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1

Quantitative biological Raman spectroscopy for non-invasive blood analysis  

E-print Network

The long term goal of this project is the measurement of clinically-relevant analytes in the blood tissue matrix of human subjects using near-infrared Raman spectroscopy, with the shorter term research directed towards ...

Shih, Wei-Chuan

2007-01-01

2

Quantitative NMR spectroscopy of biologically active substances and excipients  

Microsoft Academic Search

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

Tanja Beyer; Bernd Diehl; Ulrike Holzgrabe

2010-01-01

3

Quantitative phase spectroscopy  

PubMed Central

Quantitative phase spectroscopy is presented as a novel method of measuring the wavelength-dependent refractive index of microscopic volumes. Light from a broadband source is filtered to an ~5 nm bandwidth and rapidly tuned across the visible spectrum in 1 nm increments by an acousto-optic tunable filter (AOTF). Quantitative phase images of semitransparent samples are recovered at each wavelength using off-axis interferometry and are processed to recover relative and absolute dispersion measurements. We demonstrate the utility of this approach by (i) spectrally averaging phase images to reduce coherent noise, (ii) measuring absorptive and dispersive features in microspheres, and (iii) quantifying bulk hemoglobin concentrations by absolute refractive index measurements. Considerations of using low coherence illumination and the extension of spectral techniques in quantitative phase measurements are discussed. PMID:22567588

Rinehart, Matthew; Zhu, Yizheng; Wax, Adam

2012-01-01

4

A Quantitative Infrared Spectroscopy Experiment.  

ERIC Educational Resources Information Center

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

Krahling, Mark D.; Eliason, Robert

1985-01-01

5

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

6

Quantitative biology of single neurons  

PubMed Central

The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible. PMID:22915636

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

2012-01-01

7

Quantitative Verification Techniques for Biological Processes  

E-print Network

of a rich selection of quantitative properties. 1 Introduction Recent research has had considerable successDRAFT Quantitative Verification Techniques for Biological Processes Marta Kwiatkowska, Gethin approach but, by employing formal verification techniques, compute exact quantitative mea- sures as opposed

Oxford, University of

8

Degree: Bachelor of Science Major: Quantitative Biology  

E-print Network

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

Cakoni, Fioralba

9

QUANTITATIVE 15N NMR SPECTROSCOPY  

EPA Science Inventory

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

10

Biomolecular Plasmonics for Quantitative Biology and Nanomedicine  

PubMed Central

Free electrons in a noble metal nanoparticle can be resonantly excited, leading to their collective oscillation termed as a surface plasmon. These surface plasmons enable nanoparticles to absorb light, generate heat, transfer energy, and re-radiate incident photons. Creative designs of nanoplasmonic optical antennae (i.e. plasmon resonant nanoparticles) have become a new foundation of quantitative biology and nanomedicine. This review focuses on the recent developments in dual-functional nanoplasmonic optical antennae for label-free biosensors and nanoplasmonic gene switches. Nanoplasmonic optical antennae, functioning as biosensors to significantly enhance biochemical-specific spectral information via plasmon resonance energy transfer (PRET) and surface-enhanced Raman spectroscopy (SERS), are discussed. Nanoplasmonic optical antennae, functioning as nanoplasmonic gene switches to enable spatiotemporal regulation of genetic activity, are also reviewed. Nanoplasmonic molecular rulers and integrated photoacoustic-photothermal contrast agents are also described. PMID:20801636

Lee, Somin Eunice; Lee, Luke P.

2012-01-01

11

Teaching quantitative biology: goals, assessments, and resources.  

PubMed

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

Aikens, Melissa L; Dolan, Erin L

2014-11-01

12

Teaching quantitative biology: goals, assessments, and resources  

PubMed Central

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

Aikens, Melissa L.; Dolan, Erin L.

2014-01-01

13

Quantitative biology: where modern biology meets physical sciences  

PubMed Central

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

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

2014-01-01

14

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

E-print Network

> Microbial systems biology > Organismal systems biology > Systems ecology > Quantitative and theoretical in bacteria MICHAEL BEMAN life and environmental sciences and systems ecology > Microbial ecology and cell biology and microbial systems biology > Experimental evolution of antibiotic resistance

Uppsala Universitet

15

Journal of Quantitative Spectroscopy & Radiative Transfer 82 (2003) 505516  

E-print Network

­516 1. Introduction In the Earth's atmosphere, both in the far infrared and infrared regionsJournal of Quantitative Spectroscopy & Radiative Transfer 82 (2003) 505­516 www-4073(03)00174-2 #12;506 J. Boissoles et al. / Journal of Quantitative Spectroscopy & Radiative Transfer 82 (2003) 505

16

Journal of Quantitative Spectroscopy & Radiative Transfer 82 (2003) 544  

E-print Network

Journal of Quantitative Spectroscopy & Radiative Transfer 82 (2003) 5­44 www Spectroscopie Mol�eculaire, Universit�e Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium i Laboratoire de Spectroscopy & Radiative Transfer 82 (2003) 5­44 calculation codes: high-resolution spectroscopic parameters

Chance, Kelly

17

Quantitative thermal gradient imaging of biological surfaces  

NASA Astrophysics Data System (ADS)

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

Swanson, Curtis J.; Wingard, Christopher J.

1991-03-01

18

Quantitative cell biology: the essential role of theory  

PubMed Central

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

Howard, Jonathon

2014-01-01

19

Unraveling pancreatic islet biology by quantitative proteomics  

SciTech Connect

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

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

2011-08-01

20

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

ERIC Educational Resources Information Center

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

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

2010-01-01

21

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...

22

Quantitation of Auger and X-ray photoelectron spectroscopies  

SciTech Connect

Surface analysis using electron spectroscopies is now a well-established and continuously expanding area. With appropriate data treatment procedures, both Auger electron spectroscopy (AES, not to be confused with atomic expression spectroscopy) and X-ray photoelectron spectroscopy (XPS or ESCA) can routinely supply reliable qualitative and semiquantitative characterization of the near-surface region (top 1-100 /Angstrom/) of most solids. Complex sample matrix and instrumental parameters make quantitation of surface electron spectroscopies a real challenge. Kenneth W. Nebesny, Brian L. Mashloff, and Neal R. Armstrong of the University of Arizona describe approaches that make it possible to obtain reliable compositional information.

Nebesny, K.W.; Maschhoff, B.L.; Armstrong, N.R.

1989-04-01

23

Photon-tissue interaction model for quantitative assessment of biological tissues  

NASA Astrophysics Data System (ADS)

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

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

2014-02-01

24

Quantitative Optical Spectroscopy for Tissue Diagnosis  

Microsoft Academic Search

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

Rebecca Richards-Kortum; Eva Sevick-Muraca

1996-01-01

25

Amateur Spectroscopy: From Qualitative to Quantitative Analysis  

NASA Astrophysics Data System (ADS)

Spectroscopy is a new field of study for the amateur. This type of explor- ation by an amateur is the result of the availability of several types of off-the-shelf spectrometers, which can be coupled to a CCD camera. For the most part, amateurs pursuing this area have done so more from a qualitative standpoint: stellar classification and identification of the more prominent emission and absorption lines in stars and gas clouds. However, a spectrum contains much more valuable information about the physics of the region under survey. My talk will describe my initial efforts in the use of synthetic spectroscopy and how it can be used to determine a variety of stellar para- meters such as temperature and abundances. The process involves the creation of stellar atmospheric models where a variety of variables can be altered and the resulting spectrum fitted to the actual spectrum obtained at the tele- scope to find the best fit.

Mais, D. E.

2002-05-01

26

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

PubMed Central

Biology of the twenty-first century is an increasingly quantitative science. Undergraduate biology education therefore needs to provide opportunities for students to develop fluency in the tools and language of quantitative disciplines. Quantitative literacy (QL) is important for future scientists as well as for citizens, who need to interpret numeric information and data-based claims regarding nearly every aspect of daily life. To address the need for QL in biology education, we incorporated quantitative concepts throughout a semester-long introductory biology course at a large research university. Early in the course, we assessed the quantitative skills that students bring to the introductory biology classroom and found that students had difficulties in performing simple calculations, representing data graphically, and articulating data-driven arguments. In response to students' learning needs, we infused the course with quantitative concepts aligned with the existing course content and learning objectives. The effectiveness of this approach is demonstrated by significant improvement in the quality of students' graphical representations of biological data. Infusing QL in introductory biology presents challenges. Our study, however, supports the conclusion that it is feasible in the context of an existing course, consistent with the goals of college biology education, and promotes students' development of important quantitative skills. PMID:20810965

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

2010-01-01

27

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

ERIC Educational Resources Information Center

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

Feser, Jason; Vasaly, Helen; Herrera, Jose

2013-01-01

28

Quantitative Auger electron spectroscopy of SiC  

Microsoft Academic Search

The article is devoted to quantitative Auger electron spectroscopy (AES) of silicon carbide (SiC). It compares the results obtained by various procedures applied to LVV and KLL Auger peaks of silicon (Si) for determining the Auger current. We have found that reliable results for the content of Si in SiC can be achieved by the method in which the Auger

R. Kosiba; J. Liday; G. Ecke; O. Ambacher; J. Breza; P. Vogrin?i?

2006-01-01

29

Journal of Quantitative Spectroscopy & Radiative Transfer 105 (2007) 164165  

E-print Network

Journal of Quantitative Spectroscopy & Radiative Transfer 105 (2007) 164­165 Book review Cloud Library''. The title of the book is ambitious, and one immediately wonders whether the topic of cloud optics can be covered comprehensively on just 276 pages. In fact, my impression is that the author

30

Understanding Quantitative Genetics in the Systems Biology Era  

PubMed Central

Biology is now entering the new era of systems biology and exerting a growing influence on the future development of various disciplines within life sciences. In early classical and molecular periods of Biology, the theoretical frames of classical and molecular quantitative genetics have been systematically established, respectively. With the new advent of systems biology, there is occurring a paradigm shift in the field of quantitative genetics. Where and how the quantitative genetics would develop after having undergone its classical and molecular periods? This is a difficult question to answer exactly. In this perspective article, the major effort was made to discuss the possible development of quantitative genetics in the systems biology era, and for which there is a high potentiality to develop towards "systems quantitative genetics". In our opinion, the systems quantitative genetics can be defined as a new discipline to address the generalized genetic laws of bioalleles controlling the heritable phenotypes of complex traits following a new dynamic network model. Other issues from quantitative genetic perspective relating to the genetical genomics, the updates of network model, and the future research prospects were also discussed. PMID:19173038

Zhu, Mengjin; Yu, Mei; Zhao, Shuhong

2009-01-01

31

Photoacoustic resonance spectroscopy for biological tissue characterization  

NASA Astrophysics Data System (ADS)

By "listening to photons," photoacoustics allows the probing of chromosomes in depth beyond the optical diffusion limit. Here we report the photoacoustic resonance effect induced by multiburst modulated laser illumination, which is theoretically modeled as a damped mass-string oscillator and a resistor-inductor-capacitor (RLC) circuit. Through sweeping the frequency of multiburst modulated laser, the photoacoustic resonance effect is observed experimentally on phantoms and porcine tissues. Experimental results demonstrate different spectra for each phantom and tissue sample to show significant potential for spectroscopic analysis, fusing optical absorption and mechanical vibration properties. Unique RLC circuit parameters are extracted to quantitatively characterize phantom and biological tissues.

Gao, Fei; Feng, Xiaohua; Zheng, Yuanjin; Ohl, Claus-Dieter

2014-06-01

32

A Transformative Model for Undergraduate Quantitative Biology Education  

PubMed Central

The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions. PMID:20810949

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

2010-01-01

33

RIKEN Quantitative Biology Center Cell Dynamics Research Core  

E-print Network

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

Fukai, Tomoki

34

RIKEN Quantitative Biology Center Cell Dynamics Research Core  

E-print Network

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

Fukai, Tomoki

35

Quantitative Genetic Interactions Reveal Layers of Biological Modularity  

PubMed Central

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

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

2010-01-01

36

Development of Electron Energy Loss Spectroscopy in the Biological Sciences  

PubMed Central

The high sensitivity of electron energy loss spectroscopy (EELS) for detecting light elements at the nanoscale makes it a valuable technique for application to biological systems. In particular, EELS provides quantitative information about elemental distributions within subcellular compartments, specific atoms bound to individual macromolecular assemblies, and the composition of bionanoparticles. The EELS data can be acquired either in the fixed beam energy-filtered transmission electron microscope (EFTEM) or in the scanning transmission electron microscope (STEM), and recent progress in the development of both approaches has greatly expanded the range of applications for EELS analysis. Near single atom sensitivity is now achievable for certain elements bound to isolated macromolecules, and it becomes possible to obtain three-dimensional compositional distributions from sectioned cells through EFTEM tomography. PMID:23049161

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

2012-01-01

37

Method for depth-resolved quantitation of optical properties in layered media using spatially modulated quantitative spectroscopy  

PubMed Central

We have demonstrated that spatially modulated quantitative spectroscopy (SMoQS) is capable of extracting absolute optical properties from homogeneous tissue simulating phantoms that span both the visible and near-infrared wavelength regimes. However, biological tissue, such as skin, is highly structured, presenting challenges to quantitative spectroscopic techniques based on homogeneous models. In order to more accurately address the challenges associated with skin, we present a method for depth-resolved optical property quantitation based on a two layer model. Layered Monte Carlo simulations and layered tissue simulating phantoms are used to determine the efficacy and accuracy of SMoQS to quantify layer specific optical properties of layered media. Initial results from both the simulation and experiment show that this empirical method is capable of determining top layer thickness within tens of microns across a physiological range for skin. Layer specific chromophore concentration can be determined to <±10% the actual values, on average, whereas bulk quantitation in either visible or near infrared spectroscopic regimes significantly underestimates the layer specific chromophore concentration and can be confounded by top layer thickness. PMID:21806282

Saager, Rolf B.; Truong, Alex; Cuccia, David J.; Durkin, Anthony J.

2011-01-01

38

Quantitative polarized Raman spectroscopy in highly turbid bone tissue  

NASA Astrophysics Data System (ADS)

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

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

2010-05-01

39

Quantum integrable systems. Quantitative methods in biology  

E-print Network

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. Particularly, with this model one can study the mutual transformation of coding/non coding parts in a genome or the presence of an error threshold. The assembly of oligomeric proteins is an important phenomenon which interests the majority of proteins in a cell. I participated to the creation of the project "Gemini" which has for purpose the investigation of the structural data of the interfaces of such proteins. The objective is to differentiate the role of amino acids and determine the presence of patterns characterizing certain geometries.

Giovanni Feverati

2011-01-19

40

Quantitation and detection of vanadium in biologic and pollution materials  

NASA Technical Reports Server (NTRS)

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

Gordon, W. A.

1974-01-01

41

A Transformative Model for Undergraduate Quantitative Biology Education  

ERIC Educational Resources Information Center

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

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

2010-01-01

42

A Transformative Model for Undergraduate Quantitative Biology Education  

E-print Network

Essay A Transformative Model for Undergraduate Quantitative Biology Education David C. Usher,* Tobin A. Driscoll, Prasad Dhurjati,§ John A. Pelesko, Louis F. Rossi, Gilberto Schleiniger, Kathleen correspondence to: David C. Usher (dusher@udel.edu). *D.C.U. and T.A.D. contributed equally to this study. © 2010

Driscoll, Toby

43

Infusing Quantitative Approaches throughout the Biological Sciences Curriculum  

ERIC Educational Resources Information Center

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

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

2013-01-01

44

Toward Integration: From Quantitative Biology to Mathbio-Biomath?  

ERIC Educational Resources Information Center

In response to the call of "BIO2010" for integrating quantitative skills into undergraduate biology education, 30 Howard Hughes Medical Institute (HHMI) Program Directors at the 2006 HHMI Program Directors Meeting established a consortium to investigate, implement, develop, and disseminate best practices resulting from the integration of math and…

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

2010-01-01

45

Optimized quantitative magnetic resonance spectroscopy for clinical routine.  

PubMed

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

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

2013-07-01

46

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

ERIC Educational Resources Information Center

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

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

2014-01-01

47

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

PubMed Central

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

Rinsler, M G

1981-01-01

48

Surface-sensitive polarized Raman spectroscopy of biological tissue  

E-print Network

Surface-sensitive polarized Raman spectroscopy of biological tissue Zachary J. Smith and Andrew J even confounding signals.1 Raman spectroscopy of such a layered me- dium will in general detect this method to Raman scattering in two two-layer models with a highly diffusing lower layer of glucose powder

Berger, Andrew J.

49

Quantitative Cherenkov emission spectroscopy for tissue oxygenation assessment  

PubMed Central

Measurements of Cherenkov emission in tissue during radiation therapy are shown to enable estimation of hemoglobin oxygen saturation non-invasively, through spectral fitting of the spontaneous emissions from the treated tissue. Tissue oxygenation plays a critical role in the efficacy of radiation therapy to kill tumor tissue. Yet in-vivo measurement of this has remained elusive in routine use because of the complexity of oxygen measurement techniques. There is a spectrally broad emission of Cherenkov light that is induced during the time of irradiation, and as this travels through tissue from the point of the radiation deposition, the tissue absorption and scatter impart spectral changes. These changes can be quantified by diffuse spectral fitting of the signal. Thus Cherenkov emission spectroscopy is demonstrated for the first time quantitatively in vitro and qualitatively in vivo, and has potential for real-time online tracking of tissue oxygen during radiation therapy when fully characterized and developed. PMID:22418319

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

2012-01-01

50

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

E-print Network

symmetry from photon spectroscopies. I. Reflection infrared vibrational spectroscopy Atul N. Parikh-ray reflectivity, uv-visible spectroscopic ellipsometry, and infrared reflection spectroscopy. Further, the theory spectroscopy and involves quantitative decomposition of the isotropic imaginary optical function (k) spectrum

Parikh, Atul N.

51

A Method for Quantitative Mapping of Thick Oil Spills Using Imaging Spectroscopy  

E-print Network

A Method for Quantitative Mapping of Thick Oil Spills Using Imaging Spectroscopy By Roger N. Clark (AVIRIS) Team, 2010, A method for quantitative mapping of thick oil spills using imaging spectroscopy: U ....................................................................................................................................................14 Figures 1. Image of oil emulsion from the Deepwater Horizon oil spill in the Gulf of Mexico off

Torgersen, Christian

52

Quantitative analysis of the dentin adhesive interface by Auger spectroscopy.  

PubMed

The ultimate success of a dentin adhesive bond is dependent in large part on specific conditions at the interface between the tooth and the adhesive. Most current dentin adhesive systems use some sort of pre-treatment to demineralize the first few microns of the dentin surface, leaving a meshwork of collagen into which the adhesive resin can penetrate, infiltrate, and polymerize. The general hypothesis tested in this experiment was that the penetration and distribution of adhesive resin into the demineralized zone are a function of the conditioner used as a pre-treatment for the adhesive application. Four commercially available adhesive systems were modified to incorporate hydroxyethylthiomethacrylate (HETMA), a sulfur-substituted, traceable analogue of 2-hydroxyethylmethacrylate (HEMA), thereby allowing for a qualitative measurement of the amount and distribution of monomer in the treated dentin substrate by energy-dispersive x-ray spectroscopy (EDS) and a quantitative measurement by Auger electron spectroscopy (AES). The dentin pre-treatments investigated were: (1) 10% citric acid/3% ferric chloride, (2) 10% maleic acid, (3) 2.5% nitric acid, and (4) an alcoholic solution of HEMA with a phosphorus acid ester. These pre-treatments were applied to freshly extracted teeth that had been sectioned to expose the dentin and ground to simulate the smeared layer. After the appropriate pre-treatment was applied, a 10% (v/v) solution of HETMA in acetone was applied to the surface, followed by the corresponding adhesive resin, which was then polymerized. The samples were then processed for observation by scanning transmission electron microscopy (STEM), AES, and STEM/EDS analysis. The results indicated significant differences in the ability of HETMA to penetrate the dentin surface conditioned by the four pretreatments investigated here. This study also demonstrated that AES and STEM/EDS could be used in a correlative fashion to determine the distribution of HETMA within or adjacent to the treated dentin surface. PMID:8708132

Eick, J D; Miller, R G; Robinson, S J; Bowles, C Q; Gutshall, P L; Chappelow, C C

1996-04-01

53

Quantitative nano-mechanics of biological cells with AFM  

NASA Astrophysics Data System (ADS)

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

Sokolov, Igor

2013-03-01

54

Lessons Learned from Quantitative Dynamical Modeling in Systems Biology  

PubMed Central

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

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

2013-01-01

55

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

E-print Network

Qualitative and quantitative analysis of chlorinated solvents using Raman spectroscopy and machine is the identification of solvents into chlorinated or non-chlorinated. In this work we have used Raman spectroscopy. Keywords: Raman spectroscopy, hazardous materials, chlorinated solvents, non-chlorinated solvents

Madden, Michael

56

Positron annihilation spectroscopy of biological tissue in 11C irradiation  

NASA Astrophysics Data System (ADS)

Positron annihilation spectroscopy (PAS) spectra of biological tissue in 11C irradiation are reported and spatial resolution coefficient of positron emission tomography (PET) obtained from the PAS spectrum is discussed for 11C irradiation. A PAS spectrum of the biological tissue with water is the same as that of the water pool phantom in 11C irradiation. However, a PAS spectrum of the biological tissue with less water differs from that of the water pool phantom. The PET spatial resolution coefficient depends on the kind of biological tissue. However, the PET spatial resolution coefficient, 0.00243? ± ?0.00014, can be used as a common value of maximum limit.

Sakurai, Hiroshi; Itoh, Fumitake; Hirano, Yoshiyuki; Nitta, Munetaka; Suzuki, Kosuke; Kato, Daisuke; Yoshida, Eiji; Nishikido, Fumihiko; Wakizaka, Hidekatsu; Kanai, Tatsuaki; Yamaya, Taiga

2014-11-01

57

Quantitation of secondary structure in ATR infrared spectroscopy  

PubMed Central

Polarized attenuated total reflection infrared spectroscopy of aligned membranes provides essential information on the secondary structure content and orientation of the associated membrane proteins. Quantitation of the relative content of different secondary structures, however, requires allowance for geometric relations of the electric field components (E(x), E(y), E(z)) of the evanescent wave, and of the components of the infrared transition moments, in combining absorbances (A() and A( perpendicular)) measured with radiation polarized parallel with and perpendicular to, respectively, the plane of incidence. This has hitherto not been done. The appropriate combination for exact evaluation of relative integrated absorbances is A() + (2E(z)(2)/E(y)(2) - E(x)(2)/E(y)(2))A( perpendicular), where z is the axis of ordering that is normal to the membrane plane, and the x-axis lies in the membrane plane within the plane of incidence. This combination can take values in the range approximately from A() - 0.4A( perpendicular) to A() + 2.7A( perpendicular), depending on experimental conditions and the attenuated total reflection crystal used. With unpolarized radiation, this correction is not possible. Similar considerations apply to the dichroic ratios of multicomponent bands, which are also treated. PMID:10545362

Marsh, D

1999-01-01

58

Terahertz time-domain spectroscopy of biological tissues  

SciTech Connect

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

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

2008-07-31

59

Effect of photobleaching on calibration model development in biological Raman spectroscopy  

NASA Astrophysics Data System (ADS)

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

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

2011-01-01

60

Computational Laser Spectroscopy in a Biological Tissue  

PubMed Central

We present a numerical spectroscopic study of visible and infrared laser radiation in a biological tissue. We derive a solution of a general two-dimensional time dependent radiative transfer equation in a tissue-like medium. The used model is suitable for many situations especially when the external source is time-dependent or continuous. We use a control volume-discrete ordinate method associated with an implicit three-level second-order time differencing scheme. We consider a very thin rectangular biological-tissue-like medium submitted to a visible or a near infrared light sources. The RTE is solved for a set of different wavelength source. All sources are assumed to be monochromatic and collimated. The energetic fluence rate is computed at a set of detector points on the boundaries. According to the source type, we investigate either the steady-state or transient response of the medium. The used model is validated in the case of a heterogeneous tissue-like medium using referencing experimental results from the literature. Also, the developed model is used to study changes on transmitted light in a rat-liver tissue-like medium. Optical properties depend on the source wavelength and they are taken from the literature. In particular, light-transmission in the medium is studied for continuous wave and for short pulse. PMID:20396377

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

2010-01-01

61

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

ERIC Educational Resources Information Center

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

Hill, Devon W.; And Others

1988-01-01

62

Quantitative photopyroelectricout-of-phase spectroscopy of amorphous silicon thin films deposited on crystalline silicon  

E-print Network

Quantitative photopyroelectricout-of-phase spectroscopy of amorphous silicon thin films deposited on crystalline silicon CONSTANTINOSCHRISTOFIDES,ANDREASMANDELIS,AND ALBERTENGEL Phorouco~tsricutzcl Phororhertnal trans- mission and thermal-wave spectroscopic measurements of amorphous Si thin films, deposited

Mandelis, Andreas

63

Quantitative Determination of DNA-Ligand Binding Using Fluorescence Spectroscopy  

ERIC Educational Resources Information Center

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

Healy, Eamonn F.

2007-01-01

64

Microscope laser light scattering spectroscopy of single biological cells  

Microsoft Academic Search

A microscope laser light scattering setup was developed, allowing us to do intensity autocorrelation spectroscopy on the light\\u000a scattered from a volume as small as (2 ?m)3. This non-invasive technique makes cytoplasmic studies possible inside single live biological cells. The effect of osmotic\\u000a swelling and shrinking on the diffusion coefficient of hemoglobin inside intact red blood cells is shown as

I. Nishio; J. Peetermans; T. Tanaka

1985-01-01

65

Microfluidic Biochip for Impedance Spectroscopy of Biological Species  

Microsoft Academic Search

This paper describes the fabrication and characterization of a microelectronic device for the electrical interrogation and impedance spectroscopy of biological species. Key features of the device include an all top-side processing for the formation of fluidic channels, planar fluidic interface ports, integrated metal electrodes for impedance measurements, and a glass cover sealing the non-planar topography of the chip using spin-on-glass

R. Go´mez; R. Bashir; A. Sarikaya; M. R. Ladisch; J. Sturgis; J. P. Robinson; T. Geng; A. K. Bhunia; H. L. Apple; S. Wereley

2001-01-01

66

Biological evolution of replicator systems: towards a quantitative approach.  

PubMed

The aim of this work is to study the features of a simple replicator chemical model of the relation between kinetic stability and entropy production under the action of external perturbations. We quantitatively explore the different paths leading to evolution in a toy model where two independent replicators compete for the same substrate. To do that, the same scenario described originally by Pross (J Phys Org Chem 17:312-316, 2004) is revised and new criteria to define the kinetic stability are proposed. Our results suggest that fast replicator populations are continually favored by the effects of strong stochastic environmental fluctuations capable to determine the global population, the former assumed to be the only acting evolution force. We demonstrate that the process is continually driven by strong perturbations only, and that population crashes may be useful proxies for these catastrophic environmental fluctuations. As expected, such behavior is particularly enhanced under very large scale perturbations, suggesting a likely dynamical footprint in the recovery patterns of new species after mass extinction events in the Earth's geological past. Furthermore, the hypothesis that natural selection always favors the faster processes may give theoretical support to different studies that claim the applicability of maximum principles like the Maximum Metabolic Flux (MMF) or Maximum Entropy Productions Principle (MEPP), seen as the main goal of biological evolution. PMID:23494128

Martin, Osmel; Horvath, J E

2013-04-01

67

Direct and quantitative broadband absorptance micro/nano spectroscopy using FTIR and bilayer cantilever probes  

E-print Network

Optical properties of micro/nano materials are important for many applications in biology, optoelectronics, and energy. In this thesis, a method is described to directly measure the quantitative absorptance spectra of ...

Hsu, Wei-Chun

2012-01-01

68

High-Resolution Waveguide THz Spectroscopy of Biological Molecules?  

PubMed Central

Abstract Low-frequency vibrational modes of biological molecules consist of intramolecular modes, which are dependent on the molecule as a whole, as well as intermolecular modes, which arise from hydrogen-bonding interactions and van der Waals forces. Vibrational modes thus contain important information about conformation dynamics of biological molecules, and can also be used for identification purposes. However, conventional Fourier transform infrared spectroscopy and terahertz time-domain spectroscopy (THz-TDS) often result in broad, overlapping features that are difficult to distinguish. The technique of waveguide THz-TDS has been recently developed, resulting in sharper features. For this technique, an ordered polycrystalline film of the molecule is formed on a metal sample plate. This plate is incorporated into a metal parallel-plate waveguide and probed via waveguide THz-TDS. The planar order of the film reduces the inhomogeneous broadening, and cooling of the samples to 77K reduces the homogenous broadening. This combination results in the line-narrowing of THz vibrational modes, in some cases to an unprecedented degree. Here, this technique has been demonstrated with seven small biological molecules, thymine, deoxycytidine, adenosine, D-glucose, tryptophan, glycine, and L-alanine. The successful demonstration of this technique shows the possibilities and promise for future studies of internal vibrational modes of large biological molecules. PMID:17933879

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

2008-01-01

69

Quantitative Measurement of Trans-Fats by Infrared Spectroscopy  

ERIC Educational Resources Information Center

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

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

2007-01-01

70

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

NASA Astrophysics Data System (ADS)

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

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

2014-07-01

71

Direct and quantitative photothermal absorption spectroscopy of individual particulates  

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

72

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

EPA Science Inventory

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

73

CONFOCAL MICROSCOPY SYSTEM PERFORMANCE: SPECTROSCOPY AND FOUNDATIONS FOR QUANTITATION  

EPA Science Inventory

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

74

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

EPA Science Inventory

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

75

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

NASA Astrophysics Data System (ADS)

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.

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

2009-09-01

76

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

SciTech Connect

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

Watson, J.D.; Siniscalco, M.

1986-01-01

77

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

NASA Astrophysics Data System (ADS)

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.

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

78

Machine learning methods for quantitative analysis of Raman spectroscopy data  

NASA Astrophysics Data System (ADS)

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

Madden, Michael G.; Ryder, Alan G.

2003-03-01

79

Quantitative Raman spectroscopy for the analysis of carrot bioactives.  

PubMed

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

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

2013-03-20

80

Quantitative Mueller matrix fluorescence spectroscopy for precancer detection.  

PubMed

Quantitative fluorescence spectroscopic Mueller matrix measurements from the connective tissue regions of human cervical tissue reveal intriguing fluorescence diattenuation and polarizance effects. Interestingly, the estimated fluorescence linear diattenuation and polarizance parameters were considerably reduced in the precancerous tissues as compared to the normal ones. These polarimetry effects of the autofluorescence were found to originate from anisotropically organized collagen molecular structures present in the connective tissues. Consequently, the reduction of the magnitude of these polarimetric parameters at higher grades of precancer was attributed to the loss of anisotropic organization of collagen, which was also confirmed by control experiments. These results indicate that fluorescence spectral diattenuation and polarizance parameters may serve as potentially useful diagnostic metrics. PMID:24562117

Jagtap, J; Chandel, S; Das, N; Soni, J; Chatterjee, S; Pradhan, A; Ghosh, N

2014-01-15

81

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

SciTech Connect

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

Not Available

1986-01-01

82

Quantitative data generation for systems biology: the impact of randomisation, calibrators and  

E-print Network

Quantitative data generation for systems biology: the impact of randomisation, calibrators with chemiluminescence detection. So far, the data generated by immunoblotting have been primarily qualitative networks through mathematical modelling based on experimental data. The current lack of reliable

Timmer, Jens

83

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

ERIC Educational Resources Information Center

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

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

2008-01-01

84

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

E-print Network

Quantitative structural and textural assessment of laminar pyrocarbons through Raman spectroscopy 6759, 45067 Orléans cedex 2, France Abstract In pyrocarbon materials, the width of the Raman D band be explained by the presence of sp3 -like line defects. Keywords: Pyrolytic carbons; Optical microscopy; Raman

Boyer, Edmond

85

Sub-terahertz resonance spectroscopy of biological macromolecules and cells  

NASA Astrophysics Data System (ADS)

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

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

2013-05-01

86

Advances in Quantitative UV-Visible Spectroscopy for Clinical and Pre-clinical Application in Cancer  

PubMed Central

Summary Methods of optical spectroscopy which provide quantitative, physically or physiologically meaningful measures of tissue properties are an attractive tool for the study, diagnosis, prognosis, and treatment of various cancers. Recent development of methodologies to convert measured reflectance and fluorescence spectra from tissue to cancer-relevant parameters such as vascular volume, oxygenation, extracellular matrix extent, metabolic redox states, and cellular proliferation have significantly advanced the field of tissue optical spectroscopy. The number of publications reporting quantitative tissue spectroscopy results in the UV-visible wavelength range has increased sharply in the last 3 years, and includes new and emerging studies which correlate optically-measured parameters with independent measures such as immunohistochemistry, which should aid in increased clinical acceptance of these technologies. PMID:19268567

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

2009-01-01

87

Theoretical Population Biology 59, 175 184 (2001) Quantitative Genetics in the Age of Genomics  

E-print Network

Theoretical Population Biology 59, 175 184 (2001) MINIREVIEW Quantitative Genetics in the Age and I recently attempted to summarize the current state of quantitative genetics (Lynch and Walsh, 1998 the hallmark of a scientifically healthy and active field. As the age of genomics ushers in, continued dramatic

Walsh, Bruce

88

Amines as extracting agents for the quantitative determinations of actinides in biological samples  

Microsoft Academic Search

The present manuscript reviews the use of amines (primary, secondary and tertiary chains and quaternary ammonium salts) as extracting agents for the quantitative determination of actinides in biological samples. Among the primary amines, only Primene, JM-T is used to determine Pu in urine and bone. No one has investigated the possibility of using secondary amines to quantitatively extract actinides from

N. P. Singh

1987-01-01

89

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

NASA Technical Reports Server (NTRS)

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

Felzer, Benjamin; Hauff, Phoebe; Goetz, Alexander F. H.

1994-01-01

90

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

PubMed

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

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

1995-01-01

91

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

NASA Astrophysics Data System (ADS)

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

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

2010-11-01

92

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

NASA Astrophysics Data System (ADS)

The behavior of light after interacting with a biological medium reveals a wealth of information that may be used to distinguish between normal and disease states. This may be achieved by simply imaging the morphology of tissues or individual cells, and/or by more sophisticated methods that quantify specific surrogate biomarkers of disease. To this end, the work presented in this dissertation demonstrates novel tools derived from low coherence interferometry (LCI) that quantitatively measure wavelength-dependent scattering and absorption properties of biological samples, with high spectral resolution and micrometer spatial resolution, to provide insight into disease states. The presented work first describes a dual window (DW) method, which decomposes a signal sampled in a single domain (in this case the frequency domain) to a distribution that simultaneously contains information from both the original domain and the conjugate domain (here, the temporal or spatial domain). As the name suggests, the DW method utilizes two independently adjustable windows, each with different spatial and spectral properties to overcome limitations found in other processing methods that seek to obtain the same information. A theoretical treatment is provided, and the method is validated through simulations and experiments. With this tool, the spatially dependent spectral behavior of light after interacting with a biological medium may be analyzed to extract parameters of interest, such as the scattering and absorption properties. The DW method is employed to investigate scattering properties of samples using Fourier domain LCI (fLCI). In this method, induced temporal coherence effects provide insight into structural changes in dominant scatterers, such as cell nuclei within tissue, which can reveal the early stages of cancerous development. fLCI is demonstrated in complex, three-dimensional samples using a scattering phantom and an ex-vivo animal model. The results from the latter study show that fLCI is able to detect changes in the morphology of tissues undergoing precancerous development. The DW method is also employed to enable a novel form of optical coherence tomography (OCT), an imaging modality that uses coherence gating to obtain micrometer-scale, cross-sectional information of tissues. The novel method, named molecular imaging true color spectroscopic OCT (METRiCS OCT), analyses the depth dependent absorption of light to ascertain quantitative information of chromophore concentration, such as hemoglobin. The molecular information is also processed to yield a true color representation of the sample, a unique capability of this approach. A number of experiments, including hemoglobin absorbing phantoms and in-vivo imaging of a chick embryo model and dorsal skinfold window chamber model, demonstrate the power of the method. The final method presented in this dissertation, consists of a spectroscopic approach that interrogates the dispersive biochemical properties of samples to independently probe the scattering and absorption coefficients. To demonstrate this method, named non-linear phase dispersion spectroscopy (NLDS), a careful analysis of LCI signals is presented. The method is verified using measurements from samples that scatter and absorb light. Lastly, NLDS is combined with phase microscopy to achieve molecular imaging with sub-micron spatial resolution. Imaging of red blood cells (RBCs) shows that the method enables highly sensitive measurements that can quantify hemoglobin content from single RBCs.

Robles, Francisco E.

93

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

NASA Astrophysics Data System (ADS)

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

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

2012-03-01

94

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

NASA Astrophysics Data System (ADS)

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.

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

1994-09-01

95

Combinatorial epigenetic patterns as quantitative predictors of chromatin biology  

PubMed Central

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

2014-01-01

96

Stochastic modelling for quantitative description of heterogeneous biological systems  

Microsoft Academic Search

Two related developments are currently changing traditional approaches to computational systems biology modelling. First, stochastic models are being used increasingly in preference to deterministic models to describe biochemical network dynamics at the single-cell level. Second, sophisticated statistical methods and algorithms are being used to fit both deterministic and stochastic models to time course and other experimental data. Both frameworks are

Darren J. Wilkinson

2009-01-01

97

Using Fourier transform IR spectroscopy to analyze biological materials.  

PubMed

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

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

2014-08-01

98

Fourier transform infrared spectroscopy quantitative analysis of SF6 partial discharge decomposition components  

NASA Astrophysics Data System (ADS)

Gas-insulated switchgear (GIS) internal SF6 gas produces specific decomposition components under partial discharge (PD). By detecting these characteristic decomposition components, such information as the type and level of GIS internal insulation deterioration can be obtained effectively, and the status of GIS internal insulation can be evaluated. SF6 was selected as the background gas for Fourier transform infrared spectroscopy (FTIR) detection in this study. SOF2, SO2F2, SO2, and CO were selected as the characteristic decomposition components for system analysis. The standard infrared absorption spectroscopy of the four characteristic components was measured, the optimal absorption peaks were recorded and the corresponding absorption coefficient was calculated. Quantitative detection experiments on the four characteristic components were conducted. The volume fraction variation trend of four characteristic components at different PD time were analyzed. And under five different PD quantity, the quantitative relationships among gas production rate, PD time, and PD quantity were studied.

Zhang, Xiaoxing; Liu, Heng; Ren, Jiangbo; Li, Jian; Li, Xin

2015-02-01

99

Fourier transform infrared spectroscopy quantitative analysis of SF6 partial discharge decomposition components.  

PubMed

Gas-insulated switchgear (GIS) internal SF6 gas produces specific decomposition components under partial discharge (PD). By detecting these characteristic decomposition components, such information as the type and level of GIS internal insulation deterioration can be obtained effectively, and the status of GIS internal insulation can be evaluated. SF6 was selected as the background gas for Fourier transform infrared spectroscopy (FTIR) detection in this study. SOF2, SO2F2, SO2, and CO were selected as the characteristic decomposition components for system analysis. The standard infrared absorption spectroscopy of the four characteristic components was measured, the optimal absorption peaks were recorded and the corresponding absorption coefficient was calculated. Quantitative detection experiments on the four characteristic components were conducted. The volume fraction variation trend of four characteristic components at different PD time were analyzed. And under five different PD quantity, the quantitative relationships among gas production rate, PD time, and PD quantity were studied. PMID:25459612

Zhang, Xiaoxing; Liu, Heng; Ren, Jiangbo; Li, Jian; Li, Xin

2015-02-01

100

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

E-print Network

A research associate level Developmental Biology/Cell Biology/Biochemistry Experimentalist and funding availability. Send CV, research summary and 2 papers or projects, along with a brief statement cell or developmental biology, pharmacology, toxicology, cell biology, or biochemistry and experience

Menczer, Filippo

101

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

PubMed Central

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.

Lu, Rongwen; Zhang, Qiuxiang; Zhi, Yanan

2015-01-01

102

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

Microsoft Academic Search

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

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

2006-01-01

103

Quantitative Imaging of Single Upconversion Nanoparticles in Biological Tissue  

PubMed Central

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

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

104

Quantitative Analysis of Dynamic Association in Live Biological Fluorescent Samples  

PubMed Central

Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed. Point-pattern matching provides a measure of correspondence between two point-sets under various changes between the sets. Thus, it can be used for robust quantitative analysis of vesicle association between image channels. Results for a large set of synthetic images shows that the novel association method based on point-pattern matching demonstrates robust capability to detect association of closely located vesicles in live cell-microscopy where traditional colocalization methods fail to produce results. In addition, the method outperforms compared Iterated Closest Points registration method. Results for fixed and live experimental data shows the association method to perform comparably to traditional methods in colocalization studies for fixed cells and to perform favorably in association studies for live cells. PMID:24728133

Mäki, Anita; Huttunen, Heikki; Marjomäki, Varpu

2014-01-01

105

Quantitative analysis of polymorphic mixtures of ranitidine hydrochloride by Raman spectroscopy and principal components analysis.  

PubMed

Ranitidine hydrochloride exists as two polymorphs, forms I and II, both of which are used to manufacture commercial tablets. Raman spectroscopy can be used to differentiate the two forms but univariate methods of quantitative analysis of one polymorph as an impurity in the other lack sensitivity. We have applied principal components analysis (PCA) of Raman spectra to binary mixtures of the two polymorphs and to binary mixtures prepared by adding one polymorph to powdered tablets of the other. Based on absorption measurements of seven spectral regions, it was found that >97% of the spectral variation was accounted for by three principal components. Quantitative calibration models generated by multiple linear regression predicted a detection limit and quantitation limit for either forms I or II in mixtures of the two of 0.6 and 1.8%, respectively. This study demonstrates that PCA of Raman spectroscopic data provides a sensitive method for the quantitative analysis of polymorphic impurities of drugs in commercial tablets with a quantitation limit of less than 2%. PMID:12445565

Pratiwi, Destari; Fawcett, J Paul; Gordon, Keith C; Rades, Thomas

2002-11-01

106

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

NASA Astrophysics Data System (ADS)

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

Cerussi, Albert Edward

1999-09-01

107

Quantitative EFTEM mapping of near physiological calcium concentrations in biological specimens  

PubMed Central

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

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

2009-01-01

108

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

PubMed

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

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

2009-02-01

109

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

PubMed Central

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

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

2014-01-01

110

Elemental Analysis of Environmental and Biological Samples Using Laser?Induced Breakdown Spectroscopy and Pulsed Raman Spectroscopy  

Microsoft Academic Search

Laser?induced breakdown spectroscopy (LIBS) and a relatively new technique, pulsed Raman spectroscopy (P?RAMS) are used in this investigation to measure the elemental composition of soils and heterogeneous biological matrices. The LIBS method was used effectively to determine the elemental concentration of carbon and nitrogen in soils, and the presence of metal contaminants in invertebrates. The P?RAMS method was used in

Madhavi Z. Martin; Stan D. Wullschleger; Charles T. Garten Jr; Anthony V. Palumbo; John G. Smith

2005-01-01

111

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

ERIC Educational Resources Information Center

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

Bazzi, Ali; Kreuz, Bette; Fischer, Jeffrey

2004-01-01

112

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

E-print Network

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

Wang, Quidong

113

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

Microsoft Academic Search

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

Peter J. E. Goss; Jean Peccoud

1998-01-01

114

Fluorescence correlation spectroscopy: Statistical analysis and biological applications  

NASA Astrophysics Data System (ADS)

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

Saffarian, Saveez

2002-01-01

115

Detection of Biological Materials Using Ion Mobility Spectroscopy  

SciTech Connect

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

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

1999-03-01

116

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

NASA Astrophysics Data System (ADS)

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

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

2008-03-01

117

Quantitative analysis of slurry sample by laser-induced breakdown spectroscopy.  

PubMed

Laser-induced breakdown spectroscopy (LIBS) has been employed for the analysis of slurry samples. Quantitative analysis of slurry samples is crucial and challenging. The problems associated with slurry samples include splashing, surface turbulence, and the difficulties of obtaining reproducible samples due to sedimentation. The LIBS analysis has achieved limited success due to inherent disadvantages when applied to slurry samples. In order to achieve improved measurement precision and accuracy, a spin-on-glass sampling method was evaluated. Five elements (Al, Ca, Fe, Ni, and Si) were examined in five slurry simulants containing varying amounts of each ion. Three calibration models were developed by using univariate calibration, multiple linear regression, and partial least square regression. LIBS analysis results obtained from the partial least square regression model were determined to be the best fit to results obtained from inductively coupled plasma optical emission spectroscopy analysis. PMID:21424178

Ayyalasomayajula, Krishna K; Dikshit, Vivek; Yueh, Fang Yu; Singh, Jagdish P; Smith, Laura T

2011-07-01

118

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

NASA Astrophysics Data System (ADS)

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.

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

2015-01-01

119

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

PubMed

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

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

2014-05-01

120

Quantification of skeletal muscle mitochondrial function by (31) P magnetic resonance spectroscopy techniques: a quantitative review.  

PubMed

Magnetic resonance spectroscopy (MRS) can give information about cellular metabolism in vivo which is difficult to obtain in other ways. In skeletal muscle, non-invasive (31) P MRS measurements of the post-exercise recovery kinetics of pH, [PCr], [Pi] and [ADP] contain valuable information about muscle mitochondrial function and cellular pH homeostasis in vivo, but quantitative interpretation depends on understanding the underlying physiology. Here, by giving examples of the analysis of (31) P MRS recovery data, by some simple computational simulation, and by extensively comparing data from published studies using both (31) P MRS and invasive direct measurements of muscle O2 consumption in a common analytical framework, we consider what can be learnt quantitatively about mitochondrial metabolism in skeletal muscle using MRS-based methodology. We explore some technical and conceptual limitations of current methods, and point out some aspects of the physiology which are still incompletely understood. PMID:24773619

Kemp, G J; Ahmad, R E; Nicolay, K; Prompers, J J

2015-01-01

121

Quantitative emission from femtosecond microplasmas for laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

An ongoing study of the scaling of Laser-Induced Breakdown Spectroscopy (LIBS) to microjoule pulse energies is being conducted to quantify the LIBS process. The use of microplasmas for LIBS requires good understanding of the emission scaling in order to maximize the sensitivity of the LIBS technique at low energies. The quantitative scaling of emission of Al, Cu and Si microplasmas from 100 ?J down to 100 nJ is presented. The scaling of line emission from major and minor constituents in Al 5052 alloy is investigated and evaluated for analytical LIBS. Ablated crater volume scaling and emission efficiency for Si microplasmas are investigated.

Taschuk, M. T.; Kirkwood, S. E.; Tsui, Y. Y.; Fedosejevs, R.

2007-04-01

122

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

PubMed

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

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

2013-09-01

123

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

SciTech Connect

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.

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

124

Comprehensive, quantitative bioprocess productivity monitoring using fluorescence EEM spectroscopy and chemometrics.  

PubMed

This study demonstrates the application of fluorescence excitation-emission matrix (EEM) spectroscopy to the quantitative predictive analysis of recombinant glycoprotein production cultured in a Chinese hamster ovary (CHO) cell fed-batch process. The method relies on the fact that EEM spectra of complex solutions are very sensitive to compositional change. As the cultivation progressed, changes in the emission properties of various key fluorophores (e.g., tyrosine, tryptophan, and the glycoprotein product) showed significant differences, and this was used to follow culture progress via multiple curve resolution alternating least squares (MCR-ALS). MCR-ALS clearly showed the increase in the unique dityrosine emission from the product glycoprotein as the process progressed, thus provided a qualitative tool for process monitoring. For the quantitative predictive modelling of process performance, the EEM data was first subjected to variable selection and then using the most informative variables, partial least-squares (PLS) regression was implemented for glycoprotein yield prediction. Accurate predictions with relative errors of between 2.3 and 4.6% were obtained for samples extracted from the 100 to 5000 L scale bioreactors. This study shows that the combination of EEM spectroscopy and chemometric methods of evaluation provides a convenient method for monitoring at-line or off-line the productivity of industrial fed-batch mammalian cell culture processes from the small to large scale. This method has applicability to the advancement of process consistency, early problem detection, and quality-by-design (QbD) practices. PMID:24504094

Li, Boyan; Shanahan, Michael; Calvet, Amandine; Leister, Kirk J; Ryder, Alan G

2014-04-01

125

Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy  

NASA Astrophysics Data System (ADS)

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

Cao, Binghua; Fan, Mengbao

2010-10-01

126

Raman spectroscopy of biological material: results from the RAAD common sample set phase II  

NASA Astrophysics Data System (ADS)

Raman spectroscopy is just one of the diverse set of detection techniques which, under the CB Rapid Agent Aerosol Detection (RAAD) program, are being evaluated for their ability to detect and identify biological materials. In order to compare and contrast different techniques, a Common Sample Set composed of threat simulants, interferents and growth media was provided to all RAAD participants. The samples were investigated using both normal Raman and surface-enhanced Raman spectroscopy. This paper focuses on near-infrared Raman data from the Common Sample Set bacterial simulants. Results are also given from a principal component analysis performed on these samples. These measurements provide and initial assessment of the detection and discrimination capability of Raman spectroscopy as applied to biological materials. Despite the challenges facing this detection method, Raman spectroscopy is emerging as a rapid and information-rich method of investigating biological threats.

Gonser, Kristina R.; Christesen, Steven D.; Guicheteau, Jason A.

2004-12-01

127

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

NASA Astrophysics Data System (ADS)

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.

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

2006-02-01

128

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

NASA Astrophysics Data System (ADS)

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

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

2014-10-01

129

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

NASA Astrophysics Data System (ADS)

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

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

1998-04-01

130

Quantitative Determination of Ligand Densities on Nanomaterials by X-ray Photoelectron Spectroscopy.  

PubMed

X-ray photoelectron spectroscopy (XPS) is a nearly universal method for quantitative characterization of both organic and inorganic layers on surfaces. When applied to nanoparticles, the analysis is complicated by the strong curvature of the surface and by the fact that the electron attenuation length can be comparable to the diameter of the nanoparticles, making it necessary to explicitly include the shape of the nanoparticle to achieve quantitative analysis. We describe a combined experimental and computational analysis of XPS data for molecular ligands on gold nanoparticles. The analysis includes scattering in both Au core and organic shells and is valid even for nanoparticles having diameters comparable to the electron attenuation length (EAL). To test this model, we show experimentally how varying particle diameter from 1.3 to 6.3 nm leads to a change in the measured AC/AAu peak area ratio, changing by a factor of 15. By analyzing the data in a simple computational model, we demonstrate that ligand densities can be obtained, and, moreover, that the actual ligand densities for these nanoparticles are a constant value of 3.9 ± 0.2 molecules nm(-2). This model can be easily extended to a wide range of core-shell nanoparticles, providing a simple pathway to extend XPS quantitative analysis to a broader range of nanomaterials. PMID:25514372

Torelli, Marco D; Putans, Rebecca A; Tan, Yizheng; Lohse, Samuel E; Murphy, Catherine J; Hamers, Robert J

2015-01-28

131

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

PubMed

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

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

2013-07-29

132

Qualitative and Quantitative Analysis of Systems and Synthetic Biology Constructs using P Systems.  

PubMed

Computational models are perceived as an attractive alternative to mathematical models (e.g., ordinary differential equations). These models incorporate a set of methods for specifying, modeling, testing, and simulating biological systems. In addition, they can be analyzed using algorithmic techniques (e.g., formal verification). This paper shows how formal verification is utilized in systems and synthetic biology through qualitative vs quantitative analysis. Here, we choose two well-known case studies: quorum sensing in P. aeruginosas and pulse generator. The paper reports verification analysis of two systems carried out using some model checking tools, integrated to the Infobiotics Workbench platform, where system models are based on stochastic P systems. PMID:25090609

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

2015-01-16

133

Systems biology is the quantitative and qualitative study of interactions among the components of biological systems,  

E-print Network

of metabolites and other biologicals that are already produced by host organism Production of modified or new.5% of this amount is used in non-food applications 170 billion tons of biomass 75% carbohydrates 20% lignin 5 polymerization of monomers Organic/inorganic hybrids O * C H2 * OHR n m #12;#12;Enhanced production

Narasayya, Vivek

134

Application of Optical Imaging and Spectroscopy to Radiation Biology  

PubMed Central

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

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

2013-01-01

135

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

PubMed Central

Surface-enhanced Raman spectroscopy (SERS) has been used in a variety of biological applications due to its high sensitivity and specificity. Here, we report a SERS-based biosensing approach for quantitative detection of biomolecules. A SERS substrate bearing gold-decorated silicon nanopillars is functionalized with aptamers for sensitive and specific detection of target molecules. In this study, TAMRA-labeled vasopressin molecules in the picomolar regime (1 pM to 1 nM) are specifically captured by aptamers on the nanostructured SERS substrate and monitored by using an automated SERS signal mapping technique. From the experimental results, we show concentration-dependent SERS responses in the picomolar range by integrating SERS signal intensities over a scanning area. It is also noted that our signal mapping approach significantly improves statistical reproducibility and accounts for spot-to-spot variation in conventional SERS quantification. Furthermore, we have developed an analytical model capable of predicting experimental intensity distributions on the substrates for reliable quantification of biomolecules. Lastly, we have calculated the minimum needed area of Raman mapping for efficient and reliable analysis of each measurement. Combining our SERS mapping analysis with an aptamer-functionalized nanopillar substrate is found to be extremely efficient for detection of low-abundance biomolecules. PMID:23713574

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

2013-01-01

136

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

SciTech Connect

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

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

1994-10-11

137

Quantitative determination of the O({sup 3}P) density via visible cavity-enhanced spectroscopy  

SciTech Connect

A simple method has been developed to quantitatively measure the ground state oxygen atom, O({sup 3}P), density. The technique exploits cavity-enhanced spectroscopy to probe the relatively weak O({sup 1}D)(leftarrow)O({sup 3}P{sub 1}) transition near 636 nm. O({sup 3}P{sub 1}) densities of approximately 3.4x10{sup 14} at./cm{sup 3} were measured in an inductively coupled plasma produced within a high-finesse optical cavity, and a minimum detectable atom state density of 1.3x10{sup 12} at./cm{sup 3} was determined. The absorption profile yielded a translational temperature of 453 K. The technique can be readily extended to other atomic species.

Gupta, Manish; Owano, Thomas; Baer, Douglas; O'Keefe, Anthony [Los Gatos Research, 67 East Evelyn Avenue, Suite 3, Mountain View, California 94041 (United States)

2006-12-11

138

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

PubMed

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

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

2014-01-30

139

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

NASA Astrophysics Data System (ADS)

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

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

140

Raman and multichannel Raman spectroscopy of biological systems  

NASA Astrophysics Data System (ADS)

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

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

1991-05-01

141

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

PubMed

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

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

2015-01-01

142

An artificial neural network approach to laser-induced breakdown spectroscopy quantitative analysis  

NASA Astrophysics Data System (ADS)

The usual approach to laser-induced breakdown spectroscopy (LIBS) quantitative analysis is based on the use of calibration curves, suitably built using appropriate reference standards. More recently, statistical methods relying on the principles of artificial neural networks (ANN) are increasingly used. However, ANN analysis is often used as a ‘black box’ system and the peculiarities of the LIBS spectra are not exploited fully. An a priori exploration of the raw data contained in the LIBS spectra, carried out by a neural network to learn what are the significant areas of the spectrum to be used for a subsequent neural network delegated to the calibration, is able to throw light upon important information initially unknown, although already contained within the spectrum. This communication will demonstrate that an approach based on neural networks specially taylored for dealing with LIBS spectra would provide a viable, fast and robust method for LIBS quantitative analysis. This would allow the use of a relatively limited number of reference samples for the training of the network, with respect to the current approaches, and provide a fully automatizable approach for the analysis of a large number of samples.

D'Andrea, Eleonora; Pagnotta, Stefano; Grifoni, Emanuela; Lorenzetti, Giulia; Legnaioli, Stefano; Palleschi, Vincenzo; Lazzerini, Beatrice

2014-09-01

143

Usefulness of quantitative proton MR spectroscopy in the differentiation of benign and malignant meningioma.  

PubMed

This study was aimed to explore the value of quantitative proton MR spectroscopy (1H-MRS) in the differentiation of benign and malignant meningioma. 23 cases, including 19 benign (grade I) and 4 malignant (grade II-III) meningiomas, underwent single voxel 1H-MRS (TR/TE = 2000 ms/68, 136, 272 ms). T2 relaxation time of tissue water and choline were estimated by an exponential decay model. Choline concentration was calculated using tissue water as the internal reference, and corrected according to intra-voxel cystic/necrotic parts. Tissue water T2 of benign and malignant meningiomas were (105 +/- 41) ms and (151 +/- 42) ms, respectively. The difference was statistically significant (P = 0.033). While Choline T2 of benign and malignant meningiomas were (242 +/- 73) ms and (316 +/- 102) ms respectively, the difference was not significant (P = 0.105). Choline concentration was (2.86 +/- 0.86) mmol/ kg wet weight in benign meningiomas and (3.53 +/- 0.60) mmol/kg wet weight in malignant ones; after correction they increased to (2.98 +/- 0.93)mmol/kg wet weight and (4.58 +/- 1.22) mmol/kg wet weight, respectively, and the difference was significant (P = 0.019). In conclusion, quantitative 1H-MRS is useful for the differentiation of benign and malignant meningioma by T2 relaxation time and absolute choline concentration. PMID:22295694

Yue, Qiang; Isobe, Tomonori; Shibata, Yasushi; Kawamura, Hiraku; Anno, Izumi; Matsumura, Akira

2011-12-01

144

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

SciTech Connect

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

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

2009-12-27

145

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

PubMed

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

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

2011-07-01

146

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

SciTech Connect

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

Not Available

1993-12-31

147

Detection of Taurine in Biological Tissues by 33S NMR Spectroscopy  

NASA Astrophysics Data System (ADS)

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

Musio, Roberta; Sciacovelli, Oronzo

2001-12-01

148

Metabolome 2.0: quantitative genetics and network biology of metabolic phenotypes.  

PubMed

The characterization of the metabolome has rapidly evolved over two decades, from early developments in analytical chemistry to systems biology. Metabolites and small molecules are not independent; they are organized in biochemical pathways and in a wider metabolic network, which is itself dependent on various genetic and signaling networks for its regulation. Recent advances in genomics, transcriptomics, proteomics and metabolomics have been matched by the development of publicly available repositories, which have helped shaping a new generation of integrative studies using metabolite measurements in molecular epidemiology and genetic studies. Although the environment influences metabolism, the identification of the genetic determinants of metabolic phenotypes (metabotypes) was made possible by the development of metabotype quantitative trait locus (mQTL) mapping and metabolomic genome-wide association studies (mGWAS) in a rigorous statistical genetics framework, deriving associations between metabolite concentrations and genetic polymorphisms. However, given the complexity of the biomolecular events involved in the regulation of metabolic patterns, alternative network biology approaches have also been recently introduced, such as integrated metabolome and interactome mapping (iMIM). This unprecedented convergence of metabolic biochemistry, quantitative genetics and network biology already has had a strong impact on the role of the metabolome in biomedical sciences, and this review gives a foretaste of its anticipated successes in eventually delivering personalized medicine. PMID:22868675

Dumas, Marc-Emmanuel

2012-10-01

149

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

ERIC Educational Resources Information Center

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

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

2006-01-01

150

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

Microsoft Academic Search

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

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

2004-01-01

151

Quantitative Optical Spectroscopy: A Robust Tool for Direct Measurement of Breast Cancer Vascular Oxygenation and Total Hemoglobin Content In vivo  

Microsoft Academic Search

We propose the use of a robust, biopsy needle-based, fiber- optic tool for routine clinical quantification of tumor oxygenation at the time of diagnostic biopsy for breast cancer. The purpose of this study was to show diffuse reflectance spectroscopy as a quantitative tool to measure oxygenation levels in the vascular compartment of breast cancers in vivo via an optical biopsy

J. Quincy Brown; Lee G. Wilke; Joseph Geradts; Stephanie A. Kennedy; Gregory M. Palmer; Nirmala Ramanujam

2009-01-01

152

Quantitative Fourier transform infrared spectroscopy of binary mixtures of fatty acid esters using partial least squares regression  

Microsoft Academic Search

This work describes a quantitative spectroscopic method for the analysis of binary mixtures of fatty acid esters using multivariate data models based upon Fourier Transform Infra Red (FT-IR) spectroscopy. Multivariate calibration of binary mixtures has been performed using Partial Least Squares regression (PLS), with two approaches being applied for fitting the inner relation namely a standard linear function and a

Emma S. Haines; Anthony D. Walmsley; Stephen J. Haswell

1997-01-01

153

MR of Hypoxic Encephalopathy in Children after Near Drowning: Correlation with Quantitative Proton MR Spectroscopy and Clinical Outcome  

Microsoft Academic Search

BACKGROUND AND PURPOSE: Quantitative MR spectroscopy has a proved role in the investigation of hypoxia caused by near drowning. To date, no studies have addressed the MR imaging changes that may also accompany this condition. The purpose of this study was to describe the MR imaging findings in children with hypoxic encephalopathy caused by near drowning and to compare these

David J. Dubowitz; Stefan Bluml; Edgardo Arcinue; Rosalind B. Dietrich

154

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

PubMed

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

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

2014-04-01

155

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

PubMed Central

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

Creath, Katherine; Goldstein, Goldie

2012-01-01

156

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

PubMed Central

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

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

157

CMOS based sensor for dielectric spectroscopy of biological cell suspension  

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

158

Broadband Plasmon Waveguide Resonance Spectroscopy for Probing Biological Thin Films  

PubMed Central

A commercially available spectrometer has been modified to perform plasmon waveguide resonance (PWR) spectroscopy over a broad spectral bandwidth. When compared to surface plasmon resonance (SPR), PWR has the advantage of allowing measurements in both s- and p-polarizations on a waveguide surface that is silica or glass rather than a noble metal. Here the waveguide is a BK7 glass slide coated with silver and silica layers. The resonance wavelength is sensitive to the optical thickness of the medium adjacent to the silica layer. The sensitivity of this technique is characterized and compared with broadband SPR both experimentally and theoretically. The sensitivity of spectral PWR is comparable to that of spectral SPR for samples with refractive indices close to that of water. The hydrophilic surface of the waveguide allows supported lipid bilayers to be formed spontaneously by vesicle fusion; in contrast, the surface of an SPR chip requires chemical modification to create a supported lipid membrane. Broadband PWR spectroscopy should be a useful technique to study biointerfaces, including ligand binding to transmembrane receptors and adsorption of peripheral proteins on ligand-bearing membranes. PMID:19796490

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

2010-01-01

159

Broadband plasmon waveguide resonance spectroscopy for probing biological thin films.  

PubMed

A commercially available spectrometer has been modified to perform plasmon waveguide resonance (PWR) spectroscopy over a broad spectral bandwidth. When compared to surface plasmon resonance (SPR), PWR has the advantage of allowing measurements in both s- and p-polarizations on a waveguide surface that is silica or glass rather than a noble metal. Here the waveguide is a BK7 glass slide coated with silver and silica layers. The resonance wavelength is sensitive to the optical thickness of the medium adjacent to the silica layer. The sensitivity of this technique is characterized and compared with broadband SPR both experimentally and theoretically. The sensitivity of spectral PWR is comparable to that of spectral SPR for samples with refractive indices close to that of water. The hydrophilic surface of the waveguide allows supported lipid bilayers to be formed spontaneously by vesicle fusion; in contrast, the surface of an SPR chip requires chemical modification to create a supported lipid membrane. Broadband PWR spectroscopy should be a useful technique to study biointerfaces, including ligand binding to transmembrane receptors and adsorption of peripheral proteins on ligand-bearing membranes. PMID:19796490

Zhang, Han; Orosz, Kristina S; Takahashi, Hiromi; Saavedra, S Scott

2009-09-01

160

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

NASA Technical Reports Server (NTRS)

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

Hoehler, Tori M.

2010-01-01

161

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

NASA Astrophysics Data System (ADS)

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

Wang, Qiang; Ma, Yehao; Wang, Xiaowei

2012-06-01

162

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

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

163

Mechanical Properties of Complex Biological Systems using AFM-Based Force Spectroscopy  

E-print Network

Mechanical Properties of Complex Biological Systems using AFM-Based Force Spectroscopy jointed chain definition................. 16 1.9 Schematic of wormlike chain definition.................................. 43 2.6 Axial charge distribution in collagen D-period............... 44 2.7 AFM scan of acid

La Rosa, Andres H.

164

Raman spectroscopy of biological material: results from the RAAD common sample set phase II  

Microsoft Academic Search

Raman spectroscopy is just one of the diverse set of detection techniques which, under the CB Rapid Agent Aerosol Detection (RAAD) program, are being evaluated for their ability to detect and identify biological materials. In order to compare and contrast different techniques, a Common Sample Set composed of threat simulants, interferents and growth media was provided to all RAAD participants.

Kristina R. Gonser; Steven D. Christesen; Jason A. Guicheteau

2004-01-01

165

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 be used for identification purposes. However, conventional Fourier transform infrared spectroscopy and terahertz time- domain spectroscopy (THz-TDS) often result in broad, overlapping features that are difficult

166

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

NASA Astrophysics Data System (ADS)

A systematic calculation of the backscattering factor in quantitative analysis by Auger electron spectroscopy has been performed for the primary electron beam of energy from the threshold energy of inner-shell ionization to 30 keV at the incident angle of 0°-89° and for principal Auger transition and Auger electrons emitted from over 28 pure elements at an emission angle of 0°-89° by using a Monte Carlo simulation method. The calculation employs a general definition of backscattering factor, Casnati's ionization cross section, up-to-date Monte Carlo model of electron scattering, and a large number of electron trajectories to ensure less statistical error. Both the configuration geometry of concentric hemispherical analyzer and the cylindrical mirror analyzer for Auger electron detection are considered in the calculation. The calculated backscattering factors are found to describe very well an experimental dependence of Auger electron intensity on primary energy and on incident angle for Si, Cu, Ag, and W in literature. The calculated numerical values of backscattering factor are stored in an open and online database at http://micro.ustc.edu.cn/BSFDataBase/BFAES.htm.

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

2008-12-01

167

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

NASA Astrophysics Data System (ADS)

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

Fan, Yuxia; Cheng, Fang; Xie, Lijuan

2010-04-01

168

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

PubMed

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

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

2014-12-10

169

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

PubMed Central

Quantitative orientation measurements by attenuated total reflectance (ATR) infrared spectroscopy require the accurate knowledge of the dichroic ratio and of the mean-square electric fields along the three axes of the ATR crystal. In this paper, polarized ATR spectra of single supported bilayers of the phospholipid dimyristoylphosphatidic acid covered by either air or water have been recorded and the dichroic ratio of the bands due to the methylene stretching vibrations has been calculated. The mean-square electric field amplitudes were calculated using three formalisms, namely the Harrick thin film approximation, the two-phase approximation, and the thickness- and absorption-dependent one. The results show that for dry bilayers, the acyl chain tilt angle varies with the formalism used, while no significant variations are observed for the hydrated bilayers. To test the validity of the different formalisms, s- and p-polarized ATR spectra of a 40-A lipid layer were simulated for different acyl chain tilt angles. The results show that the thickness- and absorption-dependent formalism using the mean values of the electric fields over the film thickness gives the most accurate values of acyl chain tilt angle in dry lipid films. However, for lipid monolayers or bilayers, the tilt angle can be determined with an acceptable accuracy using the Harrick thin film approximation. Finally, this study shows clearly that the uncertainty on the determination of the tilt angle comes mostly from the experimental error on the dichroic ratio and from the knowledge of the refractive index. PMID:9876167

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

1999-01-01

170

Quantitative identification of metastable magnesium carbonate minerals by solid-state (13)c NMR spectroscopy.  

PubMed

In the conversion of CO2 to mineral carbonates for the permanent geosequestration of CO2, there are multiple magnesium carbonate phases that are potential reaction products. Solid-state (13)C NMR is demonstrated as an effective tool for distinguishing magnesium carbonate phases and quantitatively characterizing magnesium carbonate mixtures. Several of these mineral phases include magnesite, hydromagnesite, dypingite, and nesquehonite, which differ in composition by the number of waters of hydration or the number of crystallographic hydroxyl groups. These carbonates often form in mixtures with nearly overlapping (13)C NMR resonances which makes their identification and analysis difficult. In this study, these phases have been investigated with solid-state (13)C NMR spectroscopy, including both static and magic-angle spinning (MAS) experiments. Static spectra yield chemical shift anisotropy (CSA) lineshapes that are indicative of the site-symmetry variations of the carbon environments. MAS spectra yield isotropic chemical shifts for each crystallographically inequivalent carbon and spin-lattice relaxation times, T1, yield characteristic information that assist in species discrimination. These detailed parameters, and the combination of static and MAS analyses, can aid investigations of mixed carbonates by (13)C NMR. PMID:25437754

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

2015-01-01

171

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

NASA Astrophysics Data System (ADS)

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.

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

2014-11-01

172

Spectroscopy of Multilayered Biological Tissues for Diabetes Care  

NASA Astrophysics Data System (ADS)

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

Yudovsky, Dmitry

173

A diffuse reflectance spectroscopy system to study biological tissues  

NASA Astrophysics Data System (ADS)

Diffuse reflectance spectroscopy (DRS) is a technique that allows the study of the structural and biochemical condition of tissues in a noninvasive-nonionizing way. DRS has been widely used in biomedical applications, mainly as an alternative to biopsy. Generally, the technique consists in the irradiation of a specific zone of a tissue with a reference spectrum. Then, the reemitted by the tissue light is detected. The changes suffered by the backscattered spectrum (after light-tissue interaction) with respect to the incident one carry information about the tissue properties. This work presents a novel system designed and developed to use DRS in biomedical applications. The system uses a LED as a light source and a specially designed optical fiber probe as a mean to deliver the light to the tissue surface, and to collect the reemitted photons from the studied sample. This probe was designed to accomplish two different tasks: to increase the sensitivity of the diagnosis; and to study the radial dependence of the backscattered light. The measuring probe was built in a way that allows taking readings when the exerted pressure on the tissue reaches certain predetermined values.

de la Cadena, A.; Stolik, S.; de la Rosa, J. M.

2013-11-01

174

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

PubMed Central

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

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

2012-01-01

175

First quantitative measurements by IR spectroscopy of dioxins and furans by means of broadly tunable quantum cascade lasers  

NASA Astrophysics Data System (ADS)

We demonstrate the possibility of a quantitative analysis of the concentration of several dioxins and furans, among the most toxic ones, by only using infrared absorption laser spectroscopy. Two broadly tunable quantum cascade lasers, emitting in the mid-infrared, have been used to measure the absorption spectra of dioxins and furans, dissolved in CCl4, in direct absorption mode. The minimum detectable concentrations are inferred by analyzing diluted samples. A comparison between this technique and standard Fourier transform spectroscopy has been carried out and an analysis of future perspectives is reported.

Siciliani de Cumis, M.; D’Amato, F.; Viciani, S.; Patrizi, B.; Foggi, P.; Galea, C. L.

2013-02-01

176

Quantitative Determination of 3-Aminopropylsilane on the Surface of FE3O4 Nanoparticles by Attenuated Total Reflection Infrared Spectroscopy  

NASA Astrophysics Data System (ADS)

A technique for quantitative analysis of 3-aminopropylsilane on the surface of chemically modified Fe3O4 magnetic nanoparticles in the concentration range 0.32-3.03 mmol/g was developed using attenuated total reflection infrared spectroscopy. The technique was based on the ratios of band areas corresponding to Fe-O vibrations of the nanoparticles and Si-O vibrations of the coating as a function of the Si mass fraction in the nanocomposite that was determined by inductively coupled plasma atomic-emission spectroscopy.

Demin, A. M.; Koryakova, O. V.; Krasnov, V. P.

2014-09-01

177

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

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

178

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

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

179

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

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

180

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

PubMed

The present study focuses on predicting the concentration of intracellular storage polymers in enhanced biological phosphorus removal (EBPR) systems. For that purpose, quantitative image analysis techniques were developed for determining the intracellular concentrations of PHA (PHB and PHV) with Nile blue and glycogen with aniline blue staining. Partial least squares (PLS) were used to predict the standard analytical values of these polymers by the proposed methodology. Identification of the aerobic and anaerobic stages proved to be crucial for improving the assessment of PHA, PHB and PHV intracellular concentrations. Current Nile blue based methodology can be seen as a feasible starting point for further enhancement. Glycogen detection based on the developed aniline blue staining methodology combined with the image analysis data proved to be a promising technique, toward the elimination of the need for analytical off-line measurements. PMID:23498684

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

2013-04-01

181

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

NASA Astrophysics Data System (ADS)

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

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

2014-07-01

182

Quantification of Biological Interactions with Particle Image Cross-Correlation Spectroscopy (PICCS)  

Microsoft Academic Search

A multitude of biological processes that involve multiple interaction partners are observed by two-color microscopy. Here we describe an analysis method for the robust quantification of correlation between signals in different color channels: particle image cross-correlation spectroscopy (PICCS). The method, which exploits the superior positional accuracy obtained in single-object and single-molecule microscopy, can extract the correlation fraction and length scale.

Stefan Semrau; Laurent Holtzer; Marcos González-Gaitán; Thomas Schmidt

2011-01-01

183

Quasi-elastic light scattering spectroscopy of single biological cells under a microscope  

NASA Astrophysics Data System (ADS)

A microscope laser light scattering setup has been developed that allows to carry out the intensity autocorrelation spectroscopy of the light scattered from a volume as small as (2 . tm)3. This noninvasive technique makes cytoplasmic studies possible inside single live biological cells. The technique has been proven powerful as revealed in the studies of hemoglobin aggregation within sickle red blood cells crystallin synthesis in the lens fiber cells and secretion of protein containing granules in the acinar cells. 1.

Tanaka, Toyoichi; Nishio, Izumi; Peetermans, Joyce; Gorti, Sridhar

1991-05-01

184

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

PubMed

Near-infrared (NIR) spectroscopy has come of age and is now prominent among major analytical technologies after the NIR region was discovered in 1800, revived and developed in the early 1950s and put into practice in the 1970s. Since its first use in the cereal industry, it has become the quality control method of choice for many more applications due to the advancement in instrumentation, computing power and multivariate data analysis. NIR spectroscopy is also increasingly used during basic research performed to better understand complex biological systems, e.g. by means of studying characteristic water absorption bands. The shorter NIR wavelengths (800-2500 nm), compared to those in the mid-infrared (MIR) range (2500-15?000 nm) enable increased penetration depth and subsequent non-destructive, non-invasive, chemical-free, rapid analysis possibilities for a wide range of biological materials. A disadvantage of NIR spectroscopy is its reliance on reference methods and model development using chemometrics. NIR measurements and predictions are, however, considered more reproducible than the usually more accurate and precise reference methods. The advantages of NIR spectroscopy contribute to it now often being favoured over other spectroscopic (colourimetry and MIR) and analytical methods, using chemicals and producing chemical waste, such as gas chromatography (GC) and high performance liquid chromatography (HPLC). This tutorial review intends to provide a brief overview of the basic theoretical principles and most investigated applications of NIR spectroscopy. In addition, it considers the recent development, principles and applications of NIR hyperspectral imaging. NIR hyperspectral imaging provides NIR spectral data as a set of images, each representing a narrow wavelength range or spectral band. The advantage compared to NIR spectroscopy is that, due to the additional spatial dimension provided by this technology, the images can be analysed and visualised as chemical images providing identification as well as localisation of chemical compounds in non-homogenous samples. PMID:25156745

Manley, Marena

2014-12-21

185

Quantitative gas chromatography-mass spectrometry isomer-specific measurement of hydroxy fatty acids in biological samples and food as a marker of lipid peroxidation.  

PubMed

We have developed a capillary gas chromatography-mass spectrometry method for the quantitative analysis of individual positional isomers of monohydroxy fatty acids derived from linoleic, arachidonic, eicosapentaenoic, or docosahexaenoic acid. Peroxidation of a particular polyunsaturated fatty acid results already in a complex mixture of positional isomers of hydroperoxy and hydroxy fatty acids. Catalytic hydrogenation of lipid extracts produces stable saturated hydroxy lipids from the complex mixtures typical of oxidized biological samples, simultaneously simplifying the analytical problem and eliminating oxidation artifacts. After saponification and methylation, monohydroxy fatty acid methyl esters are purified by solid-phase extraction and partially resolved using a CP Sil 19 column following on-column derivatization of the hydroxy groups with tetramethylammonium hydroxide. The resulting methoxy fatty acid methyl esters are subjected to electron impact mass spectroscopy. Two characteristic ions are produced for each positional isomer. Quantitative measurements were achieved by using odd chain C17 and C19 monohydroxy fatty acids as internal standards. The limit of detection of individual hydroxy fatty acid isomers is dependent on the total number of ions monitored. Monitoring 11 pairs of ions simultaneously gives limits of detection of 10 ng. Sensitivity is much higher by monitoring fewer ions and as little as 0.2 ng of a single isomer can be detected. The method has been applied for the quantitative analysis of hydroxy (plus hydroperoxy) fatty acids in plasma, adipose tissue, oils, and foods. To date over 1000 samples have been analyzed using the method described in this paper. PMID:9177726

Wilson, R; Smith, R; Wilson, P; Shepherd, M J; Riemersma, R A

1997-05-15

186

BIOLOGY OF REPRODUCTION 43, 525-542 (1990) Quantitative and Qualitative Characteristics of the Stages and Transitions in the Cycle  

E-print Network

BIOLOGY OF REPRODUCTION 43, 525-542 (1990) Quantitative and Qualitative Characteristics are illustrated for testes fixed by vascular perfusion and embedded in plastic resins. Improved cellular in this stage. Although the resolution of cellular detail was greatly improved with the use of plastics

Hess, Rex A.

187

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

PubMed Central

It is shown that dark-field images collected in the scanning transmission electron microscope (STEM) at two different camera lengths yield quantitative distributions of both the heavy and light atoms in a stained biological specimen. Quantitative analysis of the paired STEM images requires knowledge of the elastic scattering cross sections, which are calculated from the NIST Elastic-Scattering Cross-Section Database. The results reveal quantitative information about the distribution of fixative and stain within the biological matrix, and provide a basis for assessing detection limits for heavy metal clusters used to label intracellular proteins. In sectioned cells that have been stained only with osmium tetroxide, we find an average of 1.2 ± 0.1 Os atom per nm3, corresponding to an atomic ratio of Os:C atoms of approximately 0.02, which indicates that small heavy atom clusters of Undecagold and Nanogold can be detected in lightly stained specimens. PMID:18359249

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

2009-01-01

188

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

PubMed

Metabolite concentration measurements in in vivo NMR are generally performed under partially saturated conditions, with correction for partial saturation performed after data collection using a measured saturation factor. Here, we present an experimental test of the hypothesis that quantitation errors can occur due to application of such saturation factor corrections in changing systems. Thus, this extends our previous theoretical work on quantitation errors due to varying saturation factors. We obtained results for two systems frequently studied by 31P NMR, the ischemic rat heart and the electrically stimulated rat gastrocnemius muscle. The results are interpreted in light of previous theoretical work which defined the degree of saturation occurring in a one-pulse experiment for a system with given spin-lattice relaxation times, T(1)s, equilibrium magnetizations, M(0)s, and reaction rates. We found that (i) the assumption of constancy of saturation factors leads to quantitation errors on the order of 40% in inorganic phosphate; (ii) the dominant contributor to the quantitation errors in inorganic phosphate is most likely changes in T(1); (iii) T(1) and M(0) changes between control and intervention periods, and chemical exchange contribute to different extents to quantitation errors in phosphocreatine and gamma-ATP; (iv) relatively small increases in interpulse delay substantially decreased quantitation errors for metabolites in ischemic rat hearts; (v) random error due to finite SNR led to approximately 4% error in quantitation, and hence was a substantially smaller contributor than were changes in saturation factors. PMID:12713964

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

2003-04-01

189

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

NASA Astrophysics Data System (ADS)

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

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

2003-04-01

190

Quantitative phase-amplitude microscopy II: differential interference contrast imaging for biological TEM.  

PubMed

Although phase contrast microscopy is widespread in optical microscopy, it has not been as widely adopted in transmission electron microscopy (TEM), which has therefore to a large extent relied on staining techniques to yield sufficient contrast. Those methods of phase contrast that are used in biological electron microscopy have been limited by factors such as the need for small phase shifts in very thin samples, the requirement for difficult experimental conditions, or the use of complex data analysis methods. We here demonstrate a simple method for quantitative TEM phase microscopy that is suitable for large phase shifts and requires only two images. We present a TEM phase image of unstained Radula sp. (liverwort spore). We show how the image may be transformed into the differential interference contrast image format familiar from optical microscopy. The phase images contain features not visible with the other imaging modalities. The resulting technique should permit phase contrast TEM to be performed almost as readily as phase contrast optical microscopy. PMID:12067364

McMahon, P J; Barone-Nugent, E D; Allman, B E; Nugent, K A

2002-06-01

191

Quantitative Raman Spectroscopy to monitor microbial metabolism in situ under pressure  

NASA Astrophysics Data System (ADS)

Although high hydrostatic pressure (HHP) biotopes are ubiquitous on Earth, little is known about the metabolism of piezophile organisms. Cell culture under HHP can be technically challenging, and equipment- dependent. In addition, the depressurization step required for analysis can lead to erroneous data. Therefore, to understand how piezophile organisms react to pressure, it is crucial to be able to monitor their activity in situ under HHP. We developed the use of Quantitative Raman Spectroscopy (QRS, 1) to monitor in situ the metabolism of organic molecules. This technique is based on the specific spectral signature of an analyte from which its concentration can be deduced. An application of this technique to the monitoring of alcoholic fermentation by the piezotolerant micro-eucaryote Saccharomyces cerevisiae is presented. Ethanol fermentation from glucose was monitored during 24h from ambient P up to 100 MPa in the low- pressure Diamond Anvil Cell (lpDAC, 2). The experimental compression chamber consisted in a 300 ?m-thick Ni gasket in which a 500 ?m-diameter hole was drilled. Early-stationnary yeast cells were inoculated into fresh low-fluorescence medium containing 0.15 M of glucose. Ethanol concentration was determined in situ by QRS using the symmetric C-C stretching mode of ethanol at 878 cm-1 normalizing the data to the intensity of the sulfate S-O stretching mode at 980 cm-1. In our setup, the detection limit of ethanol is lower than 0.05 mM with a precision below 1%. At ambient P, ethanol production in the lpDAC and in control experiments proceeds with the same kinetics. Thus, yeast is not affected by its confinement. This is further confirmed by its ability to bud with a generation time similar to control experiments performed in glass tubes at ambient pressure inside the lpDAC. Ethanol production by yeast occurs to at least 65 MPa (3). At 10 MPa, fermentation proceeds 3 times faster than at ambient P. Fermentation rates decrease linearly from 20 to at least 65 MPa. No ethanol was detected at 100 MPa. From these data, the pressure at which ethanol fermentation stops in yeast was calculated to be 87±7 MPa. These results indicate that the activity of one or several enzymes of the glycolytic pathway is enhanced at low pressure. At higher pressure, they become progressively repressed, and are completely inhibited above 87 MPa. Our in situ monitoring constitutes a direct demonstration of yeast metabolism in situ under pressure up to 100 MPa. Our data agree with previous ex-situ data by Abe and Horikoshi (4). However, we observed that ethanol production is not completely inhibited around 50 MPa as predicted, but could be detected at significantly higher pressures (up to 87 MPa). QSR is a powerful method to monitor microbial activities, since almost any organic molecule with a carbon chain ranging from 1 to 6 carbon can be detected and quantified. The only limitation of QSR is that the Raman spectrum of the molecule exhibits at least one peak not masked by the spectrum of the growth medium. 1 Pelletier M J Appl Spectr 57:20A-42A, 2003 2 Daniel I, Oger P, Picard A, Cardon H and Chervin J-C (submitted to Rev Sci Instr) 3 Picard A, Daniel I, Montagnac G and Oger P (submitted to Extremophiles) 4 Abe F and Horikoshi K Extremophiles 1: 89-93, 1997

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

2006-12-01

192

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

PubMed Central

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

Wang, Yuling; Irudayaraj, Joseph

2013-01-01

193

Quantification of biological interactions with particle image cross-correlation spectroscopy (PICCS).  

PubMed

A multitude of biological processes that involve multiple interaction partners are observed by two-color microscopy. Here we describe an analysis method for the robust quantification of correlation between signals in different color channels: particle image cross-correlation spectroscopy (PICCS). The method, which exploits the superior positional accuracy obtained in single-object and single-molecule microscopy, can extract the correlation fraction and length scale. We applied PICCS to correlation measurements in living tissues. The morphogen Decapentaplegic (Dpp) was imaged in wing imaginal disks of fruit fly larvae and we quantified what fraction of early endosomes contained Dpp. PMID:21463595

Semrau, Stefan; Holtzer, Laurent; González-Gaitán, Marcos; Schmidt, Thomas

2011-04-01

194

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

NASA Astrophysics Data System (ADS)

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

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

1995-02-01

195

Coherent optical spectroscopy in a biological semiconductor quantum dot-DNA hybrid system  

PubMed Central

We theoretically investigate coherent optical spectroscopy of a biological semiconductor quantum dot (QD) coupled to DNA molecules. Coupling with DNAs, the linear optical responses of the peptide QDs will be enhanced significantly in the simultaneous presence of two optical fields. Based on this technique, we propose a scheme to measure the vibrational frequency of DNA and the coupling strength between peptide QD and DNA in all-optical domain. Distinct with metallic quantum dot, biological QD is non-toxic and pollution-free to environment, which will contribute to clinical medicine experiments. This article leads people to know more about the optical behaviors of DNAs-quantum dot system, with the currently popular pump-probe technique. PMID:22340277

2012-01-01

196

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

PubMed

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

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

2013-09-11

197

Real time quantitative Raman spectroscopy of supported metal oxide catalysts without the need of an internal standard.  

PubMed

In continuation to the possibility of using a combined operando Raman/UV-Vis-NIR set-up for conducting qualitative Raman spectroscopy, the possibilities for quantitative Raman spectroscopic measurements of supported metal oxide catalysts under working conditions without the need of an internal standard have been explored. The dehydrogenation of propane over an industrial-like 13 wt% Cr/Al203 catalyst was used as a model system. During reaction, the catalytic solid was continuously monitored by both UV-Vis-NIR and Raman spectroscopy. As the dehydrogenation proceeds, the catalyst gradually darkens due to coke formation and consequently the UV-Vis-NIR diffuse reflectance and Raman scattered signal progressively decrease in intensity. The formation of coke was confirmed with TEOM, TGA and Raman. The measured Raman spectra can be used as a quantitative measure of the amount of carbonaceous deposits at the catalyst surface provided that a correction factor G(R(infinity)) is applied. This factor can be directly calculated from the corresponding UV-Vis-NIR diffuse reflectance spectra. The validity of the approach is compared with one, in which an internal boron nitride standard is added to the catalytic solid. It will be shown that the proposed methodology allows measurement of the amount of carbonaceous deposits on a catalyst material inside a reactor as a function of reaction time and catalyst bed height. As a consequence, an elegant technique for on-line process control of e.g. an industrial propane dehydrogenation reactor emerges. PMID:19785192

Tinnemans, S J; Kox, M H F; Nijhuis, T A; Visser, T; Weckhuysen, B M

2005-01-01

198

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

PubMed

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

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

2014-05-01

199

Expanding the limits of human blood metabolite quantitation using NMR spectroscopy.  

PubMed

A current challenge in metabolomics is the reliable quantitation of many metabolites. Limited resolution and sensitivity combined with the challenges associated with unknown metabolite identification have restricted both the number and the quantitative accuracy of blood metabolites. Focused on alleviating this bottleneck in NMR-based metabolomics, investigations of pooled human serum combining an array of 1D/2D NMR experiments at 800 MHz, database searches, and spiking with authentic compounds enabled the identification of 67 blood metabolites. Many of these (?1/3) are new compared with those reported previously as a part of the Human Serum Metabolome Database. In addition, considering both the high reproducibility and quantitative nature of NMR as well as the sensitivity of NMR chemical shifts to altered sample conditions, experimental protocols and comprehensive peak annotations are provided here as a guide for identification and quantitation of the new pool of blood metabolites for routine applications. Further, investigations focused on the evaluation of quantitation using organic solvents revealed a surprisingly poor performance for protein precipitation using acetonitrile. One-third of the detected metabolites were attenuated by 10-67% compared with methanol precipitation at the same solvent-to-serum ratio of 2:1 (v/v). Nearly 2/3 of the metabolites were further attenuated by up to 65% upon increasing the acetonitrile-to-serum ratio to 4:1 (v/v). These results, combined with the newly established identity for many unknown metabolites in the NMR spectrum, offer new avenues for human serum/plasma-based metabolomics. Further, the ability to quantitatively evaluate nearly 70 blood metabolites that represent numerous classes, including amino acids, organic acids, carbohydrates, and heterocyclic compounds, using a simple and highly reproducible analytical method such as NMR may potentially guide the evaluation of samples for analysis using mass spectrometry. PMID:25485990

Nagana Gowda, G A; Gowda, Yashas N; Raftery, Daniel

2015-01-01

200

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

SciTech Connect

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

Drukker, Karen, E-mail: kdrukker@uchicago.edu; Giger, Maryellen L.; Li, Hui [Department of Radiology, University of Chicago, Chicago, Illinois 60637 (United States)] [Department of Radiology, University of Chicago, Chicago, Illinois 60637 (United States); Duewer, Fred; Malkov, Serghei; Joe, Bonnie; Kerlikowske, Karla; Shepherd, John A. [Radiology Department, University of California, San Francisco, California 94143 (United States)] [Radiology Department, University of California, San Francisco, California 94143 (United States); Flowers, Chris I. [Department of Radiology, University of South Florida, Tampa, Florida 33612 (United States)] [Department of Radiology, University of South Florida, Tampa, Florida 33612 (United States); Drukteinis, Jennifer S. [Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612 (United States)] [Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612 (United States)

2014-03-15

201

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

Microsoft Academic Search

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

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

2002-01-01

202

Quantitative determination of saturated and unsaturated fatty acids in edible oils by infrared spectroscopy and chemometrics  

Microsoft Academic Search

The fatty acids of eight edible oil samples with varying composition were saponified, esterified into methyl esters and analysed by gas chromatography. These composition values were used in calculating the composition of 25 syntheic edible oil mixtures containing a wide range of saturation and unsaturation. All these 33 oils were then analysed by infrared spectroscopy using single reflectance technique. The

Alfred A. Christy; Per K. Egeberg

2006-01-01

203

Quantitative arsenic speciation in mine tailings using X-ray absorption spectroscopy  

Microsoft Academic Search

X-ray absorption fine structure spectroscopy (XAFS) was used to determine arsenic (As) oxidation state, local coordination (to a radius of 7Aaround As), and the relative proportion of different As species in model compounds and three California mine wastes: fully oxidized tailings (Ruth Mine), partially oxidized tailings (Argonaut Mine), and roast- ed sulfide ore (Spenceville Mine). Mineralogy was characterized by Rietveld

ANDREA L. FOSTER; GORDON E. BROWN JR; TRACY N. TINGLE; GEORGE A. PARKS

204

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

PubMed

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

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

2014-12-01

205

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

206

[Qualitative and quantitative research on sulfur fumigation of Angelicae Dahuricae Radix (Baizhi) by near-infrared spectroscopy].  

PubMed

The contents of coumarins in the sulfur fumigated Angelicae Dahuricae Radix (Baizhi, ADR) were reduced significantly. To achieve the quality control of ADR, the qualitative identification of sulfur fumigated ADR and quantitative model of imperatorin content should be established. The near-infrared (NIR) spectrograms of non-sulfur and sulfur fumigated ADR were collected by NIR diffuse reflectance spectroscopy technology and pretreated by the method of first derivative derivation and vector normalization. The Ward's Algorithm method was used for the cluster analysis. The non-sulfur and sulfur fumigated ADR can be quickly identified in the range of 8,806. 0-3 811.0 cm(-1) based on the cluster analysis. The NIR quantitative model of imperatorin was established by the contents of imperatorin determined by HPLC in combination with partial least squares regression analysis. According to the calibration model established in this study, correlation coefficients (R2), the root-mean-square error of cross-validation (RMSECV), and the root-mean-square error of prediction (RMSEP) for imperatorin were 0.982 8, 0.006 8, 0.011 8, respectively. The quantitative model of imperatorin can be applied to determine the content of imperatorin in ADR accurately. PMID:25282896

Wu, Xiao-Yi; Chao, Zhi-Mao; Sun, Wen; Wang, Chun

2014-05-01

207

Quantitative detection of uric Acid by electrochemical-surface enhanced Raman spectroscopy using a multilayered au/ag substrate.  

PubMed

Uric acid is a potential important biomarker in urine and serum samples for early diagnosis of preeclampsia, a life-threatening hypertensive disorder that occurs during pregnancy. Preeclampsia is a leading cause of maternal death, especially in developing nation settings. Quantitative detection of uric acid for rapid and routine diagnosis of early preeclampsia using electrochemical-surface enhanced Raman spectroscopy (EC-SERS) is presented herein. A uniform EC-SERS active Au/Ag substrate was developed by depositing nearly monodisperse gold and silver nanoparticles on the carbon working electrode surface of screen printed electrodes. The multilayered Au/Ag substrates were characterized by electron microscopy and used for quantitative detection of uric acid in 0.1 M NaF and synthetic urine at clinically relevant concentrations. These results showed a linear relationship between the EC-SERS signal intensity and the uric acid concentration. Relative errors calculated for selected concentrations were all within the Clinical Laboratory Improvement Amendments (CLIA) criterion for uric acid analysis (±17%). It is believed that routine and early diagnosis of disease could be possible through such quantitative detection of biomarkers in patient samples using this EC-SERS method. PMID:25483146

Zhao, Lili; Blackburn, Jonathan; Brosseau, Christa L

2015-01-01

208

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

E-print Network

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 growth in nature. Adhesive and viscoelastic properties of bacteria play important roles at different

Dutcher, John

209

Application of electron energy loss spectroscopy and electron spectroscopic imaging to aluminum determination in biological tissue.  

PubMed

Electron energy loss spectroscopy (EELS) is a high spatial resolution electron microscopic technique with the potential to quantify elements at the subcellular level. The presence of each element is demonstrated by the electron energy loss edge at the energy characteristic of that element. The area of the edge may indicate the quantity of element present. Electron spectroscopic imaging (ESI) is a similar technique generating graphic images of elemental localization in the specimens. An ESI of an aluminum (Al)-loaded rabbit hippocampus showed Al only in pyramidal cell lysosomes, but no EELS edge could be obtained. To determine the sensitivity of EELS for Al and to be able to adjust the instrument to optimal operating conditions, standards containing 50-5000 ppm Al were produced. An Al-chloride: dicyclohexano-18-crown-6 (Al: crown) complex was synthesized. The purity of the complex was confirmed by nuclear magnetic resonance (NMR) spectroscopy and the percentage of Al in the complex was determined by electrothermal atomic absorption spectroscopy (ETAAS). The complex was introduced into a biological tissue embedding resin (Spurr medium) and appeared to be compatible with the resin at Al concentrations < or = 500 ppm. EELS signals from the Al K edge could be obtained at a spatial resolution of 3.3 nm in a 30-nm thick section from 2.78 x 10(-21) g of Al, representing a sample concentration of 1% Al. PMID:8148210

Xie, X; Yokel, R A; Markesbery, W R

1994-01-01

210

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

NASA Astrophysics Data System (ADS)

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

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

2010-02-01

211

Quantitative determination of emerging contaminants, solvent stabilizers and fullerene nanomaterials, in biological and environmental systems.  

E-print Network

??To determine the impact of emerging environmental contaminants on human and environmental health, quantitative analytical methods are required. Analysis of emerging contaminants is hampered by… (more)

Isaacson, Carl W.

2007-01-01

212

Quantitative modeling of electron spectroscopy intensities for supported nanoparticles: The hemispherical cap model for non-normal detection  

NASA Astrophysics Data System (ADS)

Nanoparticles of one element or compound dispersed across the surface of another substrate element or compound form the basis for many materials of great technological importance, such as heterogeneous catalysts, fuel cells and other electrocatalysts, photocatalysts, chemical sensors and biomaterials. They also form during film growth by deposition in many fabrication processes. The average size and number density of such nanoparticles are often very important, and these can be estimated with electron microscopy or scanning tunneling microscopy. However, this is very time consuming and often unavailable with sufficient resolution when the particle size is ~ 1 nm. Because the probe depth of electron spectroscopies like X-Ray Photoelectron Spectroscopy (XPS) or Auger Electron Spectroscopy (AES) is ~ 1 nm, these provide quantitative information on both the total amount of adsorbed material when it is in the form of such small nanoparticles, and the particle thickness. For electron spectroscopy conducted with electron detection normal to the surface, Diebold et al. (1993) derived analytical relationships between the signal intensities for the adsorbate and substrate and the particles' average size and number density, under the assumption that all the particles have hemispherical shape and the same radius. In this paper, we report a simple angle- and particle-size-dependent correction factor that can be applied to these analytical expressions so that they can also be extended to measurements made at other detection angles away from the surface normal. This correction factor is computed using numerical integration and presented for use in future modeling. This correction factor is large (> 2) for angles beyond 60°, so comparing model predictions to measurements at both 0° and ? 60° will also provide a new means for testing the model's assumptions (hemispherical shape and fixed size particles). The ability to compare the hemispherical cap model at several angles simultaneously also should enable more accurate estimates of surface structural parameters when elastic diffraction effects cause strong peaks in the angular distributions of emitted electrons.

Sharp, James C.; Campbell, Charles T.

2015-02-01

213

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

Microsoft Academic Search

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

Yung-keun Kwon; Kwang-hyun Cho

2008-01-01

214

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

NASA Astrophysics Data System (ADS)

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

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

2007-03-01

215

Quantitative characterisation of H-Mordenite zeolite structure by infrared spectroscopy using benzene adsorption  

Microsoft Academic Search

Infrared spectroscopy has been used to characterise the Brönsted acidity, the hydroxyls of H-Mordenite (HM) zeolite and the interaction of hydroxyls with benzene molecules. After pre-treatment under dry oxygen and then under vacuum at 723 K, three hydroxyl groups at 3749, 3660 and 3608 cm?1, assigned to terminal silanol, extraframework Al–OH and framework bridged Si–OH–Al species, respectively, have been detected.

Bao-Lian Su; Valérie Norberg

2001-01-01

216

[Quantitative determination of parameters of substrate using near-infrared spectroscopy technique].  

PubMed

Soilless culture has many virtues, such as space saving, time saving, etc.. It has become one of the technologies which developed fastest in agricultural products. The selection of substrate is one of the keys to determining the success of soilless culture. Therefore, it is important to rapidly determine the parameters of substrate. In the present paper, moisture, electronic conductivity and pH values of substrate were tested by near-infrared (NIR) spectroscopy. The spectra were preprocessed by baseline correction and derivative. Partial least squares (PLS) regression model was built using different wave bands. It was found that baseline drift was improved after correction. NIR spectroscopy can be used to determine EC value of substrate. The correlation coefficient r, root-mean-square error of the cross validation (RMSECV), relative percent difference (RPD) and bias of the optimum PLS was 0.923 6, 634 micros x cm(-1), 3.11 and 19.8 micros x cm(-1), respectively, when the best wave band was 4 246.7 - 7 502.2 cm(-1) and the best factor was 7. NIR spectroscopy technique can also be used to predict moisture of substrate although the accuracy of model should be improved. However, it can not be used to predict pH value of substrate. PMID:22242487

Yu, Yong-Hua

2011-11-01

217

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

PubMed

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

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

2008-01-01

218

Quantitative determination of captopril and prednisolone in tablets by FT-Raman spectroscopy  

Microsoft Academic Search

A procedure for the quantitative determination of captopril and prednisolone in commercial tablets based on partial least squares (PLS) and principal component regression (PCR) treatment of FT-Raman spectroscopic data is described. In the studied medicines active pharmaceutical ingredients (APIs) constitute 4.2–16.7% of the tablet mass. Results obtained from calibration models built using unnormalised spectra were compared with the values found

Sylwester Mazurek; Roman Szostak

2006-01-01

219

Rapid separation and quantitation of curcuminoids combining pseudo two dimensional liquid flash chromatography and NMR spectroscopy  

PubMed Central

Rapid separation, characterization and quantitation of curcuminoids are important owing to their numerous pharmacological properties including antimicrobial, antiviral, antifungal, anticancer, and anti-inflammatory activities. In the present study, pseudo two dimensional liquid flash chromatography was used for the separation of four curcuminoids (curcumin, demethoxy curcumin, bisdemethoxy curcumin and dihydro bisdemethoxy curcumin) for the first time. Silica and diol columns were used for separation of curcuminoids using gradient mobile phase. The separated peaks were monitored at 244, 360 nm to obtain four compounds. The purity of compounds were determined by rapid quantitative 1H NMR (qNMR) using 3-(trimethylsilyl) propionic-(2,2,3,3-d4) acid sodium salt (TSP-d4) (0.012%) in D2O. These results were compared with those obtained by HPLC method. The purity of isolated curcuminoids using pseudo 2D chromatography was found to be in the range of 92.4–95.45%. The structures of these compounds were characterized unambiguously using 13C (APT) NMR spectra. The developed pseudo 2D separation technique has the advantage of simplified automation with shorter run time compared to conventional separation techniques. The method that combines rapid pseudo 2D separation and simple quantitation using qNMR reported herein can be of wide utility for routine analysis of curcuminoids in complex mixtures. PMID:24013126

Jayaprakasha, G. K.; Gowda, G.A. Nagana; Marquez, Sixto; Patil, Bhimanagouda S.

2013-01-01

220

Thin-film quantitative microanalysis of the cation composition in ceramics with ultrathin-window-type energy-dispersive X-ray spectroscopy in a transmission electron microscope  

Microsoft Academic Search

Quantative elemental microanalysis of the cation composition in ceramics was examined by ultrathin-window-type energy-dispersive X-ray spectroscopy (EDS) in a transmission electron microscope. One object of this investigation was the development of a quantitative analysis method by which absorption correction can be carried out. Another was to determine how anions in ceramics are treated in quantitative elemental analysis. The two-beam intensity

Junya Kondoh; Shiomi Kikuchi; Yoichi Timii; Yasuhiko Ito

1997-01-01

221

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

PubMed Central

Third-generation synchrotron radiation sources pose difficult challenges for energy-dispersive detectors for XAFS because of their count rate limitations. One solution to this problem is the bent crystal Laue analyzer (BCLA), which removes most of the undesired scatter and fluorescence before it reaches the detector, effectively eliminating detector saturation due to background. In this paper experimental measurements of BCLA performance in conjunction with a 13-element germanium detector, and a quantitative analysis of the signal-to-noise improvement of BCLAs are presented. The performance of BCLAs are compared with filters and slits. PMID:22514172

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

2012-01-01

222

Qualitative and Quantitative Control of Carbonated Cola Beverages Using 1H NMR Spectroscopy  

PubMed Central

1H Nuclear magnetic resonance (NMR) spectroscopy (400 MHz) was used in the context of food surveillance to develop a reliable analytical tool to differentiate brands of cola beverages and to quantify selected constituents of the soft drinks. The preparation of the samples required only degassing and addition of 0.1% of TSP in D2O for locking and referencing followed by adjustment of pH to 4.5. The NMR spectra obtained can be considered as “fingerprints” and were analyzed by principal component analysis (PCA). Clusters from colas of the same brand were observed, and significant differences between premium and discount brands were found. The quantification of caffeine, acesulfame-K, aspartame, cyclamate, benzoate, hydroxymethylfurfural (HMF), sulfite ammonia caramel (E 150D), and vanillin was simultaneously possible using external calibration curves and applying TSP as internal standard. Limits of detection for caffeine, aspartame, acesulfame-K, and benzoate were 1.7, 3.5, 0.8, and 1.0 mg/L, respectively. Hence, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of soft drinks and quantification of selected constituents. PMID:22356160

2012-01-01

223

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

NASA Astrophysics Data System (ADS)

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

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

2003-12-01

224

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

PubMed

We present a device and method for performing vector transmission spectroscopy on biological specimens at terahertz (THz) frequencies. The device consists of artificial dielectric birefringence obtained from silicon microfluidic grating structures. The device can measure the complex dielectric function of a liquid, across a wide THz band of 2 to 5.5 THz, using a Fourier transform infrared spectrometer. Measurement data from a range of liquid specimens, including sucrose, salmon deoxyribonucleic acid (DNA), herring DNA, and bovine serum albumin protein solution in water are presented. The specimen handling is simple, using a microfluidic channel. The transmission through the device is improved significantly and thus the measurement accuracy and bandwidth are increased. PMID:22734784

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

2012-06-01

225

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

PubMed Central

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

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

2011-01-01

226

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

NASA Technical Reports Server (NTRS)

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

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

2010-01-01

227

Biosynthesis of drug metabolites and quantitation using NMR spectroscopy for use in pharmacologic and drug metabolism studies.  

PubMed

The contribution of drug metabolites to the pharmacologic and toxicologic activity of a drug can be important; however, for a variety of reasons metabolites can frequently be difficult to synthesize. To meet the need of having samples of drug metabolites for further study, we have developed biosynthetic methods coupled with quantitative NMR spectroscopy (qNMR) to generate solutions of metabolites of known structure and concentration. These quantitative samples can be used in a variety of ways when a synthetic sample is unavailable, including pharmacologic assays, standards for in vitro work to help establish clearance pathways, and/or as analytical standards for bioanalytical work to ascertain exposure, among others. We illustrate five examples of metabolite biosynthesis and qNMR. The types of metabolites include one glucuronide and four oxidative products. Concentrations of the isolated metabolite stock solutions ranged from 0.048 to 8.3 mM, with volumes from approximately 0.04 to 0.150 ml in hexadeutarated dimethylsulfoxide. These specific quantified isolates were used as standards in the drug discovery setting as substrates in pharmacology assays, for bioanalytical assays to establish exposure, and in variety of routine absorption, distribution, metabolism, and excretion assays, such as protein binding and determining blood-to-plasma ratios. The methods used to generate these materials are described in detail with the objective that these methods can be generally used for metabolite biosynthesis and isolation. PMID:25053618

Walker, Gregory S; Bauman, Jonathan N; Ryder, Tim F; Smith, Evan B; Spracklin, Douglas K; Obach, R Scott

2014-10-01

228

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

PubMed Central

The electronic structures of Cu2S and CuS have been under intense scrutiny, with the aim of understanding the relationship between their electronic structures and commercially important physical properties. Here, X-ray absorption and emission spectroscopic data have been analyzed using a quantitative, molecular orbital (MO) based approach to understand the electronic structure of these two complex systems. Cu2S is shown to have a significant amount of Cu2+ sites and therefore Cu0 centers. The presence of low-valent Cu is correlated with the electrical conductivity of Cu2S, especially at high temperatures. CuS is shown to have tetrahedral Cu2+ and trigonal Cu1+ sites, with crystal planes that have alternating high and low charge on the Cu centers. These alternating charges may contribute to internal energy transitions required for photoluminescence properties. The in-depth electronic structure solutions presented here not only solve a complicated much-debated problem, but also demonstrate the strength of quantitative MO based approach to X-ray spectroscopies PMID:23781327

Kumar, Prashant; Nagarajan, Rajamani

2013-01-01

229

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

NASA Astrophysics Data System (ADS)

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

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

2012-08-01

230

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

SciTech Connect

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

Mukherjee, Dibyendu [ORNL; Cheng, Mengdawn [ORNL

2008-01-01

231

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

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

232

Quantitation of Organics in Supercritical Fluid Aging Experiments Using FTIR Spectroscopy  

SciTech Connect

Aging is a natural process in which hydrophobic organic contaminants slowly accumulate in the mineral pores and organic matter of soils and sediments. Contaminants in aged soils exhibit decreased bioavailability and slow release to the environment. Therefore, aging may have a significant influence on the applicability and effectiveness of remediation strategies (e.g., bioremediation and natural attenuation) and the accuracy of numerical transport models. Previous research in our laboratory has demonstrated that circulating supercritical carbon dioxide can be used to rapidly prepare artificially aged materials for studying slow-release behavior. In this investigation, FTIR spectroscopy was evaluated as a means of monitoring the progress of the aging process in real time. Solvent interferences, measurement sensitivity for selected halocarbons and the influence of temperature and pressure on the FTIR spectra were assessed. Application of this methodology to monitoring the incorporation of carbon tetrachloride into natural soils will be discussed.

Thompson, Christopher J.; Riley, Robert G.; Amonette, James E.; Gassman, Paul L.

2004-03-31

233

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

PubMed

The concentration of Mn and Si in different kinds of steels was determined by laser-induced breakdown spectroscopy (LIBS). The multivariate quadratic nonlinear function was adopted for calibration. Samples including common alloy steels, stainless steels and carbon tool steels were analyzed. The matrix effect was serious because of large difference in compositions of different kinds of steels and strong line overlaps in steel spectra. Therefore, the common calibration methods that only use one analytical line to calibrate the complex chemical compositions of alloy steels will lose much information. The multivariate calibration methods, however, can utilize more information of spectra, successfully reduce the matrix effect and improve the measurement repeatability and accuracy of LIBS. Compared with the common calibration method based on one analytical line, the relative standard deviation was reduced from above 20% to below 10%, and the accuracy was increased by more than 5 times for Mn and more than 6 times for Si. PMID:21322202

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

2010-12-01

234

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

PubMed Central

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

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

2013-01-01

235

Structural investigation of biological material in aqueous environment by means of infrared-ATR spectroscopy.  

PubMed

Infrared attenuated total reflection (ATR) spectroscopy may be used to investigate biological material (e.g., membranes, proteins, erythrocytes etc.) under biological conditions provided that adhesion of the sample can be achieved in aqueous environment. Uncharged lipid multilayer model membranes can be attached by hydrophobic interaction when hydrophobic internal reflection plates (e.g., ZnSe, CdTe) are used. However, if an electric field is applied across the membrane, germanium reflection elements would be preferred because of their low electric resistance (approximately 50 omega cm). This material can also be used if cells or proteins are linked chemically to the ATR plate because of the hydrophilic surface which is similar to that of glass and, thus, enables chemical modification by silanization. It has turned out that good adhesion of uncharged and negatively charged model membranes to germanium plates is achieved when they are coated with a monomolecular layer of aminopropylsilane. There is some evidence that erythrocytes remain more stable when adsorbed to a polymerized aminosilane coating (organic silanization) rather than to the corresponding monolayer (aqueous silanization). Negatively charged germanium surfaces have been obtained by succinylation of the aminosilane coating. Furthermore it has been demonstrated that proteins can be bound to the aminosilane coating by means of carbodiimide. Immobilized acetylcholinesterase was still enzymatically active. PMID:540124

Hofer, P; Fringeli, U P

1979-12-01

236

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

PubMed

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

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

2014-11-01

237

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

NASA Astrophysics Data System (ADS)

Four newly synthesized poly (propylene amine) dendrimers from first and second generation modified with 1,8-naphthalimide units in the dendrimer periphery have been investigated as ligands for the detection of heavy metal ions (Al3+, Sb2+, As2+, Cd2+ and Pb2+) by surface-enhanced Raman spectroscopy. Calibration curves were established for all metal ions between the concentration ranges of  1 x 10-6 to 5 x 10-4 M. It has been shown that these dendrimers can be coordinated, especially with different metal ions. Using dendrimer molecules and silver colloids at the same time allowed us to obtain an SERS signal from the abovementioned metal ions at very low concentrations. Principle component analysis (PCA) analysis was also applied to the collected SERS data. Four differentPCA models were developed to accomplish the discrimination of five metal ions, which interacted with each of the four dendrimer molecules, separately. A detailed investigation was performed in the present study to provide the basis of a new approach for heavy metal detection.

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

2013-12-01

238

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

PubMed

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

Mazzei, Pierluigi; Piccolo, Alessandro

2012-06-01

239

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

PubMed Central

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

Leitermann, Frank; Syldatk, Christoph; Hausmann, Rudolf

2008-01-01

240

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

NASA Astrophysics Data System (ADS)

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

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

2005-11-01

241

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

PubMed

Four newly synthesized poly (propylene amine) dendrimers from first and second generation modified with 1,8-naphthalimide units in the dendrimer periphery have been investigated as ligands for the detection of heavy metal ions (Al(3+), Sb(2+), As(2+), Cd(2+) and Pb(2+)) by surface-enhanced Raman spectroscopy. Calibration curves were established for all metal ions between the concentration ranges of 1 x 10(-6) to 5 x 10(-4) M. It has been shown that these dendrimers can be coordinated, especially with different metal ions. Using dendrimer molecules and silver colloids at the same time allowed us to obtain an SERS signal from the abovementioned metal ions at very low concentrations. Principle component analysis (PCA) analysis was also applied to the collected SERS data. Four different PCA models were developed to accomplish the discrimination of five metal ions, which interacted with each of the four dendrimer molecules, separately. A detailed investigation was performed in the present study to provide the basis of a new approach for heavy metal detection. PMID:23973576

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

2013-12-01

242

Quantitative determination of acetylsalicylic acid and acetaminophen in tablets by FT-Raman spectroscopy.  

PubMed

A procedure for quantitative determination of acetylsalicylic acid and acetaminophen in pharmaceuticals by PLS (partial least squares) and PCR (principal component regression) treatment of FT (Fourier transform)-Raman spectroscopic data is proposed. The proposed method was tested on powdered samples. Three chemometric models were built: the first, for samples consisting of an active substance diluted by lactose, starch and talc; the second, in which a simple inorganic salt was applied as an internal standard and additions were not taken into account; and the third, in which a model was constructed for a commercial pharmaceutical, where all constituents of the tablet were known. By utilising selected spectral ranges and by changing the chemometric conditions it is possible to carry out fast and precise analysis of the active component content in medicines on the basis of the simplified chemometric models. The proposed method was tested on five commercial tablets. The results were compared with data obtained by intensity ratio and pharmacopoeial methods. To appraise the quality of the models, the relative standard error of predictions (RSEPs) were calculated for calibration and prediction data sets. These were 0.7-2.0% and 0.8-2.3%, respectively, for the different PLS models. Application of these models to the Raman spectra of commercial tablets containing acetylsalicylic acid gave RSEP values of 1.3-2.0% and a mean accuracy of 1.2-1.7% with a standard deviation of 0.6-1.2%. PMID:11827382

Szostak, Roman; Mazurek, Sylwester

2002-01-01

243

Vibrational Spectroscopy and Chemometrics for Rapid, Quantitative Analysis of Bitter Acids in Hops (Humulus lupulus).  

PubMed

Hops, Humulus lupulus, are grown worldwide for use in the brewing industry to impart characteristic flavor and aroma to finished beer. Breeders produce many varietal crosses with the aim of improving and diversifying commercial hops varieties. The large number of crosses critical to a successful breeding program imposes high demands on the supporting chemical analytical laboratories. With the aim of reducing the analysis time associated with hops breeding, quantitative partial least-squares regression (PLS-R) models have been produced, relating reference data acquired by the industrial standard HPLC and UV methods, to vibrational spectra of the same, chemically diverse hops sample set. These models, produced from rapidly acquired infrared (IR), near-infrared (NIR), and Raman spectra, were appraised using standard statistical metrics. Results demonstrated that all three spectroscopic methods could be used for screening hops for ?-acid, total bitter acids, and cohumulone concentrations in powdered hops. Models generated from Raman and IR spectra also showed potential for use in screening hops varieties for xanthohumol concentrations. NIR analysis was performed using both a standard benchtop spectrometer and a portable NIR spectrometer, with comparable results obtained by both instruments. Finally, some important vibrational features of cohumulone, colupulone, and xanthohumol were assigned using DFT calculations, which allow more insightful interpretation of PLS-R latent variable plots. PMID:25485767

Killeen, Daniel P; Andersen, David H; Beatson, Ron A; Gordon, Keith C; Perry, Nigel B

2014-12-31

244

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

NASA Astrophysics Data System (ADS)

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

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

2011-07-01

245

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

PubMed Central

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

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

2012-01-01

246

Quantitation of Bacillus clausii in biological samples by real-time polymerase chain reaction.  

PubMed

A real-time PCR assay targeting the highly specific erm34 sequence of Bacillus clausii DNA was developed and optimized. The quantitative assay showed a sensitivity level of 10(2) CFU/microl of sample. The method may represent a useful tool for monitoring the role of B. clausii as probiotic in vivo. PMID:16318892

Perotti, Mario; Mancini, Nicasio; Cavallero, Annalisa; Carletti, Silvia; Canducci, Filippo; Burioni, Roberto; Clementi, Massimo

2006-06-01

247

Highly-accelerated quantitative 2D and 3D localized spectroscopy with linear algebraic modeling (SLAM) and sensitivity encoding  

PubMed Central

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

Zhang, Yi; Gabr, Refaat E.; Zhou, Jinyuan; Weiss, Robert G.; Bottomley, Paul A.

2013-01-01

248

Quantitative analysis of double-stranded DNA amplified by a polymerase chain reaction employing surface-enhanced Raman spectroscopy.  

PubMed

Surface-enhanced Raman spectroscopy (SERS) was utilized for the quantitative analysis of double-stranded (ds) DNA amplified by a polymerase chain reaction (PCR). 4?, 6-Diamidino-2-phenylindole dihydrochloride (DAPI), which intercalates into ds-DNA but does not form a complex with single-stranded (ss) DNA, was added to a DNA solution after amplification by PCR. When the solution was mixed, including ds-DNA-DAPI complexes and free DAPI with silver colloid sol, only free DAPI was adsorbed on the colloid surface. The dye on the colloid gave very intense SERS signals with excitation at 514.5 nm, whereas DAPI engaging in the intercalation with ds-DNA did not show any SERS signal. The SERS spectrum of DAPI on the colloid showed a strong band at 1610 cm(-1) due to the C?N stretching mode, and a linear relationship was observed between the peak intensity of the C?N stretching band and the concentration of free DAPI. Therefore one can determine the concentration of free DAPI by the SERS measurement. The more ds-DNA there is in the solution, the less free DAPI there is. Thus it is possible to quantitatively analyze the ds-DNA amplified by PCR indirectly by using SERS. The correlation coefficient between the peak intensity of the C?N stretching band and the concentration of ds-DNA amplified by PCR was calculated to be 0.988 for a concentration range from 0.1 to 1.3 mg/ml. PMID:18268650

Dou, X; Takama, T; Yamaguchi, Y; Hirai, K; Yamamoto, H; Doi, S; Ozaki, Y

1998-02-01

249

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

NASA Astrophysics Data System (ADS)

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

Manceau, Alain; Nagy, Kathryn L.

2012-12-01

250

Quantitative antimony speciation in shooting-range soils by EXAFS spectroscopy  

NASA Astrophysics Data System (ADS)

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 Å, indicative of metallic Sb(0). While part of this Sb(0) may be hosted by unweathered bullet fragments consisting of PbSb alloy, Pb L III-edge XAS of the soil with the highest fraction (0.75) of Sb(0) showed no metallic Pb, but only Pb 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 Å, 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 Å 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.

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

2006-07-01

251

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

NASA Astrophysics Data System (ADS)

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

Sowoidnich, Kay; Kronfeldt, Heinz-Detlef

2012-06-01

252

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

NASA Astrophysics Data System (ADS)

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

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

2007-04-01

253

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

PubMed Central

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

Korsunsky, Ilya; McGovern, Kathleen; LaGatta, Tom; Olde Loohuis, Loes; Grosso-Applewhite, Terri; Griffeth, Nancy; Mishra, Bud

2014-01-01

254

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

PubMed Central

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

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

2011-01-01

255

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

USGS Publications Warehouse

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

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

2010-01-01

256

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

Microsoft Academic Search

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

Xoaquín Moreira; Rafael Zas; Luis Sampedro

257

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

258

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

Microsoft Academic Search

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

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

2006-01-01

259

Qualitative and quantitative analysis of CO2 and CH4 dissolved in water and seawater using laser Raman spectroscopy.  

PubMed

Laboratory experiments have been performed using laser Raman spectroscopy to analyze carbon dioxide (CO(2)) and methane (CH(4)) dissolved in water and seawater. Dissolved CO(2) is characterized by bands at approximately 1275 and 1382 Deltacm(-1). Dissolved CH(4) is characterized by a dominant band at approximately 2911 Deltacm(-1). The laboratory instrumentation used for this work is equivalent to the sea-going Raman instrument, DORISS (Deep Ocean Raman In Situ Spectrometer). Limits of quantification and calibration curves were determined for each species. The limits of quantification are approximately 10 mM for CO(2) and approximately 4 mM for CH(4). A ratio technique is used to obtain quantitative information from Raman spectra: the gas bands are referenced to the O-H stretching band of water. The calibration curves relating band height ratios to gas concentration are linear and valid for a range of temperatures, pressures, and salinities. Current instrumentation is capable of measuring the highest dissolved gas concentration observed in end-member hydrothermal fluids. Further development work is needed to improve sensitivity and optimize operational configurations. PMID:20615296

White, Sheri N

2010-07-01

260

In vivo quantitative near-infrared spectroscopy in skeletal muscle and bone during rest and isometric exercise  

NASA Astrophysics Data System (ADS)

In this study quantitative near-infrared-spectroscopy (NIRS) was investigated as a potential tool to measure local O2 consumption (mVO2) in human bone (tibia) in comparison with muscle (musculus tibialis anterior). Both tissues were examined at rest and during 80% maximum voluntary isometric muscle contraction. Fifteen subjects were tested. Local variations in oxy-hemoglobin (O2Hb), desoxy-hemoglobin (HHb), and total hemoglobin (tHb) were investigated with a continuously operating NIRS system. mVO2 was determined in phases of applied arterial occlusion. At rest mVO2 was five times higher in muscle than in bone. However, both mVO2 values showed a distinct correlation with skin-fold thickness. At rest and only in bone we recorded a periodical variation of O2Hb. HHb was almost constant. This variation of O2Hb and the resulting variation in tHb indicated chances in blood volume, which are not compatible with the solid nature of bone. During muscle contraction, mVO2 in muscle increased about twenty fold. As expected, mVO2 in bone did not significantly increase during muscle contraction. In conclusion, NIRS was confirmed as a valid method to determine the excess mVO2 in muscle during contraction. For mVO2 measurements in bone more sophisticated localization techniques are required to separate the effects derived from bone and skin.

Klasing, Manfred; Zange, Jochen

2003-10-01

261

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

PubMed

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

2014-10-01

262

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

PubMed

Measurement of radical concentrations is important in understanding the chemical kinetics involved in combustion. Application of optical techniques allows for the nonintrusive determination of specific radical concentrations. One of the most challenging problems for investigators is to obtain flame data that are independent of the collisional environment. We seek to obviate this difficulty by the use of picosecond pump-probe absorption spectroscopy. A picosecond pump-probe absorption model is developed by rate-equation analysis. Implications are discussed for a laser-pulse width that is much smaller than the excited-state lifetime of the absorbing atom or molecule. The possibility of quantitative, quenching-independent concentration measurements is discussed, and detection limits for atomic sodium and the hydroxyl radical are estimated. For a three-level absorber-emitter, the model leads to a novel pump-probe strategy, called dual-beam asynchronous optical sampling, that can be used to obtain both the electronic quenching-rate coefficient and the doublet mixing-rate coefficient during a single measurement. We discuss the successful demonstration of the technique in a companion paper [Appl. Opt. 34, XXX (1995)]. PMID:21037640

Fiechtner, G J; King, G B; Laurendeau, N M

1995-02-20

263

Towards a non-invasive quantitative analysis of the organic components in museum objects varnishes by vibrational spectroscopies: methodological approach.  

PubMed

The compositions of ancient varnishes are mainly determined destructively by separation methods coupled to mass spectrometry. In this study, a methodology for non-invasive quantitative analyses of varnishes by vibrational spectroscopies is proposed. For that, experimental simplified varnishes of colophony and linseed oil were prepared according to 18th century traditional recipes with an increasing mass concentration ratio of colophony/linseed oil. FT-Raman and IR analyses using ATR and non-invasive reflectance modes were done on the "pure" materials and on the different mixtures. Then, a new approach involving spectral decomposition calculation was developed considering the mixture spectra as a linear combination of the pure materials ones, and giving a relative amount of each component. Specific spectral regions were treated and the obtained results show a good accuracy between the prepared and calculated amounts of the two compounds. We were thus able to detect and quantify from 10% to 50% of colophony in linseed oil using non-invasive techniques that can also be conducted in situ with portable instruments when it comes to museum varnished objects and artifacts. PMID:25127604

Daher, Céline; Pimenta, Vanessa; Bellot-Gurlet, Ludovic

2014-11-01

264

Electron Momentum Spectroscopy and Its Applications to Molecules of Biological Interest  

NASA Astrophysics Data System (ADS)

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

Wang, Feng

2007-11-01

265

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

SciTech Connect

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

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

1985-08-01

266

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

PubMed

This article describes a Java-based graphical user interface for the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo/medical MR spectroscopy data. We have found that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI system. We also have established that MR quantitation algorithms, programmed in the past in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI). PMID:11334636

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

2001-07-01

267

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

Microsoft Academic Search

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

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

2005-01-01

268

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

NASA Astrophysics Data System (ADS)

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

Carlson, Philip Joseph

269

Quantitative Applications of Deep-Sea Raman Spectroscopy: Geochemistry of 1,4- thioxane in sea water  

NASA Astrophysics Data System (ADS)

We have developed quantitative Raman spectroscopic techniques for the novel detection of dissolved species in sea water to determine their fundamental properties. In this example we use a field-deployable Raman system to determine the solubility of 1,4-thioxane (TO) in sea water as 0.65 to 0.63 mol/kg H2O between 4.5°C and 25.0°C (which varies greatly from an earlier report of 2.75 mol/kg H2O), and to assess the conditions under which it may form a hydrate. TO is of unusual environmental interest as a breakdown product of the chemical weapon mustard gas, and thus development of non-contact field- deployable sensing techniques is highly desirable. Raman spectroscopy has typically been considered as only a qualitative technique due to the complexity of the optical path and the substantial changes in components between different instruments. We show here that by self-referencing to the ubiquitous water peaks (the water ?2 mode from 1500 to 1800 cm-1) we can derive quantitative information with a precision of ± 4%, and provide essential new information. The long-term fate of large quantities of chemical weapons disposed of in the ocean some 50 years ago is poorly known. Part of this lacking knowledge can be attributed to the hazards associated with the direct study of these materials leaving ocean scientists vulnerable when sampling in inadequately marked sites. Mustard gas (1,1'-thiobis[2-chloroethane]) represents the largest tonnage of material disposed of until the 1972 London Convention banned such activities. Thus there is strong interest in determining the fate and lifetime of these materials, their decomposition products, and the extent of the affected zones. We have earlier shown that TO forms a hydrate with a help-gas, such as methane or hydrogen sulfide, and that the temperature, pressure and reducing conditions required for hydrate formation commonly occur at known disposal sites. In fact, a mixed TO hydrate is more stable than methane hydrate by almost 10°C. Here we show that in the presence of hydrate formation, as with other hydrate guest molecules, the TO solubility trend was reversed and solubility decreased in response to lower temperatures. The relatively low solubility in water coupled with the ability to form a hydrate within marine sediments can greatly decrease molecular mobility and increase chemical lifetime. Mixing will reduce concentrations of TO in the ocean water column below the detection limits established here. But the solubility data reveals the concentrations that will characterize marine pore waters at such sites, and these are readily detectable. Development of pore water Raman sensing techniques are underway.

Zhang, X.; Hester, K. C.; Walz, P. M.; Peltzer, E. T.; Brewer, P. G.

2008-12-01

270

Nanoplasmonics-enabled On-Demand and Systematic Intracellular Gene Regulation for Quantitative Biology and Therapeutics  

PubMed Central

This review focuses on the recent developments in nanoplasmonic technologies for on-demand and systematic intracellular gene regulation. Types of nanoplasmonic carriers and DNA/RNA cargo are described. Strategies to liberate cargo from their carriers using light are reviewed. Nanoplasmonic technologies enable on-demand and systematic silencing of endogenous intracellular genes. In addition to inhibitory effects, exogenous foreign genes are also introduced and expressed on-demand using nanoplasmonic technologies. The magnitude and timing of genetic activities can therefore be systematically controlled on-demand. Equipped with new nanoplasmonic technologies to directly probe the intracellular space, quantitative approaches should capture many dynamic activities within living systems that were otherwise previously impossible to control using conventional methods. PMID:20888286

Lee, Somin Eunice; Lee, Luke P.

2012-01-01

271

Common biology of craving across legal and illegal drugs - a quantitative meta-analysis of cue-reactivity brain response.  

PubMed

The present quantitative meta-analysis set out to test whether cue-reactivity responses in humans differ across drugs of abuse and whether these responses constitute the biological basis of drug craving as a core psychopathology of addiction. By means of activation likelihood estimation, we investigated the concurrence of brain regions activated by cue-induced craving paradigms across studies on nicotine, alcohol and cocaine addicts. Furthermore, we analysed the concurrence of brain regions positively correlated with self-reported craving in nicotine and alcohol studies. We found direct overlap between nicotine, alcohol and cocaine cue reactivity in the ventral striatum. In addition, regions of close proximity were observed in the anterior cingulate cortex (ACC; nicotine and cocaine) and amygdala (alcohol, nicotine and cocaine). Brain regions of concurrence in drug cue-reactivity paradigms that overlapped with brain regions of concurrence in self-reported craving correlations were found in the ACC, ventral striatum and right pallidum (for alcohol). This first quantitative meta-analysis on drug cue reactivity identifies brain regions underlying nicotine, alcohol and cocaine dependency, i.e. the ventral striatum. The ACC, right pallidum and ventral striatum were related to drug cue reactivity as well as self-reported craving, suggesting that this set of brain regions constitutes the core circuit of drug craving in nicotine and alcohol addiction. PMID:21261758

Kühn, Simone; Gallinat, Jürgen

2011-04-01

272

Quantitative Proteomics Reveals Factors Regulating RNA Biology as Dynamic Targets of Stress-induced SUMOylation in Arabidopsis *  

PubMed Central

The stress-induced attachment of small ubiquitin-like modifier (SUMO) to a diverse collection of nuclear proteins regulating chromatin architecture, transcription, and RNA biology has been implicated in protecting plants and animals against numerous environmental challenges. In order to better understand stress-induced SUMOylation, we combined stringent purification of SUMO conjugates with isobaric tag for relative and absolute quantification mass spectrometry and an advanced method to adjust for sample-to-sample variation so as to study quantitatively the SUMOylation dynamics of intact Arabidopsis seedlings subjected to stress. Inspection of 172 SUMO substrates during and after heat shock (37 °C) revealed that stress mostly increases the abundance of existing conjugates, as opposed to modifying new targets. Some of the most robustly up-regulated targets participate in RNA processing and turnover and RNA-directed DNA modification, thus implicating SUMO as a regulator of the transcriptome during stress. Many of these targets were also strongly SUMOylated during ethanol and oxidative stress, suggesting that their modification is crucial for general stress tolerance. Collectively, our quantitative data emphasize the importance of SUMO to RNA-related processes protecting plants from adverse environments. PMID:23197790

Miller, Marcus J.; Scalf, Mark; Rytz, Thérèse C.; Hubler, Shane L.; Smith, Lloyd M.; Vierstra, Richard D.

2013-01-01

273

Heterogeneous reaction rates in an ionic liquid: quantitative results from two-dimensional multiple population-period transient spectroscopy.  

PubMed

The hypotheses that ionic liquids are structurally heterogeneous at the molecular level and, even further, that this heterogeneity can transfer to the rates of reactions run in ionic liquids is being actively debated. Here, this hypothesis is tested using multiple population-period transient spectroscopy (MUPPETS), an emerging type of multidimensional measurement that resolves the kinetics of subensembles within a heterogeneous sample. A previous MUPPETS study of the excited-state twisting and electronic relaxation of auramine indicated that an ionic-liquid solvent induces rate dispersion due to a combination of heterogeneous and homogeneous processes, but those data could not quantitatively separate these contributions [Khurmi, C.; Berg, M. A. J. Phys. Chem. Lett.2010, 1, 161]. New MUPPETS data that include phase resolution and subtraction of thermal gratings are presented here and are successfully modeled. The total range of reaction rates (10--90%) is a factor of 70. If the solvent effect is viewed as a set of local viscosities, the viscosity distribution is broad and highly asymmetric. However, if the solvent is viewed as changing a reaction barrier, the data correspond to a Gaussian distribution of barrier heights. The relaxation of each subensemble is nonexponential with an initial induction period, but the shape of the decay is invariant across the rate distribution. A small (2%), long-lived component is identified as a part of the homogeneous kinetic scheme and thus as a secondary channel for excited-state relaxation, not as an impurity or alternative ground-state form of auramine. On the basis of these results, we suggest that the primary cause of rate heterogeneity is a long-lived local electric field acting on the charge redistribution during the reaction. PMID:21630702

Sahu, Kalyanasis; Kern, Sean J; Berg, Mark A

2011-07-14

274

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

PubMed Central

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

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

2002-01-01

275

Determining enzyme kinetics for systems biology with nuclear magnetic resonance spectroscopy.  

PubMed

Enzyme kinetics for systems biology should ideally yield information about the enzyme's activity under in vivo conditions, including such reaction features as substrate cooperativity, reversibility and allostery, and be applicable to enzymatic reactions with multiple substrates. A large body of enzyme-kinetic data in the literature is based on the uni-substrate Michaelis-Menten equation, which makes unnatural assumptions about enzymatic reactions (e.g., irreversibility), and its application in systems biology models is therefore limited. To overcome this limitation, we have utilised NMR time-course data in a combined theoretical and experimental approach to parameterize the generic reversible Hill equation, which is capable of describing enzymatic reactions in terms of all the properties mentioned above and has fewer parameters than detailed mechanistic kinetic equations; these parameters are moreover defined operationally. Traditionally, enzyme kinetic data have been obtained from initial-rate studies, often using assays coupled to NAD(P)H-producing or NAD(P)H-consuming reactions. However, these assays are very labour-intensive, especially for detailed characterisation of multi-substrate reactions. We here present a cost-effective and relatively rapid method for obtaining enzyme-kinetic parameters from metabolite time-course data generated using NMR spectroscopy. The method requires fewer runs than traditional initial-rate studies and yields more information per experiment, as whole time-courses are analyzed and used for parameter fitting. Additionally, this approach allows real-time simultaneous quantification of all metabolites present in the assay system (including products and allosteric modifiers), which demonstrates the superiority of NMR over traditional spectrophotometric coupled enzyme assays. The methodology presented is applied to the elucidation of kinetic parameters for two coupled glycolytic enzymes from Escherichia coli (phosphoglucose isomerase and phosphofructokinase). 31P-NMR time-course data were collected by incubating cell extracts with substrates, products and modifiers at different initial concentrations. NMR kinetic data were subsequently processed using a custom software module written in the Python programming language, and globally fitted to appropriately modified Hill equations. PMID:24957764

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

2012-01-01

276

Paparamborde: a software dedicated to quantitative mapping of biological samples using scanning transmission ion microscopy  

NASA Astrophysics Data System (ADS)

Paparamborde, Programme d'Analyse des PArticules RAlenties dans la Matière de BORDEaux, a software dedicated to the scanning transmission ion microscopy (STIM) analysis of biological samples was developed. The programme includes the reconstruction of the median and/or mean energy loss image of the sample, as well as accurate calculation of sample thickness performed over the whole or a part of the scanned surface. The calculation is based on the conversion of transmitted particle energy into areal density of matter (?g/cm 2) and uses SRIM code for the stopping power calculation. A new routine for the calculation of X-ray absorption correction factors (XCF), as needed for PIXE quantification of trace element, has been added in the latest version of Paparamborde, allowing the thickness heterogeneity of sample to be properly taken into account in the calculation of XCF.

Devès, G.; Michelet-Habchi, C.; Ortega, R.

2005-04-01

277

Synthesis, biological activity, and hologram quantitative structure-activity relationships of novel allatostatin analogues.  

PubMed

Cockroach-type allatostatins (FGLamides) (ASTs) can inhibit the production of juvenile hormone in vitro, and they therefore are regarded as possible insect growth regulator (IGR) candidates for pest control. However, several shortcomings, such as the absence of in vivo effects, rapid degradation, and high production costs, preclude their practical use in pest management. To discover new IGRs, 25 novel analogues of pentapeptide (Y/FXFGLa) were designed and synthesized with different aromatic acids, fatty acids, and dicarboxylic acids as the Y/FX region replacements on the basis of previous results. Their bioactivities in vitro were determined, and the results showed that eight analogues (K14, K15, K17, K18, K19, K23, K24, and K25) were more active than the lead, core region pentapeptide. The IC(50) values of K15 and K24 (IC(50) = 1.79 and 5.32 nM, respectively) were even lower than that of the natural AST, Dippu-AST 1(IC(50) = 8 nM), which indicated both analogues have better activity than Dippu-AST 1; particularly, K15 has better activity than most natural Dippu-ASTs. A predictable and statistically meaningful hologram quantitative structure-activity relationship (HQSAR) model of 32 AST analogues (28 as training sets and 4 as test sets) was obtained. The final model suggested that a potent AST analogue should contain an aromatic group, a linker of appropriate length, and the FGLa portion. These results will be useful in the design of new AST analogues that are structurally related to the training set compounds. PMID:19950981

Kai, Zhen-Peng; Huang, Juan; Xie, Yong; Tobe, Stephen S; Ling, Yun; Zhang, Li; Zhao, Yi-Chen; Yang, Xin-Ling

2010-03-10

278

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

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

279

Quantitation of cytokinins in biological samples using antibodies against zeatin riboside.  

PubMed

The cross-reactivity of antibodies elicited in rabbits against zeatin riboside, to a wide range of naturally occurring cytokinins, was examined. As well as to zeatin riboside, the antisera cross-reacted to a considerable extent with zeatin, lupinic acid, zeatin-9-glucoside, zeatin riboside 5'-monophosphate and to a much lesser, but measurable extent, with dihydrozeatin riboside and dihydrozeatin. Chromatographic methods were devised which allowed separation of all these cross-reactive compounds. Four biological samples, extracts of immature Zea mays kernels, immature seeds of Lupinus luteus, and Datura innoxia crown gall tumor tissue, and a sample of Agrobacterium tumefaciens culture supernatant, were purified by these chromatographic methods, using [(3)H]zeatin riboside as a recovery marker, and at each stage of the purification process, were subjected to radioimmunoassay over a range of dilutions. At each stage of sample purification, sample dilution curves were found to be parallel to the standard curve. Sample cytokinin levels estimated by radioimmunoassay were in close agreement to those available in the literature for similar samples assayed by alternative methods. However, in some samples, unknown cross-reacting compounds were detected. PMID:16663745

Badenoch-Jones, J; Letham, D S; Parker, C W; Rolfe, B G

1984-08-01

280

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

PubMed

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

West, Geoffrey B; Brown, James H

2005-05-01

281

[Application of near infrared spectroscopy to qualitative identification and quantitative determination of Puccinia strii formis f. sp. tritici and P. recondita f. sp. tritici].  

PubMed

To realize qualitative identification and quantitative determination of Puccinia strii formis f. sp. tritici (Pst) and P. recondita f. sp. tritici (Prt), a qualitative identification model was built using near infrared reflectance spectroscopy (NIRS) combined with distinguished partial least squares (DPLS), and a quantitative determination model was built using NIRS combined with quantitative partial least squares (QPLS). In this study, 100 pure samples including 50 samples of Pst and 50 samples of Prt were obtained, and 120 mixed samples including three replicates of mixed urediospores of the two kinds of pathogen in different proportions (the content of Pst was within the range of 2. 5% 100% with 2. 5% as the gradient) were obtained. Then the spectra of the samples were collected using MPA spectrometer, respectively. Both pure samples and mixed samples were divided into training set and testing set with the ratio equal to 2:1. Qualitative identification model and quantitative determination model were built using internal cross-validation method in the spectral region 4,000--10,000 cm(-1) based on the training sets from pure samples and mixed samples, respectively. The results showed that the identification rates of the Pst-Prt qualitative identification model for training set and testing set were both up to 100. 00% when scatter correction was used as the preprocessing method of the spectra and the number of principal components was 3. When 'range normalization + scatter correction' was used as the preprocessing method of the spectra and the number of principal components was 6, determination coefficient (RZ), standard error of calibration (SEC) and average absolute relative deviation(AARD) of the Pst-Prt quantitative determination model for training set were 99.36%, 2.31% and 8.94%, respectively, and R2, standard error of prediction (SEP) and AARD for testing set were 99.37%, 2.29% and 5. 0%, respectively. The results indicated that qualitative identification and quantitative determination of Pst and Prt using near infrared spectroscopy technology are feasible and that the Pst-Prt qualitative identification model and the Pst-Prt quantitative determination model built in this study were reliable and stable. A new method based on NIRS was provided for qualitative identification and quantitative determination of plant pathogen in this study. PMID:25208382

Li, Xiao-Long; Ma, Zhan-Hong; Zhao, Long-Lian; Li, Jun-Hui; Wang, Hai-Guang

2014-03-01

282

Imaging and quantitative data acquisition of biological cell walls with Atomic Force Microscopy and Scanning Acoustic Microscopy  

SciTech Connect

This chapter demonstrates the feasibility of Atomic Force Microscopy (AFM) and High Frequency Scanning Acoustic Microscopy (HF-SAM) as tools to characterize biological tissues. Both the AFM and the SAM have shown to provide imaging (with different resolution) and quantitative elasticity measuring abilities. Plant cell walls with minimal disturbance and under conditions of their native state have been examined with these two kinds of microscopy. After descriptions of both the SAM and AFM, their special features and the typical sample preparation is discussed. The sample preparation is focused here on epidermal peels of onion scales and celery epidermis cells which were sectioned for the AFM to visualize the inner surface (closest to the plasma membrane) of the outer epidermal wall. The nm-wide cellulose microfibrils orientation and multilayer structure were clearly observed. The microfibril orientation and alignment tend to be more organized in older scales compared with younger scales. The onion epidermis cell wall was also used as a test analog to study cell wall elasticity by the AFM nanoindentation and the SAM V(z) feature. The novelty in this work was to demonstrate the capability of these two techniques to analyze isolated, single layered plant cell walls in their natural state. AFM nanoindentation was also used to probe the effects of Ethylenediaminetetraacetic acid (EDTA), and calcium ion treatment to modify pectin networks in cell walls. The results suggest a significant modulus increase in the calcium ion treatment and a slight decrease in EDTA treatment. To complement the AFM measurements, the HF-SAM was used to obtain the V(z) signatures of the onion epidermis. These measurements were focused on documenting the effect of pectinase enzyme treatment. The results indicate a significant change in the V(z) signature curves with time into the enzyme treatment. Thus AFM and HF-SAM open the door to a systematic nondestructive structure and mechanical property study of complex biological cell walls. A unique feature of this approach is that both microscopes allow the biological samples to be examined in their natural fluid (water) environment.

Tittmann, B. R. [Penn State; Xi, X. [Penn State

2014-09-01

283

Semi-quantitative evaluation of genotoxic activity of chemical substances and evidence for a biological threshold of genotoxic activity.  

PubMed

In Japan, the Chemical Substances Control Law requires evaluation of the genotoxic potential of chemical substances semi-quantitatively by application of a ranking system. During the past 10 years under the law, 1049 new chemical substances were evaluated by a reverse mutation assay in bacteria (RMA) and a chromosome aberration test in cultured mammalian cells (CAT). Of them, 130 (12.4%) were positive in the RMA and 402 (38.3%) were positive in the CAT. Eighty (7.6%) were positive in both tests. Fifty (4.8%) were positive only in the RMA, 322 (30.7%) were positive only in the CAT, and 452 (43.1%) were positive in either the RMA or the CAT. Thus, the tests complement each other in detecting genotoxic substances in vitro. To explore the "threshold" concept, we compared the genotoxic responses of Salmonella typhimurium tester strains with and without DNA repair capacity. Recently constructed strains of TA1535 lacking O(6)-methylguanine DNA methyltransferase genes (ogt(ST) or ada(ST) and ogt(ST)) showed dose-related increases in the number of revertants induced by N-ethyl-N'-nitro-N-nitrosoguanidine, methyl methanesulfonate, dimethylnitrosamine, and ethylnitrosourea, while in the same dose ranges the parental strain TA1535 did not. This finding suggests that there is a threshold at which all DNA damage induced by low dose levels of genotoxic chemicals are repaired. That biological threshold seems to exist for both DNA and non-DNA targeting chemicals. PMID:10633181

Sofuni, T; Hayashi, M; Nohmi, T; Matsuoka, A; Yamada, M; Kamata, E

2000-01-01

284

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

SciTech Connect

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

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

2011-09-01

285

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

PubMed Central

There are several practical and intertangled issues which make the experiments of nuclear resonant vibrational spectroscopy (NRVS) on biological samples difficult to perform. The sample temperature is one of the most important issues. In NRVS the real sample temperatures can be very different from the readings on the temperature sensors. In this study the following have been performed: (i) citing and analyzing various existing NRVS data to assess the real sample temperatures during the NRVS measurements and to understand their trends with the samples’ loading conditions; (ii) designing several NRVS measurements with (Et4N)[FeCl4] to verify these trends; and (iii) proposing a new sample-loading procedure to achieve significantly lower real sample temperatures and to balance among the intertangled experimental issues in biological NRVS measurements. PMID:22338688

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

2012-01-01

286

Qualitative and simultaneous quantitative analysis of cimetidine polymorphs by ultraviolet-visible and shortwave near-infrared diffuse reflectance spectroscopy and multivariate calibration models.  

PubMed

The object of the present study was to investigate the feasibility of applying ultraviolet-visible and shortwave near-infrared diffuse reflectance spectroscopy (UV-vis-SWNIR DRS) coupled with chemometrics in qualitative and simultaneous quantitative analysis of drug polymorphs, using cimetidine as a model drug. Three polymorphic forms (A, B and D) and a mixed crystal (M1) of cimetidine, obtained by preparation under different crystallization conditions, were characterized by microscopy, X-ray powder diffraction (XRPD) and infrared spectroscopy (IR). The discriminant models of four forms (A, B, D and M1) were established by discriminant partial least squares (PLS-DA) using different pretreated spectra. The R and RMSEP of samples in the prediction set by discriminant model with original spectra were 0.9959 and 0.1004. Among the quantitative models of binary mixtures (A and D) established by partial least squares (PLS) and least squares-support vector machine (LS-SVM) with different pretreated spectra, the LS-SVM models based on original and MSC spectra had better prediction effect with a R of 1.0000 and a RMSEP of 0.0134 for form A, and a R of 1.0000 and a RMSEP of 0.0024 for form D. For ternary mixtures, the established PLS quantitative models based on normalized spectra had relatively better prediction effect for forms A, B and D with R of 0.9901, 0.9820 and 0.9794 and RMSEP of 0.0471, 0.0529 and 0.0594, respectively. This research indicated that UV-vis-SWNIR DRS can be used as a simple, rapid, nondestructive qualitative and quantitative method for the analysis of drug polymorphs. PMID:25497893

Feng, Yuyan; Li, Xiangling; Xu, Kailin; Zou, Huayu; Li, Hui; Liang, Bing

2015-02-01

287

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...

288

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

NASA Astrophysics Data System (ADS)

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

Best, Stephen P.; Cheah, Mun Hon

2010-02-01

289

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

PubMed Central

Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques. PMID:23710244

Zhang, Chi; Myers, John; Chen, Zhan

2013-01-01

290

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

PubMed Central

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

Muñoz Morales, Aarón A.; Vázquez y Montiel, Sergio

2012-01-01

291

Ordered silicon nanocones arrays for label-free DNA quantitative analysis by surface-enhanced Raman spectroscopy  

NASA Astrophysics Data System (ADS)

Ordered vertical silicon nanocones arrays coated with silver nanoparticles (AgNPs@SiNCs) are developed as surface-enhanced Raman scattering (SERS)-active substrate, which features good uniformity and reliable reproducibility of SERS signals. Label-free DNA at low concentrations (10-8 M) could be quantitatively analyzed via SERS using the AgNPs@SiNCs. The Raman peak at 732 cm-1 due to adenine breathing mode was selected as an endogenous Raman marker for quantitative detection of label-free DNA. The AgNPs@SiNCs as high-performance SERS-active substrates are attractive for surface enhancement mechanism investigation and biochemical sensing applications.

Xu, Ting-Ting; Huang, Jian-An; He, Li-Fang; He, Yao; Su, Shao; Lee, Shuit-Tong

2011-10-01

292

Cellular phone-based image acquisition and quantitative ratiometric method for detecting cocaine and benzoylecgonine for biological and forensic applications.  

PubMed

Here we describe the first report of using low-cost cellular or web-based digital cameras to image and quantify standardized rapid immunoassay strips as a new point-of-care diagnostic and forensics tool with health applications. Quantitative ratiometric pixel density analysis (QRPDA) is an automated method requiring end-users to utilize inexpensive (? $1 USD/each) immunotest strips, a commonly available web or mobile phone camera or scanner, and internet or cellular service. A model is described whereby a central computer server and freely available IMAGEJ image analysis software records and analyzes the incoming image data with time-stamp and geo-tag information and performs the QRPDA using custom JAVA based macros (http://www.neurocloud.org). To demonstrate QRPDA we developed a standardized method using rapid immunotest strips directed against cocaine and its major metabolite, benzoylecgonine. Images from standardized samples were acquired using several devices, including a mobile phone camera, web cam, and scanner. We performed image analysis of three brands of commercially available dye-conjugated anti-cocaine/benzoylecgonine (COC/BE) antibody test strips in response to three different series of cocaine concentrations ranging from 0.1 to 300 ng/ml and BE concentrations ranging from 0.003 to 0.1 ng/ml. This data was then used to create standard curves to allow quantification of COC/BE in biological samples. Across all devices, QRPDA quantification of COC and BE proved to be a sensitive, economical, and faster alternative to more costly methods, such as gas chromatography-mass spectrometry, tandem mass spectrometry, or high pressure liquid chromatography. The limit of detection was determined to be between 0.1 and 5 ng/ml. To simulate conditions in the field, QRPDA was found to be robust under a variety of image acquisition and testing conditions that varied temperature, lighting, resolution, magnification and concentrations of biological fluid in a sample. To determine the effectiveness of the QRPDA method for quantifying cocaine in biological samples, mice were injected with a sub-locomotor activating dose of cocaine (5 mg/kg; i.p.) and were found to have detectable levels of COC/BE in their urine (160.6 ng/ml) and blood plasma (8.1 ng/ml) after 15-30 minutes. By comparison rats self-administering cocaine in a 4 hour session obtained a final BE blood plasma level of 910 ng/ml with an average of 62.5 infusions. It is concluded that automated QRPDA is a low-cost, rapid and highly sensitive method for the detection of COC/BE with health, forensics, and bioinformatics application and the potential to be used with other rapid immunotest strips directed at several other targets. Thus, this report serves as a general reference and method describing the use of image analysis of lateral flow rapid test strips. PMID:22879741

Cadle, Brian A; Rasmus, Kristin C; Varela, Juan A; Leverich, Leah S; O'Neill, Casey E; Bachtell, Ryan K; Cooper, Donald C

2010-01-01

293

Homogeneity testing and quantitative analysis of manganese (Mn) in vitrified Mn-doped glasses by laser-induced breakdown spectroscopy (LIBS)  

NASA Astrophysics Data System (ADS)

Laser-induced breakdown spectroscopy (LIBS), an atomic emission spectroscopy method, has rapidly grown as one of the best elemental analysis techniques over the past two decades. Homogeneity testing and quantitative analysis of manganese (Mn) in manganese-doped glasses have been carried out using an optimized LIBS system employing a nanosecond ultraviolet Nd:YAG laser as the source of excitation. The glass samples have been prepared using conventional vitrification methods. The laser pulse irradiance on the surface of the glass samples placed in air at atmospheric pressure was about 1.7×109 W/cm2. The spatially integrated plasma emission was collected and imaged on to the spectrograph slit using an optical-fiber-based collection system. Homogeneity was checked by recording LIBS spectra from different sites on the sample surface and analyzing the elemental emission intensities for concentration determination. Validation of the observed LIBS results was done by comparison with scanning electron microscope- energy dispersive X-ray spectroscopy (SEM-EDX) surface elemental mapping. The analytical performance of the LIBS system has been evaluated through the correlation of the LIBS determined concentrations of Mn with its certified values. The results are found to be in very good agreement with the certified concentrations.

Unnikrishnan, V. K.; Nayak, Rajesh; Kartha, V. B.; Santhosh, C.; Sonavane, M. S.; Yeotikar, R. G.; Shah, M. L.; Gupta, G. P.; Suri, B. M.

2014-09-01

294

Near infrared spectroscopy in combination with chemometrics as a process analytical technology (PAT) tool for on-line quantitative monitoring of alcohol precipitation.  

PubMed

The application of near infrared (NIR) spectroscopy for on-line quantitative monitoring of alcohol precipitation of the Danhong injection was investigated. For the NIR measurements, two fiber optic probes designed to transmit NIR radiation through a 2mm path length flow cell were applied to collect spectra in real-time. Particle swarm optimization- (PSO-) based least square support vector machines (LS-SVM) and partial least squares (PLS) models were developed for quantitative analysis of the critical intermediate quality attributes: the soluble solid content (SSC) and concentrations of danshensu (DSS), protocatechuic aldehyde (PA), hydroxysafflor yellow A (HSYA) and salvianolic acid B (SAB). The optimal models were then used for on-line quantitative monitoring of alcohol precipitation. The results showed that the PSO-based LS-SVM with a radial basis function (RBF) kernel was slightly better than the conventional PLS method, even though both methods exhibited satisfactory fitting results and predictive abilities. In this study, successful models were built and applied on-line; these models proffer real-time data and instant feedback about alcohol precipitation. PMID:23357639

Jin, Ye; Wu, Zengzeng; Liu, Xuesong; Wu, Yongjiang

2013-04-15

295

Salicylate Detection by Complexation with Iron(III) and Optical Absorbance Spectroscopy: An Undergraduate Quantitative Analysis Experiment  

ERIC Educational Resources Information Center

An experiment for the undergraduate quantitative analysis laboratory involving applications of visible spectrophotometry is described. Salicylate, a component found in several medications, as well as the active by-product of aspirin decomposition, is quantified. The addition of excess iron(III) to a solution of salicylate generates a deeply…

Mitchell-Koch, Jeremy T.; Reid, Kendra R.; Meyerhoff, Mark E.

2008-01-01

296

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

Microsoft Academic Search

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

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

2011-01-01

297

Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.  

PubMed

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of ?-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment. PMID:22634414

Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

2012-09-01

298

Rapid quantitative assessment of the adulteration of virgin olive oils with hazelnut oils using Raman spectroscopy and chemometrics.  

PubMed

The authentication of extra virgin olive oil and its adulteration with lower-priced oils are serious problems in the olive oil industry. In addition to the obvious effect on producer profits, adulteration can also cause severe health and safety problems. A number of techniques, including chromatographic and spectroscopic methods, have recently been employed to assess the purity of olive oils. In this study Raman spectroscopy together with multivariate and evolutionary computational-based methods have been employed to assess the ability of Raman spectroscopy to discriminate between chemically very closely related oils. Additionally, the levels of hazelnut oils used to adulterate extra virgin olive oil were successfully quantified using partial least squares and genetic programming. PMID:14518936

López-Díez, E Consuelo; Bianchi, Giorgio; Goodacre, Royston

2003-10-01

299

Identification and Quantitation of Phosphorus Metabolites in Yeast Neutral pH Extracts by Nuclear Magnetic Resonance Spectroscopy  

Microsoft Academic Search

31P NMR spectroscopy offers a possibility to obtain a survey of all low-molecular-weight phosphorylated compounds in yeast. The yeast cells have been extracted using chloroform into a neutral aqueous phase. The use of high fields and the neutral pH extracts, which are suitable for NMR analysis, results in well-resolved 31P NMR spectra. Two-dimensional NMR experiments, such as proton-detected heteronuclear single

Anita Teleman; Peter Richard; Mervi Toivari; Merja Penttilä

1999-01-01

300

High-Resolution NMR Spectroscopy: An Alternative Fast Tool for Qualitative and Quantitative Analysis of Diacylglycerol (DAG) Oil  

Microsoft Academic Search

Multinuclear (1H, 13C, 31P) and multidimensional NMR spectroscopy was employed for the analysis of diacylglycerol (DAG) oil and the quantification\\u000a of its acylglycerols and acyl chains composition. A number of gradient selected two dimensional NMR techniques (TOCSY, HSQC-DEPT,\\u000a HSQC-TOCSY, and HMBC) facilitated the assignment of the complex one dimensional 1H- and 13C-NMR spectra. In several cases, the aforementioned 2D-NMR techniques

Emmanuel Hatzakis; Alexia Agiomyrgianaki; Sarantos Kostidis; Photis Dais

301

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

NASA Astrophysics Data System (ADS)

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.

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

2011-03-01

302

UV extended supercontinuum source for time resolved and steady state spectroscopy for biological and chemical molecules  

NASA Astrophysics Data System (ADS)

The spectrum of the supercontinuum generated by a femtosecond Ti:Sapphire laser beam in photonic crystal fiber (PCF) is increased into the UV using small core diameter PCF with zero dispersion wavelength (ZDW) shorter 600 nm. A flat spectrum is generated that spans from 350 to 1000 nm. The SC was used as an excitation source for fluorescence spectroscopy. Fluorescence spectra can be detected from dye molecules, and native molecules in tissues samples with excitation from wavelengths extracted from ultrafast SC light in the spectral range between 350 to 500 nm using narrow bandpass filters. A Streak Camera was used for time-resolved fluorescence measurements.

Alfano, R. R.; Kartazaev, V.; Zeylikovich, I.; Das, B.; Nolan, D.

2010-02-01

303

Raman spectroscopy provides a rapid, non-invasive method for quantitation of starch in live, unicellular microalgae.  

PubMed

Conventional methods for quantitation of starch content in cells generally involve starch extraction steps and are usually labor intensive, thus a rapid and non-invasive method will be valuable. Using the starch-producing unicellular microalga Chlamydomonas reinhardtii as a model, we employed a customized Raman spectrometer to capture the Raman spectra of individual single cells under distinct culture conditions and along various growth stages. The results revealed a nearly linear correlation (R(2) = 0.9893) between the signal intensity at 478 cm(-1) and the starch content of the cells. We validated the specific correlation by showing that the starch-associated Raman peaks were eliminated in a mutant strain where the AGPase (ADP-glucose pyrophosphorylase) gene was disrupted and consequentially the biosynthesis of starch blocked. Furthermore, the method was validated in an industrial algal strain of Chlorella pyrenoidosa. This is the first demonstration of starch quantitation in individual live cells. Compared to existing cellular starch quantitation methods, this single-cell Raman spectra-based approach is rapid, label-free, non-invasive, culture-independent, low-cost, and potentially able to simultaneously track multiple metabolites in individual live cells, therefore should enable many new applications. PMID:24906189

Ji, Yuetong; He, Yuehui; Cui, Yanbin; Wang, Tingting; Wang, Yun; Li, Yuanguang; Huang, Wei E; Xu, Jian

2014-12-01

304

Estimation of regional hemoglobin concentration in biological tissues using diffuse reflectance spectroscopy with a novel spectral interpretation algorithm  

NASA Astrophysics Data System (ADS)

Both in medical research and clinical settings, regional hemoglobin concentrations ([Hb]) in the microcirculation of biological tissues are highly sought. Diffuse reflectance spectroscopy has been proven to be a favorable method by which to detect regional [Hb]. This paper introduces a new algorithm to retrieve [Hb] information from diffuse reflectance spectra. The proposed algorithm utilizes the natural logarithmic operation and the differential wavelet transform to effectively quench the scattering effects, and then employs the concept of isosbestic wavelength in the transformed spectra to reduce the effects of hemoglobin oxygenation. As a result, the intensity at the defined isosbestic wavelength of the transformed spectra is a good indicator of [Hb] estimation. The algorithm was derived and validated using theoretical spectra produced by Monte Carlo simulation of photon migration. Its accuracy was further evaluated using liquid tissue phantoms, and its clinical utility with an in vivo clinical study of brain tumors. The results demonstrate the applicability of the algorithm for real-time [Hb] estimations from diffuse reflectance spectra, acquired by means of a fiber-optic spectroscopy system.

Chen, P.; Fernald, B.; Lin, W.

2011-07-01

305

Testing biological liquid samples using modified m-line spectroscopy method  

NASA Astrophysics Data System (ADS)

Non-chemical method of detection of sugar concentration in biological (animal and plant source) liquids has been investigated. Simplified set was build to show the easy way of carrying out the survey and to make easy to gather multiple measurements for error detecting and statistics. Method is suggested as easy and cheap alternative for chemical methods of measuring sugar concentration, but needing a lot effort to be made precise.

Augusciuk, Elzbieta; Rybi?ski, Grzegorz

2005-09-01

306

Relationship between the v2PO4/amide III ratio assessed by Raman spectroscopy and the calcium content measured by quantitative backscattered electron microscopy in healthy human osteonal bone  

NASA Astrophysics Data System (ADS)

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 ?) 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.

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

307

Infrared fiber optic evanescent wave spectroscopy: applications in biology and medicine  

NASA Astrophysics Data System (ADS)

A new powerful and highly sensitive technique for non-invasive biomedical diagnostics in vivo has been developed using Infrared Fiberoptic Evanescent Wave Fourier Transform Spectroscopy (FEW-FTIR). This compact and portable method allows to detect functional chemical groups and bonds via vibrational spectroscopy directly from surfaces including living tissue. Such differences and similarities in molecular structure of tissue and materials can be evaluated online. Operating in the attenuated total reflection (ATR) regime in the middle-infrared (MIR) range, the FEW-FTIR technique provides direct contact between the fiber probe and tissue for non-destructive, non-invasive, fast and remote (few meters) diagnostics and quality control of materials. This method utilizes highly flexible and extremely low loss unclad fibers, for example silver halide fibers. Applications of this method include investigations of normal skin, precancerous and cancerous conditions, monitoring of the process of aging, allergic reactions and radiation damage to the skin. This setup is suitable as well for the detection of the influence of environmental factors (sun, water, pollution, and weather) on skin surfaces. The FEW-FTIR technique is very promising also for fast histological examinations in vitro. In this review, we present recent investigations of skin, breast, lung, stomach, kidney tissues in vivo and ex vivo (during surgery) to define the areas of tumor localization. The main advantages of the FEW-FTIR technique for biomedical, clinical, and environmental applications are discussed.

Afanasyeva, Natalia I.; Bruch, Reinhard F.; Katzir, Abraham

1999-04-01

308

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

Microsoft Academic Search

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

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

2002-01-01

309

Free-electron laser spectroscopy in biology, medicine, and materials science; Proceedings of the Meeting, Los Angeles, CA, Jan. 22, 1993  

Microsoft Academic Search

Various papers on FEL spectroscopy in biology, medicine, and materials science are presented. Individual topics addressed include: Vanderbilt University FEL Center, FIR FEL facility at the University of California\\/Santa Barbara, FEL research facilities and opportunities at Duke, facilities at the Stanford Picosecond FEL Center, FIR nonlinear response of electrons in semiconductor nanostructures, FIR harmonic generation from semiconductor heterostructures, intrinsic response

H. A. Schwettman

1993-01-01

310

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

NASA Astrophysics Data System (ADS)

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.

Nawar, Said; Buddenbaum, Henning; Hill, Joachim

2014-05-01

311

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

SciTech Connect

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.

Keller, E.L.

2000-06-27

312

Acquisition and Retention of Quantitative Communication Skills in an Undergraduate Biology Curriculum: Long-Term Retention Results  

NSDL National Science Digital Library

The purpose of this study was to assess some of the effects of a nontraditional, experimental learning approach designed to improve rapid acquisition and long-term retention of quantitative communication skills (QCS) such as descriptive and inferential st

Chevalier, Cary D.; Ashley, David C.; Rushin, John W.

2010-05-01

313

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

NASA Astrophysics Data System (ADS)

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.

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

2013-11-01

314

Determination of diquat in biological materials by electron spin resonance spectroscopy.  

PubMed

An electron spin resonance (ESR) method already in use for the quantitative analysis of paraquat was applied to the analysis of diquat in blood, serum, urine, tissue homogenates and several drinks without purification of the samples. The diquat radical produced with ascorbic acid at alkaline pH was much more stable than that produced with the commonly used sodium dithionite. Radical decay in solutions covered with n-hexane was less than 5% after 60 min over a wide range of ascorbic acid concentrations. In 0.2 N NaOH solution 85% of the radicals was present even after 24 h. The limit of detection was 0.3 micrograms/ml and the required amount of sample was 0.1 ml. When both diquat and paraquat were present in a sample the diquat was first extracted with 1-butanol prior to the ESR measurement, because both species were converted to the radicals. PMID:2176021

Minakata, K; Suzuki, O; Kumazawa, T; Asano, M; Harada, N

1990-01-01

315

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

SciTech Connect

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

Phillips, D.C.

2006-05-16

316

Quantitative analysis of melamine by multi-way partial least squares model with two-dimensional near-infrared correlation spectroscopy  

NASA Astrophysics Data System (ADS)

A new approach for quantitative analysis of melamine in milk was proposed based on two-dimensional (2D) correlation near-infrared spectroscopy and multi-way partial least squares (N-PLS) in this paper. 40 pure milk samples and 40 milk samples adulterated with different contents of melamine were prepared. The near-infrared transmittance spectra of all samples were measured at room temperature. Then 2D NIR-NIR correlation spectroscopy under the perturbation of adulterant concentration was calculated and N-PLS model for the melamine concentration was established with 2D correlation spectra (28x51x51). For the prediction set, the root mean square errors of prediction (RMSEP) for melamine concentration was 0.067 g/L and the coefficient correlation between actual reference values and predicted values was 0.999, which means the model has good predictive ability. For comparison purpose, partial least squares (PLS) model was also built using the conventional one-dimensional near-infrared spectra (28x51), where the RMSEP and the coefficient correlation were 0.079 g/L and 0.998, respectively. The average relative prediction error was 22.9% for N-PLS model; whereas it was 122.4% for PLS model. The N-PLS models yielded relatively low RMSEP and average relative prediction error as compared to PLS model. Therefore, N-PLS method was more robust than PLS method for accurate quantification of the concentration of melamine in milk.

Yang, Renjie; Liu, Rong; Xu, Kexin; Yang, Yanrong

2014-03-01

317

Quantitative compositional profiling of conjugated quantum dots with single atomic layer depth resolution via time-of-flight medium-energy ion scattering spectroscopy.  

PubMed

We report the quantitative compositional profiling of 3-5 nm CdSe/ZnS quantum dots (QDs) conjugated with a perfluorooctanethiol (PFOT) layer using the newly developed time-of-flight (TOF) medium-energy ion scattering (MEIS) spectroscopy with single atomic layer resolution. The collection efficiency of TOF-MEIS is 3 orders of magnitude higher than that of conventional MEIS, enabling the analysis of nanostructured materials with minimized ion beam damage and without ion neutralization problems. The spectra were analyzed using PowerMEIS ion scattering simulation software to allow a wide acceptance angle. Thus, the composition and core-shell structure of the CdSe cores and ZnS shells were determined with a 3% composition uncertainty and a 0.2-nm depth resolution. The number of conjugated PFOT molecules per QD was also quantified. The size and composition of the QDs were consistent with those obtained from high-resolution transmission electron microscopy and X-ray photoelectron spectroscopy, respectively. We suggest TOF-MEIS as a nanoanalysis technique to successfully elucidate the core-shell and conjugated layer structures of QDs, which is critical for the practical application of QDs in various nano- and biotechnologies. PMID:24350771

Jung, Kang-Won; Yu, Hyunung; Min, Won Ja; Yu, Kyu-Sang; Sortica, M A; Grande, Pedro L; Moon, DaeWon

2014-01-21

318

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

PubMed

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

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

2013-04-01

319

Quantitative Analysis of Adulterations in Oat Flour by FT-NIR Spectroscopy, Incomplete Unbalanced Randomized Block Design, and Partial Least Squares  

PubMed Central

This paper developed a rapid and nondestructive method for quantitative analysis of a cheaper adulterant (wheat flour) in oat flour by NIR spectroscopy and chemometrics. Reflectance FT-NIR spectra in the range of 4000 to 12000?cm?1 of 300 oat flour objects adulterated with wheat flour were measured. The doping levels of wheat flour ranged from 5% to 50% (w/w). To ensure the generalization performance of the method, both the oat and the wheat flour samples were collected from different producing areas and an incomplete unbalanced randomized block (IURB) design was performed to include the significant variations that may be encountered in future samples. Partial least squares regression (PLSR) was used to develop calibration models for predicting the levels of wheat flour. Different preprocessing methods including smoothing, taking second-order derivative (D2), and standard normal variate (SNV) transformation were investigated to improve the model accuracy of PLS. The root mean squared error of Monte Carlo cross-validation (RMSEMCCV) and root mean squared error of prediction (RMSEP) were 1.921 and 1.975 (%, w/w) by D2-PLS, respectively. The results indicate that NIR and chemometrics can provide a rapid method for quantitative analysis of wheat flour in oat flour. PMID:25143857

Wang, Ning; Zhang, Xingxiang; Yu, Zhuo; Li, Guodong; Zhou, Bin

2014-01-01

320

Identification and Quantitation of Phenylalanine in the Brain of Patients with Phenylketonuria by Means of Localized in Vivo1H Magnetic-Resonance Spectroscopy  

NASA Astrophysics Data System (ADS)

Localized proton MR spectroscopy was used to identify phenylalanine (PHE) and to quantitate its cerebral concentration in patients with type I phenylketonuria (PKU). Data acquisition was optimized for the detection of low-concentration metabolites, using a short TE (20 ms) double Hahn-echo localization sequence for large volumes within the head coil and for smaller volumes using a surface coil, Previously described methods to quantitate localized MR spectra were extended to cover the case of low-concentration metabolites, unevenly distributed in three brain compartments and measured in difference spectra only. PHE content was determined in difference spectra of four PKU patients with respect to normals and in one patient before and after an oral load of L-PHE, PHE concentrations of 0.3 to 0.6 mmol/kg brain tissue were obtained, resulting in a concentration gradient for PHE between blood and brain tissue of 2.4 to 3.0, No significant changes were found for the abundant metabolites in gray or white matter. Previously reported MRI changes were confirmed to be due to increased cerebro-spinal-fluid-like spaces.

Kreis, R.; Pietz, J.; Penzien, J.; Herschkowitz, N.; Boesch, C.

321

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

SciTech Connect

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

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

2006-03-15

322

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

PubMed Central

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

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

2012-01-01

323

Quantitative analysis of sodium carbonate and sodium bicarbonate in solid mixtures using Fourier transform infrared spectroscopy (FT-IR).  

PubMed

An analytical methodology is proposed based on constant ratio and absorbance correction methods to quantify sodium carbonate, Na?CO? (1450 cm?¹), and sodium bicarbonate, NaHCO? (1000 cm?¹, 1923 cm?¹), in solid mixtures using Fourier transform infrared (FT-IR) spectroscopy. Potassium ferricyanide, K?Fe(CN)? (2117cm?¹), was used as an internal standard to get characteristic parameters. NaHCO? was quantified using the constant ratio method. Spectral interference of NaHCO? in Na?CO? (1450 cm?¹) was corrected using the absorbance correction method. The corrected absorbance was successfully applied to quantify Na?CO? (1450 cm?¹) in the mixture using the constant ratio method. The results obtained for simulated samples were satisfactory (relative standard deviation less than 7%) for all samples. PMID:23876722

Joshi, Shailesh; Kalyanasundaram, Sivasubramanian; Balasubramanian, Venkatraman

2013-08-01

324

A quantitative study of the intracellular dynamics of fluorescently labelled glyco-gold nanoparticles via fluorescence correlation spectroscopy.  

PubMed

The dynamic behaviour of gold nanoparticles functionalised with glucose (Glc-Au NPs) has been studied here by means of fluorescence correlation spectroscopy (FCS). Meaningful data on the state of aggregation and dynamics of Glc-Au NPs fluorescently-labelled with HiLyte Fluor647 (Glc-Au-Hi NPs) in the intracellular environment were obtained. Moreover, the work presented here shows that FCS can be used to visualise the presence of single NPs or NP aggregates following uptake and to estimate, locally, NP concentrations within the cell. FCS measurements become possible after applying a "prebleaching" methodology, when the immobile NP fraction has been effectively removed and thus significant FCS data has been recorded. In this study, Glc-Au-Hi NPs have been incubated with HepG2 cells and their diffusion time in the intracellular environment has been measured and compared with their diffusion value in water and cell media. PMID:24639360

Murray, Richard A; Qiu, Yuan; Chiodo, Fabrizio; Marradi, Marco; Penadés, Soledad; Moya, Sergio E

2014-07-01

325

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

326

Assessment of capillary anion exchange ion chromatography tandem mass spectrometry for the quantitative profiling of the phosphometabolome and organic acids in biological extracts.  

PubMed

Metabolic profiling has become an important tool in biological research, and the chromatographic separation of metabolites coupled with mass spectrometric detection is the most frequently used approach for such studies. The establishment of robust chromatographic methods for comprehensive coverage of the anionic metabolite pool is especially challenging. In this study, the development of a capillary ion exchange chromatography (capIC) - negative ESI tandem mass spectrometry (MS/MS) workflow for the quantitative profiling of the phosphometabolome (e.g., sugar phosphates and nucleotides) is presented. The chromatographic separation and MS/MS conditions were optimized, and the precision of repetitive injections and accuracy in terms of error percentage to true concentration were assessed. The precision is excellent for a capillary flow system with an average CV% of 8.5% for a 50-fmol standard injection and in the lower 2.4-4.4% range for higher concentrations (500-7500fmol). The limit of detection (LOD) ranges from 1 to 100nM (5-500fmol injected on column), and the limit of quantitation (LOQ) ranges from 1 to 500nM (5-2500fmol injected on column). A fast gradient method with the injection of 50% methanol in water between analytical samples is needed to eliminate carry-over and ensure optimal re-equilibration of the column. Finally, the quantitative applicability of the system was tested on real biological matrices using the constant-volume standard addition method (SAM). Extracts of the human kidney Hek293 cell line were spiked with increasing concentrations of standards to determine the concentration of each metabolite in the sample. Forty-four metabolites were detected with an average uncertainty of 4.1%. Thus, the capIC-MS/MS method exhibits excellent selectivity, sensitivity and precision for the quantitative profiling of the phosphometabolome. PMID:25454131

Kvitvang, Hans F N; Kristiansen, Kåre A; Bruheim, Per

2014-11-28

327

High-resolution nuclear magnetic resonance spectroscopy of biological tissues using projected magic angle spinning.  

PubMed

High-resolution NMR spectra of materials subject to anisotropic broadening are usually obtained by rotating the sample about the magic angle, which is 54.7 degrees to the static magnetic field. In projected magic angle spinning (p-MAS), the sample is spun about two angles, neither of which is the magic angle. This provides a method of obtaining isotropic spectra while spinning at shallow angles. The p-MAS experiment may be used in situations where spinning the sample at the magic angle is not possible due to geometric or other constraints, allowing the choice of spinning angle to be determined by factors such as the shape of the sample, rather than by the spin physics. The application of this technique to bovine tissue samples is demonstrated as a proof of principle for future biological or medical applications. PMID:16032677

Martin, Rachel W; Jachmann, Rebecca C; Sakellariou, Dimitris; Nielsen, Ulla Gro; Pines, Alexander

2005-08-01

328

High-resolution NMR spectroscopy of biological tissues usingprojected Magic Angle Spinning  

SciTech Connect

High-resolution NMR spectra of materials subject toanisotropic broadening are usually obtained by rotating the sample aboutthe magic angle, which is 54.7 degrees to the static magnetic field. Inprojected Magic Angle Spinning (p-MAS), the sample is spun about twoangles, neither of which is the magic angle. This provides a method ofobtaining isotropic spectra while spinning at shallow angles. The p-MASexperiment may be used in situations where spinning the sample at themagic angle is not possible due to geometric or other constraints,allowing the choice of spinning angle to be determined by factors such asthe shape of the sample, rather than by the spin physics. The applicationof this technique to bovine tissue samples is demonstrated as a proof ofprinciple for future biological or medical applications.

Martin, Rachel W.; Jachmann, Rebecca C.; Sakellariou, Dimitris; Nielsen, Ulla Gro; Pines, Alexander

2005-01-27

329

Adsorption and coadsorption on Ni(100): Quantitative applications of auger electron spectroscopy to the elements C, P, Pb, Sn  

NASA Astrophysics Data System (ADS)

Quantitative AES has been applied to simple adsorbates on Ni(100). Methods previously developed for calibration, involving coadsorption of a "contaminant" with an adsorbed metal vapour, are difficult to apply because of the tendency of the metal to adsorb on top of the contaminant in the case of carbon and to cause desorption in the case of phosphorus. A calibration for carbon can be made, however, by means of a simple analysis. A calibration for phosphorus is based on interpretations of the LEED patterns near a "saturation" coverage where evidence is found for compact monolayer arrangements. The segregation of phosphorus from the bulk was not reversible in the temperature range studied (500-700°C).

Oda, Osamu; Rhead, Gordon E.

1980-02-01

330

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

PubMed Central

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

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

1997-01-01

331

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

SciTech Connect

This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

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

2013-01-01

332

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

NASA Astrophysics Data System (ADS)

This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

Martin, Madhavi Z.; Labbe, Nicole; Wagner, Rebekah J.

333

Remote detection of similar biological materials using femtosecond filament-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

We demonstrated the feasibility of remote detection and differentiation of some very similar agricultural-activity related bioaerosols, namely barley, corn, and wheat grain dusts, through nonlinear fluorescence of fragments induced by the high-intensity inside filaments of femtosecond laser pulses in air. The signals were detected in Lidar configuration with targets located at 4.7 m away from the detection system. All the species showed identical spectra, namely those from molecular C2 and CN bands, as well as atomic Si, C, Mg, Al, Na, Ca, Mn, Fe, Sr and K lines. These identical spectral bands and lines reveal similar chemical compositions; however, the relative intensities of the spectra are different showing different element abundances from these three bio-targets. The intensity ratios of different elemental lines were used to distinguish these three samples. Good reproducibility was obtained. We expect that this technique could be used at long distance and thus played as a sensor of similar biological hazards for public and defense security.

Xu, H. L.; Méjean, G.; Liu, W.; Kamali, Y.; Daigle, J.-F.; Azarm, A.; Simard, P. T.; Mathieu, P.; Roy, G.; Simard, J.-R.; Chin, S. L.

2007-03-01

334

Quantitative elemental localisation in leaves and stems of nickel hyperaccumulating shrub Hybanthusfloribundus subsp. floribundus using micro-PIXE spectroscopy  

NASA Astrophysics Data System (ADS)

Hybanthusfloribundus (Lindl.) F.Muell. subsp. floribundus is a native Australian nickel (Ni) hyperaccumulating shrub and a promising species for rehabilitation and phytoremediation of Ni tailings. Spatial localisation and quantification of Ni in leaf and stem tissues of H.floribundus subsp. floribundus was studied using micro-proton-induced X-ray emission (micro-PIXE) spectroscopy. Young plants, grown in a potting mix under controlled glasshouse conditions were exposed to Ni concentrations of 0 and 26 mM kg -1 for 20 weeks. Leaf and stem samples were hand-sectioned and freeze-dried prior to micro-PIXE analysis. Elemental distribution maps of leaves revealed Ni concentration of 7800 mg kg -1 dry weight (DW) in whole leaf sections, which was identical to the bulk tissue analysis. Elemental maps showed that Ni was preferentially localised in the adaxial epidermis (10,000 mg kg -1 DW) and reached a maximum of up to 10,000 mg kg -1 DW in the leaf margin. Freeze-dried stem sections from the same plants contained lower Ni than leaf tissues (1800 mg kg -1 versus 7800 mg kg -1 DW, respectively), however did not resolve a clear pattern of compartmentalisation across different anatomical regions. Our results suggest localisation in epidermal cells is an important physiological mechanism involved in Ni accumulation and tolerance in leaves of H.floribundus subsp. floribundus.

Kachenko, Anthony G.; Singh, Balwant; Bhatia, Naveen P.; Siegele, Rainer

2008-02-01

335

Quantitative Proton MR Spectroscopy as a Biomarker of Tumor Necrosis in the Rabbit VX2 Liver Tumor  

PubMed Central

Purpose To compare metabolic magnetic resonance (MR) imaging findings (ie, quantification of tumor choline concentration) with percentage of necrosis on pathologic examination in rabbits bearing VX2 liver tumors. Materials and Methods VX2 tumors were implanted in the livers of 16 rabbits. MR imaging was performed with a 1.5-T MR scanner and extremity coil, and a hydrogen-1 (1H) proton MR spectroscopy (1H MRS) imaging protocol was used. Rabbits were euthanized immediately after imaging, and the tumor was harvested and sliced at 4-mm intervals in the axial plane. Choline concentration was calculated and was compared with the percentage of tumor necrosis on pathologic examination. Results Mean tumor size at pathologic examination was 16 mm (range, 12-22 mm). Mean percentage of necrosis at pathologic examination was 22% (range, 4%-44%). Choline concentration showed a relatively high inverse correlation with percentage of necrosis on pathologic examination, with an r value of 0.78 (P < .002). Conclusions Choline concentration showed a relatively high inverse correlation with tumor necrosis on pathologic examination. Therefore, 1H MRS may be useful to assess tumor necrosis. PMID:21620723

Buijs, Manon; Vossen, Josephina A.; Geschwind, Jean-Francois H.; Salibi, Nouha; Pan, Li; Ventura, Veronica Prieto; Liapi, Eleni; Lee, Kwang Hun; Kamel, Ihab R.

2015-01-01

336

High sensitivity quantitative lipidomics analysis of fatty acids in biological samples by gas chromatography–mass spectrometry  

Microsoft Academic Search

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

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

2011-01-01

337

Quantitative Analysis of Biological Membrane Lipids at the Low Picomole Level by Nano-Electrospray Ionization Tandem Mass Spectrometry  

Microsoft Academic Search

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

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

1997-01-01

338

2D IR Spectroscopy using Four-Wave Mixing, Pulse Shaping, and IR Upconversion: A Quantitative Comparison  

PubMed Central

Recent technological advances have led to major changes in the apparatuses used to collect 2D IR spectra. Pulse shaping offers several advantages including rapid data collection, inherent phase stability, and phase cycling capabilities. Visible array detection via upconversion allows the use of visible detectors that are cheaper, faster, more sensitive, and less noisy than IR detectors. However, despite these advantages, many researchers are reluctant to implement these technologies. Here we present a quantitative study of the S/N of 2D IR spectra collected with a traditional four-wave mixing (FWM) apparatus, with a pulse shaping apparatus, and with visible detection via upconversion to address the question of whether or not weak chromophores at low concentrations are still accessible with such an apparatus. We find that the enhanced averaging capability of the pulse shaping apparatus enables the detection of small signals that would be challenging to measure even with the traditional FWM apparatus, and we demonstrate this ability on a sample of cyanylated dihydrofolate reductase (DHFR). PMID:23687988

Rock, William; Li, Yun-Liang; Pagano, Philip; Cheatum, Christopher M.

2013-01-01

339

Quantitative evaluation on activated property-tunable bulk liquid water with reduced hydrogen bonds using deconvoluted Raman spectroscopy.  

PubMed

Interesting properties of water with distinguishable hydrogen-bonding structure on interfacial phase or in confined environment have drawn wide attentions. However, these unique properties of water are only found within the interfacial phase and confined environment, thus, their applications are limited. In addition, quantitative evaluation on these unique properties associating with the enhancement of water's physical and chemical activities represents a notable challenge. Here we report a practicable production of free-standing liquid water at room temperature with weak hydrogen-bonded structure naming Au nanoparticles (NPs)-treated (AuNT) water via treating by plasmon-induced hot electron transfer occurred on resonantly illuminated gold NPs (AuNPs). Compared to well-known untreated bulk water (deionized water), the prepared AuNT water exhibits many distinct activities in generally physical and chemical reactions, such as high solubilities to NaCl and O2. Also, reducing interaction energy within water molecules provides lower overpotential and higher efficiency in electrolytic hydrogen production. In addition, these enhanced catalytic activities of AuNT water are tunable by mixing with deionized water. Also, most of these tunable activities are linearly proportional to its degree of nonhydrogen-bonded structure (DNHBS), which is derived from the O-H stretching in deconvoluted Raman spectrum. PMID:25471522

Chen, Hsiao-Chien; Mai, Fu-Der; Yang, Kuang-Hsuan; Chen, Liang-Yih; Yang, Chih-Ping; Liu, Yu-Chuan

2015-01-01

340

Application of quantitative (19) F nuclear magnetic resonance spectroscopy in tape-stripping experiments with natural microemulsions.  

PubMed

The skin penetration of flufenamic acid (Fluf) and fluconazole (Fluc) from innovative natural microemulsions was investigated in tape-stripping experiments on pig ears. The formulations were based on the eudermic surfactants lecithin, sucrose laurate, alkylpolyglycoside or a mixture thereof. The quantification of the penetrated drug amounts was executed by (19) F nuclear magnetic resonance (NMR) in comparison with high-performance liquid chromatography (HPLC). The data obtained by the (19) F NMR method were confirmed by additional quantitative studies using HPLC. An excellent linear correlation was found for Fluf as well as for Fluc between (19) F NMR and HPLC data. This work presents a strategy outlining the use of (19) F NMR to selectively monitor the skin penetration routes of fluorinated compounds. Fluc penetrated generally well into the stratum corneum with the significantly highest amounts from the sucrose laurate microemulsion on the tape strips 1-5. Similarly, the highest amounts of penetrated Fluf could be observed from the formulation based on sucrose laurate. In addition, NMR self-diffusion studies were conducted and revealed a bicontinuous microstructure of the investigated microemulsions. The skin penetration results are in good agreement with the obtained (19) F NMR self-diffusion coefficients of the active compounds in the microemulsion systems. PMID:23794482

Schwarz, Julia C; Hoppel, Magdalena; Kählig, Hanspeter; Valenta, Claudia

2013-08-01

341

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

NASA Astrophysics Data System (ADS)

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.

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

2014-02-01

342

Raman Spectroscopy.  

ERIC Educational Resources Information Center

Reviews literature on Raman spectroscopy from late 1981 to late 1983. Topic areas include: instrumentation and sampling; liquids and solutions; gases and matrix isolation; biological molecules; polymers; high-temperature and high-pressure studies; Raman microscopy; thin films and surfaces; resonance-enhanced and surface-enhanced spectroscopy; and…

Gerrard, Donald L.

1984-01-01

343

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

NASA Astrophysics Data System (ADS)

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.

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

2014-11-01

344

33S nuclear magnetic resonance spectroscopy of biological samples obtained with a laboratory model 33S cryogenic probe.  

PubMed

(33)S nuclear magnetic resonance (NMR) spectroscopy is limited by inherently low NMR sensitivity because of the quadrupolar moment and low gyromagnetic ratio of the (33)S nucleus. We have developed a 10 mm (33)S cryogenic NMR probe, which is operated at 9-26 K with a cold preamplifier and a cold rf switch operated at 60 K. The (33)S NMR sensitivity of the cryogenic probe is as large as 9.8 times that of a conventional 5 mm broadband NMR probe. The (33)S cryogenic probe was applied to biological samples such as human urine, bile, chondroitin sulfate, and scallop tissue. We demonstrated that the system can detect and determine sulfur compounds having SO(4)(2-) anions and -SO(3)(-) groups using the (33)S cryogenic probe, as the (33)S nuclei in these groups are in highly symmetric environments. The NMR signals for other common sulfur compounds such as cysteine are still undetectable by the (33)S cryogenic probe, as the (33)S nuclei in these compounds are in asymmetric environments. If we shorten the rf pulse width or decrease the rf coil diameter, we should be able to detect the NMR signals for these compounds. PMID:20515157

Hobo, Fumio; Takahashi, Masato; Saito, Yuta; Sato, Naoki; Takao, Tomoaki; Koshiba, Seizo; Maeda, Hideaki

2010-05-01

345

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

NASA Astrophysics Data System (ADS)

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.

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

2014-07-01

346

QUANTITATIVE SPECTROSCOPY OF BLUE SUPERGIANT STARS IN THE DISK OF M81: METALLICITY, METALLICITY GRADIENT, AND DISTANCE  

SciTech Connect

The quantitative spectral analysis of low-resolution ({approx}5 A) Keck LRIS spectra of blue supergiants in the disk of the giant spiral galaxy M81 is used to determine stellar effective temperatures, gravities, metallicities, luminosities, interstellar reddening, and a new distance using the flux-weighted gravity-luminosity relationship. Substantial reddening and extinction are found with E(B - V) ranging between 0.13 and 0.38 mag and an average value of 0.26 mag. The distance modulus obtained after individual reddening corrections is 27.7 {+-} 0.1 mag. The result is discussed with regard to recently measured tip of the red giant branch and Cepheid distances. The metallicities (based on elements such as iron, titanium, magnesium) are supersolar ( Almost-Equal-To 0.2 dex) in the inner disk (R {approx}< 5 kpc) and slightly subsolar ( Almost-Equal-To - 0.05 dex) in the outer disk (R {approx}> 10 kpc) with a shallow metallicity gradient of 0.034 dex kpc{sup -1}. The comparison with published oxygen abundances of planetary nebulae and metallicities determined through fits of Hubble Space Telescope color-magnitude diagrams indicates a late metal enrichment and a flattening of the abundance gradient over the last 5 Gyr. This might be the result of gas infall from metal-rich satellite galaxies. Combining these M81 metallicities with published blue supergiant abundance studies in the Local Group and the Sculptor Group, a galaxy mass-metallicity relationship based solely on stellar spectroscopic studies is presented and compared with recent studies of Sloan Digital Sky Survey star-forming galaxies.

Kudritzki, Rolf-Peter; Urbaneja, Miguel A.; Gazak, Zachary; Bresolin, Fabio [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States); Przybilla, Norbert [Dr. Remeis-Sternwarte Bamberg and ECAP, D-96049 Bamberg (Germany); Gieren, Wolfgang; Pietrzynski, Grzegorz, E-mail: kud@ifa.hawaii.edu, E-mail: urbaneja@ifa.hawaii.edu, E-mail: zgazak@ifa.hawaii.edu, E-mail: bresolin@ifa.hawaii.edu, E-mail: przybilla@sternwarte.uni-erlangen.de, E-mail: wgieren@astro-udec.cl, E-mail: pietrzyn@astrouw.edu.pl [Departamento de Astronomia, Universidad de Concepcion, Casilla 160-C, Concepcion (Chile)

2012-03-01

347

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...

348

The Effects of Instructional Approaches on the Improvement of Reasoning in Introductory College Biology: A Quantitative Review of Research  

ERIC Educational Resources Information Center

The majority of undergraduates lack advanced reasoning patterns, which are necessary for significant achievement in college science courses. The purpose of this paper is to review the studies of various instructional practices in introductory college biology courses that claim to develop reasoning. Most of these were non-traditional,…

Daempfle, Peter A.

2006-01-01

349

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

Microsoft Academic Search

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)

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

350

Preparation of freeze-dried cryosections for quantitative X-ray microanalysis of electrolytes in biological soft tissues  

Microsoft Academic Search

A procedure is described which allows the evaluation of wet weight concentrations of diffusible substances in biological soft tissue on a cellular level by the use of energy dispersive X-ray microanalysis. Epithelia of frog skin and toad urinary bladder were used to prepare freeze-dried cryosections without the use of chemical fixatives, cryoprotectants, floating solutions or coating materials.

A. Dörge; R. Rick; K. Gehring; K. Thurau

1978-01-01

351

Scanning transmission ion microscopy mass measurements for quantitative trace element analysis within biological samples and validation using atomic force microscopy thickness measurements  

NASA Astrophysics Data System (ADS)

We used the nuclear microprobe techniques, micro-PIXE (particle-induced X-ray emission), micro-RBS (Rutherford backscattering spectrometry) and scanning transmission ion microscopy (STIM) in order to perform the characterization of trace element content and spatial distribution within biological samples (dehydrated cultured cells, tissues). The normalization of PIXE results was usually expressed in terms of sample dry mass as determined by micro-RBS recorded simultaneously to micro-PIXE. However, the main limit of RBS mass measurement is the sample mass loss occurring during irradiation and which could be up to 30% of the initial sample mass. We present here a new methodology for PIXE normalization and quantitative analysis of trace element within biological samples based on dry mass measurement performed by mean of STIM. The validation of STIM cell mass measurements was obtained in comparison with AFM sample thickness measurements. Results indicated the reliability of STIM mass measurement performed on biological samples and suggested that STIM should be performed for PIXE normalization. Further information deriving from direct confrontation of AFM and STIM analysis could as well be obtained, like in situ measurements of cell specific gravity within cells compartment (nucleolus and cytoplasm).

Devès, Guillaume; Cohen-Bouhacina, Touria; Ortega, Richard

2004-10-01

352

AUGER ELECTRON SPECTROSCOPY  

E-print Network

Qualitative Chemical Analysis by AES Auger electronAuger electron spectroscopy can provide quantitative chemical analysischemical analysis can be performed. Since both the adsorbate and the substrate Auger

Somorjai, G.A.

2010-01-01

353

Time-Resolved Quantitative Measurement of OH HO2 and CH2O in Fuel Oxidation Reactions by High Resolution IR Absorption Spectroscopy.  

SciTech Connect

Combined with a Herriott-type multi-pass slow flow reactor, high-resolution differential direct absorption spectroscopy has been used to probe, in situ and quantitatively, hydroxyl (OH), hydroperoxy (HO 2 ) and formaldehyde (CH 2 O) molecules in fuel oxidation reactions in the reactor, with a time resolution of about 1 micro-second. While OH and CH 2 O are probed in the mid-infrared (MIR) region near 2870nm and 3574nm respectively, HO 2 can be probed in both regions: near-infrared (NIR) at 1509nm and MIR at 2870nm. Typical sensitivities are on the order of 10 10 - 10 11 molecule cm -3 for OH at 2870nm, 10 11 molecule cm -3 for HO 2 at 1509nm, and 10 11 molecule cm -3 for CH 2 O at 3574nm. Measurements of multiple important intermediates (OH and HO 2 ) and product (CH 2 O) facilitate to understand and further validate chemical mechanisms of fuel oxidation chemistry.

Huang, Haifeng; Rotavera, Brandon; Taatjes, Craig A.

2014-08-01

354

Quantitative characterization of optical and physiological parameters in normal breasts using time-resolved spectroscopy: in vivo results of 19 Singapore women  

NASA Astrophysics Data System (ADS)

We report the quantitative measurements of optical and physiological parameters of normal breasts from 19 Singapore women by using time-resolved diffuse optical spectroscopy. Intrinsic absorption coefficient (?a) and reduced scattering coefficients (?s') of breasts were calculated from the time-resolved photon migration data. Physiology of breasts was characterized using the concentrations of oxyhemoglobin, deoxyhemoglobin, total hemoglobin (THC), and oxygenation saturation. On average, the experiment results showed that the ?a of young women (below 40 years old) was 36 to 38% greater than that of older women (above 40 years old) and that parameter THC was approximately 42% greater. Results also showed that the THC of premenopausal women was 24.3 ?Mol/L, which was approximately 69% larger than that of postmenopausal women at 14.1 ?Mol/L. Meanwhile, the ?a of premenopausal women was approximately 60% larger than that of postmenopausal women. Correlation analysis further showed that the optical and physiological parameters of breasts were strongly influenced by changes in the women's age, menopausal states, and body mass index. These in vivo experiment results will contribute to the breast tissue diagnosis between healthy and diseased breast tissues.

Mo, Weirong; Chan, Tryphena S. S.; Chen, Ling; Chen, Nanguang

2009-11-01

355

The quantitative analysis of paraquat in biological samples by liquid chromatography-electrospray ionization-mass spectrometry.  

PubMed

A quantitative method for the analysis of paraquat in blood and tissue samples has been developed using liquid chromatography-electrospray ionization-mass spectrometry. Chromatographic separation was performed on an Atlantis HILIC silica column using a mobile phase of acetonitrile/250 mM ammonium formate in the gradient mode. The method was linear from 2 to 500 ng/mL, with a correlation coefficient of 0.998. The limits of detection and quantitation in blood were determined to be 0.5 and 2 ng/mL, respectively. Intraday precision was performed in one extraction by analyzing five aliquots of three controls with different concentrations in the established linear range. Interday precision was determined by analyzing one aliquot of each control over 10 extractions. The coefficients of variation were less than 10% for both intra- and interday assays. The method has been successfully applied to blood and tissues samples from nine cases and can be used to detect the presence of paraquat in forensic testing. PMID:21219699

Wang, Zhaohong; Wang, Zhiping; Xing, Junbo

2011-01-01

356

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

PubMed Central

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

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

2012-01-01

357

Quantitative and in toto imaging in ascidians: Working toward an image-centric systems biology of chordate morphogenesis.  

PubMed

Developmental biology relies heavily on microscopy to image the finely controlled cell behaviors that drive embryonic development. Most embryos are large enough that a field of view with the resolution and magnification needed to resolve single cells will not span more than a small region of the embryo. Ascidian embryos, however, are sufficiently small that they can be imaged in toto with fine subcellular detail using conventional microscopes and objectives. Unlike other model organisms with particularly small embryos, ascidians have a chordate embryonic body plan that includes a notochord, hollow dorsal neural tube, heart primordium and numerous other anatomical details conserved with the vertebrates. Here we compare the size and anatomy of ascidian embryos with those of more traditional model organisms, and relate these features to the capabilities of both conventional and exotic imaging methods. We review the emergence of Ciona and related ascidian species as model organisms for a new era of image-based developmental systems biology. We conclude by discussing some important challenges in ascidian imaging and image analysis that remain to be solved. genesis 53:143-159, 2015. © 2014 Wiley Periodicals, Inc. PMID:25262824

Veeman, Michael; Reeves, Wendy

2015-01-01

358

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)

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.

Yuan, Zhen

2014-03-01

359

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

PubMed

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

Peerapattana, Jomjai; Otsuka, Kuniko; Otsuka, Makoto

2013-07-01

360

Multiplexed and Microparticle-based Analyses: Quantitative Tools for the Large-Scale Analysis of Biological Systems  

PubMed Central

While the term flow cytometry refers to the measurement of cells, the approach of making sensitive multiparameter optical measurements in a flowing sample stream is a very general analytical approach. The past few years have seen an explosion in the application of flow cytometry technology for molecular analysis and measurements using micro-particles as solid supports. While microsphere-based molecular analyses using flow cytometry date back three decades, the need for highly parallel quantitative molecular measurements that has arisen from various genomic and proteomic advances has driven the development in particle encoding technology to enable highly multiplexed assays. Multiplexed particle-based immunoassays are now common place, and new assays to study genes, protein function, and molecular assembly. Numerous efforts are underway to extend the multiplexing capabilities of microparticle-based assays through new approaches to particle encoding and analyte reporting. The impact of these developments will be seen in the basic research and clinical laboratories, as well as in drug development. PMID:16604537

Nolan, John P.; Mandy, Francis

2008-01-01

361

Fast and quantitative analysis of branched-chain amino acids in biological samples using a pillar array column.  

PubMed

In this study, a fast and quantitative determination method for branched-chain amino acids (BCAAs), namely leucine, isoleucine, and valine, was developed using a pillar array column. A pillar array column with low-dispersion turns was fabricated on a 20 × 20-mm(2) microchip using multistep ultraviolet photolithography and deep reactive ion etching. The BCAAs were fluorescently labeled with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), followed by reversed-phase separation on the pillar array column. The NBD derivatives of the three BCAAs and an internal standard (6-aminocaproic acid) were separated in 100 s. The calibration curves for the NBD-BCAAs had good linearity in the range of 0.4-20 ?M, using an internal standard. The intra- and interday precisions were found to be in the ranges of 1.42-3.80 and 2.74-6.97%, respectively. The accuracies for the NBD-BCAA were from 90.2 to 99.1%. The method was used for the analysis of sports drink and human plasma samples. The concentrations of BCAAs determined by the developed method showed good agreements with those determined using a conventional high-performance liquid chromatography system. As BCAAs are important biomarkers of some diseases, these results showed that the developed method could be a potential diagnostic tool in clinical research. PMID:23708693

Song, Yanting; Takatsuki, Katsuya; Isokawa, Muneki; Sekiguchi, Tetsushi; Mizuno, Jun; Funatsu, Takashi; Shoji, Shuichi; Tsunoda, Makoto

2013-10-01

362

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

NASA Astrophysics Data System (ADS)

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.

Cartagena-Rivera, Alexander X.

363

Full-field Hilbert phase microscopy using nearly common-path low coherence off-axis interferometry for quantitative imaging of biological cells  

NASA Astrophysics Data System (ADS)

We demonstrate single shot low coherence quantitative Hilbert phase microscopy (HPM) for the reconstruction of the two dimensional (2D) phase map of biological cells. The system is based on a compact and nearly common-path high magnification Mirau-interferometric objective lens. The spatial carrier frequency of the interference fringes was increased by means of introducing tilt in one of the arms of the interferometer, thus making the system off-axis. The system is user friendly as the interference fringes and imaging of objects with high lateral and axial resolution can be obtained quickly using a low cost commercially available microscope. Experimental results for the 2D phase map of polystyrene spheres and human red blood cells (RBCs) are presented. Hilbert transform fringe analysis was used for reconstructing the phase map and refractive index (RI) of the objects. For dynamic substances which change rapidly, single shot low coherence interferometric microscopy is an important method for obtaining the phase. Experimental results with increased field-of-view and large tilt angle are also presented. It is well known that on increasing the tilt angle for improved spatial phase sampling the object remains focused in only a small area even though the field-of-view is large. This limitation was overcome by means of vertical scanning low coherence interferometry. Due to the low coherence properties of the light source the interference occurs only at the desired location of the object, i.e., where the object is sharply focused. The object was vertically scanned and the single shot interferograms were recorded for every scan and analyzed by Hilbert transform. In this way a large area of the sample can be imaged quantitatively.

Srivastava, Vishal; Anna, Tulsi; Singh Mehta, Dalip

2012-12-01

364

Preliminary characterization of calcium chemical environment in apatitic and non-apatitic calcium phosphates of biological interest by X-ray absorption spectroscopy  

NASA Astrophysics Data System (ADS)

Several reports have mentioned the existence of non-apatitic environments of phosphate and carbonate ions in synthetic and biological poorly crystalline apatites. However there were no direct spectroscopic evidences for the existence of non-apatitic environment of calcium ions. X-ray Absorption Spectroscopy, at the K-edge of calcium, allows the discrimination between different calcium phosphates of biological interest despite great spectral similarities. A primary analysis of the spectra reveals the existence, in synthetic poorly crystalline apatites, of variable features related to the maturation stage of the sample and corresponding to the existence of non-apatitic environments of calcium ions. Although these features can also be found in several other calcium phosphate salts, and do not allow a clear identification of the ionic environments of calcium ions, they give a possibility to directly determine the maturity of poorly crystalline apatite from calcium X-ray Absorption Near Edge Structure spectra.

Eichert, D.; Salomé, M.; Banu, M.; Susini, J.; Rey, C.

2005-07-01

365

Screening biological stains with qPCR versus lateral flow immunochromatographic test strips: a quantitative comparison using analytical figures of merit.  

PubMed

Biological fluid identification is an important facet of evidence examination in forensic laboratories worldwide. While identifying bodily fluids may provide insight into which downstream DNA methods to employ, these screening techniques consume a vital portion of the available evidence, are usually qualitative, and rely on visual interpretation. In contrast, qPCR yields information regarding the amount and proportion of amplifiable genetic material. In this study, dilution series of either semen or male saliva were prepared in either buffer or female blood. The samples were subjected to both lateral flow immunochromatographic test strips and qPCR analysis. Analytical figures of merit-including sensitivity, minimum distinguishable signal (MDS) and limit of detection (LOD)-were calculated and compared between methods. By applying the theory of the propagation of random errors, LODs were determined to be 0.05 ?L of saliva for the RSID™ Saliva cards, 0.03 ?L of saliva for Quantifiler(®) Duo, and 0.001 ?L of semen for Quantifiler(®) Duo. In conclusion, quantitative PCR was deemed a viable and effective screening method for subsequent DNA profiling due to its stability in different matrices, sensitivity, and low limits of detection. PMID:24117798

Oechsle, Crystal Simson; Haddad, Sandra; Sgueglia, Joanne B; Grgicak, Catherine M

2014-01-01

366

Mössbauer Spectroscopy  

Microsoft Academic Search

Mössbauer spectroscopy, based on the recoilless resonance emission and absorption of gamma photons observed with certain atomic nuclei, is a powerful investigating tool in most disciplines of natural science ranging from physics to chemistry to biology. This nuclear method makes it possible to measure the energy difference between nuclear energy levels to an extremely high resolution (up to 13-15 decimals).

E. Kuzmann; Z. Homonnay; S. Nagy; K. Nomura

2011-01-01

367

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

SciTech Connect

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.

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

368

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.

2012-01-30

369

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.

2012-01-13

370

Leo Szilard Lectureship Award Talk - Universal Scaling Laws from Cells to Cities; A Physicist's Search for Quantitative, Unified Theories of Biological and Social Structure and Dynamics  

NASA Astrophysics Data System (ADS)

Many of the most challenging, exciting and profound questions facing science and society, from the origins of life to global sustainability, fall under the banner of ``complex adaptive systems.'' This talk explores how scaling can be used to begin to develop physics-inspired quantitative, predictive, coarse-grained theories for understanding their structure, dynamics and organization based on underlying mathematisable principles. Remarkably, most physiological, organisational and life history phenomena in biology and socio-economic systems scale in a simple and ``universal'' fashion: metabolic rate scales approximately as the 3/4-power of mass over 27 orders of magnitude from complex molecules to the largest organisms. Time-scales (such as lifespans and growth-rates) and sizes (such as genome lengths and RNA densities) scale with exponents which are typically simple multiples of 1/4, suggesting that fundamental constraints underlie much of the generic structure and dynamics of living systems. These scaling laws follow from dynamical and geometrical properties of space-filling, fractal-like, hierarchical branching networks, presumed optimised by natural selection. This leads to a general framework that potentially captures essential features of diverse systems including vasculature, ontogenetic growth, cancer, aging and mortality, sleep, cell size, and DNA nucleotide substitution rates. Cities and companies also scale: wages, profits, patents, crime, disease, pollution, road lengths scale similarly across the globe, reflecting underlying universal social network dynamics which point to general principles of organization transcending their individuality. These have dramatic implications for global sustainability: innovation and wealth creation that fuel social systems, left unchecked, potentially sow the seeds for their inevitable collapse.

West, Geoffrey

2013-04-01

371

Quantitative measurement of biological substances in daily-life environment with the little-finger-size one-shot spectroscopic tomography  

NASA Astrophysics Data System (ADS)

In daily-life environment, the quantitative measurement of biological substances, such as the blood glucose level in the human skin, is strongly required to realize the non-invasive healthcare apparatus. Fourier-spectroscopic-tomography of the little-finger-size with high time-resolution and with the strong robustness for mechanical vibrations is proposed. The proposed method is a kind of near-common-path interferometer with spatial phase-shift method. We install the transmission-type relative-inclined phase-shifter on the optical Fourier transform plane of the infinity corrected optical system. The phase shifter is constructed with the cuboid and wedge prisms to give the relative phase-shift spatially between each half-flux of the objective beams. The interferograms from each single-bright-point on an objective surface in a line are formed as fringe patterns on 2-dimensional imaging array devices. And because the proposed method is based on the imaging optics, only emitted rays from a focal plane can contribute forming of interferograms. Thus, the measurement plane can be limited onto the focal plane only. From the spectroscopic tomography, only at a localized vessel area in human skins, we can get the pinpointed near-infrared spectroscopic data. And we can expect the improvement of the determination precision, because a Fourier spectroscopic-character is acquired from multiple intensity data in accordance with amount of phase-shift. From the statistical point of view, the gradation of detector is improved with the square root of sample number, based on t-distribution. We constructed the statistical model to assure the determination accuracy, and demonstrated the feasibility of the glucose sensor using liquid cells.

Ishida, Akane; Sato, Shun; Nakada, Sho; Suzuki, Satoru; Abeygunawardhana, P. K. W.; Wada, Kenji; Nishiyama, Akira; Ishimaru, Ichiro

2014-02-01

372

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

PubMed

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

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

2014-01-01

373

Quantitative dispersion microscopy  

PubMed Central

Refractive index dispersion is an intrinsic optical property and a useful source of contrast in biological imaging studies. In this report, we present the first dispersion phase imaging of living eukaryotic cells. We have developed quantitative dispersion microscopy based on the principle of quantitative phase microscopy. The dual-wavelength quantitative phase microscope makes phase measurements at 310 nm and 400 nm wavelengths to quantify dispersion (refractive index increment ratio) of live cells. The measured dispersion of living HeLa cells is found to be around 1.088, which agrees well with that measured directly for protein solutions using total internal reflection. This technique, together with the dry mass and morphology measurements provided by quantitative phase microscopy, could prove to be a useful tool for distinguishing different types of biomaterials and studying spatial inhomogeneities of biological samples. PMID:21113234

Fu, Dan; Choi, Wonshik; Sung, Yongjin; Yaqoob, Zahid; Dasari, Ramachandra R.; Feld, Michael

2010-01-01

374

Study of energetic-particle-irradiation induced biological effect on Rhizopus oryzae through synchrotron-FTIR micro-spectroscopy  

NASA Astrophysics Data System (ADS)

Energetic particles exist ubiquitously and cause varied biological effects such as DNA strand breaks, lipid peroxidation, protein modification, cell apoptosis or death. An emerging biotechnology based on ion-beam technique has been developed to serve as an effective tool for mutation breeding of crops and microbes. In order to improve the effectiveness of ion-beam biotechnology for mutation breeding, it is indispensible to gain a better understanding of the mechanism of the interactions between the energetic ions and biological systems which is still elusive. A new trend is to conduct more comprehensive research which is based on micro-scaled observation of the changes of the cellular structures and compositions under the interactions. For this purpose, advanced synchrotron FTIR (s-FTIR) microscopy was employed to monitor the cellular changes of single fungal hyphae under irradiation of ?-particles from 241Am. Intracellular contents of ROS, MDA, GSSG/GSH and activities of CAT and SOD were measured via biochemical assay. Ion-irradiation on Rhizopus oryzae causes localized vacuolation, autolysis of cell wall and membrane, lipid peroxidation, DNA damage and conformational changes of proteins, which have been clearly revealed by the s-FTIR microspectroscopy. The different changes of cell viability, SOD and CAT activities can be explained by the ROS-involved chemical reactions. Evidently, the elevated level of ROS in hyphal cells upon irradiation plays the key role in the caused biological effect. This study demonstrates that s-FTIR microspectroscopy is an effective tool to study the damage of fungal hyphae caused by ionizing radiation and it facilitates the exploit of the mechanism for the interactions between the energetic ions and biological systems.

Liu, Jinghua; Qi, Zeming; Huang, Qing; Wei, Xiaoli; Ke, Zhigang; Fang, Yusheng; Tian, Yangchao; Yu, Zengliang

2013-01-01

375

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

Microsoft Academic Search

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)

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

2005-01-01

376

Quantitative estimation of NH3 partial pressure in H2 desorbed from the Li-N-H system by Raman spectroscopy.  

PubMed

The partial pressure of NH3 gas estimated by Raman spectroscopy indicates that approximately 0.1% NH3 inevitably contaminates the H2 desorbed from a hydrogen storage material composed of LiH and LiNH2 at any temperature up to 400 degrees C in a closed system. PMID:15959577

Hino, Satoshi; Ichikawa, Takayuki; Ogita, Norio; Udagawa, Masayuki; Fujii, Hironobu

2005-06-28

377

Nanostructural Differentiation between Live and Dead Escherichia coli Cells Using FT-IR Spectroscopy and Comparison of Detection Limits to Quantitative PCR (qPCR)  

Microsoft Academic Search

Fourier-transform infrared spectroscopy (FT-IR) utilizes nanostructural differences between bacterial cells for the rapid identification, classification, and differentiation of many species of bacteria, but most studies have used only live cells. A rapid and reliable method for determining the total number of live and dead bacterial cells in a food could prevent the distribution of unsafe products to consumers. In this

A. J. Deering; B. L. Reuhs; L. J. Mauer

2010-01-01

378

Quantitative Chemical Imaging with Multiplex Stimulated Raman Scattering Microscopy  

PubMed Central

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

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

2012-01-01

379

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)

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.

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

1989-01-01

380

Implementation of Traditional and Real-World Cooperative Learning Techniques in Quantitative Analysis Including Near Infrared Spectroscopy for Analysis of Live Fish  

Microsoft Academic Search

It is important for a modern quantitative analysis laboratory course to contain gravimetric and volumetric analysis exercises implemented with standard unknowns. By analyzing unknowns, students learn crucial laboratory skills. It is also advantageous to introduce real-world samples and cooperative learning structure into the lab course. A one-semester sophomore course at Idaho State University is divided into two parts: students individually

Tracy P. Houghton; John H. Kalivas

2000-01-01

381

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

PubMed Central

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

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

2007-01-01

382

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

SciTech Connect

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.

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

383

X-Ray Absorption Spectroscopy of Metallobiomolecules  

E-print Network

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

Scott, Robert A.

384

X-Ray Absorption Spectroscopy of Metallobiomolecules  

E-print Network

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

Scott, Robert A.

385

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

NASA Technical Reports Server (NTRS)

One of the principal means by which organic compounds are detected and identified in space is by infrared spectroscopy. Past IR telescopic and laboratory studies have shown that much of the carbon in the interstellar medium (ISM) is in complex organic species but the distribution, abundance and evolutionary relationships of these materials are not well understood. The Astrobiology Explorer (ABE) is a MIDEX mission concept designed to conduct IR spectroscopic observations to detect and identify these materials and address outstanding problems in astrobiology, astrochemistry, and astrophysics. ABE's core science program includes observations of planetary nebulae and stellar outflows, protostellar objects, Solar System objects, and galaxies, and lines of sight through dense molecular clouds and the diffuse ISM. ABE is a cryogenically-cooled 60 cm diameter space telescope equipped with 3 cross-dispersed R-2000 spectrometers that share a single common slit. Each spectrometer measures one spectral octave and together cover the entire 2.5-20 micron region simultaneously. The spectrometers use state-of-the-art InSb and Si:As 1024x1024 pixel detectors. ABE would operate in a heliocentric, Earth drift-away orbit and have a core science mission lasting approximately 1.5 years. ABE is currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corp.

Sandford, Scott A.; Ennico, Kimberly; Allamandola, Louis; Bregman, Jesse; Greene, Thomas; Hudgins, Douglas

2002-01-01

386

Quantitative determination of iron oxidation states in minerals using Fe L 2,3 -edge electron energy-loss near-edge structure spectroscopy  

Microsoft Academic Search

The Fe L\\u000a 2,3-edge spectra for a range of natural minerals and synthetic solid solutions have been measured using the technique of parallel\\u000a electron energy-loss spectroscopy (PEELS) recorded in a transmission electron microscope (TEM). The Fe L\\u000a \\u000a 2,3\\u000a -edges of the minerals are characterised by two white-line features and exhibit electron energy-loss near-edge structure (ELNES)\\u000a characteristic of Fe valence state.

P. A. van Aken; B. Liebscher; V. J. Styrsa

1998-01-01

387

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

SciTech Connect

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.

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

388

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

NASA Technical Reports Server (NTRS)

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.

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

2002-01-01

389

Infrared differential-absorption Mueller matrix spectroscopy and neural network-based data fusion for biological aerosol standoff detection.  

PubMed

An active spectrophotopolarimeter sensor and support system were developed for a military/civilian defense feasibility study concerning the identification and standoff detection of biological aerosols. Plumes of warfare agent surrogates gamma-irradiated Bacillus subtilis and chicken egg white albumen (analytes), Arizona road dust (terrestrial interferent), water mist (atmospheric interferent), and talcum powders (experiment controls) were dispersed inside windowless chambers and interrogated by multiple CO(2) laser beams spanning 9.1-12.0 microm wavelengths (lambda). Molecular vibration and vibration-rotation activities by the subject analyte are fundamentally strong within this "fingerprint" middle infrared spectral region. Distinct polarization-modulations of incident irradiance and backscatter radiance of tuned beams generate the Mueller matrix (M) of subject aerosol. Strings of all 15 normalized elements {M(ij)(lambda)/M(11)(lambda)}, which completely describe physical and geometric attributes of the aerosol particles, are input fields for training hybrid Kohonen self-organizing map feed-forward artificial neural networks (ANNs). The properly trained and validated ANN model performs pattern recognition and type-classification tasks via internal mappings. A typical ANN that mathematically clusters analyte, interferent, and control aerosols with nil overlap of species is illustrated, including sensitivity analysis of performance. PMID:20090802

Carrieri, Arthur H; Copper, Jack; Owens, David J; Roese, Erik S; Bottiger, Jerold R; Everly, Robert D; Hung, Kevin C

2010-01-20

390

Undergraduate Quantitative  

E-print Network

Undergraduate Quantitative Research Methods with: Childhood Studies | Geography | Politics | Social.ac.uk/study The University of Bristol is introducing a new quantitative research methods pathway to a range of social science new courses, work placements and pathways to Why enhance your degree with quantitative research

Bristol, University of

391

Comparison of digestion procedures used for the determination of boron in biological tissues by ICP-AES (inductively-coupled, plasma-atomic emission spectroscopy)  

SciTech Connect

A study was designed to identify the most accurate and reliable procedures for the digestion of biological tissues prior to the determination of boron by inductively-coupled, plasma-atomic emission spectroscopy (ICP-AES). The four procedures used in this study were an acid bomb digestion and digestions performed in test tubes using perchloric acid and hydrogen peroxide, nitric acid and hydrogen peroxide, and nitric acid alone. Digestions using nitric acid and hydrogen peroxide and nitric acid alone were performed in a manner analogous to the perchloric acid/hydrogen peroxide procedure. The tissues used in the study were from dogs that had been administered a boron compound (Na{sub 2}B{sub 12}H{sub 11}SH) and included two brain tissues, a liver and a tongue. These tissues were selected in order to eliminate results that may be due to surface spiking only. None of the test tube procedures were successful in completely dissolving the samples, as was evidenced by residual color and a coagulated precipitate. The amount of precipitate was much larger for the brain tissues in all cases. The acid bomb digestion and the perchloric acid/hydrogen peroxide procedures gave comparable boron concentrations for all of the tissues in this study. 2 refs., 1 tab.

Bauer, W.F.; Miller, D.L.; Steele, S.M.

1988-01-01

392

A quantitative study of valence electron transfer in the skutterudite compound CoP(3) by combining x-ray induced Auger and photoelectron spectroscopy.  

PubMed

We use the sum of the ionization and Auger energy, the so-called Auger parameter, measured from the x-ray photoelectron spectrum, to study the valence electron distribution in the skutterudite CoP(3). The electron transfer between Co and P was estimated using models relating changes in Auger parameter values to charge transfer. It was found that each P atom gains 0.24 e(-), and considering the unit formula CoP(3) this is equivalent to a donation of 0.72 e(-) per Co atom. This is in agreement with a recent electron energy-loss spectroscopy study, which indicates a charge transfer of 0.77 e(-)/atom from Co to P. PMID:21694059

Diplas, S; Prytz, O; Karlsen, O B; Watts, J F; Taftø, J

2007-06-20

393

Prostate Cancer Metastases Alter Bone Mineral and Matrix Composition Independent of Effects on Bone Architecture in Mice A Quantitative Study Using microCT and Raman Spectroscopy  

PubMed Central

Prostate cancer is the most common primary tumor and the second leading cause of cancer-related deaths in men in the United States. Prostate cancer bone metastases are characterized by abnormal bone remodeling processes and result in a variety of skeletal morbidities. Prevention of skeletal complications is a crucial element in prostate cancer management. This study investigated prostate cancer-induced alterations in the molecular composition and morphological structure of metastasis-bearing bones in a mouse model of prostate cancer using Raman spectroscopy and micro-computed tomography (microCT). LNCaP C4-2B prostate cancer cells were injected into the right tibiae of 5-week old male SCID mice. Upon sacrifice at 8 weeks post tumor inoculation, two out of the ten tumor-bearing tibiae showed only osteoblastic lesions in the radiographs, 4 osteolytic lesions only and 4 mixed with osteoblastic and osteolytic lesions.. Carbonate substitution was significantly increased while there was a marked reduction in the level of collagen mineralization, mineral crystallinity, and carbonate:matrix ratio in the cortex of the intact tumor-bearing tibiae compared to contralateral controls. MicroCT analysis revealed a significant reduction in bone volume/total volume, trabecular number and trabecular thickness, as well as significant increase in bone surface/volume ratio in tibiae with osteolytic lesions, suggesting active bone remodeling and bone loss. None of the changes in bone compositional properties were correlated with lesion area from radiographs or the changes in bone architecture from microCT. This study indicates that LNCaP C4-2B prostate cancer metastases alter bone tissue composition independent of changes in architecture, and altered bone quality may be an important contributor to fracture risk in these patients. Raman spectroscopy may provide a new avenue of investigation into interactions between tumor and bone microenvironment. PMID:23867219

Bi, Xiaohong; Sterling, Julie A.; Merkel, Alyssa R.; Perrien, Daniel S.; Nyman, Jeffry; Mahadevan-Jansen, Anita

2013-01-01

394

Quantitative use of electron energy-loss spectroscopy Mo-M2,3 edges for the study of molybdenum oxides.  

PubMed

Because of the large energy separation between O-K and Mo-L2,3 edges, extracting precise and reliable chemical information from core-loss EELS analyze of molybdenum oxides has always been a challenge. In this regard Mo-M2,3 edges represents an interesting alternative as they are situated close to the O-K edges. They should allow thus the extraction of a wealth of chemical information from the same spectra. However the main difficulty to overcome in order to work properly with these edges is the delayed maxima of the Mo-M4,5 edges which hinders the automated background subtraction with the usual inverse power low function. In this study we propose another background subtraction method specifically designed to overcome this obstacle and we apply it to the study of MoO3 and MoO2. We are able to show that quantitative chemical information can be precisely and accurately determined from the joined analyze of O-K and Mo-M2,3 edges. In particular k-factors are derived as a function of the integration window width and standard errors close to 2% are reported. The possibility to discriminate the two oxides thanks to chemical shifts and energy-loss near-edge structures is also investigated and discussed. Furthermore the M3/M2 ratios are derived and are found to be strongly dependent on the local chemical environment. This result is confirmed by multiplet calculations for which the crystal field parameters have been determined by ab initio calculations. The whole methodology as well as the conclusions presented in this paper should be easily transposable to any transitions metal oxides of the 4d family. This work should open a new and easier way regarding the quantitative EELS analyses of these compounds. PMID:25464154

Lajaunie, L; Boucher, F; Dessapt, R; Moreau, P

2015-02-01

395

Quantitative Gas Chromatography–Mass Spectrometry Isomer-Specific Measurement of Hydroxy Fatty Acids in Biological Samples and Food as a Marker of Lipid Peroxidation  

Microsoft Academic Search

We have developed a capillary gas chromatography–mass spectrometry method for the quantitative analysis of individual positional isomers of monohydroxy fatty acids derived from linoleic, arachidonic, eicosapentaenoic, or docosahexaenoic acid. Peroxidation of a particular polyunsaturated fatty acid results already in a complex mixture of positional isomers of hydroperoxy and hydroxy fatty acids. Catalytic hydrogenation of lipid extracts produces stable saturated hydroxy

R. Wilson; R. Smith; P. Wilson; M. J. Shepherd; R. A. Riemersma

1997-01-01

396

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)

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.

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

2014-03-01

397

Easy and cheap fabrication of ordered pyramidal-shaped plasmonic substrates for detection and quantitative analysis using surface-enhanced Raman spectroscopy.  

PubMed

In this work we present a simple approach for the fabrication of periodically ordered pyramidal-shaped metallic nanostructures and demonstrate their efficiency as SERS active substrates. Our method for the fabrication of the plasmonic substrate is based on nanoimprint lithography and exploits the thermal properties of two classes of polymers, thermoplastics and hydrogels. During the heating process the thermoplastic polymers will start to melt whereas the hydrogel polymers will form a solid due to the evaporation of water molecules adsorbed during the dissolving process. Using this approach we fabricate highly ordered pyramidal-shaped nanostructures using the texture of a commercial DVD as the initial mold. This technique represents a low-cost alternative to the classical lithography techniques, allowing the fabrication over large areas (~cm(2)) of periodically ordered nanostructures in a controlled and reproducible manner. The SERS efficiency of the fabricated substrate is demonstrated through the detection of urea molecules found in the fingerprint. In addition, due to the periodicity of the pyramidal-shaped structures, the fabricated substrate can be successfully employed to correlate the intensity of the specific SERS peak of urea with the molecules concentration, offering thus the possibility of developing a quantitative SERS renal sensor. PMID:23817626

Leordean, Cosmin; Gabudean, Ana-Maria; Canpean, Valentin; Astilean, Simion

2013-09-01

398

Mössbauer Spectroscopy  

NASA Astrophysics Data System (ADS)

Mössbauer spectroscopy, based on the recoilless resonance emission and absorption of ? photons observed with certain atomic nuclei, is a powerful investigating tool in most disciplines of natural science ranging from physics to chemistry to biology. This nuclear method makes it possible to measure the energy difference between nuclear energy levels to an extremely high resolution (up to 13-15 decimals). This resolution is required to measure the slight variation of nuclear energy levels caused by electric monopole, electric quadrupole, and magnetic dipole interactions between the electrons and the nucleus. Mössbauer nuclides being at different microenvironments act as local probes for the sensitive detection of the hyperfine interactions. Such interactions reflect changes in the electronic, magnetic, geometric, or defect structure as well as in the lattice vibrations, serving as a basis for a variety of applications. In this chapter, the principles and some practical aspects of Mössbauer spectroscopy are described.

Kuzmann, E.; Homonnay, Z.; Nagy, S.; Nomura, K.

399

Quantitative detection of siRNA and single-stranded oligonucleotides: relationship between uptake and biological activity of siRNA  

Microsoft Academic Search

The quantitative detection of oligomeric nucleic acids including short double-stranded RNA in cells and tissues becomes increasingly important. Here, we describe a method for the detection of siRNA inextracts prepared from mammalian cells, which is based on liquid hybridization with a 32P-labelled probe followed by a nuclease protection step. The limit of detection of absolute amounts of siRNA is in

Marita Overhoff; Winfried Wunsche; Georg Sczakiel

2004-01-01

400

Quantitative spatially resolved measurement of tissue chromophore concentrations using photoacoustic spectroscopy: application to the measurement of blood oxygenation and haemoglobin concentration.  

PubMed

A new approach based on pulsed photoacoustic spectroscopy for non-invasively quantifying tissue chromophore concentrations with high spatial resolution has been developed. The technique is applicable to the quantification of tissue chromophores such as oxyhaemoglobin (HbO(2)) and deoxyhaemoglobin (HHb) for the measurement of physiological parameters such as blood oxygen saturation (SO(2)) and total haemoglobin concentration. It can also be used to quantify the local accumulation of targeted contrast agents used in photoacoustic molecular imaging. The technique employs a model-based inversion scheme to recover the chromophore concentrations from photoacoustic measurements. This comprises a numerical forward model of the detected time-dependent photoacoustic signal that incorporates a multiwavelength diffusion-based finite element light propagation model to describe the light transport and a time-domain acoustic model to describe the generation, propagation and detection of the photoacoustic wave. The forward model is then inverted by iteratively fitting it to measurements of photoacoustic signals acquired at different wavelengths to recover the chromophore concentrations. To validate this approach, photoacoustic signals were generated in a tissue phantom using nanosecond laser pulses between 740 nm and 1040 nm. The tissue phantom comprised a suspension of intralipid, blood and a near-infrared dye in which three tubes were immersed. Blood at physiological haemoglobin concentrations and oxygen saturation levels ranging from 2% to 100% was circulated through the tubes. The signal amplitude from different temporal sections of the detected photoacoustic waveforms was plotted as a function of wavelength and the forward model fitted to these data to recover the concentrations of HbO(2) and HHb, total haemoglobin concentration and SO(2). The performance was found to compare favourably to that of a laboratory CO-oximeter with measurement resolutions of +/-3.8 g l(-1) (+/-58 microM) and +/-4.4 g l(-1) (+/-68 microM) for the HbO(2) and HHb concentrations respectively and +/-4% for SO(2) with an accuracy in the latter in the range -6%-+7%. PMID:17183133

Laufer, Jan; Delpy, Dave; Elwell, Clare; Beard, Paul

2007-01-01

401

Quantitative glycomics strategies.  

PubMed

The correlations between protein glycosylation and many biological processes and diseases are increasing the demand for quantitative glycomics strategies enabling sensitive monitoring of changes in the abundance and structure of glycans. This is currently attained through multiple strategies employing several analytical techniques such as capillary electrophoresis, liquid chromatography, and mass spectrometry. The detection and quantification of glycans often involve labeling with ionic and/or hydrophobic reagents. This step is needed in order to enhance detection in spectroscopic and mass spectrometric measurements. Recently, labeling with stable isotopic reagents has also been presented as a very viable strategy enabling relative quantitation. The different strategies available for reliable and sensitive quantitative glycomics are herein described and discussed. PMID:23325767

Mechref, Yehia; Hu, Yunli; Desantos-Garcia, Janie L; Hussein, Ahmed; Tang, Haixu

2013-04-01

402

Spectroscopy of divertor plasmas  

SciTech Connect

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.

Isler, R.C.

1995-12-31

403

Fiber Laser Based Nonlinear Spectroscopy  

E-print Network

practical. A nonlinear spectroscopy tool based on a single fiber laser, with electrically controlled wavelength-tuning and spectral resolution enhanced by a pulse shaping technique, will efficiently produce optical excitation that allows quantitative...

Adany, Peter

2012-08-31

404

Different design of enzyme-triggered CO-releasing molecules (ET-CORMs) reveals quantitative differences in biological activities in terms of toxicity and inflammation  

PubMed Central

Acyloxydiene–Fe(CO)3 complexes can act as enzyme-triggered CO-releasing molecules (ET-CORMs). Their biological activity strongly depends on the mother compound from which they are derived, i.e. cyclohexenone or cyclohexanedione, and on the position of the ester functionality they harbour. The present study addresses if the latter characteristic affects CO release, if cytotoxicity of ET-CORMs is mediated through iron release or inhibition of cell respiration and to what extent cyclohexenone and cyclohexanedione derived ET-CORMs differ in their ability to counteract TNF-? mediated inflammation. Irrespective of the formulation (DMSO or cyclodextrin), toxicity in HUVEC was significantly higher for ET-CORMs bearing the ester functionality at the outer (rac-4), as compared to the inner (rac-1) position of the cyclohexenone moiety. This was paralleled by an increased CO release from the former ET-CORM. Toxicity was not mediated via iron as EC50 values for rac-4 were significantly lower than for FeCl2 or FeCl3 and were not influenced by iron chelation. ATP depletion preceded toxicity suggesting impaired cell respiration as putative cause for cell death. In long-term HUVEC cultures inhibition of VCAM-1 expression by rac-1 waned in time, while for the cyclohexanedione derived rac-8 inhibition seems to increase. NF?B was inhibited by both rac-1 and rac-8 independent of I?B? degradation. Both ET-CORMs activated Nrf-2 and consequently induced the expression of HO-1. This study further provides a rational framework for designing acyloxydiene–Fe(CO)3 complexes as ET-CORMs with differential CO release and biological activities. We also provide a better understanding of how these complexes affect cell-biology in mechanistic terms. PMID:25009775

Stamellou, E.; Storz, D.; Botov, S.; Ntasis, E.; Wedel, J.; Sollazzo, S.; Krämer, B.K.; van Son, W.; Seelen, M.; Schmalz, H.G.; Schmidt, A.; Hafner, M.; Yard, B.A.

2014-01-01

405

Different design of enzyme-triggered CO-releasing molecules (ET-CORMs) reveals quantitative differences in biological activities in terms of toxicity and inflammation.  

PubMed

Acyloxydiene-Fe(CO)3 complexes can act as enzyme-triggered CO-releasing molecules (ET-CORMs). Their biological activity strongly depends on the mother compound from which they are derived, i.e. cyclohexenone or cyclohexanedione, and on the position of the ester functionality they harbour. The present study addresses if the latter characteristic affects CO release, if cytotoxicity of ET-CORMs is mediated through iron release or inhibition of cell respiration and to what extent cyclohexenone and cyclohexanedione derived ET-CORMs differ in their ability to counteract TNF-? mediated inflammation. Irrespective of the formulation (DMSO or cyclodextrin), toxicity in HUVEC was significantly higher for ET-CORMs bearing the ester functionality at the outer (rac-4), as compared to the inner (rac-1) position of the cyclohexenone moiety. This was paralleled by an increased CO release from the former ET-CORM. Toxicity was not mediated via iron as EC50 values for rac-4 were significantly lower than for FeCl2 or FeCl3 and were not influenced by iron chelation. ATP depletion preceded toxicity suggesting impaired cell respiration as putative cause for cell death. In long-term HUVEC cultures inhibition of VCAM-1 expression by rac-1 waned in time, while for the cyclohexanedione derived rac-8 inhibition seems to increase. NF?B was inhibited by both rac-1 and rac-8 independent of I?B? degradation. Both ET-CORMs activated Nrf-2 and consequently induced the expression of HO-1. This study further provides a rational framework for designing acyloxydiene-Fe(CO)3 complexes as ET-CORMs with differential CO release and biological activities. We also provide a better understanding of how these complexes affect cell-biology in mechanistic terms. PMID:25009775

Stamellou, E; Storz, D; Botov, S; Ntasis, E; Wedel, J; Sollazzo, S; Krämer, B K; van Son, W; Seelen, M; Schmalz, H G; Schmidt, A; Hafner, M; Yard, B A

2014-01-01

406

Quantitation of diethylene glycol and its metabolites by gas chromatography mass spectrometry or ion chromatography mass spectrometry in rat and human biological samples.  

PubMed

The misuse of the commonly used chemical diethylene glycol (DEG) has lead to many poisonings worldwide. Methods were developed for analysis of DEG and its potential metabolites; ethylene glycol, glycolic acid, oxalic acid, diglycolic acid and hydroxyethoxy acetic acid in human urine, serum and cerebrospinal fluid samples, collected following a DEG-associated poisoning in the Republic of Panama during 2006. In addition, methods were developed for rat blood, urine, kidney and liver tissue to support toxicokinetic analysis during the conduct of DEG acute toxicity studies in the rat. Sample analysis was conducted using two techniques; ion chromatography with suppressed conductivity and negative ion electrospray ionization with MS detection or with gas chromatography using electron impact ionization or methane negative chemical ionization with MS detection. Stable-isotope-labeled analogs of each analyte were employed as quantitative internal standards in the assays. PMID:24668490

Perala, Adam W; Filary, Mark J; Bartels, Michael J; McMartin, Kenneth E

2014-05-01

407

Quantitative NMR  

NSDL National Science Digital Library

This site features a learning module focused on principles and practice of NMR for quantitative analysis, an application less commonly associated with the technique than is structure determination. Links to simulation packages are included.

Korir, Albert K.; Larive, Cynthia K.

2011-07-18

408

Application of Raman spectroscopy technology to studying Sudan I  

NASA Astrophysics Data System (ADS)

Being an industrial dye, the Sudan I may have a toxic effect after oral intake on the body, and has recently been shown to cause cancer in rats, mice and rabbits. Because China and some other countries have detected the Sudan I in samples of the hot chilli powder and the chilli products, it is necessary to study the characteristics of this dye. As one kind of molecule scattering spectroscopy, Raman spectroscopy is characterized by the frequency excursion caused by interactions of molecules and photons. The frequency excursion reflects the margin between certain two vibrational or rotational energy states, and shows the information of the molecule. Because Raman spectroscopy can provides quick, easy, reproducible, and non-destructive analysis, both qualitative and quantitative, with no sample preparation required, Raman spectroscopy has been a particularly promising technique for analyzing the characteristics and structures of molecules, especially organic ones. Now, it has a broad application in biological, chemical, environmental and industrial applications. This paper firstly introduces Sudan I dye and the Raman spectroscopy technology, and then describes its application to the Sudan I. Secondly, the fingerprint spectra of the Sudan I are respectively assigned and analyzed in detail. Finally, the conclusion that the Raman spectroscopy technology is a powerful tool to determine the Sudan I is drawn.

Li, Gang; Zhang, Guoping; Chen, Chen

2006-06-01

409

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)

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.

Peng, Hanchuan; Long, Fuhui

410

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

PubMed

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

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

2014-10-01

411

Quantitative determination of butylated hydroxyanisole, butylated hydroxytoluene, and tert-butyl hydroquinone in oils, foods, and biological fluids by high-performance liquid chromatography with fluorometric detection.  

PubMed

Concentrations of synthetic antioxidants butylated hydroxyanisole, butylated hydroxytoluene, and tert-butyl hydroquinone were quantified using a high-performance liquid chromatograph with spectrofluorometric detector. The antioxidants were separated and eluted on a reversed-phase column by gradient of a mixture of H2O/acetonitrile/acetic acid (66.5: 28.5:5, by vol) and a mixture of acetonitrile/acetic acid (95:5, vol/vol). The eluants were monitored at emission and excitation wavelengths of 310 and 280 nm, respectively. Calibration curves obtained using peak areas against concentration showed high coefficients of multiple determination (R2 > 0.99) for all antioxidants. Known concentrations of added antioxidant standards were recoverable within 98-99% from oils and over 93% from mouse blood. This method requires minimum sample extraction and purification before analysis and provides a relatively high percentage recovery. The method has been applied successfully for the measurement of antioxidant concentrations in oils, dried foods, and biological fluids. PMID:9870910

Yankah, V V; Ushio, H; Ohshima, T; Koizumi, C

1998-11-01

412

Infrared quantitative spectroscopy and planetary atmospheres  

NASA Astrophysics Data System (ADS)

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.

Flaud, J.-M.

2009-04-01

413

Direct and quantitative absorptive spectroscopy of nanowires  

E-print Network

Photonic nanostructures exhibit unique optical properties that are attractive in many different applications. However, measuring the optical properties of individual nanostructures, in particular the absorptive properties, ...

Tong, Jonathan Kien-Kwok

2012-01-01