical systems. PMID:27458740

  12. Detection of biological contaminants on foods and food surfaces using laser-induced breakdown spectroscopy (LIBS).

    PubMed

    Multari, Rosalie A; Cremers, David A; Dupre, Jo Anne M; Gustafson, John E

    2013-09-11

    The rapid detection of biological contaminants, such as Escherichia coli O157:H7 and Salmonella enterica , on foods and food-processing surfaces is important to ensure food safety and streamline the food-monitoring process. Laser-induced breakdown spectroscopy (LIBS) is an ideal candidate technology for this application because sample preparation is minimal and results are available rapidly (seconds to minutes). Here, multivariate regression analysis of LIBS data is used to differentiate the live bacterial pathogens E. coli O157:H7 and S. enterica on various foods (eggshell, milk, bologna, ground beef, chicken, and lettuce) and surfaces (metal drain strainer and cutting board). The type (E. coli or S. enterica) of bacteria could be differentiated in all cases studied along with the metabolic state (viable or heat killed). This study provides data showing the potential of LIBS for the rapid identification of biological contaminants using spectra collected directly from foods and surfaces.

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

    NASA Astrophysics Data System (ADS)

    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

    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.

  14. Quantitative changes in sets of proteins as markers of biological response

    SciTech Connect

    Giometti, C.S.; Taylor, J.; Gemmell, M.A.; Tollaksen, S.L. ); Lalwani, N.D.; Reddy, J.K. )

    1990-01-01

    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.

  15. Quantitative nanoscale imaging of orientational order in biological filaments by polarized superresolution microscopy

    PubMed Central

    Valades Cruz, Cesar Augusto; Shaban, Haitham Ahmed; Kress, Alla; Bertaux, Nicolas; Monneret, Serge; Mavrakis, Manos; Savatier, Julien; Brasselet, Sophie

    2016-01-01

    Essential cellular functions as diverse as genome maintenance and tissue morphogenesis rely on the dynamic organization of filamentous assemblies. For example, the precise structural organization of DNA filaments has profound consequences on all DNA-mediated processes including gene expression, whereas control over the precise spatial arrangement of cytoskeletal protein filaments is key for mechanical force generation driving animal tissue morphogenesis. Polarized fluorescence is currently used to extract structural organization of fluorescently labeled biological filaments by determining the orientation of fluorescent labels, however with a strong drawback: polarized fluorescence imaging is indeed spatially limited by optical diffraction, and is thus unable to discriminate between the intrinsic orientational mobility of the fluorophore labels and the real structural disorder of the labeled biomolecules. Here, we demonstrate that quantitative single-molecule polarized detection in biological filament assemblies allows not only to correct for the rotational flexibility of the label but also to image orientational order of filaments at the nanoscale using superresolution capabilities. The method is based on polarized direct stochastic optical reconstruction microscopy, using dedicated optical scheme and image analysis to determine both molecular localization and orientation with high precision. We apply this method to double-stranded DNA in vitro and microtubules and actin stress fibers in whole cells. PMID:26831082

  16. Quantitative assessment of image motion blur in diffraction images of moving biological cells

    NASA Astrophysics Data System (ADS)

    Wang, He; Jin, Changrong; Feng, Yuanming; Qi, Dandan; Sa, Yu; Hu, Xin-Hua

    2016-02-01

    Motion blur (MB) presents a significant challenge for obtaining high-contrast image data from biological cells with a polarization diffraction imaging flow cytometry (p-DIFC) method. A new p-DIFC experimental system has been developed to evaluate the MB and its effect on image analysis using a time-delay-integration (TDI) CCD camera. Diffraction images of MCF-7 and K562 cells have been acquired with different speed-mismatch ratios and compared to characterize MB quantitatively. Frequency analysis of the diffraction images shows that the degree of MB can be quantified by bandwidth variations of the diffraction images along the motion direction. The analytical results were confirmed by the p-DIFC image data acquired at different speed-mismatch ratios and used to validate a method of numerical simulation of MB on blur-free diffraction images, which provides a useful tool to examine the blurring effect on diffraction images acquired from the same cell. These results provide insights on the dependence of diffraction image on MB and allow significant improvement on rapid biological cell assay with the p-DIFC method.

  17. Using Softer X-ray Absorption Spectroscopy to Probe Biological Systems

    SciTech Connect

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

    2005-01-01

    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.

  18. High-Resolution Two-Dimensional J-Resolved NMR Spectroscopy for Biological Systems

    PubMed Central

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

    2014-01-01

    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

  19. Residual DNA analysis in biologics development: review of measurement and quantitation technologies and future directions.

    PubMed

    Wang, Xing; Morgan, Donna M; Wang, Gan; Mozier, Ned M

    2012-02-01

    Residual DNA (rDNA) is comprised of deoxyribonucleic acid (DNA) fragments and longer length molecules originating from the host organism that may be present in samples from recombinant biological processes. Although similar in basic structural base pair units, rDNA may exist in different sizes and physical forms. Interest in measuring rDNA in recombinant products is based primarily on demonstration of effective purification during manufacturing, but also on some hypothetical concerns that, in rare cases, depending on the host expression system, some DNA sequences may be potentially infectious or oncogenic (e.g., HIV virus and the Ras oncogene, respectively). Recent studies suggest that a sequence known as long interspersed nucleotide element-1 (LINE-1), widely distributed in the mammalian genome, is active as a retrotransposon that can be transcribed to RNA, reverse-transcribed into DNA and inserts into a new site in genome. This integration process could potentially disrupt critical gene functions or induce tumorigenesis in mammals. Genomic DNA from microbial sources, on the other hand, could add to risk of immunogenicity to the target recombinant protein being expressed, due to the high CpG content and unmethylated DNA sequence. For these and other reasons, it is necessary for manufacturers to show clearance of DNA throughout production processes and to confirm low levels in the final drug substance using an appropriately specific and quantitative analytical method. The heterogeneity of potential rDNA sequences that might be makes the testing of all potential analytes challenging. The most common methodology for rDNA quantitation used currently is real-time polymerase chain reaction (RT-PCR), a robust and proven technology. Like most rDNA quantitation methods, the specificity of RT-PCR is limited by the sequences to which the primers are directed. To address this, primase-based whole genome amplification is introduced herein. This paper will review the recent

  20. Quantitative probe of the transition metal redox in battery electrodes through soft x-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Qinghao; Qiao, Ruimin; Wray, L. Andrew; Chen, Jun; Zhuo, Zengqing; Chen, Yanxue; Yan, Shishen; Pan, Feng; Hussain, Zahid; Yang, Wanli

    2016-10-01

    Most battery positive electrodes operate with a 3d transition-metal (TM) reaction centre. A direct and quantitative probe of the TM states upon electrochemical cycling is valuable for understanding the detailed cycling mechanism and charge diffusion in the electrodes, which is related with many practical parameters of a battery. This review includes a comprehensive summary of our recent demonstrations of five different types of quantitative analysis of the TM states in battery electrodes based on soft x-ray absorption spectroscopy and multiplet calculations. In LiFePO4, a system of a well-known two-phase transformation type, the TM redox could be strictly determined through a simple linear combination of the two end-members. In Mn-based compounds, the Mn states could also be quantitatively evaluated, but a set of reference spectra with all the three possible Mn valences needs to be deliberately selected and considered in the fitting. Although the fluorescence signals suffer the self-absorption distortion, the multiplet calculations could consider the distortion effect, which allows a quantitative determination of the overall Ni oxidation state in the bulk. With the aid of multiplet calculations, one could also achieve a quasi-quantitative analysis of the Co redox evolution in LiCoO2 based on the energy position of the spectroscopic peak. The benefit of multiplet calculations is more important for studying electrode materials with TMs of mixed spin states, as exemplified by the quantitative analysis of the mixed spin Na2-x Fe2(CN)6 system. At the end, we showcase that such quantitative analysis could provide valuable information for optimizing the electrochemical performance of Na0.44MnO2 electrodes for Na-ion batteries. The methodology summarized in this review could be extended to other energy application systems with TM redox centre for detailed analysis, for example, fuel cell and catalytic materials.

  1. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    DOE PAGES

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-03-10

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof’ electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies o1 eV can be ‘safely’ investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with nomore » observable radiation damage. Furthermore, the technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ~10nm, simultaneously combined with imaging in the electron microscope.« less

  2. Experimental demonstration of quantitation errors in MR spectroscopy resulting from saturation corrections under changing conditions

    NASA Astrophysics Data System (ADS)

    Galbán, Craig J.; Ellis, Scott J.; Spencer, Richard G. S.

    2003-04-01

    Metabolite concentration measurements in in vivo NMR are generally performed under partially saturated conditions, with correction for partial saturation performed after data collection using a measured saturation factor. Here, we present an experimental test of the hypothesis that quantitation errors can occur due to application of such saturation factor corrections in changing systems. Thus, this extends our previous theoretical work on quantitation errors due to varying saturation factors. We obtained results for two systems frequently studied by 31P NMR, the ischemic rat heart and the electrically stimulated rat gastrocnemius muscle. The results are interpreted in light of previous theoretical work which defined the degree of saturation occurring in a one-pulse experiment for a system with given spin-lattice relaxation times, T1s, equilibrium magnetizations, M0s, and reaction rates. We found that (i) the assumption of constancy of saturation factors leads to quantitation errors on the order of 40% in inorganic phosphate; (ii) the dominant contributor to the quantitation errors in inorganic phosphate is most likely changes in T1; (iii) T1 and M0 changes between control and intervention periods, and chemical exchange contribute to different extents to quantitation errors in phosphocreatine and γ-ATP; (iv) relatively small increases in interpulse delay substantially decreased quantitation errors for metabolites in ischemic rat hearts; (v) random error due to finite SNR led to approximately 4% error in quantitation, and hence was a substantially smaller contributor than were changes in saturation factors.

  3. Quantitative Raman Spectroscopy to monitor microbial metabolism in situ under pressure

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

    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 μm-thick Ni gasket in which a 500 μm-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

  4. Standoff detection of chemical and biological threats using laser-induced breakdown spectroscopy.

    PubMed

    Gottfried, Jennifer L; De Lucia, Frank C; Munson, Chase A; Miziolek, Andrzej W

    2008-04-01

    Laser-induced breakdown spectroscopy (LIBS) is a promising technique for real-time chemical and biological warfare agent detection in the field. We have demonstrated the detection and discrimination of the biological warfare agent surrogates Bacillus subtilis (BG) (2% false negatives, 0% false positives) and ovalbumin (0% false negatives, 1% false positives) at 20 meters using standoff laser-induced breakdown spectroscopy (ST-LIBS) and linear correlation. Unknown interferent samples (not included in the model), samples on different substrates, and mixtures of BG and Arizona road dust have been classified with reasonable success using partial least squares discriminant analysis (PLS-DA). A few of the samples tested such as the soot (not included in the model) and the 25% BG:75% dust mixture resulted in a significant number of false positives or false negatives, respectively. Our preliminary results indicate that while LIBS is able to discriminate biomaterials with similar elemental compositions at standoff distances based on differences in key intensity ratios, further work is needed to reduce the number of false positives/negatives by refining the PLS-DA model to include a sufficient range of material classes and carefully selecting a detection threshold. In addition, we have demonstrated that LIBS can distinguish five different organophosphate nerve agent simulants at 20 meters, despite their similar stoichiometric formulas. Finally, a combined PLS-DA model for chemical, biological, and explosives detection using a single ST-LIBS sensor has been developed in order to demonstrate the potential of standoff LIBS for universal hazardous materials detection.

  5. Optimized Pulse Parameters for Reducing Quantitation Errors Due to Saturation Factor Changes in Magnetic Resonance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Galbán, Craig J.; Spencer, Richard G. S.

    2002-06-01

    We present an analysis of the effects of chemical exchange and changes in T1 on metabolite quantitation for heart, skeletal muscle, and brain using the one-pulse experiment for a sample which is subject to temporal variation. We use an optimization algorithm to calculate interpulse delay times, TRs, and flip angles, θ, resulting in maximal root-mean-squared signal-to-noise per unit time ( S/ N) for all exchanging species under 5 and 10% constraints on quantitation errors. The optimization yields TR and θ pairs giving signal-to-noise per unit time close or superior to typical literature values. Additional simulations were performed to demonstrate explicitly the dependence of the quantitation errors on pulse parameters and variations in the properties of the sample, such as may occur after an intervention. We find that (i) correction for partial saturation in accordance with the usual analysis neglecting variations in metabolite concentrations and rate constants may readily result in quantitation errors of 15% or more; the exact degree of error depends upon the details of the system under consideration; (ii) if T1's vary as well, significantly larger quantitation errors may occur; and (iii) optimal values of pulse parameters may minimize errors in quantitation with minimal S/ N loss.

  6. Quantitative determination of fatty acid chain composition in pork meat products by high resolution 1H NMR spectroscopy.

    PubMed

    Siciliano, Carlo; Belsito, Emilia; De Marco, Rosaria; Di Gioia, Maria Luisa; Leggio, Antonella; Liguori, Angelo

    2013-01-15

    High resolution (1)H NMR spectroscopy was proposed for the determination of the fatty acid chain profile of lipids in pork meat products during ripening. Two typical Mediterranean PDO salami produced in Calabria, a region in the Southern Italy, were chosen as a case of study. Quantitative NMR analysis provided the fatty acid chain profiles of total lipid extracts. The transesterification of total lipid extracts furnished FAME mixtures that enabled quantitation of fatty acid acyl chains in the acylglycerol and FFA portions. In all cases, oleyl chains were predominant, and high amounts of polyunsaturated fatty acid chains were observed. The proposed spectroscopic method allowed also the estimation of the most important nutritional parameters of dry fermented meat products.

  7. Quantitative spectroscopy of hot stars: accurate atomic data applied on a large scale as driver of recent breakthroughs

    NASA Astrophysics Data System (ADS)

    Przybilla, Norbert; Schaffenroth, Veronika; Nieva, Maria-Fernanda

    2015-08-01

    OB-type stars present hotbeds for non-LTE physics because of their strong radiation fields that drive the atmospheric plasma out of local thermodynamic equilibrium. We report on recent breakthroughs in the quantitative analysis of the optical and UV-spectra of OB-type stars that were facilitated by application of accurate and precise atomic data on a large scale. An astophysicist's dream has come true, by bringing observed and model spectra into close match over wide parts of the observed wavelength ranges. This facilitates tight observational constraints to be derived from OB-type stars for wide applications in astrophysics. However, despite the progress made, many details of the modelling may be improved further. We discuss atomic data needs in terms of laboratory measurements and also ab-initio calculations. Particular emphasis is given to quantitative spectroscopy in the near-IR, which will be in focus in the era of the upcoming extremely large telescopes.

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

    PubMed

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

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

    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 γ = 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.

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

    PubMed

    Zhang, Yong; Cong, Qian; Xie, Yunfei; JingxiuYang; Zhao, Bing

    2008-12-15

    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 gamma=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.

  11. Quantitative description of photoexcited scanning tunneling spectroscopy and its application to the GaAs(110) surface

    NASA Astrophysics Data System (ADS)

    Schnedler, M.; Portz, V.; Weidlich, P. H.; Dunin-Borkowski, R. E.; Ebert, Ph.

    2015-06-01

    A quantitative description of photoexcited scanning tunneling spectra is developed and applied to photoexcited spectra measured on p -doped nonpolar GaAs(110) surfaces. Under illumination, the experimental spectra exhibit an increase of the tunnel current at negative sample voltages only. In order to analyze the experimental data quantitatively, the potential and charge-carrier distributions of the photoexcited tip-vacuum-semiconductor system are calculated by solving the Poisson as well as the hole and electron continuity equations by a finite-difference algorithm. On this basis, the different contributions to the tunnel current are calculated using an extension of the model of Feenstra and Stroscio to include the light-excited carrier concentrations. The best fit of the calculated tunnel currents to the experimental data is obtained for a tip-induced band bending, which is limited by the partial occupation of the C3 surface state by light-excited electrons. The tunnel current at negative voltages is then composed of a valence band contribution and a photoinduced tunnel current of excited electrons in the conduction band. The quantitative description of the tunnel current developed here is generally applicable and provides a solid foundation for the quantitative interpretation of photoexcited scanning tunneling spectroscopy.

  12. Trace iodine quantitation in biological samples by mass spectrometric methods: the optimum internal standard.

    PubMed

    Dyke, Jason V; Dasgupta, Purnendu K; Kirk, Andrea B

    2009-07-15

    Accurate quantitation of iodine in biological samples is essential for studies of nutrition and medicine, as well as for epidemiological studies for monitoring intake of this essential nutrient. Despite the importance of accurate measurement, a standardized method for iodine analysis of biological samples is yet to be established. We have evaluated the effectiveness of (72)Ge, (115)In, and (129)I as internal standards for measurement of iodine in milk and urine samples by induction coupled plasma mass spectrometry (ICP-MS) and of (35)Cl(18)O(4)(-), (129)I(-), and 2-chlorobenzenesulfonate (2-CBS) as internal standards for ion chromatography-tandem mass spectrometry (IC-MS/MS). We found recovery of iodine to be markedly low when IC-MS/MS was used without an internal standard. Percent recovery was similarly low using (35)Cl(18)O(4) as an internal standard for milk and unpredictable when used for urine. 2-Chlorobenzebenzenesulfonate provided accurate recovery of iodine from milk, but overestimated iodine in urine samples by as much as a factor of 2. Percent recovery of iodine from milk and urine using ICP-MS without an internal standard was approximately 120%. Use of (115)In predicted approximately 60% of known values for both milk and urine samples. (72)Ge provided reasonable and consistent percent recovery for iodine in milk samples (approximately 108%) but resulted in approximately 80% recovery of iodine from urine. Use of (129)I as an internal standard resulted in excellent recovery of iodine from both milk and urine samples using either IC-MS/MS and ICP-MS.

  13. QUANTITATIVE ULTRAVIOLET SPECTROSCOPY IN WEATHERING OF A MODEL POLYESTER-URETHANE COATING. (R828081E01)

    EPA Science Inventory

    Spectroscopy was used to quantify the effects of ultraviolet light on a model polyester–urethane coating as it degraded in an accelerated exposure chamber. An explorative calculation of the effective dosage absorbed by the coatings was made and, depending on the quantum...

  14. Quantitative analyses of glass via laser-induced breakdown spectroscopy in argon

    NASA Astrophysics Data System (ADS)

    Gerhard, C.; Hermann, J.; Mercadier, L.; Loewenthal, L.; Axente, E.; Luculescu, C. R.; Sarnet, T.; Sentis, M.; Viöl, W.

    2014-11-01

    We demonstrate that elemental analysis of glass with a measurement precision of about 10% can be performed via calibration-free laser-induced breakdown spectroscopy. Therefore, plasma emission spectra recorded during ultraviolet laser ablation of different glasses are compared to the spectral radiance computed for a plasma in local thermodynamic equilibrium. Using an iterative calculation algorithm, we deduce the relative elemental fractions and the plasma properties from the best agreement between measured and computed spectra. The measurement method is validated in two ways. First, the LIBS measurements are performed on fused silica composed of more than 99.9% of SiO2. Second, the oxygen fractions measured for heavy flint and barite crown glasses are compared to the values expected from the glass composing oxides. The measured compositions are furthermore compared with those obtained by X-ray photoelectron spectroscopy and energy-dispersive X-ray spectroscopy. It is shown that accurate LIBS analyses require spectra recording with short enough delays between laser pulse and detector gate, when the electron density is larger than 1017 cm- 3. The results show that laser-induced breakdown spectroscopy based on accurate plasma modeling is suitable for elemental analysis of complex materials such as glasses, with an analytical performance comparable or even better than that obtained with standard techniques.

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

    PubMed Central

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

    2013-01-01

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

  16. CSML2SBML: a novel tool for converting quantitative biological pathway models from CSML into SBML.

    PubMed

    Li, Chen; Nagasaki, Masao; Ikeda, Emi; Sekiya, Yayoi; Miyano, Satoru

    2014-07-01

    CSML and SBML are XML-based model definition standards which are developed with the aim of creating exchange formats for modeling, visualizing and simulating biological pathways. In this article we report a release of a format convertor for quantitative pathway models, namely CSML2SBML. It translates models encoded by CSML into SBML without loss of structural and kinetic information. The simulation and parameter estimation of the resulting SBML model can be carried out with compliant tool CellDesigner for further analysis. The convertor is based on the standards CSML version 3.0 and SBML Level 2 Version 4. In our experiments, 11 out of 15 pathway models in CSML model repository and 228 models in Macrophage Pathway Knowledgebase (MACPAK) are successfully converted to SBML models. The consistency of the resulting model is validated by libSBML Consistency Check of CellDesigner. Furthermore, the converted SBML model assigned with the kinetic parameters translated from CSML model can reproduce the same dynamics with CellDesigner as CSML one running on Cell Illustrator. CSML2SBML, along with its instructions and examples for use are available at http://csml2sbml.csml.org. PMID:24881961

  17. Antiproliferative Pt(IV) complexes: synthesis, biological activity, and quantitative structure-activity relationship modeling.

    PubMed

    Gramatica, Paola; Papa, Ester; Luini, Mara; Monti, Elena; Gariboldi, Marzia B; Ravera, Mauro; Gabano, Elisabetta; Gaviglio, Luca; Osella, Domenico

    2010-09-01

    Several Pt(IV) complexes of the general formula [Pt(L)2(L')2(L'')2] [axial ligands L are Cl-, RCOO-, or OH-; equatorial ligands L' are two am(m)ine or one diamine; and equatorial ligands L'' are Cl- or glycolato] were rationally designed and synthesized in the attempt to develop a predictive quantitative structure-activity relationship (QSAR) model. Numerous theoretical molecular descriptors were used alongside physicochemical data (i.e., reduction peak potential, Ep, and partition coefficient, log Po/w) to obtain a validated QSAR between in vitro cytotoxicity (half maximal inhibitory concentrations, IC50, on A2780 ovarian and HCT116 colon carcinoma cell lines) and some features of Pt(IV) complexes. In the resulting best models, a lipophilic descriptor (log Po/w or the number of secondary sp3 carbon atoms) plus an electronic descriptor (Ep, the number of oxygen atoms, or the topological polar surface area expressed as the N,O polar contribution) is necessary for modeling, supporting the general finding that the biological behavior of Pt(IV) complexes can be rationalized on the basis of their cellular uptake, the Pt(IV)-->Pt(II) reduction, and the structure of the corresponding Pt(II) metabolites. Novel compounds were synthesized on the basis of their predicted cytotoxicity in the preliminary QSAR model, and were experimentally tested. A final QSAR model, based solely on theoretical molecular descriptors to ensure its general applicability, is proposed.

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

    PubMed

    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

    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.

  19. Synthesis, biological activities, and quantitative structure-activity relationship (QSAR) study of novel camptothecin analogues.

    PubMed

    Wu, Dan; Zhang, Shao-Yong; Liu, Ying-Qian; Wu, Xiao-Bing; Zhu, Gao-Xiang; Zhang, Yan; Wei, Wei; Liu, Huan-Xiang; Chen, An-Liang

    2015-05-13

    In continuation of our program aimed at the development of natural product-based pesticidal agents, three series of novel camptothecin derivatives were designed, synthesized, and evaluated for their biological activities against T. Cinnabarinus, B. brassicae, and B. xylophilus. All of the derivatives showed good-to-excellent activity against three insect species tested, with LC50 values ranging from 0.00761 to 0.35496 mmol/L. Remarkably, all of the compounds were more potent than CPT against T. Cinnabarinus, and compounds 4d and 4c displayed superior activity (LC50 0.00761 mmol/L and 0.00942 mmol/L, respectively) compared with CPT (LC50 0.19719 mmol/L) against T. Cinnabarinus. Based on the observed bioactivities, preliminary structure-activity relationship (SAR) correlations were also discussed. Furthermore, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model using comparative molecular field analysis (CoMFA) was built. The model gave statistically significant results with the cross-validated q2 values of 0.580 and correlation coefficient r2 of 0.991 and  of 0.993. The QSAR analysis indicated that the size of the substituents play an important in the activity of 7-modified camptothecin derivatives. These findings will pave the way for further design, structural optimization, and development of camptothecin-derived compounds as pesticidal agents.

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

    PubMed

    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

    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

  1. CSML2SBML: a novel tool for converting quantitative biological pathway models from CSML into SBML.

    PubMed

    Li, Chen; Nagasaki, Masao; Ikeda, Emi; Sekiya, Yayoi; Miyano, Satoru

    2014-07-01

    CSML and SBML are XML-based model definition standards which are developed with the aim of creating exchange formats for modeling, visualizing and simulating biological pathways. In this article we report a release of a format convertor for quantitative pathway models, namely CSML2SBML. It translates models encoded by CSML into SBML without loss of structural and kinetic information. The simulation and parameter estimation of the resulting SBML model can be carried out with compliant tool CellDesigner for further analysis. The convertor is based on the standards CSML version 3.0 and SBML Level 2 Version 4. In our experiments, 11 out of 15 pathway models in CSML model repository and 228 models in Macrophage Pathway Knowledgebase (MACPAK) are successfully converted to SBML models. The consistency of the resulting model is validated by libSBML Consistency Check of CellDesigner. Furthermore, the converted SBML model assigned with the kinetic parameters translated from CSML model can reproduce the same dynamics with CellDesigner as CSML one running on Cell Illustrator. CSML2SBML, along with its instructions and examples for use are available at http://csml2sbml.csml.org.

  2. Foqus: a FORTRAN program for the quantitative analysis of x-ray spectra from thin biological specimens.

    PubMed

    Fuchs, H; Fuchs, W

    1981-01-01

    An online FORTRAN program for the quantitative analysis of energy dispersive X-ray spectra from thin biological specimens is presented. The methods of background suppression by digital filtering and peak deconvolution by linear least-squares fitting with measured peak profiles are used. The continuum quantitation method for spectra from thin biological sections as proposed by Hall is applied. The performance of the computer program, utilizing the facilities of a disk operating system, is demonstrated. The routines were optimized for speed, resulting in a run-time of less than 5 seconds on a 16 bit minicomputer for a full quantitation for 7 elements of an energy dispersive thin section X-ray spectrum, including an optional absorption correction. Since no assembly language subroutines are implemented, the restrictions for the use of the program with different computer systems are minimized.

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

    NASA Astrophysics Data System (ADS)

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

    2004-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

    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.

  5. Review of short-wave infrared spectroscopy and imaging methods for biological tissue characterization.

    PubMed

    Wilson, Robert H; Nadeau, Kyle P; Jaworski, Frank B; Tromberg, Bruce J; Durkin, Anthony J

    2015-03-01

    We present a review of short-wave infrared (SWIR, defined here as ∼1000 to 2000 nm) spectroscopy and imaging techniques for biological tissue optical property characterization. Studies indicate notable SWIR absorption features of tissue constituents including water (near 1150, 1450, and 1900 nm), lipids (near 1040, 1200, 1400, and 1700 nm), and collagen (near 1200 and 1500 nm) that are much more prominent than corresponding features observed in the visible and near-infrared (VIS-NIR, defined here as ∼400 to 1000 nm). Furthermore, the wavelength dependence of the scattering coefficient has been observed to follow a power-law decay from the VIS-NIR to the SWIR region. Thus, the magnitude of tissue scattering is lower at SWIR wavelengths than that observed at VIS or NIR wavelengths, potentially enabling increased penetration depth of incident light at SWIR wavelengths that are not highly absorbed by the aforementioned chromophores. These aspects of SWIR suggest that the tissue spectroscopy and imaging in this range of wavelengths have the potential to provide enhanced sensitivity (relative to VIS-NIR measurements) to chromophores such as water and lipids, thereby helping to characterize changes in the concentrations of these chromophores due to conditions such as atherosclerotic plaque, breast cancer, and burns. PMID:25803186

  6. Review of short-wave infrared spectroscopy and imaging methods for biological tissue characterization

    PubMed Central

    Wilson, Robert H.; Nadeau, Kyle P.; Jaworski, Frank B.; Tromberg, Bruce J.; Durkin, Anthony J.

    2015-01-01

    Abstract. We present a review of short-wave infrared (SWIR, defined here as ∼1000 to 2000 nm) spectroscopy and imaging techniques for biological tissue optical property characterization. Studies indicate notable SWIR absorption features of tissue constituents including water (near 1150, 1450, and 1900 nm), lipids (near 1040, 1200, 1400, and 1700 nm), and collagen (near 1200 and 1500 nm) that are much more prominent than corresponding features observed in the visible and near-infrared (VIS-NIR, defined here as ∼400 to 1000 nm). Furthermore, the wavelength dependence of the scattering coefficient has been observed to follow a power-law decay from the VIS-NIR to the SWIR region. Thus, the magnitude of tissue scattering is lower at SWIR wavelengths than that observed at VIS or NIR wavelengths, potentially enabling increased penetration depth of incident light at SWIR wavelengths that are not highly absorbed by the aforementioned chromophores. These aspects of SWIR suggest that the tissue spectroscopy and imaging in this range of wavelengths have the potential to provide enhanced sensitivity (relative to VIS-NIR measurements) to chromophores such as water and lipids, thereby helping to characterize changes in the concentrations of these chromophores due to conditions such as atherosclerotic plaque, breast cancer, and burns. PMID:25803186

  7. Rapid Quantitative Determination of Squalene in Shark Liver Oils by Raman and IR Spectroscopy.

    PubMed

    Hall, David W; Marshall, Susan N; Gordon, Keith C; Killeen, Daniel P

    2016-01-01

    Squalene is sourced predominantly from shark liver oils and to a lesser extent from plants such as olives. It is used for the production of surfactants, dyes, sunscreen, and cosmetics. The economic value of shark liver oil is directly related to the squalene content, which in turn is highly variable and species-dependent. Presented here is a validated gas chromatography-mass spectrometry analysis method for the quantitation of squalene in shark liver oils, with an accuracy of 99.0 %, precision of 0.23 % (standard deviation), and linearity of >0.999. The method has been used to measure the squalene concentration of 16 commercial shark liver oils. These reference squalene concentrations were related to infrared (IR) and Raman spectra of the same oils using partial least squares regression. The resultant models were suitable for the rapid quantitation of squalene in shark liver oils, with cross-validation r (2) values of >0.98 and root mean square errors of validation of ≤4.3 % w/w. Independent test set validation of these models found mean absolute deviations of the 4.9 and 1.0 % w/w for the IR and Raman models, respectively. Both techniques were more accurate than results obtained by an industrial refractive index analysis method, which is used for rapid, cheap quantitation of squalene in shark liver oils. In particular, the Raman partial least squares regression was suited to quantitative squalene analysis. The intense and highly characteristic Raman bands of squalene made quantitative analysis possible irrespective of the lipid matrix.

  8. Rapid Quantitative Determination of Squalene in Shark Liver Oils by Raman and IR Spectroscopy.

    PubMed

    Hall, David W; Marshall, Susan N; Gordon, Keith C; Killeen, Daniel P

    2016-01-01

    Squalene is sourced predominantly from shark liver oils and to a lesser extent from plants such as olives. It is used for the production of surfactants, dyes, sunscreen, and cosmetics. The economic value of shark liver oil is directly related to the squalene content, which in turn is highly variable and species-dependent. Presented here is a validated gas chromatography-mass spectrometry analysis method for the quantitation of squalene in shark liver oils, with an accuracy of 99.0 %, precision of 0.23 % (standard deviation), and linearity of >0.999. The method has been used to measure the squalene concentration of 16 commercial shark liver oils. These reference squalene concentrations were related to infrared (IR) and Raman spectra of the same oils using partial least squares regression. The resultant models were suitable for the rapid quantitation of squalene in shark liver oils, with cross-validation r (2) values of >0.98 and root mean square errors of validation of ≤4.3 % w/w. Independent test set validation of these models found mean absolute deviations of the 4.9 and 1.0 % w/w for the IR and Raman models, respectively. Both techniques were more accurate than results obtained by an industrial refractive index analysis method, which is used for rapid, cheap quantitation of squalene in shark liver oils. In particular, the Raman partial least squares regression was suited to quantitative squalene analysis. The intense and highly characteristic Raman bands of squalene made quantitative analysis possible irrespective of the lipid matrix. PMID:26620374

  9. Quantitative determination of citric acid in seminal plasma by using Raman spectroscopy.

    PubMed

    Huang, Zufang; Chen, Xiwen; Li, Yongzeng; Chen, Jinhua; Lin, Juqiang; Wang, Jing; Lei, Jinping; Chen, Rong

    2013-07-01

    In this study, Raman spectroscopy was first used to study the linear relationship between Raman spectral intensities and citric acid concentrations in aqueous solution. By using the specific Raman band of 942 cm(-1), concentrations of citric acid ranging from 2 to 20 mg/mL were observed linearly (R(2) = 0.993), and the limit of detection was 1.0 mg/mL. Then, citric acid detection in clinical seminal plasma ultrafiltrate samples was performed, and the intensity of the Raman-specific peak demonstrates a good linear correlation (R(2) = 0.946) with citric acid concentrations determined by the enzymatic method. Our results showed that Raman spectroscopy has the potential of being applied to detect concentrations of citric acid in seminal plasma in clinic.

  10. Quantitative determination of the human breast milk macronutrients by near-infrared Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Motta, Edlene d. C. M.; Zângaro, Renato A.; Silveira, Landulfo, Jr.

    2012-03-01

    This work proposes the evaluation of the macronutrient constitution of human breast milk based on the spectral information provided by near-infrared Raman spectroscopy. Human breast milk (5 mL) from a subject was collected during the first two weeks of breastfeeding and stocked in -20°C freezer. Raman spectra were measured using a Raman spectrometer (830 nm excitation) coupled to a fiber based Raman probe. Spectra of human milk were dominated by bands of proteins, lipids and carbohydrates in the 600-1800 cm-1 spectral region. Raman spectroscopy revealed differences in the biochemical constitution of human milk depending on the time of breastfeeding startup. This technique could be employed to develop a classification routine for the milk in Human Milk Banking (HMB) depending on the nutritional facts.

  11. [Study on the application of ridge regression to near-infrared spectroscopy quantitative analysis and optimum wavelength selection].

    PubMed

    Zhang, Man; Liu, Xu-Hua; He, Xiong-Kui; Zhang, Lu-Da; Zhao, Long-Lian; Li, Jun-Hui

    2010-05-01

    In the present paper, taking 66 wheat samples for testing materials, ridge regression technology in near-infrared (NIR) spectroscopy quantitative analysis was researched. The NIR-ridge regression model for determination of protein content was established by NIR spectral data of 44 wheat samples to predict the protein content of the other 22 samples. The average relative error was 0.015 18 between the predictive results and Kjeldahl's values (chemical analysis values). And the predictive results were compared with those values derived through partial least squares (PLS) method, showing that ridge regression method was deserved to be chosen for NIR spectroscopy quantitative analysis. Furthermore, in order to reduce the disturbance to predictive capacity of the quantitative analysis model resulting from irrelevant information, one effective way is to screen the wavelength information. In order to select the spectral information with more content information and stronger relativity with the composition or the nature of the samples to improve the model's predictive accuracy, ridge regression was used to select wavelength information in this paper. The NIR-ridge regression model was established with the spectral information at 4 wavelength points, which were selected from 1 297 wavelength points, to predict the protein content of the 22 samples. The average relative error was 0.013 7 and the correlation coefficient reached 0.981 7 between the predictive results and Kjeldahl's values. The results showed that ridge regression was able to screen the essential wavelength information from a large amount of spectral information. It not only can simplify the model and effectively reduce the disturbance resulting from collinearity information, but also has practical significance for designing special NIR analysis instrument for analyzing specific component in some special samples. PMID:20672604

  12. [Study on the application of ridge regression to near-infrared spectroscopy quantitative analysis and optimum wavelength selection].

    PubMed

    Zhang, Man; Liu, Xu-Hua; He, Xiong-Kui; Zhang, Lu-Da; Zhao, Long-Lian; Li, Jun-Hui

    2010-05-01

    In the present paper, taking 66 wheat samples for testing materials, ridge regression technology in near-infrared (NIR) spectroscopy quantitative analysis was researched. The NIR-ridge regression model for determination of protein content was established by NIR spectral data of 44 wheat samples to predict the protein content of the other 22 samples. The average relative error was 0.015 18 between the predictive results and Kjeldahl's values (chemical analysis values). And the predictive results were compared with those values derived through partial least squares (PLS) method, showing that ridge regression method was deserved to be chosen for NIR spectroscopy quantitative analysis. Furthermore, in order to reduce the disturbance to predictive capacity of the quantitative analysis model resulting from irrelevant information, one effective way is to screen the wavelength information. In order to select the spectral information with more content information and stronger relativity with the composition or the nature of the samples to improve the model's predictive accuracy, ridge regression was used to select wavelength information in this paper. The NIR-ridge regression model was established with the spectral information at 4 wavelength points, which were selected from 1 297 wavelength points, to predict the protein content of the 22 samples. The average relative error was 0.013 7 and the correlation coefficient reached 0.981 7 between the predictive results and Kjeldahl's values. The results showed that ridge regression was able to screen the essential wavelength information from a large amount of spectral information. It not only can simplify the model and effectively reduce the disturbance resulting from collinearity information, but also has practical significance for designing special NIR analysis instrument for analyzing specific component in some special samples.

  13. Quantitative Determination of Fluorine Content in Blends of Polylactide (PLA)–Talc Using Near Infrared Spectroscopy

    PubMed Central

    Tamburini, Elena; Tagliati, Chiara; Bonato, Tiziano; Costa, Stefania; Scapoli, Chiara; Pedrini, Paola

    2016-01-01

    Near-infrared spectroscopy (NIRS) has been widely used for quantitative and/or qualitative determination of a wide range of matrices. The objective of this study was to develop a NIRS method for the quantitative determination of fluorine content in polylactide (PLA)-talc blends. A blending profile was obtained by mixing different amounts of PLA granules and talc powder. The calibration model was built correlating wet chemical data (alkali digestion method) and NIR spectra. Using FT (Fourier Transform)-NIR technique, a Partial Least Squares (PLS) regression model was set-up, in a concentration interval of 0 ppm of pure PLA to 800 ppm of pure talc. Fluorine content prediction (R2cal = 0.9498; standard error of calibration, SEC = 34.77; standard error of cross-validation, SECV = 46.94) was then externally validated by means of a further 15 independent samples (R2EX.V = 0.8955; root mean standard error of prediction, RMSEP = 61.08). A positive relationship between an inorganic component as fluorine and NIR signal has been evidenced, and used to obtain quantitative analytical information from the spectra. PMID:27490548

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

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

    PubMed

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

    2010-01-01

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

  16. A Practical Approach to Quantitative Processing and Analysis of Small Biological Structures by Fluorescent Imaging

    PubMed Central

    Noller, Crystal M.; Boulina, Maria; McNamara, George; Szeto, Angela; McCabe, Philip M.

    2016-01-01

    Standards in quantitative fluorescent imaging are vaguely recognized and receive insufficient discussion. A common best practice is to acquire images at Nyquist rate, where highest signal frequency is assumed to be the highest obtainable resolution of the imaging system. However, this particular standard is set to insure that all obtainable information is being collected. The objective of the current study was to demonstrate that for quantification purposes, these correctly set acquisition rates can be redundant; instead, linear size of the objects of interest can be used to calculate sufficient information density in the image. We describe optimized image acquisition parameters and unbiased methods for processing and quantification of medium-size cellular structures. Sections of rabbit aortas were immunohistochemically stained to identify and quantify sympathetic varicosities, >2 μm in diameter. Images were processed to reduce background noise and segment objects using free, open-access software. Calculations of the optimal sampling rate for the experiment were based on the size of the objects of interest. The effect of differing sampling rates and processing techniques on object quantification was demonstrated. Oversampling led to a substantial increase in file size, whereas undersampling hindered reliable quantification. Quantification of raw and incorrectly processed images generated false structures, misrepresenting the underlying data. The current study emphasizes the importance of defining image-acquisition parameters based on the structure(s) of interest. The proposed postacquisition processing steps effectively removed background and noise, allowed for reliable quantification, and eliminated user bias. This customizable, reliable method for background subtraction and structure quantification provides a reproducible tool for researchers across biologic disciplines. PMID:27182204

  17. Mammographic quantitative image analysis and biologic image composition for breast lesion characterization and classification

    SciTech Connect

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

    2014-03-15

    Purpose: To investigate whether biologic image composition of mammographic lesions can improve upon existing mammographic quantitative image analysis (QIA) in estimating the probability of malignancy. Methods: The study population consisted of 45 breast lesions imaged with dual-energy mammography prior to breast biopsy with final diagnosis resulting in 10 invasive ductal carcinomas, 5 ductal carcinomain situ, 11 fibroadenomas, and 19 other benign diagnoses. Analysis was threefold: (1) The raw low-energy mammographic images were analyzed with an established in-house QIA method, “QIA alone,” (2) the three-compartment breast (3CB) composition measure—derived from the dual-energy mammography—of water, lipid, and protein thickness were assessed, “3CB alone”, and (3) information from QIA and 3CB was combined, “QIA + 3CB.” Analysis was initiated from radiologist-indicated lesion centers and was otherwise fully automated. Steps of the QIA and 3CB methods were lesion segmentation, characterization, and subsequent classification for malignancy in leave-one-case-out cross-validation. Performance assessment included box plots, Bland–Altman plots, and Receiver Operating Characteristic (ROC) analysis. Results: The area under the ROC curve (AUC) for distinguishing between benign and malignant lesions (invasive and DCIS) was 0.81 (standard error 0.07) for the “QIA alone” method, 0.72 (0.07) for “3CB alone” method, and 0.86 (0.04) for “QIA+3CB” combined. The difference in AUC was 0.043 between “QIA + 3CB” and “QIA alone” but failed to reach statistical significance (95% confidence interval [–0.17 to + 0.26]). Conclusions: In this pilot study analyzing the new 3CB imaging modality, knowledge of the composition of breast lesions and their periphery appeared additive in combination with existing mammographic QIA methods for the distinction between different benign and malignant lesion types.

  18. A Practical Approach to Quantitative Processing and Analysis of Small Biological Structures by Fluorescent Imaging.

    PubMed

    Noller, Crystal M; Boulina, Maria; McNamara, George; Szeto, Angela; McCabe, Philip M; Mendez, Armando J

    2016-09-01

    Standards in quantitative fluorescent imaging are vaguely recognized and receive insufficient discussion. A common best practice is to acquire images at Nyquist rate, where highest signal frequency is assumed to be the highest obtainable resolution of the imaging system. However, this particular standard is set to insure that all obtainable information is being collected. The objective of the current study was to demonstrate that for quantification purposes, these correctly set acquisition rates can be redundant; instead, linear size of the objects of interest can be used to calculate sufficient information density in the image. We describe optimized image acquisition parameters and unbiased methods for processing and quantification of medium-size cellular structures. Sections of rabbit aortas were immunohistochemically stained to identify and quantify sympathetic varicosities, >2 μm in diameter. Images were processed to reduce background noise and segment objects using free, open-access software. Calculations of the optimal sampling rate for the experiment were based on the size of the objects of interest. The effect of differing sampling rates and processing techniques on object quantification was demonstrated. Oversampling led to a substantial increase in file size, whereas undersampling hindered reliable quantification. Quantification of raw and incorrectly processed images generated false structures, misrepresenting the underlying data. The current study emphasizes the importance of defining image-acquisition parameters based on the structure(s) of interest. The proposed postacquisition processing steps effectively removed background and noise, allowed for reliable quantification, and eliminated user bias. This customizable, reliable method for background subtraction and structure quantification provides a reproducible tool for researchers across biologic disciplines. PMID:27182204

  19. Quantitation and biological properties of released and cell-bound lipooligosaccharides from nontypeable Haemophilus influenzae.

    PubMed Central

    Gu, X X; Tsai, C M; Apicella, M A; Lim, D J

    1995-01-01

    Nontypeable Haemophilus influenzae (NTHi) is a major pathogen causing otitis media in children. NTHi releases lipooligosaccharide (LOS) as outer membrane fragments during its growth. The release of LOS may play an important role in the pathogenicity of otitis media caused by this organism. The amounts of LOS in bacterial cells and growth media for five NTHi strains were determined by quantitative silver staining after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These strains were estimated to have 1.6 x 10(6) to 4.8 x 10(6) LOS molecules per bacterium. During a 3-day growth period, these NTHi strains released variable but significant amounts of LOS into the growth medium. Cells started to release detectable amounts of LOS into the medium at 2 to 5 h and continued to do so for up to 48 or 72 h. The concentrations of LOS in the culture supernatants released by these five strains were 10 to 55 micrograms/ml at 24 h and 40 to 100 micrograms/ml at 72 h, which was 34 to 189% of the cell-bound LOS concentration. The biological properties of released and cell-bound LOSs from two representative strains were compared. Released LOS showed an approximately 10-fold increase in inducing human monocytes to produce tumor necrosis factor alpha, interleukin 1 beta, and interleukin 6, a 13- to 28-fold increase in mouse lethal toxicity, and a 16- to 37-fold increase in the clotting of Limulus amebocyte lysate. These results suggested that released LOS or its inflammatory mediators play a more important role than the LOS in bacteria in the pathogenicity of otitis media caused by this organism. PMID:7558327

  20. Application of solid phase microextraction for quantitation of polyunsaturated fatty acids in biological fluids.

    PubMed

    Birjandi, Afsoon Pajand; Mirnaghi, Fatemeh Sadat; Bojko, Barbara; Wąsowicz, Marcin; Pawliszyn, Janusz

    2014-12-16

    Development of a straightforward strategy for simultaneous quantitative analysis of nonesterified fatty acids (NEFA) species in biofluids is a challenging task because of the extreme complexity of fatty acid distribution in biological matrices. In this study, we present a direct immersion solid phase microextraction method coupled to a liquid chromatography-mass spectrometry platform (DI-SPME- HPLC-ESI -MS) for determination of unconjugated fatty acids (FA) in fish and human plasma. The proposed method was fully validated according to bioanalytical method validation guidelines. The LOD and LOQ were in the range of 0.5-2 and 5-12 ng/mL, respectively, with a linear dynamic range of 100 fold for each compound. Absolute and relative matrix effects were comprehensively evaluated and found to be in the acceptable range of 91-116%. The affinity constant (Ka) of individual FAs to protein albumin was determined to be 9.2 × 10(4) to 4.3 × 10(5) M(-1). The plasma protein binding (PPB%) was calculated and found to be in the range of 98.0-99.7% for different polyunsaturated fatty acids (PUFAs). The PUFAs under study were found at a high concentration range in fish plasma, whereas only a few were within quantification range in control human plasma. The method was successfully applied for monitoring PUFA changes during the operation in plasma samples obtained from patients undergoing cardiac surgery with the use of cardiopulmonary bypass (CPB). The most significant contribution induced by surgery was noticed in the concentration level of α-linolenic acid (18:3, ALA), arachidonic acid (20:4, AA), and docosahexanoic acid (22:6, DHA) soon after administration of CPB in all cases. PMID:25403310

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

    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.

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

    PubMed

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

    2013-07-01

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

  3. Qualitative and quantitative control of carbonated cola beverages using ¹H NMR spectroscopy.

    PubMed

    Maes, Pauline; Monakhova, Yulia B; Kuballa, Thomas; Reusch, Helmut; Lachenmeier, Dirk W

    2012-03-21

    ¹H Nuclear magnetic resonance (NMR) spectroscopy (400 MHz) was used in the context of food surveillance to develop a reliable analytical tool to differentiate brands of cola beverages and to quantify selected constituents of the soft drinks. The preparation of the samples required only degassing and addition of 0.1% of TSP in D₂O for locking and referencing followed by adjustment of pH to 4.5. The NMR spectra obtained can be considered as "fingerprints" and were analyzed by principal component analysis (PCA). Clusters from colas of the same brand were observed, and significant differences between premium and discount brands were found. The quantification of caffeine, acesulfame-K, aspartame, cyclamate, benzoate, hydroxymethylfurfural (HMF), sulfite ammonia caramel (E 150D), and vanillin was simultaneously possible using external calibration curves and applying TSP as internal standard. Limits of detection for caffeine, aspartame, acesulfame-K, and benzoate were 1.7, 3.5, 0.8, and 1.0 mg/L, respectively. Hence, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of soft drinks and quantification of selected constituents.

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

    SciTech Connect

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

    2002-12-04

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

  5. Introduction: Andrew Thomson and the Centre for Metalloprotein Spectroscopy and Biology at the University of East Anglia.

    PubMed

    Wilson, Michael T

    2008-12-01

    The present article briefly relates the early history and growth of the Centre for Metalloprotein Spectroscopy and Biology at UEA (University of East Anglia) under the joint directorship of A.J. Thomson and C. Greenwood, and charts the exceptional success that this centre has had in fostering bioinorganic chemistry in the U.K. and the impact that it has had internationally.

  6. Quantitative real-time monitoring of dryer effluent using fiber optic near-infrared spectroscopy.

    PubMed

    Harris, S C; Walker, D S

    2000-09-01

    This paper describes a method for real-time quantitation of the solvents evaporating from a dryer. The vapor stream in the vacuum line of a dryer was monitored in real time using a fiber optic-coupled acousto-optic tunable filter near-infrared (AOTF-NIR) spectrometer. A balance was placed in the dryer, and mass readings were recorded for every scan of the AOTF-NIR. A partial least-squares (PLS) calibration was subsequently built based on change in mass over change in time for solvents typically used in a chemical manufacturing plant. Controlling software for the AOTF-NIR was developed. The software collects spectra, builds the PLS calibration model, and continuously fits subsequently collected spectra to the calibration, allowing the operator to follow the mass loss of solvent from the dryer. The results indicate that solvent loss can be monitored and quantitated in real time using NIR for the optimization of drying times. These time-based mass loss values have also been used to calculate "dynamic" vapor density values for the solvents. The values calculated are in agreement with values determined from the ideal gas law and could prove valuable as tools to measure temperature or pressure indirectly. PMID:10944383

  7. Performance evaluation of Laser Induced Breakdown Spectroscopy (LIBS) for quantitative analysis of rare earth elements in phosphate glasses

    NASA Astrophysics Data System (ADS)

    Devangad, Praveen; Unnikrishnan, V. K.; Nayak, Rajesh; Tamboli, M. M.; Muhammed Shameem, K. M.; Santhosh, C.; Kumar, G. A.; Sardar, D. K.

    2016-02-01

    In the current study, we have determined the elemental compositions of synthesized rare earth doped phosphate glasses using a laboratory Laser-Induced Breakdown Spectroscopy (LIBS) system. LIBS spectra of this rare earth (samarium (Sm), thulium (Tm) and ytterbium (Yb)) doped glass samples with known composition are recorded using a highly sensitive detector. Major atomic emission lines of Sm, Tm and Yb found in LIBS spectra are reported. By considering the atomic emission line of phosphorous as an internal standard, calibration curves were constructed for all the rare earth concentrations. Very good linear regression coefficient (R2) values were obtained using this technique. Analytical predictive skill of LIBS was studied further using leave-one-out method. Low values of the reported correlation uncertainty between measured LIBS concentration ratio and certified concentration ratio confirms that LIBS technique has great potential for quantitative analysis of rare earth elements in glass matrix.

  8. The quantitative determination of FeS2 phases in coal by means of 57Fe Mössbauer spectroscopy

    USGS Publications Warehouse

    Evans, B.J.; King, Hobart M.; Renton, John J.; Stiller, A.

    1990-01-01

    A knowledge of the concentration of pyrite and marcasite in coals can provide important insight into the genesis of coal deposits. Determinations of the relative amounts of pyrite and marcasite by traditional methods of coal analysis are, however, beset with many difficulties. Using 57Fe Mössbauer spectroscopy and a mild chemical treatment with hydrofluoric acid, a technique has been devised for the quantitative determination of the relative concentrations of pyrite and marcasite in samples of whole coals or their low-temperature ashes. The sample preparation procedure is comparable to less accurate methods. Good qualitative agreement has been obtained between ore microscopic and Mössbauer spectroscopic techniques for a series of extensively investigated whole coal samples.

  9. Micro-laser-induced breakdown spectroscopy technique: a powerful method for performing quantitative surface mapping on conductive and nonconductive samples

    NASA Astrophysics Data System (ADS)

    Menut, Denis; Fichet, Pascal; Lacour, Jean-Luc; Rivoallan, Annie; Mauchien, Patrick

    2003-10-01

    Laser-induced breakdown spectroscopy (LIBS) has been applied mainly to bulk analysis of solids, liquids, and gases and less frequently for elemental microanalysis of solid surfaces. A micro-LIBS device devoted to analysis of the distribution of elements on surfaces is described. This device offers rapid access with a 3-μm spatial resolution to the microchemical structures of both conductive and nonconductive samples. Quantitative microchemical results of applications to ceramics are reported. By the use of a time-resolved acquisition spectrum, cerium in a uranium matrix was characterized with a cerium detection limit of 1.14%. Calibration curves obtained with manipulations during 1 year facilitated evaluations of reproducibility and repeatability. A 2% single-shot repeatability with a calibration reproducibility of ~7% is reported.

  10. Micro-laser-induced breakdown spectroscopy technique: a powerful method for performing quantitative surface mapping on conductive and nonconductive samples.

    PubMed

    Menut, Denis; Fichet, Pascal; Lacour, Jean-Luc; Rivoallan, Annie; Mauchien, Patrick

    2003-10-20

    Laser-induced breakdown spectroscopy (LIBS) has been applied mainly to bulk analysis of solids, liquids, and gases and less frequently for elemental microanalysis of solid surfaces. A micro-LIBS device devoted to analysis of the distribution of elements on surfaces is described. This device offers rapid access with a 3-microm spatial resolution to the microchemical structures of both conductive and nonconductive samples. Quantitative microchemical results of applications to ceramics are reported. By the use of a time-resolved acquisition spectrum, cerium in a uranium matrix was characterized with a cerium detection limit of 1.14%. Calibration curves obtained with manipulations during 1 year facilitated evaluations of reproducibility and repeatability. A 2% single-shot repeatability with a calibration reproducibility of approximately 7% is reported.

  11. Improving the quantitative accuracy of cerebral oxygen saturation in monitoring the injured brain using atlas based Near Infrared Spectroscopy models.

    PubMed

    Clancy, Michael; Belli, Antonio; Davies, David; Lucas, Samuel J E; Su, Zhangjie; Dehghani, Hamid

    2016-08-01

    The application of Near Infrared Spectroscopy (NIRS) for the monitoring of the cerebral oxygen saturation within the brain is well established, albeit using temporal data that can only measure relative changes of oxygenation state of the brain from a baseline. The focus of this investigation is to demonstrate that hybridisation of existing near infrared probe designs and reconstruction techniques can pave the way to produce a system and methods that can be used to monitor the absolute oxygen saturation in the injured brain. Using registered Atlas models in simulation, a novel method is outlined by which the quantitative accuracy and practicality of NIRS for specific use in monitoring the injured brain, can be improved, with cerebral saturation being recovered to within 10.1 ± 1.8% of the expected values. PMID:27003677

  12. Analysis of poly-β-hydroxyalkonates (PHA) during the enhanced biological phosphorus removal process using FTIR spectroscopy.

    PubMed

    Li, Wei-hua; Mao, Qin-yan; Liu, Yi-xin; Sheng, Guo-ping; Yu, Han-qing; Huang, Xian-huai; Liu, Shao-geng; Ling, Qi; Yan, Guo-bing

    2014-06-01

    Enhanced biological phosphorus removal (EBPR) is the main phosphorus removal technique for wastewater treatment. During the anaerobic-aerobic alternative process, the activated sludge experienced the anaerobic storage of polyhydroxy-β-alkonates (PHA) and aerobic degradation, corresponding the infrared peak intensity of sludge at 1 740 cm(-1) increased in the aerobic phase and declined in the anaerobic phase. Compared with PHA standard, this peak was indentified to attribute the carbonyl of PHA. The overlapping peaks of PHA, protein I and II bands were separated using Gaussian peak fitting method. The infrared peak area ratios of PHA versus protein I had a good relationship with the PHA contents measured by gas chromatography, and the correlation coefficient was 0.873. Thus, the ratio of the peak area of PHA versus protein I can be considered as the indicator of the PHA content in the sludge. The infrared spectra of 1 480-1 780 cm(-1) was selected, normalized and transferred to the absorption data. Combined with the chromatography analysis of PHA content in the sludge sample, a model between the Fourier-transform infrared spectroscopy (ETIR) spectra of the sludge and PHA content was established, which could be used for the prediction of the PHA content in the unknown sample. The PHA content in the sludge sample could be acquired by the infrared spectra of the sludge sample and the established model, and the values fitted well with the results obtained from chromatograph. The results would provide a novel analysis method for the rapid characterization and quantitative determination of the intracellular PHA content in the activated sludge.

  13. Analysis of poly-β-hydroxyalkonates (PHA) during the enhanced biological phosphorus removal process using FTIR spectroscopy.

    PubMed

    Li, Wei-hua; Mao, Qin-yan; Liu, Yi-xin; Sheng, Guo-ping; Yu, Han-qing; Huang, Xian-huai; Liu, Shao-geng; Ling, Qi; Yan, Guo-bing

    2014-06-01

    Enhanced biological phosphorus removal (EBPR) is the main phosphorus removal technique for wastewater treatment. During the anaerobic-aerobic alternative process, the activated sludge experienced the anaerobic storage of polyhydroxy-β-alkonates (PHA) and aerobic degradation, corresponding the infrared peak intensity of sludge at 1 740 cm(-1) increased in the aerobic phase and declined in the anaerobic phase. Compared with PHA standard, this peak was indentified to attribute the carbonyl of PHA. The overlapping peaks of PHA, protein I and II bands were separated using Gaussian peak fitting method. The infrared peak area ratios of PHA versus protein I had a good relationship with the PHA contents measured by gas chromatography, and the correlation coefficient was 0.873. Thus, the ratio of the peak area of PHA versus protein I can be considered as the indicator of the PHA content in the sludge. The infrared spectra of 1 480-1 780 cm(-1) was selected, normalized and transferred to the absorption data. Combined with the chromatography analysis of PHA content in the sludge sample, a model between the Fourier-transform infrared spectroscopy (ETIR) spectra of the sludge and PHA content was established, which could be used for the prediction of the PHA content in the unknown sample. The PHA content in the sludge sample could be acquired by the infrared spectra of the sludge sample and the established model, and the values fitted well with the results obtained from chromatograph. The results would provide a novel analysis method for the rapid characterization and quantitative determination of the intracellular PHA content in the activated sludge. PMID:25358156

  14. [Quantitative analysis of Mn and Si of alloy steels by laser-induced breakdown spectroscopy].

    PubMed

    Sun, Lan-Xiang; Yu, Hai-Bin; Xin, Yong; Cong, Zhi-Bo

    2010-12-01

    The concentration of Mn and Si in different kinds of steels was determined by laser-induced breakdown spectroscopy (LIBS). The multivariate quadratic nonlinear function was adopted for calibration. Samples including common alloy steels, stainless steels and carbon tool steels were analyzed. The matrix effect was serious because of large difference in compositions of different kinds of steels and strong line overlaps in steel spectra. Therefore, the common calibration methods that only use one analytical line to calibrate the complex chemical compositions of alloy steels will lose much information. The multivariate calibration methods, however, can utilize more information of spectra, successfully reduce the matrix effect and improve the measurement repeatability and accuracy of LIBS. Compared with the common calibration method based on one analytical line, the relative standard deviation was reduced from above 20% to below 10%, and the accuracy was increased by more than 5 times for Mn and more than 6 times for Si.

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

    NASA Astrophysics Data System (ADS)

    Sowoidnich, Kay; Kronfeldt, Heinz-Detlef

    2012-06-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

    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.

  17. Quantitative determination of molecular structure in multilayered thin films of biaxial and lower symmetry from photon spectroscopies. I. Reflection infrared vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Parikh, Atul N.; Allara, David L.

    1992-01-01

    A semitheoretical formalism based on classical electromagnetic wave theory has been developed for application to the quantitative treatment of reflection spectra from multilayered anisotropic films on both metallic and nonmetallic substrates. Both internal and external reflection experiments as well as transmission can be handled. The theory is valid for all wavelengths and is appropriate, therefore, for such experiments as x-ray reflectivity, uv-visible spectroscopic ellipsometry, and infrared reflection spectroscopy. Further, the theory is applicable to multilayered film structures of variable number of layers, each with any degree of anisotropy up to and including full biaxial symmetry. The reflectivities (and transmissivities) are obtained at each frequency by solving the wave propagation equations using a rigorous 4×4 transfer matrix method developed by Yeh in which the optical functions of each medium are described in the form of second rank (3×3) tensors. In order to obtain optical tensors for materials not readily available in single crystal form, a method has been developed to evaluate tensor elements from the complex scalar optical functions (n̂) obtained from the isotropic material with the limitations that the molecular excitations are well characterized and obey photon-dipole selection rules. This method is intended primarily for infrared vibrational spectroscopy and involves quantitative decomposition of the isotropic imaginary optical function (k) spectrum into a sum of contributions from fundamental modes, the assignment of a direction in molecular coordinates to the transition dipole matrix elements for each mode, the appropriate scaling of each k vector component in surface coordinates according to a selected surface orientation of the molecule to give a diagonal im(n̂) tensor, and the calculation of the real(n̂) spectrum tensor elements by the Kramers-Kronig transformation. Tensors for other surface orientations are generated by an

  18. Explicit Tracking of Uncertainty Increases the Power of Quantitative Rule-of-Thumb Reasoning in Cell Biology

    PubMed Central

    Johnston, Iain G.; Rickett, Benjamin C.; Jones, Nick S.

    2014-01-01

    Back-of-the-envelope or rule-of-thumb calculations involving rough estimates of quantities play a central scientific role in developing intuition about the structure and behavior of physical systems, for example in so-called Fermi problems in the physical sciences. Such calculations can be used to powerfully and quantitatively reason about biological systems, particularly at the interface between physics and biology. However, substantial uncertainties are often associated with values in cell biology, and performing calculations without taking this uncertainty into account may limit the extent to which results can be interpreted for a given problem. We present a means to facilitate such calculations where uncertainties are explicitly tracked through the line of reasoning, and introduce a probabilistic calculator called CALADIS, a free web tool, designed to perform this tracking. This approach allows users to perform more statistically robust calculations in cell biology despite having uncertain values, and to identify which quantities need to be measured more precisely to make confident statements, facilitating efficient experimental design. We illustrate the use of our tool for tracking uncertainty in several example biological calculations, showing that the results yield powerful and interpretable statistics on the quantities of interest. We also demonstrate that the outcomes of calculations may differ from point estimates when uncertainty is accurately tracked. An integral link between CALADIS and the BioNumbers repository of biological quantities further facilitates the straightforward location, selection, and use of a wealth of experimental data in cell biological calculations. PMID:25468340

  19. Explicit Tracking of Uncertainty Increases the Power of Quantitative Rule-of-Thumb Reasoning in Cell Biology

    NASA Astrophysics Data System (ADS)

    Johnston, Iain G.; Rickett, Benjamin C.; Jones, Nick S.

    2014-12-01

    "Back-of-the-envelope" or "rule-of-thumb" calculations involving rough estimates of quantities play a central scientific role in developing intuition about the structure and behaviour of physical systems, for example in so-called `Fermi problems' in the physical sciences. Such calculations can be used to powerfully and quantitatively reason about biological systems, particularly at the interface between physics and biology. However, substantial uncertainties are often associated with values in cell biology, and performing calculations without taking this uncertainty into account may limit the extent to which results can be interpreted for a given problem. We present a means to facilitate such calculations where uncertainties are explicitly tracked through the line of reasoning, and introduce a `probabilistic calculator' called Caladis, a web tool freely available at www.caladis.org, designed to perform this tracking. This approach allows users to perform more statistically robust calculations in cell biology despite having uncertain values, and to identify which quantities need to be measured more precisely in order to make confident statements, facilitating efficient experimental design. We illustrate the use of our tool for tracking uncertainty in several example biological calculations, showing that the results yield powerful and interpretable statistics on the quantities of interest. We also demonstrate that the outcomes of calculations may differ from point estimates when uncertainty is accurately tracked. An integral link between Caladis and the Bionumbers repository of biological quantities further facilitates the straightforward location, selection, and use of a wealth of experimental data in cell biological calculations.

  20. Explicit tracking of uncertainty increases the power of quantitative rule-of-thumb reasoning in cell biology.

    PubMed

    Johnston, Iain G; Rickett, Benjamin C; Jones, Nick S

    2014-12-01

    Back-of-the-envelope or rule-of-thumb calculations involving rough estimates of quantities play a central scientific role in developing intuition about the structure and behavior of physical systems, for example in so-called Fermi problems in the physical sciences. Such calculations can be used to powerfully and quantitatively reason about biological systems, particularly at the interface between physics and biology. However, substantial uncertainties are often associated with values in cell biology, and performing calculations without taking this uncertainty into account may limit the extent to which results can be interpreted for a given problem. We present a means to facilitate such calculations where uncertainties are explicitly tracked through the line of reasoning, and introduce a probabilistic calculator called CALADIS, a free web tool, designed to perform this tracking. This approach allows users to perform more statistically robust calculations in cell biology despite having uncertain values, and to identify which quantities need to be measured more precisely to make confident statements, facilitating efficient experimental design. We illustrate the use of our tool for tracking uncertainty in several example biological calculations, showing that the results yield powerful and interpretable statistics on the quantities of interest. We also demonstrate that the outcomes of calculations may differ from point estimates when uncertainty is accurately tracked. An integral link between CALADIS and the BioNumbers repository of biological quantities further facilitates the straightforward location, selection, and use of a wealth of experimental data in cell biological calculations.

  1. Quantitative analysis of cyclic dimer fatty acid content in the dimerization product by proton NMR spectroscopy.

    PubMed

    Park, Kyun Joo; Kim, Minyoung; Seok, Seunghwan; Kim, Young-Wun; Kim, Do Hyun

    2015-01-01

    In this work, (1)H NMR is utilized for the quantitative analysis of a specific cyclic dimer fatty acid in a dimer acid mixture using the pseudo-standard material of mesitylene on the basis of its structural similarity. Mesitylene and cyclic dimer acid levels were determined using the signal of the proton on the cyclic ring (δ=6.8) referenced to the signal of maleic acid (δ=6.2). The content of the cyclic dimer fatty acid was successfully determined through the standard curve of mesitylene and the reported equation. Using the linearity of the mesitylene curve, the cyclic dimer fatty acid in the oil mixture was quantified. The results suggest that the proposed method can be used to quantify cyclic compounds in mixtures to optimize the dimerization process.

  2. Quantitative degenerate four-wave mixing spectroscopy: Probes for molecular species

    SciTech Connect

    Farrow, R.; Rakestraw, D.; Paul, P.; Lucht, R.; Danehy, P.; Friedman-Hill, E.; Germann, G.

    1993-12-01

    Resonant degenerate four-wave mixing (DFWM) is currently the subject of intensive investigation as a sensitive diagnostic tool for molecular species. DFWM has the advantage of generating a coherent (beam-like) signal which results in null-background detection and provides excellent immunity to background-light interference. Since multiple one-photon resonances are involved in the signal generation process, the DFWM technique can allow sensitive detection of molecules via electronic, vibrational or rotational transitions. These properties combine to make DFWM a widely applicable diagnostic technique for the probing of molecular species. The authors are conducting fundamental and applied investigations of DFWM for quantitative measurements of trace species in reacting gases. During the past year, efforts have been focussed in two areas: (1) understanding the effects of collisional processes on the DFWM signal generation process, and (2) exploring the applicability of infrared DFWM to detect polyatomic molecules via rovibrational transitions.

  3. Quantitative analysis of ammonium salts in coking industrial liquid waste treatment process based on Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Cao, Ya-Nan; Wang, Gui-Shi; Tan, Tu; Cai, Ting-Dong; Liu, Kun; Wang, Lei; Zhu, Gong-Dong; Mei, Jiao-Xu

    2016-10-01

    Quantitative analysis of ammonium salts in the process of coking industrial liquid waste treatment is successfully performed based on a compact Raman spectrometer combined with partial least square (PLS) method. Two main components (NH4SCN and (NH4)2S2O3) of the industrial mixture are investigated. During the data preprocessing, wavelet denoising and an internal standard normalization method are employed to improve the predicting ability of PLS models. Moreover, the PLS models with different characteristic bands for each component are studied to choose a best resolution. The internal and external calibration results of the validated model show a mass percentage error below 1% for both components. Finally, the repeatabilities and reproducibilities of Raman and reference titration measurements are also discussed. Project supported by the National Natural Science Foundation of China (Grant Nos. 41405022 and 61475068).

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

    PubMed

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

    2013-11-15

    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 μm 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.

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

    PubMed

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

    2013-11-15

    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 μm 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

  6. Quantitative Analysis of Metabolic Mixtures by 2D 13C-Constant-Time TOCSY NMR Spectroscopy

    PubMed Central

    Bingol, Kerem; Zhang, Fengli; Bruschweiler-Li, Lei; Brüschweiler, Rafael

    2013-01-01

    An increasing number of organisms can be fully 13C-labeled, which has the advantage that their metabolomes can be studied by high-resolution 2D NMR 13C–13C constant-time (CT) TOCSY experiments. Individual metabolites can be identified via database searching or, in the case of novel compounds, through the reconstruction of their backbone-carbon topology. Determination of quantitative metabolite concentrations is another key task. Because significant peak overlaps in 1D NMR spectra prevents straightforward quantification through 1D peak integrals, we demonstrate here the direct use of 13C–13C CT-TOCSY spectra for metabolite quantification. This is accomplished through the quantum-mechanical treatment of the TOCSY magnetization transfer at short and long mixing times or by the use of analytical approximations, which are solely based on the knowledge of the carbon-backbone topologies. The methods are demonstrated for carbohydrate and amino-acid mixtures. PMID:23773204

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

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

    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.

  8. [Rapid Quantitative Analysis of Content of the Additive in Gasoline for Motor Vehicles by Near-Infrared Spectroscopy].

    PubMed

    Rong, Hai-teng; Song, Chun-feng; Yuan, Hong-fu; Li, Xiao-yu; Hu, Ai-qin; Xie, Jin-chun; Yan, De-lin

    2015-10-01

    A new rapid quantitative method for the determination of oxygenates and the compounds not included in the national standard in gasoline using near-infrared spectroscopy is raised by this paper. This method combine near-infrared spectroscopy with oblique projection. This experiment choose four different types of gasoline, including reconcile gasoline, FCC refined gasoline, reformed gasoline and desulfurizing gasoline. Prepare series gasoline samples containing different concentrations and different types of compounds. Using FTIR spectrometer to measure those samples and got transmission spectrums. Oblique projection method could separate quantity spectral signal from mixed spectrum signal, and using projection to calculate and analyze the separated signal to obtain the content of measured component. The deviation between this method and the real content is low, the absolute error is less than 0.8 and the relative error is less than 8%. For the actual gasoline samples, compare results of this method with gas chromatography, the absolute error are less than 0.85 and the relative error are less than 6.85%. This method solves the problem of general multivariate calibration methods. It is very significant for the development of rapid detection technology using NIR suitable for on-site and the improvement of the quality of gasoline.

  9. Laser-induced breakdown spectroscopy (LIBS) to measure quantitatively soil carbon with emphasis on soil organic carbon. A review.

    PubMed

    Senesi, Giorgio S; Senesi, Nicola

    2016-09-28

    Soil organic carbon (OC) measurement is a crucial factor for quantifying soil C pools and inventories and monitoring the inherent temporal and spatial heterogeneity and changes of soil OC content. These are relevant issues in addressing sustainable management of terrestrial OC aiming to enhance C sequestration in soil, thus mitigating the impact of increasing CO2 concentration in the atmosphere and related effects on global climate change. Nowadays, dry combustion by an elemental analyzer or wet combustion by dichromate oxidation of the soil sample are the most recommended and commonly used methods for quantitative soil OC determination. However, the unanimously recognized uncertainties and limitations of these classical laboursome methods have prompted research efforts focusing on the development and application of more advanced and appealing techniques and methods for the measurement of soil OC in the laboratory and possibly in situ in the field. Among these laser-induced breakdown spectroscopy (LIBS) has raised the highest interest for its unique advantages. After an introduction and a highlight of the LIBS basic principles, instrumentation, methodologies and supporting chemometric methods, the main body of this review provides an historical and critical overview of the developments and results obtained up-to-now by the application of LIBS to the quantitative measurement of soil C and especially OC content. A brief critical summary of LIBS advantages and limitations/drawbacks including some final remarks and future perspectives concludes this review. PMID:27619082

  10. Quantitative analysis of D-(+)-glucose in fruit juices using diffusion ordered-1H nuclear magnetic resonance spectroscopy.

    PubMed

    Cao, Ruge; Komura, Fusae; Nonaka, Airi; Kato, Takeshi; Fukumashi, Junji; Matsui, Toshiro

    2014-01-01

    This study works on D-(+)-glucose quantitative analysis using diffusion ordered-quantitative (1)H nuclear magnetic resonance spectroscopy (DOSY-qNMR), by which an analyte could be distinguished from interferences based upon a characteristic diffusion coefficient (D) in gradient magnetic fields. The D value of D-(+)-glucose in deuterium oxide at 30°C was 5.6 × 10(-10) m(2)/s at a field gradient pulse of between 5.0 × 10(-2) and 3.0 × 10(-1) T/m, distinguished from fructose, sucrose and starch. Good linearity (r(2) = 0.9998) was obtained between D-(+)-glucose (0.5-20.0 g/L) and the ratio of the resonance area of α-C1 proton (5.21 ppm) in D-(+)-glucose to that of the β-C1 proton (5.25 ppm) in D-glucuronic acid (50.0 g/L) as an internal standard. The DOSY-qNMR method was successfully applied to quantify D-(+)-glucose in orange juice (18.3 ± 1.0 g/L), apple juice (26.3 ± 0.4 g/L) and grape juice (45.6 ± 0.6 g/L); the values agreed well with a conventional F-kit glucose method.

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

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

    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.

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

    NASA Technical Reports Server (NTRS)

    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

    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.

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

    PubMed

    Meuse, Curtis W; Barker, Peter E

    2009-12-01

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

  14. Laser-induced breakdown spectroscopy (LIBS) to measure quantitatively soil carbon with emphasis on soil organic carbon. A review.

    PubMed

    Senesi, Giorgio S; Senesi, Nicola

    2016-09-28

    Soil organic carbon (OC) measurement is a crucial factor for quantifying soil C pools and inventories and monitoring the inherent temporal and spatial heterogeneity and changes of soil OC content. These are relevant issues in addressing sustainable management of terrestrial OC aiming to enhance C sequestration in soil, thus mitigating the impact of increasing CO2 concentration in the atmosphere and related effects on global climate change. Nowadays, dry combustion by an elemental analyzer or wet combustion by dichromate oxidation of the soil sample are the most recommended and commonly used methods for quantitative soil OC determination. However, the unanimously recognized uncertainties and limitations of these classical laboursome methods have prompted research efforts focusing on the development and application of more advanced and appealing techniques and methods for the measurement of soil OC in the laboratory and possibly in situ in the field. Among these laser-induced breakdown spectroscopy (LIBS) has raised the highest interest for its unique advantages. After an introduction and a highlight of the LIBS basic principles, instrumentation, methodologies and supporting chemometric methods, the main body of this review provides an historical and critical overview of the developments and results obtained up-to-now by the application of LIBS to the quantitative measurement of soil C and especially OC content. A brief critical summary of LIBS advantages and limitations/drawbacks including some final remarks and future perspectives concludes this review.

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

    SciTech Connect

    Heppenstall, R.B.; Sapega, A.A.; Izant, T.; Fallon, R.; Shenton, D.; Park, Y.S.; Chance, B. )

    1989-08-01

    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.

  16. Vibrational spectroscopy and microspectroscopy analyzing qualitatively and quantitatively pharmaceutical hot melt extrudates.

    PubMed

    Netchacovitch, L; Thiry, J; De Bleye, C; Chavez, P-F; Krier, F; Sacré, P-Y; Evrard, B; Hubert, Ph; Ziemons, E

    2015-09-10

    Since the last decade, more and more Active Pharmaceutical Ingredient (API) candidates have poor water solubility inducing low bioavailability. These molecules belong to the Biopharmaceutical Classification System (BCS) classes II and IV. Thanks to Hot-Melt Extrusion (HME), it is possible to incorporate these candidates in pharmaceutical solid forms. Indeed, HME increases the solubility and the bioavailability of these drugs by encompassing them in a polymeric carrier and by forming solid dispersions. Moreover, in 2004, the FDA's guidance initiative promoted the usefulness of Process Analytical Technology (PAT) tools when developing a manufacturing process. Indeed, the main objective when developing a new pharmaceutical process is the product quality throughout the production chain. The trend is to follow this parameter in real-time in order to react immediately when there is a bias. Vibrational spectroscopic techniques, NIR and Raman, are useful to analyze processes in-line. Moreover, off-line Raman microspectroscopy is more and more used when developing new pharmaceutical processes or when analyzing optimized ones by combining the advantages of Raman spectroscopy and imaging. It is an interesting tool for homogeneity and spatial distribution studies. This review treats about spectroscopic techniques analyzing a HME process, as well off-line as in-line, presenting their advantages and their complementarities. PMID:25704954

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

    PubMed Central

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

    2009-01-01

    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. PMID:20186729

  18. Quantitative analysis of mixed hydrofluoric and nitric acids using Raman spectroscopy with partial least squares regression.

    PubMed

    Kang, Gumin; Lee, Kwangchil; Park, Haesung; Lee, Jinho; Jung, Youngjean; Kim, Kyoungsik; Son, Boongho; Park, Hyoungkuk

    2010-06-15

    Mixed hydrofluoric and nitric acids are widely used as a good etchant for the pickling process of stainless steels. The cost reduction and the procedure optimization in the manufacturing process can be facilitated by optically detecting the concentration of the mixed acids. In this work, we developed a novel method which allows us to obtain the concentrations of hydrofluoric acid (HF) and nitric acid (HNO(3)) mixture samples with high accuracy. The experiments were carried out for the mixed acids which consist of the HF (0.5-3wt%) and the HNO(3) (2-12wt%) at room temperature. Fourier Transform Raman spectroscopy has been utilized to measure the concentration of the mixed acids HF and HNO(3), because the mixture sample has several strong Raman bands caused by the vibrational mode of each acid in this spectrum. The calibration of spectral data has been performed using the partial least squares regression method which is ideal for local range data treatment. Several figures of merit (FOM) were calculated using the concept of net analyte signal (NAS) to evaluate performance of our methodology.

  19. Quantitative analysis of arsenic in mine tailing soils using double pulse-laser induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Kwak, Ji-hyun; Lenth, Christoph; Salb, Christian; Ko, Eun-Joung; Kim, Kyoung-Woong; Park, Kihong

    2009-10-01

    A double pulse-laser induced breakdown spectroscopy (DP-LIBS) was used to determine arsenic (As) concentration in 16 soil samples collected from 5 different mine tailing sites in Korea. We showed that the use of double pulse laser led to enhancements of signal intensity (by 13% on average) and signal-to-noise ratio of As emission lines (by 165% on average) with smaller relative standard deviation compared to single pulse laser approach. We believe this occurred because the second laser pulse in the rarefied atmosphere produced by the first pulse led to the increase of plasma temperature and populations of exited levels. An internal standardization method using a Fe emission line provided a better correlation and sensitivity between As concentration and the DP-LIBS signal than any other elements used. The Fe was known as one of the major components in current soil samples, and its concentration varied not substantially. The As concentration determined by the DP-LIBS was compared with that obtained by atomic absorption spectrometry (AAS) to evaluate the current LIBS system. They are correlated with a correlation coefficient of 0.94. The As concentration by the DP-LIBS was underestimated in the high concentration range (>1000 mg-As/kg). The loss of sensitivity that occurred at high concentrations could be explained by self-absorption in the generated plasma.

  20. Quantitative endoscopic imaging elastic scattering spectroscopy: model system/tissue phantom validation

    NASA Astrophysics Data System (ADS)

    Lindsley, E. H.; Farkas, D. L.

    2008-02-01

    We have designed and built an imaging elastic scattering spectroscopy endoscopic instrument for the purpose of detecting cancer in vivo. As part of our testing and validation of the system, known targets representing potential disease states of interest were constructed using polystyrene beads of known average diameter and TiO II crystals embedded in a two-layer agarose gel. Final construction geometry was verified using a dissection microscope. The phantoms were then imaged using the endoscopic probe at a known incident angle, and the results compared to model predictions. The mathematical model that was used combines classic ray-tracing optics with Mie scattering to predict the images that would be observed by the probe at a given physical distance from a Mie-regime scattering media. This model was used generate the expected observed response for a broad range of parameter values, and these results were then used as a library to fit the observed data from the phantoms. Compared against the theoretical library, the best matching signal correlated well with known phantom material dimensions. These results lead us to believe that imaging elastic scattering can be useful in detection/diagnosis, but further refinement of the device will be necessary to detect the weak signals in a real clinical setting.

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

    PubMed

    Mazzei, Pierluigi; Piccolo, Alessandro

    2012-06-01

    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

  2. Quantitative Determination of Fusarium proliferatum Concentration in Intact Garlic Cloves Using Near-Infrared Spectroscopy

    PubMed Central

    Tamburini, Elena; Mamolini, Elisabetta; De Bastiani, Morena; Marchetti, Maria Gabriella

    2016-01-01

    Fusarium proliferatum is considered to be a pathogen of many economically important plants, including garlic. The objective of this research was to apply near-infrared spectroscopy (NIRS) to rapidly determine fungal concentration in intact garlic cloves, avoiding the laborious and time-consuming procedures of traditional assays. Preventive detection of infection before seeding is of great interest for farmers, because it could avoid serious losses of yield during harvesting and storage. Spectra were collected on 95 garlic cloves, divided in five classes of infection (from 1-healthy to 5-very highly infected) in the range of fungal concentration 0.34–7231.15 ppb. Calibration and cross validation models were developed with partial least squares regression (PLSR) on pretreated spectra (standard normal variate, SNV, and derivatives), providing good accuracy in prediction, with a coefficient of determination (R2) of 0.829 and 0.774, respectively, a standard error of calibration (SEC) of 615.17 ppb, and a standard error of cross validation (SECV) of 717.41 ppb. The calibration model was then used to predict fungal concentration in unknown samples, peeled and unpeeled. The results showed that NIRS could be used as a reliable tool to directly detect and quantify F. proliferatum infection in peeled intact garlic cloves, but the presence of the external peel strongly affected the prediction reliability. PMID:27428978

  3. Quantitative analysis of hemoglobin content in polymeric nanoparticles as blood substitutes using Fourier transform infrared spectroscopy.

    PubMed

    Shan, Xiaoqian; Chen, Ligen; Yuan, Yuan; Liu, Changsheng; Zhang, Xiaolan; Sheng, Yan; Xu, Feng

    2010-01-01

    Based on the penetrability of IR within the polymeric nanoparticles, a novel Fourier transform infrared spectroscopy (FTIR) method, with polyacrylonitrile (PAN) as the internal reference standard, was developed to quantify the hemoglobin (Hb) content in Hb-based polymeric nanoparticles (HbPN). The HbPN was fabricated by double emulsion method from poly(ethylene glycol)-poly(lactic acid)-poly(ethylene glycol) triblock copolymers. Depending on the characteristic un-overlapped IR absorbances at 1540 cm(-1) of Hb (amide II) and at 2241 cm(-1) of PAN(-C[triple bond]N), calibration equations, presenting the peak height ratio of Hb and PAN as a function of the weight ratio of Hb and PAN, were established. This new quantification method is validated and used to the determination Hb content in HbPN. Due to the good results of this calibration strategy, the proposed simple FTIR approach with minimal sample-needed and solvent-free makes it useful for routine analysis of protein content and could be also applied to any other drug/protein encapsulated particles.

  4. Quantitation of dexfenfluramine/d-norfenfluramine concentration in primate brain using 19F NMR spectroscopy.

    PubMed

    Christensen, J D; Babb, S M; Cohen, B M; Renshaw, P F

    1998-01-01

    Fluorine (19F) magnetic resonance spectroscopy (MRS) was used to quantify the combined concentration of the anorectic drug dexfenfluramine (DF) and its active metabolite d-norfenfluramine (dNF) in rhesus monkey brain. The accuracy of the MRS technique was assessed by comparison with gas chromatography. Brain 19F MRS signals were converted to brain DF + dNF concentrations after correction for signal relaxation losses and drug distribution in nonbrain tissue. Gas chromatography (GC) was used to assay brain DF and dNF concentrations following MRS evaluation. DF + dNF concentrations measured by 19F MRS averaged 104 +/- 36 microM (mean +/- SD) and GC measurements averaged 71 +/- 12 microM. Correction for the distribution of DF and its metabolites in nonbrain tissue yielded a DF + metabolite brain concentration that was within one standard deviation of the GC-derived value. The concentration of DF plus dNF measured by 19F MRS was similar to or greater than the value obtained by GC, which indicates that DF and its active metabolite dNF are fully detected by 19F MRS in primate brain in vivo. The application of these techniques to human subjects should enable the measurement of low micromolar-range brain concentrations of DF and other fluorinated drugs.

  5. [Rapid quantitative analysis of hydrocarbon composition of furfural extract oils using attenuated total reflection infrared spectroscopy].

    PubMed

    Li, Na; Yuan, Hong-Fu; Hu, Ai-Qin; Liu, Wei; Song, Chun-Feng; Li, Xiao-Yu; Song, Yi-Chang; He, Qi-Jun; Liu, Sha; Xu, Xiao-Xuan

    2014-07-01

    A set of rapid analysis system for hydrocarbon composition of heavy oils was designed using attenuated total reflection FTIR spectrometer and chemometrics to determine the hydrocarbon composition of furfural extract oils. Sixty two extract oil samples were collected and their saturates and aromatics content data were determined according to the standard NB/SH/T0509-2010, then the total contents of resins plus asphaltenes were calculated by the subtraction method in the percentage of weight. Based on the partial least squares (PLS), calibration models for saturates, aromatics, and resin+asphaltene contents were established using attenuated total reflection FTIR spectroscopy, with their SEC, 1.43%, 0.91% and 1.61%, SEP, 1.56%, 1.24% and 1.81%, respectively, meeting the accuracy and repeatability required for the standard. Compared to the present standard method, the efficiency of hydrocarbon composition analysis for furfural extract oils is significantly improved by the new method which is rapid and simple. The system could also be used for other heavy oil analysis, with excellent extension and application foreground.

  6. Quantitative detection of hemoglobin saturation on piglet brain by near-infrared frequency-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Du, Congwu; Andersen, Carol; Chance, Britton

    1997-12-01

    An approach of using phase modulation spectroscopy (PMS) system has been proposed which has single frequency, dual- wavelength with phase-only output for oximetry to minimize the influences of room light in the clinical environment. The availability of this method has been verified by laboratory experiments both in vitro and in vivo. In this study, a 200 Mhz PMS system has been used for measuring on piglet brain in vivo, to detect blood volume and saturation change during normoxia to hypoxia periods, and to monitor the brain depolarization in the hypoxic stress. Our experimental results show that the brain saturation estimated by PMS is approximately 84% and lies between arterial and venous blood values of 97% and 80% in normoxia, and tends to move close to the venous side in hypoxia. In addition, the excessive hypoxic stress triggers the brain to be bio-energetic deficits and finally introduced the neural depolarization, which can be effectively detected by recording the increment of tissue scattering.

  7. Quantitative detection of hemoglobin saturation on piglet brain by near-infrared frequency-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Du, Congwu; Andersen, Carol; Chance, Britton

    1998-01-01

    An approach of using phase modulation spectroscopy (PMS) system has been proposed which has single frequency, dual- wavelength with phase-only output for oximetry to minimize the influences of room light in the clinical environment. The availability of this method has been verified by laboratory experiments both in vitro and in vivo. In this study, a 200 Mhz PMS system has been used for measuring on piglet brain in vivo, to detect blood volume and saturation change during normoxia to hypoxia periods, and to monitor the brain depolarization in the hypoxic stress. Our experimental results show that the brain saturation estimated by PMS is approximately 84% and lies between arterial and venous blood values of 97% and 80% in normoxia, and tends to move close to the venous side in hypoxia. In addition, the excessive hypoxic stress triggers the brain to be bio-energetic deficits and finally introduced the neural depolarization, which can be effectively detected by recording the increment of tissue scattering.

  8. Fast Quantitative Analysis Of Museum Objects Using Laser-Induced Breakdown Spectroscopy And Multiple Regression Algorithms

    NASA Astrophysics Data System (ADS)

    Lorenzetti, G.; Foresta, A.; Palleschi, V.; Legnaioli, S.

    2009-09-01

    The recent development of mobile instrumentation, specifically devoted to in situ analysis and study of museum objects, allows the acquisition of many LIBS spectra in very short time. However, such large amount of data calls for new analytical approaches which would guarantee a prompt analysis of the results obtained. In this communication, we will present and discuss the advantages of statistical analytical methods, such as Partial Least Squares Multiple Regression algorithms vs. the classical calibration curve approach. PLS algorithms allows to obtain in real time the information on the composition of the objects under study; this feature of the method, compared to the traditional off-line analysis of the data, is extremely useful for the optimization of the measurement times and number of points associated with the analysis. In fact, the real time availability of the compositional information gives the possibility of concentrating the attention on the most `interesting' parts of the object, without over-sampling the zones which would not provide useful information for the scholars or the conservators. Some example on the applications of this method will be presented, including the studies recently performed by the researcher of the Applied Laser Spectroscopy Laboratory on museum bronze objects.

  9. Quantitative Determination of Fusarium proliferatum Concentration in Intact Garlic Cloves Using Near-Infrared Spectroscopy.

    PubMed

    Tamburini, Elena; Mamolini, Elisabetta; De Bastiani, Morena; Marchetti, Maria Gabriella

    2016-01-01

    Fusarium proliferatum is considered to be a pathogen of many economically important plants, including garlic. The objective of this research was to apply near-infrared spectroscopy (NIRS) to rapidly determine fungal concentration in intact garlic cloves, avoiding the laborious and time-consuming procedures of traditional assays. Preventive detection of infection before seeding is of great interest for farmers, because it could avoid serious losses of yield during harvesting and storage. Spectra were collected on 95 garlic cloves, divided in five classes of infection (from 1-healthy to 5-very highly infected) in the range of fungal concentration 0.34-7231.15 ppb. Calibration and cross validation models were developed with partial least squares regression (PLSR) on pretreated spectra (standard normal variate, SNV, and derivatives), providing good accuracy in prediction, with a coefficient of determination (R²) of 0.829 and 0.774, respectively, a standard error of calibration (SEC) of 615.17 ppb, and a standard error of cross validation (SECV) of 717.41 ppb. The calibration model was then used to predict fungal concentration in unknown samples, peeled and unpeeled. The results showed that NIRS could be used as a reliable tool to directly detect and quantify F. proliferatum infection in peeled intact garlic cloves, but the presence of the external peel strongly affected the prediction reliability. PMID:27428978

  10. Quantitative analysis of mixed hydrofluoric and nitric acids using Raman spectroscopy with partial least squares regression.

    PubMed

    Kang, Gumin; Lee, Kwangchil; Park, Haesung; Lee, Jinho; Jung, Youngjean; Kim, Kyoungsik; Son, Boongho; Park, Hyoungkuk

    2010-06-15

    Mixed hydrofluoric and nitric acids are widely used as a good etchant for the pickling process of stainless steels. The cost reduction and the procedure optimization in the manufacturing process can be facilitated by optically detecting the concentration of the mixed acids. In this work, we developed a novel method which allows us to obtain the concentrations of hydrofluoric acid (HF) and nitric acid (HNO(3)) mixture samples with high accuracy. The experiments were carried out for the mixed acids which consist of the HF (0.5-3wt%) and the HNO(3) (2-12wt%) at room temperature. Fourier Transform Raman spectroscopy has been utilized to measure the concentration of the mixed acids HF and HNO(3), because the mixture sample has several strong Raman bands caused by the vibrational mode of each acid in this spectrum. The calibration of spectral data has been performed using the partial least squares regression method which is ideal for local range data treatment. Several figures of merit (FOM) were calculated using the concept of net analyte signal (NAS) to evaluate performance of our methodology. PMID:20441916

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

    SciTech Connect

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

    1985-08-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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.

  13. Technique for examining biological materials using diffuse reflectance spectroscopy and the kubelka-munk function

    DOEpatents

    Alfano, Robert R.; Yang, Yuanlong

    2003-09-02

    Method and apparatus for examining biological materials using diffuse reflectance spectroscopy and the Kubelka-Munk function. In one aspect, the method is used to determine whether a tissue sample is cancerous or not and comprises the steps of (a) measuring the diffuse reflectance from the tissue sample at a first wavelength and at a second wavelength, wherein the first wavelength is a wavelength selected from the group consisting of 255-265 nm and wherein the second wavelength is a wavelength selected from the group consisting of 275-285 nm; (b) using the Kubelka-Munk function to transform the diffuse reflectance measurement obtained at the first and second wavelengths; and (c) comparing a ratio or a difference of the transformed Kubelka-Munk measurements at the first and second wavelengths to appropriate standards determine whether or not the tissue sample is cancerous. One can use the spectral profile of KMF between 250 nm to 300 nm to determine whether or not the tissue sample is cancerous or precancerous. According to the value at the first and second wavelengths determine whether or not the malignant tissue is invasive or mixed invasive and in situ or carcinoma in situ.

  14. Next generation techniques in the high resolution spectroscopy of biologically relevant molecules.

    PubMed

    Neill, Justin L; Douglass, Kevin O; Pate, Brooks H; Pratt, David W

    2011-04-28

    Recent advances in the technology of test and measurement equipment driven by the computer and telecommunications industries have made possible the development of a new broadband, Fourier-transform microwave spectrometer that operates on principles similar to FTNMR. This technique uses a high sample-rate arbitrary waveform generator to construct a phase-locked chirped microwave pulse that gives a linear frequency sweep over a wide frequency range in 1 μs. The chirped pulse efficiently polarizes the molecular sample at all frequencies lying within this band. The subsequent free induction decay of this polarization is measured with a high-speed digitizer and then fast Fourier-transformed to yield a broadband, frequency-resolved rotational spectrum, spanning up to 11.5 GHz and containing lines that are as narrow as 100 kHz. This new technique is called chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy. The technique offers the potential to determine the structural and dynamical properties of very large molecules solely from fully resolved pure rotational spectra. FTMW double resonance techniques employing a low-resolution UV laser facilitate an easy assignment of overlapping spectra produced by different conformers in the sample. Of particular interest are the energy landscapes of conformationally flexible molecules of biological importance, including studies of their interaction with solvent and/or other weakly bound molecules. An example is provided from the authors' work on p-methoxyphenethylamine, a neurotransmitter, and its complexes with water. PMID:21394332

  15. Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Liang, Chungwen; Jansen, Thomas L. C.; Knoester, Jasper

    2011-01-01

    We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.

  16. Electrical pulse induced biological effects using dielectric spectroscopy and mathematical models

    NASA Astrophysics Data System (ADS)

    Garner, Allen Lawrence

    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

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

    PubMed

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

    2012-03-01

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

  18. Quantitative determination of aflatoxin B1 concentration in acetonitrile by chemometric methods using terahertz spectroscopy.

    PubMed

    Ge, Hongyi; Jiang, Yuying; Lian, Feiyu; Zhang, Yuan; Xia, Shanhong

    2016-10-15

    Aflatoxins contaminate and colonize agricultural products, such as grain, and thereby potentially cause human liver carcinoma. Detection via conventional methods has proven to be time-consuming and complex. In this paper, the terahertz (THz) spectra of aflatoxin B1 in acetonitrile solutions with concentration ranges of 1-50μg/ml and 1-50μg/l are obtained and analyzed for the frequency range of 0.4-1.6THz. Linear and nonlinear regression models are constructed to relate the absorption spectra and the concentrations of 160 samples using the partial least squares (PLS), principal component regression (PCR), support vector machine (SVM), and PCA-SVM methods. Our results indicate that PLS and PCR models are more accurate for the concentration range of 1-50μg/ml, whereas SVM and PCA-SVM are more accurate for the concentration range of 1-50μg/l. Furthermore, ten unknown concentration samples extracted from mildewed maize are analyzed quantitatively using these methods. PMID:27173565

  19. Variables selection for quantitative determination of cotton content in textile blends by near infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Sun, Xu-dong; Zhou, Ming-xing; Sun, Yi-ze

    2016-07-01

    Investigations were initiated to develop near infrared (NIR) techniques coupled with variables selection method to rapidly measure cotton content in blend fabrics of cotton and polyester. Multiplicative scatter correction (MSC), smooth, first derivative (1Der), second derivative (2Der) and their combination were employed to preprocess the spectra. Monte Carlo uninformative variables elimination (MCUVE), successive projections algorithm (SPA), and genetic algorithm (GA) were performed comparatively to choose characteristic variables associated with cotton content distributions. One hundred and thirty-five and fifty-nine samples were used to calibrate models and assess the performance of the models, respectively. Through comparing the performance of partial least squares (PLS) regression models with new samples, the optimal model of cotton content was obtained with spectral pretreatment method of 2 Der-Smooth-MSC and variables selection method of MCUVE-SPA-PLS. The correlation coefficient of prediction (rp) and root mean square errors of prediction (RMSEP) were 0.988% and 2.100%, respectively. The results suggest that NIR technique combining with variables selection method of MCUVE-SPA has significant potential to quantitatively analyze cotton content in blend fabrics of cotton and polyester; moreover, it could indicate the related spectral contributions.

  20. Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers.

    PubMed

    Meng, He; Andresen, Kurt; van Noort, John

    2015-04-20

    Single-molecule techniques allow for picoNewton manipulation and nanometer accuracy measurements of single chromatin fibers. However, the complexity of the data, the heterogeneity of the composition of individual fibers and the relatively large fluctuations in extension of the fibers complicate a structural interpretation of such force-extension curves. Here we introduce a statistical mechanics model that quantitatively describes the extension of individual fibers in response to force on a per nucleosome basis. Four nucleosome conformations can be distinguished when pulling a chromatin fiber apart. A novel, transient conformation is introduced that coexists with single wrapped nucleosomes between 3 and 7 pN. Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT. Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway. These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays. PMID:25779043

  1. Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers

    PubMed Central

    Meng, He; Andresen, Kurt; van Noort, John

    2015-01-01

    Single-molecule techniques allow for picoNewton manipulation and nanometer accuracy measurements of single chromatin fibers. However, the complexity of the data, the heterogeneity of the composition of individual fibers and the relatively large fluctuations in extension of the fibers complicate a structural interpretation of such force-extension curves. Here we introduce a statistical mechanics model that quantitatively describes the extension of individual fibers in response to force on a per nucleosome basis. Four nucleosome conformations can be distinguished when pulling a chromatin fiber apart. A novel, transient conformation is introduced that coexists with single wrapped nucleosomes between 3 and 7 pN. Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT. Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway. These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays. PMID:25779043

  2. Vibrational spectroscopy and chemometrics for rapid, quantitative analysis of bitter acids in hops (Humulus lupulus).

    PubMed

    Killeen, Daniel P; Andersen, David H; Beatson, Ron A; Gordon, Keith C; Perry, Nigel B

    2014-12-31

    Hops, Humulus lupulus, are grown worldwide for use in the brewing industry to impart characteristic flavor and aroma to finished beer. Breeders produce many varietal crosses with the aim of improving and diversifying commercial hops varieties. The large number of crosses critical to a successful breeding program imposes high demands on the supporting chemical analytical laboratories. With the aim of reducing the analysis time associated with hops breeding, quantitative partial least-squares regression (PLS-R) models have been produced, relating reference data acquired by the industrial standard HPLC and UV methods, to vibrational spectra of the same, chemically diverse hops sample set. These models, produced from rapidly acquired infrared (IR), near-infrared (NIR), and Raman spectra, were appraised using standard statistical metrics. Results demonstrated that all three spectroscopic methods could be used for screening hops for α-acid, total bitter acids, and cohumulone concentrations in powdered hops. Models generated from Raman and IR spectra also showed potential for use in screening hops varieties for xanthohumol concentrations. NIR analysis was performed using both a standard benchtop spectrometer and a portable NIR spectrometer, with comparable results obtained by both instruments. Finally, some important vibrational features of cohumulone, colupulone, and xanthohumol were assigned using DFT calculations, which allow more insightful interpretation of PLS-R latent variable plots.

  3. Fiber optic based multiparametric spectroscopy in vivo: Toward a new quantitative tissue vitality index

    NASA Astrophysics Data System (ADS)

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

    2006-02-01

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

  4. [Quantitative Analysis of the Hydration Process of Mine Gas Mixture Based on Raman Spectroscopy].

    PubMed

    Zhang, Bao-yong; Yu, Yue; Wu, Qiang; Gao, Xia

    2015-07-01

    The research on micro crystal structure of mine gas hydrate is especially significant for the technology of gas hydrate separation. Using Raman spectroscopy to observe hydration process of 3 kinds of mine gas mixture on line which contains high concentration of carbon dioxide, this experiment obtained the information of the hydrate crystals including large and small cage occupancy. Meanwhile obtained the hydration number indirectly based on the statistical thermodynamic model of van der Waals and Platteeuw. The results show that cage occupancy and hydration number of mine gas hydrates change little during different growth stages. The large cages of hydrate phases are nearly full occupied by carbon dioxide and methane molecules together, with the occupancy ratios between 97.70% and 98.68%. Most of the guest molecules in large cages is carbon dioxide (78.58%-94.09%) and only a few (4.52%-19.12%) is filled with methane, it is because carbon dioxide concentration in the gas sample is higher than methane and there is competition between them. However the small cage occupancy ratios is generally low in the range from 17.93% to 82.41%, and the guest molecules are all methane. With the increase of methane concentration in gas sample, the cage occupancy both large and small which methane occupied has increased, meanwhile the large cage occupancy which methane occupied is lower than small cage. The hydration numbers of mine gas hydrate during different growth stages are between 6.13 and 7.33. Small cage occupancy has increased with the increase of methane concentration, this lead to hydration number decreases. Because of the uneven distribution of hydrate growth, the hydration numbers of 3 kinds of gas samples show irregular change during different growth stages. PMID:26717751

  5. [Quantitative Analysis of the Hydration Process of Mine Gas Mixture Based on Raman Spectroscopy].

    PubMed

    Zhang, Bao-yong; Yu, Yue; Wu, Qiang; Gao, Xia

    2015-07-01

    The research on micro crystal structure of mine gas hydrate is especially significant for the technology of gas hydrate separation. Using Raman spectroscopy to observe hydration process of 3 kinds of mine gas mixture on line which contains high concentration of carbon dioxide, this experiment obtained the information of the hydrate crystals including large and small cage occupancy. Meanwhile obtained the hydration number indirectly based on the statistical thermodynamic model of van der Waals and Platteeuw. The results show that cage occupancy and hydration number of mine gas hydrates change little during different growth stages. The large cages of hydrate phases are nearly full occupied by carbon dioxide and methane molecules together, with the occupancy ratios between 97.70% and 98.68%. Most of the guest molecules in large cages is carbon dioxide (78.58%-94.09%) and only a few (4.52%-19.12%) is filled with methane, it is because carbon dioxide concentration in the gas sample is higher than methane and there is competition between them. However the small cage occupancy ratios is generally low in the range from 17.93% to 82.41%, and the guest molecules are all methane. With the increase of methane concentration in gas sample, the cage occupancy both large and small which methane occupied has increased, meanwhile the large cage occupancy which methane occupied is lower than small cage. The hydration numbers of mine gas hydrate during different growth stages are between 6.13 and 7.33. Small cage occupancy has increased with the increase of methane concentration, this lead to hydration number decreases. Because of the uneven distribution of hydrate growth, the hydration numbers of 3 kinds of gas samples show irregular change during different growth stages.

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

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

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

  7. General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters.

    PubMed

    Hadfield, J D; Nakagawa, S

    2010-03-01

    Although many of the statistical techniques used in comparative biology were originally developed in quantitative genetics, subsequent development of comparative techniques has progressed in relative isolation. Consequently, many of the new and planned developments in comparative analysis already have well-tested solutions in quantitative genetics. In this paper, we take three recent publications that develop phylogenetic meta-analysis, either implicitly or explicitly, and show how they can be considered as quantitative genetic models. We highlight some of the difficulties with the proposed solutions, and demonstrate that standard quantitative genetic theory and software offer solutions. We also show how results from Bayesian quantitative genetics can be used to create efficient Markov chain Monte Carlo algorithms for phylogenetic mixed models, thereby extending their generality to non-Gaussian data. Of particular utility is the development of multinomial models for analysing the evolution of discrete traits, and the development of multi-trait models in which traits can follow different distributions. Meta-analyses often include a nonrandom collection of species for which the full phylogenetic tree has only been partly resolved. Using missing data theory, we show how the presented models can be used to correct for nonrandom sampling and show how taxonomies and phylogenies can be combined to give a flexible framework with which to model dependence.

  8. Quantitative spectroscopy of blue supergiants in metal-poor dwarf galaxy NGC 3109

    SciTech Connect

    Hosek, Matthew W. Jr.; Kudritzki, Rolf-Peter; Bresolin, Fabio; Urbaneja, Miguel A.; Przybilla, Norbert; Evans, Christopher J.; Pietrzyński, Grzegorz; Gieren, Wolfgang; Carraro, Giovanni E-mail: kud@ifa.hawaii.edu E-mail: Miguel.Urbaneja-Perez@uibk.ac.at E-mail: chris.evans@stfc.ac.uk E-mail: wgieren@astro-udec.cl

    2014-04-20

    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 {sub 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 [ Z-bar ] = –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 ([ Z-bar ] = –0.93 ± 0.07), suggesting a low α/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.

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

    PubMed

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

    2002-10-01

    Changes in metabolites detected by proton magnetic resonance spectroscopy ((1)H MRS) of the brain have been demonstrated in Alzheimer's disease. Our objectives were, first, longitudinally to measure absolute concentrations of metabolites in both hippocampi, the sites of early Alzheimer's disease, in patients with clinical Alzheimer's disease and controls; secondly, to separate the relative contribution of atrophy and metabolite concentration change to overall signal change; and, thirdly, to determine whether metabolite concentrations in the hippocampus relate to cognitive scores. (1)H MR spectra were acquired from a single voxel (12 x 15 x 25 mm(3) = 4.5 ml) aligned to the long axis of each hippocampus in nine probable or possible Alzheimer's disease subjects diagnosed according to the National Institute of Neurologic and Cognitive Disorders and Stroke (NINCDS) compared with 14 age-matched NINCDS-negative Alzheimer's disease controls. Metabolite concentrations were corrected for the amount of CSF present in the voxel. Hippocampal volumes were measured at the same time. The same protocol was repeated approximately 1 year later. We found that atrophy-corrected hippocampal N-acetylaspartate (NAA) concentration was lower in cognitively impaired subjects compared with controls. This was significant for the left hippocampus (baseline 87% of control, P = 0.013; and at 1 year 76% of control, P = 0.020). Hippocampal volumes also differed significantly between the groups, and decreased significantly over 1 year in the Alzheimer's disease group (12%, P = 0.017). The decrease in [NAA] over 1 year was not significant in either group. Discriminant analysis revealed that the best classification of subjects was by including both left NAA concentration and left hippocampal volume. myo-Inositol signals from these small voxels had poor signal-to-noise and demonstrated no significant changes. We conclude that (1)HMRS-detectable metabolites can be quantified from the hippocampi of

  10. Quantitative Antimony Speciation in Shooting-Range Soils by EXAFS Spectroscopy

    SciTech Connect

    Scheinost,A.; Rossberg, A.; Vantelon, D.; Xifra, I.; Kretzschmar, R.; Leuz, A.; Funke, H.; Johnson, C.

    2006-01-01

    The Sb speciation in soil samples from Swiss shooting ranges was determined using Sb K-edge X-ray absorption spectroscopy (XAS) and advanced statistical data analysis methods (iterative transformation factor analysis, ITFA). The XAS analysis was supported by a spectral data set of 13 Sb minerals and 4 sorption complexes. In spite of a high variability in geology, soil pH (3.1-7.5), Sb concentrations (1000-17,000 mg/kg) and shooting-range history, only two Sb species were identified. In the first species, Sb is surrounded solely by other Sb atoms at radial distances of 2.90, 3.35, 4.30 and 4.51 Angstroms, indicative of metallic Sb(0). While part of this Sb(0) may be hosted by unweathered bullet fragments consisting of PbSb alloy, Pb L{sub III}-edge XAS of the soil with the highest fraction (0.75) of Sb(0) showed no metallic Pb, but only Pb{sup 2+} bound to soil organic matter. This suggests a preferential oxidation of Pb in the alloy, driven by the higher standard reduction potential of Sb. In the second species, Sb is coordinated to 6 O-atoms at a distance of 1.98 Angstroms, indicative of Sb(V). This oxidation state is further supported by an edge energy of 30,496-30,497 eV for the soil samples with <10% Sb(0). Iron atoms at radial distances of 3.10 and 3.56 Angstroms from Sb atoms are in line with edge-sharing and bidentate corner-sharing linkages between Sb(O,OH)6 and Fe(O,OH)6 octahedra. While similar structural units exist in tripuhyite, the absence of Sb neighbors contradicts formation of this Fe antimonate. Hence the second species most likely consists of inner-sphere sorption complexes on Fe oxides, with edge and corner-sharing configuration occurring simultaneously. This pentavalent Sb species was present in all samples, suggesting that it is the prevailing species after weathering of metallic Sb(0) in oxic soils. No indication of Sb(III) was found.

  11. Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples.

    PubMed

    Mackie, David M; Jahnke, Justin P; Benyamin, Marcus S; Sumner, James J

    2016-01-01

    The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users' purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells.

  12. Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples

    PubMed Central

    Mackie, David M.; Jahnke, Justin P.; Benyamin, Marcus S.; Sumner, James J.

    2016-01-01

    The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users’ purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells. PMID:26977411

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

    PubMed

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

    2012-08-21

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

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

    PubMed

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

    2012-08-21

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

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

    USGS Publications Warehouse

    Clark, Roger N.; Swayze, Gregg A.; Leifer, Ira; Livo, K. Eric; Kokaly, Raymond F.; 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; ,

    2010-01-01

    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.

  16. Diffuse Optical Spectroscopy for the Quantitative Assessment of Acute Ionizing Radiation Induced Skin Toxicity Using a Mouse Model

    PubMed Central

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

    2016-01-01

    Acute skin toxicities from ionizing radiation (IR) are a common side effect from therapeutic courses of external beam radiation therapy (RT) and negatively impact patient quality of life and long term survival. Advances in the understanding of the biological pathways associated with normal tissue toxicities have allowed for the development of interventional drugs, however, current response studies are limited by a lack of quantitative metrics for assessing the severity of skin reactions. Here we present a diffuse optical spectroscopic (DOS) approach that provides quantitative optical biomarkers of skin response to radiation. We describe the instrumentation design of the DOS system as well as the inversion algorithm for extracting the optical parameters. Finally, to demonstrate clinical utility, we present representative data from a pre-clinical mouse model of radiation induced erythema and compare the results with a commonly employed visual scoring. The described DOS method offers an objective, high through-put evaluation of skin toxicity via functional response that is translatable to the clinical setting. PMID:27284926

  17. The Quantitative and Qualitative Analysis of Cohorts' Early Enrollment in Physics: concurrent with enrollment in mathematics, biology and chemistry

    NASA Astrophysics Data System (ADS)

    Lynch, Robert Bruce Rodes

    Cohorts of 48 entering biological science majors was recruited in the fall of 2007 and again in 2008 and 2009 for the Interdisciplinary Science Experience (ISE). These ISE students enrolled in their own sections of standard courses of physics, chemistry, and biology. In these courses average ISE student out-performed their non-cohort peers by up to a full letter grade. A qualitative analysis of ISE student interviews illuminates the student experience and shows how the ISE students perceived themselves to be different than their non-cohort peers. Quantitative modeling of student performance shows that higher grades are correlated with multiple factors. These factors includes admissions characteristics such as high school GPA, and SAT scores, as well as demographic information. These trends support and elaborate on the selection narratives told by participants. Additionally the quantitative model found that higher student performance is predicted by structural aspects of the ISE program, specifically the timing of course, enrolling as a freshmen in many of their courses, and the sequencing of physics and chemistry courses. There is a statistically significant benefit to student performance in general and organic chemistry courses associated with completing the first quarter of the Physics for Bio-Science majors prior to enrollment. Further the combination of quantitative and qualitative data suggest that there is a epistemological transfer of problem solving skills and outlook from the physics to the chemistry courses.

  18. Highly-accelerated quantitative 2D and 3D localized spectroscopy with linear algebraic modeling (SLAM) and sensitivity encoding

    PubMed Central

    Zhang, Yi; Gabr, Refaat E.; Zhou, Jinyuan; Weiss, Robert G.; Bottomley, Paul A.

    2013-01-01

    Noninvasive magnetic resonance spectroscopy (MRS) with chemical shift imaging (CSI) provides valuable metabolic information for research and clinical studies, but is often limited by long scan times. Recently, spectroscopy with linear algebraic modeling (SLAM) was shown to provide compartment-averaged spectra resolved in one spatial dimension with many-fold reductions in scan-time. This was achieved using a small subset of the CSI phase-encoding steps from central image k-space that maximized the signal-to-noise ratio. Here, SLAM is extended to two- and three-dimensions (2D, 3D). In addition, SLAM is combined with sensitivity-encoded (SENSE) parallel imaging techniques, enabling the replacement of even more CSI phase-encoding steps to further accelerate scan-speed. A modified SLAM reconstruction algorithm is introduced that significantly reduces the effects of signal nonuniformity within compartments. Finally, main-field inhomogeneity corrections are provided, analogous to CSI. These methods are all tested on brain proton MRS data from a total of 24 patients with brain tumors, and in a human cardiac phosphorus 3D SLAM study at 3T. Acceleration factors of up to 120-fold versus CSI are demonstrated, including speed-up factors of 5-fold relative to already-accelerated SENSE CSI. Brain metabolites are quantified in SLAM and SENSE SLAM spectra and found to be indistinguishable from CSI measures from the same compartments. The modified reconstruction algorithm demonstrated immunity to maladjusted segmentation and errors from signal heterogeneity in brain data. In conclusion, SLAM demonstrates the potential to supplant CSI in studies requiring compartment-average spectra or large volume coverage, by dramatically reducing scan-time while providing essentially the same quantitative results. PMID:24188921

  19. Highly-accelerated quantitative 2D and 3D localized spectroscopy with linear algebraic modeling (SLAM) and sensitivity encoding

    NASA Astrophysics Data System (ADS)

    Zhang, Yi; Gabr, Refaat E.; Zhou, Jinyuan; Weiss, Robert G.; Bottomley, Paul A.

    2013-12-01

    Noninvasive magnetic resonance spectroscopy (MRS) with chemical shift imaging (CSI) provides valuable metabolic information for research and clinical studies, but is often limited by long scan times. Recently, spectroscopy with linear algebraic modeling (SLAM) was shown to provide compartment-averaged spectra resolved in one spatial dimension with many-fold reductions in scan-time. This was achieved using a small subset of the CSI phase-encoding steps from central image k-space that maximized the signal-to-noise ratio. Here, SLAM is extended to two- and three-dimensions (2D, 3D). In addition, SLAM is combined with sensitivity-encoded (SENSE) parallel imaging techniques, enabling the replacement of even more CSI phase-encoding steps to further accelerate scan-speed. A modified SLAM reconstruction algorithm is introduced that significantly reduces the effects of signal nonuniformity within compartments. Finally, main-field inhomogeneity corrections are provided, analogous to CSI. These methods are all tested on brain proton MRS data from a total of 24 patients with brain tumors, and in a human cardiac phosphorus 3D SLAM study at 3T. Acceleration factors of up to 120-fold versus CSI are demonstrated, including speed-up factors of 5-fold relative to already-accelerated SENSE CSI. Brain metabolites are quantified in SLAM and SENSE SLAM spectra and found to be indistinguishable from CSI measures from the same compartments. The modified reconstruction algorithm demonstrated immunity to maladjusted segmentation and errors from signal heterogeneity in brain data. In conclusion, SLAM demonstrates the potential to supplant CSI in studies requiring compartment-average spectra or large volume coverage, by dramatically reducing scan-time while providing essentially the same quantitative results.

  20. A Promising Raman Spectroscopy Technique for the Investigation of trans and cis Cholesteryl Ester Isomers in Biological Samples.

    PubMed

    Melchiorre, Michele; Ferreri, Carla; Tinti, Anna; Chatgilialoglu, Chryssostomos; Torreggiani, Armida

    2015-05-01

    Lipid geometry is an important issue in biology and medicine. The cis-trans geometry conversion of double bonds in lipids is an endogenous process that can be mediated by sulfur-centered free radicals. Trans isomers of polyunsaturated fatty acids can be used as biological markers of free radical stress, and their presence in biological samples can be determined by synthesis and characterization of appropriate reference compounds. Fractions of plasma lipids, such as cholesteryl linoleate and arachidonate esters, are interesting targets because of their connection with membrane phospholipid turnover and their roles in cardiovascular health. In this context, Raman spectroscopy can provide a useful contribution, since Raman analysis can be performed directly on the lipid extracts without any derivatization reaction, is nondestructive, and can rapidly supply biochemical information. This study focused on the build up of Raman spectral libraries of different cis and trans isomers of cholesteryl esters to be used as references for the examination of complex biological samples and to facilitate isomer recognition. Unsaturated cholesteryl esters obtained by chemical synthesis and with different alkyl chain lengths, double bond numbers, or both, were analyzed. The potential of Raman analysis for trans isomer detection in biological samples was successfully tested on some cholesteryl ester lipid fractions from human serum. The data suggest promising applications of Raman spectroscopy in metabolomics and lipidomics.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    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 (ϕ, ψ) in a series of selectively 13C-labeled 40-residue β-amyloid (Aβ1-40) 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 Aβ1-40 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 ϕ and ψ angles between the two carbonyl labels. Although the data are not sufficient to determine ϕ and ψ 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 Aβ1-40 fibrils in 4 h or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples.

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

    PubMed Central

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

    2013-01-01

    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 (ϕ,ψ) in a series of selectively 13C-labeled 40-residue β-amyloid (Aβ1–40) 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 Aβ1–40 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 ϕ and ψ angles between the two carbonyl labels. Although the data are not sufficient to determine ϕ and ψ 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 Aβ1–40 fibrils in 4 hr or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples. PMID:23562665

  3. Novel Uses of In Vitro Data to Develop Quantitative Biological Activity Relationship Models for in Vivo Carcinogenicity Prediction.

    PubMed

    Pradeep, Prachi; Povinelli, Richard J; Merrill, Stephen J; Bozdag, Serdar; Sem, Daniel S

    2015-04-01

    The availability of large in vitro datasets enables better insight into the mode of action of chemicals and better identification of potential mechanism(s) of toxicity. Several studies have shown that not all in vitro assays can contribute as equal predictors of in vivo carcinogenicity for development of hybrid Quantitative Structure Activity Relationship (QSAR) models. We propose two novel approaches for the use of mechanistically relevant in vitro assay data in the identification of relevant biological descriptors and development of Quantitative Biological Activity Relationship (QBAR) models for carcinogenicity prediction. We demonstrate that in vitro assay data can be used to develop QBAR models for in vivo carcinogenicity prediction via two case studies corroborated with firm scientific rationale. The case studies demonstrate the similarities between QBAR and QSAR modeling in: (i) the selection of relevant descriptors to be used in the machine learning algorithm, and (ii) the development of a computational model that maps chemical or biological descriptors to a toxic endpoint. The results of both the case studies show: (i) improved accuracy and sensitivity which is especially desirable under regulatory requirements, and (ii) overall adherence with the OECD/REACH guidelines. Such mechanism based models can be used along with QSAR models for prediction of mechanistically complex toxic endpoints.

  4. Quantitative carbon analysis in coal by combining data processing and spatial confinement in laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Xiongwei; Yin, Hualiang; Wang, Zhe; Fu, Yangting; Li, Zheng; Ni, Weidou

    2015-09-01

    Online measurement of carbon content of coal is important for coal-fired power plants to realize the combustion optimization of coal-fired boilers. Given that the measurement of carbon content of coal using laser-induced breakdown spectroscopy (LIBS) suffers from low measurement accuracy because of matrix effects, our previous study has proposed a combination model to improve the measurement accuracy of carbon content of coal. The spatial confinement method, which utilizes the spectral emissions of laser-induced plasmas spatially confined by cavities for quantitative analysis, has potential to improve quantitative analysis performance. In the present study, the combination model was used for coal measurement with cylindrical cavity confinement to further improve the measurement accuracy of carbon content of coal. Results showed that measurement accuracy was improved when the combination model was used with spatial confinement method. The coefficient of determination, root-mean-square error of prediction, average relative error, and average absolute error for the combination model with cylindrical cavity confinement were 0.99, 1.35%, 1.66%, and 1.08%, respectively, whereas values for the combination model without cylindrical cavity confinement were 0.99, 1.63%, 1.82%, and 1.27%, respectively. This is the first time that the average absolute error of carbon measurement for coal analysis has achieved close to 1.0% using LIBS, which is the critical requirement set for traditional chemical processing method by Chinese national standard. These results indicated that LIBS had significant application potential for coal analysis.

  5. Quantitative Subtractively Normalized Interfacial Fourier Transform Infrared Reflection Spectroscopy Study of the Adsorption of Adenine on Au(111) Electrodes.

    PubMed

    Prieto, Francisco; Su, Zhangfei; Leitch, J Jay; Rueda, Manuela; Lipkowski, Jacek

    2016-04-26

    Quantitative subtractively normalized interfacial Fourier transform infrared reflection spectroscopy (SNIFTIRS) was used to determine the molecular orientation and identify the metal-molecular interactions responsible for the adsorption of adenine from the bulk electrolyte solution onto the surface of the Au(111) electrode. The recorded p-polarized IR spectra of the adsorbed species were subtracted from the collected s-polarized IR spectra to remove the IR contributions of the vibrational bands of the desorbed molecules that are located within the thin layer cavity of the spectroelectrochemical cell. The intense IR band around 1640 cm(-1), which is assigned to the pyrimidine ring stretching vibrations of the C5-C6 and C6-N10 bonds, and the IR band at 1380 cm(-1), which results from a combination of the ring stretching vibration of the C5-C7 bond and the in-plane CH bending vibration, were selected for the quantitative analysis measurements. The transition dipoles of these bands were evaluated by DFT calculations. Their orientations differed by 85 ± 5°. The tilt angles of adsorbed adenine molecules were calculated from the intensity of these two vibrations at different potentials. The results indicate that the molecular plane is tilted at an angle of 40° with respect to the surface normal of the electrode and rotates by 16° around its normal axis with increasing electrode potential. This orientation results from the chemical interaction between the N10 and gold atoms coupled with the π-π parallel stacking interactions between the adjacent adsorbed molecules. Furthermore, the changes in the molecular plane rotation with the electric field suggests that the N1 atom of adenine must also participate in the interaction between the molecule and metal.

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

    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.

  7. Quantitative phenotyping of powdery mildew resistance in grapevine reveals differences in host resistance biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The recent demonstration of race-specific resistance to Erysiphe necator has encouraged grapevine breeders to identify and introgress quantitative resistance genes exhibiting complementary mechanisms. In 2012, we established a phenotyping center (VitisGenPM) for detailed evaluation of resistance to...

  8. Quantitation of Bacillus clausii in biological samples by real-time polymerase chain reaction.

    PubMed

    Perotti, Mario; Mancini, Nicasio; Cavallero, Annalisa; Carletti, Silvia; Canducci, Filippo; Burioni, Roberto; Clementi, Massimo

    2006-06-01

    A real-time PCR assay targeting the highly specific erm34 sequence of Bacillus clausii DNA was developed and optimized. The quantitative assay showed a sensitivity level of 10(2) CFU/microl of sample. The method may represent a useful tool for monitoring the role of B. clausii as probiotic in vivo. PMID:16318892

  9. Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud.

    PubMed

    Burns, Malcolm; Wiseman, Gordon; Knight, Angus; Bramley, Peter; Foster, Lucy; Rollinson, Sophie; Damant, Andrew; Primrose, Sandy

    2016-01-01

    Following a report on a significant amount of horse DNA being detected in a beef burger product on sale to the public at a UK supermarket in early 2013, the Elliott report was published in 2014 and contained a list of recommendations for helping ensure food integrity. One of the recommendations included improving laboratory testing capacity and capability to ensure a harmonised approach for testing for food authenticity. Molecular biologists have developed exquisitely sensitive methods based on the polymerase chain reaction (PCR) or mass spectrometry for detecting the presence of particular nucleic acid or peptide/protein sequences. These methods have been shown to be specific and sensitive in terms of lower limits of applicability, but they are largely qualitative in nature. Historically, the conversion of these qualitative techniques into reliable quantitative methods has been beset with problems even when used on relatively simple sample matrices. When the methods are applied to complex sample matrices, as found in many foods, the problems are magnified resulting in a high measurement uncertainty associated with the result which may mean that the assay is not fit for purpose. However, recent advances in the technology and the understanding of molecular biology approaches have further given rise to the re-assessment of these methods for their quantitative potential. This review focuses on important issues for consideration when validating a molecular biology assay and the various factors that can impact on the measurement uncertainty of a result associated with molecular biology approaches used in detection of food fraud, with a particular focus on quantitative PCR-based and proteomics assays.

  10. Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud.

    PubMed

    Burns, Malcolm; Wiseman, Gordon; Knight, Angus; Bramley, Peter; Foster, Lucy; Rollinson, Sophie; Damant, Andrew; Primrose, Sandy

    2016-01-01

    Following a report on a significant amount of horse DNA being detected in a beef burger product on sale to the public at a UK supermarket in early 2013, the Elliott report was published in 2014 and contained a list of recommendations for helping ensure food integrity. One of the recommendations included improving laboratory testing capacity and capability to ensure a harmonised approach for testing for food authenticity. Molecular biologists have developed exquisitely sensitive methods based on the polymerase chain reaction (PCR) or mass spectrometry for detecting the presence of particular nucleic acid or peptide/protein sequences. These methods have been shown to be specific and sensitive in terms of lower limits of applicability, but they are largely qualitative in nature. Historically, the conversion of these qualitative techniques into reliable quantitative methods has been beset with problems even when used on relatively simple sample matrices. When the methods are applied to complex sample matrices, as found in many foods, the problems are magnified resulting in a high measurement uncertainty associated with the result which may mean that the assay is not fit for purpose. However, recent advances in the technology and the understanding of molecular biology approaches have further given rise to the re-assessment of these methods for their quantitative potential. This review focuses on important issues for consideration when validating a molecular biology assay and the various factors that can impact on the measurement uncertainty of a result associated with molecular biology approaches used in detection of food fraud, with a particular focus on quantitative PCR-based and proteomics assays. PMID:26631264

  11. Stand-off Raman spectroscopy: a powerful technique for qualitative and quantitative analysis of inorganic and organic compounds including explosives.

    PubMed

    Zachhuber, Bernhard; Ramer, Georg; Hobro, Alison; Chrysostom, Engelene T H; Lendl, Bernhard

    2011-06-01

    A pulsed stand-off Raman system has been built and optimised for the qualitative and quantitative analysis of inorganic and organic samples including explosives. The system consists of a frequency doubled Q-switched Nd:YAG laser (532 nm, 10 Hz, 4.4 ns pulse length), aligned coaxially with a 6″ Schmidt-Cassegrain telescope for the collection of Raman scattered light. The telescope was coupled via a fibre optic bundle to an Acton standard series SP-2750 spectrograph with a PI-MAX 1024RB intensified CCD camera equipped with a 500-ps gating option for detection. Gating proved to be essential for achieving high signal-to-noise ratios in the recorded stand-off Raman spectra. In some cases, gating also allowed suppression of disturbing fluorescence signals. For the first time, quantitative analysis of stand-off Raman spectra was performed using both univariate and multivariate methods of data analysis. To correct for possible variation in instrumental parameters, the nitrogen band of ambient air was used as an internal standard. For the univariate method, stand-off Raman spectra obtained at a distance of 9 m on sodium chloride pellets containing varying amounts of ammonium nitrate (0-100%) were used. For the multivariate quantification of ternary xylene mixtures (0-100%), stand-off spectra at a distance of 5 m were used. The univariate calibration of ammonium nitrate yielded R (2) values of 0.992, and the multivariate quantitative analysis yielded root mean square errors of prediction of 2.26%, 1.97% and 1.07% for o-, m- and p-xylene, respectively. Stand-off Raman spectra obtained at a distance of 10 m yielded a detection limit of 174 μg for NaClO(3). Furthermore, to assess the applicability of stand-off Raman spectroscopy for explosives detection in "real-world" scenarios, their detection on different background materials (nylon, polyethylene and part of a car body) and in the presence of interferents (motor oil, fuel oil and soap) at a distance of 20 m was also

  12. Towards a non-invasive quantitative analysis of the organic components in museum objects varnishes by vibrational spectroscopies: methodological approach.

    PubMed

    Daher, Céline; Pimenta, Vanessa; Bellot-Gurlet, Ludovic

    2014-11-01

    The compositions of ancient varnishes are mainly determined destructively by separation methods coupled to mass spectrometry. In this study, a methodology for non-invasive quantitative analyses of varnishes by vibrational spectroscopies is proposed. For that, experimental simplified varnishes of colophony and linseed oil were prepared according to 18th century traditional recipes with an increasing mass concentration ratio of colophony/linseed oil. FT-Raman and IR analyses using ATR and non-invasive reflectance modes were done on the "pure" materials and on the different mixtures. Then, a new approach involving spectral decomposition calculation was developed considering the mixture spectra as a linear combination of the pure materials ones, and giving a relative amount of each component. Specific spectral regions were treated and the obtained results show a good accuracy between the prepared and calculated amounts of the two compounds. We were thus able to detect and quantify from 10% to 50% of colophony in linseed oil using non-invasive techniques that can also be conducted in situ with portable instruments when it comes to museum varnished objects and artifacts.

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

    PubMed

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

    2003-11-01

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

  14. Quantitative and mechanistic studies using the oxygen-18 isotope shift in carbon-13 nuclear magnetic resonance spectroscopy

    SciTech Connect

    Mega, T.L.

    1989-01-01

    The {sup 18}O-isotope shift in {sup 13}C NMR spectroscopy was used to study the kinetics of oxygen exchange at the anomeric carbon atoms of several ketoses and aldoses. At 25-26{degree}C and over the pH range from 2 to 10, the relative rates of oxygen exchange for the aldoses studied increased in the following sequence: D-glucose, D-mannose, D-ribose, D-2-deoxyribose. The hydration rates for the open chain forms of the sugars were calculated and the results were analyzed in terms of steric and inductive effects by drawing analogies with the hydration kinetics of simple aldehydes and ketones. Effective molarities associated with ring closure reactions of common monosaccharides are calculated. The position of bond cleavage in the acid-catalyzed hydrolysis of sucrose was elucidated by hydrolyzing the sugar in {sup 18}O-water and assaying the incorporation of {sup 18}O into the several anomeric products using {sup 13}C NMR. Independents supporting experimental evidence was obtained using {sup 1}H NMR. A detailed investigation was made of the complex {sup 13}C NMR spectrum arising from the various {sup 18}O-isotopomers in a solution of {sup 18}O-labeled (1,4-{sup 13}C{sub 2}) succinic acid. The quantitative use of the {sup 18}O isotope shift in {sup 13}C NMR was assessed.

  15. Simple quantitative analysis of Escherichia coli K-12 internalized in baby spinach using Fourier Transform Infrared spectroscopy.

    PubMed

    Wang, Jun; Kim, Kyung Ho; Kim, Sungkyun; Kim, Yong Soo; Li, Qing X; Jun, Soojin

    2010-11-15

    Bacterial contamination continues to be a serious concern for food safety. Although washing fresh produce helps in reducing pathogen levels, pathogen internalization often limits the effectiveness of washing. When pathogens internalize in leafy vegetables, the method of identification and quantitative measurement would be called into question. This study was aimed to use Fourier Transform Infrared (FTIR) spectroscopy integrated with an attenuated total reflectance kit for quantification of Escherichia coli K-12 internalized in baby spinach. The bacteria were inoculated into vascular and intracellar tissues of spinach leaves by syringe injection and the distribution of internalized E. coli K-12 cells was confirmed under scanning electron microscopy (SEM). FTIR measurement following the preparation of bacterial suspension from spinach leaves with high speed pulverizing enabled to detect the absorbance peaks in the amide II region between 1590 and 1490 cm⁻¹ as a fingerprint for the microbes. It was found that the estimated concentrations of E. coli K-12 agreed well with the concentrations determined by plate counting with R² values of 0.98 and 0.97 in peptone water and spinach extracts, respectively. The results demonstrated that FTIR can identify and quantify E. coli K-12 in baby spinach extracts at a limit of detection of approximately 100 CFU/mL in 5 min. The developed method is expected to be suitable for the analysis of pathogenic E. coli strains and other bacterial species in fresh vegetables.

  16. In Situ Determination of Fructose Isomer Concentrations in Wine Using (13)C Quantitative Nuclear Magnetic Resonance Spectroscopy.

    PubMed

    Colombo, Cinzia; Aupic, Clara; Lewis, Andrew R; Pinto, B Mario

    2015-09-30

    A practical method for simultaneously quantifying fructose and ethanol contents in wines using (13)C quantitative nuclear magnetic resonance (qNMR) spectroscopy is reported. Less than 0.6 mL of wine is needed, and the method leaves an unmodified sample available for subsequent testing or additional analyses. The relative ratios of the five known fructose isomers in ethanolic solutions at different pH and their variations with the temperature are also reported. The data are correlated with the sweetness of wines. The technique was applied to commercially available wines, and the results are compared to other methods. Sugar levels above 0.6 g/L can also be measured. A simple adaptation of the method permits measurement of different carbohydrates using integration of single peaks for each compound, in combination with an external reference (13)C qNMR spectrum of a sample with a known concentration. The method can be applied at all stages of wine production, including grape must, during fermentation, and before and after bottling.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    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.

  18. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy

    PubMed Central

    Voltz, Karine; Léonard, Jérémie; Touceda, Patricia Tourón; Conyard, Jamie; Chaker, Ziyad; Dejaegere, Annick; Godet, Julien; Mély, Yves; Haacke, Stefan; Stote, Roland H.

    2016-01-01

    Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies. PMID:26896800

  19. Visual confrontation naming and hippocampal function: A neural network study using quantitative (1)H magnetic resonance spectroscopy.

    PubMed

    Sawrie, S M; Martin, R C; Gilliam, F G; Faught, R E; Maton, B; Hugg, J W; Bush, N; Sinclair, K; Kuzniecky, R I

    2000-04-01

    Prior research on the relationship between visual confrontation naming and hippocampal function has been inconclusive. The present study examined this relationship using quantitative (1)H magnetic resonance spectroscopy ((1)H-MRS) to operationalize the function of the left and right hippocampi. The 60-item Boston Naming Test (BNT) was used to measure naming. Our sample included 46 patients with medically intractable, focal mesial temporal lobe epilepsy who had been screened for all pathology other than mesial temporal sclerosis. Statistics included Pearson correlations and neural network analysis (multilayer perceptron and radial basis function). Baseline BNT performance correlated significantly with left (1)H-MRS hippocampal ratios. Thirty-six per cent of the variance in baseline BNT performance was explained by a neural network model using left and right (1)H-MRS ratios(creatine/N-acetylaspartate) as input. This was elevated to 49% when input from the right hippocampus was lesioned mathematically. In a second model, left (1)H-MRS hippocampal ratios were modelled using measures of semantic and episodic memory as input (including the BNT). Explained variance in left (1)H-MRS hippocampal ratios fell from 60.8 to 3.6% when input from BNT and another semantic memory measure was degraded mathematically. These results provide evidence that the speech-dominant hippocampus is a significant component of the overall neuroanatomical network of visual confrontation naming. Clinical and theoretical implications are explored.

  20. Systems biology of cancer: a challenging expedition for clinical and quantitative biologists.

    PubMed

    Korsunsky, Ilya; McGovern, Kathleen; LaGatta, Tom; Olde Loohuis, Loes; Grosso-Applewhite, Terri; Griffeth, Nancy; Mishra, Bud

    2014-01-01

    A systems-biology approach to complex disease (such as cancer) is now complementing traditional experience-based approaches, which have typically been invasive and expensive. The rapid progress in biomedical knowledge is enabling the targeting of disease with therapies that are precise, proactive, preventive, and personalized. In this paper, we summarize and classify models of systems biology and model checking tools, which have been used to great success in computational biology and related fields. We demonstrate how these models and tools have been used to study some of the twelve biochemical pathways implicated in but not unique to pancreatic cancer, and conclude that the resulting mechanistic models will need to be further enhanced by various abstraction techniques to interpret phenomenological models of cancer progression.

  1. Molecular-scale quantitative charge density measurement of biological molecule by frequency modulation atomic force microscopy in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Umeda, Kenichi; Kobayashi, Kei; Oyabu, Noriaki; Matsushige, Kazumi; Yamada, Hirofumi

    2015-07-01

    Surface charge distributions on biological molecules in aqueous solutions are essential for the interactions between biomolecules, such as DNA condensation, antibody-antigen interactions, and enzyme reactions. There has been a significant demand for a molecular-scale charge density measurement technique for better understanding such interactions. In this paper, we present the local electric double layer (EDL) force measurements on DNA molecules in aqueous solutions using frequency modulation atomic force microscopy (FM-AFM) with a three-dimensional force mapping technique. The EDL forces measured in a 100 mM KCl solution well agreed with the theoretical EDL forces calculated using reasonable parameters, suggesting that FM-AFM can be used for molecular-scale quantitative charge density measurements on biological molecules especially in a highly concentrated electrolyte.

  2. Predicting Skin Permeability from Complex Chemical Mixtures: Dependency of Quantitative Structure Permeation Relationships on Biology of Skin Model Used

    PubMed Central

    Riviere, Jim E.; Brooks, James D.

    2011-01-01

    Dermal absorption of topically applied chemicals usually occurs from complex chemical mixtures; yet, most attempts to quantitate dermal permeability use data collected from single chemical exposure in aqueous solutions. The focus of this research was to develop quantitative structure permeation relationships (QSPR) for predicting chemical absorption from mixtures through skin using two levels of in vitro porcine skin biological systems. A total of 16 diverse chemicals were applied in 384 treatment mixture combinations in flow-through diffusion cells and 20 chemicals in 119 treatment combinations in isolated perfused porcine skin. Penetrating chemical flux into perfusate from diffusion cells was analyzed to estimate a normalized dermal absorptive flux, operationally an apparent permeability coefficient, and total perfusate area under the curve from perfused skin studies. These data were then fit to a modified dermal QSPR model of Abraham and Martin including a sixth term to account for mixture interactions based on physical chemical properties of the mixture components. Goodness of fit was assessed using correlation coefficients (r2), internal and external validation metrics (qLOO2, qL25%2, qEXT2), and applicable chemical domain determinations. The best QSPR equations selected for each experimental biological system had r2 values of 0.69–0.73, improving fits over the base equation without the mixture effects. Different mixture factors were needed for each model system. Significantly, the model of Abraham and Martin could also be reduced to four terms in each system; however, different terms could be deleted for each of the two biological systems. These findings suggest that a QSPR model for estimating percutaneous absorption as a function of chemical mixture composition is possible and that the nature of the QSPR model selected is dependent upon the biological level of the in vitro test system used, both findings having significant implications when dermal

  3. Sample Preparation Approaches for iTRAQ Labeling and Quantitative Proteomic Analyses in Systems Biology.

    PubMed

    Spanos, Christos; Moore, J Bernadette

    2016-01-01

    Among a variety of global quantification strategies utilized in mass spectrometry (MS)-based proteomics, isobaric tags for relative and absolute quantitation (iTRAQ) are an attractive option for examining the relative amounts of proteins in different samples. The inherent complexity of mammalian proteomes and the diversity of protein physicochemical properties mean that complete proteome coverage is still unlikely from a single analytical method. Numerous options exist for reducing protein sample complexity and resolving digested peptides prior to MS analysis. Indeed, the reliability and efficiency of protein identification and quantitation from an iTRAQ workflow strongly depend on sample preparation upstream of MS. Here we describe our methods for: (1) total protein extraction from immortalized cells; (2) subcellular fractionation of murine tissue; (3) protein sample desalting, digestion, and iTRAQ labeling; (4) peptide separation by strong cation-exchange high-performance liquid chromatography; and (5) peptide separation by isoelectric focusing.

  4. Synthesis, biological activity, and quantitative structure-activity relationship study of azanaphthalimide and arylnaphthalimide derivatives.

    PubMed

    Braña, Miguel F; Gradillas, Ana; Gómez, Angel; Acero, Nuria; Llinares, Francisco; Muñoz-Mingarro, Dolores; Abradelo, Cristina; Rey-Stolle, Fernanda; Yuste, Mercedes; Campos, Joaquín; Gallo, Miguel A; Espinosa, Antonio

    2004-04-22

    A series of quinoline derivatives as aza analogues of the naphthalene chromophore and a series of "nonfused" tricyclic aromatic systems, in particular 5-arylquinolines and 5- or 6-aryl and heteroaryl naphthalene systems, were synthesized and evaluated for growth-inhibitory properties in several human cell lines. The analysis of quantitative structure-antitumor activity relationships for the growth-inhibitory properties is also reported. Findings suggest that these compounds may not express their cytotoxicity via interaction on DNA. PMID:15084122

  5. Hybrid random walk-linear discriminant analysis method for unwrapping quantitative phase microscopy images of biological samples

    PubMed Central

    Kim, Diane N. H.; Teitell, Michael A.; Reed, Jason; Zangle, Thomas A.

    2015-01-01

    Abstract. Standard algorithms for phase unwrapping often fail for interferometric quantitative phase imaging (QPI) of biological samples due to the variable morphology of these samples and the requirement to image at low light intensities to avoid phototoxicity. We describe a new algorithm combining random walk-based image segmentation with linear discriminant analysis (LDA)-based feature detection, using assumptions about the morphology of biological samples to account for phase ambiguities when standard methods have failed. We present three versions of our method: first, a method for LDA image segmentation based on a manually compiled training dataset; second, a method using a random walker (RW) algorithm informed by the assumed properties of a biological phase image; and third, an algorithm which combines LDA-based edge detection with an efficient RW algorithm. We show that the combination of LDA plus the RW algorithm gives the best overall performance with little speed penalty compared to LDA alone, and that this algorithm can be further optimized using a genetic algorithm to yield superior performance for phase unwrapping of QPI data from biological samples. PMID:26305212

  6. Gelsius: a literature-based workflow for determining quantitative associations between genes and biological processes.

    PubMed

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

    2013-01-01

    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/.

  7. Lab on chip optical imaging of biological sample by quantitative phase microscopy

    NASA Astrophysics Data System (ADS)

    Memmolo, P.; Miccio, L.; Merola, F.; Gennari, O.; Mugnano, M.; Netti, P. A.; Ferraro, P.

    2015-03-01

    Quantitative imaging and three dimensional (3D) morphometric analysis of flowing and not-adherent cells is an important aspect for diagnostic purposes at Lab on Chip scale. Diagnostics tools need to be quantitative, label-free and, as much as possible, accurate. In recent years digital holography (DH) has been improved to be considered as suitable diagnostic method in several research field. In this paper we demonstrate that DH can be used for retrieving 3D morphometric data for sorting and diagnosis aims. Several techniques exist for 3D morphological study as optical coherent tomography and confocal microscopy, but they are not the best choice in case of dynamic events as flowing samples. Recently, a DH approach, based on shape from silhouette algorithm (SFS), has been developed for 3D shape display and calculation of cells biovolume. Such approach, adopted in combination with holographic optical tweezers (HOT) was successfully applied to cells with convex shape. Unfortunately, it's limited to cells with convex surface as sperm cells or diatoms. Here, we demonstrate an improvement of such procedure. By decoupling thickness information from refractive index ones and combining this with SFS analysis, 3D shape of concave cells is obtained. Specifically, the topography contour map is computed and used to adjust the 3D shape retrieved by the SFS algorithm. We prove the new procedure for healthy red blood cells having a concave surface in their central region. Experimental results are compared with theoretical model.

  8. Quantitative determination of competitive molecular adsorption on gold nanoparticles using attenuated total reflectance-Fourier transform infrared spectroscopy.

    PubMed

    Tsai, De-Hao; Davila-Morris, Melissa; DelRio, Frank W; Guha, Suvajyoti; Zachariah, Michael R; Hackley, Vincent A

    2011-08-01

    Surface-sensitive quantitative studies of competitive molecular adsorption on nanoparticles were conducted using a modified attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy method. Adsorption isotherms for thiolated poly(ethylene glycol) (SH-PEG) on gold nanoparticles (AuNPs) as a function of molecular mass (1, 5, and 20 kDa) were characterized. We find that surface density of SH-PEG on AuNPs is inversely proportional to the molecular mass (M(m)). Equilibrium binding constants for SH-PEG, obtained using the Langmuir adsorption model, show the binding affinity for SH-PEG is proportional to M(m). Simultaneous competitive adsorption between mercaptopropionic acid (MPA) and 5 kDa SH-PEG (SH-PEG5K) was investigated, and we find that MPA concentration is the dominant factor influencing the surface density of both SH-PEG5K and MPA, whereas the concentration of SH-PEG5K affects only SH-PEG5K surface density. Electrospray differential mobility analysis (ES-DMA) was employed as an orthogonal characterization technique. ES-DMA results are consistent with the results obtained by ATR-FTIR, confirming our conclusions about the adsorption process in this system. Ligand displacement competitive adsorption, where the displacing molecular species is added after completion of the ligand surface binding, was also interrogated by ATR-FTIR. Results indicate that for SH-PEG increasing M(m) yields greater stability on AuNPs when measured against displacement by bovine serum albumin (BSA) as a model serum protein. In addition, the binding affinity of BSA to AuNPs is inhibited for SH-PEG conjugated AuNPs, an effect that is enhanced at higher SH-PEG M(m) values.

  9. Multiparametric monitoring of chemotherapy treatment response in locally advanced breast cancer using quantitative ultrasound and diffuse optical spectroscopy

    PubMed Central

    Tran, William T.; Childs, Charmaine; Chin, Lee; Slodkowska, Elzbieta; Sannachi, Lakshmanan; Tadayyon, Hadi; Watkins, Elyse; Wong, Sharon Lemon; Curpen, Belinda; Kaffas, Ahmed El; Al-Mahrouki, Azza; Sadeghi-Naini, Ali; Czarnota, Gregory J.

    2016-01-01

    Purpose This study evaluated pathological response to neoadjuvant chemotherapy using quantitative ultrasound (QUS) and diffuse optical spectroscopy imaging (DOSI) biomarkers in locally advanced breast cancer (LABC). Materials and Methods The institution's ethics review board approved this study. Subjects (n = 22) gave written informed consent prior to participating. US and DOSI data were acquired, relative to the start of neoadjuvant chemotherapy, at weeks 0, 1, 4, 8 and preoperatively. QUS parameters including the mid-band fit (MBF), 0-MHz intercept (SI), and the spectral slope (SS) were determined from tumor ultrasound data using spectral analysis. In the same patients, DOSI was used to measure parameters relating to tumor hemoglobin and composition. Discriminant analysis and receiver-operating characteristic (ROC) analysis was used to classify clinical and pathological response during treatment and to estimate the area under the curve (AUC). Additionally, multivariate analysis was carried out for pairwise QUS/DOSI parameter combinations using a logistic regression model. Results Individual QUS and DOSI parameters, including the (SI), oxy-hemoglobin (HbO2), and total hemoglobin (HbT) were significant markers for response after one week of treatment (p < 0.01). Multivariate (pairwise) combinations increased the sensitivity, specificity and AUC at this time; the SI + HbO2 showed a sensitivity/specificity of 100%, and an AUC of 1.0. Conclusions QUS and DOSI demonstrated potential as coincident markers for treatment response and may potentially facilitate response-guided therapies. Multivariate QUS and DOSI parameters increased the sensitivity and specificity of classifying LABC patients as early as one week after treatment. PMID:26942698

  10. Developments in laser-induced fluorescence spectroscopy for quantitative in situ measurements of free radicals in the troposphere

    NASA Astrophysics Data System (ADS)

    Heard, Dwayne

    2015-04-01

    Photo-oxidation in the troposphere is highly complex, being initiated by short lived free radical species, in the daytime dominated by the hydroxyl radical, OH. Chemical oxidation cycles, which also involve peroxy radicals (HO2 and RO2), remove natural or anthropogenic emissions (for example methane) and generate a range of secondary products, for example ozone, nitrogen dioxide, acidic and multifunctional organic species, and secondary organic aerosol, which impact on human health and climate. Owing to their short lifetime in the atmosphere, the abundance of radicals is determined solely by their rate of chemical production and loss, and not by transport. Field measurements of the concentrations of radicals and comparison with calculations using a numerical model therefore constitutes one of the very best ways to test whether the chemistry in each of these locations is understood and accurately represented in the model. Validation of the chemistry is important, as the predictions of climate and air quality models containing this chemistry are used to drive the formulation of policy and legislation. However, in situ measurements of radical species, owing to their very low abundance (often sub part per trillion) and short lifetimes (< 1 second for OH), remain extremely challenging. Laser-induced fluorescence spectroscopy (LIF) has enjoyed considerable success worldwide for the quantitative detection of radicals in a range of environments. The radicals are either excited directly by the laser (e.g. OH, IO) or are first chemically converted to OH prior to detection (e.g. HO2, RO2). Recent developments in the LIF technique for radical detection, which uses a supersonic expansion with detection at low pressure and multi kHz pulse repetition rate tunable laser systems, will be discussed, together with calibration methods to make signals absolute, and identification of potential interferences. LIF instruments have been operated on ground, ship and aircraft platforms at a

  11. Java-based graphical user interface for MRUI, a software package for quantitation of in vivo/medical magnetic resonance spectroscopy signals.

    PubMed

    Naressi, A; Couturier, C; Castang, I; de Beer, R; Graveron-Demilly, D

    2001-07-01

    This article describes a Java-based graphical user interface for the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo/medical MR spectroscopy data. We have found that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI system. We also have established that MR quantitation algorithms, programmed in the past in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI).

  12. Quantitative bioassays for measuring biologically functional gonadotropins based on eel gonadotropic receptors.

    PubMed

    Minegishi, Y; Dirks, R P; de Wijze, D L; Brittijn, S A; Burgerhout, E; Spaink, H P; van den Thillart, G E E J M

    2012-08-01

    Significant declines in eel stocks have been noted in many parts of the world. Because eel aquaculture is dependent on wild-caught juveniles, there is a need to achieve artificial reproduction. Adult eel maturation is currently induced by repeated injections of purified gonadotropin (human chorionic gonadotropin [hCG]) or pituitary extract. Thus the determination of the biological efficacy and quantification of internal levels of gonadotropic hormones is important for optimizing artificial reproduction protocols. To quantify the plasma levels of biologically functional gonadotropic hormones, we developed a bioassay for luteinizing hormone (LH) and follicle-stimulating hormone (FSH) based on the stable expression of receptors in HEK293 cells of the Japanese eel Anguilla japonica LH (ajLHR) and the European eel Anguilla anguilla FSH (aaFSHR), respectively. Such cells also contain a firefly luciferase reporter gene driven by a cAMP-responsive element (CRE-Luc). We found that the obtained stable cells, with ajLHR, responded linearly to a more than 100,000-fold concentration range of hCG diluted in saline. The cells with aaFSHR showed a linear response to a 1000-fold concentration range of salmon pituitary extract mixed with saline. The biological functionality of the LH and FSH bioassays was validated using hCG, human FSH, and pituitary extracts from salmon, carp and eel. Since the toxins in eel plasma damaged the HEK293 cells, the protocol was adapted to selectively inactivate the toxins by heating at 37°C for 24h. This process successfully enabled the monitoring of hormone levels in blood plasma sampled from hCG-injected eels. In this paper, we describe the development of gonadotropin bioassays that will be useful for improving reproduction protocols in eel aquaculture. PMID:22580328

  13. Water (H2O and D2O) molar absorptivity in the 1000-4000 cm-1 range and quantitative infrared spectroscopy of aqueous solutions.

    PubMed

    Venyaminov SYu; Prendergast, F G

    1997-06-01

    Water (H2O and D2O) molar absorptivity was measured by Fourier transform infrared transmission spectroscopy in the 1000-4000 cm-1 range at 25 degrees C. A series of assembled cells with path lengths from 1.2 to 120.5 microns was used for these measurements. The optimal path length (the path length of aqueous solution at which the IR spectrum of solute, corrected for water absorbance, has the highest signal-to-noise ratio) was calculated for all water absorbance bands. The results presented here show that the optimal path length does not depend on solute properties and is inversely proportional to the solvent (water) molar absorptivity. The maximal signal-to-noise ratio for measurements of IR spectra of aqueous solution in the 1650 cm-1 spectral region, of primary interest in biological applications, can be obtained at an optimal cell path lengths of 3-4 microns (H2O) and 40-60 microns (D2O). As an example, the signal-to-noise ratio was calculated as a function of the cell path length for the amide I (H2O) and amide I' (D2O) bands of an aqueous lysozyme solution. The molar absorptivities of water bands are several orders of magnitude weaker than those of the strongest bands of biological macromolecules in the same spectral regions. High net water absorbance in aqueous solutions is due simply to the very high molar concentration of water. A method is proposed for the quantitative measuring of the path length of the cell which exploits the molar absorptivity of the strongest water bands (stretching vibrations) or of bands which do not overlap with solute absorbance. A path length in the range from approximately 0.01 micron to approximately 1.0 mm can be determined with high precision using this technique for a samples of known concentration. Problems involved in the proper correction of strong water absorbance in IR spectra of aqueous solutions of biomolecules are discussed, including multiple reflections within the cell, the effects of pH, temperature, and

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

    PubMed Central

    2011-01-01

    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. PMID:21338175

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

    PubMed

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

    2012-07-01

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

  16. Biological Matrix Effects in Quantitative Tandem Mass Spectrometry-Based Analytical Methods: Advancing Biomonitoring

    PubMed Central

    Panuwet, Parinya; Hunter, Ronald E.; D’Souza, Priya E.; Chen, Xianyu; Radford, Samantha A.; Cohen, Jordan R.; Marder, M. Elizabeth; Kartavenka, Kostya; Ryan, P. Barry; Barr, Dana Boyd

    2015-01-01

    The ability to quantify levels of target analytes in biological samples accurately and precisely, in biomonitoring, involves the use of highly sensitive and selective instrumentation such as tandem mass spectrometers and a thorough understanding of highly variable matrix effects. Typically, matrix effects are caused by co-eluting matrix components that alter the ionization of target analytes as well as the chromatographic response of target analytes, leading to reduced or increased sensitivity of the analysis. Thus, before the desired accuracy and precision standards of laboratory data are achieved, these effects must be characterized and controlled. Here we present our review and observations of matrix effects encountered during the validation and implementation of tandem mass spectrometry-based analytical methods. We also provide systematic, comprehensive laboratory strategies needed to control challenges posed by matrix effects in order to ensure delivery of the most accurate data for biomonitoring studies assessing exposure to environmental toxicants. PMID:25562585

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

    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.

  18. A New Technique for Quantitative Determination of Dexamethasone in Pharmaceutical and Biological Samples Using Kinetic Spectrophotometric Method

    PubMed Central

    Akhoundi-Khalafi, Ali Mohammad; Shishehbore, Masoud Reza

    2015-01-01

    Dexamethasone is a type of steroidal medications that is prescribed in many cases. In this study, a new reaction system using kinetic spectrophotometric method for quantitative determination of dexamethasone is proposed. The method is based on the catalytic effect of dexamethasone on the oxidation of Orange G by bromate in acidic media. The change in absorbance as a criterion of the oxidation reaction progress was followed spectrophotometrically. To obtain the maximum sensitivity, the effective reaction variables were optimized. Under optimized experimental conditions, calibration graph was linear over the range 0.2–54.0 mg L−1. The calculated detection limit (3sb/m) was 0.14 mg L−1 for six replicate determinations of blank signal. The interfering effect of various species was also investigated. The present method was successfully applied for the determination of dexamethasone in pharmaceutical and biological samples satisfactorily. PMID:25737724

  19. Water Vapor Uptake of Ultrathin Films of Biologically Derived Nanocrystals: Quantitative Assessment with Quartz Crystal Microbalance and Spectroscopic Ellipsometry.

    PubMed

    Niinivaara, Elina; Faustini, Marco; Tammelin, Tekla; Kontturi, Eero

    2015-11-10

    Despite the relevance of water interactions, explicit analysis of vapor adsorption on biologically derived surfaces is often difficult. Here, a system was introduced to study the vapor uptake on a native polysaccharide surface; namely, cellulose nanocrystal (CNC) ultrathin films were examined with a quartz crystal microbalance with dissipation monitoring (QCM-D) and spectroscopic ellipsometry (SE). A significant mass uptake of water vapor by the CNC films was detected using the QCM-D upon increasing relative humidity. In addition, thickness changes proportional to changes in relative humidity were detected using SE. Quantitative analysis of the results attained indicated that in preference to being soaked by water at the point of hydration each individual CNC in the film became enveloped by a 1 nm thick layer of adsorbed water vapor, resulting in the detected thickness response. PMID:26461931

  20. A bench-top K X-ray fluorescence system for quantitative measurement of gold nanoparticles for biological sample diagnostics

    NASA Astrophysics Data System (ADS)

    Ricketts, K.; Guazzoni, C.; Castoldi, A.; Royle, G.

    2016-04-01

    Gold nanoparticles can be targeted to biomarkers to give functional information on a range of tumour characteristics. X-ray fluorescence (XRF) techniques offer potential quantitative measurement of the distribution of such heavy metal nanoparticles. Biologists are developing 3D tissue engineered cellular models on the centimetre scale to optimise targeting techniques of nanoparticles to a range of tumour characteristics. Here we present a high energy bench-top K-X-ray fluorescence system designed for sensitivity to bulk measurement of gold nanoparticle concentration for intended use in such thick biological samples. Previous work has demonstrated use of a L-XRF system in measuring gold concentrations but being a low energy technique it is restricted to thin samples or superficial tumours. The presented system comprised a high purity germanium detector and filtered tungsten X-ray source, capable of quantitative measurement of gold nanoparticle concentration of thicker samples. The developed system achieved a measured detection limit of between 0.2 and 0.6 mgAu/ml, meeting specifications of biologists and being approximately one order of magnitude better than the detection limit of alternative K-XRF nanoparticle detection techniques. The scatter-corrected K-XRF signal of gold was linear with GNP concentrations down to the detection limit, thus demonstrating potential in GNP concentration quantification. The K-XRF system demonstrated between 5 and 9 times less sensitivity than a previous L-XRF bench-top system, due to a fundamental limitation of lower photoelectric interaction probabilities at higher K-edge energies. Importantly, the K-XRF technique is however less affected by overlying thickness, and so offers future potential in interrogating thick biological samples.

  1. Quantitative global sensitivity analysis of a biologically based dose-response pregnancy model for the thyroid endocrine system.

    PubMed

    Lumen, Annie; McNally, Kevin; George, Nysia; Fisher, Jeffrey W; Loizou, George D

    2015-01-01

    A deterministic biologically based dose-response model for the thyroidal system in a near-term pregnant woman and the fetus was recently developed to evaluate quantitatively thyroid hormone perturbations. The current work focuses on conducting a quantitative global sensitivity analysis on this complex model to identify and characterize the sources and contributions of uncertainties in the predicted model output. The workflow and methodologies suitable for computationally expensive models, such as the Morris screening method and Gaussian Emulation processes, were used for the implementation of the global sensitivity analysis. Sensitivity indices, such as main, total and interaction effects, were computed for a screened set of the total thyroidal system descriptive model input parameters. Furthermore, a narrower sub-set of the most influential parameters affecting the model output of maternal thyroid hormone levels were identified in addition to the characterization of their overall and pair-wise parameter interaction quotients. The characteristic trends of influence in model output for each of these individual model input parameters over their plausible ranges were elucidated using Gaussian Emulation processes. Through global sensitivity analysis we have gained a better understanding of the model behavior and performance beyond the domains of observation by the simultaneous variation in model inputs over their range of plausible uncertainties. The sensitivity analysis helped identify parameters that determine the driving mechanisms of the maternal and fetal iodide kinetics, thyroid function and their interactions, and contributed to an improved understanding of the system modeled. We have thus demonstrated the use and application of global sensitivity analysis for a biologically based dose-response model for sensitive life-stages such as pregnancy that provides richer information on the model and the thyroidal system modeled compared to local sensitivity analysis.

  2. Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis *

    PubMed Central

    Miller, Marcus J.; Scalf, Mark; Rytz, Thérèse C.; Hubler, Shane L.; Smith, Lloyd M.; Vierstra, Richard D.

    2013-01-01

    The stress-induced attachment of small ubiquitin-like modifier (SUMO) to a diverse collection of nuclear proteins regulating chromatin architecture, transcription, and RNA biology has been implicated in protecting plants and animals against numerous environmental challenges. In order to better understand stress-induced SUMOylation, we combined stringent purification of SUMO conjugates with isobaric tag for relative and absolute quantification mass spectrometry and an advanced method to adjust for sample-to-sample variation so as to study quantitatively the SUMOylation dynamics of intact Arabidopsis seedlings subjected to stress. Inspection of 172 SUMO substrates during and after heat shock (37 °C) revealed that stress mostly increases the abundance of existing conjugates, as opposed to modifying new targets. Some of the most robustly up-regulated targets participate in RNA processing and turnover and RNA-directed DNA modification, thus implicating SUMO as a regulator of the transcriptome during stress. Many of these targets were also strongly SUMOylated during ethanol and oxidative stress, suggesting that their modification is crucial for general stress tolerance. Collectively, our quantitative data emphasize the importance of SUMO to RNA-related processes protecting plants from adverse environments. PMID:23197790

  3. An Integrated Quantitative Proteomics and Systems Biology Approach to Explore Synaptic Protein Profile Changes During Morphine Exposure

    PubMed Central

    Stockton, Steven D; Devi, Lakshmi A

    2014-01-01

    Morphine is a classic analgesic for the treatment of chronic pain. However, its repeated use is known to produce tolerance, physical dependence, and addiction; these properties limit its long-term therapeutic use and this has led to a quest for therapeutics without these unwanted side effects. Understanding the molecular changes in response to long-term use of morphine is likely to aid in the development of novel therapeutics for the treatment of pain. Studies examining the effects of chronic morphine administration have reported alterations in gene expression, synapse morphology, and synaptic transmission implying changes in synaptic protein profile. To fully understand the changes in protein profiles, proteomic techniques have been used. Studies using two-dimensional gel electrophoresis of various brain regions combined with mass spectrometry have found alterations in the levels of a number of proteins. However, neither the changes in brain regions relevant to morphine effects nor changes in the abundance of synaptic proteins have been clearly delineated. Recent studies employing subcellular fractionation to isolate the striatal synapse, combined with quantitative proteomics and graph theory-inspired network analyses, have begun to quantify morphine-regulated changes in synaptic proteins and facilitate the generation of networks that could serve as targets for the development of novel therapeutics for the treatment of chronic pain. Thus, an integrated quantitative proteomics and systems biology approach can be useful to identify novel targets for the treatment of pain and other disorders of the brain. PMID:24045585

  4. Quantitation, biological and physicochemical properties of cell culture-adapted porcine epidemic diarrhea coronavirus (PEDV).

    PubMed

    Hofmann, M; Wyler, R

    1989-06-01

    The porcine epidemic coronavirus (PEDV), tentatively classified as a coronavirus, was adapted to Vero cells and a plaque test developed for infectivity titration, allowing us to test the biological and biophysical properties of the virus. Growth kinetics showed peak titers of 10(5.5) plaque-forming units ml-1 15 h after infection. Filtration experiments and electron microscopy revealed a particle diameter between 100 and 200 nm. The buoyant density of the virus was 1.18. The particle lost its infectivity on treatment with lipid solvents. Virus replication could not be inhibited by 5-iodo-2'-deoxyuridine. PEDV was moderately stable at 50 degrees C, but heat sensitivity was not altered by divalent cations. At 4 degrees C, the virus was stable between pH 5.0 and 9.0, but at 37 degrees C stability was restricted to the pH range 6.5-7.5. Viral infectivity was not impaired by ultrasonication or by multiple freezing and thawing. PEDV was not neutralized by transmissible gastroenteritis virus antiserum. On the basis of the tests carried out, PEDV is a pleomorphic, enveloped RNA virus with a particle diameter of approximately 150 nm and a buoyant density of 1.18. Infectivity depends on the presence of trypsin, and infected cells show a tendency to fuse and to form syncytia. All of these properties, as well as its physicochemical characteristics, allow PEDV to be classified as a coronavirus.

  5. Quantitation of retinaldehyde in small biological samples using ultrahigh-performance liquid chromatography MS/MS

    PubMed Central

    Wang, Jinshan; Yoo, Hong Sik; Obrochta, Kristin M.; Huang, Priscilla; Napoli, Joseph L.

    2015-01-01

    We report an UHPLC-MS/MS to quantify all-trans-retinal in biological samples of limited size (15-35 mg), which is especially advantageous for use with adipose. To facilitate recovery, retinal and the internal standard 3,4-didehydroretinal were derivatized in situ into their O-ethyloximes. UHPLC resolution combined with high sensitivity and specificity of MS/MS allowed quantification of retinal-O-ethyloximes with a 5 fmol lower limit of detection and a linear range from 5 fmol to 1 pmol. This assay revealed that extra-ocular concentrations of retinal range from ~2 to 40 pmol/g in multiple tissues: the same range as all-trans-retinoic acid. All-trans-retinoic acid has high affinity (kd ≤ 0.4 nM) for its nuclear receptors (RARα, β, γ), whereas retinal has low, if any affinity for these receptors, making it unlikely that these retinal concentrations would activate RAR. We also show that the copious amount of vitamin A used in chow diets increases retinal in adipose depots 2 to 5-fold relative to levels in adipose of mice fed a vitamin A-sufficient diet, as recommended for laboratory rodents. This assay also is proficient for quantifying conversion of retinol into retinal in vitro, and therefore provides an efficient method to study metabolism of retinol in vivo and in vitro. PMID:26045160

  6. Characterisation of in vivo ovarian cancer models by quantitative 1H magnetic resonance spectroscopy and diffusion-weighted imaging.

    PubMed

    Canese, Rossella; Pisanu, Maria Elena; Mezzanzanica, Delia; Ricci, Alessandro; Paris, Luisa; Bagnoli, Marina; Valeri, Barbara; Spada, Massimo; Venditti, Massimo; Cesolini, Albino; Rodomonte, Andrea; Giannini, Massimo; Canevari, Silvana; Podo, Franca; Iorio, Egidio

    2012-04-01

    Magnetic resonance imaging (MRI) and spectroscopy (MRS) offer powerful approaches for detecting physiological and metabolic alterations in malignancies and help investigate underlying molecular mechanisms. Research on epithelial ovarian carcinoma (EOC), the gynaecological malignancy with the highest death rate characterised by frequent relapse and onset of drug resistance, could benefit from application of these molecular imaging approaches. In this study, MRI/MRS were used to characterise solid tumour models obtained by subcutaneous (s.c.) or intraperitoneal (i.p.) implantation of human SKOV3.ip cells in severe combined immunodeficiency (SCID) mice. In vivo MRI/MRS, ex vivo magic-angle-spinning (MAS), and in vitro (1)H-NMR measurements were carried out at 4.7 T, 9.4 T, and 9.4/16.5 T, respectively. MRI evaluation was performed by T1-, T2-, and diffusion-weighted (DW) multislice spin-echo imaging. The in vivo (1)H spectra of all tumour models showed a prominent resonance of total choline-containing metabolites (tCho). Quantitative in vivo MRS of both i.p. and s.c. SKOV3.ip xenografts showed that the mean tCho content was in the 2.9-4.5 mM range, with a mean PCho/tCho ratio of 0.99 ± 0.01 [23 examinations, 14-34 days post injection (dpi)], in good agreement with ex vivo and in vitro analyses. Myo-inositol ranged between 11.7 and 17.0 mM, with a trend towards higher values in i.p. xenografts at 14-16 dpi. The average apparent diffusion coefficient (ADC) values of SKOV3.ip xenografts [1.64 ± 0.11 (n = 9, i.p.) and 1.58 ± 0.03 x10(-3) mm(2)/s (n = 7, s.c.)] were in agreement with values reported for tumours from patients with EOC, while the mean vascular signal fraction (VSF) was lower (≤ 4%), probably due to the more rapid growth of preclinical models. Both s.c. and i.p. xenografts are valuable preclinical models for monitoring biochemical and physiopathological changes associated with in vivo EOC tumour growth and response to therapy, which may serve as the

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

    SciTech Connect

    Wind, Robert A.; Hu, Jian Zhi

    2005-01-01

    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.

  8. The biological effects of XTC-MIF: quantitative comparison with Xenopus bFGF.

    PubMed

    Green, J B; Howes, G; Symes, K; Cooke, J; Smith, J C

    1990-01-01

    respond to the natural inducer at least until stage 10, and perhaps until stage 10.5, this suggests that bFGF cannot be the sole inducer of mesoderm in vivo. Taken together, these results are consistent with XTC-MIF being a dorsoanterior inducer and XbFGF a ventroposterior inducer, suggesting that body pattern is established by the interaction of two types of inducing signal. This model is discussed in view of the qualitative and quantitative differences between the factors.

  9. Insight into the Local Solvent Environment of Biologically Relevant Iron-nitroysl Systems through Two-Dimensional Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Brookes, Jennifer Faith

    Iron-nitrosyl systems, particularly in the form of heme proteins, with their iron metal active sites play an important role in biological systems. Heme proteins act as storage, transporters, and receptors for nitric oxide (NO), a signaling molecule that is important in immune, nervous, and cardiovascular systems of mammals. By better understanding the local environment of the active site of NO binding heme proteins we can gain insight into disease in which the NO pathways have been implicated. This is an important step to being able to develop pharmaceuticals targeting NO pathways in humans. Sodium nitroprusside ((SNP, Na2[Fe(CN)5is NO]·2H 2O) investigated as a model system for the active site of nitric oxide binding heme proteins. Using two-dimensional infrared spectroscopy (2D IR) to obtain dephasing dynamics of the nitrosyl stretch (nuNO) in a series of solvents we are able to better understand the local environment of the more complicated metalloproteins. Rigorous line shape analysis is performed by using nonlinear response theory to simulate 2D IR spectra which are then fit to experimental data in an iterative process to extract frequency-frequency correlation functions (FFCFs). The time scales obtained are then correlated to empirical solvent polarity parameters. The analysis of the 2D IR lineshapes reveal that the spectral diffusion timescale of the nuNO in SNP varies from 0.8 -- 4 ps and is negatively correlated with the empirical solvent polarity scales. We continue to investigate NO binding of metalloproteins through 2D IR experiments on nitrophorin 4 (NP4). NP4 is a pH-sensitive NO transporter protein present in the salivary gland of the blood sucking insect Rhodius prolixus which undergoes a pH sensitive structural change between a closed and open conformation allowing for the storage and delivery of NO. The two structures are observed spectroscopically as two distinct pH-dependent nu NO frequencies at ~1904 and ~1917 cm-1. We obtain FFCFs by globally

  10. 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)

    Loubere, Paul; Fariduddin, Mohammad

    1999-03-01

    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

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

    PubMed Central

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

    2006-01-01

    High-throughput screening (HTS) of chemical compounds to identify modulators of molecular targets is a mainstay of pharmaceutical development. Increasingly, HTS is being used to identify chemical probes of gene, pathway, and cell functions, with the ultimate goal of comprehensively delineating relationships between chemical structures and biological activities. Achieving this goal will require methodologies that efficiently generate pharmacological data from the primary screen and reliably profile the range of biological activities associated with large chemical libraries. Traditional HTS, which tests compounds at a single concentration, is not suited to this task, because HTS is burdened by frequent false positives and false negatives and requires extensive follow-up testing. We have developed a paradigm, quantitative HTS (qHTS), tested with the enzyme pyruvate kinase, to generate concentration–response curves for >60,000 compounds in a single experiment. We show that this method is precise, refractory to variations in sample preparation, and identifies compounds with a wide range of activities. Concentration–response curves were classified to rapidly identify pyruvate kinase activators and inhibitors with a variety of potencies and efficacies and elucidate structure–activity relationships directly from the primary screen. Comparison of qHTS with traditional single-concentration HTS revealed a high prevalence of false negatives in the single-point screen. This study demonstrates the feasibility of qHTS for accurately profiling every compound in large chemical libraries (>105 compounds). qHTS produces rich data sets that can be immediately mined for reliable biological activities, thereby providing a platform for chemical genomics and accelerating the identification of leads for drug discovery. PMID:16864780

  12. Gelatin embedding: a novel way to preserve biological samples for terahertz imaging and spectroscopy

    NASA Astrophysics Data System (ADS)

    Fan, Shuting; Ung, Benjamin; Parrott, Edward P. J.; Pickwell-MacPherson, Emma

    2015-04-01

    Sample dehydration has traditionally been a challenging problem in ex vivo terahertz biomedical experiments as water content changes significantly affect the terahertz properties and can diminish important contrast features. In this paper, we propose a novel method to prevent sample dehydration using gelatin embedding. By looking at terahertz image data and calculating the optical properties of the gelatin-embedded sample, we find that our method successfully preserves the sample for at least 35 h, both for imaging and spectroscopy. Our novel preservation method demonstrates for the first time the capability to simultaneously maintain sample structural integrity and prevent dehydration at room temperature. This is particularly relevant for terahertz studies of freshly excised tissues but could be beneficial for other imaging and spectroscopy techniques.

  13. Raman Micro-spectroscopy Study of Healthy and Burned Biological Tissue

    NASA Astrophysics Data System (ADS)

    Zarnani, Faranak; Glosser, Robert; Idris, Ahamed

    2011-10-01

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

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

    PubMed Central

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

    2013-01-01

    Since the early 1980’s, the enhanced backscattering (EBS) phenomenon has been well-studied in a large variety of non-biological materials. Yet, until recently the use of conventional EBS for the characterization of biological tissue has been fairly limited. In this work we detail the unique ability of EBS to provide spectroscopic, polarimetric, and depth-resolved characterization of biological tissue using a simple backscattering instrument. We first explain the experimental and numerical procedures used to accurately measure and model the full azimuthal EBS peak shape in biological tissue. Next we explore the peak shape and height dependencies for different polarization channels and spatial coherence of illumination. We then illustrate the extraordinary sensitivity of EBS to the shape of the scattering phase function using suspensions of latex microspheres. Finally, we apply EBS to biological tissue samples in order to measure optical properties and observe the spatial length-scales at which backscattering is altered in early colon carcinogenesis. PMID:24163574

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

    PubMed

    West, Geoffrey B; Brown, James H

    2005-05-01

    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.

  16. X-ray diffraction and infrared spectroscopy analyses on the crystallinity of engineered biological hydroxyapatite for medical application

    NASA Astrophysics Data System (ADS)

    Poralan, G. M., Jr.; Gambe, J. E.; Alcantara, E. M.; Vequizo, R. M.

    2015-06-01

    Biological hydroxyapatite (BHAp) derived from thermally-treated fish bones was successfully produced. However, the obtained biological HAp was amorphous and thus making it unfavorable for medical application. Consequently, this research exploits and engineers the crystallinity of BHAp powders by addition of CaCO3 and investigates its degree of crystallinity using XRD and IR spectroscopy. On XRD, the HAp powders with [Ca]/[P] ratios 1.42, 1.46, 1.61 and 1.93 have degree of crystallinity equal to 58.08, 72.13, 85.79, 75.85% and crystal size equal to 0.67, 0.74, 0.75, 0.72 nm, respectively. The degree of crystallinity and crystal size of the obtained calcium deficient biological HAp powders increase as their [Ca]/[P] ratio approaches the stoichiometric ratio by addition of CaCO3 as source of Ca2+ ions. These results show the possibility of engineering the crystallinity and crystal size of biological HAp by addition of CaCO3. Moreover, the splitting factor of PO4 vibration matches the result with % crystallinity on XRD. Also, the area of phosphate-substitution site of PO4 vibration shows linear relationship (R2 = 0.994) with crystal size calculated from XRD. It is worth noting that the crystallinity of the biological HAp with [Ca]/[P] ratios 1.42 and 1.48 fall near the range 60-70% for highly resorbable HAp used in the medical application.

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

    PubMed Central

    Zhang, Chi; Myers, John; Chen, Zhan

    2013-01-01

    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. PMID:23710244

  18. [Quantitative models of Raman spectroscopy for five kinds of traditional Chinese medicine containing CaCO3 based on an improved siPLS].

    PubMed

    Chen, Long; Yuan, Ming-yang; Ming, Jing; Liu, Yi-mei; Huang, Bi-sheng; Chen, Ke-li

    2015-09-01

    The aim of this paper is to apply Raman spectroscopy technique to develop rapid quantitative models for five kinds of Traditional Chinese Medicine containing CaCO3. In the experiment, Raman spectras of 67 batch of sample including Otolithum Sciaenae, Galaxeae Os, Ophicalcitum, Calcite, Stalactite and their mixture which had different content of CaCO3 were collected, and the quantitative models were established by using an improved siPLS to optimize the characteristic spectral bands and using the CaCO3 contents which were measured by EDTA titration method as references. Compared with the results by EDTA titration, the established quantitative model for CaCO, content showed a prediction result that the average relative deviation of the prediction results is 2. 71% and the average recovery rate was 100.46%, when the content is between 0.465 4-0.999 7, and when the characteristic spectral bands of 1 290-1 280, 730-714, 700-690, 660-650, 465-460, 455-445, 405-385 cm(-1) had been optimized. The result also showed that the model using Raman spectroscopy and based on an improved siPLS can get a rapid determination for contents of 5 kinds of Traditional Chinese Medicine containing CaCO3. PMID:26983209

  19. [Application of near infrared spectroscopy to qualitative identification and quantitative determination of Puccinia strii formis f. sp. tritici and P. recondita f. sp. tritici].

    PubMed

    Li, Xiao-Long; Ma, Zhan-Hong; Zhao, Long-Lian; Li, Jun-Hui; Wang, Hai-Guang

    2014-03-01

    To realize qualitative identification and quantitative determination of Puccinia strii formis f. sp. tritici (Pst) and P. recondita f. sp. tritici (Prt), a qualitative identification model was built using near infrared reflectance spectroscopy (NIRS) combined with distinguished partial least squares (DPLS), and a quantitative determination model was built using NIRS combined with quantitative partial least squares (QPLS). In this study, 100 pure samples including 50 samples of Pst and 50 samples of Prt were obtained, and 120 mixed samples including three replicates of mixed urediospores of the two kinds of pathogen in different proportions (the content of Pst was within the range of 2. 5% 100% with 2. 5% as the gradient) were obtained. Then the spectra of the samples were collected using MPA spectrometer, respectively. Both pure samples and mixed samples were divided into training set and testing set with the ratio equal to 2:1. Qualitative identification model and quantitative determination model were built using internal cross-validation method in the spectral region 4,000--10,000 cm(-1) based on the training sets from pure samples and mixed samples, respectively. The results showed that the identification rates of the Pst-Prt qualitative identification model for training set and testing set were both up to 100. 00% when scatter correction was used as the preprocessing method of the spectra and the number of principal components was 3. When 'range normalization + scatter correction' was used as the preprocessing method of the spectra and the number of principal components was 6, determination coefficient (RZ), standard error of calibration (SEC) and average absolute relative deviation(AARD) of the Pst-Prt quantitative determination model for training set were 99.36%, 2.31% and 8.94%, respectively, and R2, standard error of prediction (SEP) and AARD for testing set were 99.37%, 2.29% and 5. 0%, respectively. The results indicated that qualitative identification

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

    PubMed Central

    Muñoz Morales, Aarón A.; Vázquez y Montiel, Sergio

    2012-01-01

    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

  1. Infrared fiber optic evanescent wave spectroscopy: applications in biology and medicine

    NASA Astrophysics Data System (ADS)

    Afanasyeva, Natalia I.; Bruch, Reinhard F.; Katzir, Abraham

    1999-04-01

    A new powerful and highly sensitive technique for non-invasive biomedical diagnostics in vivo has been developed using Infrared Fiberoptic Evanescent Wave Fourier Transform Spectroscopy (FEW-FTIR). This compact and portable method allows to detect functional chemical groups and bonds via vibrational spectroscopy directly from surfaces including living tissue. Such differences and similarities in molecular structure of tissue and materials can be evaluated online. Operating in the attenuated total reflection (ATR) regime in the middle-infrared (MIR) range, the FEW-FTIR technique provides direct contact between the fiber probe and tissue for non-destructive, non-invasive, fast and remote (few meters) diagnostics and quality control of materials. This method utilizes highly flexible and extremely low loss unclad fibers, for example silver halide fibers. Applications of this method include investigations of normal skin, precancerous and cancerous conditions, monitoring of the process of aging, allergic reactions and radiation damage to the skin. This setup is suitable as well for the detection of the influence of environmental factors (sun, water, pollution, and weather) on skin surfaces. The FEW-FTIR technique is very promising also for fast histological examinations in vitro. In this review, we present recent investigations of skin, breast, lung, stomach, kidney tissues in vivo and ex vivo (during surgery) to define the areas of tumor localization. The main advantages of the FEW-FTIR technique for biomedical, clinical, and environmental applications are discussed.

  2. Mapping nanoparticles injected into a biological tissue using laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Motto-Ros, V.; Sancey, L.; Wang, X. C.; Ma, Q. L.; Lux, F.; Bai, X. S.; Panczer, G.; Tillement, O.; Yu, J.

    2013-09-01

    We describe a setup for LIBS mapping of nanoparticles and trace metallic elements in biological organ as well as the followed experimental procedure. Mapping was performed for metallic elements such as Gd, Si, Ca and Fe, with a resolution of 100 μm on kidney slices sampled from a mouse 24 h after intravenous injection of a solution of gadolinium-based nanoparticles. An approach for quantifying Gd in the tissue is also presented with a good agreement with measurement performed by ICP-OES. We demonstrate that LIBS offers a simple and robust method to study the distribution of gadolinium-based nanoparticles in biological samples, without any labeling of the nanoparticles. The used bench-top instrumentation is fully compatible with the standard optical microscopy, which shows its large potential use in Biology and Medicine as a tool for complementary observation of trace metallic elements with respect to the classical optical observations which are generally based on the responses of biomolecules or cells.

  3. [Effect of algorithms for calibration set selection on quantitatively determining asiaticoside content in Centella total glucosides by near infrared spectroscopy].

    PubMed

    Zhan, Xue-yan; Zhao, Na; Lin, Zhao-zhou; Wu, Zhi-sheng; Yuan, Rui-juan; Qiao, Yan-jiang

    2014-12-01

    The appropriate algorithm for calibration set selection was one of the key technologies for a good NIR quantitative model. There are different algorithms for calibration set selection, such as Random Sampling (RS) algorithm, Conventional Selection (CS) algorithm, Kennard-Stone(KS) algorithm and Sample set Portioning based on joint x-y distance (SPXY) algorithm, et al. However, there lack systematic comparisons between two algorithms of the above algorithms. The NIR quantitative models to determine the asiaticoside content in Centella total glucosides were established in the present paper, of which 7 indexes were classified and selected, and the effects of CS algorithm, KS algorithm and SPXY algorithm for calibration set selection on the accuracy and robustness of NIR quantitative models were investigated. The accuracy indexes of NIR quantitative models with calibration set selected by SPXY algorithm were significantly different from that with calibration set selected by CS algorithm or KS algorithm, while the robustness indexes, such as RMSECV and |RMSEP-RMSEC|, were not significantly different. Therefore, SPXY algorithm for calibration set selection could improve the predicative accuracy of NIR quantitative models to determine asiaticoside content in Centella total glucosides, and have no significant effect on the robustness of the models, which provides a reference to determine the appropriate algorithm for calibration set selection when NIR quantitative models are established for the solid system of traditional Chinese medcine.

  4. [Effect of algorithms for calibration set selection on quantitatively determining asiaticoside content in Centella total glucosides by near infrared spectroscopy].

    PubMed

    Zhan, Xue-yan; Zhao, Na; Lin, Zhao-zhou; Wu, Zhi-sheng; Yuan, Rui-juan; Qiao, Yan-jiang

    2014-12-01

    The appropriate algorithm for calibration set selection was one of the key technologies for a good NIR quantitative model. There are different algorithms for calibration set selection, such as Random Sampling (RS) algorithm, Conventional Selection (CS) algorithm, Kennard-Stone(KS) algorithm and Sample set Portioning based on joint x-y distance (SPXY) algorithm, et al. However, there lack systematic comparisons between two algorithms of the above algorithms. The NIR quantitative models to determine the asiaticoside content in Centella total glucosides were established in the present paper, of which 7 indexes were classified and selected, and the effects of CS algorithm, KS algorithm and SPXY algorithm for calibration set selection on the accuracy and robustness of NIR quantitative models were investigated. The accuracy indexes of NIR quantitative models with calibration set selected by SPXY algorithm were significantly different from that with calibration set selected by CS algorithm or KS algorithm, while the robustness indexes, such as RMSECV and |RMSEP-RMSEC|, were not significantly different. Therefore, SPXY algorithm for calibration set selection could improve the predicative accuracy of NIR quantitative models to determine asiaticoside content in Centella total glucosides, and have no significant effect on the robustness of the models, which provides a reference to determine the appropriate algorithm for calibration set selection when NIR quantitative models are established for the solid system of traditional Chinese medcine. PMID:25881421

  5. Detection and Quantitative Analysis of Chemical Species in Hanford Tank Materials Using Raman Spectroscopy Technology: FY94Florida State University Raman Spectroscopy Report

    SciTech Connect

    Reich, F.R.

    1997-08-11

    This report provides a summary of work completed in FY-94 by FSU to develop and investigate the feasibility of using Raman spectroscopy with Hanford tank waste materials. Raman performance impacts from sample morphology, including the effects of absorption, particle size, density, color and refractive index, are discussed. An algorithm for relative species concentration measurement from Raman data is presented. An Algorithm for applying Raman to tank waste core screening is presented and discussed. A library of absorption and Raman spectra are presented that support this work.

  6. Interaction of Iron II Complexes with B-DNA. Insights from Molecular Modeling, Spectroscopy and Cellular Biology.

    NASA Astrophysics Data System (ADS)

    Gattuso, Hugo; Duchanois, Thibaut; Besancenot, Vanessa; Barbieux, Claire; Assfeld, Xavier; Becuwe, Philippe; Gros, Philippe; Grandemange, Stephanie; Monari, Antonio

    2015-12-01

    We report the characterization of the interaction between B-DNA and three terpyridin iron II complexes. Relatively long time-scale molecular dynamics is used in order to characterize the stable interaction modes. By means of molecular modeling and UV-vis spectroscopy, we prove that they may lead to stable interactions with the DNA duplex. Furthermore, the presence of larger π-conjugated moieties also leads to the appearance of intercalation binding mode. Non-covalent stabilizing interactions between the iron complexes and the DNA are also characterized and evidenced by the analysis of the gradient of the electronic density. Finally, the structural deformations induced on the DNA in the different binding modes are also evidenced. The synthesis and chemical characterization of the three complexes is reported, as well as their absorption spectra in presence of DNA duplexes to prove the interaction with DNA. Finally, their effects on human cell cultures have also been evidenced to further enlighten their biological effects.

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

    PubMed Central

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

    2009-01-01

    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. PMID:19278649

  8. Recent applications of /sup 13/C NMR spectroscopy to biological systems

    SciTech Connect

    Matwiyoff, N.A.

    1981-01-01

    Carbon-13 nuclear magnetic resonance (NMR) spectroscopy, in conjunction with carbon-13 labelling, is a powerful new analytical technique for the study of metabolic pathways and structural components in intact organelles, cells, and tissues. The technique can provide, rapidly and non-destructively, unique information about: the architecture and dynamics of structural components; the nature of the intracellular environment; and metabolic pathways and relative fluxes of individual carbon atoms. With the aid of results recently obtained by us and those reported by a number of other laboratories, the problems and potentialities of the technique will be reviewed with emphasis on: the viscosities of intracellular fluids; the structure and dynamics of the components of membranes; and the primary and secondary metabolic pathways of carbon in microorganisms, plants, and mammalian cells in culture.

  9. Selective quantitative bioanalysis of proteins in biological fluids by on-line immunoaffinity chromatography-protein digestion-liquid chromatography-mass spectrometry.

    PubMed

    Hoos, Johannes S; Sudergat, Hilke; Hoelck, Jens-Peter; Stahl, Mark; de Vlieger, Jon S B; Niessen, Wilfried M A; Lingeman, Henk; Irth, Hubertus

    2006-01-18

    A quantitative method for the determination of proteins in complex biological matrices has been developed based on the selectivity of antibodies for sample purification followed by proteolytic digestion and quantitative mass spectrometry. An immunosorbent of polyclonal anti-bovine serum albumin (BSA) antibodies immobilized on CNBR agarose is used in the on-line mode for selective sample pretreatment. Next, the purified sample is trypsin digested to obtain protein specific peptide markers. Subsequent analysis of the peptide mixture using a desalination procedure and a separation step coupled, on-line to an ion-trap mass spectrometer, reveals that this method enables selective determination of proteins in biological matrices like diluted human plasma. This approach enhances substantially the selectivity compared to common quantitative analysis executed with immunoassays and colorimetry, fluorimetry or luminescence detection. Hyphenation of the immunoaffinity chromatography with on-line digestion and chromatography-mass spectrometry is performed and a completely on-line quantification of the model protein BSA in bovine and human urine was established. A detection limit of 170 nmol/l and a quantification limit of 280 nmol/l is obtained using 50 microl of either standard or spiked biological matrix. The model system allows fully automated absolute quantitative mass spectrometric analysis of intact proteins in biological matrices without time-consuming labeling procedures.

  10. Imaging and quantitative data acquisition of biological cell walls with Atomic Force Microscopy and Scanning Acoustic Microscopy

    SciTech Connect

    Tittmann, B. R.; Xi, X.

    2014-09-01

    This chapter demonstrates the feasibility of Atomic Force Microscopy (AFM) and High Frequency Scanning Acoustic Microscopy (HF-SAM) as tools to characterize biological tissues. Both the AFM and the SAM have shown to provide imaging (with different resolution) and quantitative elasticity measuring abilities. Plant cell walls with minimal disturbance and under conditions of their native state have been examined with these two kinds of microscopy. After descriptions of both the SAM and AFM, their special features and the typical sample preparation is discussed. The sample preparation is focused here on epidermal peels of onion scales and celery epidermis cells which were sectioned for the AFM to visualize the inner surface (closest to the plasma membrane) of the outer epidermal wall. The nm-wide cellulose microfibrils orientation and multilayer structure were clearly observed. The microfibril orientation and alignment tend to be more organized in older scales compared with younger scales. The onion epidermis cell wall was also used as a test analog to study cell wall elasticity by the AFM nanoindentation and the SAM V(z) feature. The novelty in this work was to demonstrate the capability of these two techniques to analyze isolated, single layered plant cell walls in their natural state. AFM nanoindentation was also used to probe the effects of Ethylenediaminetetraacetic acid (EDTA), and calcium ion treatment to modify pectin networks in cell walls. The results suggest a significant modulus increase in the calcium ion treatment and a slight decrease in EDTA treatment. To complement the AFM measurements, the HF-SAM was used to obtain the V(z) signatures of the onion epidermis. These measurements were focused on documenting the effect of pectinase enzyme treatment. The results indicate a significant change in the V(z) signature curves with time into the enzyme treatment. Thus AFM and HF-SAM open the door to a systematic nondestructive structure and mechanical property

  11. Non-invasive chemically specific measurement of subsurface temperature in biological tissues using surface-enhanced spatially offset Raman spectroscopy.

    PubMed

    Gardner, Benjamin; Stone, Nicholas; Matousek, Pavel

    2016-06-23

    Here we demonstrate for the first time the viability of characterising non-invasively the subsurface temperature of SERS nanoparticles embedded within biological tissues using spatially offset Raman spectroscopy (SORS). The proposed analytical method (T-SESORS) is applicable in general to diffusely scattering (turbid) media and features high sensitivity and high chemical selectivity. The method relies on monitoring the Stokes and anti-Stokes bands of SERS nanoparticles in depth using SORS. The approach has been conceptually demonstrated using a SORS variant, transmission Raman spectroscopy (TRS), by measuring subsurface temperatures within a slab of porcine tissue (5 mm thick). Root-mean-square errors (RMSEs) of 0.20 °C were achieved when measuring temperatures over ranges between 25 and 44 °C. This unique capability complements the array of existing, predominantly surface-based, temperature monitoring techniques. It expands on a previously demonstrated SORS temperature monitoring capability by adding extra sensitivity stemming from SERS to low concentration analytes. The technique paves the way for a wide range of applications including subsurface, chemical-specific, non-invasive temperature analysis within turbid translucent media including: the human body, subsurface monitoring of chemical (e.g. catalytic) processes in manufacture quality and process control and research. Additionally, the method opens prospects for control of thermal treatment of cancer in vivo with direct non-invasive feedback on the temperature of mediating plasmonic nanoparticles. PMID:27049293

  12. Non-invasive chemically specific measurement of subsurface temperature in biological tissues using surface-enhanced spatially offset Raman spectroscopy.

    PubMed

    Gardner, Benjamin; Stone, Nicholas; Matousek, Pavel

    2016-06-23

    Here we demonstrate for the first time the viability of characterising non-invasively the subsurface temperature of SERS nanoparticles embedded within biological tissues using spatially offset Raman spectroscopy (SORS). The proposed analytical method (T-SESORS) is applicable in general to diffusely scattering (turbid) media and features high sensitivity and high chemical selectivity. The method relies on monitoring the Stokes and anti-Stokes bands of SERS nanoparticles in depth using SORS. The approach has been conceptually demonstrated using a SORS variant, transmission Raman spectroscopy (TRS), by measuring subsurface temperatures within a slab of porcine tissue (5 mm thick). Root-mean-square errors (RMSEs) of 0.20 °C were achieved when measuring temperatures over ranges between 25 and 44 °C. This unique capability complements the array of existing, predominantly surface-based, temperature monitoring techniques. It expands on a previously demonstrated SORS temperature monitoring capability by adding extra sensitivity stemming from SERS to low concentration analytes. The technique paves the way for a wide range of applications including subsurface, chemical-specific, non-invasive temperature analysis within turbid translucent media including: the human body, subsurface monitoring of chemical (e.g. catalytic) processes in manufacture quality and process control and research. Additionally, the method opens prospects for control of thermal treatment of cancer in vivo with direct non-invasive feedback on the temperature of mediating plasmonic nanoparticles.

  13. Quantitative detection of caffeine in human skin by confocal Raman spectroscopy--A systematic in vitro validation study.

    PubMed

    Franzen, Lutz; Anderski, Juliane; Windbergs, Maike

    2015-09-01

    For rational development and evaluation of dermal drug delivery, the knowledge of rate and extent of substance penetration into the human skin is essential. However, current analytical procedures are destructive, labor intense and lack a defined spatial resolution. In this context, confocal Raman microscopy bares the potential to overcome current limitations in drug depth profiling. Confocal Raman microscopy already proved its suitability for the acquisition of qualitative penetration profiles, but a comprehensive investigation regarding its suitability for quantitative measurements inside the human skin is still missing. In this work, we present a systematic validation study to deploy confocal Raman microscopy for quantitative drug depth profiling in human skin. After we validated our Raman microscopic setup, we successfully established an experimental procedure that allows correlating the Raman signal of a model drug with its controlled concentration in human skin. To overcome current drawbacks in drug depth profiling, we evaluated different modes of peak correlation for quantitative Raman measurements and offer a suitable operating procedure for quantitative drug depth profiling in human skin. In conclusion, we successfully demonstrate the potential of confocal Raman microscopy for quantitative drug depth profiling in human skin as valuable alternative to destructive state-of-the-art techniques. PMID:25828208

  14. Quantitative detection of caffeine in human skin by confocal Raman spectroscopy--A systematic in vitro validation study.

    PubMed

    Franzen, Lutz; Anderski, Juliane; Windbergs, Maike

    2015-09-01

    For rational development and evaluation of dermal drug delivery, the knowledge of rate and extent of substance penetration into the human skin is essential. However, current analytical procedures are destructive, labor intense and lack a defined spatial resolution. In this context, confocal Raman microscopy bares the potential to overcome current limitations in drug depth profiling. Confocal Raman microscopy already proved its suitability for the acquisition of qualitative penetration profiles, but a comprehensive investigation regarding its suitability for quantitative measurements inside the human skin is still missing. In this work, we present a systematic validation study to deploy confocal Raman microscopy for quantitative drug depth profiling in human skin. After we validated our Raman microscopic setup, we successfully established an experimental procedure that allows correlating the Raman signal of a model drug with its controlled concentration in human skin. To overcome current drawbacks in drug depth profiling, we evaluated different modes of peak correlation for quantitative Raman measurements and offer a suitable operating procedure for quantitative drug depth profiling in human skin. In conclusion, we successfully demonstrate the potential of confocal Raman microscopy for quantitative drug depth profiling in human skin as valuable alternative to destructive state-of-the-art techniques.

  15. Analytical application of laser excited shpol'skii spectroscopy: direct identification and quantitation of polynuclear aromatic compounds

    SciTech Connect

    Elsaid, A.E.

    1986-01-01

    The object of the present work is to develop a broader application base for laser exicted Shpol'skii spectroscopy. Potential problems that may emerge are identified and solutions are provided. An atlas of reference spectra useful for the selective identification of individual polycyclic aromatic hydrocarbons (PAHs) has been completed. 210 refs., 83 figs., 5 tabs. (PLG)

  16. Assessment of the maturity and biological parameters of compost produced from dairy manure and rice chaff by excitation-emission matrix fluorescence spectroscopy.

    PubMed

    Tian, Wei; Li, Lingzhi; Liu, Fang; Zhang, Zhenhua; Yu, Guanghui; Shen, Qirong; Shen, Biao

    2012-04-01

    The assessment of maturity and biological parameters is important in the composting process. In this study, excitation-emission matrix (EEM) fluorescence spectroscopy was applied to evaluate the maturity and biological parameters of compost produced from the co-composting of dairy and rice chaff. The results from a Pearson correlation analysis between traditional physico-chemical maturity indices and fluorescence regional integration (FRI) parameters showed that among the FRI parameters, P(V,n)/P(III,n) and P(V,n) were suitable for the assessment of compost maturity. Moreover, the FRI parameters could be used to evaluate biological parameters including the germination index (GI) and ribotype evolution which indicate the bacterial community structure and dynamics. P(IV,n) was the most suitable indicator for revealing the community structure and dynamics during the composting process. Fluorescence spectroscopy combined with the FRI analysis could be used as a sensitive and efficient tool for assessing compost maturity and biological parameters. PMID:22342088

  17. Ordered silicon nanocones arrays for label-free DNA quantitative analysis by surface-enhanced Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Xu, Ting-Ting; Huang, Jian-An; He, Li-Fang; He, Yao; Su, Shao; Lee, Shuit-Tong

    2011-10-01

    Ordered vertical silicon nanocones arrays coated with silver nanoparticles (AgNPs@SiNCs) are developed as surface-enhanced Raman scattering (SERS)-active substrate, which features good uniformity and reliable reproducibility of SERS signals. Label-free DNA at low concentrations (10-8 M) could be quantitatively analyzed via SERS using the AgNPs@SiNCs. The Raman peak at 732 cm-1 due to adenine breathing mode was selected as an endogenous Raman marker for quantitative detection of label-free DNA. The AgNPs@SiNCs as high-performance SERS-active substrates are attractive for surface enhancement mechanism investigation and biochemical sensing applications.

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

    PubMed

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

    2014-04-01

    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

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

    SciTech Connect

    Skelly, E.M.

    1982-01-01

    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.

  20. Resonant Mie scattering in infrared spectroscopy of biological materials--understanding the 'dispersion artefact'.

    PubMed

    Bassan, Paul; Byrne, Hugh J; Bonnier, Franck; Lee, Joe; Dumas, Paul; Gardner, Peter

    2009-08-01

    Infrared spectroscopic cytology is potentially a powerful clinical tool. However, in order for it to be successful, practitioners must be able to extract reliably a pure absorption spectrum from a measured spectrum that often contains many confounding factors. The most intractable problem to date is the, so called, dispersion artefact which most prominently manifests itself as a sharp decrease in absorbance on the high wavenumber side of the amide I band in the measured spectrum, exhibiting a derivative-like line shape. In this paper we use synchrotron radiation FTIR micro-spectroscopy to record spectra of mono-dispersed poly(methyl methacrylate) (PMMA) spheres of systematically varying size and demonstrate that the spectral distortions in the data can be understood in terms of resonant Mie scattering. A full understanding of this effect will enable us to develop strategies for deconvolving the scattering contribution and recovering the pure absorption spectrum, thus removing one of the last technological barriers to the development of clinical spectroscopic cytology.

  1. [Bone Cell Biology Assessed by Microscopic Approach. Assessment of bone quality using Raman and infrared spectroscopy].

    PubMed

    Suda, Hiromi Kimura

    2015-10-01

    Bone quality, which was defined as "the sum total of characteristics of the bone that influence the bone's resistance to fracture" at the National Institute of Health (NIH) conference in 2001, contributes to bone strength in combination with bone mass. Bone mass is often measured as bone mineral density (BMD) and, consequently, can be quantified easily. On the other hand, bone quality is composed of several factors such as bone structure, bone matrix, calcification degree, microdamage, and bone turnover, and it is not easy to obtain data for the various factors. Therefore, it is difficult to quantify bone quality. We are eager to develop new measurement methods for bone quality that make it possible to determine several factors associated with bone quality at the same time. Analytic methods based on Raman and FTIR spectroscopy have attracted a good deal of attention as they can provide a good deal of chemical information about hydroxyapatite and collagen, which are the main components of bone. A lot of studies on bone quality using Raman and FTIR imaging have been reported following the development of the two imaging systems. Thus, both Raman and FTIR imaging appear to be promising new bone morphometric techniques.

  2. HNS+ and HSN+ cations: Electronic states, spin-rovibronic spectroscopy with planetary and biological implications

    NASA Astrophysics Data System (ADS)

    Trabelsi, Tarek; Ben Yaghlane, Saida; Al Mogren, Muneerah Mogren; Francisco, Joseph S.; Hochlaf, Majdi

    2016-08-01

    Ab initio methods in conjunction with a large basis set are used to compute the potential energy surfaces of the 12 lowest electronic states of the HNS+ and HSN+ isomeric forms. These potentials are used in discussions of the metastability of these cations and plausible mechanisms for the H+/H + SN+/SN, S/S+ + NH+/NH, N/N+ + SH+/SH ion-molecule reactions. Interestingly, the low rovibrational levels of HSN+(12A″) and HNS+(12A″) electronically excited ions are predicted to be long-lived. Both ions are suggested to be a suitable candidate for light-sensitive NOṡ donor in vivo and as a possible marker for the detection of intermediates in nitrites + H2S reactions at the cellular level. The full spin rovibronic levels of HNS+ are presented, which may assist in the experimental identification of HNS+ and HSN+ ions and in elucidating their roles in astrophysical and biological media.

  3. High-resolution NMR spectroscopy of biological tissues usingprojected Magic Angle Spinning

    SciTech Connect

    Martin, Rachel W.; Jachmann, Rebecca C.; Sakellariou, Dimitris; Nielsen, Ulla Gro; Pines, Alexander

    2005-01-27

    High-resolution NMR spectra of materials subject toanisotropic broadening are usually obtained by rotating the sample aboutthe magic angle, which is 54.7 degrees to the static magnetic field. Inprojected Magic Angle Spinning (p-MAS), the sample is spun about twoangles, neither of which is the magic angle. This provides a method ofobtaining isotropic spectra while spinning at shallow angles. The p-MASexperiment may be used in situations where spinning the sample at themagic angle is not possible due to geometric or other constraints,allowing the choice of spinning angle to be determined by factors such asthe shape of the sample, rather than by the spin physics. The applicationof this technique to bovine tissue samples is demonstrated as a proof ofprinciple for future biological or medical applications.

  4. High-extinction virtually imaged phased array-based Brillouin spectroscopy of turbid biological media

    NASA Astrophysics Data System (ADS)

    Fiore, Antonio; Zhang, Jitao; Shao, Peng; Yun, Seok Hyun; Scarcelli, Giuliano

    2016-05-01

    Brillouin microscopy has recently emerged as a powerful technique to characterize the mechanical properties of biological tissue, cell, and biomaterials. However, the potential of Brillouin microscopy is currently limited to transparent samples, because Brillouin spectrometers do not have sufficient spectral extinction to reject the predominant non-Brillouin scattered light of turbid media. To overcome this issue, we combined a multi-pass Fabry-Perot interferometer with a two-stage virtually imaged phased array spectrometer. The Fabry-Perot etalon acts as an ultra-narrow band-pass filter for Brillouin light with high spectral extinction and low loss. We report background-free Brillouin spectra from Intralipid solutions and up to 100 μm deep within chicken muscle tissue.

  5. Salicylate Detection by Complexation with Iron(III) and Optical Absorbance Spectroscopy: An Undergraduate Quantitative Analysis Experiment

    ERIC Educational Resources Information Center

    Mitchell-Koch, Jeremy T.; Reid, Kendra R.; Meyerhoff, Mark E.

    2008-01-01

    An experiment for the undergraduate quantitative analysis laboratory involving applications of visible spectrophotometry is described. Salicylate, a component found in several medications, as well as the active by-product of aspirin decomposition, is quantified. The addition of excess iron(III) to a solution of salicylate generates a deeply…

  6. Near-infrared spectroscopy quantitative determination of Pefloxacin mesylate concentration in pharmaceuticals by using partial least squares and principal component regression multivariate calibration

    NASA Astrophysics Data System (ADS)

    Xie, Yunfei; Song, Yan; Zhang, Yong; Zhao, Bing

    2010-05-01

    Pefloxacin mesylate, a broad-spectrum antibacterial fluoroquinolone, has been widely used in clinical practice. Therefore, it is very important to detect the concentration of Pefloxacin mesylate. In this research, the near-infrared spectroscopy (NIRS) has been applied to quantitatively analyze on 108 injection samples, which was divided into a calibration set containing 89 samples and a prediction set containing 19 samples randomly. In order to get a satisfying result, partial least square (PLS) regression and principal components regression (PCR) have been utilized to establish quantitative models. Also, the process of establishing the models, parameters of the models, and prediction results were discussed in detail. In the PLS regression, the values of the coefficient of determination ( R2) and root mean square error of cross-validation (RMSECV) of PLS regression are 0.9263 and 0.00119, respectively. For comparison, though applying PCR method to get the values of R2 and RMSECV we obtained are 0.9685 and 0.00108, respectively. And the values of the standard error of prediction set (SEP) of PLS and PCR models are 0.001480 and 0.001140. The result of the prediction set suggests that these two quantitative analysis models have excellent generalization ability and prediction precision. However, for this PFLX injection samples, the PCR quantitative analysis model achieved more accurate results than the PLS model. The experimental results showed that NIRS together with PCR method provide rapid and accurate quantitative analysis of PFLX injection samples. Moreover, this study supplied technical support for the further analysis of other injection samples in pharmaceuticals.

  7. The use of Fourier-transform infrared spectroscopy for the quantitative determination of glucose concentration in whole blood.

    PubMed

    Shen, Y C; Davies, A G; Linfleld, E H; Elsey, T S; Taday, P F; Arnone, D D

    2003-07-01

    Fourier-transform infrared transmission spectroscopy has been used for the determination of glucose concentration in whole blood samples from 28 patients. A 4-vector partial least-squares calibration model, using the spectral range 950-1200 cm(-1), yielded a standard-error-of-prediction of 0.59 mM for an independent test set. For blood samples from a single patient, we found that the glucose concentration was proportional to the difference between the values of the second derivative spectrum at 1082 cm(-1) and 1093 cm(-1). This indicates that spectroscopy at these two specific wavenumbers alone could be used to determine the glucose concentration in blood plasma samples from a single patient, with a prediction error of 0.95 mM. PMID:12884933

  8. Homogeneity testing and quantitative analysis of manganese (Mn) in vitrified Mn-doped glasses by laser-induced breakdown spectroscopy (LIBS)

    NASA Astrophysics Data System (ADS)

    Unnikrishnan, V. K.; Nayak, Rajesh; Kartha, V. B.; Santhosh, C.; Sonavane, M. S.; Yeotikar, R. G.; Shah, M. L.; Gupta, G. P.; Suri, B. M.

    2014-09-01

    Laser-induced breakdown spectroscopy (LIBS), an atomic emission spectroscopy method, has rapidly grown as one of the best elemental analysis techniques over the past two decades. Homogeneity testing and quantitative analysis of manganese (Mn) in manganese-doped glasses have been carried out using an optimized LIBS system employing a nanosecond ultraviolet Nd:YAG laser as the source of excitation. The glass samples have been prepared using conventional vitrification methods. The laser pulse irradiance on the surface of the glass samples placed in air at atmospheric pressure was about 1.7×109 W/cm2. The spatially integrated plasma emission was collected and imaged on to the spectrograph slit using an optical-fiber-based collection system. Homogeneity was checked by recording LIBS spectra from different sites on the sample surface and analyzing the elemental emission intensities for concentration determination. Validation of the observed LIBS results was done by comparison with scanning electron microscope- energy dispersive X-ray spectroscopy (SEM-EDX) surface elemental mapping. The analytical performance of the LIBS system has been evaluated through the correlation of the LIBS determined concentrations of Mn with its certified values. The results are found to be in very good agreement with the certified concentrations.

  9. Homogeneity testing and quantitative analysis of manganese (Mn) in vitrified Mn-doped glasses by laser-induced breakdown spectroscopy (LIBS)

    SciTech Connect

    Unnikrishnan, V. K.; Nayak, Rajesh; Kartha, V. B.; Santhosh, C. E-mail: unnikrishnan.vk@manipal.edu; Sonavane, M. S.; Yeotikar, R. G.; Shah, M. L.; Gupta, G. P.; Suri, B. M.

    2014-09-15

    Laser-induced breakdown spectroscopy (LIBS), an atomic emission spectroscopy method, has rapidly grown as one of the best elemental analysis techniques over the past two decades. Homogeneity testing and quantitative analysis of manganese (Mn) in manganese-doped glasses have been carried out using an optimized LIBS system employing a nanosecond ultraviolet Nd:YAG laser as the source of excitation. The glass samples have been prepared using conventional vitrification methods. The laser pulse irradiance on the surface of the glass samples placed in air at atmospheric pressure was about 1.7×10{sup 9} W/cm{sup 2}. The spatially integrated plasma emission was collected and imaged on to the spectrograph slit using an optical-fiber-based collection system. Homogeneity was checked by recording LIBS spectra from different sites on the sample surface and analyzing the elemental emission intensities for concentration determination. Validation of the observed LIBS results was done by comparison with scanning electron microscope- energy dispersive X-ray spectroscopy (SEM-EDX) surface elemental mapping. The analytical performance of the LIBS system has been evaluated through the correlation of the LIBS determined concentrations of Mn with its certified values. The results are found to be in very good agreement with the certified concentrations.

  10. Sensitive, Rapid, Quantitative and in Vitro Method for the Detection of Biologically Active Staphylococcal Enterotoxin Type E

    PubMed Central

    Rasooly, Reuven; Do, Paula; Hernlem, Bradley

    2016-01-01

    Staphylococcus aureus is a major bacterial cause of clinical infections and foodborne illnesses through its production of a group of enterotoxins (SEs) which cause gastroenteritis and also function as superantigens to massively activate T cells. In the present study, we tested Staphylococcal enterotoxin type E (SEE), which was detected in 17 of the 38 suspected staphylococcal food poisoning incidents in a British study and was the causative agent in outbreaks in France, UK and USA. The current method for detection of enterotoxin activity is an in vivo monkey or kitten bioassay; however, this expensive procedure has low sensitivity and poor reproducibility, requires many animals, is impractical to test on a large number of samples, and raises ethical concerns with regard to the use of experimental animals. The purpose of this study is to develop rapid sensitive and quantitative bioassays for detection of active SEE. We apply a genetically engineered T cell-line expressing the luciferase reporter gene under the regulation of nuclear factor of activated T-cells response element (NFAT-RE), combined with a Raji B-cell line that presents the SEE-MHC (major histocompatibility complex) class II to the engineered T cell line. Exposure of the above mixed culture to SEE induces differential expression of the luciferase gene and bioluminescence is read out in a dose dependent manner over a 6-log range. The limit of detection of biologically active SEE is 1 fg/mL which is 109 times more sensitive than the monkey and kitten bioassay. PMID:27187474

  11. Laser spectroscopy and mass spectrometry of biologically relevant systems: chiral discrimination

    NASA Astrophysics Data System (ADS)

    Piccirillo, Susanna; Satta, Mauro; Coreno, Marcello; Catone, Daniele; Rondino, Flaminia; Scuderi, Debora; Paladini, Alessandra; Speranza, Maurizio; Giardini, Anna

    2005-06-01

    Radical ions are open-shell elusive species of paramount importance in many organic reactions and in biological processes. Oxidative bond breaking and forming involving radical ions are common process taking place in asymmetric enzyme cavities. Side-chain Cα-CΒ bond fragmentation in the radical cations of aromatic alcohols is a common process in solution [1-3], whose efficiency is enhanced in polar solvents such as water. Hydrogen-bonding between the ion and the solvent in the relevant transition structure is thought as responsible of the rate acceleration [4]. Effects of achiral and chiral microsolvation on the radical cation of R-(+)-l-phenyl-l-propanol, have been investigated. The energy thresholds of the homolytic Cα-Cβ bond breaking of R-(+)-1-phenyl-1-propanol radical cation, its mono-hydrated cluster, and its clusters with (2R,3R)-(-)-2,3-butanediol and (2S,3S)-(+)-2,3-butanediol have been studied through two color Resonant Two Photon Ionization, Photodissociation and Mass Spectrometry. The barrier of the Cα-Cβ fragmentation is appreciably higher for the unsolvated molecular ion than for its adducts with solvent molecules. Moreover, marked differences in the ethyl loss fragmentation energy are observed for the clusters with water and with the two diols. In particular the homochiral cluster with (2R, 3R)-(-)-2,3-butanediol exhibits a fragmentation barrier higher than that of the corresponding heterochiral adduct with (25, 35)-(+)-2,3-butanediol.

  12. Applications of High Resolution Laser: Induced Breakdown Spectroscopy for Environmental and Biological Samples

    NASA Astrophysics Data System (ADS)

    Martin, Madhavi Z.; Labbe, Nicole; Wagner, Rebekah J.

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  13. Applications of High Resolution Laser Induced Breakdown Spectroscopy for Environmental and Biological Samples

    SciTech Connect

    Martin, Madhavi Z; Labbe, Nicole; Wagner, Rebekah J.

    2013-01-01

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  14. HNS(+) and HSN(+) cations: Electronic states, spin-rovibronic spectroscopy with planetary and biological implications.

    PubMed

    Trabelsi, Tarek; Ben Yaghlane, Saida; Al Mogren, Muneerah Mogren; Francisco, Joseph S; Hochlaf, Majdi

    2016-08-28

    Ab initio methods in conjunction with a large basis set are used to compute the potential energy surfaces of the 12 lowest electronic states of the HNS(+) and HSN(+) isomeric forms. These potentials are used in discussions of the metastability of these cations and plausible mechanisms for the H(+)/H + SN(+)/SN, S/S(+) + NH(+)/NH, N/N(+) + SH(+)/SH ion-molecule reactions. Interestingly, the low rovibrational levels of HSN(+)(1(2)A″) and HNS(+)(1(2)A″) electronically excited ions are predicted to be long-lived. Both ions are suggested to be a suitable candidate for light-sensitive NO(⋅) donor in vivo and as a possible marker for the detection of intermediates in nitrites + H2S reactions at the cellular level. The full spin rovibronic levels of HNS(+) are presented, which may assist in the experimental identification of HNS(+) and HSN(+) ions and in elucidating their roles in astrophysical and biological media. PMID:27586922

  15. Biogenic unmodified gold nanoparticles for selective and quantitative detection of cerium using UV-vis spectroscopy and photon correlation spectroscopy (DLS).

    PubMed

    Priyadarshini, E; Pradhan, N; Panda, P K; Mishra, B K

    2015-06-15

    The ability of self-functionalized biogenic GNPs towards highly selective colorimetric detection of rare earth element cerium is being reported for the first time. GNPs underwent rapid aggregation on addition of cerium indicated by red shift of SPR peak followed by complete precipitation. Hereby, this concept of co-ordination of cerium ions onto the GNP surface has been utilized for detection of cerium. The remarkable capacity of GNPs to sensitively detect Ce without proves beneficial compared to previous reports of colorimetric sensing. MDL was 15 and 35 ppm by DLS and UV-vis spectroscopy respectively, suggesting DLS to be highly sensitive and a practical alternative in ultrasensitive detection studies. The sensing system showed a good linear fit favouring feasible detection of cerium in range of 2-50 ppm. Similar studies further showed the superior selectivity of biogenic GNPs compared to chemically synthesized counterparts. The sensing system favours on-site analysis as it overcomes need of complex instrumentation, lengthy protocols and surface modification of GNP.

  16. Fourier transform mid-infrared spectroscopy (FT-MIR) combined with chemometrics for quantitative analysis of dextrin in Danshen (Salvia miltiorrhiza) granule.

    PubMed

    Guo, Tao; Feng, Wei-Hong; Liu, Xiao-Qian; Gao, Hui-Min; Wang, Zhi-Min; Gao, Liang-Liang

    2016-05-10

    The granule of Chinese medicine (GCM) is prepared by water-soluble extract of single yinpian (WESY) of herbal medicine, and used as a drug ingredient for clinical formulation. The WESY content or corresponding yinpian amount is the most important parameter in evaluating the quality of GCM. Low WESY content reflects poor GCM. Classical quantitative methods, such as HPLC, cannot fully detect the adulteration by adding characteristic ingredients and less WESY production. GCM is composed of WESY and a high content of specific excipient. The WESY content in the GCM may be indirectly analyzed using mid-infrared spectroscopy (MIR). In this paper, a quantitative method to evaluate the quality of Danshen (Salvia miltiorrhiza) granule (DG) was developed using MIR combined with chemometrics. Appropriate characteristic quantitative regions (CQR) were extracted by selecting the spectral regions corresponding to altered excipient content in DG. The best model of dextrin content determination in DG with low RMSEC of 1.97, low RMSEP of 2.07, and excellent RPD of 5.03 (>5.0) was obtained using partial least-squares (PLS) regression, and validated using accepted values of precision and recovery. The results suggest that FT-MIR combined with PLS is a rapid and valuable analytical tool to determine the WESY in DG based on excipient content. The model enabling indirect calculation of WESY content in GCM represents a reference standard for rapid analysis of other WESYs in GCM industry. PMID:26859611

  17. Wavelet prism decomposition analysis applied to CARS spectroscopy: a tool for accurate and quantitative extraction of resonant vibrational responses.

    PubMed

    Kan, Yelena; Lensu, Lasse; Hehl, Gregor; Volkmer, Andreas; Vartiainen, Erik M

    2016-05-30

    We propose an approach, based on wavelet prism decomposition analysis, for correcting experimental artefacts in a coherent anti-Stokes Raman scattering (CARS) spectrum. This method allows estimating and eliminating a slowly varying modulation error function in the measured normalized CARS spectrum and yields a corrected CARS line-shape. The main advantage of the approach is that the spectral phase and amplitude corrections are avoided in the retrieved Raman line-shape spectrum, thus significantly simplifying the quantitative reconstruction of the sample's Raman response from a normalized CARS spectrum in the presence of experimental artefacts. Moreover, the approach obviates the need for assumptions about the modulation error distribution and the chemical composition of the specimens under study. The method is quantitatively validated on normalized CARS spectra recorded for equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose. PMID:27410113

  18. Wavelet prism decomposition analysis applied to CARS spectroscopy: a tool for accurate and quantitative extraction of resonant vibrational responses.

    PubMed

    Kan, Yelena; Lensu, Lasse; Hehl, Gregor; Volkmer, Andreas; Vartiainen, Erik M

    2016-05-30

    We propose an approach, based on wavelet prism decomposition analysis, for correcting experimental artefacts in a coherent anti-Stokes Raman scattering (CARS) spectrum. This method allows estimating and eliminating a slowly varying modulation error function in the measured normalized CARS spectrum and yields a corrected CARS line-shape. The main advantage of the approach is that the spectral phase and amplitude corrections are avoided in the retrieved Raman line-shape spectrum, thus significantly simplifying the quantitative reconstruction of the sample's Raman response from a normalized CARS spectrum in the presence of experimental artefacts. Moreover, the approach obviates the need for assumptions about the modulation error distribution and the chemical composition of the specimens under study. The method is quantitatively validated on normalized CARS spectra recorded for equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose.