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Intrinsic Raman spectroscopy for quantitative biological spectroscopy Part II  

PubMed Central

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

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



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



Princeton Diversity Programs in Molecular Biology and Quantitative & Computational Biology  

E-print Network

CASE STUDY Princeton Diversity Programs in Molecular Biology and Quantitative & Computational: Diversity Programs in Molecular Biology and Quantitative & Computational Biology Founded in 2007 in response: Molecular Biology (MOL), Quantitative & Computational Biology (QCB), Neuroscience (NEU), and Ecology


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



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



[Biologic artifacts in quantitative EEG].  


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

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




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...


Quantitative tunneling spectroscopy of nanocrystals  

SciTech Connect

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

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



Noise Spectroscopy Used in Biology  

NASA Astrophysics Data System (ADS)

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

Žacik, Michal


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.



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



Modeling the Effect of Polychromatic Light in Quantitative Absorbance Spectroscopy  

ERIC Educational Resources Information Center

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

Smith, Rachel; Cantrell, Kevin



Quantitative Photoacoustic Spectroscopy in the Frequency Domain  

NASA Astrophysics Data System (ADS)

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

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



(Luminescence and Raman spectroscopy for biological analysis)  

SciTech Connect

The traveler was invited to present a seminar on Immunofluorescence and Raman Fiberoptic Chemical Sensors'' at the Laboratory FOCAL of CEN-FAR, France. The traveler visited the CEN-FAR laboratories involved in laser-based spectroscopy and remote monitors and conducted scientific discussions with research staff at CEN-FAR. The traveler was also invited to present an invited lecture on Advances in Luminescence and Raman Spectroscopy for Chemical and Biological Analysis'' at the Laboratory of Molecular Photophysics and Photochemistry, University of Bordeaux, Talence, France. The traveler visited the laboratories involved in the development of luminescence techniques for the analysis of polyaromatic pollutants and related biomarkers. The traveler conducted discussions on potential research collaboration with scientists at the University of Bordeaux. The traveler was awarded a North atlantic Treaty Organization (NATO) Collaborative Grant to conduct joint research with Professor P. Viallet, head of the Laboratory of Quantitative Microfluorimetry, University of Perpignan. The traveler was involved in experimental luminescence studies of bioindicators of polyaromatic pollutants (DNA adducts, metabolites).

Vo-Dinh, Tuan.



Informatics and Quantitative Analysis in Biological Imaging  

NSDL National Science Digital Library

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

Jason Swedlow (University of Dundee; )



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

NASA Astrophysics Data System (ADS)

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

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



Quantitative Biology Colloquium Fall 2013 Point process species distribution models  

E-print Network

Quantitative Biology Colloquium ­ Fall 2013 Point process species distribution models Tuesdays 5-6 pm in Mathematics 402 The Quantitative Biology Colloquium.e., georeferenced presence data and GIS layers of climate). SDMs have been used

Watkins, Joseph C.


Effect of photobleaching on calibration model development in biological Raman spectroscopy  

E-print Network

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 ...

Barman, Ishan


Quantitative atomic spectroscopy for primary thermometry  

NASA Astrophysics Data System (ADS)

Quantitative spectroscopy has been used to measure accurately the Doppler broadening of atomic transitions in Rb85 vapor. By using a conventional platinum resistance thermometer and the Doppler thermometry technique, we were able to determine kB with a relative uncertainty of 4.1×10-4 and with a deviation of 2.7×10-4 from the expected value. Our experiment, using an effusive vapor, departs significantly from other Doppler-broadened thermometry (DBT) techniques, which rely on weakly absorbing molecules in a diffusive regime. In these circumstances, very different systematic effects such as magnetic sensitivity and optical pumping are dominant. Using the model developed recently by Stace and Luiten, we estimate the perturbation due to optical pumping of the measured kB value was less than 4×10-6. The effects of optical pumping on atomic and molecular DBT experiments is mapped over a wide range of beam size and saturation intensity, indicating possible avenues for improvement. We also compare the line-broadening mechanisms, windows of operation and detection limits of some recent DBT experiments.

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



Quantitative atomic spectroscopy for primary thermometry  

SciTech Connect

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

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



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




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...


Terahertz Spectroscopy of Biological Systems  

Microsoft Academic Search

\\u000a Following recent developments in instrumentation, the terahertz part of the electromagnetic spectrum, lying between the microwave\\u000a and infrared regions, now offers considerable potential for the study of the structure, dynamics and function of biological\\u000a systems. The energies involved in many key biological processes lie in the terahertz frequency range, such as protein conformational\\u000a changes and the collective motion of DNA

J. W. Bowen


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



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



Submillimeter wave spectroscopy of biological macromolecules  

NASA Astrophysics Data System (ADS)

The recently emergence of submillimeter-wave or terahertz (THz) spectroscopy of biological molecules has demonstrated the capability to detect low-frequency internal molecular vibrations involving the weakest hydrogen bonds of the DNA base pairs and/or non-bonded interactions. These multiple bonds, although having only ˜ 5% of the strength of covalent bonds, stabilize the structure of bio-polymers, by holding the two strands of the DNA double helix together, or polypeptides together in different secondary structure conformations. There will be a review of THz-frequency transmission (absorption) results for biological materials obtained from Fourier Transform Infrared (FTIR) spectroscopy during the last few years^1,2. Multiple resonances, due to low frequency vibrational modes within biological macromolecules, have been unambiguously demonstrated in qualitative agreement with theoretical prediction, thereby confirming the fundamental physical nature of observed resonance features. The discovery of resonance character of interaction between THz radiation and biological materials opens many possible applications for THz spectroscopy technique in biological sensing and biomedicine using multiple resonances as distinctive spectral fingerprints. However, many issues still require investigation. Kinetics of interactions with radiation at THz has not been studied and vibrational lifetimes have not been measured directly as a function of frequency. The strength of resonant modes of bio-molecules in aqueous environment and strong dependence of spectra on molecular orientation need explanation. Vibrational modes have not been assigned to specific motions within molecules. THz spectroscopy of bio-polymers makes it only in first steps. 1. T. Globus, D. Woolard, M. Bykhovskaia, B. Gelmont, L. Werbos, A. Samuels. International Journal of High Speed Electronics and Systems (IJHSES), 13, No. 4, 903-936 (2003). 2. T. Globus, T. Khromova, D. Woolard and B. Gelmont. Proceedings of SPIE Vol. 5268-2, 10-18 (2004)

Globus, Tatiana



Characterizing human pancreatic cancer precursor using quantitative tissue optical spectroscopy  

PubMed Central

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

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



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



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

E-print Network

to develop quantitative experiments on development and developmental defects induced by toxicological-cell simulations of environmental perturbations of early development integrating reaction-kinetic models cell or developmental biology, pharmacology, toxicology, cell biology, or biochemistry and experience

Menczer, Filippo


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



A transformative model for undergraduate quantitative biology education.  


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

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



An introduction to biological NMR spectroscopy.  


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

Marion, Dominique



An Introduction to Biological NMR Spectroscopy*  

PubMed Central

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

Marion, Dominique



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.



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.



Quantitative fiber-optic Raman spectroscopy for tissue Raman measurements  

NASA Astrophysics Data System (ADS)

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

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



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


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

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



Quantitative imaging strategies pave the way for testable biological concepts  

PubMed Central

In developmental biology, the accumulation of qualitative phenotypic descriptions has fueled the need for testable parsimonious hypotheses, giving a fresh impetus to quantitative strategies. As an illustration, thanks to the precise quantification of cell growth and microtubule behavior in a study published in BMC Plant Biology, Zhang and collaborators have identified sequential phases of polarized and isotropic growth in puzzle-shaped leaf epidermal cells, thus providing new clues to explore how growth coordination occurs in this tissue. PMID:21352557



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



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.



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.



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



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



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



Quantitative bioimpedance spectroscopy for the assessment of lymphoedema.  


The aim was to make bioimpedance spectroscopy (BIS) quantitative for assessment of lymphoedema. Apparent resistivity coefficients were determined for the intra- and extracellular water of arms in a control cohort of women (n = 66). These coefficients were used to predict water volumes in the arms of women with lymphoedema (n = 23) and a separate control group without lymphoedema (n = 13) and to compare these with total arm size measured by perometry. Total arm volume was highly correlated (r = 0.80-0.90) with arm fluid volumes predicted by BIS and the proportional increase in arm size predicted by BIS was not significantly different to that measured by perometry. BIS predicted that the increased volume in the women with lymphoedema was predominantly (60%) due to increase in extracellular fluid. BIS is capable of quantifying the volume increase in limb size seen in lymphoedema. PMID:19082708

Ward, L C; Czerniec, S; Kilbreath, S L



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



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


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

Microsoft Academic Search

A detailed characterisation of the performance of transmission Raman spectroscopy was performed from the standpoint of rapid quantitative analysis of pharmaceutical capsules using production relevant formulations comprising of active pharmaceutical ingredient (API) and 3 common pharmaceutical excipients. This research builds on our earlier studies that identified the unique benefits of transmission Raman spectroscopy compared to conventional Raman spectroscopy. These include

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



Quantitative laser-induced breakdown spectroscopy analysis of calcified tissue samples  

NASA Astrophysics Data System (ADS)

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

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



Toward integration: from quantitative biology to mathbio-biomath?  


In response to the call of BIO2010 for integrating quantitative skills into undergraduate biology education, 30 Howard Hughes Medical Institute (HHMI) Program Directors at the 2006 HHMI Program Directors Meeting established a consortium to investigate, implement, develop, and disseminate best practices resulting from the integration of math and biology. With the assistance of an HHMI-funded mini-grant, led by Karl Joplin of East Tennessee State University, and support in institutional HHMI grants at Emory and University of Delaware, these institutions held a series of summer institutes and workshops to document progress toward and address the challenges of implementing a more quantitative approach to undergraduate biology education. This report summarizes the results of the four summer institutes (2007-2010). The group developed four draft white papers, a wiki site, and a listserv. One major outcome of these meetings is this issue of CBE-Life Sciences Education, which resulted from proposals at our 2008 meeting and a January 2009 planning session. Many of the papers in this issue emerged from or were influenced by these meetings. PMID:20810946

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



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



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



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



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)



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.



Vibrational spectroscopy and the development of new force fields for biological molecules.  


The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy. PMID:12601796

Gerber, R B; Chaban, G M; Gregurick, S K; Brauer, B



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



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

SciTech Connect

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

Not Available



Quantitation of sulfate solubility in borosilicate glasses using Raman spectroscopy  

Microsoft Academic Search

Raman spectroscopy is used here as an innovative technique to investigate sulfate content in borosilicate glasses. Using Raman spectroscopy after having heated the material, the evolution of sulfate amounts can be followed as a function of temperature, time and chemical composition of the starting matrix. The accuracy of this technique was verified using electron probe micro analysis (EPMA), on two

M. Lenoir; A. Grandjean; S. Poissonnet; D. R. Neuville



Microcoil NMR spectroscopy: a novel tool for biological high throughput NMR spectroscopy.  


Microcoil NMR spectroscopy is based on the increase of coil sensitivity for smaller coil diameters (approximately 1/d). Microcoil NMR probes deliver a remarkable mass-based sensitivity increase (8- to 12-fold) when compared with commonly used 5-mm NMR probes. Although microcoil NMR probes are a well established analytical tool for small molecule liquid-state NMR spectroscopy, after spectroscopy only recently have microcoil NMR probes become available for biomolecular NMR spectroscopy. This chapter highlights differences between commercially available microcoil NMR probes suitable for biomolecular NMR spectroscopy. Furthermore, it provides practical guidance for the use of microcoil probes and shows direct applications for structural biology and structural genomics, such as optimal target screening and structure determination, among others. PMID:18542883

Hopson, Russell E; Peti, Wolfgang



Cavity ring-down spectroscopy for quantitative absorption measurements Piotr Zalicki and Richard N. Zare  

E-print Network

Cavity ring-down spectroscopy for quantitative absorption measurements Piotr Zalicki and Richard N; accepted 4 October 1994 We examine under what conditions cavity ring-down spectroscopy CRDS can be used characteristics provided that the cavity ring-down decay is exponential. We find that the exponential ring-down

Zare, Richard N.


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

E-print Network

Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy sulfur functionalities in natural organic matter from S K-edge XANES spectroscopy are presented-induced errors, inherent to the choice of a particular curve, are typically lower than 5% of total sulfur


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

E-print Network

Coded Aperture Raman Spectroscopy for Quantitative Measurements of Ethanol in a Tissue Phantom S. T of the Raman system, along with quantitative estimation results for ethanol at non-toxic levels in a lipid at physiological levels in aqueous humor, urine, and filtered blood serum.2­4 In highly-scattering media like blood

Pitsianis, Nikos P.


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.



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

PubMed Central

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

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



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



A rapid screening method for heavy metals in biological materials by emission spectroscopy.  


A semi-quantitative screening method for heavy metals in biological material is described. The metals are complexed with ammonium pyrrolidine dithiocarbamate, sodium diethyl dithiocarbamate and potassium sodium tartrate. The solutions are adjusted to pH 4 and then extracted into chloroform. The chloroform phase is evaporated onto a matrix mixture of lithium fluoride and graphite. The sample is analysed by direct current arc emission spectroscopy using a 3 metre grating spectrograph. The spectra are recorded on a photographic plate. The method is developed on aqueous and spiked samples and then applied to in vivo samples containing toxic levels of heavy metals. Atomic absorption spectroscopy is used to check standard concentrations and to monitor the efficiency of the extraction procedure. PMID:7237845

Blacklock, E C; Sadler, P A



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



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



Structures of Glycans Bound to Receptors from Saturation Transfer Difference (STD) NMR Spectroscopy: Quantitative Analysis by Using CORCEMA-ST.  


Glycan-receptor interactions are of fundamental relevance for a large number of biological processes, and their kinetics properties (medium/weak binding affinities) make them appropriated to be studied by ligand observed NMR techniques, among which saturation transfer difference (STD) NMR spectroscopy has been shown to be a very robust and powerful approach. The quantitative analysis of the results from a STD NMR study of a glycan-receptor interaction is essential to be able to translate the resulting spectral intensities into a 3D molecular model of the complex. This chapter describes how to carry out such a quantitative analysis by means of the Complete Relaxation and Conformational Exchange Matrix Approach for STD NMR (CORCEMA-ST), in general terms, and an example of a previous work on an antibody-glycan interaction is also shown. PMID:25753726

Enríquez-Navas, Pedro M; Guzzi, Cinzia; Muñoz-García, Juan C; Nieto, Pedro M; Angulo, Jesús



Direct and quantitative photothermal absorption spectroscopy of individual particulates  

SciTech Connect

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



Quantitative cathodoluminescence (CL) spectroscopy of minerals: possibilities and limitations  

Microsoft Academic Search

Summary  ¶The luminescence spectrum of a mineral contains complex information related to the intrinsic crystal and the defect structure.\\u000a For quantitative analysis of cathodoluminescence (CL) the spectra have to be deconvoluted by fitting and filtering procedures\\u000a to identify and measure individual peaks. Peak-width, peak-position and transition probability of the luminescence centres\\u000a are influenced by effects such as interactions within the defects

D. Habermann




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...



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...



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...


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



Quantitative analysis of thymine with surface-enhanced Raman spectroscopy and partial least squares (PLS) regression  

Microsoft Academic Search

Silver sol surface-enhanced Raman spectroscopy (SERS) was considered as a technique in the quantitative analysis of low-concentration\\u000a thymine. Because of the poor stability and reproducibility of SERS signal, a polymer of polyacrylic acid sodium was selected\\u000a as a stable medium to add into silver sol in order to obtain a surface-enhanced Raman spectroscopy signal. Assignments of\\u000a Raman shift for solid

Lei Zhang; Qingqing Li; Wei Tao; Bohao Yu; Yiping Du



Characterization of CdTe Detectors for Quantitative X-ray Spectroscopy  

Microsoft Academic Search

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

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



Quantitative CARS spectroscopy of CO2 and N2O.  


Experimental and theoretical investigations of the CARS spectroscopy of CO2(2v2) and N2O(v3) were carried out. The experimental spectra were measured in a heated test cell, and excellent agreement with the observed temperature dependences was obtained from numerical simulations. Assignments were made for all hot bands, and the role of collisional narrowing was quantified. Observed nonresonant susceptibility effects in pure N2O have made it possible to estimate the nonresonant background susceptibility for this molecule by using the resonant contribution as a reference calibration. PMID:18213316

Hall, R J; Stufflebeam, J H



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.



Quantitating metabolites in protein precipitated serum using NMR spectroscopy.  


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

Nagana Gowda, G A; Raftery, Daniel



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.



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.



Rapid qualitative and quantitative evaluation of deer antler ( Cervus elaphus) using near-infrared reflectance spectroscopy  

Microsoft Academic Search

Near-infrared (NIR) spectroscopy has been applied for both the qualitative and quantitative evaluation of the velvet deer antler. The most important parameters of determining the quality of velvet antler are the habitat (the country of origin) and ash content. Conventionally, the habitat is determined by examining the appearance of samples (by human eye), which lacks objectivity. Ash content is measured

Chang-Hee Cho; Young-Ah Woo; Hyo-Jin Kim; Young-Ja Chung; Sung-Yeup Chang; Hoeil Chung



Rapid quantitative analysis of Dimethoate pesticide using surface enhanced raman spectroscopy  

Technology Transfer Automated Retrieval System (TEKTRAN)

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


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.




Microsoft Academic Search

The ability of Raman spectroscopy combined with multivariate analysis (PLS and PCR) to quantify binary mixtures of polymorphic forms of carbamazepine was investigated. Accurate quantitative models were generated with limits of detection of less than 1%. The polymorphic behaviour of drugs is a major concern of the pharmaceutical industry as it may have considerable formulation, therapeutic, legal and commercial implications

C. J. Strachan; J. A. Zeitler; D. Pratiwi; K. C. Gordon; T. Rades


Terahertz spectroscopy for chemicals and biological sensing applications  

NASA Astrophysics Data System (ADS)

Terahertz (THz) radiation offers innovative sensing and imaging technologies that can provide information unavailable through other conventional electromagnetic techniques. With the advancement of THz technologies, THz sensing will impact a broad range of areas. This thesis focuses on the use of THz spectroscopy for sensing applications including explosives detection, pharmaceutical identification and biological characterization. Using both a THz time-domain spectroscopy (THz-TDS) system and a Fourier transform far-infrared spectrometer (FT-FIR), a THz spectral database of explosives and related compounds (ERCs) in the range of 0.1-20 THz was established. The transmission measurements show good agreement with the diffuse reflectance measurements, which are more feasible for practical applications. Density Functional Theory was employed to calculate structures and vibrational modes of several important ERCs and the calculated spectra are in good accordance with the experimental data in the 3-20 THz range. The detection and identification of the explosive RDX using diffusely reflected THz waves were also demonstrated. THz-TDS was applied successfully for pharmaceutical study, such as investigating drug interactions, as well as identifying hydrated and anhydrous drugs, based upon the intermolecular vibrational modes of drug substances. Dehydrations and complex solid state reactions of pharmaceutical materials were studied with THz-TDS and the reaction kinetics was successfully probed. These investigations have opened new avenues for using THz technologies in pharmaceutical science and industry. THz spectra of amino acids, purines and other biomolecules were recorded. Most of these solid-state biocompounds have THz spectral features in the 0.1-3.0 THz range. THz spectroscopy of solid-state proteins and bioactive protein micro suspensions in organic media was studied and their THz absorption features may reflect their collective vibrational modes which could be used to probe their functional 3D conformation states. Owing to the high sensitivity of differential THz-TDS, it was successfully used to sense the minute change of biological cell monolayers. The results point to a new way for biosensing applications via differential THz-TDS. As a powerful sensing technique, THz spectroscopy will continue to make profound contribution to the understanding of basic physics, chemistry and biology problems, as well as to the technological applications in chemical and biomedicine sensing areas.

Liu, Hai-Bo


Intramyocardial oxygen transport by quantitative diffuse reflectance spectroscopy in calves  

NASA Astrophysics Data System (ADS)

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

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



Quantitative Analysis of Panax ginseng by FT-NIR Spectroscopy  

PubMed Central

Near-infrared spectroscopy (NIRS), a rapid and efficient tool, was used to determine the total amount of nine ginsenosides in Panax ginseng. In the study, the regression models were established using multivariate regression methods with the results from conventional chemical analytical methods as reference values. The multivariate regression methods, partial least squares regression (PLSR) and principal component regression (PCR), were discussed and the PLSR was more suitable. Multiplicative scatter correction (MSC), second derivative, and Savitzky-Golay smoothing were utilized together for the spectral preprocessing. When evaluating the final model, factors such as correlation coefficient (R2) and the root mean square error of prediction (RMSEP) were considered. The final optimal results of PLSR model showed that root mean square error of prediction (RMSEP) and correlation coefficients (R2) in the calibration set were 0.159 and 0.963, respectively. The results demonstrated that the NIRS as a new method can be applied to the quality control of Ginseng Radix et Rhizoma. PMID:24883224

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



Gas-Phase Database for Quantitative Infrared Spectroscopy  

SciTech Connect

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

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



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

E-print Network

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

Zeng, Zhao-Bang


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



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



Exploration of Quantitative Scoring Metrics to Compare Systems Biology Modeling Approaches  

Microsoft Academic Search

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

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



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


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

Chew, Shirley L; Meyers, John A



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

NASA Astrophysics Data System (ADS)

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

Jiang, Dejun; Zhao, Shusen; Shen, Jingling



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.


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

NASA Astrophysics Data System (ADS)

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

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



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



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


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



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 PMID:24472558



Using Fourier transform IR spectroscopy to analyze biological materials.  


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



Quantitative analysis of trace metal ions in ice using laser-induced breakdown spectroscopy  

Microsoft Academic Search

This work reports on a simple, quick-freeze method for the quantitative analysis of trace metal ions in liquids applying the laser-induced breakdown spectroscopy (LIBS) technique. Using this procedure with calibrated samples, well-characterized linear working curves were determined for Na and Al water solutions over the 0.01–1% concentration range. This allowed detection limits of the order of ppm. In addition, optimum

J. O. Cáceres; J. Tornero López; H. H. Telle; A. González Ureña



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

Microsoft Academic Search

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

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



SHORT REVIEW Quantitative and evolutionary biology of alternative  

E-print Network

of alternative transcripts affects phenotypic plasticity and reaction norms JH Marden Department of Biology, 208 variation in AS affects plastic traits such as stress, anxiety, fear, egg production, muscle performance.1038/sj.hdy.6800904; published online 27 September 2006 Keywords: alternative transcripts; life history

Marden, James


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. PMID:25694947

Lu, Rongwen; Zhang, Qiuxiang; Zhi, Yanan



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

PubMed Central

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

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



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


Most quantitative models used in laser-induced breakdown spectroscopy (LIBS) are based on the hypothesis that laser-induced plasma approaches the state of local thermal equilibrium (LTE). However, the local equilibrium is possible only at a specific time segment during the evolution. As the populations of each energy level does not follow Boltzmann distribution in non-LTE condition, those quantitative models using single spectral line would be inaccurate. A multivariate nonlinear model, in which the LTE is not required, was proposed in this article to reduce the signal fluctuation and improve the accuracy of quantitative analysis. This multivariate nonlinear model was compared with the internal calibration model which is based on the LTE condition. The content of Mn in steel samples was determined by using the two models, respectively. A minor error and a minor relative standard deviation (RSD) were observed in multivariate nonlinear model. This result demonstrates that multivariate nonlinear model can improve measurement accuracy and repeatability. PMID:25752066

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



Biological invasions and phenotypic evolution: a quantitative genetic perspective  

Microsoft Academic Search

Among the many different components of global environmental change, biological invasions represent the one with the most long-term\\u000a ecological and evolutionary consequences, as effects are irreversible. Although the ecological impact of invasive species\\u000a has been under great scrutiny, its evolutionary aspects and consequences have remained less explored. Once established, an\\u000a important part of the success of an invasive species will

Leonardo D. Bacigalupe



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.



Online Interactive Teaching Modules Enhance Quantitative Proficiency of Introductory Biology Students  

PubMed Central

There is widespread agreement within the scientific and education communities that undergraduate biology curricula fall short in providing students with the quantitative and interdisciplinary problem-solving skills they need to obtain a deep understanding of biological phenomena and be prepared fully to contribute to future scientific inquiry. MathBench Biology Modules were designed to address these needs through a series of interactive, Web-based modules that can be used to supplement existing course content across the biological sciences curriculum. The effect of the modules was assessed in an introductory biology course at the University of Maryland. Over the course of the semester, students showed significant increases in quantitative skills that were independent of previous math course work. Students also showed increased comfort with solving quantitative problems, whether or not they ultimately arrived at the correct answer. A survey of spring 2009 graduates indicated that those who had experienced MathBench in their course work had a greater appreciation for the role of mathematics in modern biology than those who had not used MathBench. MathBench modules allow students from diverse educational backgrounds to hone their quantitative skills, preparing them for more complex mathematical approaches in upper-division courses. PMID:20810959

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



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


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

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



Fourier-Transform Raman Spectroscopy Of Biological Assemblies  

NASA Astrophysics Data System (ADS)

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

Levin, Ira W.; Lewis, E. Neil



Quantitative microanalysis of bile acids in biological samples. Collaborative study.  


The analysis of bile acids in biological samples has always presented a problem because of their complex nature and low concentration. Recently, newer analytical procedures for bile acids have become available, including enzymatic analysis, radioimmunoassay, thin-layer chromatography (TLC), gas chromatography, high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) with selected ion monitoring (SIM). However, they differ greatly with respect to specificity, sensitivity, accuracy and simplicity. On the other hand, the choice of analytical procedure differs according to the specific aims and the nature of biological samples to be analysed. These newer procedures have been compared in a double-blind fashion by distributing bile, plasma and urine samples to seven participating laboratories. GC-MS-SIM was found to be the most sensitive and reliable, but it requires other procedures for preliminary clean-up and fractionation steps. Enzymatic analysis is simple and gives small analytical errors but tends to over-estimate plasma bile acids. Radioimmunoassay gives variable results but is useful as a screening procedure for large numbers of plasma samples. TLC gives reliable results for biliary bile acids in experienced hands, except for differentiation between conjugated dihydroxycholanoic acids. HPLC, whether using derivatization or with fixed 3 alpha-hydroxy steroid dehydrogenase detection, is suitable for the analysis of major bile acids in normal human serum but not for the identification of unknown minor peaks. PMID:3243854

Nakayama, F



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



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



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


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

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



Quantitative sum-frequency generation vibrational spectroscopy of molecular surfaces and interfaces: lineshape, polarization, and orientation.  


Sum-frequency generation vibrational spectroscopy (SFG-VS) can provide detailed information and understanding of the molecular composition, interactions, and orientational and conformational structure of surfaces and interfaces through quantitative measurement and analysis. In this review, we present the current status of and discuss important recent developments in the measurement of intrinsic SFG spectral lineshapes and formulations for polarization measurements and orientational analysis of SFG-VS spectra. The focus of this review is to present a coherent description of SFG-VS and discuss the main concepts and issues that can help advance this technique as a quantitative analytical research tool for revealing the chemistry and physics of complex molecular surfaces and interfaces. PMID:25493712

Wang, Hong-Fei; Velarde, Luis; Gan, Wei; Fu, Li



13C NMR Spectroscopy for the Quantitative Determination of Compound Ratios and Polymer End Groups  

PubMed Central

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



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

NASA Astrophysics Data System (ADS)

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

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



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: Grading: Regular grades are awarded

Wang, Quidong


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



Quantitative analysis of oils and fats by Fourier transform Raman spectroscopy  

NASA Astrophysics Data System (ADS)

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

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


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

SciTech Connect

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

Cobley, R. J.; Brown, R. A.; Barnett, C. J.; Maffeis, T. G. G.; Penny, M. W. [Multidisciplinary Nanotechnology Centre, College of Engineering, Swansea University, Singleton Park, Swansea SA2 8PP (United Kingdom)] [Multidisciplinary Nanotechnology Centre, College of Engineering, Swansea University, Singleton Park, Swansea SA2 8PP (United Kingdom)



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.



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



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: [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)



Uv Spectroscopy in Monitoring of Biological Treatment of Washing Waters from Aromatic Polyamide Fibre Production  

Microsoft Academic Search

Aromatic polyamide fibre production wastes — aqueous solutions consisting of a mixture of dimethylacetamide and isobutyl alcohol, initial and treated with microorganisms for different times — were analyzed. Monitoring solutions with absorption in the UV region and COD allowed following biological treatment and modeling its components of the solutions. The possibility of monitoring biological treatment by UV spectroscopy was demonstrated.

A. G. Venediktova



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



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.



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.



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

SciTech Connect

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

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



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


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



Cold Spring Harbor symposia on quantitative biology: Volume 49, Recombination at the DNA level  

SciTech Connect

This volume contains full papers prepared by the participants to the 1984 Cold Springs Harbor Symposia on Quantitative Biology. This year's theme is entitled Recombination at the DNA level. The volume consists of 93 articles grouped into subject areas entitled chromosome mechanics, yeast systems, mammalian homologous recombination, transposons, mu, plant transposons/T4 recombination, topoisomerase, resolvase and gyrase, Escherichia coli general recombination, RecA, repair, leukaryotic enzymes, integration and excision of bacteriophage, site-specific recombination, and recombination in vitro.

Not Available



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

NASA Astrophysics Data System (ADS)

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

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



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



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


(1)H NMR spectroscopy was used as a method for quantitative analysis of sesquiterpene lactones present in a crude lactone fraction isolated from Arnica montana. Eight main components - tigloyl-, methacryloyl-, isobutyryl- and 2-methylbutyryl-esters of helenalin (H) and 11?,13-dihydrohelenalin (DH) were identified in the studied sample. The method allows the determination of the total amount of sesquiterpene lactones and the quantity of both type helenalin and 11?,13-dihydrohelenalin esters separately. Furthermore, 6-O-tigloylhelenalin (HT, 1), 6-O-methacryloylhelenalin (HM, 2), 6-O-tigloyl-11?,13-dihydrohelenalin (DHT, 5), and 6-O-methacryloyl-11?,13-dihydrohelenalin (DHM, 6) were quantified as individual components. PMID:20837387

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



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

NASA Astrophysics Data System (ADS)

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

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



[Quantitative analysis of slag by calibration-free laser-induced breakdown spectroscopy].  


Calibration-free laser induced breakdown spectroscopy (CF-LIBS) was employed for the quantitative analysis of slag. Nd:YAG laser ablation was performed in air. The laser-induced plasma emission was measured by an Echelle spectrometer equipped with an ICCD. The plasma temperature and electron number density were determined from Boltzmann plots and a Ca I line width, respectively. The assumption of local thermal equilibrium was validated by the Ne criterion. The concentration of oxides was obtained from the concentration of elements by using stoichiometric relation. The calculated oxide concentrations were compared with those obtained by XRF. The relative errors of major elements were less than 15%. The results indicate that this method can be employed for the analysis of major elements in multi-component complex materials without certified reference. PMID:22295779

Chen, Xing-long; Dong, Feng-zhong; Wang, Qi; Yu, Rong-hua; Liang, Yun-xian; Wang, Jing-ge; Yang, Yang; Ni, Zhi-bo; Xu, Ming-ming; Wu, Bian



Quantitating membrane bleb stiffness using AFM force spectroscopy and an optical sideview setup.  


AFM-based force spectroscopy in combination with optical microscopy is a powerful tool for investigating cell mechanics and adhesion on the single cell level. However, standard setups featuring an AFM mounted on an inverted light microscope only provide a bottom view of cell and AFM cantilever but cannot visualize vertical cell shape changes, for instance occurring during motile membrane blebbing. Here, we have integrated a mirror-based sideview system to monitor cell shape changes resulting from motile bleb behavior of Xenopus cranial neural crest (CNC) cells during AFM elasticity and adhesion measurements. Using the sideview setup, we quantitatively investigate mechanical changes associated with bleb formation and compared cell elasticity values recorded during membrane bleb and non-bleb events. Bleb protrusions displayed significantly lower stiffness compared to the non-blebbing membrane in the same cell. Bleb stiffness values were comparable to values obtained from blebbistatin-treated cells, consistent with the absence of a functional actomyosin network in bleb protrusions. Furthermore, we show that membrane blebs forming within the cell-cell contact zone have a detrimental effect on cell-cell adhesion forces, suggesting that mechanical changes associated with bleb protrusions promote cell-cell detachment or prevent adhesion reinforcement. Incorporating a sideview setup into an AFM platform therefore provides a new tool to correlate changes in cell morphology with results from force spectroscopy experiments. PMID:25710133

Gonnermann, Carina; Huang, Chaolie; Becker, Sarah F; Stamov, Dimitar R; Wedlich, Doris; Kashef, Jubin; Franz, Clemens M



Characterization of geometrical factors for quantitative angle-resolved photoelectron spectroscopy  

SciTech Connect

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

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



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


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



Quantitative Characterization of the Colloidal Stability of Metallic Nanoparticles Using UV-vis Absorbance Spectroscopy.  


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

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



Universally applicable model for the quantitative determination of lake sediment composition using fourier transform infrared spectroscopy.  


Fourier transform infrared spectroscopy (FTIRS) can provide detailed information on organic and minerogenic constituents of sediment records. Based on a large number of sediment samples of varying age (0-340,000 yrs) and from very diverse lake settings in Antarctica, Argentina, Canada, Macedonia/Albania, Siberia, and Sweden, we have developed universally applicable calibration models for the quantitative determination of biogenic silica (BSi; n = 816), total inorganic carbon (TIC; n = 879), and total organic carbon (TOC; n = 3164) using FTIRS. These models are based on the differential absorbance of infrared radiation at specific wavelengths with varying concentrations of individual parameters, due to molecular vibrations associated with each parameter. The calibration models have low prediction errors and the predicted values are highly correlated with conventionally measured values (R = 0.94-0.99). Robustness tests indicate the accuracy of the newly developed FTIRS calibration models is similar to that of conventional geochemical analyses. Consequently FTIRS offers a useful and rapid alternative to conventional analyses for the quantitative determination of BSi, TIC, and TOC. The rapidity, cost-effectiveness, and small sample size required enables FTIRS determination of geochemical properties to be undertaken at higher resolutions than would otherwise be possible with the same resource allocation, thus providing crucial sedimentological information for climatic and environmental reconstructions. PMID:21882858

Rosén, Peter; Vogel, Hendrik; Cunningham, Laura; Hahn, Annette; Hausmann, Sonja; Pienitz, Reinhard; Zolitschka, Bernd; Wagner, Bernd; Persson, Per



A Simple and Highly Sensitive Method for Magnetic Nanoparticle Quantitation Using 1H-NMR Spectroscopy  

PubMed Central

Iron oxide superparamagnetic nanoparticles (SPIONs) have drawn significant attention because of their potential impact on medical diagnosis and therapy. However, the difficulty of achieving reliable and standardized quantification of these nanoparticles has limited the uniform study of nanoparticle systems. Current measurement techniques have limited sensitivity, and are sophisticated and subject to individual instrumental settings. Here, a characterization method using proton nuclear magnetic resonance (1H-NMR) spectroscopy is presented that can quantify SPIONs regardless of surface modification. In addition to routine quantification of SPIONs during nanoparticle development, the method can also be used with in vitro nanoparticle assays and potentially with tissue samples for biodistribution studies. Specifically, measurement of water relaxivity shifts (R1 or R2) of dissolved SPION samples is correlated with nanoparticle concentration. Unmodified and dextran- and poly(ethylene glycol)-coated SPIONs gave linear correlations between SPION concentration and R1 and R2 relaxivities over five orders of magnitude, to below 10 ppb iron. Quantification of SPION concentration was also demonstrated in the presence of RAW 264.7 macrophage cells. A linear correlation between the SPION concentration and relaxivities was observed to <10 ng Fe/mL. This method is a rapid and inexpensive approach for quantitation of SPIONs and exhibits a number of advantages over many of the current methods for quantitative SPION analysis. PMID:19883608

Gunn, Jonathan; Paranji, Rajan K.; Zhang, Miqin



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

SciTech Connect

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

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



Structure Determination of Biological Macromolecules in Solution Using NMR spectroscopy  

Microsoft Academic Search

Abstract A detailed understanding of the function of a biological macromolecule,requires knowledge,of its three-dimensional structure. Most atomic-resolution structures of biological macromolecules have been solved either by x-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) in solution. This review surveys the method,of NMR structure determination. First a brief introduction to NMR and its basic concepts is presented. The

Gerhard Wider


Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications.  


This review describes the vibrational self-consistent field (VSCF) method and its other variants for computing anharmonic vibrational spectroscopy of biological molecules. The superiority and limitations of this algorithm are discussed with examples. The spectroscopic accuracy of the VSCF method is compared with experimental results and other available state-of-the-art algorithms for various biologically important systems. For large biological molecules with many vibrational modes, the scaling of computational effort is investigated. The accuracy of the vibrational spectra of biological molecules using the VSCF approach for different electronic structure methods is also assessed. Finally, a few open problems and challenges in this field are discussed. PMID:23677257

Roy, Tapta Kanchan; Gerber, R Benny



Quantitative measurement of Au and Fe in ferromagnetic nanoparticles with Laser Induced Breakdown Spectroscopy using a polymer-based gel matrix  

NASA Astrophysics Data System (ADS)

The medical applications of nanomaterials require substantial changes in the research and development stage, such as the introduction of new processes and methods, and adequate modifications of the national and international laws on the medical product registration. To accomplish this, proper parameterizations of nano-scaled products need to be developed and implemented, accompanied by suitable measuring methods. The introduction of metallic particles to medical practices requires the precise, quantitative evaluation of the production process and later quantification and characterization of the nanoparticles in biological matrices for the bioavailability and biodistribution evaluation. In order to address these issues we propose a method for the quantitative analysis of the metallic nanoparticles composition by Laser Induced Breakdown Spectroscopy (LIBS). Au/Fe ferro-magnetic nanoparticles were used to evaluate the method applicability. Since the powder form of nanoparticles spatters upon laser ablation, first we had to develop fast, convenient and quantitative method for the nano-powdered sample preparation. The proposed method is based on the polymer gelation of nanopowders or their water suspensions. It has been shown that nanopowders compositional changes throughout the production process, along with their final characterization, can be reliable performed with LIBS technique. The quantitative values obtained were successfully correlated with those derived with ICP technique.

Borowik, T.; Przyby?o, M.; Pala, K.; Otlewski, J.; Langner, M.



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



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

Microsoft Academic Search

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

Walid Tawfik; Ali Saafan


Determination of adsorption isotherm of species adsorbed on roughened silver electrodes from in situ quantitative surface enhanced Raman spectroscopy  

Microsoft Academic Search

In situ surface enhanced Raman spectroscopy (SERS) has been used to determine quantitatively coverages of hemin and\\/or its reduced counterpart irreversibly adsorbed on roughened silver electrodes as a function of the applied potential in aqueous electrolytes. Analyses of spectral data recorded at pH 3 over a wide voltage region made it possible to obtain potential dependent adsorption isotherms, from which

Wen-Bin Cai; Ionel C Stefan; Daniel A Scherson



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



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



The Lightning Rod Model: Quantitative Near-Field Spectroscopy for Extraction of Nano-Resolved Optical Constants  

E-print Network

Near-field infrared spectroscopy by elastic scattering of light from a probe tip resolves optical contrasts in materials at dramatically sub-wavelength scales across a broad energy range, with the potential for chemical identification at the nanoscale. However, current models of the probe-sample near-field interaction 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, which demonstrates superb predictive agreement with newly presented infrared near-field measurements of both SiO2 thin films and SiC, measured by tunable quantum cascade laser and nanoscale Fourier transform infrared (nanoFTIR) spectroscopy. We discuss the role of probe geometry, field retardation, and surface mode dispersion in shaping the measured near-field response. This treatment offers a route to quantit...

McLeod, Alexander S; Goldflam, M D; Gainsforth, Zack; Dominguez, Gerardo; Thiemens, Mark; Fogler, Michael M; Basov, D N



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


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



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


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



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

NASA Astrophysics Data System (ADS)

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

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



Development of a Univariate Membrane-Based Mid-Infrared Method for Protein Quantitation and Total Lipid Content Analysis of Biological Samples  

PubMed Central

Biological samples present a range of complexities from homogeneous purified protein to multicomponent mixtures. Accurate qualification of such samples is paramount to downstream applications. We describe the development of an MIR spectroscopy-based analytical method offering simultaneous protein quantitation (0.25–5?mg/mL) and analysis of total lipid or detergent species, as well as the identification of other biomolecules present in biological samples. The method utilizes a hydrophilic PTFE membrane engineered for presentation of aqueous samples in a dried format compatible with fast infrared analysis. Unlike classical quantification techniques, the reported method is amino acid sequence independent and thus applicable to complex samples of unknown composition. By comparison to existing platforms, this MIR-based method enables direct quantification using minimal sample volume (2?µL); it is well-suited where repeat access and limited sample size are critical parameters. Further, accurate results can be derived without specialized training or knowledge of IR spectroscopy. Overall, the simplified application and analysis system provides a more cost-effective alternative to high-throughput IR systems for research laboratories with minimal throughput demands. In summary, the MIR-based system provides a viable alternative to current protein quantitation methods; it also uniquely offers simultaneous qualification of other components, notably lipids and detergents. PMID:25371845

Cappione, Amedeo; Lento, Joseph; Chernokalskaya, Elena



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



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.



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

NASA Astrophysics Data System (ADS)

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

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



Quantitative Characterization of Biological Liquids for Third-Harmonic Generation Microscopy  

PubMed Central

Third-harmonic generation (THG) microscopy provides images of unstained biological samples based on spatial variations in third-order nonlinear susceptibility, refractive index, and dispersion. In this study, we establish quantitative values for the third-order nonlinear susceptibilities of several solvents (water, ethanol, glycerol), physiological aqueous (ions, amino acids, polypeptides, bovine serum albumin, glucose) and lipid (triglycerides, cholesterol) solutions as a function of solute concentration in the 1.05–1.25 ?m excitation range. We use these data in conjunction with imaging experiments to show that THG imaging with ?1.2 ?m excitation lacks specificity and sensitivity to detect physiological ion concentration changes, and that nonaqueous structures such as lipid bodies provide a more robust source of signal. Finally, we illustrate the impact of index-matching liquids in THG images. These data provide a basis for interpreting biological THG images and for developing additional applications. PMID:17085492

Débarre, Delphine; Beaurepaire, Emmanuel



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




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

ERIC Educational Resources Information Center

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

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



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.



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.



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

NASA Astrophysics Data System (ADS)

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

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



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


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

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



Elastic photoelectron-scattering effects in quantitative X-ray photoelectron spectroscopy  

NASA Astrophysics Data System (ADS)

We present improved formulae for the correction parameters Qx and ?eff that are used to account for elastic scattering of photoelectrons in quantitative X-ray photoelectron spectroscopy (XPS). The new formulae are based on new Monte Carlo simulations for 584 photoelectrons in 39 elemental solids that could be excited by Mg K? and Al K? X-rays in 315 different XPS configurations. The new simulations differed from similar earlier calculations in that differential elastic-scattering cross sections calculated from the Dirac-Hartree-Fock potential were utilized rather than those from the Thomas-Fermi-Dirac potential, a smaller analyzer acceptance angle was chosen, and the number of trajectories in each simulation was an order of magnitude larger. New values of Qx and ?eff were obtained for each photoelectron line, each X-ray source, and each XPS configuration. These Qx and ?eff values could be fitted to simple two-parameter expressions, each a function of the single-scattering albedo and the photoelectron emission angle. Values of Qx from the new predictive formula differed from the previous expression by less than 1%. Larger deviations in the values of ?eff, up to 2.5%, were found from the new fit to the ?eff parameter. The new expressions for Qx and ?eff provide a convenient means for correction of elastic-scattering effects in XPS.

Jablonski, A.; Powell, C. J.



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

PubMed Central

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

Alger, Jeffry R.



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

NASA Astrophysics Data System (ADS)

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

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



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

SciTech Connect

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

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



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


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

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



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

NASA Astrophysics Data System (ADS)

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

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



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



Random matrix theory in biological nuclear magnetic resonance spectroscopy.  

PubMed Central

The statistical theory of energy levels or random matrix theory is presented in the context of the analysis of chemical shifts of nuclear magnetic resonance (NMR) spectra of large biological systems. Distribution functions for the spacing between nearest-neighbor energy levels are discussed for uncorrelated, correlated, and random superposition of correlated energy levels. Application of this approach to the NMR spectra of a vitamin, an antibiotic, and a protein demonstrates the state of correlation of an ensemble of energy levels that characterizes each system. The detection of coherent and dissipative structures in proteins becomes feasible with this statistical spectroscopic technique. PMID:6478032

Lacelle, S



Quantitation of aliphatic suberin in Quercus suber L. cork by FTIR spectroscopy and solid-state (13)C-NMR spectroscopy.  


This work determined that the percentage of suberin in cork may be found by solid-state (13)C cross polarization/magic angle spinning (CP/MAS) NMR spectroscopy and by FTIR with photoacoustic detection (FTIR-PAS) spectroscopy. A linear relationship is found between the suberin content measured through CP/MAS spectral areas and that measured gravimetrically. Furthermore, application of a partial least squares (PLS1) regression model to the NMR and gravimetric data sets clearly correlates the two sets, enabling suberin quantification with 90% precision. Suberin quantitation by FTIR-PAS spectroscopy is also achieved by a PLS1 regression model, giving 90% accurate estimates of the percentage of suberin in cork. Therefore, (13)C-CP/MAS NMR and FTIR-PAS proved to be useful and accurate noninvasive techniques to quantify suberin in cork, thus avoiding the traditional time consuming and destructive chemical methods. PMID:11054654

Lopes, M H; Neto, C P; Barros, A S; Rutledge, D; Delgadillo, I; Gil, A M



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


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

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



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

NASA Astrophysics Data System (ADS)

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

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



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

PubMed Central

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



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


NIR Raman spectroscopy in medicine and biology: results and aspects  

NASA Astrophysics Data System (ADS)

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

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



Fluorescence correlation spectroscopy in biology, chemistry, and medicine.  


This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science. PMID:21639831

Perevoshchikova, I V; Kotova, E A; Antonenko, Y N



Quantitative skin color measurements in acanthosis nigricans patients: colorimetry and diffuse reflectance spectroscopy.  


Tristimulus colorimetry and diffuse reflectance spectroscopy (DRS) are white-light skin reflectance techniques used to measure the intensity of skin pigmentation. The tristimulus colorimeter is an instrument that measures a perceived color and the DRS instrument measures biological chromophores of the skin, including oxy- and deoxyhemoglobin, melanin and scattering. Data gathered from these tools can be used to understand morphological changes induced in skin chromophores due to conditions of the skin or their treatments. The purpose of this study was to evaluate the use of these two instruments in color measurements of acanthosis nigricans (AN) lesions. Eight patients with hyperinsulinemia and clinically diagnosable AN were seen monthly. Skin pigmentation was measured at three sites: the inner forearm, the medial aspect of the posterior neck, and anterior neck unaffected by AN. Of the three, measured tristimulus L*a*b* color parameters, the luminosity parameter L* was found to most reliably distinguish lesion from normally pigmented skin. The DRS instrument was able to characterize a lesion on the basis of the calculated melanin concentration, though melanin is a weak indicator of skin change and not a reliable measure to be used independently. Calculated oxyhemoglobin and deoxyhemoglobin concentrations were not found to be reliable indicators of AN. Tristimulus colorimetry may provide reliable methods for respectively quantifying and characterizing the objective color change in AN, while DRS may be useful in characterizing changes in skin melanin content associated with this skin condition. PMID:23017175

Pattamadilok, Bensachee; Devpura, Suneetha; Syed, Zain U; Agbai, Oma N; Vemulapalli, Pranita; Henderson, Marsha; Rehse, Steven J; Mahmoud, Bassel H; Lim, Henry W; Naik, Ratna; Hamzavi, Iltefat H



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.



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


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

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



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

SciTech Connect

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

Robert P. Lucht



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

NASA Astrophysics Data System (ADS)

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

Reichardt, Thomas Andrew


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

NASA Astrophysics Data System (ADS)

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

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



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

SciTech Connect

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

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



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.



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


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

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



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



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


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



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


This paper describes a high-performance liquid chromatographic method for the assay of quinfamide and its main metabolite, 1-(dichloroacetyl)-1,2,3,4,-tetrahydro-6-quinolinol, in plasma, urine and feces. It requires 1 ml of biological fluid, an extraction using Sep-Pack cartridges and acetonitrile for drug elution. Analysis was performed on a CN column (5 microm) using water-acetonitrile-methanol (40:50:10) as a mobile phase at 269 nm. Results showed that the assay was linear in the range between 0.08 and 2.0 microg/ml. The limit of quantitation was 0.08 microg/ml. Maximum assay coefficient of variation was 14%. Recovery obtained in plasma, urine and feces ranged from 82% to 98%. PMID:11076065

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



GeLC-MRM quantitation of mutant KRAS oncoprotein in complex biological samples  

PubMed Central

Tumor-derived mutant KRAS (v-Ki-ras-2 Kirsten rat sarcoma viral oncogene) oncoprotein is a critical driver of cancer phenotypes and a potential biomarker for many epithelial cancers. Targeted mass spectrometry analysis by multiple reaction monitoring (MRM) enables selective detection and quantitation of wild-type and mutant KRAS proteins in complex biological samples. A recently described immunoprecipitation approach (Proc. Nat. Acad. Sci. 2011, 108, 2444–2449) can be used to enrich KRAS for MRM analysis, but requires large protein inputs (2–4 mg). Here we describe sodium dodecyl sulfate-polyacrylamide gel electrophoresis-based enrichment of KRAS in a low molecular weight (20 –25 kDa) protein fraction prior to MRM analysis (GeLC-MRM). This approach reduces background proteome complexity, thus allowing mutant KRAS to be reliably quantified in low protein inputs (5–50 ?g). GeLC-MRM detected KRAS mutant variants (G12D, G13D, G12V, G12S) in a panel of cancer cell lines. GeLC-MRM-analysis of wild-type and mutant was linear with respect to protein input and showed low variability across process replicates (CV = 14%). Concomitant analysis of a peptide from the highly similar HRAS and NRAS proteins enabled correction of KRAS-targeted measurements for contributions from these other proteins. KRAS peptides were also quantified in fluid from benign pancreatic cysts and pancreatic cancers at concentrations from 0.08 – 1.1 fmol/?g protein. GeLC-MRM provides a robust, sensitive approach to quantitation of mutant proteins in complex biological samples. PMID:22671702

Halvey, Patrick J.; Ferrone, Cristina R.; Liebler, Daniel C.



High-resolution mass spectrometry for integrated qualitative and quantitative analysis of pharmaceuticals in biological matrices.  


Quantitative and qualitative high-resolution (HR) dependent and independent acquisition schemes on a QqTOF MS (with resolving power 20,000-40,000) were investigated for the analysis of pharmaceutical compounds in biological fluids. High-resolution selected reaction monitoring (HR-SRM) was found to be linear over three orders of magnitude for quantitative analysis of paracetamol in human plasma, offering a real alternative to triple quadrupole LC-SRM/MS. Metabolic stability of talinolol in microsomes was characterized by use of three different acquisition schemes: (i) information-dependent acquisition (IDA) with a TOF MS experiment as survey scan and product-ion scan as dependent scan; (ii) MS(ALL) by collecting TOF mass spectra with and without fragmentation by alternating the collision energy of the collision cell between a low (i.e., 10 eV) and high setting (i.e., 40 eV); and (iii) a novel independent acquisition mode referred to as "sequential window acquisition of all theoretical fragment-ion spectra" (SWATH) or "global precursor ions scan mode" (GPS) in which sequential precursor ions windows (typically 20 u) are used to collect the same spectrum precursor and fragment ions using a collision energy range. SWATH or GPS was found to be superior to IDA or MS(ALL) in combination with UHPLC for qualitative analysis but requires a rapidly acquiring mass spectrometer. Finally, the GPS concept was used for QUAL/QUAN analysis (i.e. integration of qualitative and quantitative analysis) of bosentan and its metabolites in urine over a concentration range from 5 to 2,500 ng mL(-1). PMID:22203371

Hopfgartner, Gérard; Tonoli, David; Varesio, Emmanuel



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



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



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

Microsoft Academic Search

Identification of glyphosate in four cases of poisoning, using nuclear magnetic resonance spectroscopy of biological fluids is reported. It has been performed by using a combination of 1H and 31P NMR analyses. Characterization of the N-(phosphonomethyl) glycine herbicide was achieved by chemical shift considerations and coupling constant patterns: CH2?(P) presents specific resonance at 3.12ppm and appears as a doublet with

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



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


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



Quantitative changes in sets of proteins as markers of biological response  

SciTech Connect

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

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



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.



High volume injections of biological samples for sensitive metabolite profiling and quantitation.  


An online preconcentration approach was developed allowing the injection of very high volumes of biological samples, thereby greatly increasing sensitivity while maintaining LC resolution. The approach was applied to the analysis of radioactive samples from both in vitro and in vivo metabolism studies where typically the concentration of radioactivity given is often limited, while sample volume is usually not. The described online preconcentration approach reduces sample preparation and, therefore, also the risk for degradation and recovery issues often seen with offline preconcentration methods. In addition to facilitating the identification and profiling of low level metabolites within a sample, the described approach also provides robust quantitative analysis of samples derived from a range of biological matrices. The application of this approach is illustrated on real life samples from different matrices and containing drugs and metabolites with a wide variety in polarity, more specifically the analysis of extracts derived from an in vitro hepatocyte incubation, 36mL of blood/acetonitrile (1/1, v/v; 28dpm/mL) and 72mL of urine/methanol (9/1, v/v; 208dpm/mL). PMID:25465008

Koppen, Valerie; Jones, Russell; Bockx, Marc; Cuyckens, Filip



Gas chromatographic-mass spectrometric quantitation of theophylline and its metabolites in biological fluids.  


In premature infants, theophylline is converted to caffeine, and the biological half-life is prolonged. To assess the metabolic alterations of theophylline during development of premature infants, a sensitive and simple method was developed which quantitated all theophylline metabolites in plasma, urine, and red blood cells. Theophylline and its metabolites in the sample were converted to the N-propyl derivative using n-propyl iodide in dimethylformamide with potassium carbonate catalysis and were analyzed under isothermal conditions on a gas chromatograph-mass spectrometer with a 3% methylsilicone-phenylsilicone column. Deuterated caffeine (caffeine-d3) was used as the internal standard. A selected ion-monitoring technique, together with 70-eV electron impact ionization mode, was used. The ion current ratios between caffeine-d3 (m/z 197) and caffeine (m/z 194), theophylline (m/z 222), 3-methylxanthine (m/z 250), 1,3-dimethyluric acid (m/z 280), and 1-methyluric acid (m/z 308) were monitored. The total analysis time was 12 min with a detection limit ranging from 500 pg to 10 ng, depending on the metabolites. With this sensitivity, sample sizes of 50-100 microliters of plasma and 0.5 ml of urine were sufficient for the analysis of all theophylline metabolites. The coefficient of variation of this method was less than 5% for the analysis of biological samples. PMID:6864499

Tserng, K Y



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

NASA Astrophysics Data System (ADS)

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

Wan, Boyong



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

NASA Astrophysics Data System (ADS)

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

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



Near- and Mid-Infrared Reflectance Spectroscopy for the Quantitative and Qualitative Analysis of Agricultural Products  

Technology Transfer Automated Retrieval System (TEKTRAN)

For several decades near-infrared diffuse reflectance spectroscopy (NIRS) has been used to determine the composition of a variety of agricultural products. More recently, diffuse reflectance Fourier transform mid-infrared spectroscopy (DRIFTS) has similarly been shown to be able to determine the co...


Quantitative femtosecond charge transfer dynamics at organic/electrode interfaces studied by core-hole clock spectroscopy.  


Organic semiconductor materials have important applications in organic electronics and other novel hybrid devices. In these devices, the transport of charge carriers across the interfaces between organic molecules and electrodes plays an important role in determining the device performance. Charge transfer dynamics at the organic/electrode interface usually occurs at the several femtoseconds timescale, and quantitative charge transfer dynamics data can been inferred using synchrotron-based core-hole clock (CHC) spectroscopy. In this research news, we have reviewed recent progress in the applications of CHC spectroscopy on the quantitative characterization of charge transfer dynamics at organic/electrode interfaces. By examining charge transfer dynamics at different types of interface, from weakly interacting van der Waals-type interfaces to interfaces with strong covalent bonds, we discuss a few factors that have been found to affect the charge transfer dynamics. We also review the application of CHC spectroscopy to quantify through-bonds and through-space charge transport in organic molecules. PMID:24692009

Cao, Liang; Gao, Xing-Yu; Wee, Andrew T S; Qi, Dong-Chen



Detecting high-grade squamous intraepithelial lesions in the cervix with quantitative spectroscopy and per-patient normalization  

PubMed Central

This study develops a spectroscopic algorithm for detection of cervical high grade squamous intraepithelial lesions (HSILs). We collected reflectance and fluorescence spectra with the quantitative spectroscopy probe to measure nine spectroscopic parameters from 43 patients undergoing standard colposcopy with directed biopsy. We found that there is improved accuracy for distinguishing HSIL from non-HSIL (low grade SIL and normal tissue) when we “normalized” spectroscopy parameters by dividing the values extracted from each clinically determined suspicious site by the corresponding value extracted from a clinically normal squamous site from the same patient. The “normalized” scattering parameter (A) at 700nm, best distinguished HSIL from non-HSIL with sensitivity and specificity of 89% and 79% suggesting that a simple, monochromatic instrument measuring only A may accurately detect HSIL. PMID:22025992

Mirkovic, Jelena; Lau, Condon; McGee, Sasha; Crum, Christopher; Badizadegan, Kamran; Feld, Michael; Stier, Elizabeth



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


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

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



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


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

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



Qualitative and quantitative analysis of oxytetracycline by near-infrared spectroscopy  

Microsoft Academic Search

Near-infrared (NIR) spectroscopy, in combination with chemometrics, enable the analysis of raw materials without time-consuming sample preparation methods. The aim of our work was to estimate critical parameters in the analytical specification of oxytetracycline, and consequently the development of a method for quantification and qualification of these parameters by NIR spectroscopy. A Karl Fischer (K.F.) titration to determine the water

Nataša Smola; Uroš Urleb



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

NASA Astrophysics Data System (ADS)

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

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



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


It is important to monitor quality of tobacco during the production of cigarette. Therefore, in order to scientifically control the tobacco raw material and guarantee the cigarette quality, fast and accurate determination routine chemical of constituents of tobacco, including the total sugar, reducing sugar, Nicotine, the total nitrogen and so on, is needed. In this study, 50 samples of tobacco from different cultivation areas were surveyed by near-infrared (NIR) spectroscopy, and the spectral differences provided enough quantitative analysis information for the tobacco. Partial least squares regression (PLSR), artificial neural network (ANN), and support vector machine (SVM), were applied. The quantitative analysis models of 50 tobacco samples were studied comparatively in this experiment using PLSR, ANN, radial basis function (RBF) SVM regression, and the parameters of the models were also discussed. The spectrum variables of 50 samples had been compressed through the wavelet transformation technology before the models were established. The best experimental results were obtained using the (RBF) SVM regression with gamma=1.5, 1.3, 0.9, and 0.1, separately corresponds to total sugar, reducing sugar, Nicotine, and total nitrogen, respectively. Finally, compared with the back propagation (BP-ANN) and PLSR approach, SVM algorithm showed its excellent generalization for quantitative analysis results, while the number of samples for establishing the model is smaller. The overall results show that NIR spectroscopy combined with SVM can be efficiently utilized for rapid and accurate analysis of routine chemical compositions in tobacco. Simultaneously, the research can serve as the technical support and the foundation of quantitative analysis of other NIR applications. PMID:18538628

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



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.



A fresh look at the validity of the diffusion approximation for modeling fluorescence spectroscopy in biological tissue.  


Fluorescence has become a widely used technique for applications in noninvasive diagnostic tissue spectroscopy. The standard model used for characterizing fluorescence photon transport in biological tissue is based on the diffusion approximation. On the premise that the total energy of excitation and fluorescent photon flows must be conserved, we derive the widely used diffusion equations in fluorescence spectroscopy and show that there must be an additional term to account for the transport of fluorescent photons. The significance of this additional term in modeling fluorescence spectroscopy in biological tissue is assessed. PMID:23366185

Handapangoda, Chintha Chamalie; Premaratne, Malin; Nahavandi, Saeid



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


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

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



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

PubMed Central

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

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



Chalcogenide glass fibers used for in situ infrared spectroscopy in biology and medicine  

NASA Astrophysics Data System (ADS)

Chalcogenide glass optical fibers possess very low optical losses in the middle infrared range from 2 to 12 mm. They were used to implement remote infrared spectroscopy, known as Fiber Evanescent Wave Spectroscopy (FEWS). Due to their hydrophobic behavior, such sensor is especially suitable for application in biology and medicine where water is a nuisance to detect relevant information. Moreover, the design of the sensor using tapered fibers enables to improve the signal to noise ratio. Then, once coupled with unsupervised analysis technique such as Principle Component Analysis (PCA), it has been shown that this tool is efficient to differentiate between obese and control mice by recording their serum FEWS spectra. The same method has been carried out to detect in situ the both phenotypes of a bacterial culture.

Keirsse, Julie; Bureau, Bruno; Boussard-Pledel, Catherine; Leroyer, P.; Ropert, M.; Dupont, Virginie; Anne, Marie L.; Ribault, C.; Sire, Olivier; Loreal, Olivier; Adam, Jean Luc



ATR-FTIR spectroscopy as a tool to probe surface adsorption on nanoparticles at the liquid-solid interface in environmentally and biologically relevant media.  


Given the importance of nanoparticle surface composition in nanotoxicology, analytical tools that can probe nanoparticle surfaces in aqueous media are crucial but remain limited. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a technique capable of in situ characterization of the liquid-solid interface to probe surface adsorption on nanoparticle surfaces in environmentally and biologically relevant media. Furthermore, given that the interfacial region in these media is dynamic, ATR-FTIR spectroscopy facilitates monitoring these dynamics by interrogating a layer of immobilized nanoparticles coated on the ATR element while changing the overlying aqueous phase. The molecular information acquired from this technique allows for the determination of the adsorption mode, including conformational and structural changes of the coordinating ligand, and can directly measure ligand displacement reactions. Furthermore, in some cases, ATR-FTIR spectroscopy can be used as a quantitative surface analytical tool. In this article, we briefly review the fundamentals of the technique and then provide several examples of using ATR-FTIR spectroscopy to probe nanoparticle surfaces in general with respect to: (i) the adsorption of different environmentally and biologically relevant coordinating ligands; (ii) competitive ligand adsorption and; (iii) the determination of kinetic and thermodynamic parameters. We have also investigated surface adsorption of TiO2 nanoparticles in different biological media typically used for toxicity studies and show that the surface composition of TiO2 nanoparticles depends to a large extent on the composition of the medium due to surface adsorption. This result has important implications for the interpretation of toxicity data as well as inter-comparisons between toxicity studies. PMID:24350328

Mudunkotuwa, Imali A; Minshid, Alaa Al; Grassian, Vicki H



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

NASA Astrophysics Data System (ADS)

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

Asami, Koji



[Qualitative and quantitative detection of beet syrup adulteration of honey by near-infrared spectroscopy: a feasibility study].  


In order to further investigate the utility of near-infrared spectroscopys (NIRS) in rapidly detecting honey adulteration, near-infrared spectroscopy in combination with chemometric methods was investigated for qualitative and quantitative detection of beet syrup adulteration of honey. Total prediction accuracy of testing set was 90.2% by partial least squares-discriminant analysis (PLS-DA) for authentic and adulterated honey samples. Total prediction accuracy of testing sets was all below 33.3% by different discriminant methods for classes of adulteration level. The quantitative analysis of adulteration level by PLS regression gave satisfying results if adulterated honey samples were got from the same one authentic honey sample: correlation coefficient (r)of actual values versus predicted values was 0.9829 and root mean square error of prediction (RMSEP) was 1.394 2 in testing set, otherwise it gave dissatisfying results for the adulterated samples from different botanical origins or the different samples of the same botanical origins. The results showed that NIRS could be applied for rapid detection of authentic and adulterated honey samples, but not for detection of classes of adulteration level and quantification of adulteration level with beet syrup. PMID:24409707

Li, Shui-Fang; Wen, Rui-Zhi; Yin, Yong; Zhou, Zi; Shan, Yang



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

NASA Astrophysics Data System (ADS)

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

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



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

NASA Astrophysics Data System (ADS)

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.

Li, Jin-Jin; Zhu, Ka-Di



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


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



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


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

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




EPA Science Inventory

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


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

E-print Network

profound impact on human health, the environment, and industrial systems. Bacterial biofilms have been in biofilms. By performing microbead force spectroscopy with a closed-loop atomic force microscope, we backgrounds, growth conditions, and environmental stresses to microbial community physiology. INTRODUCTION

Dutcher, John


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



Quantitative detection of uric acid by electrochemical-surface enhanced Raman spectroscopy using a multilayered Au/Ag substrate.  


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



Using Neutron Spectroscopy to Obtain Quantitative Composition Data of Ganymede's Surface from the Jupiter Ganymede Orbiter  

Microsoft Academic Search

Understanding the global composition of Ganymede's surface is a key goal of the Europa Jupiter System Mission (EJSM) that is being jointly planned by NASA and ESA. Current plans for obtaining surface information with the Jupiter Ganymede Orbiter (JGO) use spectral imaging measurements. While spectral imaging can provide good mineralogy-related information, quantitative data about elemental abundances can often be hindered

D. J. Lawrence; S. Maurice; G. W. Patterson; C. A. Hibbitts



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

PubMed Central

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 carcinoma in 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. PMID:24593733

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



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:; 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)



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.



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


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



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



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

NASA Astrophysics Data System (ADS)

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

Sulub, Yusuf Ismail


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

PubMed Central

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

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



Comments on the quantitative interpretation of biomembrane structure by Raman spectroscopy.  


The possibility of quantitation of information obtained from laser Raman spectra of aqueous lipid dispersions is discussed. It is shown that the all-trans chain order parameter ST introduced by Gaber and Peticolas ((1977) Biochim. Biophys. Acta 465, 260) for the characterization of biomembrane structure is of restricted applicability. This order parameter may give adequate information if polar head groups are not affected at all by the interaction resulting in trans-gauche isomerization. To demonstrate this, data on the effects of mono- and divalent ions on the all-trans chain order parameter are given. The lateral order parameter proved to be suitable for quantitative studies even in the case of ion-head group interaction. PMID:921965

Karvaly, B; Loshchilova, E



Protein analysis by 31p NMR spectroscopy in ionic liquid: quantitative determination of enzymatically created cross-links.  


Cross-linking of ?-casein by Trichoderma reesei tyrosinase (TrTyr) and Streptoverticillium mobaraense transglutaminase (Tgase) was analyzed by (31)P nuclear magnetic resonance (NMR) spectroscopy in ionic liquid (IL). According to (31)P NMR, 91% of the tyrosine side chains were cross-linked by TrTyr at high dosages. When Tgase was used, no changes were observed because a different cross-linking mechanism was operational. However, this verified the success of the phosphitylation of phenolics within the protein matrix in the IL. Atomic force microscopy (AFM) in solid state showed that disk-shaped nanoparticles were formed in the reactions with average diameters of 80 and 20 nm for TrTyr and Tgase, respectively. These data further advance the current understanding of the action of tyrosinases on proteins on molecular and chemical bond levels. Quantitative (31)P NMR in IL was shown to be a simple and efficient method for the study of protein modification. PMID:21218836

Monogioudi, Evanthia; Permi, Perttu; Filpponen, Ilari; Lienemann, Michael; Li, Bin; Argyropoulos, Dimitris; Buchert, Johanna; Mattinen, Maija-Liisa



Assessment of statistical uncertainty in the quantitative analysis of solid samples in motion using laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

Statistical uncertainty in the quantitative analysis of solid samples in motion by laser-induced breakdown spectroscopy (LIBS) has been assessed. For this purpose, a LIBS demonstrator was designed and constructed in our laboratory. The LIBS system consisted of a laboratory-scale conveyor belt, a compact optical module and a Nd:YAG laser operating at 532 nm. The speed of the conveyor belt was variable and could be adjusted up to a maximum speed of 2 m s - 1 . Statistical uncertainty in the analytical measurements was estimated in terms of precision (reproducibility and repeatability) and accuracy. The results obtained by LIBS on shredded scrap samples under real conditions have demonstrated that the analytical precision and accuracy of LIBS is dependent on the sample geometry, position on the conveyor belt and surface cleanliness. Flat, relatively clean scrap samples exhibited acceptable reproducibility and repeatability; by contrast, samples with an irregular shape or a dirty surface exhibited a poor relative standard deviation.

Cabalín, L. M.; González, A.; Ruiz, J.; Laserna, J. J.



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

SciTech Connect

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

Shao Yongni; He Yong; Mao Jingyuan



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

NASA Astrophysics Data System (ADS)

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

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



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

NASA Astrophysics Data System (ADS)

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

Ferrier, Graham; Pope, Richard J. J.



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

NASA Astrophysics Data System (ADS)

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

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



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



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

NASA Technical Reports Server (NTRS)

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

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



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



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.



Quantitative infrared spectroscopy of glucose in blood using partial least-squares analyses  

SciTech Connect

The concentration of glucose in drawn samples of human blood has been determined using attenuated total reflectance (ATR) Fourier transform infrared (FT-IR) spectroscopy and partial least-squares (PLS) multivariate calibration. A twelve sample calibration set over the physiological glucose range of 50-400 mg/deciliter (dl) resulted in an average error of 5.2 mg/dl. These results were obtained using a cross validated PLS calibration over all infrared data in the frequency range of 950-1200 cm/sup /minus/1/. These results are a dramatic improvement relative to those obtained by previous studies of this system using univariate peak height analyses. 3 refs., 3 figs.

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



Quantitative Analysis of Alcohol, Sugar, and Tartaric Acid in Alcoholic Beverages Using Attenuated Total Reflectance Spectroscopy  

PubMed Central

Mid-infrared (MIR) spectroscopy in attenuated total reflectance (ATR) mode was used for quantifying ethanol, sucrose, and tartaric acid in alcoholic beverages. One hundred synthetic samples were prepared with different ethanol, sucrose, and tartaric acid concentrations. Experiments were carried out on Bio-Rad 175 C FTS using an ATR accessory. Spectra were recorded in the wavelength region 600–4000 cm ?1 . Calibration was performed using partial least squares (PLS) algorithm. Commercially available alcoholic beverages (gin, rum, vodka, etc.) were experimented and concentration of ethanol in these samples was predicted using the developed calibration model. Chemical analysis of these commercial samples was carried out in order to compare the results. The agreement between ATR results with those of chemical analysis revealed good reliability and repeatability of the technique used. PMID:17671618

Nagarajan, R.; Gupta, A.; Bajaj, M. M.



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.



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.



The Quantitative and Qualitative Analysis of Cohorts' Early Enrollment in Physics: concurrent with enrollment in mathematics, biology and chemistry  

NASA Astrophysics Data System (ADS)

Cohorts of 48 entering biological science majors was recruited in the fall of 2007 and again in 2008 and 2009 for the Interdisciplinary Science Experience (ISE). These ISE students enrolled in their own sections of standard courses of physics, chemistry, and biology. In these courses average ISE student out-performed their non-cohort peers by up to a full letter grade. A qualitative analysis of ISE student interviews illuminates the student experience and shows how the ISE students perceived themselves to be different than their non-cohort peers. Quantitative modeling of student performance shows that higher grades are correlated with multiple factors. These factors includes admissions characteristics such as high school GPA, and SAT scores, as well as demographic information. These trends support and elaborate on the selection narratives told by participants. Additionally the quantitative model found that higher student performance is predicted by structural aspects of the ISE program, specifically the timing of course, enrolling as a freshmen in many of their courses, and the sequencing of physics and chemistry courses. There is a statistically significant benefit to student performance in general and organic chemistry courses associated with completing the first quarter of the Physics for Bio-Science majors prior to enrollment. Further the combination of quantitative and qualitative data suggest that there is a epistemological transfer of problem solving skills and outlook from the physics to the chemistry courses.

Lynch, Robert Bruce Rodes


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


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

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



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

SciTech Connect

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

Farrow, R.; Rakestraw, D.; Paul, P.; Lucht, R.; Danehy, P.; Friedman-Hill, E.; Germann, G. [Sandia National Laboratories, Livermore, CA (United States)



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


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

Henderson, Terry J; Cullinan, David B



Spectral-domain optical coherence phase microscopy for quantitative biological studies  

E-print Network

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

Joo, Chulmin, 1976-



Quantitative H and K band spectroscopy of Galactic OB-stars at medium resolution  

E-print Network

In this paper we have analyzed 25 Galactic O and early B-stars by means of H and K band spectroscopy, with the primary goal to investigate to what extent a lone near-IR spectroscopy is able to recover stellar and wind parameters derived in the optical. Most of the spectra have been taken with SUBARU IRCS, at a resolution of 12,000, and with a very high S/N (200 or better). In order to synthesize the strategic H/He lines, we have used our recent, line-blanketed version of FASTWIND. First we investigated the predicted behaviour of the strategic lines. In contradiction to what one expects from the optical in the O-star regime, almost all photospheric H/HeI/HeII H/K band lines become stronger if the gravity decreases. Concerning H and HeII, this finding is related to the behaviour of Stark broadening as a function of electron density, which in the line cores is different for members of lower (optical) and higher (IR) series. Regarding HeI, the predicted behaviour is due to some subtle NLTE effects resulting in a stronger overpopulation of the lower level when the gravity decreases. For most of our objects, we obtained good fits, except for the line cores of Br_gamma in early O-stars with significant mass-loss, where this discrepancy might be an indirect effect of clumping. After having derived the stellar and wind parameters from the IR, we have compared them to results from previous optical analyses. Overall, the IR results coincide in most cases with the optical ones within the typical errors usually quoted for the corresponding parameters, i.e, an uncertainty in Teff of 5%, in log g of 0.1 dex and in Mdot of 0.2 dex, with lower errors at higher wind densities. Outliers above the 1-sigma level where found in four cases with respect to log g and in two cases for Mdot.

T. Repolust; J. Puls; M. M. Hanson; R. -P. Kudritzki; M. R. Mokiem



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

NASA Astrophysics Data System (ADS)

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

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



Strategies for improving sensitivity and selectivity for the quantitation of biotherapeutics in biological matrix using LC-MS/MS.  


In recent years, the applicability of using LC-MS/MS as a complementary technique to traditional ligand binding assays in the absolute quantitation of therapeutic proteins in biologic matrix has been demonstrated. Protein quantitation workflow via LC-MS/MS is primarily based on a enzymatic digestion model and recent works seek to improve selectivity and sensitivity. This review focuses on recent innovations in this field and discusses the following in detail: the applicability of two-dimensional liquid chromatography and its use to improve sensitivity and alleviate matrix ion suppression; the use of derivatization agents after digestion to improve extraction and MS ionization efficiency; techniques to reduce excess protein background and their positive effects on sensitivity, selectivity, and extraction consistency; the application of immunoaffinity extraction of proteins to enrich the analyte(s) of interest while improving selectivity and sensitivity. PMID:25776016

Shen, Jim X; Liu, Guowen; Zhao, Yue



Quantitative analysis of mixed hydrofluoric and nitric acids using Raman spectroscopy with partial least squares regression.  


Mixed hydrofluoric and nitric acids are widely used as a good etchant for the pickling process of stainless steels. The cost reduction and the procedure optimization in the manufacturing process can be facilitated by optically detecting the concentration of the mixed acids. In this work, we developed a novel method which allows us to obtain the concentrations of hydrofluoric acid (HF) and nitric acid (HNO(3)) mixture samples with high accuracy. The experiments were carried out for the mixed acids which consist of the HF (0.5-3wt%) and the HNO(3) (2-12wt%) at room temperature. Fourier Transform Raman spectroscopy has been utilized to measure the concentration of the mixed acids HF and HNO(3), because the mixture sample has several strong Raman bands caused by the vibrational mode of each acid in this spectrum. The calibration of spectral data has been performed using the partial least squares regression method which is ideal for local range data treatment. Several figures of merit (FOM) were calculated using the concept of net analyte signal (NAS) to evaluate performance of our methodology. PMID:20441916

Kang, Gumin; Lee, Kwangchil; Park, Haesung; Lee, Jinho; Jung, Youngjean; Kim, Kyoungsik; Son, Boongho; Park, Hyoungkuk



Quantitative analysis of thiolated ligand exchange on gold nanoparticles monitored by (1)h NMR spectroscopy.  


We use nuclear magnetic resonance spectroscopy methods to quantify the extent of ligand exchange between different types of thiolated molecules on the surface of gold nanoparticles. Specifically, we determine ligand density values for single-moiety ligand shells and then use these data to describe ligand exchange behavior with a second, thiolated molecule. Using these techniques, we identify trends in gold nanoparticle functionalization efficiency with respect to ligand type, concentration, and reaction time as well as distinguish between functionalization pathways where the new ligand may either replace the existing ligand shell (exchange) or add to it ("backfilling"). Specifically, we find that gold nanoparticles functionalized with thiolated macromolecules, such as poly(ethylene glycol) (1 kDa), exhibit ligand exchange efficiencies ranging from 70% to 95% depending on the structure of the incoming ligand. Conversely, gold nanoparticles functionalized with small-molecule thiolated ligands exhibit exchange efficiencies as low as 2% when exposed to thiolated molecules under identical exchange conditions. Taken together, the reported results provide advances in the fundamental understanding of mixed ligand shell formation and will be important for the preparation of gold nanoparticles in a variety of biomedical, optoelectronic, and catalytic applications. PMID:25658511

Smith, Ashley M; Marbella, Lauren E; Johnston, Kathryn A; Hartmann, Michael J; Crawford, Scott E; Kozycz, Lisa M; Seferos, Dwight S; Millstone, Jill E



A rapid quantitative assay of intact paracetamol tablets by reflectance near-infrared spectroscopy.  


Near-infrared (NIR) reflectance spectroscopy was used to determine rapidly and non-destructively the content of paracetamol in bulk batches of intact Sterwin 500 mg tablets by collecting NIR spectra in the range 1100-2500 nm and using a multiple linear regression calibration method. The developed NIR method gave results comparable to the British Pharmacopoeia 1993 UV assay procedure, the standard errors of calibration and prediction being 0.48% and 0.71% m/m, respectively. The method showed good repeatability, the standard deviation and coefficient of variation for six NIR assays on the same batch on the same day being 0.14 and 0.16% m/m, respectively, while measurements over six consecutive days gave 0.31 and 0.36% m/m, respectively. Applying the calibration to a parallel test set gave a mean bias of -0.22% and a mean accuracy of 0.45%. The developed method illustrates how the full potential of NIR can be utilised and how the ICH guidelines which recommend the validation of linearity, range, accuracy and precision for pharmaceutical registration purposes can be applied. Duplicate determinations on bulk batches could be performed in under 2 min, allowing the potential use of the method on-line for real time monitoring of a running production process. PMID:10563053

Trafford, A D; Jee, R D; Moffat, A C; Graham, P



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.



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


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

Gamble, Gary R; Foulk, Jonn A



Quantitative analysis of ?-mangostin in hydrophilic ointment using near-infrared spectroscopy.  


The objective of this research was to quantify the ?-mangostin content in mangosteen pericarp (MP) ointment as a colloidal dispersion using near-infrared (NIR) spectroscopy. Various concentrations of MP (IP and EP) ointments containing both internal and external pericarps were prepared and the NIR spectra of these ointments were measured. The NIR spectrum of each ointment was correlated with ?-mangostin concentration by partial least square (PLS) regression. Validation of the models was performed and their predictive ability was also investigated. The equation and R(2) value for the prediction of ?-mangostin concentration in IP ointment were y?=?0.9843x?+?0.4441 and 0.9730 and those in EP ointment were y?=?0.9569x?+?0.1142 and 0.9136, respectively. The biases of the IP and EP ointment models were 0.23 and 0.00, respectively. The results showed that NIR could be a useful tool for the quality control of herbal medicine in hydrophilic ointment without any sample preparation. It could predict ?-mangostin content in hydrophilic ointment at very low concentration with sufficient accuracy. PMID:24517571

Peerapattana, Jomjai; Otsuka, Kuniko; Hattori, Yusuke; Otsuka, Makoto



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


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

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



Vibrational spectroscopy and chemometrics for rapid, quantitative analysis of bitter acids in hops (Humulus lupulus).  


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



Use and qualification of primary and secondary standards employed in quantitative ¹H NMR spectroscopy of pharmaceuticals.  


Standards are required in quantitative NMR (qNMR) to obtain accurate and precise results. In this study acetanilide was established and used as a primary standard. Six other chemicals were selected as secondary standards: 3,4,5-trichloropyridine, dimethylterephthalate, maleic acid, 3-sulfolene, 1,4-bis(trimethylsilyl)benzene, and 1,3,5-trimethoxybenzene. The secondary standards were quantified using the primary standard acetanilide. A protocol for qualification and periodic checks of these secondary standards was developed, and used for evaluation of the stability of the compounds. Periodic monitoring of purity was performed for several years. The purity was higher than 99% for all secondary standards. All standards maintained the initial purity during the time period of monitoring, with very small variations in purity (0.3-0.4%). The selected secondary standards were shown to be suitable qNMR standards and that periodic requalification of the standards by qNMR ensures reliable analytical results. These standards have been used in our laboratory for compliance testing of pharmaceutical active substances and approved medicinal products as well as for analysis of suspected illegal medicines. In total more than 1000 samples have been tested using both internal and external standardization and examples are given. PMID:24206940

Rundlöf, Torgny; McEwen, Ian; Johansson, Monika; Arvidsson, Torbjörn



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.



Quantitative Soil Carbon Analysis with in Situ Laser-Induced Breakdown Spectroscopy by Multivariate Analysis  

NASA Astrophysics Data System (ADS)

The Earth's oceans, forests, agricultural lands and other natural areas absorb about half of the carbon dioxide emitted from anthropogenic sources. Terrestrial carbon sequestration strategies are immediately available to bridge the gap between current terrestrial sequestration capacity and high-capacity geologic sequestration projects available in 10 to 20 years. Terrestrial carbon sequestration strategies consist of implementing land management practices aimed at decreasing CO2 emitted into the atmosphere and developing advanced measurement tools to inventory and monitor carbon processes in soils and biota. Laser-Induced Breakdown Spectroscopy (LIBS) is one of the analytical tools used to determine the total soil carbon in samples within the Big Sky and Southwest Carbon Sequestration Regional Partnerships. LIBS involves focusing a Nd:YAG laser operating at 1064nm onto the surface of the sample. The laser ablates material from the surface, generating an expanding plasma containing electronically excited ions, atoms, and small molecules. As these electronically excited species relax back to the ground state, they emit light at wavelengths characteristic of the species present in the sample. Some of this emission is directed into one of three dispersive spectrometers. The experiments discussed in this paper were completed with a person portable LIBS instrument designed and built at Los Alamos National Laboratory that uses a Kigre Laser (25mJ/pulse) and an Ocean Optics HR2000 dispersive spectrometer. This instrument was used to probe samples collected from Illinois (no-till loam), Michigan (no-till clay), and North Dakota (reduced-till sand). A new multivariate analysis technique was employed to extract concentrations to 0.5%C with significantly greater statistical accuracy than conventional univariate techniques. These MVA techniques appear to completely compensate for these matrix effects because the analysis identifies the correlations between the spectra (independent variables), the individual elements of interest (dependent variables such as Si) as well as the other elements in the matrix.

Harris, R. D.; Clegg, S. M.; Barefield, J. E.; Fessenden-Rahn, J. E.; Wiens, R. C.; Ebinger, M. H.



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.



Quantitative Physiology of the Precancerous Cervix In Vivo through Optical Spectroscopy1  

PubMed Central

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

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



[Quantitative method of determining the activity of zinc- and copper-dependent superoxide dismutase in biological material].  


The activity of superhydroxide dismutase was estimated by following rate of inhibition of non-enzymatic reduction of tetrazolium salt in reaction with superhydroxide ions, which were continuously generated in a photochemical system. The quantitative estimations were achieved by using para-nitrotetrazolium chloride, which was reduced to formazanes soluble in acetone. Formation of formazanes by the photochemical system (riboflavin + tetramethylethylene diamine + O2 + para-nitrotetrazolium chloride + light) in presence of biological material and cyanide was compared with formation of formazanes in absence of cyanide for specific estimation of Zn, Cu-dependent forms of superhydroxide dismutase. The rate of enzymatic cyanide sensitive inhibition of the photochemical formation of formazanes from paranitrotetrazolium chloride was determined by the activity of Zn, Cu-dependent superhydroxide dismutase in biological material and might be expressed in units of the activity -- un. ac. = 10/(0,026.% inhibition--1,3). PMID:595507

Chumakov, V N; Osinskaia, L F



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

E-print Network

Drosophila Genome Project ... 81 Human Genome Project ... 810 Working knowledge of multivariate statistics biology (whole organism cloning, embryo transplantation) and recombinant DNA (trans- genic organisms applied in such diverse fields as human genetics, evolution, and breeding. While the broad goals

Walsh, Bruce


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

E-print Network

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

Eydgahi, Hoda



Quantitative Modeling and Estimation in Systems Biology using Fluorescent Reporter Systems  

E-print Network

La cells containing the Tet-on expression system on stimulation by different levels doxycycline. Thus, this work describes techniques for building robust predictive models of biological systems such as regularization for solving ill-posed estimation...

Bansal, Loveleena



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

NASA Astrophysics Data System (ADS)

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.

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



Use of quantitative ultrasound to detect temperature variations in biological phantoms due to heating  

E-print Network

the envelope statistics (k parameter and µ parameter) of the backscattered echoes versus temperature of an ultrasonic imaging technique for monitoring HIFU treatment is highly medically significant. Quantitative the phantoms. Sound speed and attenuation were estimated in the phantoms versus temperature using insertion

Illinois at Urbana-Champaign, University of


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.



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 F.; Hoefen, Todd; Lundeen, Sarah; Eastwood, Michael; Green, Robert O.; Pearson, Neil; Sarture, Charles; McCubbin, Ian; Roberts, Dar; Bradley, Eliza; Steele, Denis; Ryan, Thomas; Dominguez, Roseanne; The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) Team



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



Quantitative determination of coenzyme Q10 from dietary supplements by FT-NIR spectroscopy and statistical analysis.  


A novel, time- and money-sparing method has been developed and validated for the quantitative determination of coenzyme Q10 (CoQ10) from several dietary supplements. FT-NIR spectroscopy was applied for the examination, and a calibration model was built by partial least-square regression (PLS-R) using 50 dietary supplements. The combination of FT-NIRS and multivariate calibration methods is a very fast and simple way to replace the commonly used HPLC-UV method; because in contrast with the traditional techniques, sample pretreatment and reagents are not required and no wastes are produced. The calibration models could be improved by different variable selection techniques (for instance interval PLS, interval selectivity ratio, genetic algorithm), which are very fast and user-friendly. The R (2) (goodness of calibration) and Q (2) (goodness of validation) of the variable selected models are highly increased, the R (2) values being over 0.90 and the Q (2) values being over 0.86 in every case. Fivefold cross-validation and external validation were applied. The developed method(s) could be used by quality assurance laboratories for routine measurement of coenzyme Q10 products. PMID:25662936

Rácz, Anita; Vass, Andrea; Héberger, Károly; Fodor, Marietta



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


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



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


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



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

NASA Astrophysics Data System (ADS)

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

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



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

E-print Network

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

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



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


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

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



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.



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


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

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




NSDL National Science Digital Library

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


Case studies in quantitative biology: Biochemistry on a leash and a single-molecule Hershey-Chase experiment  

NASA Astrophysics Data System (ADS)

The last 50 years of biological research has seen a marked increase in the amount of quantitative data that describes living systems. This wealth of data provides a unique opportunity to recast the pictorial level descriptions of biological processes in the language of mathematics, with the hope that such an undertaking will lead to deeper insights into the behavior of living systems. To achieve this end, we have undertaken three case studies in physical biology. In the first case study, we used statistical mechanics and polymer physics to construct a simple model that describes how flexible chains of amino acids, referred to as tethers, influence the information processing properties of signaling proteins. In the second case study, we studied the DNA ejection process of phage lambda in vitro. In particular, we used bulk and single-molecule methods to study the control parameters that govern the force and kinematics of the ejection process in vitro. In the last case study, we studied the DNA ejection process of phage lambda in vivo. We developed an assay that allows real-time monitoring of DNA ejection in vivo at the single-molecule level. We also developed a parallel system that allows the simultaneous visualization of both phage capsids and phage DNA at the single-cell level, constituting a true single-molecule Hershey-Chase experiment. The work described in this thesis outlines new tools, both in theory and experiment, that can be used to study biological systems as well as a paradigm that can be employed to mathematicize the cartoons of biology.

Van Valen, David



BioMaPS Student Seminar Series in Quantitative Biology: October 27, 2011 George Locke  

E-print Network

Morozov's Group Title: "Next Generation DNA Sequencing - the Nitty Gritty" Abstract: Cheap DNA sequencing is revolutionizing biology. Next Generation Sequencing, also known as Shotgun Sequencing, is the process of reading as emerging "Real-time sequencing" technologies. Sequencing technologies - the next generation by Michael L

Chen, Kuang-Yu


Technique for examining biological materials using diffuse reflectance spectroscopy and the kubelka-munk function  


Method and apparatus for examining biological materials using diffuse reflectance spectroscopy and the Kubelka-Munk function. In one aspect, the method is used to determine whether a tissue sample is cancerous or not and comprises the steps of (a) measuring the diffuse reflectance from the tissue sample at a first wavelength and at a second wavelength, wherein the first wavelength is a wavelength selected from the group consisting of 255-265 nm and wherein the second wavelength is a wavelength selected from the group consisting of 275-285 nm; (b) using the Kubelka-Munk function to transform the diffuse reflectance measurement obtained at the first and second wavelengths; and (c) comparing a ratio or a difference of the transformed Kubelka-Munk measurements at the first and second wavelengths to appropriate standards determine whether or not the tissue sample is cancerous. One can use the spectral profile of KMF between 250 nm to 300 nm to determine whether or not the tissue sample is cancerous or precancerous. According to the value at the first and second wavelengths determine whether or not the malignant tissue is invasive or mixed invasive and in situ or carcinoma in situ.

Alfano, Robert R.; Yang, Yuanlong



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.



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

NASA Astrophysics Data System (ADS)

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

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



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



Magnetic susceptibility effects in nuclear magnetic resonance spectroscopy of biological objects  

SciTech Connect

In this article a review is given of the impact of magnetic susceptibility variations in biological objects on the proton NMR metabolite spectra observed in these objects, and of methods to reduce this impact. Susceptibility variations arise near boundaries of inter- and intra-cellular structures, generating local dipolar field gradients. These gradients broaden the 1H NMR lines significantly, seriously hampering a quantitative analysis of the spectra and, henceforth, the utility of this technique for biochemical and biomedical applications. In this paper newly developed methods are discussed to separate the susceptibility-induced line broadening from the isotropic chemical shift information while maintaining the structural integrity of the object. To this end two methods will be considered, which both utilize a slow spinning of the sample about the so-called magic axis (magic angle spinning or MAS), namely phase-adjusted spinning sidebands (PASS) and phase-corrected magic angle turning (PHORMAT). The advantages and disadvantages of these techniques will be discussed. It will be shown that PASS offers the highest NMR sensitivity and the shortest measuring time, but requires spinning speeds of at least 30 Hz, restricting this methodology to small biological samples. PHORMAT has a reduced sensitivity and a relatively long measuring time, but with this technique spinning speeds as low as 1 Hz can be used. Hence PHORMAT can be used in larger biological objects, including live animals. The utility of PASS and PHORMAT will be illustrated with applications on excised rat liver tissue and, for the latter technique, on a live mouse subjected to 1.5 Hz magic angle spinning. It will be shown that in a 7 Tesla magnet field PASS and PHORMAT reduce the widths of the proton metabolite lines by at least an order of magnitude, and that even in a relatively low 2 Tesla field and in a live mouse these widths are reduced by almost a factor 5. Finally, the impact of molecular diffusion on the isotropic line widths, and the dependence of these line widths upon the spinning frequency in PASS and PHORMAT are discussed, and perspectives of further improving the methods and possible clinical applications of PHORMAT are given.

Wind, Robert A.; Hu, Jian Zhi



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.



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


Quantitative NMR spectroscopy of complex technical mixtures using a virtual reference: chemical equilibria and reaction kinetics of formaldehyde–water–1,3,5-trioxane  

Microsoft Academic Search

Quantitative 1H NMR spectroscopy was used to study chemical equilibria and reaction kinetics of both the formation and decomposition of 1,3,5-trioxane in aqueous formaldehyde solutions. The reaction was homogeneously catalyzed with up to 0.10 g g?1 sulfuric acid at temperatures between 360 and 383 K so that most of the experiments had to be carried out pressurized. The studied mixtures were complex due

Michael Maiwald; Thomas Grützner; Eckhard Ströfer; Hans Hasse



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

Microsoft Academic Search

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

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



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

Microsoft Academic Search

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

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



The application of HPLC and microprobe NMR spectroscopy in the identification of metabolites in complex biological matrices.  


Nuclear magnetic resonance (NMR)-based metabolomics can be used directly to identify a variety of metabolites in biological fluids and tissues. Metabolite analysis is an important part of life science and metabolomics research. However, the identification of some metabolites using NMR spectroscopy remains a big challenge owing to low abundance or signal overlap. It is important to develop a method to measure these compounds accurately. Two-dimensional NMR spectroscopy, metabolite prediction software packages, and spike-in experiments with authentic standards are often used to solve these problems, but they are costly and time-consuming. In this study, methods were developed to identify metabolites in complex biological mixtures using both high-performance liquid chromatography (HPLC) and off-line microprobe NMR spectroscopy. With use of these methods, 83 and 73 metabolites were identified in Sprague Dawley rat urine and feces, respectively. Among them, 40 and 45 metabolites, respectively, could not be identified with traditional NMR methods. Our research revealed that the combination of HPLC and NMR techniques could significantly improve the accuracy of trace and overlapped metabolite identification, while offering an effective and convenient approach to identify potential biomarkers in complex biological systems. PMID:25814271

Miao, Zhaoxia; Jin, Mengxia; Liu, Xia; Guo, Wei; Jin, Xiangju; Liu, Hongyue; Wang, Yinghong



A New Technique for Quantitative Determination of Dexamethasone in Pharmaceutical and Biological Samples Using Kinetic Spectrophotometric Method  

PubMed Central

Dexamethasone is a type of steroidal medications that is prescribed in many cases. In this study, a new reaction system using kinetic spectrophotometric method for quantitative determination of dexamethasone is proposed. The method is based on the catalytic effect of dexamethasone on the oxidation of Orange G by bromate in acidic media. The change in absorbance as a criterion of the oxidation reaction progress was followed spectrophotometrically. To obtain the maximum sensitivity, the effective reaction variables were optimized. Under optimized experimental conditions, calibration graph was linear over the range 0.2–54.0?mg?L?1. The calculated detection limit (3sb/m) was 0.14?mg?L?1 for six replicate determinations of blank signal. The interfering effect of various species was also investigated. The present method was successfully applied for the determination of dexamethasone in pharmaceutical and biological samples satisfactorily. PMID:25737724

Akhoundi-Khalafi, Ali Mohammad; Shishehbore, Masoud Reza



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

PubMed Central

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution. PMID:21338175




NSDL National Science Digital Library

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


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.



An Integrated Quantitative Proteomics and Systems Biology Approach to Explore Synaptic Protein Profile Changes During Morphine Exposure  

PubMed Central

Morphine is a classic analgesic for the treatment of chronic pain. However, its repeated use is known to produce tolerance, physical dependence, and addiction; these properties limit its long-term therapeutic use and this has led to a quest for therapeutics without these unwanted side effects. Understanding the molecular changes in response to long-term use of morphine is likely to aid in the development of novel therapeutics for the treatment of pain. Studies examining the effects of chronic morphine administration have reported alterations in gene expression, synapse morphology, and synaptic transmission implying changes in synaptic protein profile. To fully understand the changes in protein profiles, proteomic techniques have been used. Studies using two-dimensional gel electrophoresis of various brain regions combined with mass spectrometry have found alterations in the levels of a number of proteins. However, neither the changes in brain regions relevant to morphine effects nor changes in the abundance of synaptic proteins have been clearly delineated. Recent studies employing subcellular fractionation to isolate the striatal synapse, combined with quantitative proteomics and graph theory-inspired network analyses, have begun to quantify morphine-regulated changes in synaptic proteins and facilitate the generation of networks that could serve as targets for the development of novel therapeutics for the treatment of chronic pain. Thus, an integrated quantitative proteomics and systems biology approach can be useful to identify novel targets for the treatment of pain and other disorders of the brain. PMID:24045585

Stockton, Steven D; Devi, Lakshmi A



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

PubMed Central

We explore the possibility of using dynamic nuclear polarization (DNP) to enhance signals in structural studies of biological solids by solid state NMR without sample spinning. Specifically, we use 2D 13C-13C exchange spectroscopy to probe the peptide backbone torsion angles (?,?) in a series of selectively 13C-labeled 40-residue ?-amyloid (A?1–40) samples, in both fibrillar and non-fibrillar states. Experiments are carried out at 9.39 T and 8 K, using a static double-resonance NMR probe and low-power microwave irradiation at 264 GHz. In frozen solutions of A?1–40 fibrils doped with DOTOPA-TEMPO, we observe DNP signal enhancement factors of 16–21. We show that the orientation- and frequency-dependent spin polarization exchange between sequential backbone carbonyl 13C labels can be simulated accurately using a simple expression for the exchange rate, after experimentally determined homogeneous 13C lineshapes are incorporated in the simulations. The experimental 2D 13C-13C exchange spectra place constraints on the ? and ? angles between the two carbonyl labels. Although the data are not sufficient to determine ? and ? uniquely, the data do provide non-trivial constraints that could be included in structure calculations. With DNP at low temperatures, 2D 13C-13C exchange spectra can be obtained from a 3.5 mg sample of A?1–40 fibrils in 4 hr or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples. PMID:23562665

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



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

NASA Astrophysics Data System (ADS)

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

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



Quantitative analysis of drugs in biological matrices by HPLC hyphenated to fluorescence detection.  


An overview of the state-of-the art in HPLC coupled with fluorescence detection is presented. Over the last 20 years, the increasing number of methodological papers on this topic (4082 between 1994 and 2004 and 7725 between 2004 and 2014) is testament to its utility in bioanalytical applications. Compared with conventional UV absorbance detection used in HPLC, fluorescence detection can greatly enhance the sensitivity leading to limits of detection similar to those obtained with mass spectrometry, offering researchers a sensitive, robust and relatively inexpensive instrumental method. This work will focus on the analysis of pharmaceutical compounds in different biological matrices, either naturally fluorescent or derivatized with a fluorescent agent, and some of them chiral. Therapeutic applications, sample preparation and derivatization, sensitivity for each example are described. PMID:25871590

Lipka, Emmanuelle; Vaccher, Claude



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

PubMed Central

Background In this study we aimed to quantify tumor suppressor gene (TSG) promoter methylation densities levels in primary neuroblastoma tumors and cell lines. A subset of these TSGs is associated with a CpG island methylator phenotype (CIMP) in other tumor types. Methods The study panel consisted of 38 primary tumors, 7 established cell lines and 4 healthy references. Promoter methylation was determined by bisulphate Pyrosequencing for 14 TSGs; and LINE-1 repeat element methylation was used as an indicator of global methylation levels. Results Overall mean TSG Z-scores were significantly increased in cases with adverse outcome, but were unrelated to global LINE-1 methylation. CIMP with hypermethylation of three or more gene promoters was observed in 6/38 tumors and 7/7 cell lines. Hypermethylation of one or more TSG (comprising TSGs BLU, CASP8, DCR2, CDH1, RASSF1A and RASSF2) was evident in 30/38 tumors. By contrast only very low levels of promoter methylation were recorded for APC, DAPK1, NORE1A, P14, P16, TP73, PTEN and RARB. Similar involvements of methylation instability were revealed between cell line models and neuroblastoma tumors. Separate analysis of two proposed CASP8 regulatory regions revealed frequent and significant involvement of CpG sites between exon 4 and 5, but modest involvement of the exon 1 region. Conclusions/significance The results highlight the involvement of TSG methylation instability in neuroblastoma tumors and cell lines using quantitative methods, support the use of DNA methylation analyses as a prognostic tool for this tumor type, and underscore the relevance of developing demethylating therapies for its treatment. PMID:22984959



Quantitation of Cytokinins in Biological Samples Using Antibodies Against Zeatin Riboside  

PubMed Central

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 [3H]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, Jane; Letham, David S.; Parker, Charles W.; Rolfe, Barry G.



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



Quantitation, biological and physicochemical properties of cell culture-adapted porcine epidemic diarrhea coronavirus (PEDV).  


The porcine epidemic coronavirus (PEDV), tentatively classified as a coronavirus, was adapted to Vero cells and a plaque test developed for infectivity titration, allowing us to test the biological and biophysical properties of the virus. Growth kinetics showed peak titers of 10(5.5) plaque-forming units ml-1 15 h after infection. Filtration experiments and electron microscopy revealed a particle diameter between 100 and 200 nm. The buoyant density of the virus was 1.18. The particle lost its infectivity on treatment with lipid solvents. Virus replication could not be inhibited by 5-iodo-2'-deoxyuridine. PEDV was moderately stable at 50 degrees C, but heat sensitivity was not altered by divalent cations. At 4 degrees C, the virus was stable between pH 5.0 and 9.0, but at 37 degrees C stability was restricted to the pH range 6.5-7.5. Viral infectivity was not impaired by ultrasonication or by multiple freezing and thawing. PEDV was not neutralized by transmissible gastroenteritis virus antiserum. On the basis of the tests carried out, PEDV is a pleomorphic, enveloped RNA virus with a particle diameter of approximately 150 nm and a buoyant density of 1.18. Infectivity depends on the presence of trypsin, and infected cells show a tendency to fuse and to form syncytia. All of these properties, as well as its physicochemical characteristics, allow PEDV to be classified as a coronavirus. PMID:2549681

Hofmann, M; Wyler, R



Quantitative STEM mass measurement of biological macromolecules in a 300 kV TEM.  


For almost four decades, the scanning transmission electron microscope (STEM) has made significant contributions to structural biology by providing accurate determinations of the molecular masses of large protein assemblies that have arbitrary shapes and sizes. Nevertheless, STEM mass mapping has been implemented in very few laboratories, most of which have employed cold field-emission gun (FEG) electron sources operating at acceleration voltages of 100 kV and lower. Here we show that a 300 kV commercial transmission electron microscope (TEM) equipped with a thermally assisted Shottky FEG can also provide accurate STEM mass measurements. Using the recently published database of elastic-scattering cross sections from the National Institute of Standards and Technology, we show that the measured absolute mass values for tobacco mosaic virus and limpet hemocyanin didecamers agree with the known values to within better than 10%. Applying the established approach, whereby tobacco mosaic virus is added to a specimen as a calibration standard, we find that the measured molecular weight of the hemocyanin assemblies agrees with the known value to within 3%. This accuracy is achievable although only a very small fraction ( approximately 0.002) of the incident probe current of 300 kV electrons is scattered onto the annular dark-field STEM detector. FEG TEMs operating at intermediate voltages (200-400 kV) are becoming common tools for determining the structure of frozen hydrated protein assemblies. The ability to perform mass determination with the same instrument can provide important complementary information about the numbers of subunits comprising the protein assemblies whose structure is being studied. PMID:17910694

Sousa, Alioscka A; Leapman, Richard D




E-print Network

SPECTROSCOPY METHODOLOGY - Communication Quantitative Measurement of N-Acetyl-aspartyl-glutamate at 3 T Using TE-Averaged PRESS Spectroscopy and Regularized Lineshape Deconvolution Yan Zhang,1 Shizhe in conjunction with TE-averaged PRESS spectroscopy to measure N-acetyl-aspartyl-glutamate (NAAG). Averaging

Shen, Jun


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

PubMed Central

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

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



Quantitative measurement of Toll-like receptor 4 agonists adsorbed to Alhydrogel(®) by Fourier transform infrared-attenuated total reflectance spectroscopy.  


Aluminum salts have a long history as safe and effective vaccine adjuvants. In addition, aluminum salts have high adsorptive capacities for vaccine antigens and adjuvant molecules, for example, Toll-like receptor 4 (TLR4) agonists. However, the physicochemical properties of aluminum salts make direct quantitation of adsorbed molecules challenging. Typical methods for quantifying adsorbed molecules require advanced instrumentation, extreme sample processing, often destroy the sample, or rely on an indirect measurement. A simple, direct, and quantitative method for analysis of adsorbed adjuvant molecules is needed. This report presents a method utilizing Fourier transform infrared spectroscopy with a ZnSe-attenuated total reflectance attachment to directly measure low levels (<30 ?g/mL) of TLR4 agonists adsorbed on aluminum salts with minimal sample preparation. PMID:25242027

Dowling, Quinton M; Schwartz, Alicia M; Vedvick, Thomas S; Fox, Christopher B; Kramer, Ryan M



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



Detection and Quantitative Analysis of Chemical Species in Hanford Tank Materials Using Raman Spectroscopy Technology: FY94Florida State University Raman Spectroscopy Report  

Microsoft Academic Search

This report provides a summary of work completed in FY-94 by FSU to develop and investigate the feasibility of using Raman spectroscopy with Hanford tank waste materials. Raman performance impacts from sample morphology, including the effects of absorption, particle size, density, color and refractive index, are discussed. An algorithm for relative species concentration measurement from Raman data is presented. An





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...


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

PubMed Central

Since the early 1980’s, the enhanced backscattering (EBS) phenomenon has been well-studied in a large variety of non-biological materials. Yet, until recently the use of conventional EBS for the characterization of biological tissue has been fairly limited. In this work we detail the unique ability of EBS to provide spectroscopic, polarimetric, and depth-resolved characterization of biological tissue using a simple backscattering instrument. We first explain the experimental and numerical procedures used to accurately measure and model the full azimuthal EBS peak shape in biological tissue. Next we explore the peak shape and height dependencies for different polarization channels and spatial coherence of illumination. We then illustrate the extraordinary sensitivity of EBS to the shape of the scattering phase function using suspensions of latex microspheres. Finally, we apply EBS to biological tissue samples in order to measure optical properties and observe the spatial length-scales at which backscattering is altered in early colon carcinogenesis. PMID:24163574

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



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

SciTech Connect

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

Wind, Robert A.; Hu, Jian Zhi



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

NASA Astrophysics Data System (ADS)

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

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



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

SciTech Connect

Laser-induced breakdown spectroscopy (LIBS), an atomic emission spectroscopy method, has rapidly grown as one of the best elemental analysis techniques over the past two decades. Homogeneity testing and quantitative analysis of manganese (Mn) in manganese-doped glasses have been carried out using an optimized LIBS system employing a nanosecond ultraviolet Nd:YAG laser as the source of excitation. The glass samples have been prepared using conventional vitrification methods. The laser pulse irradiance on the surface of the glass samples placed in air at atmospheric pressure was about 1.7×10{sup 9} W/cm{sup 2}. The spatially integrated plasma emission was collected and imaged on to the spectrograph slit using an optical-fiber-based collection system. Homogeneity was checked by recording LIBS spectra from different sites on the sample surface and analyzing the elemental emission intensities for concentration determination. Validation of the observed LIBS results was done by comparison with scanning electron microscope- energy dispersive X-ray spectroscopy (SEM-EDX) surface elemental mapping. The analytical performance of the LIBS system has been evaluated through the correlation of the LIBS determined concentrations of Mn with its certified values. The results are found to be in very good agreement with the certified concentrations.

Unnikrishnan, V. K.; Nayak, Rajesh; Kartha, V. B.; Santhosh, C., E-mail:, E-mail: [Department of Atomic and Molecular Physics, Manipal University, Manipal (India); Sonavane, M. S. [Nuclear Recycle Board, Bhabha Atomic Research Centre, Mumbai (India); Yeotikar, R. G. [Process Development Division, Bhabha Atomic Research Centre, Mumbai (India); Shah, M. L.; Gupta, G. P.; Suri, B. M. [Laser and Plasma Technology Division, Bhabha Atomic Research Centre, Mumbai (India)



Quantitative study of Co(II) complexation by synchronous fluorescence spectroscopy with Sundarban mangrove habitat humic substances  

Microsoft Academic Search

Attempt has been made to isolate and characterize humic substances and their relative role for complexation of Co (II) in the mangrove sediment. Conditional stability constant (Kc) for Co (II) complexes with humic and fulvic acids were de- termined by studying quenching of fluorescence intensity of humic substances with Co (II) using synchronous fluorescence spectroscopy. Fulvic acid forms more stable

H. Ghatak; S. K. Mukhopadhyaya; H. Biswas; T. K. Jana


Detection and Quantitative Analysis of Chemical Species in Hanford Tank Materials Using Raman Spectroscopy Technology: FY94Florida State University Raman Spectroscopy Report  

SciTech Connect

This report provides a summary of work completed in FY-94 by FSU to develop and investigate the feasibility of using Raman spectroscopy with Hanford tank waste materials. Raman performance impacts from sample morphology, including the effects of absorption, particle size, density, color and refractive index, are discussed. An algorithm for relative species concentration measurement from Raman data is presented. An Algorithm for applying Raman to tank waste core screening is presented and discussed. A library of absorption and Raman spectra are presented that support this work.

Reich, F.R.



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



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

Microsoft Academic Search

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

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



Skin Melanin, Hemoglobin, and Light Scattering Properties can be Quantitatively Assessed In Vivo Using Diffuse Reflectance Spectroscopy  

Microsoft Academic Search

Noninvasive and real-time analysis of skin properties is useful in a wide variety of applications. In particular, the quantitative assessment of skin in terms of hemoglobin and melanin content, as well as in terms of its light scattering properties, is a challenging problem in dermatology. We present here a technique for examining human skin, based on the in vivo measurement

George Zonios; Julie Bykowski; Nikiforos Kollias



Gelatin embedding: a novel way to preserve biological samples for terahertz imaging and spectroscopy  

NASA Astrophysics Data System (ADS)

Sample dehydration has traditionally been a challenging problem in ex vivo terahertz biomedical experiments as water content changes significantly affect the terahertz properties and can diminish important contrast features. In this paper, we propose a novel method to prevent sample dehydration using gelatin embedding. By looking at terahertz image data and calculating the optical properties of the gelatin-embedded sample, we find that our method successfully preserves the sample for at least 35?h, both for imaging and spectroscopy. Our novel preservation method demonstrates for the first time the capability to simultaneously maintain sample structural integrity and prevent dehydration at room temperature. This is particularly relevant for terahertz studies of freshly excised tissues but could be beneficial for other imaging and spectroscopy techniques.

Fan, Shuting; Ung, Benjamin; Parrott, Edward P. J.; Pickwell-MacPherson, Emma



Raman Micro-spectroscopy Study of Healthy and Burned Biological Tissue  

NASA Astrophysics Data System (ADS)

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

Zarnani, Faranak; Glosser, Robert; Idris, Ahamed



Gelatin embedding: a novel way to preserve biological samples for terahertz imaging and spectroscopy.  


Sample dehydration has traditionally been a challenging problem in ex vivo terahertz biomedical experiments as water content changes significantly affect the terahertz properties and can diminish important contrast features. In this paper, we propose a novel method to prevent sample dehydration using gelatin embedding. By looking at terahertz image data and calculating the optical properties of the gelatin-embedded sample, we find that our method successfully preserves the sample for at least 35?h, both for imaging and spectroscopy. Our novel preservation method demonstrates for the first time the capability to simultaneously maintain sample structural integrity and prevent dehydration at room temperature. This is particularly relevant for terahertz studies of freshly excised tissues but could be beneficial for other imaging and spectroscopy techniques. PMID:25768394

Fan, Shuting; Ung, Benjamin; Parrott, Edward P J; Pickwell-MacPherson, Emma



[Study on temperature & EMF co-effects on insulin conformation and biological functions by fluorescence and Raman spectroscopy].  


Our previous studies had suggested that the intercellular signal molecule might be an important target of electromagnetic fields. Insulin, an intercellule signal molecule, plays a critical role in transferring life information. The studies on effects of pulsed electric fields (PEF) on insulin molecule are meaningful for explaining the mechanism of biological effects of electromagnetic fields. The PEF, which we used, with its highest electric field (2 x 10(6) V x m(-1)) coupled into the insulin buffer, was about 1 V x cm(-1) cm, with a repeating frequency of 50 Hz. In the present study, the changes of insulin conformation induced by PEF were studied by fluorescence spectroscopy. Insulin solution was exposed to 50 Hz PEF with different electric field intensities for 5-35 min, which caused a time-and dose-dependent decrease in fluorescence intensities of insulin. Further, insulin solution was exposed to PEF at different temperatures to investigate the effects of PEF co-operated with temperature on insulin. The results indicated that the difference in temperature (about 5 degrees C) could induce conflict results, which is due to the effects of PEF co-operated with temperature rather than only to the effect of temperature. The authors calculated that the increase in temperature induced by PEF was 0.07 degrees C (less than 0.1 degrees C). So the effects of PEF were scarcely explained by thermal effects, it belongs to "non-thermal effects" of electric fields. So it was concluded that temperature is a considerably important factor in "non-thermal effects" of electric fields, and the ignorance of variety of temperature probably result in the contrary conclusion. Further, Raman spectroscopy was used to investigate the details of structure of insulin treated by PEF co-operated with temperature. The results of Raman spectroscopy verified the effects of PEF co-operated with temperature on insulin. And the reductions of the S-S band intensity at 510 cm(-1), the skeletal C-C stretch band intensity at 934 cm(-1), and the content of the secondary structure of the alpha helix were observed. Both S--S linkages and alpha helix structure were important to the stabilization of insulin conformation. Modification of insulin may change the biological activity either by reducing the affinity of the hormone for the receptor or by decreasing the ability of the complex, when formed, to elicit a biological response. PMID:18800719

Yan, Zhe; Chen, Shu-de; Qiao, Deng-jiang



Trap Spectroscopy by Charge Injection and Sensing (TSCIS): A quantitative electrical technique for studying defects in dielectric stacks  

Microsoft Academic Search

Trap spectroscopy by charge injection and sensing (TSCIS) is a new, fast and powerful material analysis technique that provides detailed information on the trap density profile and trap energy level in dielectric materials. We show the measurement principle and explain the data analysis. The technique is applied to a number of example materials: SiO2, Al2O3, and Si3N4. We show that

R. Degraeve; M. Cho; B. Govoreanu; B. Kaczer; M. B. Zahid; J. Van Houdt; M. Jurczak; G. Groeseneken



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


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

SciTech Connect

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

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



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


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



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


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

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



Quantitation of active pharmaceutical ingredients and excipients in powder blends using designed multivariate calibration models by near-infrared spectroscopy.  


This research note demonstrates the simultaneous quantitation of a pharmaceutical active ingredient and three excipients in a simulated powder blend containing acetaminophen, Prosolv and Crospovidone. An experimental design approach was used in generating a 5-level (%, w/w) calibration sample set that included 125 samples. The samples were prepared by weighing suitable amount of powders into separate 20-mL scintillation vials and were mixed manually. Partial least squares (PLS) regression was used in calibration model development. The models generated accurate results for quantitation of Crospovidone (at 5%, w/w) and magnesium stearate (at 0.5%, w/w). Further testing of the models demonstrated that the 2-level models were as effective as the 5-level ones, which reduced the calibration sample number to 50. The models had a small bias for quantitation of acetaminophen (at 30%, w/w) and Prosolv (at 64.5%, w/w) in the blend. The implication of the bias is discussed. PMID:15848006

Li, Weiyong; Worosila, Gregory D



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



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



On-Site Quantitative Elemental Analysis of Metal Ions in Aqueous Solutions by Underwater Laser-Induced Breakdown Spectroscopy Combined with Electrodeposition under Controlled Potential.  


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

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



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

NASA Astrophysics Data System (ADS)

A comparison of laser-induced breakdown spectroscopy (LIBS) sensitivity in laminar liquid jets and at the surface of a static liquid has been performed. Limits of detection (LODs) have been estimated for Na, Mg, Al, Ca, Ti, V, Cr, Mn, Ni, Fe, Cu, Zn, Mo, Ag, Cd, and Ba under similar conditions using both experimental arrangements. LODs in liquid jets are found to be four times lower on average compared to measurements at static surfaces. Data acquisition rates in jet experiments are also generally higher than for static liquids due to reduced problems with splashing effects. The use of LIBS in jets has also been investigated for quantitative analysis of used lubricants. A number of contaminants have been measured in a set of used engine oils and the results compared to analysis via ICP-AES, where a good correlation is obtained.

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



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



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



Molecular force spectroscopy on cells.  


Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions. PMID:25580628

Liu, Baoyu; Chen, Wei; Zhu, Cheng



Identification and quantitative determination of carbohydrates in ethanolic extracts of two conifers using 13C NMR spectroscopy.  


We developed a method for the direct identification and quantification of carbohydrates in raw vegetable extracts using (13)C NMR spectroscopy without any preliminary step of precipitation or reduction of the components. This method has been validated (accuracy, precision and response linearity) using pure compounds and artificial mixtures before being applied to authentic ethanolic extracts of pine needles, pine wood and pine cones and fir twigs. We determined that carbohydrates represented from 15% to 35% of the crude extracts in which pinitol was the principal constituent accompanied by arabinitol, mannitol, glucose and fructose. PMID:18299126

Duquesnoy, Emilie; Castola, Vincent; Casanova, Joseph



Biogenic unmodified gold nanoparticles for selective and quantitative detection of cerium using UV-vis spectroscopy and photon correlation spectroscopy (DLS).  


The ability of self-functionalized biogenic GNPs towards highly selective colorimetric detection of rare earth element cerium is being reported for the first time. GNPs underwent rapid aggregation on addition of cerium indicated by red shift of SPR peak followed by complete precipitation. Hereby, this concept of co-ordination of cerium ions onto the GNP surface has been utilized for detection of cerium. The remarkable capacity of GNPs to sensitively detect Ce without proves beneficial compared to previous reports of colorimetric sensing. MDL was 15 and 35ppm by DLS and UV-vis spectroscopy respectively, suggesting DLS to be highly sensitive and a practical alternative in ultrasensitive detection studies. The sensing system showed a good linear fit favouring feasible detection of cerium in range of 2-50ppm. Similar studies further showed the superior selectivity of biogenic GNPs compared to chemically synthesized counterparts. The sensing system favours on-site analysis as it overcomes need of complex instrumentation, lengthy protocols and surface modification of GNP. PMID:25643600

Priyadarshini, E; Pradhan, N; Panda, P K; Mishra, B K



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

SciTech Connect

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

Skelly, E.M.



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

SciTech Connect

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

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



Quantitative analysis of trace lead in tin-base lead-free solder by laser-induced plasma spectroscopy in air at atmospheric pressure.  


A quantitative analysis of trace lead in tin-base lead-free solder was carried out with laser-induced plasma spectroscopy (LIPS). In order to evaluate the applicability of the technique for rapid in situ analytical purposes, measurements were performed in air at atmospheric pressure, and the emission characteristics of the plasma produced by a Q-switched Nd:YAG laser over a laser energy range of 10 - 90 mJ were investigated using time-resolved spectroscopy. The experimental results showed that the emission intensity of the analysis line (Pb I 405.78 nm) was maximized at a laser energy of around 30 mJ, and a time-resolved measurement of a spectrum with a delay time of 0.4 micros after the laser pulse was effective for reducing the background continuum. Based on the results, lead-free solder certified reference materials were analyzed for trace lead (concentration 174 - 1940 ppm), and a linear calibration curve was obtained with a detection limit of several tens ppm. PMID:18270425

Chen, Baozhong; Kano, Hidenori; Kuzuya, Mikio



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


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

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



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



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.


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



Quantitative NMR spectroscopy of complex technical mixtures using a virtual reference: chemical equilibria and reaction kinetics of formaldehyde-water-1,3,5-trioxane.  


Quantitative 1H NMR spectroscopy was used to study chemical equilibria and reaction kinetics of both the formation and decomposition of 1,3,5-trioxane in aqueous formaldehyde solutions. The reaction was homogeneously catalyzed with up to 0.10 g g(-1) sulfuric acid at temperatures between 360 and 383 K so that most of the experiments had to be carried out pressurized. The studied mixtures were complex due to the formation of methylene glycol and poly(oxymethylene) glycols in aqueous formaldehyde and the presence of considerable amounts of ionized species. Most common internal standards are decomposed by the hot sulfuric acid and external standards were not applicable using the flow NMR probe or pressurizable NMR sample tubes. Therefore, for the quantification of the small trioxane signals, a novel procedure was applied, in which electronically generated NMR signals were used as highly stable Virtual References (VR). The NMR decoupler channel with wave-form generator was used as the source of the reference signal, which was irradiated into the probe using the lock coil. Details on the experimental procedure are presented. It is shown that the presented method yields reliable quantitative reaction data for the complex studied mixtures. PMID:16773212

Maiwald, Michael; Grützner, Thomas; Ströfer, Eckhard; Hasse, Hans



Recovery and quantitative detection of thiabendazole on apples using a surface swab capture method followed by surface-enhanced Raman spectroscopy.  


We developed a rapid and simple method which combines a surface swab capture method and surface-enhanced Raman spectroscopy for recovery and quantitative detection of thiabendazole on apple surfaces. The whole apple surface was swabbed and the swab was vortexed in methanol releasing the pesticide. Silver dendrites were then added to bind the pesticide and used for enhancing the Raman signals. The recovery of the surface swab method was calculated to be 59.4-76.6% for intentionally contaminated apples at different levels (0.1, 0.3, 3, and 5 ppm, ?g/g per weight). After considering the releasing factor (66.6%) from the swab, the final accuracy of the swab-SERS method was calculated to be between 89.2% and 115.4%. This swab-SERS method is simple, sensitive, rapid (?10 min), and quantitative enough for QA/QC in plant procedure. This can be extended to detect other pesticides on raw agricultural produce like pears, carrots, and melons etc. PMID:24262524

He, Lili; Chen, Tuo; Labuza, Theodore P



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

Cary D. Chevalier



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.



Quantitative Study of Liver Magnetic Resonance Spectroscopy Quality at 3T Using Body and Phased Array Coils with Physical Analysis and Clinical Evaluation  

PubMed Central

This study aims to investigate the quality difference of short echo time (TE) breathhold 1H magnetic resonance spectroscopy (MRS) of the liver at 3.0T using the body and phased array coils, respectively. In total, 20 pairs of single-voxel proton spectra of the liver were acquired at 3.0T using the phased array and body coils as receivers. Consecutive stacks of breathhold spectra were acquired using the point resolved spectroscopy (PRESS) technique at a short TE of 30 ms and a repetition time (TR) of 1500 ms. The first spectroscopy sequence was “copied” for the second acquisition to ensure identical voxel positioning. The MRS prescan adjustments of shimming and water suppression, signal-to noise ratio (SNR), and major liver quantitative information were compared between paired spectra. Theoretical calculation of the SNR and homogeneity of the region of interest (ROI, 2 cm×2 cm×2 cm) using different coils loaded with 3D liver electromagnetic model of real human body was implemented in the theoretical analysis. The theoretical analysis showed that, inside the ROI, the SNR of the phase array coil was 2.8387 times larger than that of body coil and the homogeneity of the phase array coil and body coil was 80.10% and 93.86%, respectively. The experimental results showed excellent correlations between the paired data (all r > 0.86). Compared with the body coil group, the phased array group had slightly worse shimming effect and better SNR (all P values < .01). The discrepancy of the line width because of the different coils was approximately 0.8 Hz (0.00625 ppm). No significant differences of the major liver quantitative information of Cho/Lip2 height, Cho/Lip2 area, and lipid content were observed (all P values >0.05). The theoretical analysis and clinical experiment showed that the phased array coil was superior to the body coil with respect to 3.0T breathhold hepatic proton MRS. PMID:25881016

Xu, Li; Gu, Shiyong; Feng, Qianjin; Liang, Changhong; Xin, Sherman Xuegang



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


Laser-induced breakdown spectroscopy (LIBS) has been applied to the analysis of toxic metals Pb and Cd in Pb(NO3)2 and Cd(NO3)2.4H2O aqueous solutions, respectively. The plasma is generated by focusing a nanosecond Nd:YAG (?=1064?nm) laser on the surface of liquid in the homemade liquid jet configuration. With an assumption of local thermodynamic equilibrium (LTE), calibration curves of Pb and Cd were obtained at different delay times between 1 to 5??s. The temporal behavior of limit of detections (LOD) was investigated and it is shown that the minimum LODs for Pb and Cd are 4 and 68 parts in 10(6) (ppm), respectively. In order to demonstrate the correctness of the LTE assumption, plasma parameters including plasma temperature and electron density are evaluated, and it is shown that the LTE condition is satisfied at all delay times. PMID:21460994

Cheri, M Sadegh; Tavassoli, S H



Quantitative evaluation of multiple adulterants in roasted coffee by Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) and chemometrics.  


The current study presents an application of Diffuse Reflectance Infrared Fourier Transform Spectroscopy for detection and quantification of fraudulent addition of commonly employed adulterants (spent coffee grounds, coffee husks, roasted corn and roasted barley) to roasted and ground coffee. Roasted coffee samples were intentionally blended with the adulterants (pure and mixed), with total adulteration levels ranging from 1% to 66% w/w. Partial Least Squares Regression (PLS) was used to relate the processed spectra to the mass fraction of adulterants and the model obtained provided reliable predictions of adulterations at levels as low as 1% w/w. A robust methodology was implemented that included the detection of outliers. High correlation coefficients (0.99 for calibration; 0.98 for validation) coupled with low degrees of error (1.23% for calibration; 2.67% for validation) confirmed that DRIFTS can be a valuable analytical tool for detection and quantification of adulteration in ground, roasted coffee. PMID:24054633

Reis, Nádia; Franca, Adriana S; Oliveira, Leandro S



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



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


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



Combining selective sequential extractions, X-ray absorption spectroscopy, and principal component analysis for quantitative zinc speciation in soil.  


Selective sequential extractions (SSE) and, more recently, X-ray absorption fine-structure IXAFS) spectroscopy have been used to characterize the speciation of metal contaminants in soils and sediments. However, both methods have specific limitations when multiple metal species coexist in soils and sediments. In this study, we tested a combined approach, in which XAFS spectra were collected after each of 6 SSE steps, and then analyzed by multishell fitting, principal component analysis (PCA) and linear combination fits (LCF), to determine the Zn speciation in a smelter-contaminated, strongly acidic soil. In the topsoil, Zn was predominately found in the smelter-emitted minerals franklinite (60%) and sphalerite (30%) and as aqueous or outer-sphere Zn2+ (10%). In the subsoil, aqueous or outer-sphere Zn2+ prevailed (55%), but 45% of Zn was incorporated by hydroxy-Al interlayers of phyllosilicates. Formation of such Zn-bearing hydroxy-interlayers, which has been observed here for the first time, may be an important mechanism to reduce the solubility of Zn in those soils, which are too acidic to retain Zn by formation of inner-sphere sorption complexes, layered double hydroxides or phyllosilicates. The stepwise removal of Zn fractions by SSE significantly improved the identification of species by XAFS and PCA and their subsequent quantification by LCF. While SSE alone provided excellent estimates of the amount of mobile Zn species, it failed to identify and quantify Zn associated with mineral phases because of nonspecific dissolution and the precipitation of Zn oxalate. The systematic combination of chemical extraction, spectroscopy, and advanced statistical analysis allowed us to identify and quantify both mobile and recalcitrant species with high reliability and precision. PMID:12523415

Scheinost, Andreas C; Kretzschmar, Ruben; Pfister, Sabina; Roberts, Darryl R



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

E-print Network

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

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



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

E-print Network

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

Urbaneja, M A; Bresolin, F; Przybilla, N; Gieren, W; Pietrzynski, G



The Araucaria Project: The Local Group Galaxy WLM-Distance and Metallicity from Quantitative Spectroscopy of Blue Supergiants  

NASA Astrophysics Data System (ADS)

The quantitative analysis of low-resolution spectra of A and B supergiants is used to determine a distance modulus of 24.99+/-0.10 mag (995+/-46 kpc) to the Local Group galaxy WLM. The analysis yields stellar effective temperatures and gravities, which provide a distance through the flux-weighted gravity-luminosity relationship (FGLR). Our distance is 0.07 mag larger than the most recent results based on Cepheids and the tip of the red giant branch. This difference is within the 1 ? overlap of the typical uncertainties quoted in these photometric investigations. In addition, non-LTE spectral synthesis of the rich metal-line spectra (mostly iron, chromium, and titanium) of the A supergiants is carried out, which allows the determination of stellar metallicities. An average metallicity of -0.87+/-0.06 dex with respect to solar metallicity is found. Based on VLT observations for ESO Large Program 171.D-0004.

Urbaneja, Miguel A.; Kudritzki, Rolf-Peter; Bresolin, Fabio; Przybilla, Norbert; Gieren, Wolfgang; Pietrzy?ski, Grzegorz



Quantitative determination of the charge carrier concentration of ion implanted silicon by IR-near-field spectroscopy.  


We use a combination of a scattering-type near-field infrared microscope with a free-electron laser as an intense, tunable radiation source to spatially and spectrally resolve buried doped layers in silicon. To this end, boron implanted stripes in silicon are raster scanned at different wavelengths in the range from 10 to 14 µm. An analysis based on a simple Drude model for the dielectric function of the sample yields quantitatively correct values for the concentration of the activated carriers. In a control experiment at the fixed wavelength of 10.6 µm, interferometric near-field signals are recorded. The phase information gained in this experiment is fully consistent with the carrier concentration obtained in the spectrally resolved experiments. PMID:21164970

Jacob, Rainer; Winnerl, Stephan; Schneider, Harald; Helm, Manfred; Wenzel, Marc Tobias; von Ribbeck, Hans-Georg; Eng, Lukas M; Kehr, Susanne C



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



Development of a time-gated system for Raman spectroscopy of biological samples.  


A time gating system has been constructed that is capable of recording high quality Raman spectra of highly fluorescing biological samples while operating below the photodamage threshold. Using a collinear gating geometry and careful attention to power conservation, we have achieved all-optical switching with a one picosecond gating time and 5% peak gating efficiency. The energy per pulse in this instrument is more than 3 orders of magnitude weaker than previous reports. Using this system we have performed proof-of-concept experiments on a sample composed of perylene dissolved in toluene, and the stem of a Jasminum multiflorum plant, the latter case being particularly important for the study of plants used in production of cellulosic biofuels. In both cases, a high SNR spectrum of the high-wavenumber region of the spectrum was recorded in the presence of an overwhelming fluorescence background. PMID:20940895

Knorr, Florian; Smith, Zachary J; Wachsmann-Hogiu, Sebastian



Sensing Lanthanide Metal Content in Biological Tissues with Magnetic Resonance Spectroscopy  

PubMed Central

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

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



Quantitative determination of the oxidation state of iron in biotite using x-ray photoelectron spectroscopy: I. Calibration  

SciTech Connect

X-ray photoelectron spectroscopy (XPS) analyses of Fe(III)/{Sigma}Fe were calibrated with nine single crystals of biotite of known Fe(III)/{Sigma}Fe content. Peak shape parameters for the component Fe{sup 2+} and Fe{sup 3+} Fe 3p peaks were obtained by a constrained lease squares fitting method that minimized the difference between Fe(III)/{Sigma}Fe determined by XPS and wet chemistry/electron microprobe (WCEM) analyses. Fe{sup 2+} and Fe{sup 3+} peak separation was estimated from the separation of minima in the second derivative of Fe 3p spectra. The single set of derived peak parameters yielded a good linear correlation (r = 0.87) between XPS and WCEM values over the sample displaying progressive oxidation during XPS analysis resulted in Fe{sup 2} and Fe{sup 3+} component peak shapes largely consistent with the constrained least squares fitting methods. Beam damage, which appeared to be restricted to three single crystals with low {Sigma}Fe, low Fe/Mg, and high Fe(II)/{Sigma}Fe, caused increases in Fe(III)/{Sigma}Fe that were proportional to the duration of sample exposure. 60 refs., 6 figs., 7 tabs.

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



Remote quantitative analysis of cerium through a shielding window by stand-off laser-induced breakdown spectroscopy  

NASA Astrophysics Data System (ADS)

Laser-Induced Breakdown Spectroscopy (LIBS) has been considered in many applications in nuclear industry. LIBS can be an ideal technique for analyzing the inaccessible nuclear materials typically located behind a shielding window. We report the effect of optical transmittance of the shielding window on the analytical performances of stand-off LIBS for the preliminary surrogate sample of demonstration pyrochemical process, a mixture of cerium oxide (CeO2) and potassium chloride (KCl). A pulsed laser beam was focused on the surface of the sample located 1.45 m away from the stand-off LIBS device. The laser-induced plasma emission was collected through a Schmidt-Cassegrain telescope. LIBS spectra were obtained in an open path and through the shielding window. Univariate calibration curves were obtained using the integrated area of partially resolved Ce I and II lines. The limits of detection (LOD) for Ce were estimated to be 0.046 and 0.061 wt.% for the open-path and through-window analysis, respectively. We found that the through-window LOD is mainly influenced by the optical transmittance of the shielding window and therefore, the through-window LOD can be predicted from the open-path LOD and the optical transmittance of the shielding window. Also, multivariate calibration using partial least squares regression was successfully applied. The quality of calibration could be improved by the multivariate analysis.

Gong, Yongdeuk; Choi, Daewoong; Han, Bo-Young; Yoo, Jonghyun; Han, Song-Hee; Lee, Yonghoon



Standardization and validation of a new atomic absorption spectroscopy technique for determination and quantitation of aluminium adjuvant in immunobiologicals.  


In the present study, Aluminium quantification in immunobiologicals has been described using atomic absorption spectroscopy (AAS) technique. The assay was found to be linear in 25-125 microg/ml Aluminium range. The procedure was found to be accurate for different vaccines with recoveries of external additions ranging between 93.26 and 103.41%. The mean Limit of Variation (L.V.) for both intra- and inter-assay precision was calculated to be 1.62 and 2.22%, respectively. Further the procedure was found to be robust in relation to digestion temperature, alteration in acid (HNO(3) and H(2)SO(4)) ratio used for sample digestion and storage of digested vaccine samples up to a period of 15 days. After validation, AAS method was compared for its equivalency with routinely used complexometric titration method. On simultaneously applying on seven different groups of both bacterial and viral vaccines, viz., DPT, DT, TT, Hepatitis-A and B, Antirabies vaccine (cell culture) and tetravalent DPT-Hib, a high degree of positive correlation (+0.85-0.998) among AAS and titration methods was observed. Further AAS method was found to have an edge over complexometric titration method that a group of vaccines, viz., ARV (cell culture, adsorbed) and Hepatitis-A, in which Aluminium estimation is not feasible by pharmacopoeial approved complexometric titration method (possibly due to some interference in the sample matrix), this newly described and validated AAS assay procedure delivered accurate and reproducible results. PMID:17644407

Mishra, Arti; Bhalla, Sumir Rai; Rawat, Sameera; Bansal, Vivek; Sehgal, Rakesh; Kumar, Sunil



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.



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



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.


Laser spectroscopy and mass spectrometry of biologically relevant systems: chiral discrimination  

NASA Astrophysics Data System (ADS)

Radical ions are open-shell elusive species of paramount importance in many organic reactions and in biological processes. Oxidative bond breaking and forming involving radical ions are common process taking place in asymmetric enzyme cavities. Side-chain C?-C? bond fragmentation in the radical cations of aromatic alcohols is a common process in solution [1-3], whose efficiency is enhanced in polar solvents such as water. Hydrogen-bonding between the ion and the solvent in the relevant transition structure is thought as responsible of the rate acceleration [4]. Effects of achiral and chiral microsolvation on the radical cation of R-(+)-l-phenyl-l-propanol, have been investigated. The energy thresholds of the homolytic C?-C? bond breaking of R-(+)-1-phenyl-1-propanol radical cation, its mono-hydrated cluster, and its clusters with (2R,3R)-(-)-2,3-butanediol and (2S,3S)-(+)-2,3-butanediol have been studied through two color Resonant Two Photon Ionization, Photodissociation and Mass Spectrometry. The barrier of the C?-C? fragmentation is appreciably higher for the unsolvated molecular ion than for its adducts with solvent molecules. Moreover, marked differences in the ethyl loss fragmentation energy are observed for the clusters with water and with the two diols. In particular the homochiral cluster with (2R, 3R)-(-)-2,3-butanediol exhibits a fragmentation barrier higher than that of the corresponding heterochiral adduct with (25, 35)-(+)-2,3-butanediol.

Piccirillo, Susanna; Satta, Mauro; Coreno, Marcello; Catone, Daniele; Rondino, Flaminia; Scuderi, Debora; Paladini, Alessandra; Speranza, Maurizio; Giardini, Anna



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.



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



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



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

Microsoft Academic Search

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

J H Marden




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:, E-mail:, E-mail:, E-mail:, E-mail:, E-mail:, E-mail: [Departamento de Astronomia, Universidad de Concepcion, Casilla 160-C, Concepcion (Chile)



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



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

NASA Astrophysics Data System (ADS)

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

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



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


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

Edwards, C S; Christensen, P R



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

NASA Astrophysics Data System (ADS)

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

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



Molecular Biology 312 Appendix: Quantity One Manual p. 1 Using the "Quantity One" software package for Quantitative Analysis of Gels  

E-print Network

computer connected to the GelDoc system. When there are not other people waiting to use the GelDoc, you" are the commands you use to tell the program where your lanes are. Line up the frame lines with the center of each lane. Be sure the frame lines are #12;Molecular Biology 312 Appendix: Quantity One Manual p. 4 anchored

Lycan, Deborah E.


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



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

Microsoft Academic Search

High-throughput screening (HTS) of chemical compounds to identify modulators of molecular targets is a mainstay of pharmaceutical development. Increasingly, HTS is being used to identify chemical probes of gene, pathway, and cell functions, with the ultimate goal of comprehensively delineating relationships between chemical structures and biological activities. Achieving this goal will require methodologies that efficiently generate pharmacological data from the

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



Quantitative measurements by Fourier-transform infrared spectroscopy of toxic gas production during inhibition of JP-8 fires by CF(3)Br and C(3)F(7)H.  


Fourier-transform infrared spectroscopy is used to monitor gases generated during chemical inhibition of JP-8 fuel pool fires burning in air. Gas samples are taken from a location that approximates the position of an individual who is using a handheld extinguisher to subdue the fire. These gas samples are flowed through a 10-m path-length multipass optical cell placed in the sample beam of a Fourier-transform infrared spectrometer. Gas samples are analyzed before and during application of C(3)F(7)H (trade name FM200) and CF(3)Br (Halon 1301) to the fire. It is shown that application of these halogenated hydrocarbons to JP-8 pool fires produces significant quantities of acid gases (HF and HBr) and of CF(2)O. A calculation of the concentrations (in parts in 10(6)) of these gases and other gaseous combustion products, based on observed absorbances, is presented. We believe this is the first quantitative simultaneous measurement of HF, HBr, HCl, and CF(2)O production during chemical inhibition of real fires. PMID:21102803

Modiano, S H; McNesby, K L; Marsh, P E; Bolt, W; Herud, C



Quantitative measurements by Fourier-transform infrared spectroscopy of toxic gas production during inhibition of JP-8 fires by CF3Br and C3F7H  

NASA Astrophysics Data System (ADS)

Fourier-transform infrared spectroscopy is used to monitor gases generated during chemical inhibition of JP-8 fuel pool fires burning in air. Gas samples are taken from a location that approximates the position of an individual who is using a handheld extinguisher to subdue the fire. These gas samples are flowed through a 10-m path-length multipass optical cell placed in the sample beam of a Fourier-transform infrared spectrometer. Gas samples are analyzed before and during application of C3F7H (trade name FM200) and CF3Br (Halon 1301) to the fire. It is shown that application of these halogenated hydrocarbons to JP-8 pool fires produces significant quantities of acid gases (HF and HBr) and of CF2O. A calculation of the concentrations (in parts in 10 6) of these gases and other gaseous combustion products, based on observed absorbances, is presented. We believe this is the first quantitative simultaneous measurement of HF, HBr, HCl, and CF2O production during chemical inhibition of real fires.

Modiano, Steven H.; McNesby, Kevin L.; Marsh, Paul E.; Bolt, William; Herud, Craig



Implementation of Traditional and Real-World Cooperative Learning Techniques in Quantitative Analysis Including Near Infrared Spectroscopy for Analysis of Live Fish  

NASA Astrophysics Data System (ADS)

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 perform traditional unknown analyses, and as groups, they study an aquatic ecosystem simulated by a trout aquarium. Ecosystem analyses include the important chemical components of the nitrogen cycle, dissolved oxygen, and alkalinity. In addition to examining the aquatic system, trout are removed temporarily from the aquarium for analysis of lipid and moisture content using near infrared (NIR) spectroscopy. For the ecosystem investigation, students also determine costs of analyses and conduct quality-control studies. At the completion of the course, students are well versed in classical methods of analysis as well as educated on the relevance of modern technology, including up-to-date instrumentation and sophisticated multivariate calibration and prediction procedures. Course assessment results are summarized in the paper.

Houghton, Tracy P.; Kalivas, John H.



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

NASA Astrophysics Data System (ADS)

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

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



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

PubMed Central

The oxidation state of Mn in cubic SrMnO3 and orthorhombic SrMnO2.5 was investigated by electron energy loss (EEL) spectroscopy. Change in the oxidation state of Mn produced some spectral changes in the O-K edge as well as in the Mn-L2,3 edge EEL spectra. This study demonstrated that the oxidation state of Mn and the amount of oxygen vacancies in cubic SrMnO3 and orthorhombic SrMnO2.5 could be quantified by analyzing the features of the O-K edge spectrum and the Mn L3?L2 ratio in the Mn-L2,3 edge spectrum. Our quantitative analysis showed that the spectral changes in the Mn-L2,3 edge were mainly caused by the oxidation state of Mn, whereas those in the O-K edge could be sensitive to both the oxidation state of Mn and to lattice distortions. PMID:21245943

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



Quantitative measurements of loss on ignition in iron ore using laser-induced breakdown spectroscopy and partial least squares regression analysis.  


Laser-induced breakdown spectroscopy (LIBS) and partial least squares regression (PLSR) have been applied to perform quantitative measurements of a multiple-species parameter known as loss on ignition (LOI), in a combined set of run-of-mine (ROM) iron ore samples originating from five different iron ore deposits. Global calibration models based on 65 samples and their duplicates from all the deposits with LOI ranging from 0.5 to 10 wt% are shown to be successful for prediction of LOI content in pressed pellets as well as bulk ore samples. A global independent dataset comprising a further 60 samples was used to validate the model resulting in the best validation R(2) of 0.87 and root mean square error of prediction (RMSEP) of 1.1 wt% for bulk samples. A validation R(2) of 0.90 and an RMSEP of 1.0 wt% were demonstrated for pressed pellets. Data preprocessing is shown to improve the quality of the analysis. Spectra normalization options, automatic outlier removal and automatic continuum background correction, which were used to improve the performance of the PLSR method, are discussed in detail. PMID:21144150

Yaroshchyk, Pavel; Death, David L; Spencer, Steven J



The BioCAT undulator beamline 18ID: A facility for biological non-crystalline diffraction and x-ray absorption spectroscopy at the APS  

SciTech Connect

The 18ID undulator beamline of the Biophysics Collaborative Access Team at the Advanced Photon Source, Argonne, IL, USA, is a high-performance instrument designed for, and dedicated to, the study of partially ordered and disordered biological materials using the techniques of small-angle X-ray scattering, fiber diffraction, and X-ray absorption spectroscopy. The beamline and associated instrumentation are described in detail and examples of the representative experimental results are presented.

Fischetti, R.; Stepanov, S.; Rosenbaum, G.; Barrea, R.; Black, E.; Gore, D.; Heurich, R.; Kondrashkina, E.; Kropf, A.J.; Wang, S.; Zhang, K.; Irving, T.C.; Bunker, G.B. (IIT); (Georgia)




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...


Single shot white light interference microscopy with colour fringe analysis for quantitative phase imaging of biological cells  

NASA Astrophysics Data System (ADS)

To quantitatively obtain the phase map of Onion and human red blood cell (RBC) from white light interferogram we used Hilbert transform color fringe analysis technique. The three Red, Blue and Green color components are decomposed from single white light interferogram and Refractive index profile for Red, Blue and Green colour were computed in a completely non-invasive manner for Onion and human RBC. The present technique might be useful for non-invasive determination of the refractive index variation within cells and tissues and morphological features of sample with ease of operation and low cost.

Srivastava, Vishal; Mehta, D. S.



High-throughput quantitation of amino acids in rat and mouse biological matrices using stable isotope labeling and UPLC-MS/MS analysis.  


Quantifying amino acids in biological matrices is typically performed using liquid chromatography (LC) coupled with fluorescent detection (FLD), requiring both derivatization and complete baseline separation of all amino acids. Due to its high specificity and sensitivity, the use of UPLC-MS/MS eliminates the derivatization step and allows for overlapping amino acid retention times thereby shortening the analysis time. Furthermore, combining UPLC-MS/MS with stable isotope labeling (e.g., isobaric tag for relative and absolute quantitation, i.e., iTRAQ) of amino acids enables quantitation while maintaining sensitivity, selectivity and speed of analysis. In this study, we report combining UPLC-MS/MS analysis with iTRAQ labeling of amino acids resulting in the elution and quantitation of 44 amino acids within 5 min demonstrating the speed and convenience of this assay over established approaches. This chromatographic analysis time represented a 5-fold improvement over the conventional HPLC-MS/MS method developed in our laboratory. In addition, the UPLC-MS/MS method demonstrated improvements in both specificity and sensitivity without loss of precision. In comparing UPLC-MS/MS and HPLC-MS/MS results of 32 detected amino acids, only 2 amino acids exhibited imprecision (RSD) >15% using UPLC-MS/MS, while 9 amino acids exhibited RSD >15% using HPLC-MS/MS. Evaluating intra- and inter-assay precision over 3 days, the quantitation range for 32 detected amino acids in rat plasma was 0.90-497 ?M, with overall mean intra-day precision of less than 15% and mean inter-day precision of 12%. This UPLC-MS/MS assay was successfully implemented for the quantitative analysis of amino acids in rat and mouse plasma, along with mouse urine and tissue samples, resulting in the following concentration ranges: 0.98-431 ?M in mouse plasma for 32 detected amino acids; 0.62-443 ?M in rat plasma for 32 detected amino acids; 0.44-8590?M in mouse liver for 33 detected amino acids; 0.61-1241 ?M in mouse kidney for 37 detected amino acids; and 1.39-1,681 ?M in rat urine for 34 detected amino acids. The utility of the assay was further demonstrated by measuring and comparing plasma amino acid levels between pre-diabetic Zucker diabetic fatty rats (ZDF/Gmi fa/fa) and their lean littermates (ZDF/Gmi fa/?). Significant differences (P<0.001) in 9 amino acid concentrations were observed, with the majority ranging from a 2- to 5-fold increase in pre-diabetic ZDF rats on comparison with ZDF lean rats, consistent with previous literature reports. PMID:24842860

Takach, Edward; O'Shea, Thomas; Liu, Hanlan



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.



Quantitative techniques for assessing and controlling the dispersion and biological effects of multiwalled carbon nanotubes in mammalian tissue culture cells.  


In vivo studies have demonstrated that the state of dispersion of carbon nanotubes (CNTs) plays an important role in generating adverse pulmonary effects. However, little has been done to develop reproducible and quantifiable dispersion techniques to conduct mechanistic studies in vitro. This study was to evaluate the dispersion of multiwalled carbon nanotubes (MWCNTs) in tissue culture media, with particular emphasis on understanding the forces that govern agglomeration and how to modify these forces. Quantitative techniques such as hydrophobicity index, suspension stability index, attachment efficiency, and dynamic light scattering were used to assess the effects of agglomeration and dispersion of as-prepared (AP), purified (PD), or carboxylated (COOH) MWCNTs on bronchial epithelial and fibroblast cell lines. We found that hydrophobicity is the major factor determining AP- and PD-MWCNT agglomeration in tissue culture media but that the ionic strength is the main factor determining COOH-MWCNT suspendability. Bovine serum albumin (BSA) was an effective dispersant for MWCNTs, providing steric and electrosteric hindrances that are capable of overcoming hydrophobic attachment and the electrostatic screening of double layer formation in ionic media. Thus, BSA was capable of stabilizing all tube versions. Dipalmitoylphosphatidylcholine (DPPC) provided additional stability for AP-MWCNTs in epithelial growth medium (BEGM). While the dispersion state did not affect cytotoxicity, improved dispersion of AP- and PD-MWCNTs increased TGF-?1 production in epithelial cells and fibroblast proliferation. In summary, we demonstrate how quantitative techniques can be used to assess the agglomeration state of MWCNTs when conducting mechanistic studies on the effects of dispersion on tissue culture cells. PMID:21067152

Wang, Xiang; Xia, Tian; Ntim, Susana Addo; Ji, Zhaoxia; George, Saji; Meng, Huan; Zhang, Haiyuan; Castranova, Vincent; Mitra, Somenath; Nel, André E



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



Quantitative excited state spectroscopy of a single InGaAs quantum dot molecule through multi-million-atom electronic structure calculations.  


Atomistic electronic structure calculations are performed to study the coherent inter-dot couplings of the electronic states in a single InGaAs quantum dot molecule. The experimentally observed excitonic spectrum by Krenner et al (2005) Phys. Rev. Lett. 94 057402 is quantitatively reproduced, and the correct energy states are identified based on a previously validated atomistic tight binding model. The extended devices are represented explicitly in space with 15-million-atom structures. An excited state spectroscopy technique is applied where the externally applied electric field is swept to probe the ladder of the electronic energy levels (electron or hole) of one quantum dot through anti-crossings with the energy levels of the other quantum dot in a two-quantum-dot molecule. This technique can be used to estimate the spatial electron-hole spacing inside the quantum dot molecule as well as to reverse engineer quantum dot geometry parameters such as the quantum dot separation. Crystal-deformation-induced piezoelectric effects have been discussed in the literature as minor perturbations lifting degeneracies of the electron excited (P and D) states, thus affecting polarization alignment of wavefunction lobes for III-V heterostructures such as single InAs/GaAs quantum dots. In contrast, this work demonstrates the crucial importance of piezoelectricity to resolve the symmetries and energies of the excited states through matching the experimentally measured spectrum in an InGaAs quantum dot molecule under the influence of an electric field. Both linear and quadra