Sample records for quantitative biological spectroscopy

  1. Intrinsic Raman spectroscopy for quantitative biological spectroscopy Part II

    PubMed Central

    Bechtel, Kate L.; Shih, Wei-Chuan; Feld, Michael S.

    2009-01-01

    We demonstrate the effectiveness of intrinsic Raman spectroscopy (IRS) at reducing errors caused by absorption and scattering. Physical tissue models, solutions of varying absorption and scattering coefficients with known concentrations of Raman scatterers, are studied. We show significant improvement in prediction error by implementing IRS to predict concentrations of Raman scatterers using both ordinary least squares regression (OLS) and partial least squares regression (PLS). In particular, we show that IRS provides a robust calibration model that does not increase in error when applied to samples with optical properties outside the range of calibration. PMID:18711512

  2. Quantitative NMR spectroscopy of biologically active substances and excipients

    Microsoft Academic Search

    Tanja Beyer; Bernd Diehl; Ulrike Holzgrabe

    2010-01-01

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

  3. Microfluidic impedance spectroscopy as a tool for quantitative biology and biotechnology

    PubMed Central

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

    2012-01-01

    A microfluidic device that is able to perform dielectric spectroscopy is developed. The device consists of a measurement chamber that is 250??m thick and 750??m in radius. Around 1000 cells fit inside the chamber assuming average quantities for cell radius and volume fraction. This number is about 1000 folds lower than the capacity of conventional fixtures. A T-cell leukemia cell line Jurkat is tested using the microfluidic device. Measurements of deionized water and salt solutions are utilized to determine parasitic effects and geometric capacitance of the device. Physical models, including Maxwell-Wagner mixture and double shell models, are used to derive quantities for sub-cellular units. Clausius-Mossotti factor of Jurkat cells is extracted from the impedance spectrum. Effects of cellular heterogeneity are discussed and parameterized. Jurkat cells are also tested with a time domain reflectometry system for verification of the microfluidic device. Results indicate good agreement of values obtained with both techniques. The device can be used as a unique cell diagnostic tool to yield information on sub-cellular units. PMID:23853680

  4. Princeton Diversity Programs in Molecular Biology and Quantitative & Computational Biology

    E-print Network

    CASE STUDY Princeton Diversity Programs in Molecular Biology and Quantitative & Computational Biology Author Princeton University Acknowledgments. Vides estius moluptaquis aut maxime vitin peroribus: Diversity Programs in Molecular Biology and Quantitative & Computational Biology Founded in 2007 in response

  5. Degree: Bachelor of Science Major: Quantitative Biology

    E-print Network

    Cakoni, Fioralba

    Degree: Bachelor of Science Major: Quantitative Biology The College of Arts and Sciences administers an interdisciplinary major pro- gram in Quantitative Biology leading to the Bachelor of Science degree. The major provides a strong background in mathematics, biology, chemistry and physics appro

  6. Noise Spectroscopy Used in Biology

    NASA Astrophysics Data System (ADS)

    Žacik, Michal

    This thesis contains glossary topic of spectroscopic measurement methods in broad bands of frequency. There is designed experimental measurement method for simple samples and biological samples measurements for noise spectroscopy in frequency range of 0.1 - 6 GHz, using broadband noise generator. There is realized the workplace and the measurement method is verified by measuring on selected samples. Measurements a displayed and analyzed.

  7. Teaching quantitative biology: goals, assessments, and resources

    PubMed Central

    Aikens, Melissa L.; Dolan, Erin L.

    2014-01-01

    More than a decade has passed since the publication of BIO2010, calling for an increased emphasis on quantitative skills in the undergraduate biology curriculum. In that time, relatively few papers have been published that describe educational innovations in quantitative biology or provide evidence of their effects on students. Using a “backward design” framework, we lay out quantitative skill and attitude goals, assessment strategies, and teaching resources to help biologists teach more quantitatively. Collaborations between quantitative biologists and education researchers are necessary to develop a broader and more appropriate suite of assessment tools, and to provide much-needed evidence on how particular teaching strategies affect biology students' quantitative skill development and attitudes toward quantitative work. PMID:25368425

  8. Quantitative and Systems Biology (QSB) GRADUATE PROGRAM AT UC MERCED

    E-print Network

    Uppsala Universitet

    Quantitative and Systems Biology (QSB) GRADUATE PROGRAM AT UC MERCED INTERDISCIPLINARYTRAINING QSB their interdisciplinary training through QSB. EMPHASISAREAS > Molecular systems biology > Cellular systems biology > Microbial systems biology > Organismal systems biology > Systems ecology > Quantitative and theoretical

  9. Ministry of Fisheries Undergraduate Scholarships in Quantitative Marine Biology

    E-print Network

    Auckland, University of

    Ministry of Fisheries Undergraduate Scholarships in Quantitative Marine Biology Ministry scholarship in Quantitative Marine Biology - Supporting double majors in Mathematics/Statistics and Biology biology at the undergraduate level. Six scholarships ($5000 each) will be available to New Zealand

  10. Quantitative Spectroscopy of BA-type Supergiants

    E-print Network

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

    2005-09-22

    Luminous BA-SGs allow topics ranging from NLTE physics and the evolution of massive stars to the chemical evolution of galaxies and cosmology to be addressed. A hybrid NLTE technique for the quantitative spectroscopy of BA-SGs is discussed. Thorough tests and first applications of the spectrum synthesis method are presented for four bright Galactic objects. Stellar parameters are derived from spectroscopic indicators. The internal accuracy of the method allows the 1sigma-uncertainties to be reduced to BA-SGs as versatile tools for extragalactic stellar astronomy beyond the Local Group. (abridged)

  11. Quantitative Pathway Logic for Computational Biology

    Microsoft Academic Search

    Michele Baggi; Demis Ballis; Moreno Falaschi

    2009-01-01

    This paper presents an extension of Pathway Logic, called Quantitative Pathway Logic (QPL), which allows one to reason about\\u000a quantitative aspects of biological processes, such as element concentrations and reactions kinetics. Besides, it supports\\u000a the modeling of inhibitors, that is, chemicals which may block a given reaction whenever their concentration exceeds a certain\\u000a threshold. QPL models can be specified and

  12. Effect of photobleaching on calibration model development in biological Raman spectroscopy

    E-print Network

    Barman, Ishan

    A major challenge in performing quantitative biological studies using Raman spectroscopy lies in overcoming the influence of the dominant sample fluorescence background. Moreover, the prediction accuracy of a calibration ...

  13. Gerhard Wider: Technical aspects of NMR spectroscopy with biological macromolecules .... Technical aspects of NMR spectroscopy

    E-print Network

    Wider, Gerhard

    Gerhard Wider: Technical aspects of NMR spectroscopy with biological macromolecules .... -1- Technical aspects of NMR spectroscopy with biological macromolecules and studies of hydration in solution aspects of NMR spectroscopy with biological macromolecules .... -2- Contents 1. Introduction 5 2. Basic

  14. Quantitative cell biology: the essential role of theory

    PubMed Central

    Howard, Jonathon

    2014-01-01

    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. PMID:25368416

  15. Quantitation of influenza A virus in the presence of extraneous protein using electrochemical impedance spectroscopy

    Microsoft Academic Search

    Walid Mohamed Hassen; Valérie Duplan; Eric Frost; Jan J. Dubowski

    2011-01-01

    In an attempt to provide an insight into detection of specific viruses in biological samples, we report on quantitation of influenza A virus (IAV) in samples containing large amounts of extraneous bovine serum albumin (BSA), foetal bovine serum (FBS) and hepatitis B virus (HBV) vaccine. Detection was carried out using electrochemical impedance spectroscopy (EIS) with an antibody-neutravidin-thiol architecture immobilized on

  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. Journal of Quantitative Spectroscopy & Radiative Transfer 98 (2006) 189201

    E-print Network

    Guo, Zhixiong "James"

    2006-01-01

    Journal of Quantitative Spectroscopy & Radiative Transfer 98 (2006) 189­201 Correlative studies vessel parameters such as the location, size, and hemoglobin concentration of the CCA or jugular vein (JV wavelengths; Radiative transfer; Cerebral blood oxygenation; Correlations; MC simulation; Noninvasive

  18. 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...

  19. 1, 2, 3, 4: Infusing Quantitative Literacy into Introductory Biology

    ERIC Educational Resources Information Center

    Bray Speth, Elena; 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…

  20. 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

  1. 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 SPIE Vol. 5268-2, 10-18 (2004)

  2. Characterizing human pancreatic cancer precursor using quantitative tissue optical spectroscopy

    PubMed Central

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

    2013-01-01

    In a pilot study, multimodal optical spectroscopy coupled with quantitative tissue-optics models distinguished intraductal papillary mucinous neoplasm (IPMN), a common precursor to pancreatic cancer, from normal tissues in freshly excised human pancreas. A photon-tissue interaction (PTI) model extracted parameters associated with cellular nuclear size and refractive index (from reflectance spectra) and extracellular collagen content (from fluorescence spectra). The results suggest that tissue optical spectroscopy has the potential to characterize pre-cancerous neoplasms in human pancreatic tissues. PMID:24409383

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

    PubMed Central

    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. PMID:20810965

  4. Submillimeter wave spectroscopy of biological macromolecules

    Microsoft Academic Search

    Tatiana Globus

    2005-01-01

    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

  5. Quantitative analysis of anatase in Georgia kaolins using Raman spectroscopy

    Microsoft Academic Search

    Paul A. Schroeder; Nathan D. Melear; Robert J. Pruett

    2003-01-01

    Raman spectroscopy of Georgia kaolins ubiquitously show a strong Eg frequency near 144 cm?1. Analysis of the band intensity shows that under specific source, sample, and optical conditions, peak area measurements are predictable and reproducible. Using standard additions, successful quantitative techniques have been developed that allow analysis of 25% solids water slurries, which achieve anatase detection limits down to 0.3%

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

    Microsoft Academic Search

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

    1995-01-01

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

  7. 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…

  8. 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.

  9. RIKEN Quantitative Biology Center Cell Dynamics Research Core

    E-print Network

    Fukai, Tomoki

    RIKEN Quantitative Biology Center Cell Dynamics Research Core Laboratory for Cell Dynamics Design Research Core Laboratory for Synthetic Biology Laboratory for Cell-Free Protein Synthesis Observation Laboratory for Single Cell Gene Dynamics Laboratory for Cell Field Structure Laboratory for Cell

  10. RIKEN Quantitative Biology Center Cell Dynamics Research Core

    E-print Network

    Fukai, Tomoki

    RIKEN Quantitative Biology Center Cell Dynamics Research Core Laboratory for Cell Dynamics for Developmental Morphogeometry Cell Design Research Core Laboratory for Synthetic Biology Laboratory for Cell Observation Laboratory for Single Cell Gene Dynamics Laboratory for Cell Field Structure Laboratory for Cell

  11. Quantitative and Rapid DNA Detection by Laser Transmission Spectroscopy

    PubMed Central

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

    2011-01-01

    Laser transmission spectroscopy (LTS) is a quantitative and rapid in vitro technique for measuring the size, shape, and number of nanoparticles in suspension. Here we report on the application of LTS as a novel detection method for species-specific DNA where the presence of one invasive species was differentiated from a closely related invasive sister species. The method employs carboxylated polystyrene nanoparticles functionalized with short DNA fragments that are complimentary to a specific target DNA sequence. In solution, the DNA strands containing targets bind to the tags resulting in a sizable increase in the nanoparticle diameter, which is rapidly and quantitatively measured using LTS. DNA strands that do not contain the target sequence do not bind and produce no size change of the carboxylated beads. The results show that LTS has the potential to become a quantitative and rapid DNA detection method suitable for many real-world applications. PMID:22195026

  12. Quantitative and rapid DNA detection by laser transmission spectroscopy.

    PubMed

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

    2011-01-01

    Laser transmission spectroscopy (LTS) is a quantitative and rapid in vitro technique for measuring the size, shape, and number of nanoparticles in suspension. Here we report on the application of LTS as a novel detection method for species-specific DNA where the presence of one invasive species was differentiated from a closely related invasive sister species. The method employs carboxylated polystyrene nanoparticles functionalized with short DNA fragments that are complimentary to a specific target DNA sequence. In solution, the DNA strands containing targets bind to the tags resulting in a sizable increase in the nanoparticle diameter, which is rapidly and quantitatively measured using LTS. DNA strands that do not contain the target sequence do not bind and produce no size change of the carboxylated beads. The results show that LTS has the potential to become a quantitative and rapid DNA detection method suitable for many real-world applications. PMID:22195026

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

    PubMed Central

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

    2012-01-01

    Imaging mRNA with single-molecule sensitivity in live cells has become an indispensable tool for quantitatively studying RNA biology. The MS2 system has been extensively used due to its unique simplicity and sensitivity. However, the levels of the coat protein needed for consistent labeling of mRNAs limits the sensitivity and quantitation of this technology. Here, we applied fluorescence fluctuation spectroscopy to quantitatively characterize and enhance the MS2 system. Surprisingly, we found that a high fluorescence background resulted from inefficient dimerization of fluorescent protein (FP)-labeled MS2 coat protein (MCP). To mitigate this problem, we used a single-chain tandem dimer of MCP (tdMCP) that significantly increased the uniformity and sensitivity of mRNA labeling. Furthermore, we characterized the PP7 coat protein and the binding to its respective RNA stem loop. We conclude that the PP7 system performs better for RNA labeling. Finally, we used these improvements to study endogenous ?-actin mRNA, which has 24xMS2 binding sites inserted into the 3? untranslated region. The tdMCP-FP allowed uniform RNA labeling and provided quantitative measurements of endogenous mRNA concentration and diffusion. This work provides a foundation for quantitative spectroscopy and imaging of single mRNAs directly in live cells. PMID:22735544

  14. 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.

  15. 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.

  16. Mapping of local oxide properties by quantitative scanning capacitance spectroscopy

    SciTech Connect

    Brezna, W.; Harasek, S.; Lugstein, A.; Leitner, T.; Hoffmann, H.; Bertagnolli, E.; Smoliner, J. [Institut fuer Festkoerperelektronik, Technische Universitaet Wien, Floragasse 7, A-1040 Vienna (Austria); Institut fuer Angewandte Synthesechemie, Technische Universitat Wien, Getreidemarkt 9/163, A-1060 Vienna (Austria); Institut fuer Festkoerperelektronik, Technische Universitaet Wien, Floragasse 7, A-1040 Vienna (Austria)

    2005-05-01

    In this work, quantitative scanning capacitance spectroscopy was applied to investigate the local dielectric properties of a chemical vapor deposition grown ZrO{sub 2} layer on low-doped silicon. Due to self-organization effects during the growth process, the ZrO{sub 2} layer shows small, periodic thickness variations on micrometer length scales near the sample edges. The measured capacitance data and derived oxide charge densities show the same periodicity as the thickness variations. The magnitude of the change of the oxide charge density, however, cannot be explained by the small thickness variations and is attributed to a local periodic change of the growth dynamics.

  17. 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

  18. 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

  19. Quantum integrable systems. Quantitative methods in biology

    E-print Network

    Feverati, Giovanni

    2011-01-01

    Quantum integrable systems have very strong mathematical properties that allow an exact description of their energetic spectrum. From the Bethe equations, I formulate the Baxter "T-Q" relation, that is the starting point of two complementary approaches based on nonlinear integral equations. The first one is known as thermodynamic Bethe ansatz, the second one as Kl\\"umper-Batchelor-Pearce-Destri- de Vega. I show the steps toward the derivation of the equations for some of the models concerned. I study the infrared and ultraviolet limits and discuss the numerical approach. Higher rank integrals of motion can be obtained, so gaining some control on the eigenvectors. After, I discuss the Hubbard model in relation to the N = 4 supersymmetric gauge theory. The Hubbard model describes hopping electrons on a lattice. In the second part, I present an evolutionary model based on Turing machines. The goal is to describe aspects of the real biological evolution, or Darwinism, by letting evolve populations of algorithms. ...

  20. 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…

  1. 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. PMID:19783522

  2. 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

  3. 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

  4. Quantitative correlative proton and electron microprobe analysis of biological specimens

    Microsoft Academic Search

    B. Forslind; L. Kunst; K. G. Malmqvist; L. E. Carlsson; G. M. Roomans

    1985-01-01

    Summary  To investigate the possibility of quantitative correlative proton microprobe (PMP) and electron microprobe (EMP) analysis\\u000a of biological soft tissue, model specimens were analyzed by both techniques. The specimens consisted of freeze-dried sections\\u000a of gelatin containing known concentrations of nickel chloride. Both for PMP and for EMP, the signal was expressed as the ratio\\u000a of the characteristic intensity and the continuum

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

    Microsoft Academic Search

    Masakazu Aono; Ryutaro Souda

    1985-01-01

    Surface atomic structure analysis by low-energy ion scattering spectroscopy (ISS) is reviewed, with particular emphasis on quantitative surface atomic structure analysis by ISS. The important differences between ISS and Rutherford backscattering spectroscopy (RBS), some basic characteristics of ISS, a special type of ISS called impact-collision ion scattering spectroscopy (ICISS), and the general features of the shadow cone in the energy

  6. 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, proliferation, fishing, resources protection and management of specific plans.

  7. Terahertz time-domain spectroscopy of biological tissues

    SciTech Connect

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

    2008-07-31

    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)

  8. 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

  9. Syllabus for BE700 / PY895, Fall 2014 "Methods and Logic in Quantitative Biology"

    E-print Network

    Syllabus for BE700 / PY895, Fall 2014 "Methods and Logic in Quantitative Biology" Boston University Biology is in the midst of a transformation into a fully quantitative, theory-rich science. For example of theory and experiment in biology. Two (or three) important papers, read in advance by all students

  10. Practical aspects of quantitative laser Raman microprobe spectroscopy for the study of fluid inclusions

    Microsoft Academic Search

    J. D. Pasteris; B. Wopenka; J. C. Seitz

    1988-01-01

    This paper is addressed to both geologists who use laser Raman microprobe (LRM) spectroscopy to analyze fluid inclusions and to those who want to evaluate analyses done by this technique. Emphasis is on how to obtain quantitative analyses of fluid inclusions. The authors discuss the basic method of fluid inclusion analysis by LRM spectroscopy and the levels of accuracy and

  11. Biological Sensing with Terahertz Circular Dichroism Spectroscopy

    NASA Astrophysics Data System (ADS)

    Xu, J.; Ramian, G.; Scopatz, A. M.; Allen, S. J.; Plaxco, K. W.

    2003-03-01

    Chirality is believed to be a general and unique trait of life. Since biopolymers absorb broadly in the terahertz regime, we expect circular dichroism to appear everywhere but with zero-crossings as a bio-polymer specific spectroscopic signature; terahertz circular dichroism (heretofore unexplored) may provide a universal and unambiguous signature of biological systems, regardless of their genesis. We are building a novel terahertz circular dichroism spectrometer. It is being tested with a 139 gigahertz Gunn source. But, we will explore terahertz circular dichroism over a very broad frequency range, in and out of aqueous solution using the intense and broadly tunable terahertz radiation from the free electron lasers at UCSB (0.12 to 4.75 THz). Preliminary experimental results will be presented as well as coupled harmonic oscillator models for the broad terahertz frequency circular dichroism expected for these disordered systems. Supported by NASA abd ARO

  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. 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 ( ? = 532 nm, ? = 5 ns) and a frequency-doubled Nd:glass ( ? = 527 nm, ? = 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  15. Quantitative biological imaging by ptychographic x-ray diffraction microscopy

    PubMed Central

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

    2010-01-01

    Recent advances in coherent x-ray diffractive imaging have paved the way to reliable and quantitative imaging of noncompact specimens at the nanometer scale. Introduced a year ago, an advanced implementation of ptychographic coherent diffractive imaging has removed much of the previous limitations regarding sample preparation and illumination conditions. Here, we apply this recent approach toward structure determination at the nanoscale to biological microscopy. We show that the projected electron density of unstained and unsliced freeze-dried cells of the bacterium Deinococcus radiodurans can be derived from the reconstructed phase in a straightforward and reproducible way, with quantified and small errors. Thus, the approach may contribute in the future to the understanding of the highly disputed nucleoid structure of bacterial cells. In the present study, the estimated resolution for the cells was 85 nm (half-period length), whereas 50-nm resolution was demonstrated for lithographic test structures. With respect to the diameter of the pinhole used to illuminate the samples, a superresolution of about 15 was achieved for the cells and 30 for the test structures, respectively. These values should be assessed in view of the low dose applied on the order of ?1.3·105 Gy, and were shown to scale with photon fluence. PMID:20018650

  16. Journal of Quantitative Spectroscopy & Radiative Transfer 109 (2008) 19311942

    E-print Network

    2008-01-01

    with good TES sensitivity after accounting for its lower vertical sensitivity compared with the ACE FTS. r; Spectroscopy; Carbon monoxide ARTICLE IN PRESS www.elsevier.com/locate/jqsrt 0022-4073/$ - see front matter r@sciborg.uwaterloo.ca, cboone@acebox.uwaterloo.ca (C.D. Boone), bernath@uwaterloo.ca, pfb500@york.ac.uk (P.F. Bernath), linda.s.chiou

  17. Broadband reflectance spectroscopy for establishing a quantitative metric of vascular leak using the Miles assay

    NASA Astrophysics Data System (ADS)

    McMurdy, John; Reichner, Jonathan; Mathews, Zara; Markey, Mary; Intwala, Sunny; Crawford, Gregory

    2009-09-01

    Monitoring the physiological effects of biological mediators on vascular permeability is important for identifying potential targets for antivascular leak therapy. This therapy is relevant to treatments for pulmonary edema and other disorders. Current methods of quantifying vascular leak are in vitro and do not allow repeated measurement of the same animal. Using an in vivo diffuse reflectance optical method allows pharmacokinetic analysis of candidate antileak molecules. Here, vascular leak is assessed in mice and rats by using the Miles assay and introducing irritation both topically using mustard oil and intradermally using vascular endothelial growth factor (VEGF). The severity of the leak is assessed using broadband diffuse reflectance spectroscopy with a fiber reflectance probe. Postprocessing techniques are applied to extract an artificial quantitative metric of leak from reflectance spectra at vascular leak sites on the skin of the animal. This leak metric is calculated with respect to elapsed time from irritation in both mustard oil and VEGF treatments on mice and VEGF treatments on rats, showing a repeatable increase in leak metric with leak severity. Furthermore, effects of pressure on the leak metric are observed to have minimal effect on the reflectance spectra, while spatial positioning showed spatially nonuniform leak sites.

  18. 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, E-mail: gchen2@mit.edu [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)] [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Zheng, Ruiting [Key Laboratory of Radiation Beam Technology and Materials Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China)] [Key Laboratory of Radiation Beam Technology and Materials Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China); Shen, Sheng [Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States)] [Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States)

    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.

  19. Quantitative 2H NMR spectroscopy with 1H lock extender.

    PubMed

    Vignali, Carlo; Caligiani, Augusta; Palla, Gerardo

    2007-07-01

    An inexpensive external unit that allows the use of the commercial high-resolution NMR spectrometer for (2)H observation with an (1)H lock system is described. The external unit does not require any tuning, is extremely easy to use, and could be a cheaper and more straightforward alternative to the more expensive (19)F lock configuration. An application for the quantitative determination of the natural isotopic ratio (2)H/(1)H of ethanol and acetic acid is reported. PMID:17485230

  20. Journal of Quantitative Spectroscopy & Radiative Transfer 102 (2006) 2536

    E-print Network

    2006-01-01

    microscopy measurements. An automated procedure was developed to construct a realistic three of flow cytometry as a powerful technique of cell analysis and diagnosis in cell biology and clinics requires continuous improvement in instrumentation, and development of accurate and efficient modeling

  1. Model for quantitative tip-enhanced spectroscopy and the extraction of nanoscale-resolved optical constants

    NASA Astrophysics Data System (ADS)

    McLeod, Alexander S.; Kelly, P.; Goldflam, M. D.; Gainsforth, Z.; Westphal, A. J.; Dominguez, Gerardo; Thiemens, Mark H.; Fogler, Michael M.; Basov, D. N.

    2014-08-01

    Near-field infrared spectroscopy by elastic scattering of light from a probe tip resolves optical contrasts in materials at dramatically subwavelength scales across a broad energy range, with the demonstrated capacity for chemical identification at the nanoscale. However, current models of probe-sample near-field interactions still cannot provide a sufficiently quantitatively interpretation of measured near-field contrasts, especially in the case of materials supporting strong surface phonons. We present a model of near-field spectroscopy derived from basic principles and verified by finite-element simulations, demonstrating superb predictive agreement both with tunable quantum cascade laser near-field spectroscopy of SiO2 thin films and with newly presented nanoscale Fourier transform infrared (nanoFTIR) spectroscopy of crystalline SiC. We discuss the role of probe geometry, field retardation, and surface mode dispersion in shaping the measured near-field response. This treatment enables a route to quantitatively determine nanoresolved optical constants, as we demonstrate by inverting newly presented nanoFTIR spectra of an SiO2 thin film into the frequency dependent dielectric function of its mid-infrared optical phonon. Our formalism further enables tip-enhanced spectroscopy as a potent diagnostic tool for quantitative nanoscale spectroscopy.

  2. Quantitating Metabolites in Protein Precipitated Serum Using NMR Spectroscopy

    PubMed Central

    2015-01-01

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

  3. Quantitative Analysis of Spectroscopy's Study for Engine Oil Degradation Monitoring Due to Temperature Effect

    Microsoft Academic Search

    M. F. M. Idros; Sawal Ali

    2012-01-01

    This paper presents the quantitative analysis of spectroscopy measurement for engine oil degradation prediction due to the temperature effect. The main objective of this project is to study the behavior of engine oil if the continues high temperature are applied to the engine oil as compared to the effect of running condition. Two types of engine oil were used as

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

    E-print Network

    Madden, Michael

    models were developed to identify the presence of chlorinated solvents in mixtures at levels of ~5 solvent waste is chlorinated or not will determine firstly how it is transported for disposal and secondlyQualitative and quantitative analysis of chlorinated solvents using Raman spectroscopy and machine

  5. Self-absorption model in quantitative laser induced breakdown spectroscopy measurements on soils and sediments

    Microsoft Academic Search

    V. Lazic; R. Barbini; F. Colao; R. Fantoni; A. Palucci

    2001-01-01

    Application of laser induced breakdown spectroscopy (LIBS) in the quantitative analysis of elemental composition of soils with different origins and Antarctic marine sediments has been considered. The analytical method followed includes the usual plasma modeling at local thermal equilibrium (LTE) based on average temperature and electron density values, as well as spectra normalization, introduced in order to reduce the effects

  6. Quantitative elemental determination in water and oil by laser induced breakdown spectroscopy

    Microsoft Academic Search

    Pascal Fichet; Patrick Mauchien; Jean-François Wagner; Christophe Moulin

    2001-01-01

    Laser induced breakdown spectroscopy has been used to evaluate the potentiality of the technique for the determination of trace amounts of elements in different types of liquids, in the framework of nuclear applications. A specific set-up using a pulsed laser focussed with a tilted angle on the surface of the liquid is presented. It allows on-line quantitative measurements with good

  7. Quantitative multiplex CARS spectroscopy in congested spectral regions

    NASA Astrophysics Data System (ADS)

    Müller, Michiel; Rinia, Hilde A.; Bonn, Mischa; Vartiainen, Erik M.; Lisker, Melanie; van Bel, Aart

    2007-02-01

    A novel procedure is developed to describe and reproduce experimental coherent anti-Stokes Raman scattering (CARS) data, with particular emphasis on highly congested spectral regions. The approach - exemplified here with high-quality multiplex CARS data - makes use the maximum entropy method for phase retrieval. The retrieved imaginary part of the nonlinear susceptibility is shown to be equal to the spontaneous Raman spectrum. The phase retrieval procedure does not influence the noise contained in the spectra. The conversion of CARS to Raman data permits a quantitative interpretation of CARS spectra. This novel approach is demonstrated for highly congested multiplex CARS spectra of sucrose, fructose and glucose. This novel procedures enables extraction of vibrational information from multiplex CARS data without the use of a priori information of the sample.

  8. A research associate level Developmental Biology/Cell Biology/Biochemistry Experimentalist to develop quantitative

    E-print Network

    Menczer, Filippo

    A research associate level Developmental Biology/Cell Biology/Biochemistry Experimentalist cell or developmental biology, pharmacology, toxicology, cell biology, or biochemistry and experience to cell regulation, cell signaling and cell behavior to extract the underlying biological models

  9. Quantitative near infra-red spectroscopy of massive stars

    NASA Astrophysics Data System (ADS)

    Stap, F. A.; Sana, H.; de Koter, A.

    2011-12-01

    Interest in near infra-red spectroscopy of massive stars has increased dramatically over the last decades, as it offers the possibility to analyze stars embedded in dusty star forming regions and near the Galactic center. We present an analysis of both high resolution optical and, separately, high resolution VLT/CRIRES near-IR spectra in the J, H, K and L-band of nearby dwarf O-type stars. Applying a genetic fitting algorithm approach using state-of-the-art FASTWIND non-LTE atmospheres, we present a comparison of the stellar and wind properties as derived from these two spectral regimes. In this approach we retrieve the effective temperature to within a sub-type and the surface gravity to within 0.2 dex, but find a discrepancy in the mass-loss rates of 0.2 up to 1.0 dex. We find that He II 1012 nm and Brackett-? lines do not yield consistent mass-loss estimates, the former producing much lower values than H?, while Brackett-? and H? are consistent.

  10. 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.

  11. Quantitative Analysis of Panax ginseng by FT-NIR Spectroscopy.

    PubMed

    Xu, Xin-Fang; Nie, Li-Xing; Pan, Li-Li; Hao, Bian; Yuan, Shao-Xiong; Lin, Rui-Chao; Bu, Hai-Bo; Wang, Dan; Dong, Ling; Li, Xiang-Ri

    2014-01-01

    Near-infrared spectroscopy (NIRS), a rapid and efficient tool, was used to determine the total amount of nine ginsenosides in Panax ginseng. In the study, the regression models were established using multivariate regression methods with the results from conventional chemical analytical methods as reference values. The multivariate regression methods, partial least squares regression (PLSR) and principal component regression (PCR), were discussed and the PLSR was more suitable. Multiplicative scatter correction (MSC), second derivative, and Savitzky-Golay smoothing were utilized together for the spectral preprocessing. When evaluating the final model, factors such as correlation coefficient (R (2)) and the root mean square error of prediction (RMSEP) were considered. The final optimal results of PLSR model showed that root mean square error of prediction (RMSEP) and correlation coefficients (R (2)) in the calibration set were 0.159 and 0.963, respectively. The results demonstrated that the NIRS as a new method can be applied to the quality control of Ginseng Radix et Rhizoma. PMID:24883224

  12. From Classical Genetics to Quantitative Genetics to Systems Biology: Modeling Epistasis

    E-print Network

    Zeng, Zhao-Bang

    From Classical Genetics to Quantitative Genetics to Systems Biology: Modeling Epistasis David L. These two disciplines have separate approaches to measuring and interpreting epistasis, which epistasis from a classical experiment that combines the strengths of each approach. A regression analysis

  13. Exploration of Quantitative Scoring Metrics to Compare Systems Biology Modeling Approaches

    Microsoft Academic Search

    Chanchala Kaddi; Erica D. Oden; Chang F. Quo; May D. Wang

    2007-01-01

    In this paper, we report a focused case study to assess whether quantitative metrics are useful to evaluate molecular-level system biology models on cellular metabolism. Ideally, the bio-modeling community shall be able assess systems biology models based on objective and quantitative metrics. This is because metric-based model design not only can accelerate the validation process, but also can improve the

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

    SciTech Connect

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

    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.

  15. Structural changes of yellow Cameleon domains observed by quantitative FRET analysis and polarized fluorescence correlation spectroscopy.

    PubMed

    Borst, J W; Laptenok, S P; Westphal, A H; Kühnemuth, R; Hornen, H; Visser, N V; Kalinin, S; Aker, J; van Hoek, A; Seidel, C A M; Visser, A J W G

    2008-12-01

    Förster resonance energy transfer (FRET) is a widely used method for monitoring interactions between or within biological macromolecules conjugated with suitable donor-acceptor pairs. Donor fluorescence lifetimes in absence and presence of acceptor molecules are often measured for the observation of FRET. However, these lifetimes may originate from interacting and noninteracting molecules, which hampers quantitative interpretation of FRET data. We describe a methodology for the detection of FRET that monitors the rise time of acceptor fluorescence on donor excitation thereby detecting only those molecules undergoing FRET. The large advantage of this method, as compared to donor fluorescence quenching method used more commonly, is that the transfer rate of FRET can be determined accurately even in cases where the FRET efficiencies approach 100% yielding highly quenched donor fluorescence. Subsequently, the relative orientation between donor and acceptor chromophores is obtained from time-dependent fluorescence anisotropy measurements carried out under identical conditions of donor excitation and acceptor detection. The FRET based calcium sensor Yellow Cameleon 3.60 (YC3.60) was used because it changes its conformation on calcium binding, thereby increasing the FRET efficiency. After mapping distances and orientation angles between the FRET moieties in YC3.60, cartoon models of this FRET sensor with and without calcium could be created. Independent support for these representations came from experiments where the hydrodynamic properties of YC3.60 under ensemble and single-molecule conditions on selective excitation of the acceptor were determined. From rotational diffusion times as found by fluorescence correlation spectroscopy and consistently by fluorescence anisotropy decay analysis it could be concluded that the open structure (without calcium) is flexible as opposed to the rather rigid closed conformation. The combination of two independent methods gives consistent results and presents a rapid and specific methodology to analyze structural and dynamical changes in a protein on ligand binding. PMID:18790855

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  17. 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. PMID:25964049

  18. A study of the 42CrMo4 steel surface by quantitative XPS electron spectroscopy

    NASA Astrophysics Data System (ADS)

    Flori, M.; Gruzza, B.; Bideux, L.; Monier, G.; Robert-Goumet, C.

    2008-05-01

    Quantitative X-ray photoelectron spectroscopy was used to characterize the native oxide film formed on 42CrMo4 steel surface by air exposure in normal conditions. In order to determine the thickness and composition of the oxide layer we have used a stacking layer model together with experimental XPS sputtering depth profiling. At a nanoscale study, to obtain quantitative results one must take into account fundamental parameters like the attenuation depth of photoelectrons. We have found that both lepidocrocit (?-FeOOH) and magnetite (Fe 3O 4) were present and the total thickness of the oxide layer was 16 monolayers.

  19. 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.

  20. Rapid quantitation of thermal oxidation products in fats and oils by 1H-NMR spectroscopy.

    PubMed

    Yang, C M; Grey, A A; Archer, M C; Bruce, W R

    1998-01-01

    This work describes the application of high-resolution proton nuclear magnetic resonance (1H-NMR) spectroscopy to the study of the thermal peroxidation of beef tallow and corn oil under standardized conditions. The approach provides a rapid, quantitative method for determining the degree of oxidation of unsaturated fatty acids in animal and vegetable fats and oils by quantitating the decreasing intensities of 1H-NMR peaks for allylic and olefinic protons in unsaturated fatty acid chains of triglycerides and the increasing peak intensities of hydroperoxide and saturated and alpha, beta-unsaturated aldehydic protons in relation to the less labile protons in the triglyceride molecule. Two-dimensional correlation spectroscopy analysis of highly oxidized beef tallow (180 degrees C for 24 h) suggested that the unsaturated aldehydes that persisted were apparently associated with carboxy groups. PMID:9507515

  1. Self-calibrated quantitative elemental analysis by laser-induced plasma spectroscopy: application to pigment analysis

    Microsoft Academic Search

    Ilaria Borgia; Lucia M. F Burgio; Michela Corsi; Roberta Fantoni; Vincenzo Palleschi; Azenio Salvetti; Maria Cristina Squarcialupi; Elisabetta Tognoni

    2000-01-01

    A new laser-based spectroscopic technique, called calibration-free LIPS (laser-induced plasma spectroscopy), is proposed for fast and precise elemental analysis in the field of cultural heritage conservation and study. Quantitative stratigraphic results, obtained by CF-LIPS on ancient Roman frescoe samples, are shown. The application of this calibration-free procedure frees the LIPS technique from the need of reference samples or an internal

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

    Microsoft Academic Search

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

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

  3. A polarization-sensitive light field imager for multi-channel angular spectroscopy of light scattering in biological tissues

    PubMed Central

    Lu, Rongwen; Zhang, Qiuxiang; Zhi, Yanan

    2015-01-01

    Background Angular spectroscopy of light scattering can be used for quantitative analysis of cellular and subcellular properties, and thus promises a noninvasive methodology for in vivo assessment cellular integrity to complement in vitro histological examination. Spatial information is essential for accurate identification of localized abnormalities. However, conventional angular spectroscopy systems only provide single-channel measurement, which suffers from poor spatial resolution or requires time-consuming scanning over extended area. The purpose of this study was to develop a multi-channel angular spectroscopy for light field imaging in biological tissues. Materials and methods A microlens array (MLA) (8×8) based light field imager for 64-channel angular spectroscopy was developed. A pair of crossed polarizers was employed for polarization-sensitive recording to enable quantitative measurement at high signal specificity and sensitivity. The polarization-sensitive light field imager enables rapid measurement of multiple sampling volumes simultaneously at 18 ?m spatial-resolution and 3° angular-resolution. Comparative light field imaging and electrophysiological examination of freshly isolated and physiologically deteriorated lobster leg nerves have been conducted. Results Two-dimensional (2D) polarization-sensitive scattering patterns of the fresh nerves were highly elliptical, while they gradually lost the ellipticity and became rotationally symmetric (i.e., circular) as the nerves physiologically deteriorated due to repeated electrical stimulations. Characterized parameters, i.e., the ellipticity and the scattering intensity, rendered spatially various characteristics such as different values and deteriorating rates. Conclusions The polarization-sensitive light field imager is able to provide multi-channel angular spectroscopy of light scattering with both spatial and angular resolutions. The light scattering properties of nerves are highly dependent on the orientation of nerves and their physiological status. Further development of polarization-sensitive multi-channel angular spectroscopy may promise a methodology for rapid and reliable identification of localized abnormalities in biological tissues. PMID:25694947

  4. 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

  5. Using Fourier transform IR spectroscopy to analyze biological materials.

    PubMed

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

    2014-08-01

    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

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

    PubMed

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  8. Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

    PubMed Central

    2014-01-01

    Background Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is the most widely used method for characterizing the epigenetic states of chromatin on a genomic scale. With the recent availability of large genome-wide data sets, often comprising several epigenetic marks, novel approaches are required to explore functionally relevant interactions between histone modifications. Computational discovery of "chromatin states" defined by such combinatorial interactions enabled descriptive annotations of genomes, but more quantitative approaches are needed to progress towards predictive models. Results We propose non-negative matrix factorization (NMF) as a new unsupervised method to discover combinatorial patterns of epigenetic marks that frequently co-occur in subsets of genomic regions. We show that this small set of combinatorial "codes" can be effectively displayed and interpreted. NMF codes enable dimensionality reduction and have desirable statistical properties for regression and classification tasks. We demonstrate the utility of codes in the quantitative prediction of Pol2-binding and the discrimination between Pol2-bound promoters and enhancers. Finally, we show that specific codes can be linked to molecular pathways and targets of pluripotency genes during differentiation. Conclusions We have introduced and evaluated a new computational approach to represent combinatorial patterns of epigenetic marks as quantitative variables suitable for predictive modeling and supervised machine learning. To foster widespread adoption of this method we make it available as an open-source software-package – epicode at https://github.com/mcieslik-mctp/epicode. PMID:24472558

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

    PubMed Central

    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

  10. 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

  11. Fourier-Transform Raman Spectroscopy Of Biological Assemblies

    NASA Astrophysics Data System (ADS)

    Levin, Ira W.; Lewis, E. Neil

    1989-12-01

    Although the successful coupling of Raman scattered near-infrared radiation to a Michelson interferometer has recently created an outburst of intense interest in Fourier-transform (FT) Raman spectrometry," extended applications of the technique to macromolecular assemblies of biochemical and biophysical relevance have not progressed as rapidly as studies directed primarily at more conventional chemical characterizations. Since biological materials sampled with visible laser excitation sources typically emit a dominant fluorescence signal originating either from the intrinsic fluorescence of the molecular scatterer or from unrelenting contaminants, the use of near-infrared Nd:YAG laser excitation offers a convenient approach for avoiding this frequently overwhelming effect. In addition, the FT-Raman instrumentation provides a means of eliminating the deleterious resonance and decomposition effects often observed with the more accessible green and blue laser emissions. However, in choosing the incident near-infrared wavelength at, for example, 1064nm, the Raman scattered intensity decreases by factors of eighteen to forty from the Raman emissions induced by the shorter, visible excitations. Depending upon the experiment, this disadvantage is offset by the throughput and multiplex advantages afforded by the interferometric design. Thus, for most chemical systems, near-infrared FT-Raman spectroscopy, clearly provides a means for obtaining vibrational Raman spectra from samples intractable to the use of visible laser sources. In particular, for neat liquids, dilute solutions or polycrystalline materials, the ability to achieve high quality, reproducible spectra is, with moderate experience and perhaps relatively high laser powers, as straightforward as the conventional methods used to obtain Raman spectra with visible excitation and dispersive monochromators. In using near-infrared FT techniques to determine the Raman spectra of biological samples, one encounters new sets of experimental problems that may entail an initial, relatively steep learning curve. These difficulties originate particularly from the fragility of the weakly scattering aggregate paired with the dilute nature of the biochemical or cellular dispersion. Often, the Raman scattered intensity from these samples can be increased by carefully peileting the biological suspension using ultracentrifugation techniques. Since the overtone region of water, the usual medium for biological samples, absorbs radiation from both the Rayleigh signal at the exciting wavelength of the Nd:YAG laser and the longer wavelength Raman scattering from the sample, reproducible temperature measurements and temperature control become significant concerns. In these cases one appeals to internal temperature calibrations, use of deuterium oxide (D20) as a solvent (since absorptions of the laser exciting wavelength and Raman scattered photons are minimized), manipulation of incident laser spot size and the use of fiber optic bundles to carry the exciting and scattered radiation. In the present discussion we briefly cite some of the experimental approaches we have developed and experiences we have encountered in adapting near-infrared FT-Raman spectroscopy to the more challenging biophysical and biochemical systems amenable to vibrational analysis. We emphasize here the determination of the spectra of membrane assemblies and membrane related materials; in particular, we elucidate the interaction of several polyene antibiotics, including amphotericin A, amphotericin B and nystatin, with a model membrane system composed of dipalmitoylphosphatidylcholine bilayers.

  12. A method for three-dimensional quantitative observation of the microstructure of biological samples

    NASA Astrophysics Data System (ADS)

    Wang, Pengfei; Chen, Dieyan; Ma, Wanyun; Wu, Hongxin; Ji, Liang; Sun, Jialin; Lv, Danyu; Zhang, Lu; Li, Ying; Tian, Ning; Zheng, Jinggao; Zhao, Fengying

    2009-07-01

    Contemporary biology has developed into the era of cell biology and molecular biology, and people try to study the mechanism of all kinds of biological phenomena at the microcosmic level now. Accurate description of the microstructure of biological samples is exigent need from many biomedical experiments. This paper introduces a method for 3-dimensional quantitative observation on the microstructure of vital biological samples based on two photon laser scanning microscopy (TPLSM). TPLSM is a novel kind of fluorescence microscopy, which has excellence in its low optical damage, high resolution, deep penetration depth and suitability for 3-dimensional (3D) imaging. Fluorescent stained samples were observed by TPLSM, and afterward the original shapes of them were obtained through 3D image reconstruction. The spatial distribution of all objects in samples as well as their volumes could be derived by image segmentation and mathematic calculation. Thus the 3-dimensionally and quantitatively depicted microstructure of the samples was finally derived. We applied this method to quantitative analysis of the spatial distribution of chromosomes in meiotic mouse oocytes at metaphase, and wonderful results came out last.

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

    PubMed Central

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

    2009-01-01

    Although electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) provides high sensitivity for measuring the important element, calcium, in biological specimens, the technique has been difficult to apply routinely, because of long acquisition times required. Here we describe a refinement of the complementary analytical technique of energy-filtered transmission electron microscopy (EFTEM), which enables rapid imaging of large cellular regions and measurement of calcium concentrations approaching physiological levels. Extraction of precise quantitative information is possible by averaging large numbers of pixels that are contained in organelles of interest. We employ a modified two-window approach in which the behavior of the background signal in the EELS spectrum can be modeled as a function of specimen thickness t expressed in terms of the inelastic mean free path ?. By acquiring pairs of images, one above and one below the Ca L2,3 edge, together with zero-loss and unfiltered images, which are used to determine a relative thickness (t/?) map, it is possible to correct the Ca L2,3 signal for plural scattering. We have evaluated the detection limits of this technique by considering several sources of systematic errors and applied this method to determine mitochondrial total calcium concentrations in freeze-dried cryosections of rapidly frozen stimulated neurons. By analyzing 0.1 ?m2 areas of specimen regions that do not contain calcium, it was found that the standard deviation in the measurement of Ca concentrations was about 20 mmol/kg dry weight, corresponding to a Ca:C atomic fraction of approximately 2 × 10?4. Calcium concentrations in peripheral mitochondria of recently depolarized, and therefore stimulated and Ca loaded, frog sympathetic neurons were in reasonable agreement with previous data. PMID:19118952

  14. 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.

  15. Renal geology (quantitative renal stone analysis) by ‘Fourier transform infrared spectroscopy

    Microsoft Academic Search

    Iqbal Singh

    2008-01-01

    Aim  To prospectively determine the precise stone composition (quantitative analysis) by using infrared spectroscopy in patients\\u000a with urinary stone disease presenting to our clinic. To determine an ideal method for stone analysis suitable for use in a\\u000a clinical setting.\\u000a \\u000a \\u000a \\u000a Methods  After routine and a detailed metabolic workup of all patients of urolithiasis, stone samples of 50 patients of urolithiasis\\u000a satisfying the entry

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

    PubMed

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

    2014-06-01

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

  17. Quantitative spectral and orientational analysis in surface sum frequency generation vibrational spectroscopy (SFG-VS)

    NASA Astrophysics Data System (ADS)

    Wang, Hong-Fei; Gan, Wei; Lu, Rong; Rao, Yi; Wu, Bao-Hua

    Sum frequency generation vibrational spectroscopy (SFG-VS) has been proven to be a uniquely effective spectroscopic technique in the investigation of molecular structure and conformations, as well as the dynamics of molecular interfaces. However, the ability to apply SFG-VS to complex molecular interfaces has been limited by the ability to abstract quantitative information from SFG-VS experiments. In this review, we try to make assessments of the limitations, issues and techniques as well as methodologies in quantitative orientational and spectral analysis with SFG-VS. Based on these assessments, we also try to summarize recent developments in methodologies on quantitative orientational and spectral analysis in SFG-VS, and their applications to detailed analysis of SFG-VS data of various vapour/neat liquid interfaces. A rigorous formulation of the polarization null angle (PNA) method is given for accurate determination of the orientational parameter D = /, and comparison between the PNA method with the commonly used polarization intensity ratio (PIR) method is discussed. The polarization and incident angle dependencies of the SFG-VS intensity are also reviewed, in the light of how experimental arrangements can be optimized to effectively abstract crucial information from the SFG-VS experiments. The values and models of the local field factors in the molecular layers are discussed. In order to examine the validity and limitations of the bond polarizability derivative model, the general expressions for molecular hyperpolarizability tensors and their expression with the bond polarizability derivative model for C3v, C2v and C?v molecular groups are given in the two appendixes. We show that the bond polarizability derivative model can quantitatively describe many aspects of the intensities observed in the SFG-VS spectrum of the vapour/neat liquid interfaces in different polarizations. Using the polarization analysis in SFG-VS, polarization selection rules or guidelines are developed for assignment of the SFG-VS spectrum. Using the selection rules, SFG-VS spectra of vapour/diol, and vapour/n-normal alcohol (n˜ 1-8) interfaces are assigned, and some of the ambiguity and confusion, as well as their implications in previous IR and Raman assignment, are duly discussed. The ability to assign a SFG-VS spectrum using the polarization selection rules makes SFG-VS not only an effective and useful vibrational spectroscopy technique for interface studies, but also a complementary vibrational spectroscopy method in general condensed phase studies. These developments will put quantitative orientational and spectral analysis in SFG-VS on a more solid foundation. The formulations, concepts and issues discussed in this review are expected to find broad applications for investigations on molecular interfaces in the future.

  18. BioMaPS Student Seminar Series in Quantitative Biology: April 5, 2010 Asli Ertekin

    E-print Network

    Chen, Kuang-Yu

    , due to lack of structural data. Here, the structure of CDK2-AP1 is presented for the first time as oneBioMaPS Student Seminar Series in Quantitative Biology: April 5, 2010 Asli Ertekin Dr. Guy cells. This gene was found to be missing or down-regulated in many other cancer cell types

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

    Microsoft Academic Search

    Peter J. E. Goss; Jean Peccoud

    1998-01-01

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

  20. Physiology 472/572 Quantitative modeling of biological systems (3 units)

    E-print Network

    Wang, Quidong

    Physiology 472/572 Quantitative modeling of biological systems (3 units) Fall 2009 Coordinator: Timothy W. Secomb, Ph.D. Professor, Physiology and Mathematics Department of Physiology Office: 1527 E: http://www.physiology.arizona.edu/people/secomb/472572info09 Grading: Regular grades are awarded

  1. 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.

  2. Fluorescence correlation spectroscopy: Statistical analysis and biological applications

    NASA Astrophysics Data System (ADS)

    Saffarian, Saveez

    2002-01-01

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

  3. Dual-molecule spectroscopy: molecular rulers for the study of biological macromolecules

    Microsoft Academic Search

    T. Ha; Th. Enderle; D. S. Chemla; S. Weiss

    1996-01-01

    Single-molecule detection and spectroscopy by laser induced fluorescence offer many applications to life sciences. We review recent techniques and experiments based on the detection and spectroscopy of two near-by molecules. The spectroscopic signature of the light emitted from the two molecules can be used to measure the distance, orientation and relative dynamics between biological macromolecules

  4. Electron energy loss spectroscopy microanalysis and imaging in the transmission electron microscope: example of biological applications

    Microsoft Academic Search

    Marco Diociaiuti

    2005-01-01

    This paper reports original results obtained in our laboratory over the past few years in the application of both electron energy loss spectroscopy (EELS) and electron spectroscopy imaging (ESI) to biological samples, performed in two transmission electron microscopes (TEM) equipped with high-resolution electron filters and spectrometers: a Gatan model 607 single magnetic sector double focusing EEL serial spectrometer attached to

  5. High-Throughput Near-Infrared Reflectance Spectroscopy for Predicting Quantitative and Qualitative Composition Phenotypes of Individual Maize Kernels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Near-infrared reflectance (NIR) spectroscopy can be used for fast and reliable prediction of organic compounds in complex biological samples. We used a recently developed NIR spectroscopy instrument to predict starch, protein, oil, and weight of individual maize (Zea mays) seeds. The starch, prote...

  6. H2o Quantitative Analysis of Transition Zone Minerals Wadsleyite and Ringwoodite By Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Novella, D.; Bolfan-Casanova, N.; Bureau, H.; Raepsaet, C.; Montagnac, G.

    2014-12-01

    Liquid H2O covers approximately 70% of the Earth's surface but it can also be incorporated as OH- groups in nominally anhydrous minerals (NAMs) that constitute the Earth's mantle, as observed in peridotitic xenoliths. The presence of even trace amounts (ppm wt) of hydrogen in mantle minerals strongly affect the physical, chemical and rheological properties of the mantle. The Earth's transition zone (410 to 660 km depth) is particularly important in this regard since it can store large amounts of H2O (wt%) as shown by experiments and recently by a natural sample. Addressing the behavior of H2O at high depths and its potential concentration in mantle NAMs is therefore fundamental to fully comprehend global-scale processes such as plate tectonics and magmatism. We developed an innovative technique to measure the H2O content of main transition zone NAMs wadsleyite and ringwoodite by Raman spectroscopy. This technique allows to use a beam of 1-3 µm size to measure small samples that are typical for high pressure natural and synthetic specimens. High pressure polyphasic samples are indeed very challenging to be measured in terms of H2O content by the routinely used Fourier transform infra-red (FTIR) spectroscopy and ion probe mass spectroscopy analyses, making the Raman approach a valid alternative. High quality crystals of wadsleyite and ringwoodite were synthesized at high pressure and temperature in a multi-anvil press and analyzed by Raman and FTIR spectroscopy as well as elastic recoil detection analyses (ERDA) which is an absolute, standard-free technique. We will present experimental data that allow to apply Raman spectroscopy to the determination of H2O content of the most abundant minerals in the transition zone. The data gathered in this study will also permit to investigate the absorption coefficients of wadsleyite and ringwoodite that are employed in FTIR quantitative analyses.

  7. Qualitative and quantitative analysis of calcium-based microfillers using terahertz spectroscopy and imaging.

    PubMed

    Abina, Andreja; Puc, Uroš; Jegli?, Anton; Prah, Jana; Venckevi?ius, Rimvydas; Kašalynas, Irmantas; Valušis, Gintaras; Zidanšek, Aleksander

    2015-10-01

    In different industrial applications, several strictly defined parameters of calcium-based microfillers such as average particle size, particle size distribution, morphology, specific surface area, polymorphism and chemical purity, play a key role in the determination of its usefulness and effectiveness. Therefore, an analytical tool is required for rapid and non-destructive characterization of calcium-based microfillers during the synthesis process or before its use in a further manufacturing process. Since spectroscopic techniques are preferred over microscopy and thermogravimetry, particularly due to its non-destructive nature and short analysis time, we applied terahertz (THz) spectroscopy to analyse calcite microfillers concentration in polymer matrix, its granulation and chemical treatment. Based on the analysis of peak absorbance amplitude, peak frequency position, and the appearance of additional spectral features, quantitative and qualitative analysis was successfully achieved. In addition, THz imaging was also applied for both quantitative and qualitative analysis of calcium-based microfillers. By using spatial distribution map, the inhomogeneity in concentration of calcium carbonate in polymer matrix was characterized. Moreover, by THz spectroscopy and imaging different calcium compounds were detected in binary mixtures. Finally, we demonstrated that the applied spectroscopic technique offers valuable results and can be, in combination with other spectroscopic and microscopic techniques, converted to a powerful rapid analytical tool. PMID:26078145

  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. 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) available: TEM imaging, calibration experiments for the SMS instrument with gold nanoparticles, SMS images of dye doped polymer beads from a commercial source, evidence for endosome uptake, and additional SMS images of dye-doped LPNPs in EMT-6 cells, and spectra of SRfluor680/croconaine doped lipid-polymer nanoparticles. See DOI: 10.1039/C5NR01614B

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

    SciTech Connect

    Thomson, Ty M. [Selventa, One Alewife Center, Cambridge, MA 02140 (United States); Sewer, Alain, E-mail: Alain.Sewer@pmi.com [Philip Morris International R and D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel (Switzerland); Martin, Florian; Belcastro, Vincenzo [Philip Morris International R and D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel (Switzerland); Frushour, Brian P. [Selventa, One Alewife Center, Cambridge, MA 02140 (United States); Gebel, Stephan [Philip Morris International R and D, Philip Morris Research Laboratories GmbH, Edmund-Rumpler-Strasse 5, 51149 Koeln (Germany); Park, Jennifer [Selventa, One Alewife Center, Cambridge, MA 02140 (United States); Schlage, Walter K. [Philip Morris International R and D, Philip Morris Research Laboratories GmbH, Edmund-Rumpler-Strasse 5, 51149 Koeln (Germany); Talikka, Marja [Philip Morris International R and D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel (Switzerland); Vasilyev, Dmitry M.; Westra, Jurjen W. [Selventa, One Alewife Center, Cambridge, MA 02140 (United States); Hoeng, Julia; Peitsch, Manuel C. [Philip Morris International R and D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel (Switzerland)

    2013-11-01

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

  11. Method for quantitative determination of spatial polymer distribution in alginate beads using Raman spectroscopy.

    PubMed

    Heinemann, Matthias; Meinberg, Holger; Büchs, Jochen; Koss, Hans-Jürgen; Ansorge-Schumacher, Marion B

    2005-03-01

    A new method based on Raman spectroscopy is presented for non-invasive, quantitative determination of the spatial polymer distribution in alginate beads of approximately 4 mm diameter. With the experimental setup, a two-dimensional image is created along a thin measuring line through the bead comprising one spatial and one spectral dimension. For quantitative analysis of the Raman spectra, the method of indirect hard modeling was applied to make use of the information contained in the entire recorded spectra. For quantification of the alginate signals from within the beads, a calibration curve acquired from sodium alginate solutions was used after it was shown that only negligible differences occur between signals from alginate solutions and alginate gels. The distribution of alginate over the bead gel matrix was acquired with high spatial (51 microm) and time (12 s) resolution. The inhomogeneous distribution obtained using the new measuring technique is qualitatively in excellent agreement with data from the literature. In contrast to known measuring techniques, correct quantitative information about the spatial polymer distribution within the matrix was derived. It gave an alginate mass fraction of approximately 0.045 g/g at the edges and 0.02 g/g in the center of the beads. Next to the determination of mere polymer concentrations, the excellent time resolution of the presented method will enable investigation of the dynamic process of gel formation and it will also serve as a basis for investigation of mass transfer of small diffusing molecules in alginate matrices. PMID:15901307

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

    SciTech Connect

    Hedwig, Rinda; Lie, Zener Sukra; Kurniawan, Koo Hendrik [Research Center of Maju Makmur Mandiri Foundation, 40/80 Srengseng Raya, Kembangan, Jakarta Barat 11630 (Indonesia); Chumakov, Alexander Nikitich [B. I. Stepanov Institute of Physics of the National Academy of Sciences of Belarus, 68 Nezalezhnastsi Ave., Minsk 220072 (Belarus); Kagawa, Kiichiro [Department of Physics, Faculty of Education and Regional Studies, Fukui University, 9-1 bunkyo 3-chome, Fukui 910-8507 (Japan); Tjia, May On [Physics of Magnetism and Photonics Research Group, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, 10 Ganesha, Bandung 40132 (Indonesia)

    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.

  13. 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.

  14. Laser-Induced Breakdown Spectroscopy Detection and Classification of Biological Aerosols

    Microsoft Academic Search

    John D. Hybl; Gregg A. Lithgow; Steven G. Buckley

    2003-01-01

    Laser-induced breakdown spectroscopy (LIBS) is examined as a potential method for detecting airborne biological agents. A spec- trally broadband LIBS system was used for laboratory measure- ments on some common biological agent simulants. These measure- ments were compared to those of common, naturally occurring bi- ological aerosol components (pollen and fungal spores) to determine the potential of LIBS for discriminating

  15. 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 challenging Raman endoscopic applications. PMID:24160634

  16. Application of Optical Imaging and Spectroscopy to Radiation Biology

    PubMed Central

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

    2013-01-01

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

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

    SciTech Connect

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

    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.

  18. 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 11?,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 11?,13-dihydrohelenalin esters separately. Furthermore, 6-O-tigloylhelenalin (HT, 1), 6-O-methacryloylhelenalin (HM, 2), 6-O-tigloyl-11?,13-dihydrohelenalin (DHT, 5), and 6-O-methacryloyl-11?,13-dihydrohelenalin (DHM, 6) were quantified as individual components. PMID:20837387

  19. Matrix Effects in Quantitative Assessment of Pharmaceutical Tablets Using Transmission Raman and Near-Infrared (NIR) Spectroscopy.

    PubMed

    Sparén, Anders; Hartman, Madeleine; Fransson, Magnus; Johansson, Jonas; Svensson, Olof

    2015-05-01

    Raman spectroscopy can be an alternative to near-infrared spectroscopy (NIR) for nondestructive quantitative analysis of solid pharmaceutical formulations. Compared with NIR spectra, Raman spectra have much better selectivity, but subsampling was always an issue for quantitative assessment. Raman spectroscopy in transmission mode has reduced this issue, since a large volume of the sample is measured in transmission mode. The sample matrix, such as particle size of the drug substance in a tablet, may affect the Raman signal. In this work, matrix effects in transmission NIR and Raman spectroscopy were systematically investigated for a solid pharmaceutical formulation. Tablets were manufactured according to an experimental design, varying the factors particle size of the drug substance (DS), particle size of the filler, compression force, and content of drug substance. All factors were varied at two levels plus a center point, except the drug substance content, which was varied at five levels. Six tablets from each experimental point were measured with transmission NIR and Raman spectroscopy, and their concentration of DS was determined for a third of those tablets. Principal component analysis of NIR and Raman spectra showed that the drug substance content and particle size, the particle size of the filler, and the compression force affected both NIR and Raman spectra. For quantitative assessment, orthogonal partial least squares regression was applied. All factors varied in the experimental design influenced the prediction of the DS content to some extent, both for NIR and Raman spectroscopy, the particle size of the filler having the largest effect. When all matrix variations were included in the multivariate calibrations, however, good predictions of all types of tablets were obtained, both for NIR and Raman spectroscopy. The prediction error using transmission Raman spectroscopy was about 30% lower than that obtained with transmission NIR spectroscopy. PMID:25811389

  20. Characterization of geometrical factors for quantitative angle-resolved photoelectron spectroscopy

    SciTech Connect

    Martinez, Eugenie; Herrera-Gomez, Alberto; Allain, Mickael; Renault, Olivier; Faure, Alain; Chabli, Amal; Bertin, Francois [CEA, LETI, MINATEC Campus, 17 rue des Martyrs, F-38054 Grenoble Cedex 9 (France); CINVESTAV-Queretaro, Libramiento Norponiente 2000, Real de Juriquilla, Queretaro, 76000 (Mexico); CEA, LETI, MINATEC Campus, 17 rue des Martyrs, F-38054 Grenoble Cedex 9 (France)

    2012-07-15

    For conventional angle-resolved x-ray photoelectron spectroscopy (ARXPS), the area under the core-level peaks depends mainly on the in-depth distribution of chemical species at the top surface of a specimen. But the x-ray photoelectron spectroscopy (XPS) intensity is also affected by tool-related geometrical factors such as the shape of the x-ray beam, the spectrometer analysis volume, and the manipulator rotation axis. Data analysis is therefore typically based on normalization with respect to the signal from the substrate. Here, we present an original method to perform quantitative ARXPS without normalization, involving evaluation of these geometrical factors. The method is illustrated for a multiprobe XPS system using a methodology based on a specific software (XPSGeometry{sup Registered-Sign }), but is a general process that can be adapted to all types of XPS equipment, even those not specifically designed for ARXPS. In that case, this method enables bringing the sample as close as possible to the manipulator axis of rotation in order to perform automatic acquisitions.

  1. [Quantitative measurement of induced skin reddening using optical reflection spectroscopy--methodology and clinical application].

    PubMed

    Smesny, S; Riemann, S; Riehemann, S; Bellemann, M E; Sauer, H

    2001-10-01

    Optical reflection spectroscopy is a simple and quick method for the quantification of colour intensity, and is thus suitable for the determination of changes in skin reddening (erythema) due to local vasodilatation. To quantify the time course of this erythema, the oxyhaemoglobin absorption double peak with maxima at 542 and 577 nm is an appropriate parameter. A compact handheld optical spectrometer makes the technique applicable to clinical use, an example being the niacin patch test described herein. This noninvasive test provides information about the cell membrane metabolism via the skin flush induced by niacin (vitamin B3) and mediated by prostaglandin. The aim of this study was to adapt optical reflection spectroscopy to the requirements of the clinical niacin patch test. To that end, we investigated 60 healthy volunteers. Analysis of the spectroscopic data with regard to physiological covariables of niacin sensitivity revealed faster and more intense erythema in females--a gender effect that to our knowledge has not previously been reported. In the light of these results, the findings of other researchers based on semi-quantitative test methods should be reassessed, with consideration given to the gender effect. PMID:11721583

  2. Quantitative classification of cryptosporidium oocysts and giardia cysts in water using UV/vis spectroscopy

    NASA Astrophysics Data System (ADS)

    Bacon, Christina P.; Rose, J. B.; Patten, K.; Garcia-Rubio, Luis H.

    1995-05-01

    Cryptosporidium and Giardia are enteric protozoa which cause waterborne diseases. To date, the detection of these organisms in water has relied upon microscopic immunofluorescent assay technology which uses antibodies directed against the cyst and oocyst forms of the protozoa. In this paper, the uv/vis extinction spectra of aqueous dispersions of Cryptosporidium and Giardia have been studied to investigate the potential use of light scattering-spectral deconvolution techniques as a rapid method for the identification and quantification of protozoa in water. Examination of purified samples of Cryptosporidium and Giardia suggests that spectral features apparent in the short wavelength region of the uv/vis spectra contain information that may be species specific for each protozoa. The spectral characteristics, as well as the particle size analysis, determined from the same spectra, allow for the quantitative classification, identification, and possibly, the assessment of the viability of the protozoa. To further increase the sensitivity of this technique, specific antibodies direction against these organisms, labelled with FITC and rhodamine are being used. It is demonstrated that uv/vis spectroscopy provides an alternative method for the characterization of Giardia and Cryptosporidium. The simplicity and reproducibility of uv/vis spectroscopy measurements makes this technique ideally suited for the development of on-line instrumentation for the rapid detection of microorganisms in water supplies.

  3. Quantitative characterization of the colloidal stability of metallic nanoparticles using UV-vis absorbance spectroscopy.

    PubMed

    Ray, Tyler R; Lettiere, Bethany; de Rutte, Joseph; Pennathur, Sumita

    2015-03-31

    Plasmonic nanoparticles are used in a wide variety of applications over a broad array of fields including medicine, energy, and environmental chemistry. The continued successful development of this material class requires the accurate characterization of nanoparticle stability for a variety of solution-based conditions. Although many characterization methods exists, there is an absence of a unified, quantitative means for assessing the colloidal stability of plasmonic nanoparticles. We present the particle instability parameter (PIP) as a robust, quantitative, and generalizable characterization technique based on UV-vis absorbance spectroscopy to characterize colloidal instability. We validate PIP performance with both traditional and alternative characterization methods by measuring gold nanorod instability in response to different salt (NaCl) concentrations. We further measure gold nanorod stability as a function of solution pH, salt, and buffer (type and concentration), nanoparticle concentration, and concentration of free surfactant. Finally, these results are contextualized within the literature on gold nanorod stability to establish a standardized methodology for colloidal instability assessment. PMID:25730093

  4. A Reusable Electrochemical Proximity Assay for Highly Selective, Real-Time Protein Quantitation in Biological Matrices

    PubMed Central

    2015-01-01

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

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

    PubMed

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

    2014-06-11

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

  6. 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.

  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. Laser-induced breakdown spectroscopy in a biological tissue

    Microsoft Academic Search

    Hanriete P. de Souza; Egberto Munin; Leandro P. Alves; Marcela L. Redígolo; Marcos Tadeu; T. Pacheco

    2003-01-01

    The relative atomic composition of the laser-generated ablation plume in chicken myocardium is investigated by using luminescence spectroscopy. A Q-switched Nd:YAG laser emitting at 1064 nm with 9 ns pulse duration was used for the tissue ablation. The selected ou tput energy was 210 mJ and the beam was focused to a 0.8 mm diameter spot size by using a

  9. 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.

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

    PubMed

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

    2014-01-01

    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. PMID:25348877

  11. 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.

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

    PubMed Central

    Creath, Katherine; Goldstein, Goldie

    2012-01-01

    This paper describes research in developing a dynamic quantitative phase imaging microscope providing instantaneous measurements of dynamic motions within and among live cells without labels or contrast agents. It utilizes a pixelated phase mask enabling simultaneous measurement of multiple interference patterns derived using the polarization properties of light to track dynamic motions and morphological changes. Optical path difference (OPD) and optical thickness (OT) data are obtained from phase images. Two different processing routines are presented to remove background surface shape to enable quantification of changes in cell position and volume over time. Data from a number of different moving biological organisms and cell cultures are presented. PMID:23162725

  13. 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.

  14. 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 ?g/L. It is suggested that reflectance spectroscopy provides an ideal routine analytical tool for characterizing leachate samples. The outcome of this study also has implications for monitoring the environmental effect of REE mining, in particular in stream water systems by hyperspectral remote sensing.

  15. 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

  16. 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.

  17. Fast quantitative determination of platinum in liquid samples by laser-induced breakdown spectroscopy.

    PubMed

    Barreda, Flory-Anne; Trichard, Florian; Barbier, Sophie; Gilon, Nicole; Saint-Jalmes, Laurent

    2012-07-01

    The potential of laser-induced breakdown spectroscopy (LIBS) for the rapid determination of platinum in liquid silicone oils has been evaluated in the framework of on-line process control. A comparison of LIBS sensitivity between three setups designed for liquid analysis (static, liquid jet and flowing liquid) was performed using a 266 nm Nd/YAG laser irradiation. Best results were obtained using the flowing liquid setup and a similar limit of detection was obtained using the liquid jet. The effect of different buffer gases (Ar, He, N(2), etc.) on the signal sensitivity was studied in liquid jet analysis and best values were obtained with a nitrogen sheath gas. Detection limits were in the 100 mg/kg range for both setups. Quantitative determination of platinum in real liquid samples was also investigated using both liquid jet and flowing liquid setups. Calibration curves were plotted for Pt with the liquid jet and the flowing liquid setups under optimised temporal acquisition parameters (delay time and gate width). A normalisation using a silicon line was applied and recovery ranged from 3 to 15% for Pt in catalyst samples with both setups showing that LIBS is a sensitive and accurate method for on-line applications. PMID:22547353

  18. Neoadjuvant chemotherapy in breast cancer: early response prediction with quantitative MR imaging and spectroscopy

    PubMed Central

    Manton, D J; Chaturvedi, A; Hubbard, A; Lind, M J; Lowry, M; Maraveyas, A; Pickles, M D; Tozer, D J; Turnbull, L W

    2006-01-01

    A prospective study was undertaken in women undergoing neoadjuvant chemotherapy for locally advanced breast cancer in order to determine the ability of quantitative magnetic resonance imaging (MRI) and proton spectroscopy (MRS) to predict ultimate tumour response (percentage decrease in volume) or to detect early response. Magnetic resonance imaging and MRS were carried out before treatment and after the second of six treatment cycles. Pharmacokinetic parameters were derived from T1-weighted dynamic contrast-enhanced MRI, water apparent diffusion coefficient (ADC) was measured, and tissue water?:?fat peak area ratios and water T2 were measured using unsuppressed one-dimensional proton spectroscopic imaging (30 and 135?ms echo times). Pharmacokinetic parameters and ADC did not detect early response; however, early changes in water?:?fat ratios and water T2 (after cycle two) demonstrated substantial prognostic efficacy. Larger decreases in water T2 accurately predicted final volume response in 69% of cases (11/16) while maintaining 100% specificity and positive predictive value. Small/absent decreases in water?:?fat ratios accurately predicted final volume non-response in 50% of cases (3/6) while maintaining 100% sensitivity and negative predictive value. This level of accuracy might permit clinical application where early, accurate prediction of non-response would permit an early change to second-line treatment, thus sparing patients unnecessary toxicity, psychological morbidity and delay of initiation of effective treatment. PMID:16465174

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

    SciTech Connect

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

    2006-04-15

    Based on a Monte Carlo simulation method, an improved calculation of the backscattering factor in quantitative analysis by Auger electron spectroscopy has been performed by integrating several aspects of recent progresses in the related fields. The calculation used a general definition of backscattering factor, more accurate ionization cross section, up-to-date Monte Carlo model of electron inelastic scattering, and a large number of electron trajectories to ensure less statistical error. The results reveal several noticeable properties of backscattering factor, i.e., its slow variation with primary energy at higher overvoltage ratios, and dependence on the geometrical configuration of a detector. However, only for large emission angles of Auger signals a considerable angular dependence of backscattering factor is found. Specifically a calculation is carried out for detection in the solid angles of a cylindrical mirror analyzer. This backscattering factor can be less than unity for very low primary energies closing to ionization energy and/or for large incident angles. The physical cause has been detailed and analyzed.

  20. 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.

  1. 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.

  2. 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. PMID:25831066

  3. Biological tissue infrared analysis by chalcogenide glass optical fiber spectroscopy

    NASA Astrophysics Data System (ADS)

    Hocde, Sandrine; Loreal, O.; Sire, O.; Turlin, B.; Boussard-Pledel, Catherine; Le Coq, D.; Bureau, B.; Fonteneau, Gilles; Pigeon, C.; Leroyer, P.; Lucas, Jacques

    2001-01-01

    Owing to their low losses in the 2-12 micrometers region, the Te- As-Se glass fibers are used for infrared light transportation as well as sensing element based on evanescent wave absorption mechanism. The efficiency of the system is improved by tapering the fiber diameter in the sensing zone. With this kind of sensor, infrared spectra of biological tissue have been obtained. Spectra of mouse liver have been especially recorded in order to detect spectral differences between the healthy and the tumoral states of mouse liver.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  5. 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 project period, and nonperturbative numerical models of both of these techniques were developed. In addition, we developed new single-mode, injection-seeded optical parametric laser sources (OPLSs) that will be used to replace multi-mode commercial dye lasers in our experimental measurements. The use of single-mode laser radiation in our experiments will increase significantly the rigor with which theory and experiment are compared.

  6. NIR Raman spectroscopy in medicine and biology: results and aspects

    NASA Astrophysics Data System (ADS)

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

    1999-05-01

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

  7. Bioanalytics in Quantitive (Bio)imaging/Mapping of Metallic Elements in Biological Samples.

    PubMed

    Jurowski, Kamil; Buszewski, Bogus?aw; Piekoszewski, Wojciech

    2015-10-01

    The aim of this article is to describe selected analytical techniques and their applications in the quantitative mapping/(bio)imaging of metals in biological samples. This work presents the advantages and disadvantages as well as the appropriate methods of scope for research. Distribution of metals in biological samples is currently one of the most important issues in physiology, toxicology, pharmacology, and other disciplines where functional information about the distribution of metals is essential. This issue is a subject of research in (bio)imaging/mapping studies, which use a variety of analytical techniques for the identification and determination of metallic elements. Increased interest in analytical techniques enabling the (bio)imaging of metals in a variety of biological material has been observed more recently. Measuring the distribution of trace metals in tissues after a drug dose or ingestion of poison-containing metals allows for the studying of pathomechanisms and the pathophysiology of various diseases and disorders related to the management of metals in human and animal systems. PMID:25996031

  8. 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.

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

    PubMed

    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 I2/O3 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. PMID:16387540

  10. 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.

  11. Quantitative Cardiac 31P Spectroscopy at 3T Using Adiabatic Pulses

    PubMed Central

    El-Sharkawy, AbdEl-Monem; Schär, Michael; Ouwerkerk, Ronald; Weiss, Robert G.; Bottomley, Paul A.

    2011-01-01

    Cardiac phosphorus magnetic resonance spectroscopy (MRS) with surface coils promises better quantification at 3T due to improved signal-to-noise ratios and spectral resolution compared to 1.5T. However, Bloch equation and field analyses at 3T show that for efficient quantitative MRS protocols employing small-angle adiabatic (BIR4/BIRP) pulses the excitation-field is limited by RF power requirements and power deposition. When BIR4/BIRP pulse duration is increased to reduce power levels, T2-decay can introduce flip-angle dependent errors in the steady-state magnetization, causing errors in saturation corrections for metabolite quantification and in T1s measured by varying the flip-angle. A new dual-repetition-time (2TR) T1 method using frequency-sign-cycled adiabatic-half-passage pulses is introduced to alleviate power requirements, and avoid the problem related to T2 relaxation during the RF pulse. The 2TR method is validated against inversion-recovery in phantoms using a practical transmit/receive coil set designed for phosphorus MRS of the heart at depths of 9-10 cm with 4kW of pulse power. The T1s of phosphocreatine (PCr) and adenosine triphosphate (?-ATP) in the calf-muscle (n=9) at 3T are 6.8±0.3s and 5.4±0.6s respectively. For heart (n=10) the values are 5.8±0.5s (PCr) and 3.1±0.6s (?-ATP). The 2TR protocol measurements agreed with those obtained by conventional methods to within 10%. PMID:19195018

  12. Biological capacitance studies of anodes in microbial fuel cells using electrochemical impedance spectroscopy.

    PubMed

    Lu, Zhihao; Girguis, Peter; Liang, Peng; Shi, Haifeng; Huang, Guangtuan; Cai, Lankun; Zhang, Lehua

    2015-07-01

    It is known that cell potential increases while anode resistance decreases during the start-up of microbial fuel cells (MFCs). Biological capacitance, defined as the apparent capacitance attributed to biological activity including biofilm production, plays a role in this phenomenon. In this research, electrochemical impedance spectroscopy was employed to study anode capacitance and resistance during the start-up period of MFCs so that the role of biological capacitance was revealed in electricity generation by MFCs. It was observed that the anode capacitance ranged from 3.29 to 120 mF which increased by 16.8 % to 18-20 times over 10-12 days. Notably, lowering the temperature and arresting biological activity via fixation by 4 % para formaldehyde resulted in the decrease of biological capacitance by 16.9 and 62.6 %, indicating a negative correlation between anode capacitance and anode resistance of MFCs. Thus, biological capacitance of anode should play an important role in power generation by MFCs. We suggest that MFCs are not only biological reactors and/or electrochemical cells, but also biological capacitors, extending the vision on mechanism exploration of electron transfer, reactor structure design and electrode materials development of MFCs. PMID:25656699

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

    DOEpatents

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

    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.

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

    NASA Astrophysics Data System (ADS)

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

  15. Learning quantitative sequence-function relationships from high-throughput biological data

    E-print Network

    Atwal, Gurinder S

    2015-01-01

    Understanding the transcriptional regulatory code, as well as other types of information encoded within biomolecular sequences, will require learning biophysical models of sequence-function relationships from high-throughput data. Controlling and characterizing the noise in such experiments, however, is notoriously difficult. The unpredictability of such noise creates problems for standard likelihood-based methods in statistical learning, which require that the quantitative form of experimental noise be known precisely. However, when this unpredictability is properly accounted for, important theoretical aspects of statistical learning which remain hidden in standard treatments are revealed. Specifically, one finds a close relationship between the standard inference method, based on likelihood, and an alternative inference method based on mutual information. Here we review and extend this relationship. We also describe its implications for learning sequence-function relationships from real biological data. Fin...

  16. Use of gel filtration in the preparation of biological fluids for magnetic resonance spectroscopy

    Microsoft Academic Search

    David W. Hoffman; Ronald A. Venters; Suzanne F. Shedd; Leonard D. Spicer

    1990-01-01

    Analysis of biological fluids by proton magnetic resonance spectroscopy is often complicated by dynamic range problems created from the large water resonance. Gel filtration chromatography is found to be a simple and nondestructive method for exchanging DâO for HâO and for removing low molecular weight molecules from both plasma and urine, significantly improving subsequent one- and two-dimensional MRS spectra.

  17. 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 improve robustness of calibration models, signal processing methods can be used to decrease the influence of such non-constant background variation. In this dissertation, signal processing methods are also applied to NIR single-beam spectra collected during short-term and long-term studies. The prediction performance of the calibration models demonstrates, with suppression of non-constant background information by optimal wavelet processing procedures, robustness of calibration models with time can be significantly improved.

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

    SciTech Connect

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

    1990-01-01

    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.

  19. Quantitative structural and textural assessment of laminar pyrocarbons through Raman spectroscopy, electron diffraction

    E-print Network

    Boyer, Edmond

    spectroscopy; Electron energy- loss spectroscopy 1. Introduction Rough laminar pyrocarbon (RL) has been-cross when observed by polarized optical microscopy. The development of new densification methods of felts (FWHMD) is very sensitive to low energy structural defects (e.g., disorientations of the graphene layers

  20. 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 advancement in rDNA quantitation and recent findings regarding potential risks of immunogenicity, infectivity, and oncogenicity of rDNA. PMID:21956148

  1. High-Resolution Waveguide THz Spectroscopy of Biological Molecules N. Laman,* S. Sree Harsha,* D. Grischkowsky,* and Joseph S. Melingery

    E-print Network

    High-Resolution Waveguide THz Spectroscopy of Biological Molecules N. Laman,* S. Sree Harsha,* D 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

  2. Substrate and instrumental effects in quantitative Auger electron spectroscopy: the system lead on gold

    Microsoft Academic Search

    M. G. Barthes; G. E. Rhead

    1980-01-01

    New and previously published AES data on monolayer and surface compound formation during the first stages of deposition of lead on gold are critically examined. The system serves as a 'test case' for quantitative AES. Comparison of results obtained with different single crystals substrates and with different spectrometers show quantitative differences of up to a factor of two. It is

  3. 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).

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

    PubMed

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

    2012-04-01

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

  5. 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.

  6. Electric field standing wave artefacts in FTIR micro-spectroscopy of biological materials.

    PubMed

    Filik, Jacob; Frogley, Mark D; Pijanka, Jacek K; Wehbe, Katia; Cinque, Gianfelice

    2012-02-21

    FTIR absorption micro-spectroscopy is a widely used, powerful technique for analysing biological materials. In principle it is a straightforward linear absorption spectroscopy, but it can be affected by artefacts that complicate the interpretation of the data. In this article, artefacts produced by the electric-field standing-wave (EFSW) in micro-reflection-absorption (transflection) spectroscopy are investigated. An EFSW is present at reflective metallic surfaces due to the interference of incident and reflected light. The period of this standing wave is dependent on the wavelength of the radiation and can produce non-linear changes in absorbance with increasing sample thickness (non-Beer-Lambert like behaviour). A protein micro-structure was produced as a simple experimental model for a biological cell and used to evaluate the differences between FTIR spectra collected in transmission and transflection. By varying the thickness of the protein samples, the relationship between the absorbance and sample thickness in transflection was determined, and shown to be consistent with optical interference due to the EFSW coupled with internal reflection from the sample top surface. FTIR spectral image data from MCF 7 breast adenocarcinoma cells was then analysed to determine the severity of the EFSW artefact in data from a real sample. The results from these measurements confirmed that the EFSW artefact has a profound effect on transflection spectra, and in this case the main spectral variations were related to the sample thickness rather than any biochemical differences. PMID:22231204

  7. Titel DFG: Priority Programme "New frontiers in sensitivity for EPR spectroscopy: from biological cells to nano materials"

    E-print Network

    Greifswald, Ernst-Moritz-Arndt-Universität

    Titel DFG: Priority Programme "New frontiers in sensitivity for EPR spectroscopy: from biological cells to nano materials" Ziel der Ausschreibung The Priority Programme has been bringing the research areas of biological and material science together in a coordinated effort to increase the sensitivity

  8. 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

  9. Compound parabolic concentrator probe for efficient light collection in spectroscopy of biological tissue

    NASA Astrophysics Data System (ADS)

    Tanaka, Kazunori; Pacheco, Marcos T. T.; Brennan, James F., III; Itzkan, Irving; Berger, Andrew J.; Dasari, Ramachandra R.; Feld, Michael S.

    1996-02-01

    We describe a compound parabolic concentrator (CPC)-based probe for enhanced signal collection in the spectroscopy of biological tissues. Theoretical considerations governing signal enhancement compared with conventional collection methods are given. A ray-tracing program was used to analyze the throughput of CPC's with shape deviations and surface imperfections. A modified CPC shape with 99% throughput was discovered. A 4.4-mm-long CPC was manufactured and incorporated into an optical fiber-based near-infrared Raman spectrometer system. For human tissue samples, light collection was enhanced by a factor of 7 compared with collection with 0.29-NA optical fibers.

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  11. 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

  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. PMID:20672604

  13. Polarized light scattering spectroscopy for quantitative measurement of epithelial cellular structures in situ

    Microsoft Academic Search

    Vadim Backman; Rajan Gurjar; Kamran Badizadegan; Irving Itzkan; Ramachandra R. Dasari; Lev T. Perelman; Michael S. Feld

    1999-01-01

    We report an in situ method of probing the structure of living epithelial cells, based on light scattering spectroscopy with polarized light. The method makes it possible to distinguish between single backscattering from uppermost epithelial cells and multiply scattered light. The spectrum of the single backscattering component can be further analyzed to provide histological information about the epithelial cells such

  14. Quantitative micro-analysis by laser-induced breakdown spectroscopy: a review of the experimental approaches

    Microsoft Academic Search

    E. Tognoni; V Palleschi; M Corsi; G Cristoforetti

    2002-01-01

    The laser-induced breakdown spectroscopy (LIBS) technique has shown in recent years its great potential for rapid qualitative analysis of materials. Because of the lack of pre-treatment of the material, as well as the speed of analysis, not mentioning the possibility of in situ analysis, this technique offers an attractive solution for a wide range of industrial applications. As a consequence,

  15. 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. PMID:24806938

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

    PubMed

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

    2014-05-01

    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. PMID:24806938

  17. Absolute Quantitation of Bacterial Biofilm Adhesion and Viscoelasticity by Microbead Force Spectroscopy

    E-print Network

    Dutcher, John

    Absolute Quantitation of Bacterial Biofilm Adhesion and Viscoelasticity by Microbead Force of Guelph, Guelph, ON N1G 2W1, Canada ABSTRACT Bacterial biofilms are the most prevalent mode of bacterial stages of biofilm development. Following irreversible attachment of bacterial cells onto a surface

  18. 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. PMID:25468340

  19. QUANTITATIVE IMAGING AND ANALYSIS OF BIOLOGICAL SPECIMENS IN THE FIELD-EMISSION SCANNING TRANSMISSION ELECTRON MICROSCOPE: CAPABILITIES AND LIMITATIONS

    Microsoft Academic Search

    S. Brian Andrews; Natalia B. Pivovarova; Richard D. Leapman

    We have been applying a field-emission scanning transmission electron microscope (STEM) to high-resolu- tion imaging and analysis of biological specimens. This instrument is equipped with a cold\\/cryotransfer stage, dig- ital image acquisition system, energy-dispersive x-ray (EDX) detector, and electron energy loss spectrometer (EELS). It has been optimized to give low detection limits for elemental microanalysis and to provide quantitative images

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

    Microsoft Academic Search

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

    2002-01-01

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

  1. 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.

  2. Quantitative Analysis Of Agricultural Parameters Using Ger-imaging-spectroscopy Data Of The Eisac-89 Campagne

    Microsoft Academic Search

    Heike Bach; Wolfram Mauser

    1991-01-01

    During the EISAC-89 Imaging-Spectroscopy Campagne data was acquired of an agricultural test site in the Upper Rhine Valley near the City of Freiburg using the GER-IS-Scanner. An intensive ground-check of plant parameters was carried out of a 24 km2 subset of the acquired image. The ground truth data was integrated in a Geographical Information System. The GER-data was radiometrically corrected

  3. Application of Principal Component-Artificial Neural Networks in Near Infrared Spectroscopy Quantitative Analysis

    Microsoft Academic Search

    Hai-yan Ji; Zhen-hong Rao

    2006-01-01

    \\u000a The principal components of near infrared spectroscopy were calculated by nonlinear iterative partial least squares (NIPALS).\\u000a The best number of principal components was determined by cross-validation method. Thus, limited principal components that\\u000a free from noise and orthogonal each other were obtained. After standardization, these principal components were used as input\\u000a nodes of back propagation artificial neural networks (B-P ANN). ANN

  4. Quantitative antimony speciation in shooting-range soils by EXAFS spectroscopy

    Microsoft Academic Search

    Andreas C. Scheinost; Andre Rossberg; Delphine Vantelon; Irene Xifra; Ruben Kretzschmar; Ann-Kathrin Leuz; Harald Funke; C. Annette Johnson

    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

  5. Quantitative polymorph contaminant analysis in tablets using Raman and near infra-red spectroscopies.

    PubMed

    Hennigan, Michelle C; Ryder, Alan G

    2013-01-01

    The detection and quantification of alternate polymorphs of active pharmaceutical ingredients (APIs), particularly at low concentrations is a key issue for the manufacture and analysis of solid-state formulations. Each polymorph can possess unique physical and chemical properties which in turn can directly affect factors such as solubility and bioavailability. Near infra-red (NIR) and Raman spectroscopies can be used for the rapid characterisation and quantification of polymorphs in solid samples. In this study we have generated a model tablet system with two excipients and a 10% API concentration, where the API is a mixture of the FII and FIII polymorphs of piracetam. Using transmission Raman spectroscopy (TRS) and NIR spectroscopy it was possible to detect FII polymorph contamination in these model tablets with limits of detection (LODs) of 0.6 and 0.7%, respectively, with respect to the total tablet weight (or ?6-7% of the API content). The TRS method is the superior method because of the speed of analysis (?6s per sample), better sampling statistics, and because the sharper, more resolved bands in the Raman spectra allowed for easier interpretation of the spectral data. In addition the TRS used here provides facile access to the low frequency wavenumber region for analysis of solid-state lattice modes. PMID:23146243

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

    NASA Astrophysics Data System (ADS)

    Shao, Yongni; He, Yong; Mao, Jingyuan

    2007-09-01

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

  7. Relationship between the v?PO?/amide III ratio assessed by Raman spectroscopy and the calcium content measured by quantitative backscattered electron microscopy in healthy human osteonal bone.

    PubMed

    Roschger, Andreas; Gamsjaeger, Sonja; Hofstetter, Birgit; Masic, Admir; Blouin, Stéphane; Messmer, Phaedra; Berzlanovich, Andrea; Paschalis, Eleftherios P; Roschger, Paul; Klaushofer, Klaus; Fratzl, Peter

    2014-06-01

    Raman microspectroscopy and quantitative backscattered electron imaging (qBEI) of bone are powerful tools to investigate bone material properties. Both methods provide information on the degree of bone matrix mineralization. However, a head-to-head comparison of these outcomes from identical bone areas has not been performed to date. In femoral midshaft cross sections of three women, 99 regions (20×20 ?m²) were selected inside osteons and interstitial bone covering a wide range of matrix mineralization. As the focus of this study was only on regions undergoing secondary mineralization, zones exhibiting a distinct gradient in mineral content close to the mineralization front were excluded. The same regions were measured by both methods. We found a linear correlation (R²=0.75) between mineral/matrix as measured by Raman spectroscopy and the wt.?%Mineral/(100-wt.?%Mineral) as obtained by qBEI, in good agreement with theoretical estimations. The observed deviations of single values from the linear regression line were determined to reflect biological heterogeneities. The data of this study demonstrate the good correspondence between Raman and qBEI outcomes in describing tissue mineralization. The obtained correlation is likely sensitive to changes in bone tissue composition, providing an approach to detect potential deviations from normal bone. PMID:24919447

  8. quantitative determination of the AGN content in local ULIRGs through L-band spectroscopy

    E-print Network

    Risaliti, G; Sani, E

    2009-01-01

    We present a quantitative estimate of the relative AGN/starburst content in a sample of 59 nearby (z85% of the observed infrared luminosity. The subsample of sources optically classified as LINERs (31 objects) shows a similar AGN/starburst distribution as the whole sample, indicating a composite nature for this class of objects. We also show that a few ULIRGs, optically classified as starbursts, have L-band spectral features suggesting the presence of a buried AGN.

  9. Quantitative Determination of Chemical Processes by Dynamic Nuclear Polarization Enhanced Nuclear Magnetic Resonance Spectroscopy

    E-print Network

    Zeng, Haifeng

    2012-07-16

    between two spins, gives rise to the nuclear Overhauser effect (NOE),2-3 which depends on the distance between the two spins as 61/ij ijNOE r? . Distances obtained from NOE measurement and dihedral angles from scalar couplings provide geometrical... Robert R. Lucchese Jim(Xiuquan) Ji Head of Department, David H. Russell May 2012 Major Subject: Chemistry iii ABSTRACT Quantitative Determination of Chemical Processes by Dynamic Nuclear Polarization Enhanced Nuclear Magnetic Resonance...

  10. Distribution of Hydroxyl Groups in Kukersite Shale Oil: Quantitative Determination Using Fourier Transform Infrared (FT-IR) Spectroscopy.

    PubMed

    Baird, Zachariah Steven; Oja, Vahur; Järvik, Oliver

    2015-05-01

    This article describes the use of Fourier transform infrared (FT-IR) spectroscopy to quantitatively measure the hydroxyl concentrations among narrow boiling shale oil cuts. Shale oil samples were from an industrial solid heat carrier retort. Reference values were measured by titration and were used to create a partial least squares regression model from FT-IR data. The model had a root mean squared error (RMSE) of 0.44 wt% OH. This method was then used to study the distribution of hydroxyl groups among more than 100 shale oil cuts, which showed that hydroxyl content increased with the average boiling point of the cut up to about 350 °C and then leveled off and decreased. PMID:25811170

  11. Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics

    Microsoft Academic Search

    Yung-keun Kwon; Kwang-hyun Cho

    2008-01-01

    Motivation: It has been widely reported that biological networks are robust against perturbations such as mutations. On the contrary, it has also been known that biological networks are often fragile against unexpected mutations. There is a growing interest in these intriguing observations and the underlying design principle that causes such robust but fragile characteristics of biological networks. For relatively small

  12. Near-field confocal optical spectroscopy (NCOS): subdiffraction optical resolution for biological systems.

    PubMed

    Haydon, P G; Marchese-Ragona, S; Basarsky, T A; Szulczewski, M; McCloskey, M

    1996-06-01

    Optical resolution is limited by diffraction. However, in near-field microscopes sample illumination is provided through a subwavelength aperture to increase optical resolution. In this study we have evaluated the usefulness of this technique for living biological systems and report two significant improvements in this form of microscopy to enhance optical resolution for biological studies. We report a unique feedback method, photon-density feedback, which is used to monitor the registration of a near-field illumination probe with living cell membranes. In this method, the fluorescence intensity of a uniformly distributed fluorochrome is monitored while the sample is moved in the z-axis towards the probe. Upon contact between the cell membrane and the near-field probe a maximum intensity is detected. A problem with near-field microscopy is that enhanced optical resolution is only achieved within the near-field of the illuminating aperture. Thick biological specimens also fluoresce in the far-field reducing optical resolution. To reduce this problem we incorporated a confocal pinhole together with the near-field probe to enhance the resolution of this form of near-field microscopy. Finally, we demonstrate that near-field confocal optical spectroscopy does not impair physiological properties of neurons, astrocytes or mast cells, indicating that this high-resolution optical methodology will permit a new approach to the study of molecular distribution and action within living specimens. PMID:8763172

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

    SciTech Connect

    Shao Yongni; He Yong; Mao Jingyuan

    2007-09-01

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

  14. 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.

  15. Simultaneous quantitative analysis of mebendazole polymorphs A-C in powder mixtures by DRIFTS spectroscopy and ANN modeling.

    PubMed

    Kachrimanis, K; Rontogianni, M; Malamataris, S

    2010-02-01

    In the present study, a simple method, based on diffuse reflectance FTIR spectroscopy (DRIFTS) and artificial neural network (ANN) modeling is developed for the simultaneous quantitative analysis of mebendazole polymorphs A-C in powder mixtures. Spectral differences between the polymorphs are elucidated by computationally assisted band assignments on the basis of quantum chemical calculations, and subsequently, the spectra are preprocessed by calculation of 1st and 2nd derivatives. Then ANN models are fitted after PCA compression of the input space. Finally the predictive performance of the ANNs is compared with that of PLS regression. It was found that simultaneous quantitative analysis of forms A-C in powder mixtures is possible by fitting an ANN model to the 2nd derivative spectra even after PCA compression of the data (RMSEP of 1.75% for form A, 1.85% for B, and 1.65% for C), while PLS regression, applied for comparison purposes, results in acceptable predictions only within the 700-1750cm(-1) spectral range and after direct orthogonal signal correction (DOSC), with RMSEP values of 2.69%, 2.68%, and 3.40% for forms A, B, and C, respectively. Application of the ANN to commercial samples of raw material and formulation (suspension) proved its suitability for the prediction of polymorphic content. PMID:19833468

  16. 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. (Veterans Administration Medical Center, Philadelphia, PA (USA))

    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.

  17. 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.

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

    SciTech Connect

    Mukherjee, Dibyendu [ORNL; Cheng, Mengdawn [ORNL

    2008-01-01

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

  19. Near-infrared spectroscopy quantitative determination of Pefloxacin mesylate concentration in pharmaceuticals by using partial least squares and principal component regression multivariate calibration

    Microsoft Academic Search

    Yunfei Xie; Yan Song; Yong Zhang; Bing Zhao

    2010-01-01

    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.

  20. 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.

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

    PubMed Central

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

    2011-01-01

    Historically considered to be simple membrane components serving as structural elements and energy storing entities, fatty acids are now increasingly recognized as potent signaling molecules involved in many metabolic processes. Quantitative determination of fatty acids and exploration of fatty acid profiles have become common place in lipid analysis. We present here a reliable and sensitive method for comprehensive analysis of free fatty acids and fatty acid composition of complex lipids in biological material. The separation and quantitation of fatty acids is achieved by capillary gas chromatography. The analytical method uses pentafluorobenzyl bromide derivatization and negative chemical ionization gas chromatography-mass spectrometry. The chromatographic procedure provides base line separation between saturated and unsaturated fatty acids of different chain lengths as well as between most positional isomers. Fatty acids are extracted in the presence of isotope-labeled internal standards for high quantitation accuracy. Mass spectrometer conditions are optimized for broad detection capacity and sensitivity capable of measuring trace amounts of fatty acids in complex biological samples. PMID:21787881

  2. 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.

  3. Spectral-domain optical coherence phase microscopy for quantitative biological studies

    E-print Network

    Joo, Chulmin, 1976-

    2008-01-01

    Conventional phase-contrast and differential interference contrast microscopy produce high contrast images of transparent specimens such as cells. However, they do not provide quantitative information or do not have enough ...

  4. [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. PMID:25269288

  5. Quantitation of cerebral blood volume in human infants by near-infrared spectroscopy.

    PubMed

    Wyatt, J S; Cope, M; Delpy, D T; Richardson, C E; Edwards, A D; Wray, S; Reynolds, E O

    1990-03-01

    Current methods for measuring cerebral blood volume (CBV) in newborn infants are unsatisfactory. A new method is described in which the effect of a small change (5-10%) in arterial oxygen saturation (SaO2) on cerebral oxyhemoglobin [HbO2] and deoxyhemoglobin [Hb] concentration is observed by near-infrared (NIR) spectroscopy. Previous experiments in which the NIR absorption characteristics of HbO2 and Hb and the pathlength of NIR light through the brain were defined allowed changes in [HbO2] and [Hb] to be quantified from the Beer-Lambert law. It is shown here that CBV can then be derived from the expression CBV = (delta[HbO2] - delta[Hb])/(2. delta SaO2.H.R.), where H is the large vessel total hemoglobin concentration and R to the cerebral-to-large vessel hematocrit ratio. Observations on 12 newborn infants with normal brains, born at 25-40 wk of gestation and aged 10-240 h, gave a mean value for CBV of 2.22 +/- 0.40 (SD) ml/100 g, whereas mean CBV was significantly higher 3.00 +/- 1.04 ml/100 g in 10 infants with brain injury born at 24 to 42 wk of gestation and aged 4-168 h (P less than 0.05). PMID:2341336

  6. [Quantitative study on errors in evaluation of trace gases by long path differential optical absorption spectroscopy].

    PubMed

    Li, Su-Wen; Liu, Wen-Qing; Xie, Pin-Hua; Zhang, Yu-Jun; Li, Ang; Chen, Teng-Yun

    2007-07-01

    Long path differential optical absorption spectroscopy (LP-DOAS) can be used to retrieve the concentration of trace gases based on the principle of least squares. LP-DOAS permits the sensitive measurement of concentrations of trace gases. However, the calculation of a statistically sound measurement precision still remains an unsolved problem. The absorbance of atmospheric trace gases is usually very weak, so the interference caused by the occurrence of non-reproducible spectral artifacts often determines the detection limit and the measurement precision. These spectral artifacts bias the least squares fitting result in two respects. Spectral artifacts are falsely interpreted as real absorption, and spectral artifacts add non-statistical noise to spectral residuals, resulting in a significant underestimation of the least squares fitting error. Monte Carlo method was presented to investigate the evaluation errors in DOAS spectra accurately. Residual inspection by cyclic displacement was used to estimate the effect of false interpretation of the artifact structures. The evaluation of simulated atmospheric measurement spectra shows that Monte Carlo method yields a good estimate of the spectra evaluation error. It is approximately real error, factors of errors are 1.13, but errors are ordinarily underestimated by err(LSQ), and factors of errors are 3.12. PMID:17944388

  7. 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.

  8. Fast quantitative determination of microbial rhamnolipids from cultivation broths by ATR-FTIR Spectroscopy

    PubMed Central

    Leitermann, Frank; Syldatk, Christoph; Hausmann, Rudolf

    2008-01-01

    Background Vibrational spectroscopic techniques are becoming increasingly important and popular because they have the potential to provide rapid and convenient solutions to routine analytical problems. Using these techniques, a variety of substances can be characterized, identified and also quantified rapidly. Results The rapid ATR-FTIR (Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy) in time technique has been applied, which is suitable to quantify the concentrations of microbial rhamnolipids in a typical cultivation process. While the usually applied HPLC analysis requires an extensive and time consuming multi step extraction protocol for sample preparation, the ATR-FTIR-method allows the quantification of the rhamnolipids within 20 minutes. Accuracies between 0.5 g/l – 2.1 g/l for the different analytes were determined by cross validation of the calibration set. Even better accuracies between 0.28 g/l – 0.59 g/l were found for independent test samples of an arbitrarily selected cultivation. Conclusion ATR-FTIR was found to be suitable for the rapid analysis of rhamnolipids in a biotechnological process with good reproducibility in sample determination and sufficient accuracy. An improvement in accuracy through continuous expansion and validation of the reference spectra set seems very likely. PMID:18840269

  9. Metabolic responses during hemodialysis determined by quantitative (1)H NMR spectroscopy.

    PubMed

    Fujiwara, Masako; Ando, Itiro; Takeuchi, Kazuhisa; Oguma, Shiro; Sato, Hiroshi; Sekino, Hiroshi; Sato, Keisuke; Imai, Yutaka

    2015-07-10

    A large proportion of patients with end-stage renal disease have lifelong hemodialysis (HD) treatment. HD rapidly and indiscriminately removes necessary small metabolites together with uremic toxins from plasma into dialysate. To investigate metabolic responses to HD, we determined the levels of metabolites through time-course monitoring of (1)H NMR spectroscopy of dialysate during HD. The dialysate sample is stable for analysis because it contains only small metabolites without proteins. It was collected non-invasively from 9 HD patients with chronic glomerular nephropathy, at 6 time points during 4h of HD in 5 sessions. Creatinine, alanine, lactate, pyruvate and valine were simultaneously quantified on a one-dimensional single-pulse spectrum with a single standard compound. The concentration of creatinine exhibited monotonous decay with time, while that of valine decreased slowly and then maintained its levels throughout an HD. Lactate, alanine and pyruvate increased at 2-3h after the initiation of HD. They exhibited remarkable responses to HD with production from the body. The time-course of change in the 4 metabolites of lactate, pyruvate, alanine, and valine had reproducible behavior unique to each patient during the HD. This finding may be applied to distinguish metabolic status in HD patients. PMID:25886393

  10. 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.

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

    PubMed

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

    2012-08-21

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

  12. 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.

  13. Quantitative Physiology of the Precancerous Cervix In Vivo through Optical Spectroscopy1

    PubMed Central

    Chang, Vivide Tuan-Chyan; Cartwright, Peter S; Bean, Sarah M; Palmer, Greg M; Bentley, Rex C; Ramanujam, Nirmala

    2009-01-01

    Cervical cancer is the second most common female cancer worldwide. The ability to quantify physiological and morphological changes in the cervix is not only useful in the diagnosis of cervical precancers but also important in aiding the design of cost-effective detection systems for use in developing countries that lack well-established screening and diagnostic programs. We assessed the capability of a diffuse reflectance spectroscopy technique to identify contrasts in optical biomarkers that vary with different grades of cervical intraepithelial neoplasia (CIN) from normal cervical tissues. The technology consists of an optical probe and an instrument (with broadband light source, dispersive element, and detector), and a Monte Carlo algorithm to extract optical biomarker contributions including total hemoglobin (Hb) concentration, Hb saturation, and reduced scattering coefficient from the measured spectra. Among 38 patients and 89 sites examined, 46 squamous normal sites, 18 CIN 1, and 15 CIN 2+ sites were included in the analysis. Total Hb was statistically higher in CIN 2+ (18.3 ± 3.6 µM, mean ± SE) compared with normal (9.58 ± 1.91 µM) and CIN 1 (12.8 ± 2.6 µM), whereas scattering was significantly reduced in CIN 1 (8.3 ± 0.8 cm-1) and CIN 2+ (8.6 ± 1.0 cm-1) compared with normal (10.2 ± 1.1 cm-1). Hemoglobin saturation was not significantly altered in CIN 2+ compared with normal and CIN 1. The difference in total Hb is likely because of stromal angiogenesis, whereas decreased scattering can be attributed to breakdown of collagen network in the cervical stroma. PMID:19308287

  14. 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.

  15. 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

  16. Time-integrated laser-induced plasma spectroscopy in the vacuum ultraviolet for the quantitative elemental characterization of steel alloys

    NASA Astrophysics Data System (ADS)

    Khater, M. A.; van Kampen, P.; Costello, J. T.; Mosnier, J.-P.; Kennedy, E. T.

    2000-09-01

    This paper demonstrates that time-integrated space-resolved laser-induced plasma spectroscopy (TISR-LIPS) is a useful technique in the vacuum ultraviolet (VUV) for the quantitative determination of the carbon content in steels. The standard reference samples used were carbon-iron alloys containing a relatively wide concentration range of carbon (0.041-1.32%). In the experiments the output of a Q-switched Nd:YAG (1064 nm) laser, with approximately a 1 J maximum output pulse energy and approximately a 12 ns temporal pulse width, was focused onto the surface of each sample (under vacuum) in order to produce the emitting plasma. A fore-slit mounted in the target chamber allowed spatially-resolved spectral measurements in the axial direction of the plasma and provided emission lines that were almost free of the background continuum. A 1 m normal incidence vacuum spectrometer, equipped with a 1200 grooves mm-1 concave grating and a micro-channel plate/photodiode array detector combination, was used as the detection system. A particularly interesting feature of this work is the demonstration that VUV spectroscopy allows ionic lines to be used and linear calibration curves were obtained for the five carbon spectral lines (from C+ and C2+) under investigation. The limits of detection for all lines were determined; the lowest detection limit (87+/-10 ppm) was obtained from the C2+ 97.70 nm line, which compares favourably with the only available value in the literature of 100 ppm.

  17. Quantitative and dynamic measurements of biological fresh samples with X-ray phase contrast tomography.

    PubMed

    Hoshino, Masato; Uesugi, Kentaro; Tsukube, Takuro; Yagi, Naoto

    2014-11-01

    X-ray phase contrast tomography using a Talbot grating interferometer was applied to biological fresh samples which were not fixed by any fixatives. To achieve a high-throughput measurement for the fresh samples the X-ray phase contrast tomography measurement procedure was improved. The three-dimensional structure of a fresh mouse fetus was clearly depicted as a mass density map using X-ray phase contrast tomography. The mouse fetus measured in the fresh state was then fixed by formalin and measured in the fixed state. The influence of the formalin fixation on soft tissue was quantitatively evaluated by comparing the fresh and fixed samples. X-ray phase contrast tomography was also applied to the dynamic measurement of a biological fresh sample. Morphological changes of a ring-shaped fresh pig aorta were measured tomographically under different degrees of stretching. PMID:25343804

  18. 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.

  19. Molecular-scale quantitative charge density measurement of biological molecule by frequency modulation atomic force microscopy in aqueous solutions.

    PubMed

    Umeda, Kenichi; Kobayashi, Kei; Oyabu, Noriaki; Matsushige, Kazumi; Yamada, Hirofumi

    2015-07-17

    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. PMID:26120025

  20. 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 absorption data are used for in vivo risk assessments. PMID:20947718

  1. Quantitative Modeling and Estimation in Systems Biology using Fluorescent Reporter Systems

    E-print Network

    Bansal, Loveleena

    2013-12-10

    , protein localization and protein-protein interactions. This dissertation presents various techniques to facilitate modeling of biological systems containing fluorescent reporters with special attention given to challenges arising due to limited...

  2. A quantitative framework For large-scale model estimation and discrimination In systems biology

    E-print Network

    Eydgahi, Hoda

    2013-01-01

    Using models to simulate and analyze biological networks requires principled approaches to parameter estimation and model discrimination. We use Bayesian and Monte Carlo methods to recover the full probability distributions ...

  3. Quantitative analysis of WC stars: constraints on neon abundances from ISO-SWS spectroscopy

    NASA Astrophysics Data System (ADS)

    Dessart, Luc; Crowther, Paul A.; Hillier, D. John; Willis, Allan J.; Morris, Patrick W.; van der Hucht, Karel A.

    2000-06-01

    Neon abundances are derived in four Galactic WC stars - ?2Vel (WR11, WC8+O7.5III), HD156385 (WR90, WC7), HD192103 (WR135, WC8) and WR146 (WC5+O8) - using mid-infrared fine-structure lines obtained with ISO-SWS. Stellar parameters for each star are derived using the non-local thermodynamic equilibrium model atmospheric code of Hillier & Miller, together with ultraviolet (IUE), optical (INT, AAT) and infrared (UKIRT, ISO) spectroscopy. In the case of ?2Vel, we adopt very recent results from De Marco et al., who followed an identical approach. ISO-SWS data sets reveal the [Neiii] 15.5-?m line in each of our targets, while [Neii] 12.8?m, [Siv] 10.5?m and [Siii] 18.7?m are observed solely in ?2Vel. Using a method updated from Barlow et al. to account for clumped winds, we derive Ne/He=(3-4)×10-3 by number, plus S/He=6×10-5 for ?2Vel. Neon is highly enriched, such that Ne/S in ?2Vel is eight times higher than cosmic values. However, observed Ne/He ratios are a factor of 2 lower than predictions of current evolutionary models of massive stars. An imprecise mass loss and distance were responsible for the much greater discrepancy in neon content identified by Barlow et al. Our sample of WC5-8 stars span a narrow range in T* (=55-71kK), with no trend towards higher temperature at earlier spectral type, supporting earlier results for a larger sample by Koesterke & Hamann. Stellar luminosities range from 100000 to 500000Lsolar, while 10-5.1 <= M/(Msolar yr-1) <= 10-4.5, adopting clumped winds, in which volume filling factors are 10per cent. In all cases, wind performance numbers are less than 10, significantly lower than recent estimates. Carbon abundances span 0.08<=C/He<=0.25 by number, while oxygen abundances remain poorly constrained.

  4. 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.

  5. 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 ?g 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 investigated. PMID:21336938

  6. 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; The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) Team

    2010-01-01

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

  7. Studying Flow Close to an Interface by Total Internal Reflection Fluorescence Cross Correlation Spectroscopy: Quantitative Data Analysis

    E-print Network

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

    2011-11-13

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

  8. Remote Quantitative Analysis of Minerals Based on Multispectral Line-Calibrated Laser-Induced Breakdown Spectroscopy (LIBS).

    PubMed

    2014-10-01

    Laser-induced breakdown spectroscopy (LIBS) is a feasible remote sensing technique used for mineral analysis in some unapproachable places where in situ probing is needed, such as analysis of radioactive elements in a nuclear leak or the detection of elemental compositions and contents of minerals on planetary and lunar surfaces. Here a compact custom 15 m focus optical component, combining a six times beam expander with a telescope, has been built, with which the laser beam of a 1064 nm neodymium-doped yttrium aluminum garnet (Nd:YAG) laser is focused on remote minerals. The excited LIBS signals that reveal the elemental compositions of minerals are collected by another compact single lens?based signal acquisition system. In our remote LIBS investigations, the LIBS spectra of an unknown ore have been detected, from which the metal compositions are obtained. In addition, a multi-spectral line calibration (MSLC) method is proposed for the quantitative analysis of elements. The feasibility of the MSLC and its superiority over a single-wavelength determination have been confirmed by comparison with traditional chemical analysis of the copper content in the ore. PMID:25198122

  9. 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. PMID:20937537

  10. Quantitation of normal metabolite concentrations in six brain regions by in-vivo 1H-MR spectroscopy

    PubMed Central

    Minati, Ludovico; Aquino, Domenico; Bruzzone, Maria Grazia; Erbetta, Alessandra

    2010-01-01

    This study examined the concentrations of brain metabolites visible to in-vivo 1H-Magnetic Resonance Spectroscopy (1H-MRS) at 1.5 T in a sample of 28 normal subjects. Quantitation was attempted for inositol compounds, choline units, total creatine and N-acetyl moieties, using open-source software. Six brain regions were considered: frontal and parietal white matter, medial temporal lobe, thalamus, pons and cerebellum. Absolute concentrations were derived using tissue water as an internal reference and using an external reference; metabolite signal intensity ratios with respect to creatine were also calculated. The inter-individual variability was smaller for absolute concentrations (internal reference) as compared to that for signal intensity ratios. Significant regional variability in concentration was found for all metabolites, indicating that separate normative values are needed for different brain regions. The values obtained in this study can be used as reference in future studies, provided the same methodology is followed; it is confirmed that despite unsuccessful attempts in the past, smaller coefficients of variation can indeed be obtained through absolute quantification. PMID:20927223

  11. Evaluation of impedance spectroscopy for the characterization of small biological samples in tissue-based test systems.

    PubMed

    Thielecke, H; Fleckenstein, J; Bartholoma, P; Rube, C

    2004-01-01

    Marker free techniques are needed for the construction of efficient tissue-based test and sensor systems. In principle biological tissue can be characterized by impedance spectroscopy. In this paper we investigate by simulation how sensitive parameters of small biological tissue samples can be determined by impedance spectroscopy under optimal measurement conditions. Further, we experimentally evaluate whether the effects of different clinical relevant radio therapy variants on 3D in vitro tumor models are determinable and distinguishable by impedance spectroscopy using a tissue-based test system. The simulations demonstrate that changes in tissue parameters related to the extracellular space are determinable with a high sensitivity. The experiments show that the effect of different radiation dose levels on 3D in vitro tumor models can be determined and distinguished by using a capillary measurement system and impedance spectroscopy. These results are relevant for the development of tissue-based test and sensor systems using impedance spectroscopy to evaluate personalized therapy variants or new therapy approaches. PMID:17272128

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

    PubMed Central

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

    2011-01-01

    Prions are pathogens with an unusually high tolerance to inactivation and constitute a complex challenge to the re-processing of surgical instruments. On the other hand, however, they provide an informative paradigm which has been exploited successfully for the development of novel broad-range disinfectants simultaneously active also against bacteria, viruses and fungi. Here we report on the development of a methodological platform that further facilitates the use of scrapie prions as model pathogens for disinfection. We used specifically adapted serial protein misfolding cyclic amplification (PMCA) for the quantitative detection, on steel wires providing model carriers for decontamination, of 263K scrapie seeding activity converting normal protease-sensitive into abnormal protease-resistant prion protein. Reference steel wires carrying defined amounts of scrapie infectivity were used for assay calibration, while scrapie-contaminated test steel wires were subjected to fifteen different procedures for disinfection that yielded scrapie titre reductions of ?101- to ?105.5-fold. As confirmed by titration in hamsters the residual scrapie infectivity on test wires could be reliably deduced for all examined disinfection procedures, from our quantitative seeding activity assay. Furthermore, we found that scrapie seeding activity present in 263K hamster brain homogenate or multiplied by PMCA of scrapie-contaminated steel wires both triggered accumulation of protease-resistant prion protein and was further propagated in a novel cell assay for 263K scrapie prions, i.e., cerebral glial cell cultures from hamsters. The findings from our PMCA- and glial cell culture assays revealed scrapie seeding activity as a biochemically and biologically replicative principle in vitro, with the former being quantitatively linked to prion infectivity detected on steel wires in vivo. When combined, our in vitro assays provide an alternative to titrations of biological scrapie infectivity in animals that substantially facilitates the use of prions as potentially highly indicative test agents in the search for novel broad-range disinfectants. PMID:21647368

  13. Deciphering the protein-RNA recognition code: Combining large-scale quantitative methods with structural biology.

    PubMed

    Hennig, Janosch; Sattler, Michael

    2015-08-01

    RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence-specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross-linking immuno-precipitation (CLIP) and other recently developed high-throughput methods provide comprehensive, genome-wide maps of protein-RNA interactions in the cell. Structural biology gives detailed insights into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high-throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein-RNA recognition in gene regulation, as we review in this article. PMID:26059946

  14. Systems Biology of Cancer: A Challenging Expedition for Clinical and Quantitative Biologists

    PubMed Central

    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. PMID:25191654

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

    PubMed

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

    2010-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  17. 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.

  18. 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.

  19. 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.

  20. Java-based graphical user interface for MRUI, a software package for quantitation of in vivo\\/medical magnetic resonance spectroscopy signals

    Microsoft Academic Search

    A. Naressi; C. Couturier; I. Castang; R. de Beer; D. Graveron-Demilly

    2001-01-01

    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

  1. Quantitative analysis in gas chromatography\\/low power atmospheric-pressure helium microwave-induced plasma atomic emission interferometry and ion cyclotron resonance mass spectroscopy

    Microsoft Academic Search

    Loo

    1990-01-01

    The development of experimental and data analysis techniques for quantitative analysis in gas chromatography\\/low power atmospheric pressure helium microwave-induced plasma atomic emission interferometry (GC\\/HeMIPAEI) and ion cyclotron resonance mass spectroscopy (ICR\\/MS) is presented. A discussion of interferometric data analysis by discrete and fast Fourier transform (DFT and FFT, respectively) is given. Additionally, the use of two techniques (the maximum entropy

  2. Identification and quantitation of 3,4-methylenedioxy- N-methylamphetamine (MDMA, ecstasy) in human urine by 1H NMR spectroscopy. Application to five cases of intoxication

    Microsoft Academic Search

    Jonathan Liu; John Decatur; Gloria Proni; Elise Champeil

    2010-01-01

    Identification of 3,4-methylenedioxy-N-methylamphetamine (MDMA, ecstasy) in five cases of intoxication using nuclear magnetic resonance (NMR) spectroscopy of human urine is reported. A new water suppression technique PURGE (Presaturation Utilizing Relaxation Gradients and Echoes) was used. A calibration curve was obtained using spiked samples. The method gave a linear response (correlation coefficient of 0.992) over the range 0.01–1mg\\/mL. Subsequently, quantitation of

  3. Precision open-ended coaxial probes for in vivo and ex vivo dielectric spectroscopy of biological tissues at microwave frequencies

    Microsoft Academic Search

    Dijana Popovic; Leah McCartney; Cynthia Beasley; Mariya Lazebnik; Michal Okoniewski; Susan C. Hagness; John H. Booske

    2005-01-01

    Hermetic stainless-steel open-ended coaxial probes have been designed for precision dielectric spectroscopy of biological tissue, such as breast tissue, over the 0.5-20-GHz frequency range. Robust data-processing techniques have also been developed for extracting the unknown permittivity of the tissue under test from the reflection coefficient measured with the precision probe and a vector network analyzer. The first technique, referred to

  4. Some precautions in the use of time-domain dielectric spectroscopy with biological and other lossy dielectrics

    Microsoft Academic Search

    F. X. Hart

    1982-01-01

    Time-domain dielectric spectroscopy provides a rapid means of obtainingin vivo dielectric spectra of biological objects whose physiological state may be changing with time. This paper discusses precautions\\u000a which must be taken in the selection of the measuring-circuit parameters and frequency range to prevent the introduction of\\u000a artefacts into the resulting spectra. The ratio of the amplifier input resistance to the

  5. Infrared overtone spectroscopy measurements of ammonia and carbon dioxide in the effluent of a biological water processor

    Microsoft Academic Search

    R. Claps; D. Leleux; F. V. Englich; F. K. Tittel; M. E. Webber; J. B. Jeffries; R. K. Hanson; J. C. Graf; L. M. Vega

    NH3 and CO2 concentration measurements performed on a Biological Water Processor (BWP), under development at NASA-JSC for water recycling, using near infrared laser diode absorption spectroscopy are reported. The gaseous effluents from the bioreactor are a concern for potentially introducing harmful amounts of NH3 in a spacecraft environment. Furthermore, NH3 and CO2 monitoring is important for understanding the nitrogen and

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

    NASA Astrophysics Data System (ADS)

    Carlson, Philip Joseph

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

  7. Rapid and quantitative detection of the microbial spoilage of meat by fourier transform infrared spectroscopy and machine learning.

    PubMed

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

    2002-06-01

    Fourier transform infrared (FT-IR) spectroscopy is a rapid, noninvasive technique with considerable potential for application in the food and related industries. We show here that this technique can be used directly on the surface of food to produce biochemically interpretable "fingerprints." Spoilage in meat is the result of decomposition and the formation of metabolites caused by the growth and enzymatic activity of microorganisms. FT-IR was exploited to measure biochemical changes within the meat substrate, enhancing and accelerating the detection of microbial spoilage. Chicken breasts were purchased from a national retailer, comminuted for 10 s, and left to spoil at room temperature for 24 h. Every hour, FT-IR measurements were taken directly from the meat surface using attenuated total reflectance, and the total viable counts were obtained by classical plating methods. Quantitative interpretation of FT-IR spectra was possible using partial least-squares regression and allowed accurate estimates of bacterial loads to be calculated directly from the meat surface in 60 s. Genetic programming was used to derive rules showing that at levels of 10(7) bacteria.g(-1) the main biochemical indicator of spoilage was the onset of proteolysis. Thus, using FT-IR we were able to acquire a metabolic snapshot and quantify, noninvasively, the microbial loads of food samples accurately and rapidly in 60 s, directly from the sample surface. We believe this approach will aid in the Hazard Analysis Critical Control Point process for the assessment of the microbiological safety of food at the production, processing, manufacturing, packaging, and storage levels. PMID:12039738

  8. 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 number of locations worldwide, and examples from recent fieldwork involving the Leeds instruments will be presented.

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

    PubMed Central

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

    2002-01-01

    Fourier transform infrared (FT-IR) spectroscopy is a rapid, noninvasive technique with considerable potential for application in the food and related industries. We show here that this technique can be used directly on the surface of food to produce biochemically interpretable “fingerprints.” Spoilage in meat is the result of decomposition and the formation of metabolites caused by the growth and enzymatic activity of microorganisms. FT-IR was exploited to measure biochemical changes within the meat substrate, enhancing and accelerating the detection of microbial spoilage. Chicken breasts were purchased from a national retailer, comminuted for 10 s, and left to spoil at room temperature for 24 h. Every hour, FT-IR measurements were taken directly from the meat surface using attenuated total reflectance, and the total viable counts were obtained by classical plating methods. Quantitative interpretation of FT-IR spectra was possible using partial least-squares regression and allowed accurate estimates of bacterial loads to be calculated directly from the meat surface in 60 s. Genetic programming was used to derive rules showing that at levels of 107 bacteria·g?1 the main biochemical indicator of spoilage was the onset of proteolysis. Thus, using FT-IR we were able to acquire a metabolic snapshot and quantify, noninvasively, the microbial loads of food samples accurately and rapidly in 60 s, directly from the sample surface. We believe this approach will aid in the Hazard Analysis Critical Control Point process for the assessment of the microbiological safety of food at the production, processing, manufacturing, packaging, and storage levels. PMID:12039738

  10. 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.

  11. 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

  12. Spectroscopy

    NSDL National Science Digital Library

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

  13. Quantitative global sensitivity analysis of a biologically based dose-response pregnancy model for the thyroid endocrine system

    PubMed Central

    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. PMID:26074819

  14. Isotope dilution technique for quantitative analysis of endogenous trace element species in biological systems

    NASA Astrophysics Data System (ADS)

    Schaumlöffel, Dirk; Lobinski, Ryszard

    2005-04-01

    The aim of this study was to develop an inductively coupled plasma mass spectrometry (ICPMS) method for the determination of enriched species-specific mercury tracers at ng L-1 levels (ppt) in zooplankton and aquatic samples from biological tracer experiments. Applying a cold vapor sector field ICPMS method a high sensitivity was obtained, i.e., 106 cps for 1 [mu]g L-1 of natural mercury measured on 202Hg+, which in turn enabled the measurement of mercury isotope ratios with a 0.6-1.4%R.S.D. precision for a 50 ng L-1 standard. This method was used to quantify CH3201Hg+ and 200Hg2+ tracers in zooplankton from a biological tracer experiment with the aim of investigating the effects of algal density and zooplankton density on mercury bioaccumulation in zooplankton in a fresh water system. For quantification purposes a known amount of 199Hg+ was added to the zooplankton samples before digestion. The digested samples were analyzed and the resulting ICPMS spectra split into four spectra one for each of the four sources of mercury present in the sample (CH3201Hg+, 200Hg2+, 199Hg2+ and natural mercury) using algebraic de-convoluting. The CH3201Hg+ and 200Hg2+ tracers were quantified using an isotope dilution approach with the added 199Hg+. Detection limits were 0.6 and 0.2 ng L-1 for 200Hg+ and CH3201Hg+, respectively. The coefficient of variation on the tracer determinations was approximately 18% CV estimated from the analysis of real samples with tracer concentrations in the <0.1-100 ng L-1 range. The developed method was successfully applied for the determination of species-specific mercury tracers in zooplankton samples from a biological tracer experiment.

  15. 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

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

    PubMed

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

    2002-02-15

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

  17. 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 (?, ?) in a series of selectively 13C-labeled 40-residue ?-amyloid (A?1-40) samples, in both fibrillar and non-fibrillar states. Experiments are carried out at 9.39 T and 8 K, using a static double-resonance NMR probe and low-power microwave irradiation at 264 GHz. In frozen solutions of A?1-40 fibrils doped with DOTOPA-TEMPO, we observe DNP signal enhancement factors of 16-21. We show that the orientation- and frequency-dependent spin polarization exchange between sequential backbone carbonyl 13C labels can be simulated accurately using a simple expression for the exchange rate, after experimentally determined homogeneous 13C lineshapes are incorporated in the simulations. The experimental 2D 13C-13C exchange spectra place constraints on the ? and ? angles between the two carbonyl labels. Although the data are not sufficient to determine ? and ? uniquely, the data do provide non-trivial constraints that could be included in structure calculations. With DNP at low temperatures, 2D 13C-13C exchange spectra can be obtained from a 3.5 mg sample of A?1-40 fibrils in 4 h or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples.

  18. 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 (?,?) in a series of selectively 13C-labeled 40-residue ?-amyloid (A?1–40) samples, in both fibrillar and non-fibrillar states. Experiments are carried out at 9.39 T and 8 K, using a static double-resonance NMR probe and low-power microwave irradiation at 264 GHz. In frozen solutions of A?1–40 fibrils doped with DOTOPA-TEMPO, we observe DNP signal enhancement factors of 16–21. We show that the orientation- and frequency-dependent spin polarization exchange between sequential backbone carbonyl 13C labels can be simulated accurately using a simple expression for the exchange rate, after experimentally determined homogeneous 13C lineshapes are incorporated in the simulations. The experimental 2D 13C-13C exchange spectra place constraints on the ? and ? angles between the two carbonyl labels. Although the data are not sufficient to determine ? and ? uniquely, the data do provide non-trivial constraints that could be included in structure calculations. With DNP at low temperatures, 2D 13C-13C exchange spectra can be obtained from a 3.5 mg sample of A?1–40 fibrils in 4 hr or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples. PMID:23562665

  19. The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

    PubMed Central

    Kamerlin, Shina C. L.; Warshel, Arieh

    2012-01-01

    Recent years have seen dramatic improvements in computer power, allowing ever more challenging problems to be approached. In light of this, it is imperative to have a quantitative model for examining chemical reactivity, both in the condensed phase and in solution, as well as to accurately quantify physical organic chemistry (particularly as experimental approaches can often be inconclusive). Similarly, computational approaches allow for great progress in studying enzyme catalysis, as they allow for the separation of the relevant energy contributions to catalysis. Due to the complexity of the problems that need addressing, there is a need for an approach that can combine reliability with an ability to capture complex systems in order to resolve long-standing controversies in a unique way. Herein, we will demonstrate that the empirical valence bond (EVB) approach provides a powerful way to connect the classical concepts of physical organic chemistry to the actual energies of enzymatic reactions by means of computation. Additionally, we will discuss the proliferation of this approach, as well as attempts to capture its basic chemistry and repackage it under different names. We believe that the EVB approach is the most powerful tool that is currently available for studies of chemical processes in the condensed phase in general and enzymes in particular, particularly when trying to explore the different proposals about the origin of the catalytic power of enzymes. PMID:25285029

  20. Quantitative evaluation of the lactate signal loss and its spatial dependence in press localized (1)H NMR spectroscopy.

    PubMed

    Jung, W I; Bunse, M; Lutz, O

    2001-10-01

    Localized (1)H NMR spectroscopy using the 90 degrees -t(1)-180 degrees -t(1)+t(2)-180 degrees -t(2)-Acq. PRESS sequence can lead to a signal loss for the lactate doublet compared with signals from uncoupled nuclei which is dependent on the choice of t(1) and t(2). The most striking signal loss of up to 78% of the total signal occurs with the symmetrical PRESS sequence (t(1)=t(2)) at an echo time of 2/J (approximately 290 ms). Calculations have shown that this signal loss is related to the pulse angle distributions produced by the two refocusing pulses which leads to the creation of single quantum polarization transfer (PT) as well as to not directly observable states (NDOS) of the lactate AX(3) spin system: zero- and multiple-quantum coherences, and longitudinal spin orders. In addition, the chemical shift dependent voxel displacement (VOD) leads to further signal loss. By calculating the density operator for various of the echo times TE=n/J, n=1, 2, 3,..., we calculated quantitatively the contributions of these effects to the signal loss as well as their spatial distribution. A maximum signal loss of 75% can be expected from theory for the symmetrical PRESS sequence and TE=2/J for Hamming filtered sinc pulses, whereby 47% are due to the creation of NDOS and up to 28% arise from PT. Taking also the VOD effect into account (2 mT/m slice selection gradients, 20-mm slices) leads to 54% signal loss from NDOS and up to 24% from PT, leading to a maximum signal loss of 78%. Using RE-BURP pulses with their more rectangular pulse angle distributions reduces the maximum signal loss to 44%. Experiments at 1.5 T using a lactate solution demonstrated a maximum lactate signal loss for sinc pulses of 82% (52% NDOS, 30% PT) at TE=290 ms using the symmetrical PRESS sequence. The great signal loss and its spatial distribution is of importance for investigations using a symmetrical PRESS sequence at TE=2/J. PMID:11567573

  1. Quantitative Evaluation of the Lactate Signal Loss and Its Spatial Dependence in PRESS Localized 1H NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Jung, Wulf-Ingo; Bunse, Michael; Lutz, Otto

    2001-10-01

    Localized 1H NMR spectroscopy using the 90°-t1-180°-t1+t2-180°-t2-Acq. PRESS sequence can lead to a signal loss for the lactate doublet compared with signals from uncoupled nuclei which is dependent on the choice of t1 and t2. The most striking signal loss of up to 78% of the total signal occurs with the symmetrical PRESS sequence (t1=t2) at an echo time of 2/J (?290 ms). Calculations have shown that this signal loss is related to the pulse angle distributions produced by the two refocusing pulses which leads to the creation of single quantum polarization transfer (PT) as well as to not directly observable states (NDOS) of the lactate AX3 spin system: zero- and multiple-quantum coherences, and longitudinal spin orders. In addition, the chemical shift dependent voxel displacement (VOD) leads to further signal loss. By calculating the density operator for various of the echo times TE=n/J, n=1, 2, 3, …, we calculated quantitatively the contributions of these effects to the signal loss as well as their spatial distribution. A maximum signal loss of 75% can be expected from theory for the symmetrical PRESS sequence and TE=2/J for Hamming filtered sinc pulses, whereby 47% are due to the creation of NDOS and up to 28% arise from PT. Taking also the VOD effect into account (2 mT/m slice selection gradients, 20-mm slices) leads to 54% signal loss from NDOS and up to 24% from PT, leading to a maximum signal loss of 78%. Using RE-BURP pulses with their more rectangular pulse angle distributions reduces the maximum signal loss to 44%. Experiments at 1.5 T using a lactate solution demonstrated a maximum lactate signal loss for sinc pulses of 82% (52% NDOS, 30% PT) at TE=290 ms using the symmetrical PRESS sequence. The great signal loss and its spatial distribution is of importance for investigations using a symmetrical PRESS sequence at TE=2/J.

  2. 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 basis for further clinical development of noninvasive MR approaches. PMID:22020805

  3. Quantitation of retinaldehyde in small biological samples using ultrahigh-performance liquid chromatography tandem mass spectrometry.

    PubMed

    Wang, Jinshan; Yoo, Hong Sik; Obrochta, Kristin M; Huang, Priscilla; Napoli, Joseph L

    2015-09-01

    We report an ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method to quantify all-trans-retinal in biological samples of limited size (15-35mg), 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 5fmol to 1pmol. This assay revealed that extraocular concentrations of retinal range from approximately 2 to 40pmol/g in multiple tissues-the same range as all-trans-retinoic acid. All-trans-retinoic acid has high affinity (kd?0.4nM) for its nuclear receptors (RAR?, -?, and -?), 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

  4. 3-Dimensional quantitative detection of nanoparticle content in biological tissue samples after local cancer treatment

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  5. Quantitative Determination of the Biodegradable Polymer Poly(?-hydroxybutyrate) in a Recombinant Escherichia coli Strain by Use of Mid-Infrared Spectroscopy and Multivariative Statistics

    PubMed Central

    Kansiz, Mustafa; Billman-Jacobe, Helen; McNaughton, Don

    2000-01-01

    Fourier transform infrared (FTIR) spectroscopy in combination with the partial least squares (PLS) multivariative statistical technique was used for quantitative analysis of the poly(?-hydroxybutyrate) (PHB) contents of bacterial cells. A total of 237 replicate spectra from 34 samples were obtained together with gas chromatography-determined reference PHB contents. Using the PLS regression, we were able to relate the infrared spectra to the reference PHB contents, and the correlation coefficient between the measured and predicted values for the optimal model with a standard error of prediction of 1.49% PHB was 0.988. With this technique, there are no solvent requirements, sample preparation is minimal and simple, and analysis time is greatly reduced; our results demonstrate the potential of FTIR spectroscopy as an alternative to the conventional methods used for analysis of PHB in bacterial cells. PMID:10919800

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

    NASA Astrophysics Data System (ADS)

    Zhang, Hedong; Miwa, Mitsuharu; Yamashita, Yutaka; Tsuchiya, Yutaka

    1998-05-01

    Based on the microscopic Beer-Lambert law, two practical time-integrated spectroscopy (TIS) methods, called dual-wavelength spectroscopy method, and dual-wavelength and dual-site spectroscopy method, are described to determine the absolute concentration of an absorber in variously shaped turbid media. We demonstrate, for the first time, the validity of the TIS methods by means of experiments in which the absolute concentrations of an absorber in a tissue-like phantom were determined with errors less than several percent. The advantages and disadvantages of both methods are also discussed.

  7. The use of low-energy ion scattering spectroscopy for the quantitative determination of adsorption sites in surface chemistry studies

    Microsoft Academic Search

    Nancy R. Gleason; Francisco Zaera

    1997-01-01

    Ion scattering spectroscopy (ISS) was used in conjunction with temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS) for the study of the adsorption of hydrogen, oxygen, ethyl iodide, and 2-propyl iodide on Ni(100). In all those systems the decrease in Ni ISS signal intensity seen during the uptake could be explained by shielding of the Ni surface atoms by the

  8. Quantitative measurement of residual biaxial stress by Raman spectroscopy in diamond grown on a Ti alloy by chemical vapor deposition

    Microsoft Academic Search

    Joel Ager; Michael Drory

    1993-01-01

    Raman spectroscopy is used to study residual stress in diamond grown on Ti--6Al--4V by chemical vapor deposition. A general model is developed to use Raman spectroscopy to measure biaxial stress in polycrystalline, diamond-structure films. The as-grown film has 7.1 GPa of residual compressive stress, consistent with the difference in thermal-expansion coefficients between the diamond film and the substrate. Examination of

  9. FT-IR TRANSMISSION SPECTROSCOPY FOR QUANTITATION OF AMMONIUM BISULFATE IN FINE PARTICULATE MATTER COLLECTED ON TEFLON FILTERS

    EPA Science Inventory

    A quantitative measurement method for fine particle bisulfatein ammonium bisulfate collected from the ambient air onto Teflon filters is described. nfrared absorbance measurements of the Teflon filters are made before and after particle collection. ubtraction of the two spectra r...

  10. 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

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

    NASA Astrophysics Data System (ADS)

    Best, Stephen P.; Cheah, Mun Hon

    2010-02-01

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

  12. Electron paramagnetic resonance spectroscopy studies of oxidative degradation of an active pharmaceutical ingredient and quantitative analysis of the organic radical intermediates using partial least-squares regression.

    PubMed

    Williams, Helen Elizabeth; Loades, Victoria Catherine; Claybourn, Mike; Murphy, Damien Martin

    2006-01-15

    Electron paramagnetic resonance (EPR) spectroscopy was used to study the radical species formed during the oxidation of an active pharmaceutical ingredient in the solid state. It was found that the extent of radical generation correlated to the formation of an oxidative degradation product. Multifrequency EPR and electron nuclear double resonance spectroscopy gave additional information on the identity of the organic radical species involved in the oxidation process, and a mechanism was proposed for the degradation, involving the formation of both carbon-centered and peroxy radicals. The multivariate analysis technique of partial least-squares (PLS) regression was then used to determine the extent of oxidation of the active pharmaceutical ingredient from the EPR spectra. The suitability of this approach was demonstrated from its application to a series of standards. The conventional approach for the quantitative analysis of EPR spectra is to measure the peak height or to perform double integration of the spectral region containing the signal of interest. Both of these methods have intrinsic errors associated with them, particularly for weak EPR signals with a poor signal-to-noise ratio or a sloping background response. The results obtained showed that greatly improved quantitation was obtained using the PLS regression approach. PMID:16408946

  13. Natural deuterium distribution in fatty acids isolated from peanut seed oil: a site-specific study by quantitative 2H NMR spectroscopy.

    PubMed

    Duan, Jia-Rong; Billault, Isabelle; Mabon, Françoise; Robins, Richard

    2002-08-01

    Quantitative (2)H NMR spectroscopy has been used to measure the distribution of deuterium at natural abundance in long-chain fatty acids extracted from the same vegetable oil. Peanut seed oil was selected, due to its suitable oleic and linoleic acid content. The methyl esters of the fatty acids were prepared by transesterification and isolated by modified argentation column chromatography on silica. In order to measure the natural isotopic fractionation of deuterium (D) at the maximum number of positions, the purified methyl oleate and methyl linoleate were chemically cleaved and the (D/H)(i) values determined by quantitative (2)H NMR spectroscopy. It was thus possible to demonstrate that fractionation in deuterium occurs during the desaturation of oleate to linoleate. Furthermore, the previously observed distribution of deuterium at the sites of desaturation is confirmed, as is the alternating pattern of (D/H)(i), which relates to the origin of the pertinent hydrogen atoms. The data obtained are discussed in terms of the kinetic isotopic effects intrinsic to the enzymes-synthetases and desaturases-involved in the biosynthesis of fatty acids. PMID:12203973

  14. Fluorometric Quantitation of dsDNA An essential element of cellular and molecular biology is the ability to quantitate DNA in large

    E-print Network

    Raizada, Manish N.

    of nucleic acid concentration is the determination of absorbance at 260 nm (A260) as described by Matiatis et and phenol are commonly found in nucleic acid preparations. As a result, several fluorescent staining is the ability to quantitate DNA in large numbers of samples at a sensitivity that enables determination of small

  15. 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.

  16. Laser spectroscopy technique for estimating the efficiency of photosensitisers in biological media

    SciTech Connect

    Ryabova, A V; Stratonnikov, Aleksandr A; Loshchenov, V B [Natural Science Center, A.M. Prokhorov General Physics Institute, Russian Academy of Sciences, Moscow (Russian Federation)

    2006-06-30

    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). (laser biology)

  17. Detection of trace Al in model biological tissue with laser-induced breakdown spectroscopy

    E-print Network

    Rehse, Steven J.

    spectroscopy (LIBS), which is an excellent tool for trace elemental analysis, was studied as a method for a much more realistic sampling methodology were also studied, suggesting that LIBS could be a candidate harmful metals into the tissue [6]. In this paper, laser-induced breakdown spectros- copy (LIBS) has been

  18. Quantitation of the global secondary structure of globular proteins by FTIR spectroscopy: Comparison with X-ray crystallographic structure

    Microsoft Academic Search

    Thomas F. Kumosinski; Joseph J. Unruh

    1996-01-01

    Fourier transform infrared spectroscopy (FTIR) is potentially a powerful tool for determining the global secondary structure of proteins in solution, providing the spectra are analyzed using a statistically and theoretically justified methodology. We have performed FTIR experiments on 14 globular proteins and two synthetic polypeptides whose X-ray crystal structures are known to exhibit varying types and amounts of secondary structures.

  19. Quantitative Investigation of Compartmentalized Dynamics of ErbB2 Targeting Gold Nanorods in Live Cells by Single Molecule Spectroscopy

    Microsoft Academic Search

    Jiji Chen; Joseph Irudayaraj

    2009-01-01

    Understanding the diffusion dynamics and receptor uptake mechanism of nanoparticles in cancer cells is crucial to the rational design of multifunctional nanoprobes for targeting and delivery. In this report, for the first time, we quantify the localization and evaluate the diffusion times of Herceptin-conjugated gold nanorods (H-GNRs) in different cell organelles by fluorescence correlation spectroscopy (FCS) and examine the endocytic

  20. The ratio of the single and double scattering intensities in ion scattering spectroscopy as a quantitative measure of surface structures

    Microsoft Academic Search

    A. J. Algra; S. B. Luitjens; H. Borggreve; E. P. Th. M. Suurmeijer; A. L. Boers

    1982-01-01

    The ratio R of the intensities of the single and double scattering peaks observed in Ion Scattering Spectroscopy has been determined as a function of several experimental parameters. If all particles scattered through a certain scattering angle are detected with a time of flight spectrometer or when alkali ions are used as primary particles then the absolute value of R

  1. 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.

  2. Direct Quantitation and Detection of Salmonellae in Biological Samples without Enrichment, Using Two-Step Filtration and Real-Time PCR

    Microsoft Academic Search

    Petra F. G Wolffs; Kari Glencross; Romain Thibaudeau; Mansel W. Griffiths

    2006-01-01

    A new two-step filtration protocol followed by a real-time PCR assay based on SYBR green I detection was developed to directly quantitate salmonellae in two types of biological samples: i.e., chicken rinse and spent irrigation water. Four prefiltration filters, one type of final filter, and six protocols for recovery of salmonellae from the final filter were evaluated to identify an

  3. Quantitative Analysis of Simulated Illicit Street-Drug Samples Using Raman Spectroscopy and Partial Least Squares Regression

    Microsoft Academic Search

    Owen S. Fenton; Lindsey A. Tonge; Taylor H. Moot; Kimberley A. Frederick

    2011-01-01

    Modern drug laws require that a seized sample be characterized for both the illegal substances present and the quantity of each of those substances. The goal of this work was to develop a common approach to model development based on Raman spectroscopic analysis followed by partial least squares (PLS) regression that would allow us to obtain quantitative information from simulated

  4. 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

  5. Quantitative determination of cyfluthrin in n-hexane by terahertz time-domain spectroscopy with chemometrics methods

    Microsoft Academic Search

    Yuefang Hua; Hongjian Zhang; Hongliang Zhou

    2009-01-01

    Terahertz time-domain spectroscopy (THz-TDS) was used for the detection of cyfluthrin content in N-hexane solvent with the concentration range of 0.5-10 mug\\/mL. The absorbance of the solution form cyfluthrin was obtained in the frequency range between 0.5-1.5 THz. Two kinds of multivariate linear regression models were then built between the absorbance and the concentration of 15 samples, using partial least

  6. Quantitative Evaluation of the Lactate Signal Loss and Its Spatial Dependence in PRESS Localized 1H NMR Spectroscopy

    Microsoft Academic Search

    Wulf-Ingo Jung; Michael Bunse; Otto Lutz

    2001-01-01

    Localized 1H NMR spectroscopy using the 90°?t1?180°?t1+t2?180°?t2?Acq. PRESS sequence can lead to a signal loss for the lactate doublet compared with signals from uncoupled nuclei which is dependent on the choice of t1 and t2. The most striking signal loss of up to 78% of the total signal occurs with the symmetrical PRESS sequence (t1=t2) at an echo time of

  7. High-throughput quantitative biochemical characterization of algal biomass by NIR spectroscopy; multiple linear regression and multivariate linear regression analysis.

    PubMed

    Laurens, L M L; Wolfrum, E J

    2013-12-18

    One of the challenges associated with microalgal biomass characterization and the comparison of microalgal strains and conversion processes is the rapid determination of the composition of algae. We have developed and applied a high-throughput screening technology based on near-infrared (NIR) spectroscopy for the rapid and accurate determination of algal biomass composition. We show that NIR spectroscopy can accurately predict the full composition using multivariate linear regression analysis of varying lipid, protein, and carbohydrate content of algal biomass samples from three strains. We also demonstrate a high quality of predictions of an independent validation set. A high-throughput 96-well configuration for spectroscopy gives equally good prediction relative to a ring-cup configuration, and thus, spectra can be obtained from as little as 10-20 mg of material. We found that lipids exhibit a dominant, distinct, and unique fingerprint in the NIR spectrum that allows for the use of single and multiple linear regression of respective wavelengths for the prediction of the biomass lipid content. This is not the case for carbohydrate and protein content, and thus, the use of multivariate statistical modeling approaches remains necessary. PMID:24229385

  8. Molecular Force Spectroscopy on Cells

    NASA Astrophysics Data System (ADS)

    Liu, Baoyu; Chen, Wei; Zhu, Cheng

    2015-04-01

    Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

  9. Using wide-field quantitative diffuse reflectance spectroscopy in combination with high-resolution imaging for margin assessment

    NASA Astrophysics Data System (ADS)

    Kennedy, Stephanie; Mueller, Jenna; Bydlon, Torre; Brown, J. Quincy; Ramanujam, Nimmi

    2011-03-01

    Due to the large number of women diagnosed with breast cancer and the lack of intra-operative tools, breast cancer margin assessment presents a significant unmet clinical need. Diffuse reflectance spectral imaging provides a method for quantitatively interrogating margins of lumpectomy specimens. We have previously found that [?- carotene]/?s' is a diagnostically important parameter but both parameters, [?-carotene] and ?s', were derived from a low resolution parameter map and are subject to the tissue type and heterogeneity present in the breast. In this study, we used diffuse reflectance measurements from individual sites co-registered with high resolution microendoscopy (HRME) images to determine if the combined performance of these technologies could improve margin assessment. By comparing the optical parameters of [?-carotene] and ?s' to the quantitative HRME image endpoints of feature size, feature density and normalized fluorescence, we determined that adding HRME to spectral imaging can improve the specificity of our diffuse reflectance spectral imaging system.

  10. Fiber optic evanescent wave spectroscopy (FEWS) and its applications for multicomponent analysis of blood and biological fluids

    NASA Astrophysics Data System (ADS)

    Simhi, Ronit; Bunimovich, David; Sela, Ben-Ami; Katzir, Abraham

    1995-05-01

    In numerous cases the technique of Fiberoptic Evanescent Wave Spectroscopy (FEWS) offers great advantages over regular IR spectroscopic methods. It provides an easy way for measuring the absorption spectra of highly absorbing or highly scattering samples. With FEWS one can perform measurements in situ and in real time and this is potentially useful for measurements on biological samples or for the monitoring of chemical reactions. In the present work, the FEWS technique was used to analyze human blood serum using a Fourier Transform Infrared Spectrometer. A special cell based on IR transmitting non-toxic silver halide fibers was designed. Further improvements in the analysis were obtained by adopting some multivariate calibration techniques that have already been used in clinical chemistry. The blood constituents analyzed were: urea, total protein, cholesterol, uric acid and calcium. Good agreement between our results and the ordinary chemical and enzymatic methods was obtained.

  11. On-site quantitative elemental analysis of metal ions in aqueous solutions by underwater laser-induced breakdown spectroscopy combined with electrodeposition under controlled potential.

    PubMed

    Matsumoto, Ayumu; Tamura, Ayaka; Koda, Ryo; Fukami, Kazuhiro; Ogata, Yukio H; Nishi, Naoya; Thornton, Blair; Sakka, Tetsuo

    2015-02-01

    We propose a technique of on-site quantitative analysis of Zn(2+) in aqueous solution based on the combination of electrodeposition for preconcentration of Zn onto a Cu electrode and successive underwater laser-induced breakdown spectroscopy (underwater LIBS) of the electrode surface under electrochemically controlled potential. Zinc emission lines are observed with the present technique for a Zn(2+) concentration of 5 ppm. It is roughly estimated that the overall sensitivity over 10?000 times higher is achieved by the preconcentration. Although underwater LIBS suffers from the spectral deformation due to the dense plasma confined in water and also from serious shot-to-shot fluctuations, a linear calibration curve with a coefficient of determination R(2) of 0.974 is obtained in the range of 5-50 ppm. PMID:25560224

  12. Quantitative speciation of Mn-bearing particulates emitted from autos burning (methylcyclopentadienyl)manganese tricarbonyl-added gasolines using XANES spectroscopy

    SciTech Connect

    Ressler, T.; Wong, J.; Roos, J.; Smith, I.L.

    2000-03-15

    The chemical nature of Mn-containing particulates emitted from (methylcyclopentadienyl)manganese tricarbonyl-added gasoline engines has been elucidated using Mn K-edge X-ray absorption fine structure (XAFS) spectroscopy. Edge shift data from the X-ray absorption near-edge structure (SANES) spectra showed that the average Mn valence in these particulates is {approximately}2.2. Using a principal component analysis (PCA) algorithm, the number and type of probable species contained in these particulates were determined to be three, consisting of Mn{sub 3}O{sub 4}, MnSO{sub 4}{sm_bullet}H{sub 2}O, and a divalent manganese phosphate, Mn{sub 5}(PO{sub 4})[PO{sub 3}(OH)]{sub 2}{sm_bullet}4H{sub 2}O. The proportions of these Mn phases in each particulate sample were evaluated quantitatively using least-squares fitting (LSF) of the experimental XANES spectra with linear combinations of these principal component (model compound) spectra. Two groups of Mn-bearing particulates may be distinguished: group I having 4--9 wt % of Mn{sub 3}O{sub 4} and exhibiting a single intense first major absorption maximum at the Mn K-edge and group II containing 15--22 wt % of Mn{sub 3}O{sub 4} and exhibiting a doublet absorption maximum at lower intensity. Fourier transforms of the EXAFS signals were found to corroborate the XANES results. This study clearly establishes XANES spectroscopy, in combination with PCA and LSF, as a quantitative analytical tool for speciation of dilute and/or amorphous multicomponent environmental materials not easily attainable with conventional methods.

  13. Estimation of soil clay and organic matter using two quantitative methods (PLSR and MARS) based on reflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    Nawar, Said; Buddenbaum, Henning; Hill, Joachim

    2014-05-01

    A rapid and inexpensive soil analytical technique is needed for soil quality assessment and accurate mapping. This study investigated a method for improved estimation of soil clay (SC) and organic matter (OM) using reflectance spectroscopy. Seventy soil samples were collected from Sinai peninsula in Egypt to estimate the soil clay and organic matter relative to the soil spectra. Soil samples were scanned with an Analytical Spectral Devices (ASD) spectrometer (350-2500 nm). Three spectral formats were used in the calibration models derived from the spectra and the soil properties: (1) original reflectance spectra (OR), (2) first-derivative spectra smoothened using the Savitzky-Golay technique (FD-SG) and (3) continuum-removed reflectance (CR). Partial least-squares regression (PLSR) models using the CR of the 400-2500 nm spectral region resulted in R2 = 0.76 and 0.57, and RPD = 2.1 and 1.5 for estimating SC and OM, respectively, indicating better performance than that obtained using OR and SG. The multivariate adaptive regression splines (MARS) calibration model with the CR spectra resulted in an improved performance (R2 = 0.89 and 0.83, RPD = 3.1 and 2.4) for estimating SC and OM, respectively. The results show that the MARS models have a great potential for estimating SC and OM compared with PLSR models. The results obtained in this study have potential value in the field of soil spectroscopy because they can be applied directly to the mapping of soil properties using remote sensing imagery in arid environment conditions. Key Words: soil clay, organic matter, PLSR, MARS, reflectance spectroscopy.

  14. ERDA Paper: Quantitative Measurement of Chromium, Manganese, Rhenium, and Magnesium in Liquid by Laser-Induced Breakdown Spectroscopy

    SciTech Connect

    Keller, E.L.

    2000-06-27

    A technique is needed to measure Tc during the waste process at DOE Hanford site. Laser induced breakdown spectroscopy (LIBS), a laser-based, non-intrusive, and sensitive optical diagnostic technique for measuring the concentration of various atomic and molecular species in test media, has the potential to be an on-line monitor to monitor Tc in the effluent from the Tc removal column to track the technetium removal process. In this work, we evaluate the analytical figure of merit of LIBS system for the element that has similar properties to Tc.

  15. Analysis of both cobalt and selenium in feed?stuffs and in biological tissue by chelation?extraction and graphite furnace atomic absorption spectroscopy

    Microsoft Academic Search

    T. F. Brown; L. K. Zeringue

    1991-01-01

    A procedure for measuring cobalt in feedstuffs and biological tissues using ammonium pyrrolidine dithiocarbamate (APDC) and methyl isobutyl ketone (MIBK) chelation?extraction and graphite furnace atomic absorption spectroscopy is described. This procedure, except for the graphite furnace and spectrophotometer programs, is identical to another method for analysis of selenium in the same types of sample materials. Therefore, only one chelation?extraction is

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

    Microsoft Academic Search

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

    2002-01-01

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

  17. Detection of bacteria by time-resolved laser-induced breakdown spectroscopy

    Microsoft Academic Search

    Stéphane Morel; Nicolas Leone; Philippe Adam; Jacques Amouroux

    2003-01-01

    A laser-induced breakdown spectroscopy technique for analyzing biological matter for the detection of biological hazards is investigated. Eight species were considered in our experiment: six bacteria and two pollens in pellet form. The experimental setup is described, then a cumulative intensity ratio is proposed as a quantitative criterion because of its linearity and reproducibility. Time-resolved laser-induced breakdown spectroscopy (TRELIBS) exhibits

  18. Combining FT-IR spectroscopy and multivariate analysis for qualitative and quantitative analysis of the cell wall composition changes during apples development.

    PubMed

    Szymanska-Chargot, M; Chylinska, M; Kruk, B; Zdunek, A

    2015-01-22

    The aim of this work was to quantitatively and qualitatively determine the composition of the cell wall material from apples during development by means of Fourier transform infrared (FT-IR) spectroscopy. The FT-IR region of 1500-800 cm(-1), containing characteristic bands for galacturonic acid, hemicellulose and cellulose, was examined using principal component analysis (PCA), k-means clustering and partial least squares (PLS). The samples were differentiated by development stage and cultivar using PCA and k-means clustering. PLS calibration models for galacturonic acid, hemicellulose and cellulose content from FT-IR spectra were developed and validated with the reference data. PLS models were tested using the root-mean-square errors of cross-validation for contents of galacturonic acid, hemicellulose and cellulose which was 8.30 mg/g, 4.08% and 1.74%, respectively. It was proven that FT-IR spectroscopy combined with chemometric methods has potential for fast and reliable determination of the main constituents of fruit cell walls. PMID:25439873

  19. Quantitative data on blood flow during tumor PDT obtained by laser Doppler spectroscopy in the hen's egg test system

    NASA Astrophysics Data System (ADS)

    Vervoorts, Anja; Rood, H. A.; Klotz, Marcus; Moser, Joerg G.; Rosenbruch, Martin

    1995-01-01

    Oxygen supply is the most important requirement of type II photodynamic reactions. Prerequisite in photodynamic tumor therapy is an intact tumor blood flow during irradiation. Most photosensitizers destroy tumor vessels due to accumulation in endothelial cells. As a prerequisite to develop novel photosensitizing drugs an in-vivo test system is required to quantitatively assess for inertness of those sensitizers to the blood supply. We adapted and further developed a system capable of measuring the relative oxygen supply to heterotransplanted tumors on the yolk sac membrane (YSM) of fertilized chicken eggs.

  20. 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.

  1. 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

  2. In Situ Adsorption Studies at the Solid/Liquid Interface:Characterization of Biological Surfaces and Interfaces Using SumFrequency Generation Vibrational Spectroscopy, Atomic Force Microscopy,and Quartz Crystal Microbalance

    SciTech Connect

    Phillips, D.C.

    2006-05-16

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and quartz crystal microbalance (QCM) have been used to study the molecular surface structure, surface topography and mechanical properties, and quantitative adsorbed amount of biological molecules at the solid-liquid interface. The molecular-level behavior of designed peptides adsorbed on hydrophobic polystyrene and hydrophilic silica substrates has been examined as a model of protein adsorption on polymeric biomaterial surfaces. Proteins are such large and complex molecules that it is difficult to identify the features in their structure that lead to adsorption and interaction with solid surfaces. Designed peptides which possess secondary structure provide simple model systems for understanding protein adsorption. Depending on the amino acid sequence of a peptide, different secondary structures ({alpha}-helix and {beta}-sheet) can be induced at apolar (air/liquid or air/solid) interfaces. Having a well-defined secondary structure allows experiments to be carried out under controlled conditions, where it is possible to investigate the affects of peptide amino acid sequence and chain length, concentration, buffering effects, etc. on adsorbed peptide structure. The experiments presented in this dissertation demonstrate that SFG vibrational spectroscopy can be used to directly probe the interaction of adsorbing biomolecules with a surface or interface. The use of well designed model systems aided in isolation of the SFG signal of the adsorbing species, and showed that surface functional groups of the substrate are sensitive to surface adsorbates. The complementary techniques of AFM and QCM allowed for deconvolution of the effects of surface topography and coverage from the observed SFG spectra. Initial studies of biologically relevant surfaces are also presented: SFG spectroscopy was used to study the surface composition of common soil bacteria for use in bioremediation of nuclear waste.

  3. Quantitative determination of the oxidation state of iron in biotite using x-ray photoelectron spectroscopy: II. In situ analyses

    SciTech Connect

    Raeburn, S.P. [Pennsylvania State Univ., University Park, PA (United States)] [Pennsylvania State Univ., University Park, PA (United States); [Lehigh Univ., Bethlehem, PA (United States); Ilton, E.S. [Lehigh Univ., Bethlehem, PA (United States)] [Lehigh Univ., Bethlehem, PA (United States); Veblen, D.R. [Johns Hopkins Univ., Baltimore, MD (United States)] [Johns Hopkins Univ., Baltimore, MD (United States)

    1997-11-01

    X-ray photoelectron spectroscopy (XPS) was used to determine Fe(III)/{Sigma}Fe in individual biotite crystals in thin sections of ten metapelites and one syenite. The in situ XPS analyses of Fe(III)/{Sigma}Fe in biotite crystals in the metapelites were compared with published Fe(III)/{Sigma}Fe values determined by Moessbauer spectroscopy (MS) for mineral separates from the same hand samples. The difference between Fe(III)/{Sigma}Fe by the two techniques was greatest for samples with the lowest Fe(III)/{Sigma}Fe (by MS). For eight metamorphic biotites with Fe(III)/{Sigma}Fe = 9-27% comparison of the two techniques yielded a linear correlation of r = 0.94 and a statistically acceptable fit of [Fe(III)/{Sigma}Fe]{sub xps} = [Fe(III)/{Sigma}Fe]{sub ms}. The difference between Fe(III)/{Sigma}Fe by the two techniques was greater for two samples with Fe(III)/{Sigma}Fe {le} 6% (by MS). For biotite in the syenite sample, Fe(III)/{Sigma}Fe determined by both in situ XPS and bulk wet chemistry/electron probe microanalysis were similar. This contribution demonstrates that XPS can be used to analyze bulk Fe(III)/{Sigma}Fe in minerals in thin sections when appropriate precautions taken to avoid oxidation of the near-surface during preparation of samples. 25 refs., 3 figs., 4 tabs.

  4. Principles, performance, and applications of spectral reconstitution (SR) in quantitative analysis of oils by Fourier transform infrared spectroscopy (FT-IR).

    PubMed

    García-González, Diego L; Sedman, Jacqueline; van de Voort, Frederik R

    2013-04-01

    Spectral reconstitution (SR) is a dilution technique developed to facilitate the rapid, automated, and quantitative analysis of viscous oil samples by Fourier transform infrared spectroscopy (FT-IR). This technique involves determining the dilution factor through measurement of an absorption band of a suitable spectral marker added to the diluent, and then spectrally removing the diluent from the sample and multiplying the resulting spectrum to compensate for the effect of dilution on the band intensities. The facsimile spectrum of the neat oil thus obtained can then be qualitatively or quantitatively analyzed for the parameter(s) of interest. The quantitative performance of the SR technique was examined with two transition-metal carbonyl complexes as spectral markers, chromium hexacarbonyl and methylcyclopentadienyl manganese tricarbonyl. The estimation of the volume fraction (VF) of the diluent in a model system, consisting of canola oil diluted to various extents with odorless mineral spirits, served as the basis for assessment of these markers. The relationship between the VF estimates and the true volume fraction (VF(t)) was found to be strongly dependent on the dilution ratio and also depended, to a lesser extent, on the spectral resolution. These dependences are attributable to the effect of changes in matrix polarity on the bandwidth of the ?(CO) marker bands. Excellent VF(t) estimates were obtained by making a polarity correction devised with a variance-spectrum-delineated correction equation. In the absence of such a correction, SR was shown to introduce only a minor and constant bias, provided that polarity differences among all the diluted samples analyzed were minimal. This bias can be built into the calibration of a quantitative FT-IR analytical method by subjecting appropriate calibration standards to the same SR procedure as the samples to be analyzed. The primary purpose of the SR technique is to simplify preparation of diluted samples such that only approximate proportions need to be adhered to, rather than using exact weights or volumes, the marker accounting for minor variations. Additional applications discussed include the use of the SR technique in extraction-based, quantitative, automated FT-IR methods for the determination of moisture, acid number, and base number in lubricating oils, as well as of moisture content in edible oils. PMID:23601545

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

    SciTech Connect

    Prieto, P.; Morant, C.; Climent-Font, A.; Munoz, A.; Elizalde, E.; Sanz, J.M. [Departamento de Fisica Aplicada C-XII, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Departamento de Fisica Aplicada C-XII, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid, Spain and Centro de Micro-Analisis de Materiales, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Centro de Micro-Analisis de Materiales, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Departamento de Fisica Aplicada C-XII, Universidad Autonoma de Madrid, Cantoblanco, E-28049 Madrid (Spain)

    2006-03-15

    CN/TiCN/TiN multilayers and the respective single layers have been deposited on Si(100) substrates using a dual ion-beam sputtering system. Both the multilayers and the respective single layers have been chemically characterized by Auger electron spectroscopy (AES) depth profiling combined with factor analysis and by Rutherford backscattering spectrometry (RBS). The combination of AES and RBS allows a quantitative chemical characterization of the multilayer and the respective single layers. Whereas RBS has some difficulties to determine the in-depth distribution of the light elements along the multilayer, AES depth profiling enables their quantitative analysis and even their chemical state along the multilayer. On the contrary, RBS shows its advantages to determine the heavy elements, including the contaminants incorporated during the deposition process (e.g., W). Under special experimental conditions it is shown that RBS is able to determine the composition of the single layers (i.e., CN/Si, TiCN/Si, and TiN/Si) in good agreement with AES depth profiling. As a result of this complementary use we obtain a complete quantitative chemical characterization of the single layers and multilayers. In addition, the thermal stability of the multilayers upon heating for 1 h in vacuum and ambient atmospheres at 500 deg. C has been studied by AES depth profiling. The results show that whereas the multilayer is stable in vacuum it undergoes significant changes when it is heated in air. In fact, it is shown that annealing in air for 1 h causes the disappearance of the CN top layer and the oxidation of the TiCN layer that leads to the formation of TiO{sub 2} on its surface.

  6. Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples

    PubMed Central

    Renault, Marie; Shintu, Laetitia; Piotto, Martial; Caldarelli, Stefano

    2013-01-01

    High-Resolution Magic-Angle Spinning (HR-MAS) NMR spectroscopy has become an extremely versatile analytical tool to study heterogeneous systems endowed with liquid-like dynamics. Spinning frequencies of several kHz are however required to obtain NMR spectra, devoid of spinning sidebands, with a resolution approaching that of purely isotropic liquid samples. An important limitation of the method is the large centrifugal forces that can damage the structure of the sample. In this communication, we show that optimizing the sample preparation, particularly avoiding air bubbles, and the geometry of the sample chamber of the HR-MAS rotor leads to high-quality low-sideband NMR spectra even at very moderate spinning frequencies, thus allowing the use of well-established solution-state NMR procedures for the characterization of small and highly dynamic molecules in the most fragile samples, such as live cells and intact tissues. PMID:24284435

  7. Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples

    NASA Astrophysics Data System (ADS)

    Renault, Marie; Shintu, Laetitia; Piotto, Martial; Caldarelli, Stefano

    2013-11-01

    High-Resolution Magic-Angle Spinning (HR-MAS) NMR spectroscopy has become an extremely versatile analytical tool to study heterogeneous systems endowed with liquid-like dynamics. Spinning frequencies of several kHz are however required to obtain NMR spectra, devoid of spinning sidebands, with a resolution approaching that of purely isotropic liquid samples. An important limitation of the method is the large centrifugal forces that can damage the structure of the sample. In this communication, we show that optimizing the sample preparation, particularly avoiding air bubbles, and the geometry of the sample chamber of the HR-MAS rotor leads to high-quality low-sideband NMR spectra even at very moderate spinning frequencies, thus allowing the use of well-established solution-state NMR procedures for the characterization of small and highly dynamic molecules in the most fragile samples, such as live cells and intact tissues.

  8. Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples.

    PubMed

    Renault, Marie; Shintu, Laetitia; Piotto, Martial; Caldarelli, Stefano

    2013-01-01

    High-Resolution Magic-Angle Spinning (HR-MAS) NMR spectroscopy has become an extremely versatile analytical tool to study heterogeneous systems endowed with liquid-like dynamics. Spinning frequencies of several kHz are however required to obtain NMR spectra, devoid of spinning sidebands, with a resolution approaching that of purely isotropic liquid samples. An important limitation of the method is the large centrifugal forces that can damage the structure of the sample. In this communication, we show that optimizing the sample preparation, particularly avoiding air bubbles, and the geometry of the sample chamber of the HR-MAS rotor leads to high-quality low-sideband NMR spectra even at very moderate spinning frequencies, thus allowing the use of well-established solution-state NMR procedures for the characterization of small and highly dynamic molecules in the most fragile samples, such as live cells and intact tissues. PMID:24284435

  9. Correlative Instrumental Neutron Activation Analysis, Light Microscopy, Transmission Electron Microscopy, and X-ray Microanalysis for Qualitative and Quantitative Detection of Colloidal Gold Spheres in Biological Specimens

    NASA Astrophysics Data System (ADS)

    Hillyer, Julián F.; Albrecht, Ralph M.

    1998-10-01

    : Colloidal gold, conjugated to ligands or antibodies, is routinely used as a label for the detection of cell structures by light (LM) and electron microscopy (EM). To date, several methods to count the number of colloidal gold labels have been employed with limited success. Instrumental neutron activation analysis (INAA), a physical method for the analysis of the elemental composition of materials, can be used to provide a quantitative index of gold accumulation in bulk specimens. Given that gold is not naturally found in biological specimens in any substantial amount and that colloidal gold and ligand conjugates can be prepared to yield uniform bead sizes, the amount of label can be calculated in bulk biological samples by INAA. Here we describe the use of INAA, LM, transmission EM, and X-ray microanalysis (EDX) in a model to determine both distribution (localization) and amount of colloidal gold at the organ, tissue, cellular, and ultrastructural levels in whole animal systems following administration. In addition, the sensitivity for gold in biological specimens by INAA is compared with that of inductively coupled plasma mass spectrometry (ICP-MS). The correlative use of INAA, LM, TEM, and EDX can be useful, for example, in the quantitative and qualitative tracking of various labeled molecular species following administration in vivo.

  10. Atomic emission stratigraphy by laser-induced plasma spectroscopy: Quantitative depth profiling of metal thin film systems

    NASA Astrophysics Data System (ADS)

    Nagy, Tristan O.; Pacher, Ulrich; Pöhl, Hannes; Kautek, Wolfgang

    2014-05-01

    Laser-induced plasma spectroscopy (LIPS) with a frequency-quadrupled Nd:YAG laser (266 nm, pulse duration: 4 ns) was applied to a metallic layer system consisting of an electrodeposited copper layer (30 ?m) on an aluminium substrate. A stratigraphic model describing the emission signal in dependence of the pulse number was developed, which can explain several effects originating from laser ablation of various thin top layers by means of the Gaussian beam cross section character. This model was applied to trace elements through layers with thicknesses that are in the range of the resolvable depth, given by the single-pulse ablation rate, by means of empirical fitting functions. Additionally, the contribution of redeposited bulk material to the characteristic shape of emission-traces when averaging spot arrays with varying spacing could be quantified. This can be used to estimate cross-contamination in analytical applications where ablations need to be performed at close spacing.

  11. The Araucaria Project: the Local Group Galaxy WLM--Distance and metallicity from quantitative spectroscopy of blue Supergiants

    E-print Network

    M. A. Urbaneja; R. -P. Kudritzki; F. Bresolin; N. Przybilla; W. Gieren; G. Pietrzynski

    2008-05-22

    The quantitative analysis of low resolution spectra of A and B supergiants is used to determine a distance modulus of 24.99 +/- 0.10 mag (995 +/- 46 Kpc) to the Local Group galaxy WLM. The analysis yields stellar effective temperatures and gravities, which provide a distance through the Flux weighted Gravity--Luminosity Relationship (FGLR). Our distance is 0.07 mag larger than the most recent results based on Cepheids and the tip of the RGB. This difference is within the 1-sigma overlap of the typical uncertainties quoted in these photometric investigations. In addition, non-LTE spectral synthesis of the rich metal line spectra (mostly iron, chromium and titanium) of the A supergiants is carried out, which allows the determination of stellar metallicities. An average metallicity of -0.87 +/- 0.06 dex with respect to solar metallicity is found.

  12. Direct Quantitation and Detection of Salmonellae in Biological Samples without Enrichment, Using Two-Step Filtration and Real-Time PCR

    PubMed Central

    Wolffs, Petra F. G; Glencross, Kari; Thibaudeau, Romain; Griffiths, Mansel W.

    2006-01-01

    A new two-step filtration protocol followed by a real-time PCR assay based on SYBR green I detection was developed to directly quantitate salmonellae in two types of biological samples: i.e., chicken rinse and spent irrigation water. Four prefiltration filters, one type of final filter, and six protocols for recovery of salmonellae from the final filter were evaluated to identify an effective filtration protocol. This method was then combined with a real-time PCR assay based on detection of the invA gene. The best results were obtained by subsequent filtration of 100 ml of chicken rinse or 100 ml of spent irrigation water through filters with pore diameters of >40 ?m to remove large particles and of 0.22 ?m to recover the Salmonella cells. After this, the Salmonella cells were removed from the filter by vortexing in 1 ml of physiological saline, and this sample was then subjected to real-time quantitative PCR. The whole procedure could be completed within 3 h from sampling to quantitation, and cell numbers as low as 7.5 × 102 CFU per 100-ml sample could be quantified. Below this limit, qualitative detection of concentrations as low as 2.2 CFU/100 ml sample was possible on occasion. This study has contributed to the development of a simple, rapid, and reliable method for quantitation of salmonellae in food without the need for sample enrichment or DNA extraction. PMID:16751494

  13. A Novel HPLC Method for the Concurrent Analysis and Quantitation of Seven Water-Soluble Vitamins in Biological Fluids (Plasma and Urine): A Validation Study and Application

    PubMed Central

    Grotzkyj Giorgi, Margherita; Howland, Kevin; Martin, Colin; Bonner, Adrian B.

    2012-01-01

    An HPLC method was developed and validated for the concurrent detection and quantitation of seven water-soluble vitamins (C, B1, B2, B5, B6, B9, B12) in biological matrices (plasma and urine). Separation was achieved at 30°C on a reversed-phase C18-A column using combined isocratic and linear gradient elution with a mobile phase consisting of 0.01% TFA aqueous and 100% methanol. Total run time was 35 minutes. Detection was performed with diode array set at 280 nm. Each vitamin was quantitatively determined at its maximum wavelength. Spectral comparison was used for peak identification in real samples (24 plasma and urine samples from abstinent alcohol-dependent males). Interday and intraday precision were <4% and <7%, respectively, for all vitamins. Recovery percentages ranged from 93% to 100%. PMID:22536136

  14. A novel HPLC method for the concurrent analysis and quantitation of seven water-soluble vitamins in biological fluids (plasma and urine): a validation study and application.

    PubMed

    Giorgi, Margherita Grotzkyj; Howland, Kevin; Martin, Colin; Bonner, Adrian B

    2012-01-01

    An HPLC method was developed and validated for the concurrent detection and quantitation of seven water-soluble vitamins (C, B(1), B(2), B(5), B(6), B(9), B(12)) in biological matrices (plasma and urine). Separation was achieved at 30°C on a reversed-phase C18-A column using combined isocratic and linear gradient elution with a mobile phase consisting of 0.01% TFA aqueous and 100% methanol. Total run time was 35 minutes. Detection was performed with diode array set at 280 nm. Each vitamin was quantitatively determined at its maximum wavelength. Spectral comparison was used for peak identification in real samples (24 plasma and urine samples from abstinent alcohol-dependent males). Interday and intraday precision were <4% and <7%, respectively, for all vitamins. Recovery percentages ranged from 93% to 100%. PMID:22536136

  15. 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.

  16. Sensing Lanthanide Metal Content in Biological Tissues with Magnetic Resonance Spectroscopy

    PubMed Central

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

    2013-01-01

    The development and validation of MRI contrast agents consisting of a lanthanide chelate often requires a determination of the concentration of the agent in ex vivo tissue. We have developed a protocol that uses 70% nitric acid to completely digest tissue samples that contain Gd(III), Dy(III), Tm(III), Eu(III), or Yb(III) ions, or the MRI contrast agent gadodiamide. NMR spectroscopy of coaxial tubes containing a digested sample and a separate control solution of nitric acid was used to rapidly and easily measure the bulk magnetic susceptibility (BMS) shift caused by each lanthanide ion and gadodiamide. Each BMS shift was shown to be linearly correlated with the concentration of each lanthanide ion and gadodiamide in the 70% nitric acid solution and in digested rat kidney and liver tissues. These concentration measurements had outstanding precision, and also had good accuracy for concentrations ?10 mM for Tm(III) Eu(III), and Yb(III), and ?3 mM for Gd(III), gadodiamide, and Dy(III). Improved sample handling methods are needed to improve measurement accuracy for samples with lower concentrations. PMID:24152931

  17. [Visible and near infrared spectroscopy combined with recursive variable selection to quantitatively determine soil total nitrogen and organic matter].

    PubMed

    Jia, Sheng-yao; Tang, Xu; Yang, Xiang-long; Li, Guang; Zhang, Jian-ming

    2014-08-01

    In the present work, recursive variable selection methods (updating both the model coefficients and effective variables during the prediction process) were applied to maintain the predictive abilities of calibration models. This work compared the performances of partial least squares (PLS), recursive PLS (RPLS) and three recursive variable selection methods, namely vari- able importance in the projection combined with RPLS (VIP-RPLS), VIP-PLS, and uninformative variable elimination combined with PLS (UVE-PLS) for the measurement of soil total nitrogen (TN) and organic matter (OM) using Vis-NIR spectroscopy. The dataset consisted of 195 soil samples collected from eight towns in Wencheng County, Zhejiang Province, China. The entire data set was split randomly into calibration set and prediction set. The calibration set was composed of 120 samples, while the prediction set included 75 samples. The best prediction results were obtained by the VIP-RPLS model. The coefficient of determination (R2) and residual prediction deviation (RPD) were respectively 0.85, 0.86 and 2.6%, 2.7% for soil TN and OM. The results indicate that VIP-RPLS is able to capture the effective information from the latest modeling sample by recursively updating the effective variables. The proposed method VIP-RPLS has the advantages of better performance for Vis-NIR prediction of soil N and OM compared with other methods in this work. PMID:25508715

  18. [Visible and near infrared spectroscopy combined with recursive variable selection to quantitatively determine soil total nitrogen and organic matter].

    PubMed

    Jia, Sheng-yao; Tang, Xu; Yang, Xiang-long; Li, Guang; Zhang, Jian-ming

    2014-08-01

    In the present work, recursive variable selection methods (updating both the model coefficients and effective variables during the prediction process) were applied to maintain the predictive abilities of calibration models. This work compared the performances of partial least squares (PLS), recursive PLS (RPLS) and three recursive variable selection methods, namely vari- able importance in the projection combined with RPLS (VIP-RPLS), VIP-PLS, and uninformative variable elimination combined with PLS (UVE-PLS) for the measurement of soil total nitrogen (TN) and organic matter (OM) using Vis-NIR spectroscopy. The dataset consisted of 195 soil samples collected from eight towns in Wencheng County, Zhejiang Province, China. The entire data set was split randomly into calibration set and prediction set. The calibration set was composed of 120 samples, while the prediction set included 75 samples. The best prediction results were obtained by the VIP-RPLS model. The coefficient of determination (R2) and residual prediction deviation (RPD) were respectively 0.85, 0.86 and 2.6%, 2.7% for soil TN and OM. The results indicate that VIP-RPLS is able to capture the effective information from the latest modeling sample by recursively updating the effective variables. The proposed method VIP-RPLS has the advantages of better performance for Vis-NIR prediction of soil N and OM compared with other methods in this work. PMID:25474936

  19. Influence of data preprocessing on the quantitative determination of nutrient content in poultry manure by near infrared spectroscopy.

    PubMed

    Chen, L J; Xing, L; Han, L J

    2010-01-01

    With increasing concern over potential polltion from farm wastes, there is a need for rapid and robust methods that can analyze livestock manure nutrient content. The near infrared spectroscopy (NIRS) method was used to determine nutrient content in diverse poultry manure samples (n=91). Various standard preprocessing methods (derivatives, multiplicative scatter correction, Savitsky-Golay smoothing, and standard normal variate) were applied to reduce data systemic noise. In addition, a new preprocessing method known as direct orthogonal signal correction (DOSC) was tested. Calibration models for ammonium nitrogen, total potassium, total nitrogen, and total phosphorus were developed with the partial least squares (PLS) method. The results showed that all the preprocessed data improved prediction results compared with the non-preprocessing method. Compared with the other preprocessing methods, the DOSC method gave the best results. The DOSC method achieved moderately successful prediction for ammonium nitrogen, total nitrogen, and total phosphorus. However, all preprocessing methods did not provide reliable prediction for total potassium. This indicates the DOSC method, especially combined with other preprocessing methods, needs further study to allow a more complete predictive analysis of manure nutrient content. PMID:21043290

  20. Quantitative analysis of toxic metals lead and cadmium in water jet by laser-induced breakdown spectroscopy

    SciTech Connect

    Cheri, M. Sadegh; Tavassoli, S. H.

    2011-03-20

    Laser-induced breakdown spectroscopy (LIBS) has been applied to the analysis of toxic metals Pb and Cd in Pb(NO{sub 3}){sub 2} and Cd(NO{sub 3}){sub 2}.4H{sub 2}O aqueous solutions, respectively. The plasma is generated by focusing a nanosecond Nd:YAG ({lambda}=1064 nm) laser on the surface of liquid in the homemade liquid jet configuration. With an assumption of local thermodynamic equilibrium (LTE), calibration curves of Pb and Cd were obtained at different delay times between 1 to 5 {mu}s. The temporal behavior of limit of detections (LOD) was investigated and it is shown that the minimum LODs for Pb and Cd are 4 and 68 parts in 10{sup 6} (ppm), respectively. In order to demonstrate the correctness of the LTE assumption, plasma parameters including plasma temperature and electron density are evaluated, and it is shown that the LTE condition is satisfied at all delay times.

  1. Quantitative analysis of biological membrane lipids at the low picomole level by nano-electrospray ionization tandem mass?spectrometry

    PubMed Central

    Brügger, B.; Erben, G.; Sandhoff, R.; Wieland, F. T.; Lehmann, W. D.

    1997-01-01

    Nano-electrospray tandem mass spectrometry allows qualitative and quantitative analysis of complex membrane lipid mixtures at the subpicomole level. We have exploited this technique to selectively detect individual classes of phospholipids from unprocessed total cellular lipid extracts by either precursor ion or neutral loss scanning. This way phosphatidylcholine, sphingomyelin, phosphatidylinositol and -phosphates, phosphatidylethanolamine, phosphatidylserine, phosphatidylglycerol, phosphatidic acid, and their plasmalogen analogues can be detected. The optimized ionization and fragmentation conditions described together with the principle of internal standardization by nonnatural analogues allow the rapid and quantitative determination of membrane lipid compositions down to sample amounts of 1000 cells. PMID:9122196

  2. Brain Volume and Metabolism in Fetuses with Congenital Heart Disease: Evaluation with Quantitative Magnetic Resonance Imaging and Spectroscopy

    PubMed Central

    Limperopoulos, Catherine; Tworetzky, Wayne; McElhinney, Doff B.; Newburger, Jane W.; Brown, David W.; Robertson, Richard L.; Guizard, Nicolas; McGrath, Ellen; Geva, Judith; Annese, David; Dunbar-Masterson, Carolyn; Trainor, Bethany; Laussen, Peter C.; du Plessis, Adré J.

    2010-01-01

    Background Adverse neurodevelopmental outcome is an important source of morbidity in children with congenital heart disease (CHD). A significant proportion of newborns with complex CHD have abnormalities of brain size, structure, and/or function, suggesting that antenatal factors may contribute to childhood neurodevelopmental morbidity. Methods and Results Brain volume and metabolism were compared prospectively between 55 fetuses with CHD and 50 normal fetuses using 3-D volumetric magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (1H-MRS). Fetal intracranial cavity (ICV), cerebrospinal fluid, and total brain volumes (TBV) were measured by manual segmentation. 1H-MRS was used to measure the cerebral N-acetyl aspartate:choline ratio (NAA:Cho) and identify cerebral lactate. Complete fetal echocardiograms were performed. Gestational age (GA) at MRI ranged from 25 1/7 to 37 1/7 weeks (median 30 weeks). During the third trimester, there were progressive and significant declines in GA-adjusted TBV and ICV in CHD fetuses relative to controls. NAA:Cho increased progressively over the third trimester in normal fetuses, but the rate of rise was significantly slower (p<0.001) in CHD fetuses. On multivariable analysis adjusting for GA and weight percentile, cardiac diagnosis and percentage of combined ventricular output through the aortic valve were independently associated with TBV. Independent predictors of lower NAA:Cho included diagnosis, absence of antegrade aortic arch flow, and evidence of cerebral lactate (p<0.001). Conclusions Third-trimester fetuses with some forms of CHD have smaller GA- and weight-adjusted TBV than normal fetuses, and evidence of impaired neuroaxonal development and metabolism. Hemodynamic factors may play an important role in this abnormal development. PMID:20026783

  3. Quantitative proton magnetic resonance spectroscopy detects abnormalities in dorsolateral prefrontal cortex and motor cortex of patients with frontotemporal lobar degeneration

    PubMed Central

    Chawla, Sanjeev; Wang, Sumei; Moore, Peachie; Woo, John H.; Elman, Lauren; McCluskey, Leo F.; Melhem, Elias R.; Grossman, Murray

    2010-01-01

    Frontotemporal lobar degeneration (FTLD) is a neurodegenerative disease of the frontal and temporal neocortex. The single most common pathology underlying FTLD is neuronal degeneration with ubiquitin-positive but tau-negative inclusions consisting of Tar DNA binding proteins (TDP-43). Inclusions containing TDP-43 in neurons are also the most common pathology underlying motor neuron disease (MND). The present study tested the hypothesis that abnormal metabolite patterns within the dorsolateral prefrontal cortex (DLPFC) as well as the motor cortex (MC) may be observed in FTLD patients without motor disorders, using proton magnetic resonance spectroscopy (1H MRS). Twenty-six FTLD patients with cognitive damage and ten controls underwent multivoxel 1H MRS. Absolute concentrations of N-acetyl aspartate (NAA), creatine (Cr), choline (Cho) and myo-inositol (mI) were measured from the DLPFC, the MC and the parietal cortex (PC, an internal control). Statistical analyses were performed for group differences between FTLD patients and controls. Comparisons were also made across brain regions (PC and DLPFC; PC and MC) within FTLD patients. Significant reductions in NAA and Cr along with increased Cho and mI were observed in the DLPFC of FTLD patients compared to controls. Significantly lower NAA and higher Cho were also observed in the MCs of patients as compared to controls. Within the FTLD patients, both the MC and the DLPFC exhibited significantly decreased NAA and elevated Cho compared to the PC. However, only the DLPFC had significantly lower Cr and higher mI. Abnormal metabolite pattern from the MC supports the hypothesis that FTLD and MND may be closely linked. PMID:19688233

  4. A quantitative study of bioenergetics in skeletal muscle lacking carbonic anhydrase III using 31P magnetic resonance spectroscopy

    PubMed Central

    Liu, M.; Walter, G. A.; Pathare, N. C.; Forster, R. E.; Vandenborne, K.

    2007-01-01

    Oxidative slow skeletal muscle contains carbonic anhydrase III in high concentration, but its primary function remains unknown. To determine whether its lack handicaps energy metabolism and/or acid elimination, we measured the intracellular pH and energy phosphates by 31P magnetic resonance spectroscopy in hind limb muscles of wild-type and CA III knockout mice during and after ischemia and intense exercise (electrical stimulation). Thirty minutes of ischemia caused phosphocreatine (PCr) to fall and Pi to rise while pH and ATP remained constant in both strains of mice. PCr and Pi kinetics during ischemia and recovery were not significantly different between the two genotypes. From this we conclude that under neutral pH conditions resting muscle anaerobic metabolism, the rate of the creatine kinase reaction, intracellular buffering of protons, and phosphorylation of creatine by mitochondrial oxygen metabolism are not influenced by the lack of CA III. Two minutes of intense stimulation of the mouse gastrocnemius caused PCr, ATP, and pH to fall and ADP and Pi to rise, and these changes, with the exception of ATP, were all significantly larger in the CA III knockouts. The rate of return of pH and ADP to control values was the same in wild-type and mutant mice, but in the mutants PCr and Pi recovery were delayed in the first minute after stimulation. Because the tension decrease during fatigue is known to be the same in the two genotypes, we conclude that a lack of CA III impairs mitochondrial ATP synthesis. PMID:17182736

  5. Early metabolic development of posteromedial cortex and thalamus in humans analyzed via in vivo quantitative magnetic resonance spectroscopy.

    PubMed

    Degnan, Andrew J; Ceschin, Rafael; Lee, Vince; Schmithorst, Vincent J; Blüml, Stefan; Panigrahy, Ashok

    2014-11-01

    The posteromedial cortex (PMC) including the posterior cingulate, retrosplenial cortex, and medial parietal cortex/precuneus is an epicenter of cortical interactions in a wide spectrum of neural activity. Anatomic connections between PMC and thalamic components have been established in animal studies, but similar studies do not exist for the fetal and neonatal period. Magnetic resonance spectroscopy (MRS) allows for noninvasive measurement of metabolites in early development. Using single-voxel 3-T MRS, healthy term neonates (n?=?31, mean postconception age 41.5 weeks?±?3.8 weeks) were compared with control children (n?=?23, mean age 9.4 years?±?5.1 years) and young adults (n?=?10, mean age 24.1 years?±?2.6 years). LCModel-based calculations compared metabolites within medial parietal gray matter (colocalizing to the PMC), posterior thalamus, and parietal white matter voxels. Common metabolic changes existed for neuronal-axonal maturation and structural markers in the PMC, thalamus, and parietal white matter with increasing NAA and glutamate and decreasing myoinositol and choline with age. Key differences in creatine and glucose metabolism were noted in the PMC, in contrast to the thalamic and parietal white matter locations, suggesting a unique role of energy metabolism. Significant parallel metabolite developmental changes of multiple other metabolites including aspartate, glutamine, and glutathione with age were present between PMC and parietal white matter but not between PMC and thalamus. These findings offer insight into the metabolic architecture of the interface between structural and functional topology of brain networks. Further investigation unifying metabolic changes with functional and anatomic pathways may further enhance the understanding of the PMC in posterior default mode network development. PMID:24888973

  6. Quantitative X-ray photoelectron spectroscopy-based depth profiling of bioleached arsenopyrite surface by Acidithiobacillus ferrooxidans

    NASA Astrophysics Data System (ADS)

    Zhu, Tingting; Lu, Xiancai; Liu, Huan; Li, Juan; Zhu, Xiangyu; Lu, Jianjun; Wang, Rucheng

    2014-02-01

    In supergene environments, microbial activities significantly enhance sulfide oxidation and result in the release of heavy metals, causing serious contamination of soils and waters. As the most commonly encountered arsenic mineral in nature, arsenopyrite (FeAsS) accounts for arsenic contaminants in various environments. In order to investigate the geochemical behavior of arsenic during microbial oxidation of arsenopyrite, (2 3 0) surfaces of arsenopyrite slices were characterized after acidic (pH 2.00) and oxidative decomposition with or without an acidophilic microorganism Acidithiobacillus ferrooxidans. The morphology as well as chemical and elemental depth profiles of the oxidized arsenopyrite surface were investigated by scanning electron microscopy and X-ray photoelectron spectroscopy. With the mediation of bacteria, cell-shaped and acicular pits were observed on the reacted arsenopyrite surface, and the concentration of released arsenic species in solution was 50 times as high as that of the abiotic reaction after 10 days reaction. Fine-scale XPS depth profiles of the reacted arsenopyrite surfaces after both microbial and abiotic oxidation provided insights into the changes in chemical states of the elements in arsenopyrite surface layers. Within the 450 nm surface layer of abiotically oxidized arsenopyrite, Fe(III)-oxides appeared and gradually increased towards the surface, and detectable sulfite and monovalent arsenic appeared above 50 nm. In comparison, higher contents of ferric sulfate, sulfite, and arsenite were found in the surface layer of approximately 3 ?m of the microbially oxidized arsenopyrite. Intermediates, such as Fe(III)-AsS and S0, were detectable in the presence of bacteria. Changes of oxidative species derived from XPS depth profiles show the oxidation sequence is Fe > As = S in abiotic oxidation, and Fe > S > As in microbial oxidation. Based on these results, a possible reaction path of microbial oxidation was proposed in a concept model.

  7. 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.

  8. 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 C?-C? 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 C?-C? 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 C?-C? 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.

  9. Applications of High Resolution Laser Induced Breakdown Spectroscopy for Environmental and Biological Samples

    SciTech Connect

    Martin, Madhavi Z [ORNL; Labbe, Nicole [ORNL; Wagner, Rebekah J. [Pennsylvania State University, University Park, PA

    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.

  10. An improved method for the identification and quantitation of biological lipids by HPIX: using laser light-scat tering detection

    Microsoft Academic Search

    B. S. Lutzke; J. M. Braughler

    Summary We have developed a simplified and improved high performance liquid chromatography (HPLC) method for the detection and quantitation of tissue lipid using a new laser light-scattering detector (Vara model ELSD 11). This detector has a limit of sensitivity of 50 ng for neutral lipid and 200 ng for most phospholipids with excellent reproducibility. By coupling the ELSD I1 with

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

    Microsoft Academic Search

    J H Marden

    2008-01-01

    Alternative splicing (AS) of pre-messenger RNA is a common phenomenon that creates different transcripts from a single gene, and these alternative transcripts affect phenotypes. The majority of AS research has examined tissue and developmental specificity of expression of particular AS transcripts, how this specificity affects cell function, and how aberrant AS is related to disease. Few studies have examined quantitative

  12. Identification of antibody isotypes in biological fluids by means of micro-Raman spectroscopy and chemometric methods

    NASA Astrophysics Data System (ADS)

    Araujo-Andrade, C.; Pichardo-Molina, J. L.; Barbosa-Sabanero, G.; Frausto-Reyes, C.

    2008-02-01

    Clinical diagnosis of infections, generally are realized by serological methods, which identifies the antibodies presents in serum or tissue fluids of the patient. Antibodies are proteins present in our bodies that aid in the elimination of pathogens or antigens. Identification of antibodies isotypes is important because can help to predict when and whether patients will recover from infections and are commonly diagnosed by means of indirect methods such as serological test. In the other hand, the majority of these methods requires specific kits for the analysis, special sample preparation, chemical reagents, expensive equipment and require long time for getting results. In this work we show the feasibility to discriminate antibody isotypes in biological fluids like human colostrum by means of Raman spectroscopy and chemometrics. Spectra were obtained using an excitation wavelength of 514 nm over dried samples of human colostrum labeled previously as positives to specific IgG and IgM antibodies against Toxoplasma Gondii by means of ELISA test. Partial least square-discriminant analysis (PLS-DA) was used to discriminate among antibody isotypes by use second derivative of Raman spectra of colostrum samples.

  13. Sensitivity of coded aperture Raman spectroscopy to analytes beneath turbid biological tissue and tissue-simulating phantoms

    NASA Astrophysics Data System (ADS)

    Maher, Jason R.; Matthews, Thomas E.; Reid, Ashley K.; Katz, David F.; Wax, Adam

    2014-11-01

    Traditional slit-based spectrometers have an inherent trade-off between spectral resolution and throughput that can limit their performance when measuring diffuse sources such as light returned from highly scattering biological tissue. Recently, multielement fiber bundles have been used to effectively measure diffuse sources, e.g., in the field of spatially offset Raman spectroscopy, by remapping the source (or some region of the source) into a slit shape for delivery to the spectrometer. Another approach is to change the nature of the instrument by using a coded entrance aperture, which can increase throughput without sacrificing spectral resolution. In this study, two spectrometers, one with a slit-based entrance aperture and the other with a coded aperture, were used to measure Raman spectra of an analyte as a function of the optical properties of an overlying scattering medium. Power-law fits reveal that the analyte signal is approximately proportional to the number of transport mean free paths of the scattering medium raised to a power of -0.47 (coded aperture instrument) or -1.09 (slit-based instrument). These results demonstrate that the attenuation in signal intensity is more pronounced for the slit-based instrument and highlight the scattering regimes where coded aperture instruments can provide an advantage over traditional slit-based spectrometers.

  14. Evaluation of a multi-electrode bioimpedance spectroscopy tensor probe to detect the anisotropic conductivity spectra of biological tissues

    NASA Astrophysics Data System (ADS)

    Karki, Bishal; Wi, Hun; McEwan, Alistair; Kwon, Hyeuknam; In Oh, Tong; Woo, Eung Je; Seo, Jin Keun

    2014-07-01

    This paper presents bioimpedance spectroscopy measurements of anisotropic tissues using a 16 electrode probe and reconstruction method of estimating the anisotropic impedance spectrum in a local region just underneath the center of the probe. This may enable in-vivo surface bioimpedance measurements with similar performance to the ex-vivo gold standard that requires excising and placing the entire tissue sample in a unit measurement cell with uniform electric field. The multiple surface electrodes enable us to create a focused current pattern so that the resulting measured voltage is more sensitive to a local region and less sensitive to other areas. This is exploited in a reconstruction method to provide improved bioimpedance and anisotropy measurements. In this paper, we describe the current pattern for localized electrical energy concentration, performance with the spring loaded pin electrodes, data calibration and experimental results on anisotropic agar phantoms and different tissue types. The anisotropic conductivity spectra are able to differentiate insulating films of different thickness and detect their orientation. Bioimpedance spectra of biological tissues are in agreement with published data and reference instruments. The anisotropy expressed as the ratio of eigenvalues and the orientation of eigenfunctions were reconstructed at 45° intervals. This information is used to predict the underlying anisotropy of the region under the probe. Tissue measurements clearly demonstrate the expected higher anisotropy of muscle tissue compared to liver tissue and spectral changes.

  15. Microscopic emission and reflectance thermal infrared spectroscopy: instrumentation for quantitative in situ mineralogy of complex planetary surfaces.

    PubMed

    Edwards, C S; Christensen, P R

    2013-04-10

    The diversity of investigations of planetary surfaces, especially Mars, using in situ instrumentation over the last decade is unprecedented in the exploration history of our solar system. The style of instrumentation that landed spacecraft can support is dependent on several parameters, including mass, power consumption, instrument complexity, cost, and desired measurement type (e.g., chemistry, mineralogy, petrology, morphology, etc.), all of which must be evaluated when deciding an appropriate spacecraft payload. We present a laboratory technique for a microscopic emission and reflectance spectrometer for the analysis of martian analog materials as a strong candidate for the next generation of in situ instruments designed to definitively assess sample mineralogy and petrology while preserving geologic context. We discuss the instrument capabilities, signal and noise, and overall system performance. We evaluate the ability of this instrument to quantitatively determine sample mineralogy, including bulk mineral abundances. This capability is greatly enhanced. Whereas the number of mineral components observed from existing emission spectrometers is high (often >5 to 10 depending on the number of accessory and alteration phases present), the number of mineral components at any microscopic measurement spot is low (typically <2 to 3). Since this style of instrument is based on a long heritage of thermal infrared emission spectrometers sent to orbit (the thermal emission spectrometer), sent to planetary surfaces [the mini-thermal emission spectrometers (mini-TES)], and evaluated in laboratory environments (e.g., the Arizona State University emission spectrometer laboratory), direct comparisons to existing data are uniquely possible with this style of instrument. The ability to obtain bulk mineralogy and atmospheric data, much in the same manner as the mini-TESs, is of significant additional value and maintains the long history of atmospheric monitoring for Mars. Miniaturization of this instrument has also been demonstrated, as the same microscope objective has been mounted to a flight-spare mini-TES. Further miniaturization of this instrument is straightforward with modern electronics, and the development of this instrument as an arm-mounted device is the end goal. PMID:23670748

  16. A meta-classifier for detecting prostate cancer by quantitative integration of in vivo magnetic resonance spectroscopy and magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Viswanath, Satish; Tiwari, Pallavi; Rosen, Mark; Madabhushi, Anant

    2008-03-01

    Recently, in vivo Magnetic Resonance Imaging (MRI) and Magnetic Resonance Spectroscopy (MRS) have emerged as promising new modalities to aid in prostate cancer (CaP) detection. MRI provides anatomic and structural information of the prostate while MRS provides functional data pertaining to biochemical concentrations of metabolites such as creatine, choline and citrate. We have previously presented a hierarchical clustering scheme for CaP detection on in vivo prostate MRS and have recently developed a computer-aided method for CaP detection on in vivo prostate MRI. In this paper we present a novel scheme to develop a meta-classifier to detect CaP in vivo via quantitative integration of multimodal prostate MRS and MRI by use of non-linear dimensionality reduction (NLDR) methods including spectral clustering and locally linear embedding (LLE). Quantitative integration of multimodal image data (MRI and PET) involves the concatenation of image intensities following image registration. However multimodal data integration is non-trivial when the individual modalities include spectral and image intensity data. We propose a data combination solution wherein we project the feature spaces (image intensities and spectral data) associated with each of the modalities into a lower dimensional embedding space via NLDR. NLDR methods preserve the relationships between the objects in the original high dimensional space when projecting them into the reduced low dimensional space. Since the original spectral and image intensity data are divorced from their original physical meaning in the reduced dimensional space, data at the same spatial location can be integrated by concatenating the respective embedding vectors. Unsupervised consensus clustering is then used to partition objects into different classes in the combined MRS and MRI embedding space. Quantitative results of our multimodal computer-aided diagnosis scheme on 16 sets of patient data obtained from the ACRIN trial, for which corresponding histological ground truth for spatial extent of CaP is known, show a marginally higher sensitivity, specificity, and positive predictive value compared to corresponding CAD results with the individual modalities.

  17. I. Analysis of biological specimens by proton-induced x-ray emission spectroscopy (PIXE). II. Separation and purity of C{sub 60} and C{sub 70}

    SciTech Connect

    Lowe, T.P.

    1993-12-31

    This report outlines work done on the optimization of instrumental parameters and sample preparation for the analysis of biological tissue. The analysis of biological samples by PIXE provides information on interelemental interactions in tissue and body fluids. A computer program for spectrum processes and quantitation, which decomposes overlapped peaks, corrects for thick target matrix effects and calculates results without resorting to the use of standards, is explored. In part II of this dissertation, a convenient method of removing solvent from a benzene extract of graphite soot containing fullerenes using sublimation, is outlined. Separation of macroscopic quantities of the fullerenes C{sub 60} and C{sub 70} has been accomplished using a combination of selective precipitation of C{sub 60} and chromatography. C{sub 60} is selectively crystallized freezing and thawing a benzene solution of mixed fullerenes, then using the C{sub 70} enriched supernatant as starting material in the chromatographic separation of C{sub 60} and C{sub 70}. In the separation scheme, a bed of modified silica sorbent is charged with the fullerene mixture and the fullerenes are eluted using a hexanes/THF mobile phase. The methods of UV-Visible and infrared spectroscopy, as well as high performance liquid chromatography (HPLC) are evaluated for their ability to determine the purity of a C{sub 60} or C{sub 70} sample.

  18. Quantitative surface plasmon resonance spectroscopy as a probe of adsorption, diffusion, and self-assembly of biopolymers and oligonucleotides at interfaces

    NASA Astrophysics Data System (ADS)

    Georgiadis, Rosina M.; Peterlinz, Kevin A.

    1998-04-01

    In situ surface plasmon resonance (SPR) spectroscopy methods are used to investigate the process by which thin films form at solid/solutions interfaces. Representative kinetics data are presented for the adsorption of two different types of molecular adsorbates onto gold substrates. The first system involves adsorption of alginic acid, an acidic polysaccharide. The second system involves the adsorption of single-stranded DNA oligomers. Quantitative two-color SPR kinetics data are of sufficiently high quality that distinguishing between various kinetics models is now possible. Commonly used Langmuir adsorption models cannot adequately describe some of the adsorption kinetics data. However, these data are very well described by a model developed to include diffusion at the interface as well as adsorption/description. This more general model is found to work very well for a variety of chemically distinct adsorbate/substrate systems. Analysis of high quality in- situ SPR data can identify distinct differences in kinetics and many be useful for distinguishing between different types of adsorbate/surface interactions. This capability may prove very useful for gaining insight into mechanistic differences in the process by which molecular films at solid/liquid interfaces.

  19. Quantitative analyses of oxidation states for cubic SrMnO3 and orthorhombic SrMnO2.5 with electron energy loss spectroscopy

    NASA Astrophysics Data System (ADS)

    Kobayashi, S.; Tokuda, Y.; Mizoguchi, T.; Shibata, N.; Sato, Y.; Ikuhara, Y.; Yamamoto, T.

    2010-12-01

    The oxidation state of Mn in cubic SrMnO3 and orthorhombic SrMnO2.5 was investigated by electron energy loss (EEL) spectroscopy. Change in the oxidation state of Mn produced some spectral changes in the O-K edge as well as in the Mn-L2,3 edge EEL spectra. This study demonstrated that the oxidation state of Mn and the amount of oxygen vacancies in cubic SrMnO3 and orthorhombic SrMnO2.5 could be quantified by analyzing the features of the O-K edge spectrum and the Mn L3/L2 ratio in the Mn-L2,3 edge spectrum. Our quantitative analysis showed that the spectral changes in the Mn-L2,3 edge were mainly caused by the oxidation state of Mn, whereas those in the O-K edge could be sensitive to both the oxidation state of Mn and to lattice distortions.

  20. Laser-Induced Breakdown Spectroscopy: A Novel Technology for the Rapid Detection, Identification, and Discrimination of Biological Agents

    E-print Network

    Rehse, Steven J.

    Laser-Induced Breakdown Spectroscopy: A Novel Technology for the Rapid Detection, Identification. Adam, and J. Amouroux, "Detection of bacteria by time-resolved laser-induced breakdown spectroscopy, "Laser-induced breakdown spectroscopy of bacterial spores, molds, pollens, and protein: initial studies

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

    Microsoft Academic Search

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

    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

  2. The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging

    Microsoft Academic Search

    Ilya G Goldberg; Chris Allan; Jean-Marie Burel; Doug Creager; Andrea Falconi; Harry Hochheiser; Josiah Johnston; Jeff Mellen; Peter K Sorger; Jason R Swedlow

    2005-01-01

    The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML)

  3. BIOLOG

    EPA Science Inventory

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

  4. Parallel ?-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: Quantitative benchmark for the interpretation of amyloid and protein infrared spectra

    PubMed Central

    Woys, Ann Marie; Almeida, Aaron M.; Wang, Lu; Chiu, Chi Cheng; McGovern, Michael; de Pablo, Juan J.; Skinner, James L.; Gellman, Samuel H.; Zanni, Martin T.

    2012-01-01

    Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel ?-sheets. Using a synthetic macrocycle that enforces a two stranded parallel ?-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly 13C=18O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequen cies of the labels ranged from 1585 to 1595 cm?1, with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the linewidths and frequencies nearly quantitatively. Historically, the characteristic features of ?-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel ?-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm?1 linewidth. Narrower linewidths indicate that the amide I backbone is solvent protected inside the macrocycle. This work provides calculated and experimentally verified couplings for parallel ?-sheets that can be used in structure-based models to simulate and interpret the infrared spectra of ?-sheet containing proteins and protein assemblies, such as amyloid fibers. PMID:23113791

  5. Quantitative analysis in gas chromatography/low power atmospheric-pressure helium microwave-induced plasma atomic emission interferometry and ion cyclotron resonance mass spectroscopy

    SciTech Connect

    Loo, J.F.

    1990-01-01

    The development of experimental and data analysis techniques for quantitative analysis in gas chromatography/low power atmospheric pressure helium microwave-induced plasma atomic emission interferometry (GC/HeMIPAEI) and ion cyclotron resonance mass spectroscopy (ICR/MS) is presented. A discussion of interferometric data analysis by discrete and fast Fourier transform (DFT and FFT, respectively) is given. Additionally, the use of two techniques (the maximum entropy method, or MEM, and linear prediction, or LP) that have shown to produce results superior to those from the FFT is shown for synthetic and experimental NMR, optical, and mass spectral data. Visual spectral comparisons, performance results as compared to known spectral parameters, and a methodology for the implementation of the linear prediction technique is given. A low-power HeMIP was constructed and used as the excitation source for an AEI detector for gas chromatography. In general, HeMIPs have the advantage of being able to excite non-metal atoms, which comprise a large fraction of the molecules used in typical organic GC analysis. Sensitivity, detection limits, their dependence on microwave power values, and elemental emission ratios are tabulated for a series of test compounds. Results show that elemental emission ratios are independent of the structure of the compound used in this study. Suggestions for further development, from the use of a concentric-flow torch and optical filters to the removal of oxygen through the use of ultra-high purity helium, are presented. Through the use of coherent pulsed excitation, electronic quadrature detection, and data analysis by linear prediction, ICR/MS relative abundance error values for the principal isotopes of krypton have been calculated to be less than 1%.

  6. Application of NIR spectroscopy for the quality control of mangosteen pericarp powder: quantitative analysis of alpha-mangostin in mangosteen pericarp powder and capsule.

    PubMed

    Peerapattana, Jomjai; Otsuka, Kuniko; Otsuka, Makoto

    2013-07-01

    Near-infrared spectroscopy (NIR) was applied to the quantitative analysis of the concentration of alpha-mangostin (aM) in mangosteen pericarp powder (MP). The predicted results from the partial least squares chemometric method of various pretreatment data were compared to obtain the best calibration model. Two different types of containers (transparent capsules and glass vials) filled with the same samples were measured. For MP mixture in vials, the calibration model involving nine principal components (PC) could predict the amount of aM most accurately based on non-pretreatment spectral data. For MP mixture in capsules, the calibration model involving nine PC could predict the amount of aM most accurately based on first-derivative pretreatment spectra. The relationships of the calibration models for both samples had sufficiently linear plots. The standard error of cross-validation for the MP mixture in vials was lower and the R(2) values of validation were higher compared to the MP mixture in capsules. The equation for prediction of the concentration of aM in MP mixtures in vials is y = 0.9775x + 0.0425 with R(2) = 0.9950 and for those in capsules is y = 1.0264x + 0.0126 with R(2) = 0.9898. Both validation results indicated that the concentrations of aM in MP mixtures were predicted with sufficient accuracy and repeatability. NIR can be a useful tool for the quality control of herbal medicine in powder form without any sample preparation. The type and the shape of the container should be considered to obtain more accurate data. PMID:22926311

  7. Listen to photon propagation in biological tissues: quantitative optical scattering imaging and high-resolution diffuse optical tomography using photoacoustic measurements

    NASA Astrophysics Data System (ADS)

    Yuan, Zhen

    2014-03-01

    Biomedical photoacoustic tomography (PAT), as a future imaging modality, can visualize the internal structure and function of soft tissues with high spatial resolution and excellent optical contrast as well as satisfactory imaging depth. A key issue for this unique imaging technique is to recover both the optical absorption and scattering coefficients from the measured acoustic data. Previous attempts in quantitative PAT(qPAT) have been implemented to deduce the map of absorption coefficient from the absorbed energy density using either a model-based method or the invasive measurement techniques when an assumed scattering coefficient is used. However, optical scattering in biological tissue typically dominates over absorption by an order of magnitude or more. Due to this effect it is very challenging to image tissues with highly scattering and accurately recover the absorption coefficient photoacoustically. In this study we propose and validate by experiment tests that quantitative scattering map can be recovered using the measured acoustic data from one-wavelength illumination. The developed reconstruction algorithm relies on PAT and coupled diffusion equation to recover the optical absorption coefficient and energy density, and the diffusion model only to recover the optical scattering coefficients. In particular, this algorithm has the capability to resolve the crosstalk issue in diffuse optical tomography (DOT) and achieve high resolution DOT using acoustics measurements.

  8. Assessment of Technical and Biological Parameters of Volumetric Quantitative Computed Tomography in the Foot: A Phantom Study

    PubMed Central

    Smith, Kirk E.; Whiting, Bruce R.; Reiker, Gregory G.; Commean, Paul K.; Sinacore, David R.; Prior, Fred W.

    2012-01-01

    Few studies exist for bone densitometry of the whole foot. A phantom study demonstrated the sources of error and necessary controls for accurate quantitative computed tomography of the foot. A loss in bone mineral density in the small foot bones may be an early indicator of diabetic foot complications. Purpose Volumetric quantitative computed tomography (vQCT) facilitates assessment of pedal bone osteopenia, which in the presence of peripheral neuropathy may well be an early sign of diabetic foot deformity. To date, sources and magnitudes of error in foot vQCT measurements have not been reported. Methods Foot phantoms were scanned using a 64-slice CT scanner. Energy (kVp), table height, phantom size and orientation, location of “bone” inserts, insert material, location of calibration phantom, and reconstruction kernel were systematically varied during scan acquisition. Results Energy (kVp) and distance from the isocenter (table height) resulted in relative attenuation changes from ?5% to 22% and ?5% to 0%, respectively, and average bone mineral density (BMD) changes from ?0.9% to 0.0% and ?1.1% to 0.3%, respectively, compared to a baseline 120 kVp scan performed at the isocenter. BMD compared to manufacturer specified values ranged on average from ?2.2% to 0.9%. Phantom size and location of bone-equivalent material inserts resulted in relative attenuation changes of ?1.2% to 1.4% compared to the medium sized phantom. Conclusion This study demonstrated that variations in kVp and table height can be controlled using a calibration phantom scanned at the same energy and height as a foot phantom; however, error due to soft tissue thickness and location of bones within a foot cannot be controlled using a calibration phantom alone. PMID:22147208

  9. Fragmentation of peptides with intra-chain disulfide bonds in triple quadrupole mass spectrometry and its quantitative application to biological samples

    NASA Astrophysics Data System (ADS)

    Chen, Yun; Qiao, Shanlei; Wang, Ce

    2009-12-01

    A growing number of peptides are being used today in bioanalytical laboratories. Because of this, there is an increasing interest in the development of highly sensitive, specific and robust liquid chromatography/tandem mass spectrometry (LC/MS/MS) assays for the quantitative analysis of peptides in biological samples. Among the mass spectrometers previously used for peptide quantification, triple quadrupole mass spectrometers are generally not considered the instrument of choice. With this instrumentation, collision cascades or multiple fragmentations tend to generate multiple peaks that have weak intensities. This leads to a loss in detection sensitivity. However, in cases where immonium product ions were formed in abundance, it was found that peptide quantification succeeded. A common feature of these peptides is their intra-loop structure. To elucidate the usefulness of this feature in fragmentation, several peptide analytes with intra-chain disulfide bonds were investigated in this study, including a newly synthesized analog having a single amino acid substitution. The results presented here indicate that abrupt bond cleavage from the intra-loop structure of peptides could be one of the premises for intense immonium ion generation. In contrast, any preferential cleavage of peptide bonds (e.g., proline effect) that gives rise to a linearized sequence would break the intactness of the loop and prevent it from completely dissociating. In addition, the utilization of immonium product ions in LC/MS/MS was demonstrated for the determination of peptides with intra-chain disulfide bonds in biological fluids.

  10. Separation scheme for selective and quantitative isolation of cobalt from neutron-irradiated biological materials by ion exchange and extraction chromatography

    SciTech Connect

    Dybczynski, R.; Danko, B.; Maleszewska, H. [Institute of Nuclear Chemistry and Technology, Warsaw (Poland)

    1994-01-01

    Highly reliable radiochemical separation scheme for selective and quantitative isolation of trace amounts of cobalt from neutron-irradiated biological materials was elaborated. The method consists in wet-ashing of the sample with HNO{sub 3} + HClO{sub 4} (1:1) mixture plus vanadium salt (oxidation catalyst), removal of silica by evaporation with HF and separation of cobalt from accompanying ions successively on 3 columns with Dowex 1-X8[Cl{sup -}] from 0.5 M HCl, Dowex 1-X8[Cl{sup -}] from 8 M HCl + 2 M MgCl{sub 2} and tri-n-octylphosphine oxide (TOPO) supported on styrene-divinylbenzene copolymer, from 7 M HCl solution, respectively. Cobalt of very high radiochemical purity is finally recovered in 1.2 M HCl solution with practically 100% yield. The separation scheme is universally applicable, to biological samples of both animal and plant origin and was devised to become an integral part of the very accurate ({open_quotes}definitive{close_quotes}) method of cobalt determination by neutron activation analysis (NAA). Preliminary results on Co determination by NAA in some certified reference materials confirmed high reliability of the devised separation scheme.

  11. The design and characterization of a testing platform for quantitative evaluation of tread performance on multiple biological substrates.

    PubMed

    Sliker, Levin J; Rentschler, Mark E

    2012-09-01

    In this study, an experimental platform is developed to quantitatively measure the performance of robotic wheel treads in a dynamic environment. The platform imposes a dynamic driving condition for a single robot wheel, where the wheel is rotated on a translating substrate, thereby inducing slip. The normal force of the wheel can be adjusted mechanically, while the rotational velocity of the wheel and the translational velocity of the substrate can be controlled using an open-loop control system. Wheel slip and translational speed can be varied autonomously while wheel traction force is measured using a load cell. The testing platform is characterized by testing one micropatterned polydimethylsiloxane (PDMS) tread on three substrates (dry synthetic tissue, hydrated synthetic tissue, and excised porcine small bowel tissue), at three normal forces (0.10, 0.20, and 0.30 N), 13 slip ratios (-0.30 to 0.30 in increments of 0.05), and three translational speeds (2, 3, and 6 mm/s). Additionally, two wheels (micropatterned and smooth PDMS) are tested on beef liver at the same three normal forces and translational speeds for a tread comparison. An analysis of variance revealed that the platform can detect statistically significant differences between means when observing normal forces, translational speeds, slip ratios, treads, and substrates. The variance due to within (platform error, P = 1) and between trials (human error, P = 0.152) is minimal when compared to the normal force (P = 0.036), translational speed ( P = 0.059), slip ratio (P = 0), tread (P = 0.004), and substrate variances ( P = 0). In conclusion, this precision testing platform can be used to determine wheel tread performance differences on the three substrates and for each of the studied parameters. Future use of the platform could lead to an optimized micropattern-based mobility system, under given operating conditions, for implementation on a robotic capsule endoscope. PMID:22736689

  12. Improving fundamental abilities of atomic force microscopy for investigating quantitative nanoscale physical properties of complex biological systems

    NASA Astrophysics Data System (ADS)

    Cartagena-Rivera, Alexander X.

    Measurements of local material properties of complex biological systems (e.g. live cells and viruses) in their respective physiological conditions are extremely important in the fields of biophysics, nanotechnology, material science, and nanomedicine. Yet, little is known about the structure-function-property relationship of live cells and viruses. In the case of live cells, the measurements of progressive variations in viscoelastic properties in vitro can provide insight to the mechanistic processes underpinning morphogenesis, mechano-transduction, motility, metastasis, and many more fundamental cellular processes. In the case of living viruses, the relationship between capsid structural framework and the role of the DNA molecule interaction within viruses influencing their stiffness, damping and electrostatic properties can shed light in virological processes like protein subunits assembly/dissassembly, maturation, and infection. The study of mechanics of live cells and viruses has been limited in part due to the lack of technology capable of acquiring high-resolution (nanoscale, subcellular) images of its heterogeneous material properties which vary widely depending on origin and physical interaction. The capabilities of the atomic force microscope (AFM) for measuring forces and topography with sub-nm precision have greatly contributed to research related to biophysics and biomechanics during the past two decades. AFM based biomechanical studies have the unique advantage of resolving/mapping spatially the local material properties over living cells and viruses. However, conventional AFM techniques such as force-volume and quasi-static force-distance curves are too low resolution and low speed to resolve interesting biophysical processes such as cytoskeletal dynamics for cells or assembly/dissasembly of viruses. To overcome this bottleneck, a novel atomic force microscopy mode is developed, that leads to sub-10-nm resolution and sub-15-minutes mapping of local material properties of living cells and viruses in their respective physiological conditions. This advance is based on the harnessing of sub and superharmonic channels of cantilever vibration which are especially strong in liquids environments, which enable the mapping with exquisite detail of nanoscale material properties. Material properties such as storage and loss modulus or the spring and damping constant in live cells and the repulsive electrostatic force gradient, hydration layer viscosity and adhesion on viruses. By the use of this multi-harmonic dynamic AFM technique using a commercial AFM system, the local material properties of live rat fibroblast cells (RFB), red blood cells (RBC), human breast carcinoma cells (MDA-MB-231), and bacteriophage ?29 mature virions have been successfully imaged and extracted in relevant physiological conditions. Also, a novel high-speed dynamic AFM technique is developed to image at higher spatiotemporal resolution whole live cells under physiological conditions. This high-throughput technology enables the study of cellular processes in near real time frames, for example, the cytoskeleton structure dynamics of live fibroblast cells and human breast carcinoma cells. Overall, the contributions described in this thesis demonstrate the robustness and versatility of these novel advanced dynamic AFM techniques to investigate a wide range of complex biological relevant problems.

  13. Quantitative molecular methods in virology

    Microsoft Academic Search

    M. Clementi; S. Menzo; A. Manzin; P. Bagnarelli

    1995-01-01

    Summary During the past few years, significant technical effort was made to develop molecular methods for the absolute quantitation of nucleic acids in biological samples. In virology, semi-quantitative and quantitative techniques of different principle, complexity, and reliability were designed, optimized, and applied in basic and clinical researches. The principal data obtained in successful pilot applications in vivo are reported in

  14. Oriented single-crystal nuclear resonance vibrational spectroscopy of [Fe(TPP)(MI)(NO)] : quantitative sssessment of the trans effect of NO.

    SciTech Connect

    Lehnert, N.; Sage, J. T.; Silvernail, N.; Scheidt, W. R.; Alp, E. E.; Sturhahn, W.; Zhao, J. (X-Ray Science Division); (Univ. of Michigan); (Northeastern Univ.); (Univ. of Notre Dame)

    2010-01-01

    This paper presents oriented single-crystal Nuclear Resonance Vibrational Spectroscopy (NRVS) data for the six-coordinate (6C) ferrous heme-nitrosyl model complex [{sup 57}Fe(TPP)(MI)(NO)] (1; TPP{sup 2-} = tetraphenylporphyrin dianion; MI = 1-methylimidazole). The availability of these data enables for the first time the detailed simulation of the complete NRVS data, including the porphyrin-based vibrations, of a 6C ferrous heme-nitrosyl, using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Importantly, the Fe-NO stretch is split by interaction with a porphyrin-based vibration into two features, observed at 437 and 472 cm{sup -1}. The 437 cm{sup -1} feature is strongly out-of-plane (oop) polarized and shows a {sup 15}N{sup 18}O isotope shift of 8 cm{sup -1} and is therefore assigned to v(Fe-NO). The admixture of Fe-N-O bending character is small. Main contributions to the Fe-N-O bend are observed in the 520-580 cm{sup -1} region, distributed over a number of in-plane (ip) polarized porphyrin-based vibrations. The main component, assigned to {delta}{sub ip}(Fe-N-O), is identified with the feature at 563 cm{sup -1}. The Fe-N-O bend also shows strong mixing with the Fe-NO stretching internal coordinate, as evidenced by the oop NRVS intensity in the 520-580 cm{sup -1} region. Very accurate normal mode descriptions of ?(Fe-NO) and {delta}{sub ip}(Fe-N-O) have been obtained in this study. These results contradict previous interpretations of the vibrational spectra of 6C ferrous heme-nitrosyls where the higher energy feature at {approx}550 cm{sup -1} had usually been associated with v(Fe-NO). Furthermore, these results provide key insight into NO binding to ferrous heme active sites in globins and other heme proteins, in particular with respect to (a) the effect of hydrogen bonding to the coordinated NO and (b) changes in heme dynamics upon NO coordination. [Fe(TPP)(MI)(NO)] constitutes an excellent model system for ferrous NO adducts of myoglobin (Mb) mutants where the distal histidine (His64) has been removed. Comparison to the reported vibrational data for wild-type (wt) Mb-NO then shows that the effect of H bonding to the coordinated NO is weak and mostly leads to a polarization of the {pi}/{pi}* orbitals of bound NO. In addition, the observation that {delta}{sub ip}(Fe-N-O) does not correlate well with ?(N-O) can be traced back to the very mixed nature of this mode. The Fe-N(imidazole) stretching frequency is observed at 149 cm{sup -1} in [Fe(TPP)(MI)(NO)], and spectral changes upon NO binding to five-coordinate ferrous heme active sites are discussed. The obtained high-quality force constants for the Fe-NO and N-O bonds of 2.57 and 11.55 mdyn/{angstrom} can further be compared to those of corresponding 5C species, which allows for a quantitative analysis of the {sigma} trans interaction between the proximal imidazole (His) ligand and NO. This is key for the activation of the NO sensor soluble guanylate cyclase. Finally, DFT methods are calibrated against the experimentally determined vibrational properties of the Fe-N-O subunit in 1. DFT is in fact incapable of reproducing the vibrational energies and normal mode descriptions of the Fe-N-O unit well, and thus, DFT-based predictions of changes in vibrational properties upon heme modification or other perturbations of these 6C complexes have to be treated with caution.

  15. N-CPMAS nuclear magnetic resonance spectroscopy and biological stability of soil organic nitrogen in whole soil and

    E-print Network

    Weliky, David

    Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA c Earth Systems Science resonance spectroscopy. Frac- tions isolated by wet chemical extraction include amino acid-N, amino sugar is distributed as follows: proteins +peptides+amino acids, 40%; amino sugars, 5­6%; heterocyclic N, 35%; and ``NH

  16. Simultaneous multielemental analysis of some environmental and biological samples by inductively coupled plasma atomic emission spectrometry

    Microsoft Academic Search

    Shane S. Que. Hee; James R. Boyle

    1988-01-01

    The Parr bomb technique is found to be the preferred acid digestion method for multielemental analysis by simultaneous inductively coupled plasma atomic emission spectroscopy (ICP-AES) when compared with microwave and hot plate methods for many environmental and biological specimens, but especially for the latter. One digestion alone often did not produce quantitative results compared with a sequential digestion scheme. The

  17. Conservation biology Quantitative analysis of

    E-print Network

    Sanders, Nathan J.

    species affect seed-dispersal mutualisms, a synthetic examination of the effect of exotic invasive species by invasive species is unclear. Keywords: Argentine ants; exotic invasive species; seed-dispersal mutualisms & Muller-Landau 2000). However, the spread of exotic invasive species (invasive species hereafter

  18. UC Davis Quantitative Biology Courses

    NSDL National Science Digital Library

    A team of researchers and education specialists at the University of California, Davis worked together to create this set of resources for students studying biochemistry. These resources help students learn how to use computer models to answer a variety of biochemical questions. The topics covered by the learning modules offered here include acid-base chemistry, Gibbs free energy, enzyme inhibition, hemoglobin, and the Bohr effect. All told, there are ten different modules here, complete with mini-modules that teach students how to work with different graphs and other visualizations. Additionally, the site contains links to other resources in the fields of animal behavior, biomechanics, and neurobiology.

  19. UC Davis Quantitative Biology Courses

    NSDL National Science Digital Library

    2012-01-13

    A team of researchers and education specialists at the University of California, Davis worked together to create this set of resources for students studying biochemistry. These resources help students learn how to use computer models to answer a variety of biochemical questions. The topics covered by the learning modules offered here include acid-base chemistry, Gibbs free energy, enzyme inhibition, hemoglobin, and the Bohr effect. All told, there are ten different modules here, complete with mini-modules that teach students how to work with different graphs and other visualizations. Additionally, the site contains links to other resources in the fields of animal behavior, biomechanics, and neurobiology.

  20. Quantitative videomicrofluorometry: empirical methods for an automatic determination of the threshold level for fluorescent objects and application to living lymphoblastoid cell lines

    Microsoft Academic Search

    Jean Vigo; Pierre M. Viallet; Jean-Marie Salmon

    1997-01-01

    Analytical methods on individual cells are essential for studying both the functions of normal cells and the possibility to monitor pathological cells. The development of some polyvalent techniques like flow cytometry and fluorescence imaging spectroscopy has led to more and more accurate methods for analyzing heterogeneous cell populations. Unfortunately, most of the quantitative morphometric or biological parameters extracted from fluorescence

  1. A GC–MS\\/MS method for the quantitative analysis of low levels of the tyrosine metabolites maleylacetone, succinylacetone, and the tyrosine metabolism inhibitor dichloroacetate in biological fluids and tissues

    Microsoft Academic Search

    Melissa D. Zolodz; Minghong Jia; Huiping Liu; George N. Henderson; Peter W. Stacpoole

    2006-01-01

    We developed a sensitive method to quantitate the tyrosine metabolites maleylacetone (MA) and succinylacetone (SA) and the tyrosine metabolism inhibitor dichloroacetate (DCA) in biological specimens. Accumulation of these metabolites may be responsible for the toxicity observed when exposed to DCA. Detection limits of previous methods are 200ng\\/mL (1.2pmol\\/?L) (MA) and 2.6?g\\/mL (16.5pmol\\/?L) (SA) but the metabolites are likely present in

  2. Quantitative Chemical Imaging with Multiplex Stimulated Raman Scattering Microscopy

    PubMed Central

    Fu, Dan; Lu, Fa-Ke; Zhang, Xu; Freudiger, Christian; Pernik, Douglas R.; Holtom, Gary; Xie, Xiaoliang Sunney

    2012-01-01

    Stimulated Raman scattering (SRS) microscopy is a newly developed label-free chemical imaging technique that overcomes the speed limitation of confocal Raman while avoiding the nonresonant-background problem of coherent anti-Stokes Raman scattering (CARS) microscopy. Previous demonstrations were limited to single Raman band measurement. We present a novel modulation multiplexing approach that allows real-time detection of multiple species using the fast Fourier-transform. We demonstrate quantitative determination of chemical concentration of a ternary mixture. Furthermore, two imaging applications are pursued: (1) quantitative determination of oil content, as well as pigment and protein concentration in microalgae cultures; (2) 3D high resolution imaging of blood, lipids, and protein distribution in ex vivo mouse skin tissue. We believe quantitative multiplex SRS uniquely combines the advantage of fast label-free imaging with the fingerprinting capability of Raman spectroscopy and enables numerous applications lipid biology as well as biomedical imaging. PMID:22316340

  3. An assessment of the potential of laser-induced breakdown spectroscopy (LIBS) for the analysis of cesium in liquid samples of biological origin.

    PubMed

    Metzinger, Anikó; Kovács-Széles, Eva; Almási, István; Galbács, Gábor

    2014-01-01

    The present study describes the development of an analytical method for the determination of cesium in biological fluid samples (human urine and blood samples) by laser-induced breakdown spectroscopy (LIBS). The developed method is based on sample presentation by liquid-to-solid conversion, enhancing the emission signal by drying the liquid into small "pockets" created in a metal support (zinc plate), and allows the analysis to be carried out on as little as 1 ?L of sample volume, in a closed sample cell. Absolute detection limits on the Cs I 852.1 nm spectral line were calculated by the IUPAC 3? method to be 6 ng in the urine sample and 27 ng in the blood serum sample. It is estimated that LIBS may be used to detect highly elevated concentration levels of Cs in fluid samples taken from people potentially exposed to surges of Cs from non-natural sources. PMID:25014845

  4. Nanoscale investigation of the degradation mechanism of a historical chrome yellow paint by quantitative electron energy loss spectroscopy mapping of chromium species.

    PubMed

    Tan, Haiyan; Tian, He; Verbeeck, Jo; Monico, Letizia; Janssens, Koen; Van Tendeloo, Gustaaf

    2013-10-18

    Getting the picture: The investigation of 100?year old chrome yellow paint by transmission electron microscopy and spectroscopy has led to the identification of four types of core-shell particles. This nanoscale investigation has allowed a mechanism to be proposed for the darkening of some bright yellow colors in Van Gogh's paintings (e.g. in Falling leaves (Les Alyscamps), 1888). PMID:24039036

  5. Quantitative determination of wear metals in engine oils using laser-induced breakdown spectroscopy: A comparison between liquid jets and static liquids

    Microsoft Academic Search

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

    2005-01-01

    A comparison of laser-induced breakdown spectroscopy (LIBS) sensitivity in laminar liquid jets and at the surface of a static liquid has been performed. Limits of detection (LODs) have been estimated for Na, Mg, Al, Ca, Ti, V, Cr, Mn, Ni, Fe, Cu, Zn, Mo, Ag, Cd, and Ba under similar conditions using both experimental arrangements. LODs in liquid jets are

  6. Direct quantitative determination, using flameless atomic absorption spectroscopy, of metallic impurities and rare earths in nuclear solutions containing uranium, thorium, and fission products

    Microsoft Academic Search

    M. Gerardi; G. A. Pelliccia

    2009-01-01

    A method is described for direct quantitative determination of metallic and rare earths in nuclear solutions containing U, Th, and fission products from the ITREC reprocessing plant of the CNEN, CRN-Trisaia. Various tables summarize instrumental operating conditions, preparations of standards, detection limits and sensitivities, average relative standard deviation, analytical limits for the 22 investigated elements, maximum total tolerance of the

  7. Use of near infrared correlation spectroscopy for quantitation of surface iron, absorbed water and stored electronic energy in a suite of Mars soil analog materials

    NASA Technical Reports Server (NTRS)

    Coyne, Lelia M.; Banin, Amos; Carle, Glenn; Orenberg, James; Scattergood, Thomas

    1989-01-01

    A number of questions concerning the surface mineralogy and the history of water on Mars remain unresolved using the Viking analyses and Earth-based telescopic data. Identification and quantitation of iron-bearing clays on Mars would elucidate these outstanding issues. Near infrared correlation analysis, a method typically applied to qualitative and quantitative analysis of individual constituents of multicomponent mixtures, is adapted here to selection of distinctive features of a small, highly homologous series of Fe/Ca-exchanged montmorillonites and several kalinites. Independently determined measures of surface iron, relative humidity and stored electronic energy were used as constituent data for linear regression of the constituent vs. reflectance data throughout the spectral region 0.68 to 2.5 micrometers. High correlations were found in appropriate regions for all three constituents, though that with stored energy is still considered tenuous. Quantitation was improved using 1st and 2nd derivative spectra. High resolution data over a broad spectral range would be required to quantitatively identify iron-bearing clays by remotely sensed reflectance.

  8. X-Ray Absorption Spectroscopy of Metallobiomolecules

    E-print Network

    Scott, Robert A.

    2/9/07 1 X-Ray Absorption Spectroscopy of Metallobiomolecules The Outskirts of Structural Biology 9, 07] This is a tutorial about the use of X-ray Absorption Spectroscopy (XAS) in biology, RG; Eisenberger, P; Kincaid, BM "X-ray Absorption Spectroscopy of Biological Molecules" Annu. Rev

  9. X-Ray Absorption Spectroscopy of Metallobiomolecules

    E-print Network

    Scott, Robert A.

    9/6/09 1 X-Ray Absorption Spectroscopy of Metallobiomolecules The Outskirts of Structural Biology 6, 09] This is a tutorial about the use of X-ray Absorption Spectroscopy (XAS) in biology, RG; Eisenberger, P; Kincaid, BM "X-ray Absorption Spectroscopy of Biological Molecules" Annu. Rev

  10. Principles of Plasma Spectroscopy

    Microsoft Academic Search

    A. L. Osterheld

    1998-01-01

    This book gives a comprehensive treatment of plasma spectroscopy, the quantitative study of line and continuous radiation from high temperature plasmas. This highly interdisciplinary field combines elements of atomic, plasma and statistical physics, and has wide application to simulations and diagnostics of laboratory and astrophysical plasmas. Plasma spectroscopy is naturally intertwined with magnetic and inertial fusion energy science. Radiative processes

  11. A Quantitative Comparison of Instruction Format of Undergraduate Introductory Level Content Biology Courses: Traditional Lecture Approach vs. Inquiry Based for Education Majors.

    ERIC Educational Resources Information Center

    Willden, Jennifer L.; Crowther, David T.; Gubanich, Alan A.; Cannon, John R.

    The purpose of this study was to determine if there were any statistically significant differences in the pretest and posttest examination scores between students in two undergraduate biology classes taught in two fundamentally different praxes at the University of Nevada, Reno. Biology 100, an introductory biology course for non-majors, was…

  12. Dissolved organic matter fluorescence spectroscopy as a tool to estimate biological activity in a coastal zone submitted to anthropogenic inputs

    Microsoft Academic Search

    E. Parlanti; K. Wörz; L. Geoffroy; M. Lamotte

    2000-01-01

    Here we report on an investigation of the three-dimensional excitation-emission-matrix (EEM) fluorescence spectra of unconcentrated water samples collected in 1996, 1998 and 1999 at a site particularly propitious for macro-algae development. The degradation of these macro-algae was studied to determine the influence of their exudates on natural water EEM fluorescence spectra. This work demonstrates that biological activity is one of

  13. Application of Synchrotron X-Ray Microbeam Spectroscopy to the Determination of Metal Distribution and Speciation in Biological Tissues

    Microsoft Academic Search

    T. Punshon; B. P. Jackson; A. Lanzirotti; W. A. Hopkins; P. M. Bertsch; J. Burger

    2005-01-01

    Resolving the distribution and speciation of metal(loid)s within biological environmental samples is essential for understanding bioavailability, trophic transfer, and environmental risk. We used synchrotron x?ray microspectroscopy to analyze a range of samples that had been exposed to metal(loid) contamination. Microprobe x?ray fluorescence elemental mapping (µSXRF) of decomposing rhizosphere microcosms consisting of Ni? and U?contaminated soil planted with wheat (Triticum aestivum)

  14. Development of Quantitative Real-Time PCR Assays for Detection and Quantification of Surrogate Biological Warfare Agents in Building Debris and Leachate?

    PubMed Central

    Saikaly, Pascal E.; Barlaz, Morton A.; de los Reyes, Francis L.

    2007-01-01

    Evaluation of the fate and transport of biological warfare (BW) agents in landfills requires the development of specific and sensitive detection assays. The objective of the current study was to develop and validate SYBR green quantitative real-time PCR (Q-PCR) assays for the specific detection and quantification of surrogate BW agents in synthetic building debris (SBD) and leachate. Bacillus atrophaeus (vegetative cells and spores) and Serratia marcescens were used as surrogates for Bacillus anthracis (anthrax) and Yersinia pestis (plague), respectively. The targets for SYBR green Q-PCR assays were the 16S-23S rRNA intergenic transcribed spacer (ITS) region and recA gene for B. atrophaeus and the gyrB, wzm, and recA genes for S. marcescens. All assays showed high specificity when tested against 5 ng of closely related Bacillus and Serratia nontarget DNA from 21 organisms. Several spore lysis methods that include a combination of one or more of freeze-thaw cycles, chemical lysis, hot detergent treatment, bead beat homogenization, and sonication were evaluated. All methods tested showed similar threshold cycle values. The limit of detection of the developed Q-PCR assays was determined using DNA extracted from a pure bacterial culture and DNA extracted from sterile water, leachate, and SBD samples spiked with increasing quantities of surrogates. The limit of detection for B. atrophaeus genomic DNA using the ITS and B. atrophaeus recA Q-PCR assays was 7.5 fg per PCR. The limits of detection of S. marcescens genomic DNA using the gyrB, wzm, and S. marcescens recA Q-PCR assays were 7.5 fg, 75 fg, and 7.5 fg per PCR, respectively. Quantification of B. atrophaeus vegetative cells and spores was linear (R2 > 0.98) over a 7-log-unit dynamic range down to 101 B. atrophaeus cells or spores. Quantification of S. marcescens (R2 > 0.98) was linear over a 6-log-unit dynamic range down to 102 S. marcescens cells. The developed Q-PCR assays are highly specific and sensitive and can be used for monitoring the fate and transport of the BW surrogates B. atrophaeus and S. marcescens in building debris and leachate. PMID:17720820

  15. Transient absorption spectroscopy in biology using the Super-ACO storage ring FEL and the synchrotron radiation combination

    NASA Astrophysics Data System (ADS)

    Renault, Eric; Nahon, Laurent; Garzella, David; Nutarelli, Daniele; De Ninno, Giovanni; Hirsch, Matthias; Couprie, Marie Emmanuelle

    2001-12-01

    The Super-ACO storage ring FEL, covering the UV range down to 300 nm with a high average power (300 mW at 350 nm) together with a high stability and long lifetime, is a unique tool for the performance of users applications. We present here the first pump-probe two color experiments on biological species using a storage ring FEL coupled to the synchrotron radiation. The intense UV pulse of the Super-ACO FEL is used to prepare a high initial concentration of chromophores in their first singlet electronic excited state. The nearby bending magnet synchrotron radiation provides, on the other hand a pulsed, white light continuum (UV-IR), naturally synchronized with the FEL pulses and used to probe the photochemical subsequent events and the associated transient species. We have demonstrated the feasibility with a dye molecule (POPOP) observing a two-color effect, signature of excited state absorption and a temporal signature with Acridine. Applications on various chromophores of biological interest are carried out, such as the time-resolved absorption study of the first excited state of Acridine.

  16. Final report on LDRD project: Semiconductor surface-emitting microcavity laser spectroscopy for analysis of biological cells and microstructures

    SciTech Connect

    Gourley, P.L.; McDonald, A.E. [Sandia National Labs., Albuquerque, NM (United States). Nanostructure and Semiconductor Physics Dept.; Gourley, M.F. [Washington Hospital Center, DC (United States); Bellum, J. [Coherent Technologies, Boulder, CO (United States)

    1997-08-01

    This article discusses a new intracavity laser technique that uses living or fixed cells as an integral part of the laser. The cells are placed on a GaAs based semiconductor wafer comprising one half of a vertical cavity surface-emitting laser. After placement, the cells are covered with a dielectric mirror to close the laser cavity. When photo-pumped with an external laser, this hybrid laser emits coherent light images and spectra that depend sensitively on the cell size, shape, and dielectric properties. The light spectra can be used to identify different cell types and distinguish normal and abnormal cells. The laser can be used to study single cells in real time as a cell-biology lab-on-a-chip, or to study large populations of cells by scanning the pump laser at high speed. The laser is well-suited to be integrated with other micro-optical or micro-fluidic components to lead to micro-optical-mechanical systems for analysis of fluids, particulates, and biological cells.

  17. Detection and quantitative analysis of chemical species in Hanford tank materials using Raman spectroscopy technology: FY94, January 1, 1994--March 31, 1995

    SciTech Connect

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

    1995-09-12

    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.

  18. Quantitative Analysis of Microstructure in Polysiloxanes Using High Resolution Si29 NMR Spectroscopy: Investigation of Lot Variability in the LVM97 and HVM97 PDMS/PDPS Copolymers

    SciTech Connect

    ALAM, TODD M.

    2002-11-01

    The quantitative analysis of microstructure and sequence distribution in polysiloxane copolymers using high-resolution solution {sup 29}Si NMR is reported. Copolymers containing dimethylsiloxane (DMS) and diphenysiloxane (DPS) monomer units prepared with either high vinyl content (HVM) or low vinyl content (LVM) were analyzed. The average run length (R{sub exp}), the number average sequence length (l{sub A}, l{sub B}), along with the various linkage probabilities (p{sub AA}, p{sub AB}, p{sub BA}, and p{sub BB}) were determined for different production lots of the LVM97 and HVM97 samples to address the lot variability of microstructure in these materials.

  19. Determination of Three-Bond 1H3?– 31P Couplings in Nucleic Acids and Protein–Nucleic Acid Complexes by Quantitative JCorrelation Spectroscopy

    Microsoft Academic Search

    G. Marius Clore; Elizabeth C. Murphy; Angela M. Gronenborn; Ad Bax

    1998-01-01

    A new sensitive two-dimensional quantitativeJcorrelation experiment is described for measuring3JH3?–Pcouplings in nucleic acids and protein–nucleic acid complexes. The method is based on measuring the change in intensity of the1H–1H cross peaks in a constant-time1H–1H COSY experiment which occurs in the presence and absence of3JH3?–Pdephasing during the constant-time evolution period. For protein–nucleic acid complexes where the protein is13C-labeled but the nucleic

  20. Application of on-line electrochemical derivatization coupled with high-performance liquid chromatography electrospray ionization mass spectrometry for detection and quantitation of (p-chlorophenyl)aniline in biological samples.

    PubMed

    Chen, Hao; Zhang, Yanhua; Mutlib, Abdul E; Zhong, Min

    2006-04-01

    A rapid, sensitive, and specific assay for detection and quantitation of (p-chlorophenyl)aniline (CPA) in biological samples was developed. The assay was established based on rapid electrochemical oxidation of CPA to a dimerized product (1.0 V vs Pd) with the enhanced detection sensitivity of electrospray mass spectrometer (ES/MS). A "head-to-tail" dimer ([M + H]+ at m/z 217) was exhibited as the predominant species after electrochemical conversion of CPA. Optimal detection sensitivity and specificity for the dimer of CPA that was present in the biological matrix (e.g., rat urine) were achieved through on-line electrochemistry (EC) coupled with high-performance liquid chromatography tandem mass spectrometry. No matrix-associated ion suppression was observed. The limit of detection (S/N approximately 6) was 20 ng/mL, and the limit of quantitation was 50 ng/mL. The calibration curve was exhibited to be quadratic over the range of 50-2000 ng/mL with r2 > 0.99 in various biological matrixes. The assay was validated and used to study the biotransformation of p-chlorophenyl isocyanate (CPIC) to CPA in rats administered intraperitoneally with CPIC (50 mg/kg). The present LC/EC/MS/MS assay of CPA brings important technical advantages to assist in the risk assessment of new chemical entities, which have the potential to produce anilines via biotransformation. PMID:16579628

  1. In-line monitoring of extraction process of scutellarein from Erigeron breviscapus (vant.) Hand-Mazz based on qualitative and quantitative uses of near-infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Wu, Yongjiang; Jin, Ye; Ding, Haiying; Luan, Lianjun; Chen, Yong; Liu, Xuesong

    2011-09-01

    The application of near-infrared (NIR) spectroscopy for in-line monitoring of extraction process of scutellarein from Erigeron breviscapus (vant.) Hand-Mazz was investigated. For NIR measurements, two fiber optic probes designed to transmit NIR radiation through a 2 mm pathlength flow cell were utilized to collect spectra in real-time. High performance liquid chromatography (HPLC) was used as a reference method to determine scutellarein in extract solution. Partial least squares regression (PLSR) calibration model of Savitzky-Golay smoothing NIR spectra in the 5450-10,000 cm -1 region gave satisfactory predictive results for scutellarein. The results showed that the correlation coefficients of calibration and cross validation were 0.9967 and 0.9811, respectively, and the root mean square error of calibration and cross validation were 0.044 and 0.105, respectively. Furthermore, both the moving block standard deviation (MBSD) method and conformity test were used to identify the end point of extraction process, providing real-time data and instant feedback about the extraction course. The results obtained in this study indicated that the NIR spectroscopy technique provides an efficient and environmentally friendly approach for fast determination of scutellarein and end point control of extraction process.

  2. Instrument independent diffuse reflectance spectroscopy

    PubMed Central

    Yu, Bing; Fu, Henry L.; Ramanujam, Nirmala

    2011-01-01

    Diffuse reflectance spectroscopy with a fiber optic probe is a powerful tool for quantitative tissue characterization and disease diagnosis. Significant systematic errors can arise in the measured reflectance spectra and thus in the derived tissue physiological and morphological parameters due to real-time instrument fluctuations. We demonstrate a novel fiber optic probe with real-time, self-calibration capability that can be used for UV-visible diffuse reflectance spectroscopy in biological tissue in clinical settings. The probe is tested in a number of synthetic liquid phantoms over a wide range of tissue optical properties for significant variations in source intensity fluctuations caused by instrument warm up and day-to-day drift. While the accuracy for extraction of absorber concentrations is comparable to that achieved with the traditional calibration (with a reflectance standard), the accuracy for extraction of reduced scattering coefficients is significantly improved with the self-calibration probe compared to traditional calibration. This technology could be used to achieve instrument-independent diffuse reflectance spectroscopy in vivo and obviate the need for instrument warm up and post?premeasurement calibration, thus saving up to an hour of precious clinical time. PMID:21280897

  3. Quantitative analysis is changing the face of biology. An area in which it has provided particularly useful insights is the analysis of the func-

    E-print Network

    Sens, Pierre

    into organelles. Far from being inert, biological membranes are key components in sensory and signalling pathways. At the microscopic scale, biological membranes are a crowded mix of membrane proteins and their lipid partners. Our bilayer. As a concrete example, we will consider bacterial mechanosensitive channels. The structure

  4. Photoacoustic detection and optical spectroscopy of high-intensity focused ultrasound-induced thermal lesions in biologic tissue

    SciTech Connect

    Alhamami, Mosa; Kolios, Michael C.; Tavakkoli, Jahan, E-mail: jtavakkoli@ryerson.ca [Department of Physics, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3 (Canada)] [Department of Physics, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3 (Canada)

    2014-05-15

    Purpose: The aims of this study are: (a) to investigate the capability of photoacoustic (PA) method in detecting high-intensity focused ultrasound (HIFU) treatments in muscle tissuesin vitro; and (b) to determine the optical properties of HIFU-treated and native tissues in order to assist in the interpretation of the observed contrast in PA detection of HIFU treatments. Methods: A single-element, spherically concaved HIFU transducer with a centre frequency of 1 MHz was utilized to create thermal lesions in chicken breast tissuesin vitro. To investigate the detectability of HIFU treatments photoacoustically, PA detection was performed at 720 and 845 nm on seven HIFU-treated tissue samples. Within each tissue sample, PA signals were acquired from 22 locations equally divided between two regions of interest within two volumes in tissue – a HIFU-treated volume and an untreated volume. Optical spectroscopy was then carried out on 10 HIFU-treated chicken breast specimens in the wavelength range of 500–900 nm, in 1-nm increments, using a spectrophotometer with an integrating sphere attachment. The authors’ optical spectroscopy raw data (total transmittance and diffuse reflectance) were used to obtain the optical absorption and reduced scattering coefficients of HIFU-induced thermal lesions and native tissues by employing the inverse adding-doubling method. The aforementioned interaction coefficients were subsequently used to calculate the effective attenuation coefficient and light penetration depth of HIFU-treated and native tissues in the wavelength range of 500–900 nm. Results: HIFU-treated tissues produced greater PA signals than native tissues at 720 and 845 nm. At 720 nm, the averaged ratio of the peak-to-peak PA signal amplitude of HIFU-treated tissue to that of native tissue was 3.68 ± 0.25 (mean ± standard error of the mean). At 845 nm, the averaged ratio of the peak-to-peak PA signal amplitude of HIFU-treated tissue to that of native tissue was 3.75 ± 0.26 (mean ± standard error of the mean). The authors’ spectroscopic investigation has shown that HIFU-treated tissues have a greater optical absorption and reduced scattering coefficients than native tissues in the wavelength range of 500–900 nm. In fact, at 720 and 845 nm, the ratio of the optical absorption coefficient of HIFU-treated tissues to that of native tissues was 1.13 and 1.17, respectively; on the other hand, the ratio of the reduced scattering coefficient of HIFU-treated tissues to that of native tissues was 13.22 and 14.67 at 720 and 845 nm, respectively. Consequently, HIFU-treated tissues have a higher effective attenuation coefficient and a lower light penetration depth than native tissues in the wavelength range 500–900 nm. Conclusions: Using a PA approach, HIFU-treated tissues interrogated at 720 and 845 nm optical wavelengths can be differentiated from untreated tissues. Based on the authors’ spectroscopic investigation, the authors conclude that the observed PA contrast between HIFU-induced thermal lesions and untreated tissue is due, in part, to the increase in the optical absorption coefficient, the reduced scattering coefficient and, therefore, the deposited laser energy fluence in HIFU-treated tissues.

  5. The AstroBiology Explorer (ABE) MIDEX Mission Concept: Using Infrared Spectroscopy to Identify Organic Molecules in Space

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; Vincenzi, Donald (Technical Monitor)

    2002-01-01

    One of the principal means by which organic compounds are detected and identified in space is by infrared spectroscopy. Past IR studies (telescopic and laboratory) have demonstrated that much of the carbon in the interstellar medium (ISM) is in complex organic species of a variety of types, but the distribution, abundance, and evolutionary relationships of these materials are not well understood. The Astrobiology Explorer (ABE) is a MIDEAST mission concept designed to conduct IR spectroscopic observations to detect and identify these materials to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. Systematic studies include the observation of planetary nebulae and stellar outflows, protostellar objects, Solar System Objects, and galaxies, and multiple lines of sight through dense molecular clouds and the diffuse ISM. ABE will also search for evidence of D enrichment in complex molecules in all these environments. The mission is currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corp. ABE is a cryogenically-cooled 60 cm diameter space telescope equipped with 3 cryogenic cross-dispersed spectrographs that share a single common slit. The 3 spectrometers each measure single spectral octaves (2.5-5, 5-10, 10-20 microns) and together cover the entire 2.5 - 20 micron region simultaneously. The spectrometers use state-of-the-art 1024x1024 pixel detectors, with a single InSb array for the 2.5-5 micron region and two Si:As arrays for the 5-10 and 10-20 micron regions. The spectral resolution is wavelength dependent but is greater than 2000 across the entire spectral range. ABE would operate in a heliocentric, Earth drift-away orbit and is designed to take maximum advantage of this environment for cooling, thermal stability, and mission lifetime. ABE would have a core science mission lasting approximately 1.5 years.

  6. Quantitative depth-resolved photoelectron spectroscopy analysis of the interaction of energetic oxygen ions with the beryllium-tungsten alloy Be2W

    NASA Astrophysics Data System (ADS)

    Köppen, M.; Oberkofler, M.; Riesch, J.; Schmid, K.; Vollmer, A.; Linsmeier, Ch.

    2013-07-01

    The chemical reactions during the implantation of oxygen ions into a thin beryllium-tungsten alloy layer on a beryllium substrate and subsequent annealing are investigated by depth-resolved chemical analysis using X-ray photoelectron spectroscopy. By using variable photon energies at a synchrotron, identical kinetic energies of the photoelectrons from the different core levels are selected. This enables a chemical analysis at identical depth intervals for all core levels. From these sets of photoelectron spectra chemically resolved depth profiles are determined. The depth profiles allow an interpretation of the reaction and diffusion steps during implantation and annealing steps. This leads to a detailed understanding of the complex processes in a multi-component solid.

  7. Improvement of the inverse-gated-decoupling sequence for a faster quantitative analysis of various samples by 13C NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Giraudeau, Patrick; Baguet, Evelyne

    2006-05-01

    The inverse-gated-decoupling sequence enables quantitative 1H decoupled 13C spectra to be obtained. We modified this sequence so as to obtain the same result in less time for molecules containing carbons with various relaxation properties. For that, we determined the optimal 13C longitudinal-magnetization initial value for a faster relaxation while 1H decoupler is stopped. This value can be calculated precisely via the nuclear Overhauser effects, the longitudinal relaxation times, together with the determination of the relaxation rate constants of carbons while 1H are out of equilibrium. A supplementary delay of 1H decoupling and/or a series of selective pulses applied at the beginning of the recovery delay allow an acceleration of 13C longitudinal relaxation. We applied this method to the molecule of vanillin. The simultaneous quantification of all carbons was carried out with a recovery delay divided by two compared to the usual sequence.

  8. Application of a series of artificial neural networks to on-site quantitative analysis of lead into real soil samples by laser induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    Artificial neural networks were applied to process data from on-site LIBS analysis of soil samples. A first artificial neural network allowed retrieving the relative amounts of silicate, calcareous and ores matrices into soils. As a consequence, each soil sample was correctly located inside the ternary diagram characterized by these three matrices, as verified by ICP-AES. Then a series of artificial neural networks were applied to quantify lead into soil samples. More precisely, two models were designed for classification purpose according to both the type of matrix and the range of lead concentrations. Then, three quantitative models were locally applied to three data subsets. This complete approach allowed reaching a relative error of prediction close to 20%, considered as satisfying in the case of on-site analysis.

  9. A GC-MS/MS method for the quantitative analysis of low levels of the tyrosine metabolites maleylacetone, succinylacetone, and the tyrosine metabolism inhibitor dichloroacetate in biological fluids and tissues.

    PubMed

    Zolodz, Melissa D; Jia, Minghong; Liu, Huiping; Henderson, George N; Stacpoole, Peter W

    2006-06-01

    We developed a sensitive method to quantitate the tyrosine metabolites maleylacetone (MA) and succinylacetone (SA) and the tyrosine metabolism inhibitor dichloroacetate (DCA) in biological specimens. Accumulation of these metabolites may be responsible for the toxicity observed when exposed to DCA. Detection limits of previous methods are 200 ng/mL (1.2 pmol/microL) (MA) and 2.6 microg/mL (16.5 pmol/microL) (SA) but the metabolites are likely present in lower levels in biological specimens. To increase sensitivity, analytes were extracted from liver, urine, plasma and cultured nerve cells before and after dosing with DCA, derivatized to their pentafluorobenzyl esters, and analyzed via GC-MS/MS. PMID:16713404

  10. Quantitative assessment of brain tissue oxygenation in porcine models of cardiac arrest and cardiopulmonary resuscitation using hyperspectral near-infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Lotfabadi, Shahin S.; Toronov, Vladislav; Ramadeen, Andrew; Hu, Xudong; Kim, Siwook; Dorian, Paul; Hare, Gregory M. T.

    2014-03-01

    Near-infrared spectroscopy (NIRS) is a non-invasive tool to measure real-time tissue oxygenation in the brain. In an invasive animal experiment we were able to directly compare non-invasive NIRS measurements on the skull with invasive measurements directly on the brain dura matter. We used a broad-band, continuous-wave hyper-spectral approach to measure tissue oxygenation in the brain of pigs under the conditions of cardiac arrest, cardiopulmonary resuscitation (CPR), and defibrillation. An additional purpose of this research was to find a correlation between mortality due to cardiac arrest and inadequacy of the tissue perfusion during attempts at resuscitation. Using this technique we measured the changes in concentrations of oxy-hemoglobin [HbO2] and deoxy-hemoglobin [HHb] to quantify the tissue oxygenation in the brain. We also extracted cytochrome c oxidase changes ?[Cyt-Ox] under the same conditions to determine increase or decrease in cerebral oxygen delivery. In this paper we proved that applying CPR, [HbO2] concentration and tissue oxygenation in the brain increase while [HHb] concentration decreases which was not possible using other measurement techniques. We also discovered a similar trend in changes of both [Cyt-Ox] concentration and tissue oxygen saturation (StO2). Both invasive and non-invasive measurements showed similar results.

  11. A quantitative analysis of protein secondary structure of photosystem II particles and light-harvesting complex of chloroplast thylakoid membranes by FT-IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Nahar, S.; Tajmir-Riahi, H. A.; Carpentier, R.

    1994-12-01

    We report the preliminary results of protein conformational analysis of photosystem II (PSII) particles and light-harvesting complex (LHC-II) of chloroplast thylakoid membranes isolated from fresh spinach in aqueous solution at neutral pH. FT-IR spectroscopy, with its self-deconvolution and second derivative resolution enhancement as well as curve-fitting procedures, was used in the amide I region (1700-1600 cm-1), to determine the amount of each conformation present in coexistence. Spectroscopic data have shown the domination of the ?-helix (1656 cm-1) to be a major conformational component in both PSII (64%) and LHC-II (48%) systems. The ?-sheet (1626-1640 cm-1), with 17% for PSII and 21% for LHC-II, and the turn structure (1670-1680 cm-1), with 23% for LHC-II and 13% for PSII, with ?-antiparallel (1689-1691 cm-1) 8% for LHC-II and 6% for PSII, were the minor conformations present in aqueous solution.

  12. Exploring Phytoplankton Population Investigation Growth to Enhance Quantitative Literacy

    ERIC Educational Resources Information Center

    Baumgartner, Erin; Biga, Lindsay; Bledsoe, Karen; Dawson, James; Grammer, Julie; Howard, Ava; Snyder, Jeffrey

    2015-01-01

    Quantitative literacy is essential to biological literacy (and is one of the core concepts in "Vision and Change in Undergraduate Biology Education: A Call to Action"; AAAS 2009). Building quantitative literacy is a challenging endeavor for biology instructors. Integrating mathematical skills into biological investigations can help build…

  13. Quantitative analysis of deconvolved X-ray absorption near-edge structure spectra: a tool to push the limits of the X-ray absorption spectroscopy technique.

    PubMed

    D'Angelo, Paola; Migliorati, Valentina; Persson, Ingmar; Mancini, Giordano; Della Longa, Stefano

    2014-09-15

    A deconvolution procedure has been applied to K-edge X-ray absorption near-edge structure (XANES) spectra of lanthanoid-containing solid systems, namely, hexakis(dmpu)praseodymium(III) and -gadolinium(III) iodide. The K-edges of lanthanoids cover the energy range 38 (La)-65 (Lu) keV, and the large widths of the core-hole states lead to broadening of spectral features, reducing the content of structural information that can be extracted from the raw X-ray absorption spectra. Here, we demonstrate that deconvolution procedures allow one to remove most of the instrumental and core-hole lifetime broadening in the K-edge XANES spectra of lanthanoid compounds, highlighting structural features that are lost in the raw data. We show that quantitative analysis of the deconvolved K-edge XANES spectra can be profitably used to gain a complete local structural characterization of lanthanoid-containing systems not only for the nearest neighbor atoms but also for higher-distance coordination shells. PMID:25171598

  14. Robotic work station for microscale synthetic chemistry: On-line absorption spectroscopy, quantitative automated thin-layer chromatography, and multiple reactions in parallel

    NASA Astrophysics Data System (ADS)

    Lindsey, Jonathan S.; Corkan, L. Andrew; Erb, David; Powers, Gary J.

    1988-06-01

    A robotic work station has been constructed for automatically initiating and monitoring microscale chemical reactions. The work station consists of a robot with a general-purpose arm and interchangeable special-purpose hands, a carousel of seven reaction vessels, a series of stations for performing quantitative automated thin-layer chromatography (TLC), an on-line multichannel absorption spectrophotometer, sensors for verification, syringes and pumps for sample and solvent delivery, a supervisory computer for real-time data acquisition and process control, and a graphics terminal for data display. The controlling software is menu-driven and contains a scheduling algorithm that permits multiple reactions to be performed simultaneously. The automated TLC process is performed in four stages (plate dispensing, sample application, plate development, and plate densitometry), and samples are moved sequentially among these stations by the robot. The partial autonomy of these separate stations permits distributed sample processing. Four TLC plates are processed simultaneously with interleaving segmented schedules, giving a 160% increase in TLC sample throughput. The workstation can be applied to yield optimizations of synthetic reactions and to the exploration of synthetic reaction spaces. The capabilities of the workstation are demonstrated in the two-step synthesis of tetraphenylporphyrin from benzaldehyde and pyrrole in 1 h at room temperature. Kinetic data are obtained from a single-batch reaction concerning the consumption of benzaldehyde, the side reactions forming dipyrrylmethenes, and the formation of tetraphenylporphyrin.

  15. Malaria remedies of the Kenyah of the Apo Kayan, East Kalimantan, Indonesian Borneo: A quantitative assessment of local consensus as an indicator of biological efficacy

    Microsoft Academic Search

    Danna J. Leaman; J. Thor Arnason; Razali Yusuf; Harini Sangat-Roemantyo; Herwasono Soedjito; Cindy K. Angerhofer; John M. Pezzuto

    1995-01-01

    Traditional remedies have been a source of important antimalarial drugs and continue to provide novel and effective treatments, both where pharmaceuticals are not available and where the disease is increasingly resistant to commonly prescribed drugs. The Kenyah of the Apo Kayan, a remote forested plateau in Indonesian Borneo, use 17 malaria remedies derived from natural sources. A quantitative analysis of

  16. Quantitative single-molecule imaging by confocal laser scanning microscopy.

    PubMed

    Vukojevic, Vladana; Heidkamp, Marcus; Ming, Yu; Johansson, Björn; Terenius, Lars; Rigler, Rudolf

    2008-11-25

    A new approach to quantitative single-molecule imaging by confocal laser scanning microscopy (CLSM) is presented. It relies on fluorescence intensity distribution to analyze the molecular occurrence statistics captured by digital imaging and enables direct determination of the number of fluorescent molecules and their diffusion rates without resorting to temporal or spatial autocorrelation analyses. Digital images of fluorescent molecules were recorded by using fast scanning and avalanche photodiode detectors. In this way the signal-to-background ratio was significantly improved, enabling direct quantitative imaging by CLSM. The potential of the proposed approach is demonstrated by using standard solutions of fluorescent dyes, fluorescently labeled DNA molecules, quantum dots, and the Enhanced Green Fluorescent Protein in solution and in live cells. The method was verified by using fluorescence correlation spectroscopy. The relevance for biological applications, in particular, for live cell imaging, is discussed. PMID:19011092

  17. Quantitative Plant Phosphoproteomics

    PubMed Central

    Kline, Kelli G.; Barrett-Wilt, Gregory A.; Sussman, Michael R.

    2011-01-01

    Protein phosphorylation is a major post-translational modification in plants crucial for the regulation of diverse cellular functions. In the early stages of this field, efforts focused on the qualitative detection, identification, and cataloging of in vivo protein phosphorylation sites. Recently these studies have advanced into utilizing quantitative mass spectrometric measurements, capable of dynamically monitoring changes in phosphorylation levels in response to genetic and environmental alterations. This review will highlight current untargeted and targeted mass spectral technologies used for quantitative phosphoproteome measurements in plants, and provide a discussion of these phosphorylation changes in relation to important biological events. PMID:21764629

  18. Entropy analysis of muscular near-infrared spectroscopy (NIRS) signals during exercise programme of type 2 diabetic patients: quantitative assessment of muscle metabolic pattern.

    PubMed

    Molinari, Filippo; Acharya, U Rajendra; Martis, Roshan Joy; De Luca, Riccardo; Petraroli, Giuliana; Liboni, William

    2013-12-01

    Diabetes mellitus (DM) is a metabolic disorder that is widely rampant throughout the world population these days. The uncontrolled DM may lead to complications of eye, heart, kidney and nerves. The most common type of diabetes is the type 2 diabetes or insulin-resistant DM. Near-infrared spectroscopy (NIRS) technology is widely used in non-invasive monitoring of physiological signals. Three types of NIRS signals are used in this work: (i) variation in the oxygenated haemoglobin (O2Hb) concentration, (ii) deoxygenated haemoglobin (HHb), and (iii) ratio of oxygenated over the sum of the oxygenated and deoxygenated haemoglobin which is defined as: tissue oxygenation index (TOI) to analyze the effect of exercise on diabetes subjects. The NIRS signal has the characteristics of non-linearity and non-stationarity. Hence, the very small changes in this time series can be efficiently extracted using higher order statistics (HOS) method. Hence, in this work, we have used sample and HOS entropies to analyze these NIRS signals. These computer aided techniques will assist the clinicians to diagnose and monitor the health accurately and easily without any inter or intra observer variability. Results showed that after a one-year of physical exercise programme, all diabetic subjects increased the sample entropy of the NIRS signals, thus revealing a better muscle performance and an improved recruitment by the central nervous system. Moreover, after one year of physical therapy, diabetic subjects showed a NIRS muscular metabolic pattern that was not distinguished from that of controls. We believe that sample and bispectral entropy analysis is need when the aim is to compare the inner structure of the NIRS signals during muscle contraction, particularly when dealing with neuromuscular impairments. PMID:24075080

  19. "EASY: A simple tool for simultaneously removing background, deadtime and acoustic ringing in quantitative NMR spectroscopy. Part II: Improved ringing suppression, application to quadrupolar nuclei, cross polarisation and 2D NMR".

    PubMed

    Jaeger, Christian; Hemmann, Felix

    2014-01-01

    A simple experiment for Elimination of Artifacts in NMR SpectroscopY (EASY) was introduced in Part I, and it was shown that NMR probe background signals, spectral distortions due to deadtime effects, and acoustic ringing can be eliminated simultaneously from solid-state NMR spectra. In this Part II, it is shown that acoustic ringing suppression can be improved up to one order of magnitude compared to the original EASY pulse sequence by inserting a delay ? between the two data acquisition scans of the EASY pulse sequence. The achievable ringing suppression depends on the length of this delay and is limited by the spin-lattice relaxation time T1. Furthermore, EASY is considered in conjunction with NMR of quadrupolar nuclei. For strong second-order broadening, EASY can be used to acquire either pure central transition MAS patterns or pure satellite transition NMR spectra. Two further modifications to EASY are introduced. One concerns improved ringing artifact suppression in experiments in which the central transition NMR signal is amplified by Rotor Assisted Population Transfer (RAPT). The second EASY modification enables the acquisition of quantitative NMR spectra if signals with different quadrupole coupling constants are present. In addition, acoustic ringing and (11)B stator signals are removed. Finally, it is demonstrated that the basic idea of EASY for removing ringing artifacts can be realized for heteronuclear one-dimensional and hetero- and homo-nuclear multi-dimensional NMR experiments using extended phase cycling. (15)N{(1)H} CPMAS and (15)N 2D Exchange NMR spectroscopy are considered as examples. PMID:25200102

  20. Quantitative analysis

    PubMed Central

    Nevin, John A.

    1984-01-01

    Quantitative analysis permits the isolation of invariant relations in the study of behavior. The parameters of these relations can serve as higher-order dependent variables in more extensive analyses. These points are illustrated by reference to quantitative descriptions of performance maintained by concurrent schedules, multiple schedules, and signal-detection procedures. Such quantitative descriptions of empirical data may be derived from mathematical theories, which in turn can lead to novel empirical analyses so long as their terms refer to behavioral and environmental events. Thus, quantitative analysis is an integral aspect of the experimental analysis of behavior. PMID:16812400

  1. A Sensitive and Specific Procedure for Quantitation of ADR529 in Biological Fluids by High-Performance Liquid Chromatography (HPLC) with Column Switching and Amperometric Detection

    Microsoft Academic Search

    Richard C. Lewis; Barbara A. Phillips; John R. Baldwin; David T. Rossi; Prem K. Narang

    1992-01-01

    An HPLC method using electrochemical detection (ED) has been validated for the determination of ADR-529 in plasma and urine using ICRF-192 as an internal standard (IS). Prior to storage and quantitation, both plasma and urine samples require acid stabilization. Acidified plasma samples were prepared for HPLC using a two column solid-phase extraction (SPE). An aliquot of buffered plasma (i.e., pH

  2. Spectroscopy of divertor plasmas

    SciTech Connect

    Isler, R.C.

    1995-12-31

    The requirements for divertor spectroscopy are treated with respect to instrumentation and observations on present machines. Emphasis is placed on quantitative measurements.of impurity concentrations from the interpretation of spectral line intensities. The possible influence of non-Maxwellian electron distributions on spectral line excitation in the divertor is discussed. Finally the use of spectroscopy for determining plasma temperature, density, and flows is examined.

  3. In situ infrared emission spectroscopy for quantitative gas-phase measurement under high temperature reaction conditions: an analytical method for methane by means of an innovative small-volume flowing cell.

    PubMed

    Usseglio, Sandro; Thorshaug, Knut; Karlsson, Arne; Dahl, Ivar M; Nielsen, Claus J; Jens, Klaus-J; Tangstad, Elisabeth

    2010-02-01

    We have used infrared emission spectroscopy (IRES) in order to perform in situ studies under flowing gas-phase conditions. When the small-volume cell developed herein is used, we can (1) observe emission spectra from a hot gas-phase sample having an effective volume much less than one milliliter, (2) observe spectra of typical molecular species present, and (3) observe spectra of the more important molecular species down to below 10% and in some cases even as low as 1%. In addition, an analytical method has been derived in order to conduct quantitative studies under typical reaction conditions. We show that simplifications can be made in the data acquisition and handling for a direct linear correlation between band intensity and concentration with only simple background correction. The practical lower limit for methane in the present setup is approximately 0.5-1% v/v depending on the selected temperature. Our data were collected at 500, 600, and 700 degrees C, respectively. The major features of the present cell design are fairly simple and basically formed by a quartz tube (outer diameter=6 mm, inner diameter=4 mm) inside a metal pipe and two tubular ceramic heaters. This simple setup has advantages and attractive features that have extended the application of IRES to new fields and, in particular, for in situ studies of hydrocarbon reactions at different residence times at high temperature. PMID:20149274

  4. The use of multi-element aerosol particles for determining temporal variations in temperature and electron density in laser-induced plasmas in support of quantitative laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Asgill, Michael E.; Groh, Sebastian; Niemax, Kay; Hahn, David W.

    2015-07-01

    Quantitative laser-induced breakdown spectroscopy (LIBS) analysis operates on the assumption that the sample is completely dissociated and diffused within the highly energetic plasma on time-scales of analyte analysis, resulting in analyte emission ideally at the bulk plasma temperature and a signal that is linear with analyte mass concentration. However, recent studies focusing on aerosol analysis have found the heat and mass diffusion rates within laser-induced plasmas to be finite, resulting in particle-rich, locally perturbed areas within the hot bulk plasma. The goal of this study is to observe any related plasma differences, by calculating the bulk and local (i.e. analyte rich regions) plasma temperatures and electron density, to better understand the time frame of equilibrium between the local and bulk plasma properties. This study also seeks to determine whether the presence of large quantities of a matrix element can significantly alter the local plasma conditions, thereby generating matrix effects. We report the temporal profiles of particle-derived species, adding additional insight into the effect of local perturbation of plasma properties, with the conclusion that significant plasma residence (tens of microseconds) is necessary to minimize such effects.

  5. EDITORIAL: Physical Biology

    Microsoft Academic Search

    Jane Roscoe

    2004-01-01

    Physical Biology is a new peer-reviewed publication from Institute of Physics Publishing. Launched in 2004, the journal will foster the integration of biology with the traditionally more quantitative fields of physics, chemistry, computer science and other math-based disciplines. Its primary aim is to further the understanding of biological systems at all levels of complexity, ranging from the role of structure

  6. Noncovalent peptide-mediated delivery of chemically modified steric block oligonucleotides promotes splice correction: quantitative analysis of uptake and biological effect.

    PubMed

    Laufer, Sandra D; Recke, Anna Lena; Veldhoen, Sandra; Trampe, Alexander; Restle, Tobias

    2009-03-01

    Despite numerous encouraging reports in the literature, the efficiency of cell penetrating peptides (CPPs) in promoting cellular delivery of bioactive cargos is still limited. To extend our current understanding of the underlying limitations of such approaches, we performed quantitative uptake studies of different chemically modified (2'-O-methyl, LNA and PNA) steric block oligonucleotides, targeted against a mutated splice site inserted in a firefly luciferase reporter gene construct, applying the peptide carrier MPGalpha as a model system. The peptide formed stable noncovalent complexes with phosphorothioate oligonucleotide (PTO) and locked nucleic acid (LNA) modified oligonucleotides, whereas the neutral peptide nucleic acid (PNA) had to be hybridized to an unmodified DNA to allow for complex formation. Detailed quantitative uptake studies revealed comparable numbers of intracellular PTO and LNA oligonucleotides after peptide-mediated delivery. Surprisingly, the PTO derivative showed the strongest upregulation of reporter gene activity of about 100-fold followed by the PNA (40-fold) and LNA (10-fold). Electroporation and microinjection studies proved that delivery itself was not the limiting factor for the low activity of the LNA derivative. Maximal achievable reporter gene activity could be observed only after addition of chloroquine (CQ), indicative of an endosomal pathway involved. This is in line with nuclear microinjection experiments, which show that the minimal number of steric block molecules needed to trigger the observed reporter upregulation is about two orders of magnitude lower than determined after peptide or cationic lipid delivery. PMID:19196099

  7. On Quantitizing

    PubMed Central

    Sandelowski, Margarete; Voils, Corrine I.; Knafl, George

    2009-01-01

    Quantitizing, commonly understood to refer to the numerical translation, transformation, or conversion of qualitative data, has become a staple of mixed methods research. Typically glossed are the foundational assumptions, judgments, and compromises involved in converting disparate data sets into each other and whether such conversions advance inquiry. Among these assumptions are that qualitative and quantitative data constitute two kinds of data, that quantitizing constitutes a unidirectional process essentially different from qualitizing, and that counting is an unambiguous process. Among the judgments are deciding what and how to count. Among the compromises are balancing numerical precision with narrative complexity. The standpoints of “conditional complementarity,” “critical remediation,” and “analytic alternation” clarify the added value of converting qualitative data into quantitative form. PMID:19865603

  8. Quantitative surface structure analysis by low-energy ion scattering

    Microsoft Academic Search

    M. Aono

    1984-01-01

    A review is presented of low-energy ion scattering spectroscopy (ISS) as a tool for surface atomic structure analysis. Especially, quantitative surface atomic structure analysis by ISS is highlighted. An important difference between ISS and Rutherford backscattering spectroscopy (RBS), a specialization of ISS for quantitative surface atomic structure analysis, and a general feature of the shadow cone in the energy range

  9. Preparation, biological evaluation and pharmacokinetics of human anti-HER1 monoclonal antibody, Panitumumab, labeled with 86Y for quantitative PET imaging of carcinoma

    PubMed Central

    Nayak, Tapan K.; Garmestani, Kayhan; Baidoo, Kwamena E.; Milenic, Diane E.; Brechbiel, Martin W.

    2010-01-01

    Purpose Panitumumab, a human monoclonal antibody (mAb) that binds to the epidermal growth factor receptor (EGFR/HER1), was approved by the FDA in 2006 for the treatment of patients with HER1-expressing carcinoma. In this report, we describe preclinical development of 86Y-CHX-A?-DTPA-panitumumab for quantitative positron emission tomography (PET) imaging of HER1-expressing carcinoma. Experimental design Panitumumab was conjugated to CHX-A?-DTPA and radiolabeled with 86Y. In vivo biodistribution, PET imaging, blood clearance, area under the curve (AUC), area under the moment curve (AUMC) and mean residence time (MRT) were determined on mice bearing HER1-expressing human colorectal (LS-174T), prostate (PC-3) and epidermoid (A431) tumor xenografts. Receptor-specificity was demonstrated by co-injection of 0.1 mg panitumumab with the radioimmunoconjugate (RIC). Results 86Y-CHX-A?-DTPA-panitumumab was routinely prepared with a specific activity exceeding 2 GBq/mg. Biodistribution and PET imaging studies demonstrated high HER1-specific tumor uptake of the RIC. In mice bearing LS-174T, PC-3 or A431 tumors, the tumor uptake at 3 d were 34.6 ± 5.9, 22.1± 1.9 and 22.7 ± 1.7 % ID/g, respectively. The corresponding tumor uptake in mice co-injected with 0.1 mg panitumumab was 9.3 ± 1.5, 8.8 ± 0.9 and 10.0 ± 1.3 % ID/g, respectively at the same time point, demonstrating specific blockage of the receptor. Normal organ and tumor uptake quantified by PET were closely related (r2= 0.95) to values determined by biodistribution studies. LS-174T tumor had the highest AUC (96.8 ± 5.6 %ID.d.g?1) and AUMC (262.5 ± 14.9 %ID.d2.g?1), however the tumor MRT were identical for all three tumors (2.7–2.8 d). Conclusion This study demonstrates the potential of 86Y-CHX-A?-DTPA-panitumumab for quantitative non-invasive PET imaging of HER1-expressing tumors, and represents the first step towards clinical translation. PMID:20484421

  10. Ammonium chloride salting out extraction/cleanup for trace-level quantitative analysis in food and biological matrices by flow injection tandem mass spectrometry.

    PubMed

    Nanita, Sergio C; Padivitage, Nilusha L T

    2013-03-20

    A sample extraction and purification procedure that uses ammonium-salt-induced acetonitrile/water phase separation was developed and demonstrated to be compatible with the recently reported method for pesticide residue analysis based on fast extraction and dilution flow injection mass spectrometry (FED-FI-MS). The ammonium salts evaluated were chloride, acetate, formate, carbonate, and sulfate. A mixture of NaCl and MgSO4, salts used in the well-known QuEChERS method, was also tested for comparison. With thermal decomposition/evaporation temperature of <350°C, ammonium salts resulted in negligible ion source residual under typical electrospray conditions, leading to consistent method performance and less instrument cleaning. Although all ammonium salts tested induced acetonitrile/water phase separation, NH4Cl yielded the best performance, thus it was the preferred salting out agent. The NH4Cl salting out method was successfully coupled with FI/MS/MS and tested for fourteen pesticide active ingredients: chlorantraniliprole, cyantraniliprole, chlorimuron ethyl, oxamyl, methomyl, sulfometuron methyl, chlorsulfuron, triflusulfuron methyl, azimsulfuron, flupyrsulfuron methyl, aminocyclopyrachlor, aminocyclopyrachlor methyl, diuron and hexazinone. A validation study was conducted with nine complex matrices: sorghum, rice, grapefruit, canola, milk, eggs, beef, urine and blood plasma. The method is applicable to all analytes, except aminocyclopyrachlor. The method was deemed appropriate for quantitative analysis in 114 out of 126 analyte/matrix cases tested (applicability rate=0.90). The NH4Cl salting out extraction/cleanup allowed expansion of FI/MS/MS for analysis in food of plant and animal origin, and body fluids with increased ruggedness and sensitivity, while maintaining high-throughput (run time=30s/sample). Limits of quantitation (LOQs) of 0.01mgkg(-1) (ppm), the 'well-accepted standard' in pesticide residue analysis, were achieved in >80% of cases tested; while limits of detection (LODs) were typically in the range of 0.001-0.01mgkg(-1) (ppm). A comparison to a well-established HPLC/MS/MS method was also conducted, yielding comparable results, thus confirming the suitability of NH4Cl salting out FI/MS/MS for pesticide residue analysis. PMID:23473245

  11. Seeing More Is Knowing More: V3D Enables Real-Time 3D Visualization and Quantitative Analysis of Large-Scale Biological Image Data Sets

    NASA Astrophysics Data System (ADS)

    Peng, Hanchuan; Long, Fuhui

    Everyone understands seeing more is knowing more. However, for large-scale 3D microscopic image analysis, it has not been an easy task to efficiently visualize, manipulate and understand high-dimensional data in 3D, 4D or 5D spaces. We developed a new 3D+ image visualization and analysis platform, V3D, to meet this need. The V3D system provides 3D visualization of gigabyte-sized microscopy image stacks in real time on current laptops and desktops. V3D streamlines the online analysis, measurement and proofreading of complicated image patterns by combining ergonomic functions for selecting a location in an image directly in 3D space and for displaying biological measurements, such as from fluorescent probes, using the overlaid surface objects. V3D runs on all major computer platforms and can be enhanced by software plug-ins to address specific biological problems. To demonstrate this extensibility, we built a V3Dbased application, V3D-Neuron, to reconstruct complex 3D neuronal structures from high-resolution brain images. V3D-Neuron can precisely digitize the morphology of a single neuron in a fruitfly brain in minutes, with about a 17-fold improvement in reliability and tenfold savings in time compared with other neuron reconstruction tools. Using V3D-Neuron, we demonstrate the feasibility of building a high-resolution 3D digital atlas of neurite tracts in the fruitfly brain. V3D can be easily extended using a simple-to-use and comprehensive plugin interface.

  12. LASER BIOLOGY AND MEDICINE: A laser-spectroscopy system for fluorescent diagnostics and photodynamic therapy of diseases of eye retina and choroid

    NASA Astrophysics Data System (ADS)

    Meerovich, G. A.; Shevchik, S. A.; Loshchenov, M. V.; Budzinskaya, M. V.; Ermakova, N. A.; Kharnas, S. S.

    2002-11-01

    A laser-spectroscopy system for the fluorescent diagnostics and photodynamic therapy of pathologic eye-fundus changes combined with the use of the Photosens compound is developed. The system is tested on experimental animals (mice and rabbits).

  13. Infrared quantitative spectroscopy and planetary atmospheres

    NASA Astrophysics Data System (ADS)

    Flaud, J.-M.

    2009-04-01

    Optical measurements of atmospheric minor constituents are carried out using spectrometers working in the UV-visible, infrared and microwave spectral ranges. In all cases the quality of the analysis and of the interpretation of the atmospheric spectra requires the best possible knowledge of the molecular parameters of the species of interest. To illustrate this point we will concentrate on recent laboratory studies of nitric acid, chlorine nitrate and formaldehyde. Nitric acid is one of the important minor constituent of the terrestrial atmosphere. Using new and accurate experimental results concerning the spectroscopic properties of the H14NO3 and H15NO3 molecules, as well as improved theoretical methods (Perrin et al., 2004), it has been possible to generate an improved set of line parameters for these molecules in the 11.2 ?m spectral region. These line parameters were used to detect for the first time the H15NO3 molecule in the atmosphere analyzing atmospheric spectra recorded by the MIPAS experiment. The retrievals of chlorine nitrate profiles are usually performed using absorption cross sections (Birk and Wagner, 2003). Following a high resolution analysis of the ?3 and ?4bands of this species in the 12.8 ?m region wepropose, as a possibility, to use line by line calculation simulating its ?4Q-branch for the atmospheric temperature and pressure ranges. For the measurement of atmospheric formaldehyde concentrations, mid-infrared and ultraviolet absorptions are both used by ground, air or satellite instruments. It is then of the utmost importance to have consistent spectral parameters in these various spectral domains. Consequently the aim of the study performed at LISA (Gratien et al., 2007) was to intercalibrate formaldehyde spectra in the infrared and ultraviolet regions acquiring simultaneously UV and IR spectra using a common optical cell. The results of the work will be presented. Also high resolution infrared data derived from Perrin et al., 2003 have been used to determine vertical distributions from the upper troposphere to the stratopause using the high spectral resolution measurements of MIPAS (Steck et al., 2008). References: M. Birk, G. Wagner, J. Quant. Spectros. Radiat.Transfer, 82, 443, 2003. G. Brizzi, M. Carlotti, J.-M. Flaud, A. Perrin and M. Ridolfi, Geophys. Res. Lett., 34, L03802, 2006. A. Gratien, B. Picquet-Varrault, J. Orphal, E. Perraudin, J.-F. Doussin and J.-M. Flaud, J. Geophys. Res., 112, D05305, 2007. A. Perrin, F. Keller and J.-M. Flaud, J. Mol. Spectrosc., 221, 192, 2003. A. Perrin, J. Orphal, J.-M. Flaud, S. Klee, G. Mellau, H. Mader, D. Walbrodt and M. Winnewisser, J. Mol. Spectrosc, 228, 375, 2004. T. Steck, N. Glatthor, T. von Clarmann, H. Fischer, J. M. Flaud, B. Funke, U. Grabowski, M. Hopfner, S. Kellmann, A. Linden, A. Perrin, and G. P. Stiller, Atm. Chem. Phys., 8, 463, 2008.

  14. Gerhard Wider: Structure Determination of Biological Macromolecules using NMR. Structure Determination of Biological

    E-print Network

    Wider, Gerhard

    Gerhard Wider: Structure Determination of Biological Macromolecules using NMR. -1- Structure Determination of Biological Macromolecules in Solution Using NMR spectroscopy Gerhard Wider Institut fürTechniques 29, 1278­1294 (2000) #12;Gerhard Wider: Structure Determination of Biological Macromolecules using

  15. Qualitative and quantitative analysis of a group of volatile organic compounds in biological samples by HS-GC/FID: application in practical cases.

    PubMed

    Monteiro, C; Franco, J M; Proença, P; Castañera, A; Claro, A; Vieira, D N; Corte-Real, F

    2014-10-01

    A simple and sensitive procedure, using n-propanol as internal standard (IS), was developed and validated for the qualitative and quantitative analysis of a group of 11 volatile organic substances with different physicochemical properties (1-butanol, 2-propanol, acetaldehyde, ethyl acetate, acetone, acetonitrile, chloroform, diethyl ether, methanol, toluene and p-xylene) in whole blood, urine and vitreous humor. Samples were prepared by dilution with an aqueous solution of internal standard followed by Headspace Gas Chromatography with a Flame-ionization Detector (HS GC-FID) analysis. Chromatographic separation was performed using two capillary columns with different polarities (DB-ALC2: 30m×0.320mm×1.2?m and DB-ALC1: 30m×0.320mm×1.8?m), thus providing a change in the retention and elution order of volatiles. This dual column confirmation increases the specificity, since the risk of another substance co-eluting at the same time in both columns is very small. The method was linear from 5 to 1000mg/L for toluene and p-xylene, 50-1000mg/L for chloroform, and 50-2000mg/L for the remaining substances, with correlation coefficients of over 0.99 for all compounds. The limits of detection (LOD) ranged 1 to 10mg/L, while the limits of quantification (LOQ) ranged from 2 to 31mg/L. The intra-day precision (CV<6.4%), intermediate precision (CV<7.0%) and accuracy (relative error ±10%) of the method were in conformity with the criteria normally accepted in bioanalytical method validation. The method developed has been applied to forensic cases, with the advantages that it uses a small sample volume and does not require any extraction procedure as it makes use of a headspace injection technique. PMID:25124884

  16. Improved protocols for quantitative determination of metabolites from biological samples using high performance ionic-exchange chromatography with conductimetric and pulsed amperometric detection.

    PubMed

    Groussac; Ortiz; François

    2000-06-01

    Simple and reliable protocols are described for an extensive analysis of metabolites in extracts from different biological sources. The separation was performed by high performance ionic-exchange chromatography (HPIC) at alkaline pH using two types of chromatography columns and two detection methods. Organic acids and inorganic anions were separated on an ionPac AS11 column using a 0.5 to 35 mM Na0H gradient. Detection limits in the range of milligrams per liter were achieved by use of a conductivity detector equipped with an anion self-regenerating suppressor. Twelve phosphorylated compounds belonging to the glycolytic and the pentose phosphate pathways could be resolved on a CarboPac PA1 column using a Na0H/Na-acetate gradient. Quantification was achieved by pulsed amperometry with detection limits in the micromolar range. Cell extracts obtained by extraction in boiling buffered ethanol described previously could be directly injected onto HPIC columns for the separation of metabolites because the extraction procedure affected neither the retention time nor the stability of most of the metabolites, and yielded very clean chromatograms. These improved protocols were applied for a dynamic analysis of intracellular metabolites in Saccharomyces cerevisiae in response to a glucose pulse. PMID:10862877

  17. Two-dimensional correlation spectroscopy — Biannual survey 2007-2009

    NASA Astrophysics Data System (ADS)

    Noda, Isao

    2010-06-01

    The publication activities in the field of 2D correlation spectroscopy are surveyed with the emphasis on papers published during the last two years. Pertinent review articles and conference proceedings are discussed first, followed by the examination of noteworthy developments in the theory and applications of 2D correlation spectroscopy. Specific topics of interest include Pareto scaling, analysis of randomly sampled spectra, 2D analysis of data obtained under multiple perturbations, evolution of 2D spectra along additional variables, comparison and quantitative analysis of multiple 2D spectra, orthogonal sample design to eliminate interfering cross peaks, quadrature orthogonal signal correction and other data transformation techniques, data pretreatment methods, moving window analysis, extension of kernel and global phase angle analysis, covariance and correlation coefficient mapping, variant forms of sample-sample correlation, and different display methods. Various static and dynamic perturbation methods used in 2D correlation spectroscopy, e.g., temperature, composition, chemical reactions, H/D exchange, physical phenomena like sorption, diffusion and phase transitions, optical and biological processes, are reviewed. Analytical probes used in 2D correlation spectroscopy include IR, Raman, NIR, NMR, X-ray, mass spectrometry, chromatography, and others. Application areas of 2D correlation spectroscopy are diverse, encompassing synthetic and natural polymers, liquid crystals, proteins and peptides, biomaterials, pharmaceuticals, food and agricultural products, solutions, colloids, surfaces, and the like.

  18. DNA interaction studies and evaluation of biological activity of homo- and hetero-trihalide mononuclear Cu(II) Schiff base complexes. Quantitative structure-activity relationships.

    PubMed

    Chaviara, A T; Kioseoglou, E E; Pantazaki, A A; Tsipis, A C; Karipidis, P A; Kyriakidis, D A; Bolos, C A

    2008-09-01

    A new series of mixed-ligand mono- or hetero-trihalide Cu(II) complexes of the type [Cu(dienXX)Y(YZ(2))], where dienXX=Schiff dibase of diethylenetriamine with 2-thiophene-carboxaldehyde (dienSS), 2-furaldehyde (dienOO) or 2-pyrrole-2-carboxaldehyde (dienNN), Y=Cl, Br and Z=Br, I was synthesized by the reaction of the precursors of the type [Cu(dienXX)Y]Y with iodine or bromine in 1:1 molar ratio. The distorted square pyramidal configuration of the new homo- and hetero-trihalide Cu(II) mononuclear complexes was identified by C, H, N, Cu analysis, spectroscopic methods (IR, UV-visible), molar conductivity and magnetic measurements. The basal plane consists of three nitrogen atoms of the Schiff base and one halogen (terminal) atom while another axially located trihalogen moiety occupies the fifth side of the square pyramid as a YZ(2) entity, adopting an almost linear configuration. The equilibrium geometry of these complexes was further corroborated by theoretical studies at the B3LYP/DGDZVP level. A series of quantum chemical descriptors (e.g. SOMO (singly occupied molecular orbital) LUMO (lowest occupied molecular orbital), SOMO and LUMO energies, SOMO-LUMO gap, dipole moment, polarizability, molar volume, etc.) have been utilized in order to deduce quantitative structure-activity relationships (QSARs). The effect of the new compounds on the single stranded (ss), double stranded (ds) and pDNA led either to the formation of a DNA-complex cationic adduct, or to its degradation, evidenced by DNA electrophoretic mobility and DNA interaction spectroscopic titration studies. Moreover, the antimicrobial activity of Cu(II) complexes against Gram(+) and Gram(-) bacteria can be attributed to the synergistic action of the dissociation species, namely the cationic [Cu(dienXX)Y](+) and anionic [YZ(2)](-) ones. Finally, de Novo linear regression analysis correlating the bioactivity of these complexes with their structural substituents has been carried out, leading to some interesting qualitative observations/conclusions. PMID:18584877

  19. Use of Concept of Chemotherapy-Equivalent Biologically Effective Dose to Provide Quantitative Evaluation of Contribution of Chemotherapy to Local Tumor Control in Chemoradiotherapy Cervical Cancer Trials

    SciTech Connect

    Plataniotis, George A. [Department of Oncology, Aberdeen Royal Infirmary, Aberdeen (United Kingdom)], E-mail: george.plataniotis@nhs.net; Dale, Roger G. [Imperial College Healthcare NHS Trust, Charing Cross Hospital, London (United Kingdom)

    2008-12-01

    Purpose: To express the magnitude of the contribution of chemotherapy to local tumor control in chemoradiotherapy cervical cancer trials in terms of the concept of the biologically effective dose. Methods and Materials: The local control rates of both arms of each study (radiotherapy vs. radiotherapy plus chemotherapy) reported from randomized controlled trials of concurrent chemoradiotherapy for cervical cancer were reviewed and expressed using the Poisson model for tumor control probability (TCP) as TCP = exp(-exp E), where E is the logarithm of cell kill. By combining the two TCP values from each study, we calculated the chemotherapy-related log cell kill as Ec = ln[(lnTCP{sub Radiotherapy})/(lnTCP{sub Chemoradiotherapy})]. Assuming a range of radiosensitivities ({alpha} = 0.1-0.5 Gy{sup -1}) and taking the calculated log cell kill, we calculated the chemotherapy-BED, and using the linear quadratic model, the number of 2-Gy fractions corresponding to each BED. The effect of a range of tumor volumes and radiosensitivities ({alpha} Gy{sup -1}) on the TCP was also explored. Results: The chemotherapy-equivalent number of 2-Gy fractions range was 0.2-4 and was greater in tumors with lower radiosensitivity. In those tumors with intermediate radiosensitivity ({alpha} = 0.3 Gy{sup -1}), the equivalent number of 2-Gy fractions was 0.6-1.3, corresponding to 120-260 cGy of extra dose. The opportunities for clinically detectable improvement are only available in tumors with intermediate radiosensitivity with {alpha} = 0.22-0.28 Gy{sup -1}. The dependence of TCP on the tumor volume decreases as the radiosensitivity increases. Conclusion: The results of our study have shown that the contribution of chemotherapy to the TCP in cervical cancer is expected to be clinically detectable in larger and less-radiosensitive tumors.

  20. Quantitative biomedical mass spectrometry

    NASA Astrophysics Data System (ADS)

    de Leenheer, Andrép; Thienpont, Linda M.

    1992-09-01

    The scope of this contribution is an illustration of the capabilities of isotope dilution mass spectrometry (IDMS) for quantification of target substances in the biomedical field. After a brief discussion of the general principles of quantitative MS in biological samples, special attention will be paid to new technological developments or trends in IDMS from selected examples from the literature. The final section will deal with the use of IDMS for accuracy assessment in clinical chemistry. Methodological aspects considered crucial for avoiding sources of error will be discussed.

  1. Protein Quantitation Using Mass Spectrometry

    PubMed Central

    Zhang, Guoan; Ueberheide, Beatrix M.; Waldemarson, Sofia; Myung, Sunnie; Molloy, Kelly; Eriksson, Jan; Chait, Brian T.; Neubert, Thomas A.; Fenyö, David

    2013-01-01

    Mass spectrometry is a method of choice for quantifying low-abundance proteins and peptides in many biological studies. Here, we describe a range of computational aspects of protein and peptide quantitation, including methods for finding and integrating mass spectrometric peptide peaks, and detecting interference to obtain a robust measure of the amount of proteins present in samples. PMID:20835801

  2. Imaging with Raman Spectroscopy

    PubMed Central

    Zhang, Yin; Hong, Hao; Cai, Weibo

    2010-01-01

    Raman spectroscopy, based on the inelastic scattering of a photon, has been widely used as an analytical tool in many research fields. Recently, Raman spectroscopy has also been explored for biomedical applications (e.g. cancer diagnosis) because it can provide detailed information on the chemical composition of cells and tissues. For imaging applications, several variations of Raman spectroscopy have been developed to enhance its sensitivity. This review article will provide a brief summary of Raman spectroscopy-based imaging, which includes the use of coherent anti-Stokes Raman spectroscopy (CARS, primarily used for imaging the C-H bond in lipids), surface-enhanced Raman spectroscopy (SERS, for which a variety of nanoparticles can be used as contrast agents), and single-walled carbon nanotubes (SWNTs, with its intrinsic Raman signal). The superb multiplexing capability of SERS-based Raman imaging can be extremely powerful in future research where different agents can be attached to different Raman tags to enable the interrogation of multiple biological events simultaneously in living subjects. The primary limitations of Raman imaging in humans are those also faced by other optical techniques, in particular limited tissue penetration. Over the last several years, Raman spectroscopy imaging has advanced significantly and many critical proof-of-principle experiments have been successfully carried out. It is expected that imaging with Raman Spectroscopy will continue to be a dynamic research field over the next decade. PMID:20497112

  3. Biology 494 Biology Internship

    E-print Network

    Wurtele, Eve Syrkin

    Biology 494 Biology Internship Guidelines The Biology Program encourages students to seek out and participate in internship opportunities that have a clear biological focus. Internships may be arranged may receive credit in Biology 494 (Biology Internship) for participation in internships, regardless

  4. Quantitative phase microscopy with asynchronous digital holography

    PubMed Central

    Brown, William J.; Wax, Adam

    2009-01-01

    We demonstrate a new method of measuring quantitative phase in imaging of biological materials. This method, asynchronous digital holography, employs knowledge of a moving fringe created by acousto-optic modulators to execute phase-shifting interferometry using two near-simultaneous interferograms. The method can be used to obtain quantitative phase images of dynamic biological samples on millisecond time scales. We present results on a standard sample, and on live cell samples. PMID:19532543

  5. Electronic Spectroscopy & Dynamics

    SciTech Connect

    Mark Maroncelli, Nancy Ryan Gray

    2010-06-08

    The Gordon Research Conference (GRC) on Electronic Spectroscopy and Dynamics was held at Colby College, Waterville, NH from 07/19/2009 thru 07/24/2009. The Conference was well-attended with participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. The GRC on Electronic Spectroscopy & Dynamics showcases some of the most recent experimental and theoretical developments in electronic spectroscopy that probes the structure and dynamics of isolated molecules, molecules embedded in clusters and condensed phases, and bulk materials. Electronic spectroscopy is an important tool in many fields of research, and this GRC brings together experts having diverse backgrounds in physics, chemistry, biophysics, and materials science, making the meeting an excellent opportunity for the interdisciplinary exchange of ideas and techniques. Topics covered in this GRC include high-resolution spectroscopy, biological molecules in the gas phase, electronic structure theory for excited states, multi-chromophore and single-molecule spectroscopies, and excited state dynamics in chemical and biological systems.

  6. Evaluation of ultrasound-assisted extraction as sample pre-treatment for quantitative determination of rare earth elements in marine biological tissues by inductively coupled plasma-mass spectrometry.

    PubMed

    Costas, M; Lavilla, I; Gil, S; Pena, F; de la Calle, I; Cabaleiro, N; Bendicho, C

    2010-10-29

    In this work, the determination of rare earth elements (REEs), i.e. Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu in marine biological tissues by inductively coupled-mass spectrometry (ICP-MS) after a sample preparation method based on ultrasound-assisted extraction (UAE) is described. The suitability of the extracts for ICP-MS measurements was evaluated. For that, studies were focused on the following issues: (i) use of clean up of extracts with a C18 cartridge for non-polar solid phase extraction; (ii) use of different internal standards; (iii) signal drift caused by changes in the nebulization efficiency and salt deposition on the cones during the analysis. The signal drift produced by direct introduction of biological extracts in the instrument was evaluated using a calibration verification standard for bracketing (standard-sample bracketing, SSB) and cumulative sum (CUSUM) control charts. Parameters influencing extraction such as extractant composition, mass-to-volume ratio, particle size, sonication time and sonication amplitude were optimized. Diluted single acids (HNO(3) and HCl) and mixtures (HNO(3)+HCl) were evaluated for improving the extraction efficiency. Quantitative recoveries for REEs were achieved using 5 mL of 3% (v/v) HNO(3)+2% (v/v) HCl, particle size <200 ?m, 3 min of sonication time and 50% of sonication amplitude. Precision, expressed as relative standard deviation from three independent extractions, ranged from 0.1 to 8%. In general, LODs were improved by a factor of 5 in comparison with those obtained after microwave-assisted digestion (MAD). The accuracy of the method was evaluated using the CRM BCR-668 (mussel tissue). Different seafood samples of common consumption were analyzed by ICP-MS after UAE and MAD. PMID:20951856

  7. Biological detector and method

    DOEpatents

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

    2014-04-15

    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  8. Biological detector and method

    DOEpatents

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

    2013-02-26

    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  9. Quantitative Bioscience for the 21st Century

    NSDL National Science Digital Library

    ALAN HASTINGS, PETER ARZBERGER, BEN BOLKER, SCOTT COLLINS, ANTHONY R. IVES, NORMAN A. JOHNSON, and MARGARET A. PALMER (; )

    2005-06-01

    This peer-reviewed article from BioScience is about the use of quantitative research in biology. Using a carefully chosen set of examples, we illustrate the importance and ubiquity of quantitative reasoning in the biological sciences. The examples range across many different levels of biological organization, from diseases through ecosystems, and the problems addressed range from basic to applied. In addition to the overall theme that mathematical and statistical approaches are essential for understanding biological systems, three particular and interacting mathematical themes emerge. First, nonlinearity is pervasive; second, inclusion of stochasticity is essential; and third, issues of scale are common to all applications of quantitative approaches. Future progress in understanding many biological systems will depend on continued applications and developments in these three areas, and on understanding how nonlinearity, stochasticity, and scale interact.

  10. Raman spectroscopy: the gateway into tomorrow's virology

    Microsoft Academic Search

    Phelps J Lambert; Audy G Whitman; Ossie F Dyson; Shaw M Akula

    2006-01-01

    In the molecular world, researchers act as detectives working hard to unravel the mysteries surrounding cells. One of the researchers' greatest tools in this endeavor has been Raman spectroscopy. Raman spectroscopy is a spectroscopic technique that measures the unique Raman spectra for every type of biological molecule. As such, Raman spectroscopy has the potential to provide scientists with a library

  11. Quantitative proteomic analysis of HIV-1 infected CD4+ T cells reveals an early host response in important biological pathways: Protein synthesis, cell proliferation, and T-cell activation

    SciTech Connect

    Navare, Arti T.; Sova, Pavel; Purdy, David E.; Weiss, Jeffrey M. [Department of Microbiology, University of Washington, Seattle, WA (United States)] [Department of Microbiology, University of Washington, Seattle, WA (United States); Wolf-Yadlin, Alejandro [Department of Genome Sciences, University of Washington, Seattle, WA (United States)] [Department of Genome Sciences, University of Washington, Seattle, WA (United States); Korth, Marcus J.; Chang, Stewart T.; Proll, Sean C. [Department of Microbiology, University of Washington, Seattle, WA (United States)] [Department of Microbiology, University of Washington, Seattle, WA (United States); Jahan, Tahmina A. [Proteomics Resource, UW Medicine at South Lake Union, Seattle, WA (United States)] [Proteomics Resource, UW Medicine at South Lake Union, Seattle, WA (United States); Krasnoselsky, Alexei L.; Palermo, Robert E. [Department of Microbiology, University of Washington, Seattle, WA (United States)] [Department of Microbiology, University of Washington, Seattle, WA (United States); Katze, Michael G., E-mail: honey@uw.edu [Department of Microbiology, University of Washington, Seattle, WA (United States); Washington National Primate Research Center, University of Washington, Seattle, WA (United States)

    2012-07-20

    Human immunodeficiency virus (HIV-1) depends upon host-encoded proteins to facilitate its replication while at the same time inhibiting critical components of innate and/or intrinsic immune response pathways. To characterize the host cell response on protein levels in CD4+ lymphoblastoid SUP-T1 cells after infection with HIV-1 strain LAI, we used mass spectrometry (MS)-based global quantitation with iTRAQ (isobaric tag for relative and absolute quantification). We found 266, 60 and 22 proteins differentially expressed (DE) (P-value{<=}0.05) at 4, 8, and 20 hours post-infection (hpi), respectively, compared to time-matched mock-infected samples. The majority of changes in protein abundance occurred at an early stage of infection well before the de novo production of viral proteins. Functional analyses of these DE proteins showed enrichment in several biological pathways including protein synthesis, cell proliferation, and T-cell activation. Importantly, these early changes before the time of robust viral production have not been described before.

  12. METABOLOMICS IN SYSTEMS BIOLOGY

    Microsoft Academic Search

    Wolfram Weckwerth

    2003-01-01

    ? Abstract The primary aim of “omic”,technologies is the nontargeted,identifica- tion of all gene products (transcripts, proteins, and metabolites) present in a specific biological sample. By their nature, these technologies reveal unexpected properties of biological systems. A second,and more,challenging aspect of omic technologies is the refined analysis of quantitative dynamics,in biological systems. For metabolomics, gas and liquid chromatography coupled to

  13. Studies of the electronic structure and biological activity of chosen 1,4-benzodiazepines by 35Cl NQR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Bronisz, K.; Ostafin, M.; Poleshchuk, O. Kh.; Mielcarek, J.; Nogaj, B.

    2006-11-01

    Selected derivatives of 1,4-benzodiazepine: lorazepam, lormetazepam, oxazepam and temazepam, used as active substances in anxiolytic drugs, have been studied by 35Cl NQR method in order to find the correlation between electronic structure and biological activity. The 35Cl NQR resonance frequencies ( ?Q) measured at 77 K have been correlated with the following parameters characterising their biological activity: biological half-life period ( t0.5), affinity to benzodiazepine receptor (IC 50) and mean dose equivalent. The results of experimental study of some benzodiazepine derivatives by nuclear quadrupole resonance of 35Cl nuclei are compared with theoretical results based on DFT calculations which were carried out by means of Gaussian'98 W software.

  14. Investigation of statistics strategies for improving the discriminating power of laser-induced breakdown spectroscopy for chemical and biological warfare agent simulants

    Microsoft Academic Search

    Chase A. Munson; Frank C. De Lucia; Thuvan Piehler; Kevin L. McNesby; Andrzej W. Miziolek

    2005-01-01

    Laser-induced breakdown spectroscopy spectra of bacterial spores, molds, pollens and nerve agent simulants have been acquired. The performance of several statistical methodologies–linear correlation, principal components analysis, and soft independent model of class analogy–has been evaluated for their ability to differentiate between the various samples. The effect of data selection (total spectra, peak intensities, and intensity ratios) and pre-treatments (e.g., averaging)

  15. Molecular Biology Biology 311

    E-print Network

    Lycan, Deborah E.

    Molecular Biology Biology 311 Fall 2013 Syllabus Instructor: Dr. Deborah Lycan Class: MWF 9@lclark.edu Website: http://legacy.lclark.edu/~lycan/Bio311/molecbiohomepage.html Textbook: Molecular Biology: Alberts et al., Molecular Biology of the Cell 4th edition (2002) Darnell et al., Molecular Cell Biology

  16. Theoretical Physics in Cellular Biology

    E-print Network

    Theoretical Physics in Cellular Biology: Some Illustrative Case Studies Living matter obeys in many areas of biology. This truism is becoming ever more relevant with the rapid growth of the ability of biological experiment to produce large amounts of quantitative data: comprehending that data surely

  17. Synthesis and quantitative analysis of plasma-targeted metabolites of catechin and epicatechin.

    PubMed

    Blount, Jack W; Redan, Benjamin W; Ferruzzi, Mario G; Reuhs, Bradley L; Cooper, Bruce R; Harwood, John S; Shulaev, Vladimir; Pasinetti, Giulio; Dixon, Richard A

    2015-03-01

    Grape seed polyphenolic extract (GSPE) rich in the flavan-3-ols (+)-catechin and (-)-epicatechin beneficially modulates Alzheimer's Disease phenotypes in animal models. The parent molecules in the extract are converted to a series of methylated and glucuronidated derivatives. To fully characterize these metabolites and establish a robust quantitative assay of their levels in biological fluids, we have implemented a partial synthetic approach utilizing chemical methylation followed by enzymatic glucuronidation. Liquid chromatography/time-of-flight mass spectrometry (LC-TOF-MS) and nuclear magnetic resonance (NMR) spectroscopy were used to assign unequivocal structures to the compounds. An analytical method using solid-phase extraction and LC-MS/MS in selective reaction monitoring mode (SRM) was validated for their quantitation in plasma. These studies provide a basis for improvements in future work on the bioavailability, metabolism, and mechanism of action of metabolites derived from dietary flavan-3-ols in a range of interventions. PMID:25671729

  18. Quantitative Analysen

    NASA Astrophysics Data System (ADS)

    Hübner, Philipp

    Der heilige Gral jeglicher Analytik ist, den wahren Wert bestimmen zu können. Dies bedingt quantitative Messmethoden, welche in der molekularen Analytik nun seit einiger Zeit zur Verfügung stehen. Das generelle Problem bei der Quantifizierung ist, dass wir meistens den wahren Wert weder kennen noch bestimmen können! Aus diesem Grund behelfen wir uns mit Annäherungen an den wahren Wert, indem wir aus Laborvergleichsuntersuchungen den Median oder den (robusten) Mittelwert berechnen oder indem wir einen Erwartungswert (expected value) aufgrund der Herstellung des Probenmaterials berechnen. Bei diesen Versuchen der Annäherung an den wahren Wert findet beabsichtigterweise eine Normierung der Analytik statt, entweder nach dem demokratischen Prinzip, dass die Mehrheit bestimmt oder durch zur Verfügungsstellung von geeignetem zertifiziertem Referenzmaterial. Wir müssen uns folglich bewusst sein, dass durch dieses Vorgehen zwar garantiert wird, dass die Mehrheit der Analysenlaboratorien gleich misst, wir jedoch dabei nicht wissen, ob alle gleich gut oder allenfalls gleich schlecht messen.

  19. Raman spectroscopy for noninvasive glucose measurements

    E-print Network

    Enejder, Annika M. K.

    We report the first successful study of the use of Raman spectroscopy for quantitative, noninvasive (“transcutaneous”) measurement of blood analytes, using glucose as an example. As an initial evaluation of the ability of ...

  20. Early detection of high-grade squamous intraepithelial lesions in the cervix with quantitative spectroscopic imaging

    E-print Network

    Lau, Condon

    Quantitative spectroscopy has recently been extended from a contact-probe to wide-area spectroscopic imaging to enable mapping of optical properties across a wide area of tissue. We train quantitative spectroscopic imaging ...

  1. Quantitative Biology Initiative Executive Committee Meeting Notes

    E-print Network

    (from the Leroi grant) and that student support for conferences may be available from the Grad School. b, conferences, bioinformatics workshop, stimulating preparation of grant proposals, and running the QB grad, Bob Cukier, and Charles Ofria Agenda: 1. Announcements: a. The Molecular Biophysics Training Grant

  2. Quarkonium spectroscopy

    SciTech Connect

    Scharre, D.L.

    1981-06-01

    Recent experimental investigations of heavy quark-antiquark bound state systems are reviewed. Results from SPEAR on charmonium spectroscopy and from DORIS and CESR on bottomonium spectroscopy are presented. The current status of the search for top is also discussed.

  3. Optical and Electron Spectrometry of Molecules of Biological Interest

    NASA Astrophysics Data System (ADS)

    Marinkovi?, B. P.; Milosavljevi?, A. R.; Maljkovi?, J. B.; Ševi?, D.; Petruševski, B. A.; Filipovi?, D. M.; Terzi?, M.; Pej?ev, V.

    2007-11-01

    Optical absorption and emission spectroscopy together with low energy electron interaction (elastic scattering, excitation, ionization, resonances) with biologically relevant molecules (nitrogen, oxygen, water, alcohols, tetrahydrofuran, tetrahydrofurfuril alcohol, 3-hydroxytetrahydrofuran, pyrimidine, glycine, alanine) are studied in order to understand radiation damage and to investigate the presence of pollutants in the atmosphere. Versatile high resolution electron spectrometers are used in the present study of electron-molecule interactions. Energy loss spectra were recorded for these molecules in order to identify electronic transitions from ground state to both allowed and optically forbidden states. Optical emission spectra have been recorded from gas discharge processes by low resolution optical spectrometer (Ocean Optics 2000). Also, electronic spectra were compared with high resolution synchrotron photoabsorption spectra where these spectra had been available. Experimental methods of absorption-based laser spectroscopy were reviewed being of the most widely used analytical tools for detection of a specific molecule and quantitative measurements, based on the Beer-Lambert absorption law.

  4. MathBench Biology Modules: Web-Based Math for All Biology Undergraduates

    ERIC Educational Resources Information Center

    Nelson, Karen C.; Marbach-Ad, Gili; Schneider, Katie; Thompson, Katerina V.; Shields, Patricia A.; Fagan, William F.

    2009-01-01

    Historically, biology has not been a heavily quantitative science, but this is changing rapidly (Ewing 2002; Gross 2000; Hastings and palmer 2003; Jungck 2005; Steen 2005). Quantitative approaches now constitute a key tool for modern biologists, yet undergraduate biology courses remain largely qualitative and descriptive. Although biology majors…

  5. BOOK REVIEW: Principles of Plasma Spectroscopy

    Microsoft Academic Search

    H. R. Griem

    1998-01-01

    This book gives a comprehensive treatment of plasma spectroscopy, the quantitative study of line and continuous radiation from high temperature plasmas. This highly interdisciplinary field combines elements of atomic, plasma and statistical physics, and has wide application to simulations and diagnostics of laboratory and astrophysical plasmas. Plasma spectroscopy is naturally intertwined with magnetic and inertial fusion energy science. Radiative processes

  6. Cobalt complexes with pyrazole ligands as catalyst precursors for the peroxidative oxidation of cyclohexane: X-ray absorption spectroscopy studies and biological applications.

    PubMed

    Silva, Telma F S; Martins, Luísa M D R S; Guedes da Silva, M Fátima C; Kuznetsov, Maxim L; Fernandes, Alexandra R; Silva, Ana; Pan, Chun-Jern; Lee, Jyh-Fu; Hwang, Bing-Joe; Pombeiro, Armando J L

    2014-04-01

    [CoCl(?-Cl)(Hpz(Ph))3]2 (1) and [CoCl2(Hpz(Ph))4] (2) were obtained by reaction of CoCl2 with HC(pz(Ph))3 and Hpz(Ph), respectively (Hpz(Ph)=3-phenylpyrazole). The compounds were isolated as air-stable solids and fully characterized by IR and far-IR spectroscopy, MS(ESI+/-), elemental analysis, cyclic voltammetry (CV), controlled potential electrolysis, and single-crystal X-ray diffraction. Electrochemical studies showed that 1 and 2 undergo single-electron irreversible Co(II)?Co(III) oxidations and Co(II)?Co(I) reductions at potentials measured by CV, which also allowed, in the case of dinuclear complex 1, the detection of electronic communication between the Co centers through the chloride bridging ligands. The electrochemical behavior of models of 1 and 2 were also investigated by density functional theory (DFT) methods, which indicated that the vertical oxidation of 1 and 2 (that before structural relaxation) affects mostly the chloride and pyrazolyl ligands, whereas adiabatic oxidation (that after the geometry relaxation) and reduction are mostly metal centered. Compounds 1 and 2 and, for comparative purposes, other related scorpionate and pyrazole cobalt complexes, exhibit catalytic activity for the peroxidative oxidation of cyclohexane to cyclohexanol and cyclohexanone under mild conditions (room temperature, aqueous H2O2). In?situ X-ray absorption spectroscopy studies indicated that the species derived from complexes 1 and 2 during the oxidation of cyclohexane (i.e., Ox-1 and Ox-2, respectively) are analogous and contain a Co(III) site. Complex 2 showed low in?vitro cytotoxicity toward the HCT116 colorectal carcinoma and MCF7 breast adenocarcinoma cell lines. PMID:24482364

  7. Marine Biology

    E-print Network

    Zaffino, Kyle

    2013-01-01

    this  door. ”   Marine  Biology   I  joined  the  military  RIVERSIDE   Marine  Biology   A Thesis submitted in partialBiology                                                                                                                        

  8. Relative versus absolute quantitation in disease glycomics.

    PubMed

    Moh, Edward S X; Thaysen-Andersen, Morten; Packer, Nicolle H

    2015-04-01

    The glycome of a diagnostic biological material such as blood, urine, saliva, tissue, or cell cultures comprises of a vast array of structurally distinct glycans attached to the protein complement. Aberrant glycan structures and distributions result from changes in specific glycosyltransferase activities and have different biological significance, making proper quantitation of glycans highly important. In this review, common HPLC/CE and LC-MS/MS-based methods for glycomics, their advantages and disadvantages, will be discussed with respect to the main quantitative strategies. With the increasing interest in absolute quantitation for glycomics, we discuss absolute and relative glycome quantitation and how it affects the resulting conclusions drawn from glycomics studies. We argue that while absolute quantitation of glycomes may be attractive for some areas of clinical glycomics, relative quantitation of glycans remains the most informative and time/cost-effective method to obtain biological insight into the regulation of the cellular glycosylation machinery and the synthesis of the resultant glycan structures in most research questions due to the enzymatic relatedness of the biosynthesized glycans. Recent developments in multiplexing of glycomes by the introduction of stable isotopic labeling of glycans show promise for providing another level of information to the existing benefits of relative quantitation. PMID:25684231

  9. NEW TECHNOLOGY Role of Frequency Domain Optical Spectroscopy

    E-print Network

    Fantini, Sergio

    ISS Inc., Champaign, Illinois Objective: Inability of continuous wave (CW) optical spectroscopyNEW TECHNOLOGY Role of Frequency Domain Optical Spectroscopy in the Detection of Neonatal Brain objective was to assess whether, and to what extent, the use of quantitative frequency domain spectroscopy

  10. Near-infrared spectroscopy for intracoronary detection of lipid-rich plaques to understand atherosclerotic plaque biology in man and guide clinical therapy.

    PubMed

    Erlinge, D

    2015-08-01

    Ischaemic heart disease is the leading cause of death worldwide. The common denominator for plaques causing acute coronary syndrome (ACS) is lipid accumulation, either as a lipid core or lipid pools. An intracoronary imaging device to detect lipid-rich plaques (LRPs) could therefore identify most of the plaques causing ACS and sudden death. Near-infrared spectroscopy combined with intravascular ultrasound (NIRS-IVUS) is a promising new intracoronary imaging method that is able to specifically quantify lipid accumulation measured as the lipid core burden index (LCBI). NIRS-IVUS is highly specific for the identification of ST-elevation myocardial infarction (STEMI) and non-ST-elevation myocardial infarction (NSTEMI) culprit plaques usually in the form of a circular LRP. NIRS-IVUS may assist in defining the aetiology of coronary events. The effect of cholesterol-lowering therapy on the lipid core can be measured in coronary plaques in patients, and NIRS-IVUS may be a useful tool for drug development in phase II studies as a surrogate end-point for future ACS. Plaques with a high LCBI have an increased risk of peri-procedural events. NIRS-IVUS can help to define the diameter and length of stents to avoid procedure-related complications. Increased coronary LCBI predicts a higher risk of future cardiovascular events. Lipid core detection using NIRS may help to identify vulnerable plaques to treat them before they cause ACS or sudden death. PMID:26096457

  11. High resolution UV resonance enhanced two-photon ionization spectroscopy with mass selection of biologically relevant molecules in the gas phase

    NASA Astrophysics Data System (ADS)

    Chervenkov, S.; Wang, P. Q.; Karaminkov, R.; Chakraborty, T.; Braun, Juergen E.; Neusser, Hans J.

    2005-04-01

    The high resolution Doppler-free resonance-enhanced two-photon ionization (R2PI) spectroscopy with mass selection of jet-cooled (2-12 K) molecular species is a powerful experimental method providing comprehensive information on both isolated molecules and molecular clusters. We have demonstrated for the first time that this technique can be applied to large molecules and provides detailed information on their conformational structure. It allows rotationally resolved (FWHM = 70 MHz) spectra of the vibronic bands of the S1<--S0 electronic transition of the studied molecular systems to be measured. A specially designed computer-assisted fitting routine based on genetic algorithms is used to determine their rotational constants in the ground and excited electronic states, respectively, and the transition moment ratio. To interpret the experimental information and to discriminate and unambiguously assign the observed approach to the study of the neurotransmitter molecule, ephedrine. The results elucidate the role of the intramolecular hydrogen bonds stabilizing the respective conformations and affecting their intrinsic properties.

  12. Ratiometric biological nanosensors.

    PubMed

    Fisher, Kate M; Campbell, Colin J

    2014-08-01

    The measurement of intracellular analytes has been key in understanding cellular processes and function, and the use of biological nanosensors has revealed the spatial and temporal variation in their concentrations. In particular, ratiometric nanosensors allow quantitative measurements of analyte concentrations. The present review focuses on the recent advances in ratiometric intracellular biological nanosensors, with an emphasis on their utility in measuring analytes that are important in cell function. PMID:25109976

  13. Low-loss Electron Energy-loss Spectroscopy and Dielectric Function of Biological and Geological Polymorphs of CaCO(3).

    PubMed

    Katti; Qian; Frech; Sarikaya

    1999-09-01

    : Previous work on microstructural characterization has shown variations in terms of defects and organization of nanostructures in the two polymorphs of calcium carbonate, calcite, and aragonite in mollusc shells. Large variations in mechanical properties are observed between these sections which have been attributed to variations in composite microstructure as well as intrinsic properties of the inorganic phases. Here we present local low-loss electron energy-loss spectroscopic (EELS) study of calcitic and aragonitic regions of abalone shell that were compared to geological (single-crystal) counterpart polymorphs to reveal intrinsic differences that could be related to organismal effects in biomineralization. In both sets of samples, local dielectric function is computed using Kramer-Kronig analysis. The electronic structures of biogenic and geological calcitic materials are not significantly different. On the other hand, electronic structure of biogenic aragonite is remarkably different from that of geological aragonite. This difference is attributed to the increased contribution from single electron excitations in biogenic aragonite as compared to that of geological aragonite. Furthermore, an apparent bound characteristic of the Re(1/epsilon) is observed for biological samples which suggests a "quasi-plasmon"-like nature of the collective excitations. Implications of these changes are discussed in the context of macromolecular involvement in the making of the microstructures and properties in biogenic phases. PMID:10473681

  14. Quantitation of carcinogen bound protein adducts by fluorescence measurements

    NASA Astrophysics Data System (ADS)

    Gan, Liang-Shang; Otteson, Michael S.; Doxtader, Mark M.; Skipper, Paul L.; Dasari, Ramachandra R.; Tannenbaum, Steven R.

    1989-01-01

    A highly significant correlation of aflatoxin B 1 serum albumin adduct level with daily aflatoxin B 1 intake was observed in a molecular epidemiological study of aflatoxin carcinogenesis which used conventional fluorescence spectroscopy methods for adduct quantitation. Synchronous fluorescence spectroscopy and laser induced fluorescence techniques have been employed to quantitate antibenzo[ a]pyrene diol epoxide derived globin peptide adducts. Fast and efficient methods to isolate the peptide adducts as well as eliminate protein fluorescence background are described. A detection limit of several femtomoles has been achieved. Experimental and technical considerations of low temperature synchronous fluorescence spectroscopy and fluorescence line narrowing to improve the detection sensitivities are also presented.

  15. Turbidity corrected Raman spectroscopy for blood analyte detection

    PubMed Central

    Barman, Ishan; Singh, Gajendra P.; Dasari, Ramachandra R.; Feld, Michael S.

    2010-01-01

    A major challenge in quantitative biological Raman spectroscopy, particularly as applied to transcutaneous Raman spectroscopy measurements, is overcoming the deleterious effects of scattering and absorption (turbidity). The Raman spectral information is distorted by multiple scattering and absorption events in the surrounding medium, thereby diminishing the prediction capability of the calibration model. To account for these distortions, we present a novel analytical method, that we call turbidity corrected Raman spectroscopy (TCRS), which is based on the photon migration approach and employs alternate acquisition of diffuse reflectance and Raman spectra. We demonstrate that on application of TCRS, the widely varying Raman spectra observed from a set of tissue phantoms having the same concentration of Raman scatterers but different turbidities tend to collapse onto a single spectral profile. Furthermore, in a prospective study employing physical tissue models with varying turbidities and randomized concentrations of Raman scatterers and interferents, a 20% reduction in prediction error is obtained by applying the turbidity correction procedure to the observed Raman spectra. PMID:19413337

  16. Basic Principles of Spectroscopy

    NASA Astrophysics Data System (ADS)

    Penner, Michael H.

    Spectroscopy deals with the production, measurement, and interpretation of spectra arising from the interaction of electromagnetic radiation with matter. There are many different spectroscopic methods available for solving a wide range of analytical problems. The methods differ with respect to the species to be analyzed (such as molecular or atomic spectroscopy), the type of radiation-matter interaction to be monitored (such as absorption, emission, or diffraction), and the region of the electromagnetic spectrum used in the analysis. Spectroscopic methods are very informative and widely used for both quantitative and qualitative analyses. Spectroscopic methods based on the absorption or emission of radiation in the ultraviolet (UV), visible (Vis), infrared (IR), and radio (nuclear magnetic resonance, NMR) frequency ranges are most commonly encountered in traditional food analysis laboratories. Each of these methods is distinct in that it monitors different types of molecular or atomic transitions. The basis of these transitions is explained in the following sections.

  17. BIOLOGICAL SCIENCES Contemporary biological science

    E-print Network

    BIOLOGICAL SCIENCES Contemporary biological science covers a range of diverse and overlapping in cellular and molecular biology. Wichita State University's Department of Biological Sciences offers courses in most aspects of contemporary biological science. Our required core courses will expose you

  18. Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes

    PubMed Central

    Ruprecht, Verena; Wieser, Stefan; Marguet, Didier; Schütz, Gerhard J.

    2011-01-01

    Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresolution chronoscopy) are still lacking. Here, we show that recently introduced spot-variation fluorescence correlation spectroscopy allows for sensing transient confinement times of membrane constituents at dramatically improved resolution. Using standard diffraction-limited optics, spot-variation fluorescence correlation spectroscopy captures signatures of single retardation events far below the transit time of the tracer through the focal spot. We provide an analytical description of special cases of transient binding of a tracer to pointlike traps, or association of a tracer with nanodomains. The influence of trap mobility and the underlying binding kinetics are quantified. Experimental approaches are suggested that allow for gaining quantitative mechanistic insights into the interaction processes of membrane constituents. PMID:21641330

  19. Examination of pterins using surface-enhanced Raman spectroscopy using low-volume samples

    NASA Astrophysics Data System (ADS)

    Mehigan, Sam; Smyth, Ciarán.; McCabe, Eithne M.

    2013-02-01

    Raman spectroscopy is a very useful tool for analysing compounds, however its ability to detect low concentrations of a substance are very limited. Surface Enhanced Raman Spectroscopy (SERS) overcomes that issue and is reported to have achieved single molecule detection. Its main shortcoming is the reproducibility of SERS spectra. The variation in signal strength prevents SERS from being usable as a quantitative analytical technique. This variability have been investigated in this work and key factors in improving reproducibility have been considered. Pterins, such as xanthopterin are studied in this paper. Pterins are a group of biological compounds that are found in nature in colour pigmentation and in mammal's metabolic pathways. Moreover, they have been identified in abnormal concentrations in the urine of people suffering from certain kinds of cancer. The potential for pterin's use as a cancer diagnostic points to the importance of SERS detection for pterins.

  20. Digital PCR and Quantitation

    E-print Network

    Perkins, Richard A.

    Applied Genetics Digital PCR and Quantitation Ross Haynes Research Biologist, Applied Genetics Group Forensics@NIST 2012 Meeting Gaithersburg, MD November 28, 2012 #12;Applied Genetics Agenda · Why quantitate with qPCR? · How digital PCR Will Help Quantitation · Quantitative PCR versus Digital PCR

  1. Pathway information for systems biology

    Microsoft Academic Search

    Michael P. Cary; Gary D. Bader; Chris Sander

    2005-01-01

    Pathway information is vital for successful quantitative modeling of biological systems. The almost 170 online pathway databases vary widely in coverage and representation of biological processes, making their use extremely difficult. Future pathway information systems for querying, visualization and analysis must support standard exchange formats to successfully integrate data on a large scale. Such integrated systems will greatly facilitate the

  2. Vibrational Spectroscopy and Astrobiology

    NASA Technical Reports Server (NTRS)

    Chaban, Galina M.; Kwak, D. (Technical Monitor)

    2001-01-01

    Role of vibrational spectroscopy in solving problems related to astrobiology will be discussed. Vibrational (infrared) spectroscopy is a very sensitive tool for identifying molecules. Theoretical approach used in this work is based on direct computation of anharmonic vibrational frequencies and intensities from electronic structure codes. One of the applications of this computational technique is possible identification of biological building blocks (amino acids, small peptides, DNA bases) in the interstellar medium (ISM). Identifying small biological molecules in the ISM is very important from the point of view of origin of life. Hybrid (quantum mechanics/molecular mechanics) theoretical techniques will be discussed that may allow to obtain accurate vibrational spectra of biomolecular building blocks and to create a database of spectroscopic signatures that can assist observations of these molecules in space. Another application of the direct computational spectroscopy technique is to help to design and analyze experimental observations of ice surfaces of one of the Jupiter's moons, Europa, that possibly contains hydrated salts. The presence of hydrated salts on the surface can be an indication of a subsurface ocean and the possible existence of life forms inhabiting such an ocean.

  3. Quantitative Mineralogical Characterization of Oregon Erionite

    NASA Astrophysics Data System (ADS)

    Dogan, A.; Dogan, M.; Ballirano, P.

    2006-12-01

    Erionite has been classified as Group-I Human Carcinogen by the IARC Working Group. Fibrogenetic potential of erionite varies from low to high yield of mesothelioma. This may require quantitative characterization of physicochemical properties of erionite before any experimental design. The toxicity of the mineral is such that quantitative characterization of erionite is extremely important. Yet, often the erionite specimens were incompletely or incorrectly characterized throwing doubt on the results of the work. For example, none of the Turkish erionite published until recently had balance error (E%) less than 10%, and Mg cation of the type specimen of erionite-Ca from Maze, Niigita Prefecture, Japan is more than 0.8. In the present study, erionite sample near Rome, Oregon have been quantitatively characterized using powder x-ray diffraction, Reitveld refinement, scanning electron microscopy, energy dispersive spectroscopy, inductively coupled plasma - mass spectroscopy, and Massbauer spectroscopy. The cell parameters of the erionite-K from Oregon is computed as a=13.2217(2) Å and c=15.0671 Å; chemical composition of the erionite as major oxides, rare earth elements and other trace elements, are characterized quantitatively. Crystal chemistries of the erionite are computed based upon the quidelines of the IMAA zeolite report of 1997.

  4. Quantitative determination of the absorption spectraof chromophores in strongly scattering

    E-print Network

    Fantini, Sergio

    the efficiencyand ease ofuse ofthe LED technique, whichlends itself to in vivo spectroscopy of biological tissues the endogenous chromophores are When this research was performed, B. Barbieri was with ISS, Inc., 2604 North

  5. Combinational pixel-by-pixel and object-level classifying, segmenting, and agglomerating in performing quantitative image analysis that distinguishes between healthy non-cancerous and cancerous cell nuclei and delineates nuclear, cytoplasm, and stromal material objects from stained biological tissue materials

    DOEpatents

    Boucheron, Laura E

    2013-07-16

    Quantitative object and spatial arrangement-level analysis of tissue are detailed using expert (pathologist) input to guide the classification process. A two-step method is disclosed for imaging tissue, by classifying one or more biological materials, e.g. nuclei, cytoplasm, and stroma, in the tissue into one or more identified classes on a pixel-by-pixel basis, and segmenting the identified classes to agglomerate one or more sets of identified pixels into segmented regions. Typically, the one or more biological materials comprises nuclear material, cytoplasm material, and stromal material. The method further allows a user to markup the image subsequent to the classification to re-classify said materials. The markup is performed via a graphic user interface to edit designated regions in the image.

  6. TOPICAL REVIEW: Prospects for in vivo Raman spectroscopy

    Microsoft Academic Search

    E. B. Hanlon; R. Manoharan; T.-W. Koo; K. E. Shafer; J. T. Motz; M. Fitzmaurice; J. R. Kramer; I. Itzkan; R. R. Dasari; M. S. Feld

    2000-01-01

    Raman spectroscopy is a potentially important clinical tool for real-time diagnosis of disease and in situ evaluation of living tissue. The purpose of this article is to review the biological and physical basis of Raman spectroscopy of tissue, to assess the current status of the field and to explore future directions. The principles of Raman spectroscopy and the molecular level

  7. [Studies of biologic activation associated with molecular receptor increase and tumor response in ChL6/L6 protocol patients; Studies in phantoms; Quantitative SPECT; Preclinical studies; and Clinical studies]. DOE annual report, 1994--95

    SciTech Connect

    DeNardo, S.J.

    1995-12-31

    The authors describe results which have not yet been published from their associated studies listed in the title. For the first, they discuss Lym-1 single chain genetically engineered molecules, analysis of molecular genetic coded messages to enhance tumor response, and human dosimetry and therapeutic human use radiopharmaceuticals. Studies in phantoms includes a discussion of planar image quantitation, counts coincidence correction, organ studies, tumor studies, and {sup 90}Y quantitation with Bremsstrahlung imaging. The study on SPECT discusses attenuation correction and scatter correction. Preclinical studies investigated uptake of {sup 90}Y-BrE-3 in mice using autoradiography. Clinical studies discuss image quantitation verses counts from biopsy samples, S factors for radiation dose calculation, {sup 67}Cu imaging studies for lymphoma cancer, and {sup 111}In MoAb imaging studies for breast cancer to predict {sup 90}Y MoAb therapy.

  8. IR Spectroscopy

    NSDL National Science Digital Library

    Reich, Ieva

    These organic chemistry quiz questions from the JCE question bank focus on the topic of Infrared Spectroscopy. Students can use these as review material or to prepare for exams. Answer keys are made available to teachers for a small fee.

  9. Amateur Spectroscopy

    NSDL National Science Digital Library

    The main objective of this website is to teach the amateur astronomer how to perform spectroscopy. The first part of the website is dedicated to establishing a theoretical foundation, in which the process of spectroscopy is explained: how spectral lines are created, the operation of a spectroscope, and grating spectroscopy. Later on, all these concepts are applied to astronomy, specifically to stars. Using spectroscopy, astronomers are able to identify the composition of stars, which leads to a classification catalog dependent on the spectral lines observed. Several spectra, from different objects like supernovae and stars are presented for the user to observe, along with distinctive spectral lines from some chemical elements. Finally, this website motivates amateurs by suggesting several project ideas along with a list of references and instrument suppliers.

  10. Quantitative measurement of cyanide species in simulated ferrocyanide Hanford waste

    SciTech Connect

    Bryan, S.A.; Pool, K.H.; Matheson, J.D.

    1993-02-01

    Analytical methods for the quantification of cyanide species in Hanford simulated high-level radioactive waste were pursued in this work. Methods studied include infrared spectroscopy (solid state and solution), Raman spectroscopy, Moessbauer spectroscopy, X-ray diffraction, scanning electron microscopy-electron dispersive spectroscopy (SEM-EDS), and ion chromatography. Of these, infrared, Raman, X-ray diffraction, and ion chromatography techniques show promise in the concentration range of interest. Quantitation limits for these latter four techniques were demonstrated to be approximately 0.1 wt% (as cyanide) using simulated Hanford wastes.

  11. EM Algorithm for Mapping Quantitative Trait Loci in Multivalent Tetraploids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multivalent tetraploids that include many plant species, such as potato, sugarcane and rose, are of paramount importance to agricultural production and biological research. Quantitative trait locus (QTL) mapping in multivalent tetraploids is challenged by their unique cytogenetic properties, such ...

  12. Biological Technicians

    MedlinePLUS

    ... biological and medical scientists conduct laboratory tests and experiments. Work Environment Biological technicians typically work in laboratories. ... biological and medical scientists conduct laboratory tests and experiments. Duties Biological technicians typically do the following: Set ...

  13. Applications of Process Algebra in Systems Biology

    E-print Network

    Goldschmidt, Christina

    Applications of Process Algebra in Systems Biology Nicolas Wu a a Brasenose College, University in systems biology. This survey reveals that although progress has been made in using process algebra are suggested. 1 Introduction The aim of systems biology is to be able to formally and quantitatively reason

  14. Biology Online

    NSDL National Science Digital Library

    Richard Lees

    Biology Online provides a dictionary of biological terms, tutorials, and biology-related links categorized into dozens of subfields. The tutorials cover the following topics: adaptation, cell biology, developmental biology, freshwater ecology, genetics and evolution, neurology, regulation in biological systems, and the origin and evolution of life.

  15. ARGET–ATRP Synthesis and Characterization of PNIPAAm Brushes for Quantitative Cell Detachment Studies

    PubMed Central

    Shivapooja, Phanindhar; Ista, Linnea K.; Canavan, Heather E.; Lopez, Gabriel P.

    2012-01-01

    Stimuli responsive (or “smart”) polymer brushes represent a non-toxic approach for achieving release of biofouling layers. Thermo-responsive poly(N-isopropylacrylamide) (PNIPAAm) polymer brushes have been shown to modulate bacterial adhesion and release through transition between temperatures above and below the lower critical solution temperature (LCST ~32 °C) of PNIPAAm in water. In this article, we describe a convenient method to synthesize grafted PNIPAAm brushes over large areas for biological studies using a relatively simple and rapid method which allows atom transfer radical polymerization (ATRP) in presence of air using the activator regenerated electron transfer (ARGET) mechanism. PNIPAAm brushes were characterized using X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectroscopy, Fourier transform infrared spectroscopy, ellipsometry, and contact angle measurements. Our studies demonstrate that uniform, high purity PNIPAAm brushes with controlled and high molecular weight can be easily produced over large areas using ARGET–ATRP. We also report the use of a spinning disk apparatus to systematically and quantitatively study the detachment profiles of bacteria from PNIPAAm surfaces under a range (0–400 dyne/cm2) of shear stresses. PMID:22589075

  16. Quantitative imaging as cancer biomarker

    NASA Astrophysics Data System (ADS)

    Mankoff, David A.

    2015-03-01

    The ability to assay tumor biologic features and the impact of drugs on tumor biology is fundamental to drug development. Advances in our ability to measure genomics, gene expression, protein expression, and cellular biology have led to a host of new targets for anticancer drug therapy. In translating new drugs into clinical trials and clinical practice, these same assays serve to identify patients most likely to benefit from specific anticancer treatments. As cancer therapy becomes more individualized and targeted, there is an increasing need to characterize tumors and identify therapeutic targets to select therapy most likely to be successful in treating the individual patient's cancer. Thus far assays to identify cancer therapeutic targets or anticancer drug pharmacodynamics have been based upon in vitro assay of tissue or blood samples. Advances in molecular imaging, particularly PET, have led to the ability to perform quantitative non-invasive molecular assays. Imaging has traditionally relied on structural and anatomic features to detect cancer and determine its extent. More recently, imaging has expanded to include the ability to image regional biochemistry and molecular biology, often termed molecular imaging. Molecular imaging can be considered an in vivo assay technique, capable of measuring regional tumor biology without perturbing it. This makes molecular imaging a unique tool for cancer drug development, complementary to traditional assay methods, and a potentially powerful method for guiding targeted therapy in clinical trials and clinical practice. The ability to quantify, in absolute measures, regional in vivo biologic parameters strongly supports the use of molecular imaging as a tool to guide therapy. This review summarizes current and future applications of quantitative molecular imaging as a biomarker for cancer therapy, including the use of imaging to (1) identify patients whose tumors express a specific therapeutic target; (2) determine whether the drug reaches the target; (3) identify an early response to treatment; and (4) predict the impact of therapy on long-term outcomes such as survival. The manuscript reviews basic concepts important in the application of molecular imaging to cancer drug therapy, in general, and will discuss specific examples of studies in humans, and highlight future directions, including ongoing multi-center clinical trials using molecular imaging as a cancer biomarker.

  17. TIME-RESOLVED VIBRATIONAL SPECTROSCOPY

    SciTech Connect

    Andrei Tokmakoff, MIT (Conference Chair) [Conference Chair; Paul Champion, Northeastern University; Edwin J. Heilweil, NIST; Keith A. Nelson, MIT; Larry Ziegler, Boston University

    2009-05-14

    This document contains the Proceedings from the 14th International Conference on Time-Resolved Vibrational Spectroscopy, which was held in Meredith, NH from May 9-14, 2009. The study of molecular dynamics in chemical reaction and biological processes using time-resolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE�s Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time-resolved spectroscopy is central to all five of DOE�s grand challenges for fundamental energy science. The Time-Resolved Vibrational Spectroscopy conference is organized biennially to bring the leaders in this field from around the globe together with young scientists to discuss the most recent scientific and technological advances. The latest technology in ultrafast infrared, Raman, and terahertz spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  18. Robust network calibration and therapy design in systems biology

    E-print Network

    Kim, Bo S. (Bo Sung)

    2010-01-01

    Mathematical modeling of biological networks is under active research, receiving attention for its ability to quantitatively represent the modeler's systems-level understanding of network functionalities. Computational ...

  19. Laser-induced plasma spectroscopy: principles, methods and applications

    SciTech Connect

    Lazic, Violeta; Colao, Francesco; Fantoni, Roberta; Spizzichino, Valeria [ENEA, FIS-LAS, V. E. Fermi 45, Frascati (RM) (Italy); Jovicevic, Sonja [Institute of Physics, 11080 Belgrade, Pregrevica 118 (Serbia and Montenegro)

    2006-12-01

    Principles of the Laser Induced Plasma Spectroscopy and its advances are reported. Methods for obtaining quantitative analyses are described, together with discussion of some applications and the specific problems.

  20. Photoacoustic spectroscopy of condensed matter

    NASA Technical Reports Server (NTRS)

    Somoano, R. B.

    1978-01-01

    Photoacoustic spectroscopy is a new analytical tool that provides a simple nondestructive technique for obtaining information about the electronic absorption spectrum of samples such as powders, semisolids, gels, and liquids. It can also be applied to samples which cannot be examined by conventional optical methods. Numerous applications of this technique in the field of inorganic and organic semiconductors, biology, and catalysis have been described. Among the advantages of photoacoustic spectroscopy, the signal is almost insensitive to light scattering by the sample and information can be obtained about nonradiative deactivation processes. Signal saturation, which can modify the intensity of individual absorption bands in special cases, is a drawback of the method.

  1. A Holistic Approach to Marine Eco-Systems Biology

    E-print Network

    Follows, Michael J.

    With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical ...

  2. THz-Spectroscopy of Biological Molecules

    Microsoft Academic Search

    T. R. Globus; D. L. Woolard; T. Khromova; T. W. Crowe; M. Bykhovskaia; B. L. Gelmont; J. Hesler; A. C. Samuels

    2003-01-01

    The terahertz frequency absorption spectraof DNA molecules reflect low-frequencyinternal helical vibrations involvingrigidly bound subgroups that are connectedby the weakest bonds, including thehydrogen bonds of the DNA base pairs,and\\/or non-bonded interactions. Althoughnumerous difficulties make the directidentification of terahertz phonon modes inbiological materials very challenging, ourresearch has shown that such measurementsare both possible and fruitful. Spectra ofdifferent DNA samples reveal a large

  3. Infrared Spectroscopy

    NSDL National Science Digital Library

    C. P. Sherman Hsu

    This 38-page PDF document is a chapter from the Handbook of Instrumental Techniques for Analytical Chemistry. The chapter explains how infrared spectroscopy works (no comma) along with its general uses, common applications, range and limitations. Also included are spectrometer designs, information about sample preparation, analytical methods, related methods such as gas chromotography and diffuse reflectance, and costs and instrument vendors.

  4. Treatment assessment of radiotherapy using MR functional quantitative imaging

    PubMed Central

    Chang, Zheng; Wang, Chunhao

    2015-01-01

    Recent developments in magnetic resonance (MR) functional quantitative imaging have made it a potentially powerful tool to assess treatment response in radiation therapy. With its abilities to capture functional information on underlying tissue characteristics, MR functional quantitative imaging can be valuable in assessing treatment response and as such to optimize therapeutic outcome. Various MR quantitative imaging techniques, including diffusion weighted imaging, diffusion tensor imaging, MR spectroscopy and dynamic contrast enhanced imaging, have been investigated and found useful for assessment of radiotherapy. However, various aspects including data reproducibility, interpretation of biomarkers, image quality and data analysis impose challenges on applications of MR functional quantitative imaging in radiotherapy assessment. All of these challenging issues shall be addressed to help us understand whether MR functional quantitative imaging is truly beneficial and contributes to future development of radiotherapy. It is evident that individualized therapy is the future direction of patient care. MR functional quantitative imaging might serves as an indispensable tool towards this promising direction. PMID:25628799

  5. Quantitative Measurements of HO2 and other products of n-butane oxidation (H2O2, H2O, CH2O, and C2H4) at elevated temperatures by direct coupling of a jet-stirred reactor with sampling nozzle and cavity ring-down spectroscopy (cw-CRDS).

    PubMed

    Djehiche, Mokhtar; Le Tan, Ngoc Linh; Jain, Chaithanya D; Dayma, Guillaume; Dagaut, Philippe; Chauveau, Christian; Pillier, Laure; Tomas, Alexandre

    2014-11-26

    For the first time quantitative measurements of the hydroperoxyl radical (HO2) in a jet-stirred reactor were performed thanks to a new experimental setup involving fast sampling and near-infrared cavity ring-down spectroscopy at low pressure. The experiments were performed at atmospheric pressure and over a range of temperatures (550-900 K) with n-butane, the simplest hydrocarbon fuel exhibiting cool flame oxidation chemistry which represents a key process for the auto-ignition in internal combustion engines. The same technique was also used to measure H2O2, H2O, CH2O, and C2H4 under the same conditions. This new setup brings new scientific horizons for characterizing complex reactive systems at elevated temperatures. Measuring HO2 formation from hydrocarbon oxidation is extremely important in determining the propensity of a fuel to follow chain-termination pathways from R + O2 compared to chain branching (leading to OH), helping to constrain and better validate detailed chemical kinetics models. PMID:25381864

  6. Quantitative spectroscopic imaging for noninvasive early cancer detection

    PubMed Central

    Yu, Chung-Chieh; Lau, Condon; O’Donoghue, Geoff; Mirkovic, Jelena; McGee, Sasha; Galindo, Luis; Elackattu, Alphi; Stier, Elizabeth; Grillone, Gregory; Badizadegan, Kamran; Dasari, Ramachandra R.; Feld, Michael S.

    2008-01-01

    We report a fully quantitative spectroscopy imaging instrument for wide area detection of early cancer (dysplasia). This instrument provides quantitative maps of tissue biochemistry and morphology, making it a potentially powerful surveillance tool for objective early cancer detection. We describe the design, construction, calibration, and first clinical application of this new system. We demonstrate its accuracy using physical tissue models. We validate its diagnostic ability on a resected colon adenoma, and demonstrate feasibility of in vivo imaging in the oral cavity. PMID:18825262

  7. Development of fiber optic sensor based on laser Raman spectroscopy

    Microsoft Academic Search

    Vidhu Shekhar Tiwari

    2008-01-01

    Laser Raman Spectroscopy (LRS) has received worldwide acknowledgement as a powerful molecular 'finger print' technique. The Raman spectrum of sample contains useful information such as molecular identity, composition, constituent's concentration ratio etc. These information are manifested in the Raman spectrum in band heights, peak wavelength, band areas etc. The basis of quantitative analysis in Raman spectroscopy lies in the measurement

  8. Nanoscale Electromechanics of Ferroelectric and Biological Systems: A New Dimension in Scanning Probe Microscopy

    SciTech Connect

    Kalinin, Sergei V [ORNL; Rodriguez, Brian J [ORNL; Jesse, Stephen [ORNL; Karapetian, Edgar [ORNL; Mirman, B [Suffolk University, Boston; Eliseev, E. A. [National Academy of Science of Ukraine, Kiev, Ukraine; Morozovska, A. N. [National Academy of Science of Ukraine, Kiev, Ukraine

    2007-01-01

    Functionality of biological and inorganic systems ranging from nonvolatile computer memories and microelectromechanical systems to electromotor proteins and cellular membranes is ultimately based on the intricate coupling between electrical and mechanical phenomena. In the past decade, piezoresponse force microscopy (PFM) has been established as a powerful tool for nanoscale imaging, spectroscopy, and manipulation of ferroelectric and piezoelectric materials. Here, we give an overview of the fundamental image formation mechanism in PFM and summarize recent theoretical and technological advances. In particular, we show that the signal formation in PFM is complementary to that in the scanning tunneling microscopy (STM) and atomic force microscopy (AFM) techniques, and we discuss the implications. We also consider the prospect of extending PFM beyond ferroelectric characterization for quantitative probing of electromechanical behavior in molecular and biological systems and high-resolution probing of static and dynamic polarization switching processes in low-dimensional ferroelectric materials and heterostructures.

  9. Total internal reflection Raman spectroscopy.

    PubMed

    Woods, David A; Bain, Colin D

    2012-01-01

    Total internal reflection (TIR) Raman spectroscopy is an experimentally straightforward, surface-sensitive technique for obtaining chemically specific spectroscopic information from a region within approximately 100-200 nm of a surface. While TIR Raman spectroscopy has long been overshadowed by surface-enhanced Raman scattering, with modern instrumentation TIR Raman spectra can be acquired from sub-nm thick films in only a few seconds. In this review, we describe the physical basis of TIR Raman spectroscopy and illustrate the performance of the technique in the diverse fields of surfactant adsorption, liquid crystals, lubrication, polymer films and biological interfaces, including both macroscopic structures such as the surfaces of leaves, and microscopic structures such as lipid bilayers. Progress, and challenges, in using TIR Raman to obtain depth profiles with sub-diffraction resolution are described. PMID:22003492

  10. Modular languages for systems and synthetic biology 

    E-print Network

    Pedersen, Michael

    2010-01-01

    Systems biology is a rapidly growing field which seeks a refined quantitative understanding of organisms, particularly studying how molecular species such as metabolites, proteins and genes interact in cells to form the ...

  11. Electronic spectroscopies

    Microsoft Academic Search

    B. M. Weckhuysen; R. A. Schoonheydt

    2000-01-01

    Diffuse reflectance spectroscopy (DRS) in the ultraviolet, visible and near-infrared\\u000aregion is a versatile spectroscopic technique, as both d-d and charge transfer\\u000atransitions of supported TMI can be probed. One of the advantages of electronic\\u000aspectroscopy is that the obtained information is directly chemical since the outer shell\\u000aelectrons of the TMI are probed and provide information about the oxidation

  12. Impedance spectroscopy

    Microsoft Academic Search

    J. Ross Macdonald

    1992-01-01

    Impedance spectroscopy (IS) is a general term that subsumes the small-signal measurement of the linear electrical response\\u000a of a material of interest (including electrode effects) and the subsequent analysis of the response to yield useful information\\u000a about the physicochemical properties of the system. Analysis is generally carried out in the frequency domain, although measurements\\u000a are sometimes made in the time

  13. Surface analysis with Auger electron spectroscopy

    NASA Astrophysics Data System (ADS)

    Grant, J. T.

    Experimental aspects of Auger electron spectroscopy (AES) as applied to solid surfaces are reviewed. Areas considered include instrumentation, methods of excitation, acquisition of spectra, chemical effects, quantitative analysis, depth profiling and mapping. This review is designed to give the reader a comprehensive view of experimental aspects of AES with suitable references for more detailed information.

  14. Fundamental quantitative analysis of microbial activity in aquifer bioreclamation; and Modeling the transport of biologically and chemically reactive solutes in a two-dimensional, heterogeneous intermediate scale system. Semi-annual progress report, August 1991--March 1992

    SciTech Connect

    Rittmann, B.E.; Valocchi, A.J. [Illinois Univ., Urbana, IL (United States). Dept. of Civil Engineering; Baveye, P. [Cornell Univ., Ithaca, NY (United States). Dept. of Agronomy

    1992-12-31

    This report is the semi-annual progress report for the second half of the third year. The project has four primary areas: (1) biodegradation of poorly soluble organic contaminants; (2) dual-limitation kinetics of electron donors and acceptors; (3) two-dimensional modeling of biofilm reactions in nonhomogeneous porous media; and (4) biologically induced clogging in porous media. For each area, this report presents a brief summary of the previous progress, as well as reporting this period`s progress. In addition plans for future work are included.

  15. Laser Spectroscopy

    NASA Astrophysics Data System (ADS)

    Katori, H.; Yoneda, H.; Nakagawa, K.; Shimizu, F.

    2010-02-01

    Anderson localization of matter-waves in a controlled disorder: a quantum simulator? / A. Aspect ... [et al.] -- Squeezing and entanglement in a Bose-Einstein condensate / C. Gross ... [et al.] -- New physics in dipolar Bose-Einstein condensates / Y. Kawaguchi, H. Saito, and M. Ueda -- Observation of vacuum fluctuations in a spinor Bose-Einstein condensate / C. Klempt ... [et al.] -- Negative-index media for matter waves / F. Perales ... [et al.] -- Entanglement of two individual atoms using the Rydberg blockade / A. Browaeys ... [et al.] -- Array of mesoscopic ensembles on a magnetic atom chip / A. F. Tauschinsky ... [et al.] -- Stability of the proton-to-electron mass ratio tested with molecules using an optical link to primary clock / A. Amy-Klein ... [et al.] -- Metastable helium: lifetime measurements using cold atoms as a test of QED / K. G. H. Baldwin ... [et al.] -- Optical lattice clocks with single occupancy bosons and spin-polarized fermions toward 10[symbol] accuracy / M. Takamoto ... [et al.] -- Frequency measurements of Al[symbol] and Hg[symbol] optical standards / W. M. Itano ... [et al.] -- Switching of light with light using cold atoms inside a hollow optical fiber / M. Bajcsy ... [et al.] -- Room-temperature atomic ensembles for quantum memory and magnetometry / K. Jensen ... [et al.] -- Components for multi-photon non-classical state preparation and measurement / G. Puentes ... [et al.] -- Quantum field state measurement and reconstruction in a cavity by quantum nondemolition photon counting / M. Brune ... [et al.] -- XUV frequency comb spectroscopy / C. Gohle ... [et al.] -- Ultrahigh-repetition-rate pulse train with absolute-phase control produced by an adiabatic raman process / M. Katsuragawa ... [et al.] -- Strongly correlated bosons and fermions in optical lattices / S. Will ... [et al.] -- Bragg spectroscopy of ultracold bose gases in optical lattices / L. Fallani ... [et al.] -- Synthetic quantum many-body systems / C. Guerlin ... [et al.] -- Ultracold Ytterbium atoms in optical lattices / S. Sugawa ... [et al.] -- Ultracold polar molecules in the rovibrational ground state / J. Deiglmayr ... [et al.] -- Polar molecules near quantum degeneracy / J. Ye and D. S. Jin -- Production of a quantum gas of rovibronic ground-state molecules in an optical lattice / J. G. Danzl ... [et al.] -- Recent progress in x-ray nonlinear optics / K. Tamasaku, K. Sawada, and T. Ishikawa -- Gas in scattering media absorption spectroscopy - laser spectroscopy in unconventional environments / S. Svanberg -- Laser spectroscopy on relativistic ion beams / S. Reinhardt ... [et al.] -- Single frequency microcavity lasers and applications / L. Xu ... [et al.].

  16. Automated Quantitative Live Cell Fluorescence Microscopy

    PubMed Central

    Fero, Michael; Pogliano, Kit

    2010-01-01

    Advances in microscopy automation and image analysis have given biologists the tools to attempt large scale systems-level experiments on biological systems using microscope image readout. Fluorescence microscopy has become a standard tool for assaying gene function in RNAi knockdown screens and protein localization studies in eukaryotic systems. Similar high throughput studies can be attempted in prokaryotes, though the difficulties surrounding work at the diffraction limit pose challenges, and targeting essential genes in a high throughput way can be difficult. Here we will discuss efforts to make live-cell fluorescent microscopy based experiments using genetically encoded fluorescent reporters an automated, high throughput, and quantitative endeavor amenable to systems-level experiments in bacteria. We emphasize a quantitative data reduction approach, using simulation to help develop biologically relevant cell measurements that completely characterize the cell image. We give an example of how this type of data can be directly exploited by statistical learning algorithms to discover functional pathways. PMID:20591990

  17. Renaissance in diatomic spectroscopy

    NASA Astrophysics Data System (ADS)

    Tiemann, Eberhard; Knöckel, Horst

    2013-07-01

    New technological developments resulted in several periods of renaissances of spectroscopy, the period on microwaves and later the period with lasers, and led to developments of new models for description of observations, thus to understanding the underlying physics. Today, the exciting period of cold molecules has started and demands for new data from molecular spectroscopy and completion in their modeling. This contribution will describe the status of understanding before the era of "cold molecules" and note open questions when entering the field of cold molecules. Because large varieties of cold molecules are studied, like deeply bound (about 1eV) or very weakly bound (less than 10-7 eV) ones, the spectroscopic tools and the theoretical descriptions have to be largely extended. We will describe recent success regarding different molecules of diatomic alkaliand alkaline-earth atoms as examples and will show how to use the often huge body of spectroscopic data for obtaining predictions for optimal paths to produce ultra cold molecules in a desired molecular state. It is very exciting to combine the results of spectroscopy and of studies of ultra cold ensembles which are influenced by their atom-to-molecule changeover. This allows already to complete the understanding of the electronic structure of atom pairs from infinite internuclear separation down to the range of strongly overlapping electronic distribution in some cases (e.g. KRb or KCs). However, enhanced effort is required for describing quantitatively the discoveries, already published or expected, like a contribution to the field hunting for signatures of time dependence of fundamental constants. For molecules with their rotational and vibrational motion the ratio of electron mass-to-nuclear mass as a fundamental constant shows up as an obvious attraction for spectroscopic studies.

  18. FACSS XXII - the 22nd annual conference of the Federation of Analytical Chemistry and Spectroscopy Societies

    SciTech Connect

    NONE

    1995-12-31

    This document contains abstracts of reports which were presented at The 22nd Annual Conference of the Federation of Analytical Chemistry and Spectroscopy Societies. Abstracts are included under the following topics: Raman spectroscopy; near infrared spectroscopy; gas chromatography; chemometrics; surface analysis techniques; raman microspectroscopy; ICP-MS and solids analysis; biological sensing; industrial raman spectroscopy; luminescence spectroscopy in biology and environment; sample preparation; analytical applications of synchrotron radiation; spectroscopy and microscopy at electrochemical interfaces; sensors; speciation in elemental analysis; materials and surfaces; electrochemistry; glow discharge spectrometry; flow injection methods; raman imaging; atomic absorption spectrometry; instrumentation development; environmental analysis; thermal analysis; automation; and infrared microscopy.

  19. Absolute measurements of local chromophore concentrations using pulsed photoacoustic spectroscopy

    NASA Astrophysics Data System (ADS)

    Laufer, J.; Elwell, C.; Delpy, D.; Beard, P.

    2006-02-01

    Photoacoustic spectroscopy has the potential to make non-invasive, spatially resolved measurements of absolute chromophore concentrations. This has a wide range of possible applications, for example the mapping of endogenous chromophores such as oxy- (HbO II) and deoxyhaemoglobin (HHb) or externally administered contrast agents designed to target specific tissues or molecular processes. In this study we used near-infrared photoacoustic spectroscopy to determine the absolute concentrations of HbO II and HHb in a tissue phantom. The phantom consisted of three blood filled capillaries (Ø460microns) suspended at depths between 3mm and 9mm in a 2.5% Intralipid solution which also contained 2% blood in order to simulate the background optical attenuation in biological tissue. The blood oxygen saturation (SO II) of the blood circulating in the capillaries was varied using a membrane oxygenator. At each SO II level, nanosecond pulses emitted by an OPO laser system that was tuneable over the wavelength range from 740nm to 1040nm illuminated the phantom. The generated photoacoustic waves were recorded using a single Fabry-Perot ultrasound detector and used to obtain a depth profile of the location of the tubes. The amplitudes of the part of the photoacoustic signal that corresponded to the capillaries and the surface of the Intralipid/blood mixture were plotted as a function of wavelength. The output of a diffusion theory based model of the wavelength dependence of the photoacoustic signal amplitude was then fitted to these spectra. This enabled the quantitative determination of absolute HbO II and HHb concentrations in the capillaries and the Intralipid/blood mixture from which the total haemoglobin concentrations and blood SO II were calculated. Based on these measurements, the smallest chromophore concentrations that can be detected in biological tissue were estimated.

  20. Biolog phenotype microarrays.

    PubMed

    Shea, April; Wolcott, Mark; Daefler, Simon; Rozak, David A

    2012-01-01

    Phenotype microarrays nicely complement traditional genomic, transcriptomic, and proteomic analysis by offering opportunities for researchers to ground microbial systems analysis and modeling in a broad yet quantitative assessment of the organism's physiological response to different metabolites and environments. Biolog phenotype assays achieve this by coupling tetrazolium dyes with minimally defined nutrients to measure the impact of hundreds of carbon, nitrogen, phosphorous, and sulfur sources on redox reactions that result from compound-induced effects on the electron transport chain. Over the years, we have used Biolog's reproducible and highly sensitive assays to distinguish closely related bacterial isolates, to understand their metabolic differences, and to model their metabolic behavior using flux balance analysis. This chapter describes Biolog phenotype microarray system components, reagents, and methods, particularly as they apply to bacterial identification, characterization, and metabolic analysis. PMID:22639219