Sample records for absorption-biological reduction integrated

  1. Error Reduction Methods for Integrated-path Differential-absorption Lidar Measurements

    NASA Technical Reports Server (NTRS)

    Chen, Jeffrey R.; Numata, Kenji; Wu, Stewart T.

    2012-01-01

    We report new modeling and error reduction methods for differential-absorption optical-depth (DAOD) measurements of atmospheric constituents using direct-detection integrated-path differential-absorption lidars. Errors from laser frequency noise are quantified in terms of the line center fluctuation and spectral line shape of the laser pulses, revealing relationships verified experimentally. A significant DAOD bias is removed by introducing a correction factor. Errors from surface height and reflectance variations can be reduced to tolerable levels by incorporating altimetry knowledge and "log after averaging", or by pointing the laser and receiver to a fixed surface spot during each wavelength cycle to shorten the time of "averaging before log".

  2. Pathway of FeEDTA transformation and its impact on performance of NOx removal in a chemical absorption-biological reduction integrated process

    PubMed Central

    Li, Wei; Zhao, Jingkai; Zhang, Lei; Xia, Yinfeng; Liu, Nan; Li, Sujing; Zhang, Shihan

    2016-01-01

    A novel chemical absorption-biological reduction (CABR) integrated process, employing ferrous ethylenediaminetetraacetate (Fe(II)EDTA) as a solvent, is deemed as a potential option for NOx removal from the flue gas. Previous work showed that the Fe(II)EDTA concentration was critical for the NOx removal in the CABR process. In this work, the pathway of FeEDTA (Fe(III)/Fe(II)-EDTA) transformation was investigated to assess its impact on the NOx removal in a biofilter. Experimental results revealed that the FeEDTA transformation involved iron precipitation and EDTA degradation. X-ray photoelectron spectroscopy analysis confirmed the iron was precipitated in the form of Fe(OH)3. The iron mass balance analysis showed 44.2% of the added iron was precipitated. The EDTA degradation facilitated the iron precipitation. Besides chemical oxidation, EDTA biodegradation occurred in the biofilter. The addition of extra EDTA helped recover the iron from the precipitation. The transformation of FeEDTA did not retard the NO removal. In addition, EDTA rather than the iron concentration determined the NO removal efficiency. PMID:26743930

  3. Absorptive coding metasurface for further radar cross section reduction

    NASA Astrophysics Data System (ADS)

    Sui, Sai; Ma, Hua; Wang, Jiafu; Pang, Yongqiang; Feng, Mingde; Xu, Zhuo; Qu, Shaobo

    2018-02-01

    Lossless coding metasurfaces and metamaterial absorbers have been widely used for radar cross section (RCS) reduction and stealth applications, which merely depend on redirecting electromagnetic wave energy into various oblique angles or absorbing electromagnetic energy, respectively. Here, an absorptive coding metasurface capable of both the flexible manipulation of backward scattering and further wideband bistatic RCS reduction is proposed. The original idea is carried out by utilizing absorptive elements, such as metamaterial absorbers, to establish a coding metasurface. We establish an analytical connection between an arbitrary absorptive coding metasurface arrangement of both the amplitude and phase and its far-field pattern. Then, as an example, an absorptive coding metasurface is demonstrated as a nonperiodic metamaterial absorber, which indicates an expected better performance of RCS reduction than the traditional lossless coding metasurface and periodic metamaterial-absorber. Both theoretical analysis and full-wave simulation results show good accordance with the experiment.

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

    PubMed Central

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

    2012-01-01

    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

  5. [Gas Concentration Measurement Based on the Integral Value of Absorptance Spectrum].

    PubMed

    Liu, Hui-jun; Tao, Shao-hua; Yang, Bing-chu; Deng, Hong-gui

    2015-12-01

    The absorptance spectrum of a gas is the basis for the qualitative and quantitative analysis of the gas by the law of the Lambert-Beer. The integral value of the absorptance spectrum is an important parameter to describe the characteristics of the gas absorption. Based on the measured absorptance spectrum of a gas, we collected the required data from the database of HIT-RAN, and chose one of the spectral lines and calculated the integral value of the absorptance spectrum in the frequency domain, and then substituted the integral value into Lambert-Beer's law to obtain the concentration of the detected gas. By calculating the integral value of the absorptance spectrum we can avoid the more complicated calculation of the spectral line function and a series of standard gases for calibration, so the gas concentration measurement will be simpler and faster. We studied the changing trends of the integral values of the absorptance spectrums versus temperature. Since temperature variation would cause the corresponding variation in pressure, we studied the changing trends of the integral values of the absorptance spectrums versus both the pressure not changed with temperature and changed with the temperature variation. Based on the two cases, we found that the integral values of the absorptance spectrums both would firstly increase, then decrease, and finally stabilize with temperature increasing, but the ranges of specific changing trend were different in the two cases. In the experiments, we found that the relative errors of the integrated values of the absorptance spectrum were much higher than 1% and still increased with temperature when we only considered the change of temperature and completely ignored the pressure affected by the temperature variation, and the relative errors of the integrated values of the absorptance spectrum were almost constant at about only 1% when we considered that the pressure were affected by the temperature variation. As the integral value

  6. Model reduction in mathematical pharmacology : Integration, reduction and linking of PBPK and systems biology models.

    PubMed

    Snowden, Thomas J; van der Graaf, Piet H; Tindall, Marcus J

    2018-03-26

    In this paper we present a framework for the reduction and linking of physiologically based pharmacokinetic (PBPK) models with models of systems biology to describe the effects of drug administration across multiple scales. To address the issue of model complexity, we propose the reduction of each type of model separately prior to being linked. We highlight the use of balanced truncation in reducing the linear components of PBPK models, whilst proper lumping is shown to be efficient in reducing typically nonlinear systems biology type models. The overall methodology is demonstrated via two example systems; a model of bacterial chemotactic signalling in Escherichia coli and a model of extracellular regulatory kinase activation mediated via the extracellular growth factor and nerve growth factor receptor pathways. Each system is tested under the simulated administration of three hypothetical compounds; a strong base, a weak base, and an acid, mirroring the parameterisation of pindolol, midazolam, and thiopental, respectively. Our method can produce up to an 80% decrease in simulation time, allowing substantial speed-up for computationally intensive applications including parameter fitting or agent based modelling. The approach provides a straightforward means to construct simplified Quantitative Systems Pharmacology models that still provide significant insight into the mechanisms of drug action. Such a framework can potentially bridge pre-clinical and clinical modelling - providing an intermediate level of model granularity between classical, empirical approaches and mechanistic systems describing the molecular scale.

  7. INVESTIGATION OF REDUCTION OF ABSORPTION OF RADIOACTIVE MATERIAL BY MEANS OF ASTRINGENTS (in German)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lehrnbecher, W.

    1963-02-01

    An attempt was made to use the astringent properties of two substances, adrenalin and tannin, for reducing skin absorption of radioactive substances on female Wistar rats. The effect of 1/2% adrenalin emulsion and of a 2% tannin solution on the absorption of a BETA -emitting substance (Sr/sup 89/Cl/sub 2/ solution) was observed over three periods of 30, 60, and 90 min. A reduction of absorption was found after using adrenalin and tanning. The effect of adrenalin was small, particularly over prolonged periods of observation, and there was a marked reduction of absorption resulting from the use of tannin during allmore » periods of observation-. A method is described that permits an estimate of the reduction in skin absorption of BETA rays. (P.C.H.)« less

  8. Tuning the nonlinear optical absorption of reduced graphene oxide by chemical reduction.

    PubMed

    Shi, Hongfei; Wang, Can; Sun, Zhipei; Zhou, Yueliang; Jin, Kuijuan; Redfern, Simon A T; Yang, Guozhen

    2014-08-11

    Reduced graphene oxides with varying degrees of reduction have been produced by hydrazine reduction of graphene oxide. The linear and nonlinear optical properties of both graphene oxide as well as the reduced graphene oxides have been measured by single beam Z-scan measurement in the picosecond region. The results reveal both saturable absorption and two-photon absorption, strongly dependent on the intensity of the pump pulse: saturable absorption occurs at lower pump pulse intensity (~1.5 GW/cm2 saturation intensity) whereas two-photon absorption dominates at higher intensities (≥5.7 GW/cm2). Intriguingly, we find that the two-photon absorption coefficient (from 1.5 cm/GW to 4.5cm/GW) and the saturation intensity (from 1 GW/cm2 to 2 GW/cm2) vary with chemical reduction, which is ascribed to the varying concentrations of sp2 domains and sp2 clusters in the reduced graphene oxides. Our results not only provide an insight into the evolution of the nonlinear optical coefficient in reduced graphene oxide, but also suggest that chemical engineering techniques may usefully be applied to tune the nonlinear optical properties of various nano-materials, including atomically thick graphene sheets.

  9. Nonlinear absorption in biological tissue for high intensity focused ultrasound.

    PubMed

    Liu, Xiaozhou; Li, Junlun; Gong, Xiufen; Zhang, Dong

    2006-12-22

    In recent years the propagation of the high intensity focused ultrasound (HIFU) in biological tissue is an interesting area due to its potential applications in non-invasive treatment of disease. The base principle of these applications is the heat effect generated by ultrasound absorption. In order to control therapeutic efficiency, it is important to evaluate the heat generation in biological tissue irradiated by ultrasound. In his paper, based on the Khokhlov-Zabolotkaya-Kuznetsov (KZK) equation in frequency-domain, the numerical simulations of nonlinear absorption in biological tissues for high intensity focused ultrasound are performed. We find that ultrasound thermal transfer effect will be enhanced with the increasing of initial acoustic intensity due to the high harmonic generation. The concept of extra absorption factor is introduced to describe nonlinear absorption in biological tissue for HIFU. The theoretical results show that the heat deposition induced by the nonlinear theory can be nearly two times as large as that predicated by linear theory. Then, the influence of the diffraction effect on the position of the focus in HIFU is investigated. It is shown that the sound focus moves toward the transducer compared with the geometry focus because of the diffraction of the sound wave. The position of the maximum heat deposition is shifted to the geometry focus with the increase of initial acoustic intensity because the high harmonics are less diffraction. Finally, the temperature in the porcine fat tissue changing with the time is predicated by Pennes' equation and the experimental results verify the nonlinear theoretical prediction.

  10. Sulphate absorption across biological membranes.

    PubMed

    Mitchell, Stephen C; Waring, Rosemary H

    2016-01-01

    1. Sulphonation is unusual amongst the common Phase II (condensation; synthetic) reactions experienced by xenobiotics, in that the availability of the conjugating agent, sulphate, may become a rate-limiting factor. This sulphate is derived within the body via the oxygenation of sulphur moieties liberated from numerous ingested compounds including the sulphur-containing amino acids. Preformed inorganic sulphate also makes a considerable contribution to this pool. 2. There has been a divergence of opinion as to whether or not inorganic sulphate may be readily absorbed from the gastrointestinal tract and this controversy still continues in some quarters. Even more so, is the vexing question of potential absorption of inorganic sulphate via the lungs and through the skin. 3. This review examines the relevant diverse literature and concludes that sulphate ions may move across biological membranes by means of specific transporters and, although the gastrointestinal tract is by far the major portal of entry, some absorption across the lungs and the skin may take place under appropriate circumstances.

  11. FREQUENCY-DEPENDENT ABSORPTION OF ELECTROMAGNETIC ENERGY IN BIOLOGICAL TISSUE

    EPA Science Inventory

    The frequency-dependent absorption of electromagnetic energy in biological tissue is illustrated by use of the Debye equations, model calculations for different irradiation conditions, and measured electrical properties (conductivity and permittivity) of different tissues. Four s...

  12. Importance of Air Absorption During Mechanical Integrity Testing

    NASA Astrophysics Data System (ADS)

    Arnold, Fredric C.

    1990-11-01

    Wells used for injection of liquid industrial waste into deep saline aquifers are required to be periodically tested for mechanical integrity. A generally accepted method to demonstrate mechanical integrity is to pressurize the casing-tubing annulus and monitor any decline in pressure. If air is used to pressurize the annulus, uncertainty may exist in differentiating between absorption of air into water in the annulus and loss of pressure due to the absence of mechanical integrity. An analytical model of air absorbance has been derived and used to quantify the pressure decline due to dissolving and diffusion of the air in annular water. A parameteric study was made to determine when annular pressure decline due to absorption of air is significant.

  13. SPATIAL DISTRIBUTIONS OF ABSORPTION, LOCAL SUPPRESSION, AND EMISSIVITY REDUCTION OF SOLAR ACOUSTIC WAVES IN MAGNETIC REGIONS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chou, D.-Y.; Yang, M.-H.; Zhao Hui

    Observed acoustic power in magnetic regions is lower than the quiet Sun because of absorption, emissivity reduction, and local suppression of solar acoustic waves in magnetic regions. In the previous studies, we have developed a method to measure the coefficients of absorption, emissivity reduction, and local suppression of sunspots. In this study, we go one step further to measure the spatial distributions of three coefficients in two active regions, NOAA 9055 and 9057. The maps of absorption, emissivity reduction, and local suppression coefficients correlate with the magnetic map, including plage regions, except the emissivity reduction coefficient of NOAA 9055 wheremore » the emissivity reduction coefficient is too weak and lost among the noise.« less

  14. [Acoustic detection of absorption of millimeter-band electromagnetic waves in biological objects].

    PubMed

    Polnikov, I G; Putvinskiĭ, A V

    1988-01-01

    Principles of photoacoustic spectroscopy were applied to elaborate a new method for controlling millimeter electromagnetic waves absorption in biological objects. The method was used in investigations of frequency dependence of millimeter wave power absorption in vitro and in vivo in the commonly used experimental irradiation systems.

  15. Integrated Path Differential Absorption Lidar Optimizations Based on Pre-Analyzed Atmospheric Data for ASCENDS Mission Applications

    NASA Technical Reports Server (NTRS)

    Pliutau, Denis; Prasad, Narasimha S.

    2012-01-01

    In this paper a modeling method based on data reductions is investigated which includes pre analyzed MERRA atmospheric fields for quantitative estimates of uncertainties introduced in the integrated path differential absorption methods for the sensing of various molecules including CO2. This approach represents the extension of our existing lidar modeling framework previously developed and allows effective on- and offline wavelength optimizations and weighting function analysis to minimize the interference effects such as those due to temperature sensitivity and water vapor absorption. The new simulation methodology is different from the previous implementation in that it allows analysis of atmospheric effects over annual spans and the entire Earth coverage which was achieved due to the data reduction methods employed. The effectiveness of the proposed simulation approach is demonstrated with application to the mixing ratio retrievals for the future ASCENDS mission. Independent analysis of multiple accuracy limiting factors including the temperature, water vapor interferences, and selected system parameters is further used to identify favorable spectral regions as well as wavelength combinations facilitating the reduction in total errors in the retrieved XCO2 values.

  16. Spectrophotometer-Integrating-Sphere System for Computing Solar Absorptance

    NASA Technical Reports Server (NTRS)

    Witte, William G., Jr.; Slemp, Wayne S.; Perry, John E., Jr.

    1991-01-01

    A commercially available ultraviolet, visible, near-infrared spectrophotometer was modified to utilize an 8-inch-diameter modified Edwards-type integrated sphere. Software was written so that the reflectance spectra could be used to obtain solar absorptance values of 1-inch-diameter specimens. A descriptions of the system, spectral reflectance, and software for calculation of solar absorptance from reflectance data are presented.

  17. Theory of absorption integrated optical sensor of gaseous materials

    NASA Astrophysics Data System (ADS)

    Egorov, A. A.

    2010-10-01

    The eigen and noneigen (leaky) modes of a three-layer planar integrated optical waveguide are described. The dispersion relation of a three-layer planar waveguide and other dependences are derived, and the cutoff conditions are analyzed. The diagram of propagation constants of the guided and radiation modes of an irregular asymmetric three-layer waveguide and the dependence of the electric field amplitudes of radiation modes of substrate on vertical coordinate in a tantalum integrated optical waveguide are presented. The operating principles of an absorption integrated optical waveguide sensor are investigated. The dependences of sensitivity of an integrated optical waveguide sensor on the sensory cell length, the coupling efficiency of the laser radiation into the waveguide, the absorption cross-section of the studied material, and the level of additive statistical noise are investigated. Some of the prospective areas of application of integrated-optical waveguide sensors are outlined.

  18. Vertical electro-absorption modulator design and its integration in a VCSEL

    NASA Astrophysics Data System (ADS)

    Marigo-Lombart, L.; Calvez, S.; Arnoult, A.; Thienpont, H.; Almuneau, G.; Panajotov, K.

    2018-04-01

    Electro-absorption modulators, either embedded in CMOS technology or integrated with a semiconductor laser, are of high interest for many applications such as optical communications, signal processing and 3D imaging. Recently, the integration of a surface-normal electro-absorption modulator into a vertical-cavity surface-emitting laser has been considered. In this paper we implement a simple quantum well electro-absorption model and design and optimize an asymmetric Fabry-Pérot semiconductor modulator while considering all physical properties within figures of merit. We also extend this model to account for the impact of temperature on the different parameters involved in the calculation of the absorption, such as refractive indices and exciton transition broadening. Two types of vertical modulator structures have been fabricated and experimentally characterized by reflectivity and photocurrent measurements demonstrating a very good agreement with our model. Finally, preliminary results of an electro-absorption modulator vertically integrated with a vertical-cavity surface-emitting laser device are presented, showing good modulation performances required for high speed communications.

  19. Determination of optical coefficients of biological tissue from a single integrating-sphere

    NASA Astrophysics Data System (ADS)

    Zhang, Lianshun; Shi, Aijuan; Lu, Hongguang

    2012-01-01

    The detection of interactions between light and tissue can be used to characterize the optical properties of the tissue. The development is described of a method that determines optical coefficients of biological tissue from a single optical reflectance spectrum measured with an integrating-sphere. The experimental system incorporated a DH-2000 deuterium tungsten halogen light source, a USB4000-VIS-NIR miniature fiber optic spectrometer and an integrating-sphere. Fat emulsion and ink were used to mimic the scattering and absorbing properties of tissue in the tested sample. The measured optical reflectance spectrums with different scattering and absorbing properties were used to train a back-propagation neural network (BPNN). Then the neural network (BPNN) was used to determine the optical coefficients of biological tissue from a single optical reflectance spectrum measured with an integrating-sphere. Tests on tissue-simulation phantoms showed the relative errors of this technique to be 7% for the reduced scattering coefficient and 15% for the absorption coefficients. The optical properties of human skin were also measured in vivo.

  20. A Two Micron Coherent Differential Absorption Lidar Development

    NASA Technical Reports Server (NTRS)

    Yu, Jirong; Petros, Mulugeta; Chen, Songsheng; Bai, Yingxin; Petzar, Paul J.; Trieu, Bo C.; Koch, Grady J.; Beyon, Jeffrey Y.; VanValkenburg, Randal L.; Kavaya, Michael J.; hide

    2010-01-01

    A pulsed, 2-micron coherent Differential Absorption Lidar (DIAL)/Integrated Path Differential Absorption (IPDA) transceiver, developed under the Laser Risk Reduction Program (LRRP) at NASA, is integrated into a fully functional lidar instrument. This instrument measures atmospheric CO2 profiles (by DIAL) from a ground platform. It allows the investigators to pursue subsequent in science-driven deployments, and provides a unique tool for Active Sensing of CO2 Emissions over Night, Days, and Seasons (ASCENDS) validation that was strongly advocated in the recent ASCENDS Workshop. Keywords: Differential Absorption Lidar, Near Infrared Laser,

  1. Integrating Rehabilitation Engineering Technology With Biologics

    PubMed Central

    Collinger, Jennifer L.; Dicianno, Brad E.; Weber, Douglas J.; Cui, Xinyan Tracy; Wang, Wei; Brienza, David M.; Boninger, Michael L.

    2017-01-01

    Rehabilitation engineers apply engineering principles to improve function or to solve challenges faced by persons with disabilities. It is critical to integrate the knowledge of biologics into the process of rehabilitation engineering to advance the field and maximize potential benefits to patients. Some applications in particular demonstrate the value of a symbiotic relationship between biologics and rehabilitation engineering. In this review we illustrate how researchers working with neural interfaces and integrated prosthetics, assistive technology, and biologics data collection are currently integrating these 2 fields. We also discuss the potential for further integration of biologics and rehabilitation engineering to deliver the best technologies and treatments to patients. Engineers and clinicians must work together to develop technologies that meet clinical needs and are accessible to the intended patient population. PMID:21703573

  2. BiologicalNetworks 2.0 - an integrative view of genome biology data

    PubMed Central

    2010-01-01

    Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other) and their relations (interactions, co-expression, co-citations, and other). The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org. PMID:21190573

  3. Direct observation of single layer graphene oxide reduction through spatially resolved, single sheet absorption/emission microscopy.

    PubMed

    Sokolov, Denis A; Morozov, Yurii V; McDonald, Matthew P; Vietmeyer, Felix; Hodak, Jose H; Kuno, Masaru

    2014-06-11

    Laser reduction of graphene oxide (GO) offers unique opportunities for the rapid, nonchemical production of graphene. By tuning relevant reduction parameters, the band gap and conductivity of reduced GO can be precisely controlled. In situ monitoring of single layer GO reduction is therefore essential. In this report, we show the direct observation of laser-induced, single layer GO reduction through correlated changes to its absorption and emission. Absorption/emission movies illustrate the initial stages of single layer GO reduction, its transition to reduced-GO (rGO) as well as its subsequent decomposition upon prolonged laser illumination. These studies reveal GO's photoreduction life cycle and through it native GO/rGO absorption coefficients, their intrasheet distributions as well as their spatial heterogeneities. Extracted absorption coefficients for unreduced GO are α405 nm ≈ 6.5 ± 1.1 × 10(4) cm(-1), α520 nm ≈ 2.1 ± 0.4 × 10(4) cm(-1), and α640 nm ≈ 1.1 ± 0.3 × 10(4) cm(-1) while corresponding rGO α-values are α405 nm ≈ 21.6 ± 0.6 × 10(4) cm(-1), α520 nm ≈ 16.9 ± 0.4 × 10(4) cm(-1), and α640 nm ≈ 14.5 ± 0.4 × 10(4) cm(-1). More importantly, the correlated absorption/emission imaging provides us with unprecedented insight into GO's underlying photoreduction mechanism, given our ability to spatially resolve its kinetics and to connect local rate constants to activation energies. On a broader level, the developed absorption imaging is general and can be applied toward investigating the optical properties of other two-dimensional materials, especially those that are nonemissive and are invisible to current single molecule optical techniques.

  4. Biological sludge solubilisation for reduction of excess sludge production in wastewater treatment process.

    PubMed

    Yamaguchi, T; Yao, Y; Kihara, Y

    2006-01-01

    A novel sludge disintegration system (JFE-SD system) was developed for the reduction of excess sludge production in wastewater treatment plants. Chemical and biological treatments were applied to disintegrate excess sludge. At the first step, to enhance biological disintegration, the sludge was pretreated with alkali. At the second step, the sludge was disintegrated by biological treatment. Many kinds of sludge degrading microorganisms integrated the sludge. The efficiency of the new sludge disintegration system was confirmed in a full-scale experiment. The JFE-SD system reduced excess sludge production by approximately 50% during the experimental period. The quality of effluent was kept at quite a good level. Economic analysis revealed that this system could significantly decrease the excess sludge treatment cost.

  5. Absorption of CO2 from modified flue gases of power generation Tarahan chemically using NaOH and Na2CO3 and biologically using microalgae

    NASA Astrophysics Data System (ADS)

    Purba, Elida; Agustina, Dewi; Putri Pertama, Finka; Senja, Fita

    2018-03-01

    This research was carried out on the absorption of CO2 from the modified flue gases of power generation Tarahan using NaOH (sodium hydroxide) and Na2CO3 (sodium carbonate). The operation was conducted in a packed column absorber and then the output gases from the packed column was fed into photo-bioreactor for biological absorption. In the photo-bioreactor, two species of microalgae, N. occulata and T. chuii, were cultivated to both absorb CO2 gas and to produce biomass for algal oil. The aims of this research were, first, to determine the effect of absorbent flow rate on the reduction of CO2 and on the decrease of output gas temperature, second, to determine the characteristics of methyl ester obtained from biological absorption process. Flow rates of the absorbent were varied as 1, 2, and 3 l/min. The concentrations of NaOH and Na2CO3 were 1 M at a constant gas flow rate of 6 l/min. The output concentrations of CO2 from the absorber was analyzed using Gas Chromatography 2014-AT SHIMADZU Corp 08128. The results show that both of the absorbents give different trends. From the absorption using NaOH, it can be concluded that the higher the flow rate, the higher the absorption rate obtained. The highest flow rate achieved maximum absorption of 100%. On the other hand, absorption with Na2CO3 revealed the opposite trend where the higher the flow rates the lower the absorption rate. The highest absorption using Na2CO3 was obtained with the lowest flow rate, 1 l/min, that was 45,5%. As the effect of flow rate on output gas temperature, the temperature decreased with increasing flow rates for both absorbents. The output gas temperature for NaOH and Na2CO3 were consecutively 35 °C and 31 °C with inlet gas temperature of 50°C. Absorption of CO2 biologically resulted a reduction of CO2 up to 60% from the input gas concentration. Algal oil was extracted with mixed hexane and chloroform to obtain algal oil. Extracted oil was transesterified to methyl ester using sodium

  6. Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization.

    PubMed

    Yang, Jiaoyun; Wang, Haipeng; Ding, Huitong; An, Ning; Alterovitz, Gil

    2017-01-19

    Visualizing data by dimensionality reduction is an important strategy in Bioinformatics, which could help to discover hidden data properties and detect data quality issues, e.g. data noise, inappropriately labeled data, etc. As crowdsourcing-based synthetic biology databases face similar data quality issues, we propose to visualize biobricks to tackle them. However, existing dimensionality reduction methods could not be directly applied on biobricks datasets. Hereby, we use normalized edit distance to enhance dimensionality reduction methods, including Isomap and Laplacian Eigenmaps. By extracting biobricks from synthetic biology database Registry of Standard Biological Parts, six combinations of various types of biobricks are tested. The visualization graphs illustrate discriminated biobricks and inappropriately labeled biobricks. Clustering algorithm K-means is adopted to quantify the reduction results. The average clustering accuracy for Isomap and Laplacian Eigenmaps are 0.857 and 0.844, respectively. Besides, Laplacian Eigenmaps is 5 times faster than Isomap, and its visualization graph is more concentrated to discriminate biobricks. By combining normalized edit distance with Isomap and Laplacian Eigenmaps, synthetic biology biobircks are successfully visualized in two dimensional space. Various types of biobricks could be discriminated and inappropriately labeled biobricks could be determined, which could help to assess crowdsourcing-based synthetic biology databases' quality, and make biobricks selection.

  7. Integrating rehabilitation engineering technology with biologics.

    PubMed

    Collinger, Jennifer L; Dicianno, Brad E; Weber, Douglas J; Cui, Xinyan Tracy; Wang, Wei; Brienza, David M; Boninger, Michael L

    2011-06-01

    Rehabilitation engineers apply engineering principles to improve function or to solve challenges faced by persons with disabilities. It is critical to integrate the knowledge of biologics into the process of rehabilitation engineering to advance the field and maximize potential benefits to patients. Some applications in particular demonstrate the value of a symbiotic relationship between biologics and rehabilitation engineering. In this review we illustrate how researchers working with neural interfaces and integrated prosthetics, assistive technology, and biologics data collection are currently integrating these 2 fields. We also discuss the potential for further integration of biologics and rehabilitation engineering to deliver the best technologies and treatments to patients. Engineers and clinicians must work together to develop technologies that meet clinical needs and are accessible to the intended patient population. Copyright © 2011 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

  8. Model Order Reduction Algorithm for Estimating the Absorption Spectrum

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Van Beeumen, Roel; Williams-Young, David B.; Kasper, Joseph M.

    The ab initio description of the spectral interior of the absorption spectrum poses both a theoretical and computational challenge for modern electronic structure theory. Due to the often spectrally dense character of this domain in the quantum propagator’s eigenspectrum for medium-to-large sized systems, traditional approaches based on the partial diagonalization of the propagator often encounter oscillatory and stagnating convergence. Electronic structure methods which solve the molecular response problem through the solution of spectrally shifted linear systems, such as the complex polarization propagator, offer an alternative approach which is agnostic to the underlying spectral density or domain location. This generality comesmore » at a seemingly high computational cost associated with solving a large linear system for each spectral shift in some discretization of the spectral domain of interest. In this work, we present a novel, adaptive solution to this high computational overhead based on model order reduction techniques via interpolation. Model order reduction reduces the computational complexity of mathematical models and is ubiquitous in the simulation of dynamical systems and control theory. The efficiency and effectiveness of the proposed algorithm in the ab initio prediction of X-ray absorption spectra is demonstrated using a test set of challenging water clusters which are spectrally dense in the neighborhood of the oxygen K-edge. On the basis of a single, user defined tolerance we automatically determine the order of the reduced models and approximate the absorption spectrum up to the given tolerance. We also illustrate that, for the systems studied, the automatically determined model order increases logarithmically with the problem dimension, compared to a linear increase of the number of eigenvalues within the energy window. Furthermore, we observed that the computational cost of the proposed algorithm only scales quadratically with respect

  9. Integrating systems biology models and biomedical ontologies

    PubMed Central

    2011-01-01

    Background Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. Results We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. Conclusions We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms. PMID:21835028

  10. The staircase method: integrals for periodic reductions of integrable lattice equations

    NASA Astrophysics Data System (ADS)

    van der Kamp, Peter H.; Quispel, G. R. W.

    2010-11-01

    We show, in full generality, that the staircase method (Papageorgiou et al 1990 Phys. Lett. A 147 106-14, Quispel et al 1991 Physica A 173 243-66) provides integrals for mappings, and correspondences, obtained as traveling wave reductions of (systems of) integrable partial difference equations. We apply the staircase method to a variety of equations, including the Korteweg-De Vries equation, the five-point Bruschi-Calogero-Droghei equation, the quotient-difference (QD)-algorithm and the Boussinesq system. We show that, in all these cases, if the staircase method provides r integrals for an n-dimensional mapping, with 2r, then one can introduce q <= 2r variables, which reduce the dimension of the mapping from n to q. These dimension-reducing variables are obtained as joint invariants of k-symmetries of the mappings. Our results support the idea that often the staircase method provides sufficiently many integrals for the periodic reductions of integrable lattice equations to be completely integrable. We also study reductions on other quad-graphs than the regular {\\ Z}^2 lattice, and we prove linear growth of the multi-valuedness of iterates of high-dimensional correspondences obtained as reductions of the QD-algorithm.

  11. Improvement of infrared single-photon detectors absorptance by integrated plasmonic structures

    PubMed Central

    Csete, Mária; Sipos, Áron; Szalai, Anikó; Najafi, Faraz; Szabó, Gábor; Berggren, Karl K.

    2013-01-01

    Plasmonic structures open novel avenues in photodetector development. Optimized illumination configurations are reported to improve p-polarized light absorptance in superconducting-nanowire single-photon detectors (SNSPDs) comprising short- and long-periodic niobium-nitride (NbN) stripe-patterns. In OC-SNSPDs consisting of ~quarter-wavelength dielectric layer closed by a gold reflector the highest absorptance is attainable at perpendicular incidence onto NbN patterns in P-orientation due to E-field concentration at the bottom of nano-cavities. In NCAI-SNSPDs integrated with nano-cavity-arrays consisting of vertical and horizontal gold segments off-axis illumination in S-orientation results in polar-angle-independent perfect absorptance via collective resonances in short-periodic design, while in long-periodic NCAI-SNSPDs grating-coupled surface waves promote EM-field transportation to the NbN stripes and result in local absorptance maxima. In NCDAI-SNSPDs integrated with nano-cavity-deflector-array consisting of longer vertical gold segments large absorptance maxima appear in 3p-periodic designs due to E-field enhancement via grating-coupled surface waves synchronized with the NbN stripes in S-orientation, which enable to compensate fill-factor-related retrogression. PMID:23934331

  12. Data integration in biological research: an overview.

    PubMed

    Lapatas, Vasileios; Stefanidakis, Michalis; Jimenez, Rafael C; Via, Allegra; Schneider, Maria Victoria

    2015-12-01

    Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

  13. Methods for biological data integration: perspectives and challenges

    PubMed Central

    Gligorijević, Vladimir; Pržulj, Nataša

    2015-01-01

    Rapid technological advances have led to the production of different types of biological data and enabled construction of complex networks with various types of interactions between diverse biological entities. Standard network data analysis methods were shown to be limited in dealing with such heterogeneous networked data and consequently, new methods for integrative data analyses have been proposed. The integrative methods can collectively mine multiple types of biological data and produce more holistic, systems-level biological insights. We survey recent methods for collective mining (integration) of various types of networked biological data. We compare different state-of-the-art methods for data integration and highlight their advantages and disadvantages in addressing important biological problems. We identify the important computational challenges of these methods and provide a general guideline for which methods are suited for specific biological problems, or specific data types. Moreover, we propose that recent non-negative matrix factorization-based approaches may become the integration methodology of choice, as they are well suited and accurate in dealing with heterogeneous data and have many opportunities for further development. PMID:26490630

  14. Integration of culture and biology in human development.

    PubMed

    Mistry, Jayanthi

    2013-01-01

    The challenge of integrating biology and culture is addressed in this chapter by emphasizing human development as involving mutually constitutive, embodied, and epigenetic processes. Heuristically rich constructs extrapolated from cultural psychology and developmental science, such as embodiment, action, and activity, are presented as promising approaches to the integration of cultural and biology in human development. These theoretical notions are applied to frame the nascent field of cultural neuroscience as representing this integration of culture and biology. Current empirical research in cultural neuroscience is then synthesized to illustrate emerging trends in this body of literature that examine the integration of biology and culture.

  15. Dimension reduction techniques for the integrative analysis of multi-omics data

    PubMed Central

    Zeleznik, Oana A.; Thallinger, Gerhard G.; Kuster, Bernhard; Gholami, Amin M.

    2016-01-01

    State-of-the-art next-generation sequencing, transcriptomics, proteomics and other high-throughput ‘omics' technologies enable the efficient generation of large experimental data sets. These data may yield unprecedented knowledge about molecular pathways in cells and their role in disease. Dimension reduction approaches have been widely used in exploratory analysis of single omics data sets. This review will focus on dimension reduction approaches for simultaneous exploratory analyses of multiple data sets. These methods extract the linear relationships that best explain the correlated structure across data sets, the variability both within and between variables (or observations) and may highlight data issues such as batch effects or outliers. We explore dimension reduction techniques as one of the emerging approaches for data integration, and how these can be applied to increase our understanding of biological systems in normal physiological function and disease. PMID:26969681

  16. Integrating sphere-based photoacoustic setup for simultaneous absorption coefficient and Grüneisen parameter measurements of biomedical liquids

    NASA Astrophysics Data System (ADS)

    Villanueva, Yolanda; Hondebrink, Erwin; Petersen, Wilma; Steenbergen, Wiendelt

    2015-03-01

    A method for simultaneously measuring the absorption coefficient μa and Grüneisen parameter Γ of biological absorbers in photoacoustics is designed and implemented using a coupled-integrating sphere system. A soft transparent tube with inner diameter of 0.58mm is used to mount the liquid absorbing sample horizontally through the cavity of two similar and adjacent integrating spheres. One sphere is used for measuring the sample's μa using a continuous halogen light source and a spectrometer fiber coupled to the input and output ports, respectively. The other sphere is used for simultaneous photoacoustic measurement of the sample's Γ using an incident pulsed light with wavelength of 750nm and a flat transducer with central frequency of 5MHz. Absolute optical energy and pressure measurements are not necessary. However, the derived equations for determining the sample's μa and Γ require calibration of the setup using aqueous ink dilutions. Initial measurements are done with biological samples relevant to biomedical imaging such as human whole blood, joint and cyst fluids. Absorption of joint and cyst fluids is enhanced using a contrast agent like aqueous indocyanine green dye solution. For blood sample, measured values of μa = 0.580 +/- 0.016 mm-1 and Γ = 0.166 +/- 0.006 are within the range of values reported in literature. Measurements with the absorbing joint and cyst fluid samples give Γ values close to 0.12, which is similar to that of water and plasma.

  17. Semantic Web meets Integrative Biology: a survey.

    PubMed

    Chen, Huajun; Yu, Tong; Chen, Jake Y

    2013-01-01

    Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB.

  18. Compact characterization of liquid absorption and emission spectra using linear variable filters integrated with a CMOS imaging camera

    NASA Astrophysics Data System (ADS)

    Wan, Yuhang; Carlson, John A.; Kesler, Benjamin A.; Peng, Wang; Su, Patrick; Al-Mulla, Saoud A.; Lim, Sung Jun; Smith, Andrew M.; Dallesasse, John M.; Cunningham, Brian T.

    2016-07-01

    A compact analysis platform for detecting liquid absorption and emission spectra using a set of optical linear variable filters atop a CMOS image sensor is presented. The working spectral range of the analysis platform can be extended without a reduction in spectral resolution by utilizing multiple linear variable filters with different wavelength ranges on the same CMOS sensor. With optical setup reconfiguration, its capability to measure both absorption and fluorescence emission is demonstrated. Quantitative detection of fluorescence emission down to 0.28 nM for quantum dot dispersions and 32 ng/mL for near-infrared dyes has been demonstrated on a single platform over a wide spectral range, as well as an absorption-based water quality test, showing the versatility of the system across liquid solutions for different emission and absorption bands. Comparison with a commercially available portable spectrometer and an optical spectrum analyzer shows our system has an improved signal-to-noise ratio and acceptable spectral resolution for discrimination of emission spectra, and characterization of colored liquid’s absorption characteristics generated by common biomolecular assays. This simple, compact, and versatile analysis platform demonstrates a path towards an integrated optical device that can be utilized for a wide variety of applications in point-of-use testing and point-of-care diagnostics.

  19. Compact characterization of liquid absorption and emission spectra using linear variable filters integrated with a CMOS imaging camera.

    PubMed

    Wan, Yuhang; Carlson, John A; Kesler, Benjamin A; Peng, Wang; Su, Patrick; Al-Mulla, Saoud A; Lim, Sung Jun; Smith, Andrew M; Dallesasse, John M; Cunningham, Brian T

    2016-07-08

    A compact analysis platform for detecting liquid absorption and emission spectra using a set of optical linear variable filters atop a CMOS image sensor is presented. The working spectral range of the analysis platform can be extended without a reduction in spectral resolution by utilizing multiple linear variable filters with different wavelength ranges on the same CMOS sensor. With optical setup reconfiguration, its capability to measure both absorption and fluorescence emission is demonstrated. Quantitative detection of fluorescence emission down to 0.28 nM for quantum dot dispersions and 32 ng/mL for near-infrared dyes has been demonstrated on a single platform over a wide spectral range, as well as an absorption-based water quality test, showing the versatility of the system across liquid solutions for different emission and absorption bands. Comparison with a commercially available portable spectrometer and an optical spectrum analyzer shows our system has an improved signal-to-noise ratio and acceptable spectral resolution for discrimination of emission spectra, and characterization of colored liquid's absorption characteristics generated by common biomolecular assays. This simple, compact, and versatile analysis platform demonstrates a path towards an integrated optical device that can be utilized for a wide variety of applications in point-of-use testing and point-of-care diagnostics.

  20. Behavioral and Biological Effects of Resonant Electromagnetic Absorption in Rats.

    DTIC Science & Technology

    1976-11-01

    for 23-550 MHz, biological phantom materials to simulate tissue properties, monopole -above-ground radiation chamber, design of a waveguide slot array...Resonant Electromagnetic Power Absorption in Rats" L T OF FTCTIF S A,’L i .LIS SFigure Pa 1 A photograiph of the monopole -above-gruund radiation...and mice without ground effects (L/2b = 3.25 where 21Tb is the "average" circumference of the animals) ........ .................... ... 20 8

  1. Biological condition gradient: Applying a framework for determining the biological integrity of coral reefs

    EPA Science Inventory

    The goals of the U.S. Clean Water Act (CWA) are to restore and maintain the chemical, physical and biological integrity of water resources. Although clean water is a goal, another is to safeguard biological communities by defining levels of biological integrity to protect aquatic...

  2. Enhanced broadband absorption in nanowire arrays with integrated Bragg reflectors

    NASA Astrophysics Data System (ADS)

    Aghaeipour, Mahtab; Pettersson, Håkan

    2018-05-01

    A near-unity unselective absorption spectrum is desirable for high-performance photovoltaics. Nanowire (NW) arrays are promising candidates for efficient solar cells due to nanophotonic absorption resonances in the solar spectrum. The absorption spectra, however, display undesired dips between the resonance peaks. To achieve improved unselective broadband absorption, we propose to enclose distributed Bragg reflectors (DBRs) in the bottom and top parts of indium phosphide (InP) NWs, respectively. We theoretically show that by enclosing only two periods of In0.56Ga0.44As/InP DBRs, an unselective 78% absorption efficiency (72% for NWs without DBRs) is obtained at normal incidence in the spectral range from 300 nm to 920 nm. Under oblique light incidence, the absorption efficiency is enhanced up to about 85% at an incidence angle of 50°. By increasing the number of DBR periods from two to five, the absorption efficiency is further enhanced up to 95% at normal incidence. In this work, we calculated optical spectra for InP NWs, but the results are expected to be valid for other direct band gap III-V semiconductor materials. We believe that our proposed idea of integrating DBRs in NWs offers great potential for high-performance photovoltaic applications.

  3. Model reduction in integrated controls-structures design

    NASA Technical Reports Server (NTRS)

    Maghami, Peiman G.

    1993-01-01

    It is the objective of this paper to present a model reduction technique developed for the integrated controls-structures design of flexible structures. Integrated controls-structures design problems are typically posed as nonlinear mathematical programming problems, where the design variables consist of both structural and control parameters. In the solution process, both structural and control design variables are constantly changing; therefore, the dynamic characteristics of the structure are also changing. This presents a problem in obtaining a reduced-order model for active control design and analysis which will be valid for all design points within the design space. In other words, the frequency and number of the significant modes of the structure (modes that should be included) may vary considerably throughout the design process. This is also true as the locations and/or masses of the sensors and actuators change. Moreover, since the number of design evaluations in the integrated design process could easily run into thousands, any feasible order-reduction method should not require model reduction analysis at every design iteration. In this paper a novel and efficient technique for model reduction in the integrated controls-structures design process, which addresses these issues, is presented.

  4. Integrative Systems Biology for Data Driven Knowledge Discovery

    PubMed Central

    Greene, Casey S.; Troyanskaya, Olga G.

    2015-01-01

    Integrative systems biology is an approach that brings together diverse high throughput experiments and databases to gain new insights into biological processes or systems at molecular through physiological levels. These approaches rely on diverse high-throughput experimental techniques that generate heterogeneous data by assaying varying aspects of complex biological processes. Computational approaches are necessary to provide an integrative view of these experimental results and enable data-driven knowledge discovery. Hypotheses generated from these approaches can direct definitive molecular experiments in a cost effective manner. Using integrative systems biology approaches, we can leverage existing biological knowledge and large-scale data to improve our understanding of yet unknown components of a system of interest and how its malfunction leads to disease. PMID:21044756

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  7. Delivering the Benefits of Chemical-Biological Integration in ...

    EPA Pesticide Factsheets

    Slide Presentation at the German Cheminformatics Conference on Delivering the Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA. Presentation at the German Cheminformatics Conference on Delivering the Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA.

  8. Compact characterization of liquid absorption and emission spectra using linear variable filters integrated with a CMOS imaging camera

    PubMed Central

    Wan, Yuhang; Carlson, John A.; Kesler, Benjamin A.; Peng, Wang; Su, Patrick; Al-Mulla, Saoud A.; Lim, Sung Jun; Smith, Andrew M.; Dallesasse, John M.; Cunningham, Brian T.

    2016-01-01

    A compact analysis platform for detecting liquid absorption and emission spectra using a set of optical linear variable filters atop a CMOS image sensor is presented. The working spectral range of the analysis platform can be extended without a reduction in spectral resolution by utilizing multiple linear variable filters with different wavelength ranges on the same CMOS sensor. With optical setup reconfiguration, its capability to measure both absorption and fluorescence emission is demonstrated. Quantitative detection of fluorescence emission down to 0.28 nM for quantum dot dispersions and 32 ng/mL for near-infrared dyes has been demonstrated on a single platform over a wide spectral range, as well as an absorption-based water quality test, showing the versatility of the system across liquid solutions for different emission and absorption bands. Comparison with a commercially available portable spectrometer and an optical spectrum analyzer shows our system has an improved signal-to-noise ratio and acceptable spectral resolution for discrimination of emission spectra, and characterization of colored liquid’s absorption characteristics generated by common biomolecular assays. This simple, compact, and versatile analysis platform demonstrates a path towards an integrated optical device that can be utilized for a wide variety of applications in point-of-use testing and point-of-care diagnostics. PMID:27389070

  9. Superficial heat reduction technique for a hybrid microwave-optical device.

    PubMed

    Al-Armaghany, A; Tong, K; Leung, T S

    2013-01-01

    Microwave applicator in the form of a circularly polarized microstrip patch antenna is proposed to provide localized deep heating in biological tissue, which causes blood vessels to dilate leading to changes in tissue oxygenation. These changes are monitored by an integrated optical system for studying thermoregulation in different parts of the human body. Using computer simulations, this paper compares circularly and linearly polarized antennas in terms of the efficiency of depositing electromagnetic (EM) energy and the heating patterns. The biological model composes of the skin, fat and muscle layers with appropriate dielectric and thermal properties. The results show that for the same specific absorption rate (SAR) in the muscle, the circularly polarized antenna results in a lower SAR in the skin-fat interface than the linearly polarized antenna. The thermal distribution is also presented based on the biological heat equation. The proposed circularly polarized antenna shows heat reduction in the superficial layers in comparison to the linearly polarized antenna.

  10. Integrative biological analysis for neuropsychopharmacology.

    PubMed

    Emmett, Mark R; Kroes, Roger A; Moskal, Joseph R; Conrad, Charles A; Priebe, Waldemar; Laezza, Fernanda; Meyer-Baese, Anke; Nilsson, Carol L

    2014-01-01

    Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches--proteomics, transcriptomics, metabolomics, and glycomics--have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studies that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine.

  11. Integrative Biological Analysis For Neuropsychopharmacology

    PubMed Central

    Emmett, Mark R; Kroes, Roger A; Moskal, Joseph R; Conrad, Charles A; Priebe, Waldemar; Laezza, Fernanda; Meyer-Baese, Anke; Nilsson, Carol L

    2014-01-01

    Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches—proteomics, transcriptomics, metabolomics, and glycomics—have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studes that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine. PMID:23800968

  12. The fate of calcium carbonate nanoparticles administered by oral route: absorption and their interaction with biological matrices.

    PubMed

    Lee, Jeong-A; Kim, Mi-Kyung; Kim, Hyoung-Mi; Lee, Jong Kwon; Jeong, Jayoung; Kim, Young-Rok; Oh, Jae-Min; Choi, Soo-Jin

    2015-01-01

    Orally administered particles rapidly interact with biological fluids containing proteins, enzymes, electrolytes, and other biomolecules to eventually form particles covered by a corona, and this corona potentially affects particle uptake, fate, absorption, distribution, and elimination in vivo. This study explored relationships between the biological interactions of calcium carbonate particles and their biokinetics. We examined the effects of food grade calcium carbonates of different particle size (nano [N-Cal] and bulk [B-Cal]: specific surface areas of 15.8 and 0.83 m(2)/g, respectively) on biological interactions in in vitro simulated physiological fluids, ex vivo biofluids, and in vivo in gastrointestinal fluid. Moreover, absorption and tissue distribution of calcium carbonates were evaluated following a single dose oral administration to rats. N-Cal interacted more with biomatrices than bulk materials in vitro and ex vivo, as evidenced by high fluorescence quenching ratios, but it did not interact more actively with biomatrices in vivo. Analysis of coronas revealed that immunoglobulin, apolipoprotein, thrombin, and fibrinogen, were the major corona proteins, regardless of particle size. A biokinetic study revealed that orally delivered N-Cal was more rapidly absorbed into the blood stream than B-Cal, but no significant differences were observed between the two in terms of absorption efficiencies or tissue distributions. Both calcium carbonates were primarily present as particulate forms in gastrointestinal fluids but enter the circulatory system in dissolved Ca(2+), although both types showed partial phase transformation to dicalcium phosphate dihydrate. Relatively low dissolution (about 4%), no remarkable protein-particle interaction, and the major particulate fate of calcium carbonate in vivo gastrointestinal fluids can explain its low oral absorption (about 4%) regardless of particle size. We conclude that calcium carbonate nanoparticles can act more

  13. Integrating paleobiology, archeology, and history to inform biological conservation.

    PubMed

    Rick, Torben C; Lockwood, Rowan

    2013-02-01

    The search for novel approaches to establishing ecological baselines (reference conditions) is constrained by the fact that most ecological studies span the past few decades, at most, and investigate ecosystems that have been substantially altered by human activities for decades, centuries, or more. Paleobiology, archeology, and history provide historical ecological context for biological conservation, remediation, and restoration. We argue that linking historical ecology explicitly with conservation can help unify related disciplines of conservation paleobiology, conservation archeobiology, and environmental history. Differences in the spatial and temporal resolution and extent (scale) of prehistoric, historic, and modern ecological data remain obstacles to integrating historical ecology and conservation biology, but the prolonged temporal extents of historical ecological data can help establish more complete baselines for restoration, document a historical range of ecological variability, and assist in determining desired future conditions. We used the eastern oyster (Crassostrea virginica) fishery of the Chesapeake Bay (U.S.A.) to demonstrate the utility of historical ecological data for elucidating oyster conservation and the need for an approach to conservation that transcends disciplinary boundaries. Historical ecological studies from the Chesapeake have documented dramatic declines (as much as 99%) in oyster abundance since the early to mid-1800 s, changes in oyster size in response to different nutrient levels from the sixteenth to nineteenth centuries, and substantial reductions in oyster accretion rates (from 10 mm/year to effectively 0 mm/year) from the Late Holocene to modern times. Better integration of different historical ecological data sets and increased collaboration between paleobiologists, geologists, archeologists, environmental historians, and ecologists to create standardized research designs and methodologies will help unify prehistoric

  14. Relationship between light scattering and absorption due to cytochrome c oxidase reduction during loss of tissue viability in brains of rats

    NASA Astrophysics Data System (ADS)

    Kawauchi, Satoko; Sato, Shunichi; Ooigawa, Hidetoshi; Nawashiro, Hiroshi; Ishihara, Miya; Kikuchi, Makoto

    2008-02-01

    We performed simultaneous measurement of light scattering and absorption due to reduction of cytochrome c oxidase as intrinsic optical signals that are related to morphological characteristics and energy metabolism, respectively, for rat brains after oxygen/glucose deprivation by saline infusion. To detect change in light scattering, we determined the wavelength that was the most insensitive to change in light absorption due to the reduction of cytochrome c oxidase on the basis of multiwavelength analysis of diffuse reflectance data set for each rat. Then the relationships between scattering signal and absorption signals related to the reductions of heme aa 3 (605 nm) and CuA (830 nm) in cytochrome c oxidase were examined. Measurements showed that after starting saline infusion, the reduction of heme aa 3 started first; thereafter triphasic, large scattering change occurred (200-300 s), during which the reduction of CuA started. Despite such complex behaviors of IOSs, almost linear correlations were seen between the scattering signal and the heme aa 3-related absorption signal, while a relatively large animal-to-animal variation was observed in the correlation between the scattering signal and CuA-related absorption signal. Transmission electron microscopic observation revealed that dendritic swelling and mitochondrial deformation occurred in the cortical surface tissue after the triphasic scattering change. These results suggest that mitochondrial energy failure accompanies morphological alteration in the brain tissue and results in change in light scattering; light scattering will become an important indicator of tissue viability in brain.

  15. Variance Reduction Factor of Nuclear Data for Integral Neutronics Parameters

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chiba, G., E-mail: go_chiba@eng.hokudai.ac.jp; Tsuji, M.; Narabayashi, T.

    We propose a new quantity, a variance reduction factor, to identify nuclear data for which further improvements are required to reduce uncertainties of target integral neutronics parameters. Important energy ranges can be also identified with this variance reduction factor. Variance reduction factors are calculated for several integral neutronics parameters. The usefulness of the variance reduction factors is demonstrated.

  16. The contribution of malabsorption to the reduction in net energy absorption after long-limb Roux-en-Y gastric bypass.

    PubMed

    Odstrcil, Elizabeth A; Martinez, Juan G; Santa Ana, Carol A; Xue, Beiqi; Schneider, Reva E; Steffer, Karen J; Porter, Jack L; Asplin, John; Kuhn, Joseph A; Fordtran, John S

    2010-10-01

    Roux-en-Y gastric bypass (RYGB) restricts food intake, and when the Roux limb is elongated to 150 cm, the procedure is believed to induce malabsorption. Our objective was to measure total reduction in intestinal absorption of combustible energy after RYGB and the extent to which this was due to restriction of food intake or malabsorption of ingested macronutrients. Long-limb RYGB was performed in 9 severely obese patients. Dietary intake and intestinal absorption of fat, protein, carbohydrate, and combustible energy were measured before and at 2 intervals after bypass. By using coefficients of absorption to measure absorptive function, equations were developed to calculate the daily gram and kilocalorie quantities of ingested macronutrients that were not absorbed because of malabsorption or restricted food intake. Coefficients of fat absorption were 92 ± 1.3% before bypass, 72 ± 5.5% 5 mo after bypass, and 68 ± 8.7% 14 mo after bypass. There were no statistically significant effects of RYGB on protein or carbohydrate absorption coefficients, although protein coefficients decreased substantially in some patients. Five months after bypass, malabsorption reduced absorption of combustible energy by 124 ± 57 kcal/d, whereas restriction of food intake reduced energy absorption by 2062 ± 271 kcal/d. Fourteen months after bypass, malabsorption reduced energy absorption by 172 ± 60 kcal/d compared with 1418 ± 171 kcal/d caused by restricted food intake. On average, malabsorption accounted for ≈6% and 11% of the total reduction in combustible energy absorption at 5 and 14 mo, respectively, after this gastric bypass procedure.

  17. The Physics of Marine Biology.

    ERIC Educational Resources Information Center

    Conn, Kathleen

    1992-01-01

    Discusses ways in which marine biology can be integrated into the physics classroom. Topics suggested for incorporation include the harmonic motion of ocean waves, ocean currents, the interaction of visible light with ocean water, pressure, light absorption, and sound transfer in water. (MDH)

  18. Interactions between Biological and Abiotic Pathways in the Reduction of Chlorinated Solvents

    EPA Science Inventory

    While biologically mediated reductive dechlorination continues to be a significant focus of chlorinated solvent remediation, there has been an increased interest in abiotic reductive processes for the remediation of chlorinated solvents. In situ chemical reduction (ISCR) uses zer...

  19. Absorption spectroscopy of microalgae, cyanobacteria, and dissolved organic matter: Measurements in an integrating sphere cavity

    NASA Astrophysics Data System (ADS)

    Pogosyan, S. I.; Durgaryan, A. M.; Konyukhov, I. V.; Chivkunova, O. B.; Merzlyak, M. N.

    2009-12-01

    A device for integrating cavity absorption measurements (ICAM) with an internal diameter of 80 mm suitable for field research is described. The spectral features of the light absorption by some cyanobacteria, green algae, and diatoms in the integrating sphere were studied and the dependences of the absorption on the cell concentration were determined in comparison with the conventional measurements in a 1-cm cuvette. The sensitivity of the chlorophyll estimation with the ICAM reached 0.2-0.5 mg m-3. The results of the ICAM application for the direct analysis of the natural phytoplankton and dissolved organic (“yellow“) matter in the Black Sea and the Sea of Japan are described.

  20. A review on machine learning principles for multi-view biological data integration.

    PubMed

    Li, Yifeng; Wu, Fang-Xiang; Ngom, Alioune

    2018-03-01

    Driven by high-throughput sequencing techniques, modern genomic and clinical studies are in a strong need of integrative machine learning models for better use of vast volumes of heterogeneous information in the deep understanding of biological systems and the development of predictive models. How data from multiple sources (called multi-view data) are incorporated in a learning system is a key step for successful analysis. In this article, we provide a comprehensive review on omics and clinical data integration techniques, from a machine learning perspective, for various analyses such as prediction, clustering, dimension reduction and association. We shall show that Bayesian models are able to use prior information and model measurements with various distributions; tree-based methods can either build a tree with all features or collectively make a final decision based on trees learned from each view; kernel methods fuse the similarity matrices learned from individual views together for a final similarity matrix or learning model; network-based fusion methods are capable of inferring direct and indirect associations in a heterogeneous network; matrix factorization models have potential to learn interactions among features from different views; and a range of deep neural networks can be integrated in multi-modal learning for capturing the complex mechanism of biological systems.

  1. Plasmonic Structure Integrated Single-Photon Detector Configurations to Improve Absorptance and Polarization Contrast

    PubMed Central

    Csete, Mária; Szekeres, Gábor; Szenes, András; Szalai, Anikó; Szabó, Gábor

    2015-01-01

    Configurations capable of maximizing both the absorption component of system detection efficiency and the achievable polarization contrast were determined for 1550 nm polarized light illumination of different plasmonic structure integrated superconducting nanowire single-photon detectors (SNSPDs) consisting of p = 264 nm and P = 792 nm periodic niobium nitride (NbN) patterns on silica substrate. Global effective NbN absorptance maxima appear in case of p/s-polarized light illumination in S/P-orientation (γ = 90°/0° azimuthal angle) and the highest polarization contrast is attained in S-orientation of all devices. Common nanophotonical origin of absorptance enhancement is collective resonance on nanocavity gratings with different profiles, which is promoted by coupling between localized modes in quarter-wavelength metal-insulator-metal nanocavities and laterally synchronized Brewster-Zenneck-type surface waves in integrated SNSPDs possessing a three-quarter-wavelength-scaled periodicity. The spectral sensitivity and dispersion characteristics reveal that device design specific optimal configurations exist. PMID:25654724

  2. The fate of calcium carbonate nanoparticles administered by oral route: absorption and their interaction with biological matrices

    PubMed Central

    Lee, Jeong-A; Kim, Mi-Kyung; Kim, Hyoung-Mi; Lee, Jong Kwon; Jeong, Jayoung; Kim, Young-Rok; Oh, Jae-Min; Choi, Soo-Jin

    2015-01-01

    Background Orally administered particles rapidly interact with biological fluids containing proteins, enzymes, electrolytes, and other biomolecules to eventually form particles covered by a corona, and this corona potentially affects particle uptake, fate, absorption, distribution, and elimination in vivo. This study explored relationships between the biological interactions of calcium carbonate particles and their biokinetics. Methods We examined the effects of food grade calcium carbonates of different particle size (nano [N-Cal] and bulk [B-Cal]: specific surface areas of 15.8 and 0.83 m2/g, respectively) on biological interactions in in vitro simulated physiological fluids, ex vivo biofluids, and in vivo in gastrointestinal fluid. Moreover, absorption and tissue distribution of calcium carbonates were evaluated following a single dose oral administration to rats. Results N-Cal interacted more with biomatrices than bulk materials in vitro and ex vivo, as evidenced by high fluorescence quenching ratios, but it did not interact more actively with biomatrices in vivo. Analysis of coronas revealed that immunoglobulin, apolipoprotein, thrombin, and fibrinogen, were the major corona proteins, regardless of particle size. A biokinetic study revealed that orally delivered N-Cal was more rapidly absorbed into the blood stream than B-Cal, but no significant differences were observed between the two in terms of absorption efficiencies or tissue distributions. Both calcium carbonates were primarily present as particulate forms in gastrointestinal fluids but enter the circulatory system in dissolved Ca2+, although both types showed partial phase transformation to dicalcium phosphate dihydrate. Relatively low dissolution (about 4%), no remarkable protein–particle interaction, and the major particulate fate of calcium carbonate in vivo gastrointestinal fluids can explain its low oral absorption (about 4%) regardless of particle size. Conclusion We conclude that calcium

  3. Challenges and opportunities in absorption, distribution, metabolism, and excretion studies of therapeutic biologics.

    PubMed

    Xu, Xin; Vugmeyster, Yulia

    2012-12-01

    With the advancement of biotechnology in the last two decades, optimized and novel modalities and platforms of biologic moieties have emerged rapidly in drug discovery pipelines. In addition, new technologies for delivering therapeutic biologics (e.g., needle-free devices, nanoparticle complexes), as well as novel approaches for disease treatments (e.g., stem cell therapy, individualized medicine), continue to be developed. While pharmacokinetic studies are routinely carried out for therapeutic biologics, experiments that elucidate underlying mechanisms for clearance and biodistribution or identify key factors that govern absorption, distribution, metabolism, and excretion (ADME) of biologics often are not thoroughly conducted. Realizing the importance of biologics as therapeutic agents, pharmaceutical industry has recently begun to move the research focus from small molecules only to a blended portfolio consisting of both small molecules and biologics. This trend brings many opportunities for scientists working in the drug disposition research field. In anticipation of these opportunities and associated challenges, this review highlights impact of ADME studies on clinical and commercial success of biologics, with a particular focus on emerging applications and technologies and linkage with mechanistic pharmacokinetic/pharmacodynamic modeling and biomarker research.

  4. Integrating Mathematics into the Introductory Biology Laboratory Course

    ERIC Educational Resources Information Center

    White, James D.; Carpenter, Jenna P.

    2008-01-01

    Louisiana Tech University has an integrated science curriculum for its mathematics, chemistry, physics, computer science, biology-research track and secondary mathematics and science education majors. The curriculum focuses on the calculus sequence and introductory labs in biology, physics, and chemistry. In the introductory biology laboratory…

  5. The demonstration of a novel sulfur cycle-based wastewater treatment process: sulfate reduction, autotrophic denitrification, and nitrification integrated (SANI®) biological nitrogen removal process.

    PubMed

    Lu, Hui; Wu, Di; Jiang, Feng; Ekama, George A; van Loosdrecht, Mark C M; Chen, Guang-Hao

    2012-11-01

    Saline water supply has been successfully practiced for toilet flushing in Hong Kong since 1950s, which saves 22% of freshwater in Hong Kong. In order to extend the benefits of saline water supply into saline sewage management, we have recently developed a novel biological organics and nitrogen removal process: the Sulfate reduction, Autotrophic denitrification, and Nitrification Integrated (SANI®) process. The key features of this novel process include elimination of oxygen demand in organic matter removal and production of minimal sludge. Following the success of a 500-day lab-scale trial, this study reports a pilot scale evaluation of this novel process treating 10 m(3) /day of 6-mm screened saline sewage in Hong Kong. The SANI® pilot plant consisted of a sulfate reduction up-flow sludge bed (SRUSB) reactor, an anoxic bioreactor for autotrophic denitrification and an aerobic bioreactor for nitrification. The plant was operated at a steady state for 225 days, during which the average removal efficiencies of both chemical oxygen demand (COD) and total suspended solids (TSS) at 87% and no excess sludge was purposefully withdrawn. Furthermore, a tracer test revealed 5% short circuit flow and a 34.6% dead zone in the SRUSB, indicating a good possibility to further optimize the treatment capacity of the process for full-scale application. Compared with conventional biological nitrogen removal processes, the SANI® process reduces 90% of waste sludge, which saves 35% of the energy and reduces 36% of fossil CO(2) emission. The SANI® process not only eliminates the major odor sources originating from primary treatment and subsequent sludge treatment and disposal during secondary saline sewage treatment, but also promotes saline water supply as an economic and sustainable solution for water scarcity and sewage treatment in water-scarce coastal areas. Copyright © 2012 Wiley Periodicals, Inc.

  6. The entropy reduction engine: Integrating planning, scheduling, and control

    NASA Technical Reports Server (NTRS)

    Drummond, Mark; Bresina, John L.; Kedar, Smadar T.

    1991-01-01

    The Entropy Reduction Engine, an architecture for the integration of planning, scheduling, and control, is described. The architecture is motivated, presented, and analyzed in terms of its different components; namely, problem reduction, temporal projection, and situated control rule execution. Experience with this architecture has motivated the recent integration of learning. The learning methods are described along with their impact on architecture performance.

  7. Integrating cell biology and proteomic approaches in plants.

    PubMed

    Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

    2017-10-03

    Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

  8. Energy for biologic sulfate reduction in a hydrothermally formed ocean on Europa

    NASA Astrophysics Data System (ADS)

    Zolotov, Mikhail Y.; Shock, Everett L.

    2003-04-01

    Formation of a sulfate-bearing ocean on Jupiter's satellite Europa by quenched hydrothermal fluids provides a source of metabolic energy for low-temperature sulfate-reducing organisms that use dissolved H2 as an electron donor. Inhibition of thermodynamically favorable sulfate reduction in cooled hydrothermal fluids creates the potential for biologic reduction. Both high temperature and reduced conditions of ocean-forming hydrothermal solutions favor sulfate reduction in quenched fluids. The maximum amount of energy available to support autotrophic sulfate reduction is on the order of a few kilojoules per kilogram of water and is limited by the low abundances of either H2 or sulfate in ocean-forming fluids. Although this irreplaceable energy source might have supported early life on Europa, maintenance of biologic sulfate reduction throughout the ocean's history would require a supply of organic compounds from endogenic sources or from the satellite's surface.

  9. Integrative Radiation Biology

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Barcellos-Hoff, Mary Helen

    We plan to study tissue-level mechanisms important to human breast radiation carcinogenesis. We propose that the cell biology of irradiated tissues reveals a coordinated multicellular damage response program in which individual cell contributions are primarily directed towards suppression of carcinogenesis and reestablishment of homeostasis. We identified transforming growth factor β1 (TGFβ) as a pivotal signal. Notably, we have discovered that TGFβ suppresses genomic instability by controlling the intrinsic DNA damage response and centrosome integrity. However, TGFβ also mediates disruption of microenvironment interactions, which drive epithelial to mesenchymal transition in irradiated human mammary epithelial cells. This apparent paradox of positive andmore » negative controls by TGFβ is the topic of the present proposal. First, we postulate that these phenotypes manifest differentially following fractionated or chronic exposures; second, that the interactions of multiple cell types in tissues modify the responses evident in this single cell type culture models. The goals are to: 1) study the effect of low dose rate and fractionated radiation exposure in combination with TGFβ on the irradiated phenotype and genomic instability of non-malignant human epithelial cells; and 2) determine whether stromal-epithelial interactions suppress the irradiated phenotype in cell culture and the humanized mammary mouse model. These data will be used to 3) develop a systems biology model that integrates radiation effects across multiple levels of tissue organization and time. Modeling multicellular radiation responses coordinated via extracellular signaling could have a significant impact on the extrapolation of human health risks from high dose to low dose/rate radiation exposure.« less

  10. An effective way to reduce water absorption to terahertz

    NASA Astrophysics Data System (ADS)

    Wu, Yaxiong; Su, Bo; He, Jingsuo; Zhang, Cong; Zhang, Hongfei; Zhang, Shengbo; Zhang, Cunlin

    2018-01-01

    Since many vibrations and rotational levels of biomolecules fall within the THz band, THz spectroscopy can be used to identify biological samples. In addition, most biomolecules need to maintain their biological activity in a liquid environment, but water as polar substance has strong absorption to the THz wave. Thus, it is difficult to detect the sample information in aqueous solution using THz wave. In order to prevent the information of biological samples were masked in the solution, many research methods were used to explore how to reduce the water absorption of terahertz. In this paper, we have developed a real-time chemical methodology through transmission Terahertz time-domain spectroscopy (THz-TDS) system. The material of Zeonor 1020r is used as substrate and cover plate, and PDMS as channel interlayer. The transmission of the empty microfluidic chip is more than 80% in the range of 0.2-2.6 THz by THz-TDS system. Then, experiments were carried out using chips, which were filled with different volumes of 1, 2- propanediol, and it has been proved that the microfluidic chip could reduce the water absorption of terahertz. Finally, in order to further explore the reduction of terahertz to water absorption, we inject different concentrations of electrolyte to the chip. The results show that with the addition of different electrolytes, terahertz transmission line has evident changes. It can be taken into account that the electrolyte has different effects about the hydrogen bonds in the aqueous solution. Some of them can promote water molecules clusters, while others destroy them. Based on the basis of microfluidic chip, the discovery of this phenomenon can provide a way that reduces water absorption of terahertz. This work has laid a solid foundation for the subsequent study in reducing water absorption of terahertz.

  11. Defining the biological integrity of coral reefs using a biological condition gradient framework

    EPA Science Inventory

    Under authority of the Clean Water Act (CWA), the US EPA is committed to protecting the biological integrity of tropical ecosystems, including mangroves, seagrasses and coral reefs that lie within the 3-mile limit of the territorial seas. The biological condition gradient (BCG) w...

  12. ENFIN a network to enhance integrative systems biology.

    PubMed

    Kahlem, Pascal; Birney, Ewan

    2007-12-01

    Integration of biological data of various types and development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing both an adapted infrastructure to connect databases and platforms to enable the generation of new bioinformatics tools as well as the experimental validation of computational predictions. We will give an overview of the projects tackled within ENFIN and discuss the challenges associated with integration for systems biology.

  13. Delivering The Benefits of Chemical-Biological Integration in ...

    EPA Pesticide Factsheets

    Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intention of this research program is to quickly evaluate thousands of chemicals for potential risk but with much reduced cost relative to historical approaches. This work involves computational and data driven approaches including high-throughput screening, modeling, text-mining and the integration of chemistry, exposure and biological data. We have developed a number of databases and applications that are delivering on the vision of developing a deeper understanding of chemicals and their effects on exposure and biological processes that are supporting a large community of scientists in their research efforts. This presentation will provide an overview of our work to bring together diverse large scale data from the chemical and biological domains, our approaches to integrate and disseminate these data, and the delivery of models supporting computational toxicology. This abstract does not reflect U.S. EPA policy. Presentation at ACS TOXI session on Computational Chemistry and Toxicology in Chemical Discovery and Assessement (QSARs).

  14. Determination of Death: A Scientific Perspective on Biological Integration

    PubMed Central

    Condic, Maureen L.

    2016-01-01

    Human life is operationally defined by the onset and cessation of organismal function. At postnatal stages of life, organismal integration critically and uniquely requires a functioning brain. In this article, a distinction is drawn between integrated and coordinated biologic activities. While communication between cells can provide a coordinated biologic response to specific signals, it does not support the integrated function that is characteristic of a living human being. Determining the loss of integrated function can be complicated by medical interventions (i.e., “life support”) that uncouple elements of the natural biologic hierarchy underlying our intuitive understanding of death. Such medical interventions can allow living human beings who are no longer able to function in an integrated manner to be maintained in a living state. In contrast, medical intervention can also allow the cells and tissues of an individual who has died to be maintained in a living state. To distinguish between a living human being and living human cells, two criteria are proposed: either the persistence of any form of brain function or the persistence of autonomous integration of vital functions. Either of these criteria is sufficient to determine a human being is alive. PMID:27075193

  15. Integrated anaerobic/aerobic biological treatment for intensive swine production.

    PubMed

    Bortone, Giuseppe

    2009-11-01

    Manure processing could help farmers to effectively manage nitrogen (N) surplus load. Many pig farms have to treat wastewater. Piggery wastewater treatment is a complex challenge, due to the high COD and N concentrations and low C/N ratio. Anaerobic digestion (AD) could be a convenient pre-treatment, particularly from the energetic view point and farm income, but this causes further reduction of C/N ratio and makes denitrification difficult. N removal can only be obtained integrating anaerobic/aerobic treatment by taking into account the best use of electron donors. Experiences gained in Italy during development of integrated biological treatment approaches for swine manure, from bench to full scale, are reported in this paper. Solid/liquid separation as pre-treatment of raw manure is an efficient strategy to facilitate liquid fraction treatment without significantly lowering C/N ratio. In Italy, two full scale SBRs showed excellent efficiency and reliability. Current renewable energy policy and incentives makes economically attractive the application of AD to the separated solid fraction using high solid anaerobic digester (HSAD) technology. Economic evaluation showed that energy production can reduce costs up to 60%, making sustainable the overall treatment.

  16. Quantitative filter technique measurements of spectral light absorption by aquatic particles using a portable integrating cavity absorption meter (QFT-ICAM).

    PubMed

    Röttgers, Rüdiger; Doxaran, David; Dupouy, Cecile

    2016-01-25

    The accurate determination of light absorption coefficients of particles in water, especially in very oligotrophic oceanic areas, is still a challenging task. Concentrating aquatic particles on a glass fiber filter and using the Quantitative Filter Technique (QFT) is a common practice. Its routine application is limited by the necessary use of high performance spectrophotometers, distinct problems induced by the strong scattering of the filters and artifacts induced by freezing and storing samples. Measurements of the sample inside a large integrating sphere reduce scattering effects and direct field measurements avoid artifacts due to sample preservation. A small, portable, Integrating Cavity Absorption Meter setup (QFT-ICAM) is presented, that allows rapid measurements of a sample filter. The measurement technique takes into account artifacts due to chlorophyll-a fluorescence. The QFT-ICAM is shown to be highly comparable to similar measurements in laboratory spectrophotometers, in terms of accuracy, precision, and path length amplification effects. No spectral artifacts were observed when compared to measurement of samples in suspension, whereas freezing and storing of sample filters induced small losses of water-soluble pigments (probably phycoerythrins). Remaining problems in determining the particulate absorption coefficient with the QFT-ICAM are strong sample-to-sample variations of the path length amplification, as well as fluorescence by pigments that is emitted in a different spectral region than that of chlorophyll-a.

  17. ORAC-DR -- integral field spectroscopy data reduction

    NASA Astrophysics Data System (ADS)

    Todd, Stephen

    ORAC-DR is a general-purpose automatic data-reduction pipeline environment. This document describes its use to reduce integral field unit (IFU) data collected at the United Kingdom Infrared Telescope (UKIRT) with the UIST instrument.

  18. Modeling the thermo-acoustic effects of thermal-dependent speed of sound and acoustic absorption of biological tissues during focused ultrasound hyperthermia.

    PubMed

    López-Haro, S A; Gutiérrez, M I; Vera, A; Leija, L

    2015-10-01

    To evaluate the effects of thermal dependence of speed of sound (SOS) and acoustic absorption of biological tissues during noninvasive focused ultrasound (US) hyperthermia therapy. A finite element (FE) model was used to simulate hyperthermia therapy in the liver by noninvasive focused US. The model consisted of an ultrasonic focused transducer radiating a four-layer biological medium composed of skin, fat, muscle, and liver. The acoustic field and temperature distribution along the layers were obtained after 15 s of hyperthermia therapy using the bio-heat equation. The model solution was found with and without the thermal dependence of SOS and acoustic absorption of biological tissues. The inclusion of the thermal dependence of the SOS generated an increment of 0.4 mm in the longitudinal focus axis of the acoustic field. Moreover, results indicate an increment of the hyperthermia area (zone with temperature above 43 °C), and a maximum temperature difference of almost 3.5 °C when the thermal dependence of absorption was taken into account. The increment of the achieved temperatures at the treatment zone indicated that the effects produced by the thermal dependence of SOS and absorption must be accounted for when planning hyperthermia treatment in order to avoid overheating undesired regions.

  19. Reduction of the capillary water absorption of foamed concrete by using the porous aggregate

    NASA Astrophysics Data System (ADS)

    Namsone, E.; Sahmenko, G.; Namsone, E.; Korjakins, A.

    2017-10-01

    The article reports on the research of reduction of the capillary water absorption of foamed concrete (FC) by using the porous aggregate such as the granules of expanded glass (EG) and the cenospheres (CS). The EG granular aggregate is produced by using recycled glass and blowing agents, melted down in high temperature. The unique structure of the EG granules is obtained where the air is kept closed inside the pellet. The use of the porous aggregate in the preparation process of the FC samples provides an opportunity to improve some physical and mechanical properties of the FC, classifying it as a product of high-performance. In this research the FC samples were produced by adding the EG granules and the CS. The capillary water absorption of hardened samples has been verified. The pore size distribution has been determined by microscope. It is a very important characteristic, specifically in the cold climate territories-where temperature often falls below zero degrees. It is necessary to prevent forming of the micro sized pores in the final structure of the material as it reduces its water absorption capacity. In addition, at a below zero temperature water inside these micro sized pores can increase them by expanding the stress on their walls during the freezing process. Research of the capillary water absorption kinetics can be practical for prevision of the FC durability.

  20. Physical integrity: the missing link in biological monitoring and TMDLs.

    PubMed

    Asmus, Brenda; Magner, Joseph A; Vondracek, Bruce; Perry, Jim

    2009-12-01

    The Clean Water Act mandates that the chemical, physical, and biological integrity of our nation's waters be maintained and restored. Physical integrity has often been defined as physical habitat integrity, and as such, data collected during biological monitoring programs focus primarily on habitat quality. However, we argue that channel stability is a more appropriate measure of physical integrity and that channel stability is a foundational element of physical habitat integrity in low-gradient alluvial streams. We highlight assessment tools that could supplement stream assessments and the Total Maximum Daily Load stressor identification process: field surveys of bankfull cross-sections; longitudinal thalweg profiles; particle size distribution; and regionally calibrated, visual, stream stability assessments. Benefits of measuring channel stability include a more informed selection of reference or best attainable stream condition for an Index of Biotic Integrity, establishment of a baseline for monitoring changes in present and future condition, and indication of channel stability for investigations of chemical and biological impairments associated with sediment discontinuity and loss of habitat quality.

  1. Design of Miniaturized Double-Negative Material for Specific Absorption Rate Reduction in Human Head

    PubMed Central

    Faruque, Mohammad Rashed Iqbal; Islam, Mohammad Tariqul

    2014-01-01

    In this study, a double-negative triangular metamaterial (TMM) structure, which exhibits a resounding electric response at microwave frequency, was developed by etching two concentric triangular rings of conducting materials. A finite-difference time-domain method in conjunction with the lossy-Drude model was used in this study. Simulations were performed using the CST Microwave Studio. The specific absorption rate (SAR) reduction technique is discussed, and the effects of the position of attachment, the distance, and the size of the metamaterials on the SAR reduction are explored. The performance of the double-negative TMMs in cellular phones was also measured in the cheek and the tilted positions using the COMOSAR system. The TMMs achieved a 52.28% reduction for the 10 g SAR. These results provide a guideline to determine the triangular design of metamaterials with the maximum SAR reducing effect for a mobile phone. PMID:25350398

  2. Design of miniaturized double-negative material for specific absorption rate reduction in human head.

    PubMed

    Faruque, Mohammad Rashed Iqbal; Islam, Mohammad Tariqul

    2014-01-01

    In this study, a double-negative triangular metamaterial (TMM) structure, which exhibits a resounding electric response at microwave frequency, was developed by etching two concentric triangular rings of conducting materials. A finite-difference time-domain method in conjunction with the lossy-Drude model was used in this study. Simulations were performed using the CST Microwave Studio. The specific absorption rate (SAR) reduction technique is discussed, and the effects of the position of attachment, the distance, and the size of the metamaterials on the SAR reduction are explored. The performance of the double-negative TMMs in cellular phones was also measured in the cheek and the tilted positions using the COMOSAR system. The TMMs achieved a 52.28% reduction for the 10 g SAR. These results provide a guideline to determine the triangular design of metamaterials with the maximum SAR reducing effect for a mobile phone.

  3. Brushing Your Spacecrafts Teeth: A Review of Biological Reduction Processes for Planetary Protection Missions

    NASA Technical Reports Server (NTRS)

    Pugel, D. E. (Betsy); Rummel, J. D.; Conley, Catharine

    2017-01-01

    Much like keeping your teeth clean, where you brush away biofilms that your dentist calls "plaque," there are various methods to clean spaceflight hardware of biological contamination, known as biological reduction processes. Different approaches clean your hardware's "teeth" in different ways and with different levels of effectiveness. We know that brushing at home with a simple toothbrush is convenient and has a different level of impact vs. getting your teeth cleaned at the dentist. In the same way, there are some approaches to biological reduction that may require simple tools or more complex implementation approaches (think about sonicating or just soaking your dentures, vs. brushing them). There are also some that are more effective for different degrees of cleanliness and still some that have materials compatibility concerns. In this article, we review known and NASA-certified approaches for biological reduction, pointing out materials compatibility concerns and areas where additional research is needed.

  4. Brushing Your Spacecrafts Teeth: A Review of Biological Reduction Processes for Planetary Protection Missions

    NASA Technical Reports Server (NTRS)

    Pugel, D.E. (Betsy); Rummel, J. D.; Conley, C. A.

    2017-01-01

    Much like keeping your teeth clean, where you brush away biofilms that your dentist calls plaque, there are various methods to clean spaceflight hardware of biological contamination, known as biological reduction processes. Different approaches clean your hardwares teeth in different ways and with different levels of effectiveness. We know that brushing at home with a simple toothbrush is convenient and has a different level of impact vs. getting your teeth cleaned at the dentist. In the same way, there are some approaches to biological reduction that may require simple tools or more complex implementation approaches (think about sonicating or just soaking your dentures, vs. brushing them). There are also some that are more effective for different degrees of cleanliness and still some that have materials compatibility concerns. In this article, we review known and NASA-certified approaches for biological reduction, pointing out materials compatibility concerns and areas where additional research is needed.

  5. Shape component analysis: structure-preserving dimension reduction on biological shape spaces.

    PubMed

    Lee, Hao-Chih; Liao, Tao; Zhang, Yongjie Jessica; Yang, Ge

    2016-03-01

    Quantitative shape analysis is required by a wide range of biological studies across diverse scales, ranging from molecules to cells and organisms. In particular, high-throughput and systems-level studies of biological structures and functions have started to produce large volumes of complex high-dimensional shape data. Analysis and understanding of high-dimensional biological shape data require dimension-reduction techniques. We have developed a technique for non-linear dimension reduction of 2D and 3D biological shape representations on their Riemannian spaces. A key feature of this technique is that it preserves distances between different shapes in an embedded low-dimensional shape space. We demonstrate an application of this technique by combining it with non-linear mean-shift clustering on the Riemannian spaces for unsupervised clustering of shapes of cellular organelles and proteins. Source code and data for reproducing results of this article are freely available at https://github.com/ccdlcmu/shape_component_analysis_Matlab The implementation was made in MATLAB and supported on MS Windows, Linux and Mac OS. geyang@andrew.cmu.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Designing integrated computational biology pipelines visually.

    PubMed

    Jamil, Hasan M

    2013-01-01

    The long-term cost of developing and maintaining a computational pipeline that depends upon data integration and sophisticated workflow logic is too high to even contemplate "what if" or ad hoc type queries. In this paper, we introduce a novel application building interface for computational biology research, called VizBuilder, by leveraging a recent query language called BioFlow for life sciences databases. Using VizBuilder, it is now possible to develop ad hoc complex computational biology applications at throw away costs. The underlying query language supports data integration and workflow construction almost transparently and fully automatically, using a best effort approach. Users express their application by drawing it with VizBuilder icons and connecting them in a meaningful way. Completed applications are compiled and translated as BioFlow queries for execution by the data management system LifeDB, for which VizBuilder serves as a front end. We discuss VizBuilder features and functionalities in the context of a real life application after we briefly introduce BioFlow. The architecture and design principles of VizBuilder are also discussed. Finally, we outline future extensions of VizBuilder. To our knowledge, VizBuilder is a unique system that allows visually designing computational biology pipelines involving distributed and heterogeneous resources in an ad hoc manner.

  7. Open-path FTIR data reduction algorithm with atmospheric absorption corrections: the NONLIN code

    NASA Astrophysics Data System (ADS)

    Phillips, William; Russwurm, George M.

    1999-02-01

    This paper describes the progress made to date in developing, testing, and refining a data reduction computer code, NONLIN, that alleviates many of the difficulties experienced in the analysis of open path FTIR data. Among the problems that currently effect FTIR open path data quality are: the inability to obtain a true I degree or background, spectral interferences of atmospheric gases such as water vapor and carbon dioxide, and matching the spectral resolution and shift of the reference spectra to a particular field instrument. This algorithm is based on a non-linear fitting scheme and is therefore not constrained by many of the assumptions required for the application of linear methods such as classical least squares (CLS). As a result, a more realistic mathematical model of the spectral absorption measurement process can be employed in the curve fitting process. Applications of the algorithm have proven successful in circumventing open path data reduction problems. However, recent studies, by one of the authors, of the temperature and pressure effects on atmospheric absorption indicate there exist temperature and water partial pressure effects that should be incorporated into the NONLIN algorithm for accurate quantification of gas concentrations. This paper investigates the sources of these phenomena. As a result of this study a partial pressure correction has been employed in NONLIN computer code. Two typical field spectra are examined to determine what effect the partial pressure correction has on gas quantification.

  8. Airborne Measurements of CO2 Column Absorption and Range Using a Pulsed Direct-Detection Integrated Path Differential Absorption Lidar

    NASA Technical Reports Server (NTRS)

    Abshire, James B.; Riris, Haris; Weaver, Clark J.; Mao, Jianping; Allan, Graham R.; Hasselbrack, William E.; Browell, Edward V.

    2013-01-01

    We report on airborne CO2 column absorption measurements made in 2009 with a pulsed direct-detection lidar operating at 1572.33 nm and utilizing the integrated path differential absorption technique. We demonstrated these at different altitudes from an aircraft in July and August in flights over four locations in the central and eastern United States. The results show clear CO2 line shape and absorption signals, which follow the expected changes with aircraft altitude from 3 to 13 km. The lidar measurement statistics were also calculated for each flight as a function of altitude. The optical depth varied nearly linearly with altitude, consistent with calculations based on atmospheric models. The scatter in the optical depth measurements varied with aircraft altitude as expected, and the median measurement precisions for the column varied from 0.9 to 1.2 ppm. The altitude range with the lowest scatter was 810 km, and the majority of measurements for the column within it had precisions between 0.2 and 0.9 ppm.

  9. Optical and biological properties of plasma-treated Neurospora crassa spores as studied by absorption, circular dichroism, and Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Lee, Geon Joon; Park, Gyungsoon; Choi, Eun Ha

    2017-11-01

    We studied the effect of plasma treatment on the optical, structural and biological properties of Neurospora crassa ( N. crassa) spores. An atmospheric-pressure plasma jet (APPJ) was used to generate reactive oxygen and nitrogen species in aqueous solution. The APPJ treatment of N. crassa spores in water significantly reduced the viability of spores. The reduction in the spore viability can be attributed to the reactive species from the plasma itself and those derived from the reaction of plasma radicals with aqueous solution. These structural modifications were contingent on the medium in which N. crassa spores were suspended; plasma treatment of N. crassa spores in PBS did not significantly affect the viability of spores as compared with N. crassa spores in water. Scanning electron microscopy images and circular dichroism spectra indicated that the spore cell wall was damaged by plasma treatment. The optical absorption spectrum of untreated N. crassa spores exhibited two resonance absorption bands at approximately λ1 ≈ 260 nm and λ2 ≈ 472 nm, originating from deoxyribonucleic acid (DNA) and β-carotene. The Raman spectrum of untreated N. crassa spores exhibited three main peaks at 1519, 1157 and 1006 cm -1, attributed to β-carotene inside the cell wall. The Raman spectra showed that the APPJ treatment of N. crassa spores in water caused degradation of β-carotene, affecting the viability of spores.

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Skelly, E.M.

    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,more » 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.« less

  12. Integrative Physiology 2.0’: integration of systems biology into physiology and its application to cardiovascular homeostasis

    PubMed Central

    Kuster, Diederik W D; Merkus, Daphne; van der Velden, Jolanda; Verhoeven, Adrie J M; Duncker, Dirk J

    2011-01-01

    Since the completion of the Human Genome Project and the advent of the large scaled unbiased ‘-omics’ techniques, the field of systems biology has emerged. Systems biology aims to move away from the traditional reductionist molecular approach, which focused on understanding the role of single genes or proteins, towards a more holistic approach by studying networks and interactions between individual components of networks. From a conceptual standpoint, systems biology elicits a ‘back to the future’ experience for any integrative physiologist. However, many of the new techniques and modalities employed by systems biologists yield tremendous potential for integrative physiologists to expand their tool arsenal to (quantitatively) study complex biological processes, such as cardiac remodelling and heart failure, in a truly holistic fashion. We therefore advocate that systems biology should not become/stay a separate discipline with ‘-omics’ as its playing field, but should be integrated into physiology to create ‘Integrative Physiology 2.0’. PMID:21224228

  13. Age-related reduction of adaptive brain response during semantic integration is associated with gray matter reduction.

    PubMed

    Zhu, Zude; Yang, Fengjun; Li, Dongning; Zhou, Lianjun; Liu, Ying; Zhang, Ying; Chen, Xuezhi

    2017-01-01

    While aging is associated with increased knowledge, it is also associated with decreased semantic integration. To investigate brain activation changes during semantic integration, a sample of forty-eight 25-75 year-old adults read sentences with high cloze (HC) and low cloze (LC) probability while functional magnetic resonance imaging was conducted. Significant age-related reduction of cloze effect (LC vs. HC) was found in several regions, especially the left middle frontal gyrus (MFG) and right inferior frontal gyrus (IFG), which play an important role in semantic integration. Moreover, when accounting for global gray matter volume reduction, the age-cloze correlation in the left MFG and right IFG was absent. The results suggest that brain structural atrophy may disrupt brain response in aging brains, which then show less brain engagement in semantic integration.

  14. The observation of biology implemented by integrated religion values in integrated Islamic school (Decriptive Study in X Integrated Senior Hight School Tasikmalaya)

    NASA Astrophysics Data System (ADS)

    Nurjanah, E.; Adisendjaja, Y. H.; Kusumastuti, M. N.

    2018-05-01

    The learning Integrated Religious value is one of the efforts to increase the motivation of learning and building the student character. This study aims to describe the application of Biology learning integrated religion values in Integrated Islamic School. Research methods used in this research is descriptive. Participants in this study involved the headmaster, headmaster of curriculum, biology teachers, boarding school teachers, the lead of boarding schools, and students. The instruments used are interview, observation and the student questionnaire about learning biology. The results showed that learning in X school consists of two curriculums, there was the curriculum of national education and curriculum of boarding school. The curriculum of national education referred to 2013 curriculum and boarding school curriculum referred to the curriculum of Salafi boarding school (Kitab Kuning). However, in its learning process not delivered integrated. The main obstacle to implementing the learning integrated religious values are 1) the background of general teacher education did not know of any connection between biology subject and subject that are studied in boarding school; 2) schools did not form the teaching team; 3) unavailability of materials integrated religious values.

  15. A Biochemical Magic Frequency Based on the Reduction Level of Biological Carbon

    NASA Technical Reports Server (NTRS)

    Weber, Arthur L.

    1995-01-01

    We have calculated the average number of electron pairs required for the chemical reduction of carbon dioxide to biological carbon using (a) estimates of the reducing equivalents (electron pairs) needed to synthesize biomolecules from carbon dioxide, and (b) measurements of the molecular composition of different organisms. These calculations showed that the carbon of the Earth's biosphere is at the reduction level of formaldehyde that requires two electron pairs per carbon atom to be synthesized from carbon dioxide. This was also the reduction level of cellular carbon when fuel stored as lipid was not used in the estimate. Since this chemical characteristic of life is probably universal, it could be the one thing we know about other carbon-based life in the universe, and the one thing that other intelligent life knows about us. We believe that this common knowledge that biological carbon throughout the universe is at the reduction level of formaldehyde could lead to the selection of the 72.83814 GHz line of the 0, 0, 0 yields 1, 1, 1 rotational transition of formaldehyde as a frequency for interstellar communication.

  16. Integrated three-dimensional photonic nanostructures for achieving near-unity solar absorption and superhydrophobicity

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kuang, Ping; Lin, Shawn-Yu, E-mail: sylin@rpi.edu; Hsieh, Mei-Li

    2015-06-07

    In this paper, we proposed and realized 3D photonic nanostructures consisting of ultra-thin graded index antireflective coatings (ARCs) and woodpile photonic crystals. The use of the integrated ARC and photonic crystal structure can achieve broadband, broad-angle near unity solar absorption. The amorphous silicon based photonic nanostructure experimentally shows an average absorption of ∼95% for λ = 400–620 nm over a wide angular acceptance of θ = 0°–60°. Theoretical studies show that a Gallium Arsenide (GaAs) based structure can achieve an average absorption of >95% for λ = 400–870 nm. Furthermore, the use of the slanted SiO{sub 2} nanorod ARC surface layer by glancing angle deposition exhibits Cassie-Baxter statemore » wetting, and superhydrophobic surface is obtained with highest water contact angle θ{sub CB} ∼ 153°. These properties are fundamentally important for achieving maximum solar absorption and surface self-cleaning in thin film solar cell applications.« less

  17. Physical constraints on biological integral control design for homeostasis and sensory adaptation.

    PubMed

    Ang, Jordan; McMillen, David R

    2013-01-22

    Synthetic biology includes an effort to use design-based approaches to create novel controllers, biological systems aimed at regulating the output of other biological processes. The design of such controllers can be guided by results from control theory, including the strategy of integral feedback control, which is central to regulation, sensory adaptation, and long-term robustness. Realization of integral control in a synthetic network is an attractive prospect, but the nature of biochemical networks can make the implementation of even basic control structures challenging. Here we present a study of the general challenges and important constraints that will arise in efforts to engineer biological integral feedback controllers or to analyze existing natural systems. Constraints arise from the need to identify target output values that the combined process-plus-controller system can reach, and to ensure that the controller implements a good approximation of integral feedback control. These constraints depend on mild assumptions about the shape of input-output relationships in the biological components, and thus will apply to a variety of biochemical systems. We summarize our results as a set of variable constraints intended to provide guidance for the design or analysis of a working biological integral feedback controller. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  18. Plasmonic nanopatch array with integrated metal–organic framework for enhanced infrared absorption gas sensing

    DOE PAGES

    Chong, Xinyuan; Kim, Ki-joong; Zhang, Yujing; ...

    2017-06-06

    In this letter, we present a nanophotonic device consisting of plasmonic nanopatch array (NPA) with integrated metal–organic framework (MOF) for enhanced infrared absorption gas sensing. By designing a gold NPA on a sapphire substrate, we are able to achieve enhanced optical field that spatially overlaps with the MOF layer, which can adsorb carbon dioxide (CO 2) with high capacity. Additionally, experimental results show that this hybrid plasmonic–MOF device can effectively increase the infrared absorption path of on-chip gas sensors by more than 1100-fold. Lastly, the demonstration of infrared absorption spectroscopy of CO 2 using the hybrid plasmonic–MOF device proves amore » promising strategy for future on-chip gas sensing with ultra-compact size.« less

  19. Plasmonic nanopatch array with integrated metal–organic framework for enhanced infrared absorption gas sensing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chong, Xinyuan; Kim, Ki-joong; Zhang, Yujing

    In this letter, we present a nanophotonic device consisting of plasmonic nanopatch array (NPA) with integrated metal–organic framework (MOF) for enhanced infrared absorption gas sensing. By designing a gold NPA on a sapphire substrate, we are able to achieve enhanced optical field that spatially overlaps with the MOF layer, which can adsorb carbon dioxide (CO 2) with high capacity. Additionally, experimental results show that this hybrid plasmonic–MOF device can effectively increase the infrared absorption path of on-chip gas sensors by more than 1100-fold. Lastly, the demonstration of infrared absorption spectroscopy of CO 2 using the hybrid plasmonic–MOF device proves amore » promising strategy for future on-chip gas sensing with ultra-compact size.« less

  20. Characteristics of sludge reduction in an integrated pretreatment and aerobic digestion process.

    PubMed

    Hwang, S; Jang, H; Lee, M; Song, J; Kim, S

    2006-01-01

    In this study, integrated pretreatments and aerobic digestion processes were investigated in order to provide a feasible alternative that can achieve effective sludge reduction. An ozone treatment in the presence of ionic manganese, a catalyst, increased the sludge reduction ratio three times higher than that of a single ozonation, presumably due to an increase in OH radical production. The ozone treatment yielded the effective sludge reduction ratio with an increasing ozone dosage, and an effective dosage of the catalyst was found to be 4 mg-Mn/g-TS. When a mechanical pretreatment and an ozone/catalyst were applied in a series, the integrated process, even at a half mechanical intensity and a half level of ozone dosage, showed higher and faster sludge reduction than each single process did. In addition, the integrated pretreatment process showed the highest dewaterability of the treated sludges. A ratio of sludge cake generation, which was newly introduced to quantify overall performance of sludge treatment processes, showed that the integrated pretreatment followed by the aerobic digestion yielded approximately a half of the sludge cake volume compared to the single aerobic digestion. Therefore, the integrated pretreatment can be a feasible method for the effective reduction of total suspended solid and the final volume.

  1. Integration of a molten carbonate fuel cell with a direct exhaust absorption chiller

    NASA Astrophysics Data System (ADS)

    Margalef, Pere; Samuelsen, Scott

    A high market value exists for an integrated high-temperature fuel cell-absorption chiller product throughout the world. While high-temperature, molten carbonate fuel cells are being commercially deployed with combined heat and power (CHP) and absorption chillers are being commercially deployed with heat engines, the energy efficiency and environmental attributes of an integrated high-temperature fuel cell-absorption chiller product are singularly attractive for the emerging distributed generation (DG) combined cooling, heating, and power (CCHP) market. This study addresses the potential of cooling production by recovering and porting the thermal energy from the exhaust gas of a high-temperature fuel cell (HTFC) to a thermally activated absorption chiller. To assess the practical opportunity of serving an early DG-CCHP market, a commercially available direct fired double-effect absorption chiller is selected that closely matches the exhaust flow and temperature of a commercially available HTFC. Both components are individually modeled, and the models are then coupled to evaluate the potential of a DG-CCHP system. Simulation results show that a commercial molten carbonate fuel cell generating 300 kW of electricity can be effectively coupled with a commercial 40 refrigeration ton (RT) absorption chiller. While the match between the two "off the shelf" units is close and the simulation results are encouraging, the match is not ideal. In particular, the fuel cell exhaust gas temperature is higher than the inlet temperature specified for the chiller and the exhaust flow rate is not sufficient to achieve the potential heat recovery within the chiller heat exchanger. To address these challenges, the study evaluates two strategies: (1) blending the fuel cell exhaust gas with ambient air, and (2) mixing the fuel cell exhaust gases with a fraction of the chiller exhaust gas. Both cases are shown to be viable and result in a temperature drop and flow rate increase of the

  2. [THE PHYSICAL CHEMICAL, BIOLOGICAL BASICS OF CELLS ABSORPTION OF UNESTERIFIED FATTY ACIDS; ALBUMIN, CAVEOLIN, CLATHRIN AND LIPID-BINDING PROTEINS OF CYTOPLASM (THE LECTURE)].

    PubMed

    Titov, V N; Shoibonov, B B

    2016-03-01

    From aposition of phylogenetic theory of general pathology, obesity and metabolic syndrome are pathology of fatty cells. However, the first is a pathology of phylogenetically early visceral fatty cells of omentum. They supply with substratum of energy realization of biologic function of trophology, homeostasis, endoecology and adaptation. The visceral fatty cells of omentum have no receptors to insulin and synthesize adaptively insulin and they are not characterized by biologic reaction of proliferation. The obesity is a pathology of late in phylogenesis subcutaneous adpocytes. They are insulin-dependent and supply with substratum of energy realization of one biologic function of locomotion--movement at the expense of constriction of cross-striated miocytes. The adipocytes in terms of adaptation synthesize humoral mediator adponectin and actively implement biologic function of proliferation. Under both aphysiologic conditions increases passive by gradient of concentration, absorption by cells albumin-unbound free fatty acids in unionized form in micellae's composition. The passive aphysiologic absorption of free fatty acids by cells which under intracellular compartmentalization don't oxidize mitochondria results in synthesis, accumulation of triglycerides in cytoplasm of cells which don't implement it physiologically. The aphysiologic absorption of free fatty acids by cells, their etherification in triglyceride, in particular, in phylogenetically late β-cells of islets and either late cardiomyocytes which fatty acids don't synthesize de novo results in development of aphysiologic processes and disorder of function. From position of biology, these cells in vivo are subjected to loss similar to apoptosis. The formation of corpuscles of apoptosis compromise biologic function of endoecology activating biologic reaction of inflammation.

  3. Integrated Modular Teaching of Human Biology for Primary Care Practitioners

    ERIC Educational Resources Information Center

    Glasgow, Michael S.

    1977-01-01

    Describes the use of integrated modular teaching of the human biology component of the Health Associate Program at Johns Hopkins University, where the goal is to develop an understanding of the sciences as applied to primary care. Discussion covers the module sequence, the human biology faculty, goals of the human biology faculty, laboratory…

  4. Chemometric analysis of correlations between electronic absorption characteristics and structural and/or physicochemical parameters for ampholytic substances of biological and pharmaceutical relevance.

    PubMed

    Judycka-Proma, U; Bober, L; Gajewicz, A; Puzyn, T; Błażejowski, J

    2015-03-05

    Forty ampholytic compounds of biological and pharmaceutical relevance were subjected to chemometric analysis based on unsupervised and supervised learning algorithms. This enabled relations to be found between empirical spectral characteristics derived from electronic absorption data and structural and physicochemical parameters predicted by quantum chemistry methods or phenomenological relationships based on additivity rules. It was found that the energies of long wavelength absorption bands are correlated through multiparametric linear relationships with parameters reflecting the bulkiness features of the absorbing molecules as well as their nucleophilicity and electrophilicity. These dependences enable the quantitative analysis of spectral features of the compounds, as well as a comparison of their similarities and certain pharmaceutical and biological features. Three QSPR models to predict the energies of long-wavelength absorption in buffers with pH=2.5 and pH=7.0, as well as in methanol, were developed and validated in this study. These models can be further used to predict the long-wavelength absorption energies of untested substances (if they are structurally similar to the training compounds). Copyright © 2014 Elsevier B.V. All rights reserved.

  5. [Humanities in medical education: between reduction and integration].

    PubMed

    Han, Taehee

    2015-09-01

    Reductive logic has been a major reasoning style in development of modern biomedical sciences. However, when "medical humanities" is developed by reductive reasoning, integrative and holistic values of humanities tend to be weakened. In that sense, identity and significance of "medical humanities" continue to be controversial despite of its literal clarity. Humanities in medical education should be established by strengthening humanistic and socialistic aspects of regular medical curriculum as well as developing individual "medical humanities" programs.

  6. Plaque reduction over time of an integrated oral hygiene system.

    PubMed

    Nunn, Martha E; Ruhlman, C Douglas; Mallatt, Philip R; Rodriguez, Sally M; Ortblad, Katherine M

    2004-10-01

    This article compares the efficacy of a prototype integrated system (the IntelliClean System from Sonicare and Crest) in the reduction of supragingival plaque to that of a manual toothbrush and conventional toothpaste. The integrated system was compared to a manual toothbrush with conventional toothpaste in a randomized, single-blinded, parallel, 4-week, controlled clinical trial with 100 subjects randomized to each treatment group. There was a low dropout rate, with 89 subjects in the manual toothbrush group (11% loss to follow-up) and 93 subjects in the integrated system group (7% loss to follow-up) completing the study. The Turesky modification of the Quigley and Hein Plaque Index was used to assess full-mouth plaque scores for each subject. Prebrushing plaque scores were obtained at baseline and at 4 weeks after 14 to 20 hours of plaque accumulation. A survey also was conducted at the conclusion of the study to determine the attitude toward the two oral hygiene systems. The integrated system was found to significantly reduce overall and interproximal prebrushing plaque scores over 4 weeks, both by 8.6%, demonstrating statistically significant superiority in overall plaque reduction (P = .002) and interproximal plaque reduction (P < .001) compared to the manual toothbrush with conventional toothpaste, which showed no significant reduction in either overall plaque or interproximal plaque. This study demonstrates that the IntelliClean System from Sonicare and Crest is superior to a manual toothbrush with conventional toothpaste in reducing overall plaque and interproximal plaque over time.

  7. Carbon Monoxide as an Electron Donor for the Biological Reduction of Sulphate

    PubMed Central

    Parshina, Sofiya N.; Sipma, Jan; Henstra, Anne Meint; Stams, Alfons J. M.

    2010-01-01

    Several strains of Gram-negative and Gram-positive sulphate-reducing bacteria (SRB) are able to use carbon monoxide (CO) as a carbon source and electron donor for biological sulphate reduction. These strains exhibit variable resistance to CO toxicity. The most resistant SRB can grow and use CO as an electron donor at concentrations up to 100%, whereas others are already severely inhibited at CO concentrations as low as 1-2%. Here, the utilization, inhibition characteristics, and enzymology of CO metabolism as well as the current state of genomics of CO-oxidizing SRB are reviewed. Carboxydotrophic sulphate-reducing bacteria can be applied for biological sulphate reduction with synthesis gas (a mixture of hydrogen and carbon monoxide) as an electron donor. PMID:20628586

  8. Integrated Chemistry and Biology for First-Year College Students

    ERIC Educational Resources Information Center

    Abdella, Beth R. J.; Walczak, Mary M.; Kandl, Kim A.; Schwinefus, Jeffrey J.

    2011-01-01

    A three-course sequence for first-year students that integrates beginning concepts in biology and chemistry has been designed. The first two courses that emphasize chemistry and its capacity to inform biological applications are described here. The content of the first course moves from small to large particles with an emphasis on membrane…

  9. Future of Chemical Engineering: Integrating Biology into the Undergraduate ChE Curriculum

    ERIC Educational Resources Information Center

    Mosto, Patricia; Savelski, Mariano; Farrell, Stephanie H.; Hecht, Gregory B.

    2007-01-01

    Integrating biology in the chemical engineering curriculum seems to be the future for chemical engineering programs nation and worldwide. Rowan University's efforts to address this need include a unique chemical engineering curriculum with an intensive biology component integrated throughout from freshman to senior years. Freshman and Sophomore…

  10. Integration of chemical and biological treatments for textile industry wastewater: a possible zero-discharge system.

    PubMed

    Lee, H H; Chen, G; Yue, P L

    2001-01-01

    Theoretical and experimental studies have established that integrated treatment systems (mostly chemical and biological) for various industrial wastewaters can achieve better quality of treatment and can be cost-effective. In the present study, the objective is to minimize the use of process water in the textile industry by an economical recycle and reuse scheme. The textile wastewater was first characterized in terms of COD, BOD5, salinity and color. In order to recycle such wastewater, the contaminants should be mineralized and/or removed according to the reusable textile water quality standards. Typical results show that this is achievable. An economic analysis has been conducted on the proposed integrated system. The economic analysis shows that the integrated system is economically more attractive than any of the single treatment technologies for achieving the same target of treatment. The information presented in this paper provides a feasible option for the reduction of effluent discharges in the textile industry.

  11. Large integrated absorption enhancement in plasmonic solar cells by combining metallic gratings and antireflection coatings.

    PubMed

    Munday, Jeremy N; Atwater, Harry A

    2011-06-08

    We describe an ultrathin solar cell architecture that combines the benefits of both plasmonic photovoltaics and traditional antireflection coatings. Spatially resolved electron generation rates are used to determine the total integrated current improvement under AM1.5G solar illumination, which can reach a factor of 1.8. The frequency-dependent absorption is found to strongly correlate with the occupation of optical modes within the structure, and the improved absorption is mainly attributed to improved coupling to guided modes rather than localized resonant modes.

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

    PubMed Central

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

    2010-01-01

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

  13. Operando Soft X-ray Absorption Spectroscopic Study on a Solid Oxide Fuel Cell Cathode during Electrochemical Oxygen Reduction.

    PubMed

    Nakamura, Takashi; Oike, Ryo; Kimura, Yuta; Tamenori, Yusuke; Kawada, Tatsuya; Amezawa, Koji

    2017-05-09

    An operando soft X-ray absorption spectroscopic technique, which enabled the analysis of the electronic structures of the electrode materials at elevated temperature in a controlled atmosphere and electrochemical polarization, was established and its availability was demonstrated by investigating the electronic structural changes of an La 2 NiO 4+δ dense-film electrode during an electrochemical oxygen reduction reaction. Clear O K-edge and Ni L-edge X-ray absorption spectra could be obtained below 773 K under an atmospheric pressure of 100 ppm O 2 /He, 0.1 % O 2 /He, and 1 % O 2 /He gas mixtures. Considerable spectral changes were observed in the O K-edge X-ray absorption spectra upon changing the PO2 and application of electrical potential, whereas only small spectral changes were observed in Ni L-edge X-ray absorption spectra. A pre-edge peak of the O K-edge X-ray absorption spectra, which reflects the unoccupied partial density of states of Ni 3d-O 2p hybridization, increased or decreased with cathodic or anodic polarization, respectively. The electronic structural changes of the outermost orbital of the electrode material due to electrochemical polarization were successfully confirmed by the operando X-ray absorption spectroscopic technique developed in this study. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. An integrative approach to inferring biologically meaningful gene modules.

    PubMed

    Cho, Ji-Hoon; Wang, Kai; Galas, David J

    2011-07-26

    The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO) annotation in construction of gene modules in order to gain better functional association. We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM) that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

  15. An integrative approach to inferring biologically meaningful gene modules

    PubMed Central

    2011-01-01

    Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO) annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM) that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level. PMID:21791051

  16. Integrating Introductory Biology and General Chemistry Laboratories.

    ERIC Educational Resources Information Center

    Godrick, Elizabeth; Hartman, Standish

    2000-01-01

    Introduces a science laboratory integrating biology and chemistry courses that includes four modules: (1) the fundamental process of reactions; (2) a semester-long project on the chemical assay of ascorbic acid; (3) human metabolism of Vitamin C; and (4) an open-ended project on the manipulation of macromolecules. (YDS)

  17. ECOLOGICAL IMPACT OF INTEGRATED CHEMICAL AND BIOLOGICAL AQUATIC WEED CONTROL

    EPA Science Inventory

    This final report presents results of a four-year study of the ecological impacts of chemical, biological, and integrated methods of aquatic weed control. Biological and water quality changes occurred as abundance of macrophytic vegetation was altered by natural factors or manage...

  18. A general model for the absorption of ultrasound by biological tissues and experimental verification.

    PubMed

    Jongen, H A; Thijssen, J M; van den Aarssen, M; Verhoef, W A

    1986-02-01

    In this paper, a closed-form expression is derived for the absorption of ultrasound by biological tissues. In this expression, the viscothermal and viscoelastic theories of relaxation processes are combined. Three relaxation time distribution functions are introduced, and it is assumed that each of these distributions can be described by an identical and simple hyperbolic function. Several simplifying assumptions had to be made to enable the experimental verification of the derived closed-form expression of the absorption coefficient. The simplified expression leaves two degrees of freedom and it was fitted to the experimental data obtained from homogenized beef liver. The model produced a considerably better fit to the data than other, more pragmatic models for the absorption coefficient as a function of frequency that could be found in the literature. Scattering in beef liver was estimated indirectly from the difference between attenuation in in vitro liver tissue as compared to absorption in a homogenate. The frequency dependence of the scattering coefficient could be described by a power law with a power of the order of 2. A comparable figure was found in direct backscattering measurements, performed at our laboratory with the same liver samples [Van den Aarssen et al., J. Acoust. Soc. Am. (to be published)]. A model for scattering recently proposed by Sehgal and Greenleaf [Ultrason. Imag. 6, 60-80 (1984)] was fitted to the scattering data as well. This latter model enabled the estimation of a maximum scatterer distance, which appeared to be of the order of 25 micron.

  19. Real-time trace gas sensor using a multimode diode laser and multiple-line integrated cavity enhanced absorption spectroscopy.

    PubMed

    Karpf, Andreas; Rao, Gottipaty N

    2015-07-01

    We describe and demonstrate a highly sensitive trace gas sensor based on a simplified design that is capable of measuring sub-ppb concentrations of NO2 in tens of milliseconds. The sensor makes use of a relatively inexpensive Fabry-Perot diode laser to conduct off-axis cavity enhanced spectroscopy. The broad frequency range of a multimode Fabry-Perot diode laser spans a large number of absorption lines, thereby removing the need for a single-frequency tunable laser source. The use of cavity enhanced absorption spectroscopy enhances the sensitivity of the sensor by providing a pathlength on the order of 1 km in a small volume. Off-axis alignment excites a large number of cavity modes simultaneously, thereby reducing the sensor's susceptibility to vibration. Multiple-line integrated absorption spectroscopy (where one integrates the absorption spectra over a large number of rovibronic transitions of the molecular species) further improves the sensitivity of detection. Relatively high laser power (∼400  mW) is used to compensate for the low coupling efficiency of a broad linewidth laser to the optical cavity. The approach was demonstrated using a 407 nm diode laser to detect trace quantities of NO2 in zero air. Sensitivities of 750 ppt, 110 ppt, and 65 ppt were achieved using integration times of 50 ms, 5 s, and 20 s respectively.

  20. BioInt: an integrative biological object-oriented application framework and interpreter.

    PubMed

    Desai, Sanket; Burra, Prasad

    2015-01-01

    BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

  1. WISB: Warwick Integrative Synthetic Biology Centre

    PubMed Central

    McCarthy, John

    2016-01-01

    Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary ‘build to apply’ and ‘build to understand’ approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. PMID:27284024

  2. WISB: Warwick Integrative Synthetic Biology Centre.

    PubMed

    McCarthy, John

    2016-06-15

    Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. © 2016 The Author(s).

  3. Light Absorption in Arctic Sea Ice - Black Carbon vs Chlorophyll

    NASA Astrophysics Data System (ADS)

    Ogunro, O. O.; Wingenter, O. W.; Elliott, S.; Hunke, E. C.; Flanner, M.; Wang, H.; Dubey, M. K.; Jeffery, N.

    2015-12-01

    The fingerprint of climate change is more obvious in the Arctic than any other place on Earth. This is not only because the surface temperature there has increased at twice the rate of global mean temperature but also because Arctic sea ice extent has reached a record low of 49% reduction relative to the 1979-2000 climatology. Radiation absorption through black carbon (BC) deposited on Arctic snow and sea ice surface is one of the major hypothesized contributors to the decline. However, we note that chlorophyll-a absorption owing to increasing biology activity in this region could be a major competitor during boreal spring. Modeling of sea-ice physical and biological processes together with experiments and field observations promise rapid progress in the quality of Arctic ice predictions. Here we develop a dynamic ice system module to investigate discrete absorption of both BC and chlorophyll in the Arctic, using BC deposition fields from version 5 of Community Atmosphere Model (CAM5) and vertically distributed layers of chlorophyll concentrations from Sea Ice Model (CICE). To this point, our black carbon mixing ratios compare well with available in situ data. Both results are in the same order of magnitude. Estimates from our calculations show that sea ice and snow around the Canadian Arctic Archipelago and Baffin Bay has the least black carbon absorption while values at the ice-ocean perimeter in the region of the Barents Sea peak significantly. With regard to pigment concentrations, high amounts of chlorophyll are produced in Arctic sea ice by the bottom microbial community, and also within the columnar pack wherever substantial biological activity takes place in the presence of moderate light. We show that the percentage of photons absorbed by chlorophyll in the spring is comparable to the amount attributed to BC, especially in areas where the total deposition rates are decreasing with time on interannual timescale. We expect a continuous increase in

  4. Omics Integration in Biology and Medicine Workshop | Office of Cancer Clinical Proteomics Research

    Cancer.gov

    The focus of this meeting will be on the emerging field of integrating disparate omic data from genomics, proteomics, glycomics, etc. in order to better understand key biological processes and also improve clinical practice. Discussants will focus on identifying the technical and biological barriers in omic integration, with solutions to build a consensus towards data integration in bioscience and to better define phenotypes.

  5. Bayesian integration of position and orientation cues in perception of biological and non-biological forms.

    PubMed

    Thurman, Steven M; Lu, Hongjing

    2014-01-01

    Visual form analysis is fundamental to shape perception and likely plays a central role in perception of more complex dynamic shapes, such as moving objects or biological motion. Two primary form-based cues serve to represent the overall shape of an object: the spatial position and the orientation of locations along the boundary of the object. However, it is unclear how the visual system integrates these two sources of information in dynamic form analysis, and in particular how the brain resolves ambiguities due to sensory uncertainty and/or cue conflict. In the current study, we created animations of sparsely-sampled dynamic objects (human walkers or rotating squares) comprised of oriented Gabor patches in which orientation could either coincide or conflict with information provided by position cues. When the cues were incongruent, we found a characteristic trade-off between position and orientation information whereby position cues increasingly dominated perception as the relative uncertainty of orientation increased and vice versa. Furthermore, we found no evidence for differences in the visual processing of biological and non-biological objects, casting doubt on the claim that biological motion may be specialized in the human brain, at least in specific terms of form analysis. To explain these behavioral results quantitatively, we adopt a probabilistic template-matching model that uses Bayesian inference within local modules to estimate object shape separately from either spatial position or orientation signals. The outputs of the two modules are integrated with weights that reflect individual estimates of subjective cue reliability, and integrated over time to produce a decision about the perceived dynamics of the input data. Results of this model provided a close fit to the behavioral data, suggesting a mechanism in the human visual system that approximates rational Bayesian inference to integrate position and orientation signals in dynamic form analysis.

  6. Non linear optical investigations of silver nanoparticles synthesised by curcumin reduction

    NASA Astrophysics Data System (ADS)

    Dhanya, N. P.

    2017-11-01

    Metal nanoparticles have considerable applications in assorted fields like medicine, biology, photonics, metallurgy etc. Optical applications of Silver nanoparticles are of significant interest among researchers nowadays. In this paper, we report a single step chemical reduction of silver nanoparticles with Curcumin both as a reducing and stabilising agent at room temperature. Structural, plasmonic and non linear optical properties of the prepared nanoparticles are explored using Scanning Electron Microscope, Transmission Electron Microscope, UV absorption spectrometry, Spectroflurometry and Z scan. UV-Vis absorption studies affirm the Surface Plasmon Resonance (SPR) absorption and spectroflurometric studies announce the emission spectrum of the prepared silvernanoparticles at 520 nm. SEM and TEM images uphold the existence of uniform sized, spherical silvernanoparticles. Nonlinear optical studies are accomplished with the open aperture z scan technique in the nanosecond regime. The nonlinearity is in virtue of saturable absorption, two-photon absorption and excited state absorption. The marked nonlinearity and optical limiting of the Curcumin reduced silvernanoparticles enhances its photonic applications.

  7. Network-based drug discovery by integrating systems biology and computational technologies

    PubMed Central

    Leung, Elaine L.; Cao, Zhi-Wei; Jiang, Zhi-Hong; Zhou, Hua

    2013-01-01

    Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple ‘-omics’ databases. The newly developed algorithm- or network-based computational models can tightly integrate ‘-omics’ databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various ‘-omics’ platforms and computational tools would accelerate development of network-based drug discovery and network medicine. PMID:22877768

  8. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    PubMed Central

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  9. Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

    PubMed

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-10-11

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  10. Reduction of cross-polarized reflection to enhance dual-band absorption

    NASA Astrophysics Data System (ADS)

    Kundu, Debidas; Mohan, Akhilesh; Chakrabarty, Ajay

    2016-11-01

    In this paper, cross-polarized reflection from a periodic array of metal-dielectric-metal resonator units is reduced to improve its absorbing performance. Through this simple and typical example, it is shown that some reported absorbers are actually poor absorbers but efficient polarization converters, when the cross-polarized reflection is considered. Using a frequency selective surface, sandwiched between the top layer and the ground plane, the cross-polarized reflection is reduced by 7.2 dB at 5.672 GHz and 8.5 dB at 9.56 GHz, while negligibly affecting the co-polarized reflection reduction performance. The polarization conversion ratio is reduced from 90. 74% to 34.12% and 98.51% to 27.2% and total absorption is improved up to 80% from 26% and 21% around the two resonant frequencies. The reflection characteristics of the proposed absorber are quantitatively analyzed using interference theory, where the near field coupling of the resonant geometries and ground is taken into account. Measurement results show good agreement with both the numerically simulated and theoretical results.

  11. Integrated Bio-Entity Network: A System for Biological Knowledge Discovery

    PubMed Central

    Bell, Lindsey; Chowdhary, Rajesh; Liu, Jun S.; Niu, Xufeng; Zhang, Jinfeng

    2011-01-01

    A significant part of our biological knowledge is centered on relationships between biological entities (bio-entities) such as proteins, genes, small molecules, pathways, gene ontology (GO) terms and diseases. Accumulated at an increasing speed, the information on bio-entity relationships is archived in different forms at scattered places. Most of such information is buried in scientific literature as unstructured text. Organizing heterogeneous information in a structured form not only facilitates study of biological systems using integrative approaches, but also allows discovery of new knowledge in an automatic and systematic way. In this study, we performed a large scale integration of bio-entity relationship information from both databases containing manually annotated, structured information and automatic information extraction of unstructured text in scientific literature. The relationship information we integrated in this study includes protein–protein interactions, protein/gene regulations, protein–small molecule interactions, protein–GO relationships, protein–pathway relationships, and pathway–disease relationships. The relationship information is organized in a graph data structure, named integrated bio-entity network (IBN), where the vertices are the bio-entities and edges represent their relationships. Under this framework, graph theoretic algorithms can be designed to perform various knowledge discovery tasks. We designed breadth-first search with pruning (BFSP) and most probable path (MPP) algorithms to automatically generate hypotheses—the indirect relationships with high probabilities in the network. We show that IBN can be used to generate plausible hypotheses, which not only help to better understand the complex interactions in biological systems, but also provide guidance for experimental designs. PMID:21738677

  12. ENFIN--A European network for integrative systems biology.

    PubMed

    Kahlem, Pascal; Clegg, Andrew; Reisinger, Florian; Xenarios, Ioannis; Hermjakob, Henning; Orengo, Christine; Birney, Ewan

    2009-11-01

    Integration of biological data of various types and the development of adapted bioinformatics tools represent critical objectives to enable research at the systems level. The European Network of Excellence ENFIN is engaged in developing an adapted infrastructure to connect databases, and platforms to enable both the generation of new bioinformatics tools and the experimental validation of computational predictions. With the aim of bridging the gap existing between standard wet laboratories and bioinformatics, the ENFIN Network runs integrative research projects to bring the latest computational techniques to bear directly on questions dedicated to systems biology in the wet laboratory environment. The Network maintains internally close collaboration between experimental and computational research, enabling a permanent cycling of experimental validation and improvement of computational prediction methods. The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet.

  13. Enhanced light absorption in waveguide Schottky photodetector integrated with ultrathin metal/silicide stripe.

    PubMed

    Guo, Jingshu; Wu, Zhiwei; Zhao, Yanli

    2017-05-01

    We investigate the light absorption enhancement in waveguide Schottky photodetector integrated with ultrathin metal/silicide stripe, which can provide high internal quantum efficiency. By using aab0-quasi-TE hybrid modes for the first time, a high absorptance of 95.6% is achieved in 5 nm thick Au stripe with area of only 0.14 μm2, without using resonance structure. In theory, the responsivity, dark current, and 3dB bandwidth of the corresponding device are 0.146 A/W, 8.03 nA, and 88 GHz, respectively. For most silicides, the quasi-TM mode should be used in this device, and an optimized PtSi device has a responsivity of 0.71 A/W and a dark current of 35.9 μA.

  14. PathJam: a new service for integrating biological pathway information.

    PubMed

    Glez-Peña, Daniel; Reboiro-Jato, Miguel; Domínguez, Rubén; Gómez-López, Gonzalo; Pisano, David G; Fdez-Riverola, Florentino

    2010-10-28

    Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.

  15. Aerosol Absorption Measurements in MILAGRO.

    NASA Astrophysics Data System (ADS)

    Gaffney, J. S.; Marley, N. A.; Arnott, W. P.; Paredes-Miranda, L.; Barnard, J. C.

    2007-12-01

    During the month of March 2006, a number of instruments were used to determine the absorption characteristics of aerosols found in the Mexico City Megacity and nearby Valley of Mexico. These measurements were taken as part of the Department of Energy's Megacity Aerosol Experiment - Mexico City (MAX-Mex) that was carried out in collaboration with the Megacity Interactions: Local and Global Research Observations (MILAGRO) campaign. MILAGRO was a joint effort between the DOE, NSF, NASA, and Mexican agencies aimed at understanding the impacts of a megacity on the urban and regional scale. A super-site was operated at the Instituto Mexicano de Petroleo in Mexico City (designated T-0) and at the Universidad Technologica de Tecamac (designated T-1) that was located about 35 km to the north east of the T-0 site in the State of Mexico. A third site was located at a private rancho in the State of Hidalgo approximately another 35 km to the northeast (designated T-2). Aerosol absorption measurements were taken in real time using a number of instruments at the T-0 and T-1 sites. These included a seven wavelength aethalometer, a multi-angle absorption photometer (MAAP), and a photo-acoustic spectrometer. Aerosol absorption was also derived from spectral radiometers including a multi-filter rotating band spectral radiometer (MFRSR). The results clearly indicate that there is significant aerosol absorption by the aerosols in the Mexico City megacity region. The absorption can lead to single scattering albedo reduction leading to values below 0.5 under some circumstances. The absorption is also found to deviate from that expected for a "well-behaved" soot anticipated from diesel engine emissions, i.e. from a simple 1/lambda wavelength dependence for absorption. Indeed, enhanced absorption is seen in the region of 300-450 nm in many cases, particularly in the afternoon periods indicating that secondary organic aerosols are contributing to the aerosol absorption. This is likely due

  16. Multi-Group Reductions of LTE Air Plasma Radiative Transfer in Cylindrical Geometries

    NASA Technical Reports Server (NTRS)

    Scoggins, James; Magin, Thierry Edouard Bertran; Wray, Alan; Mansour, Nagi N.

    2013-01-01

    Air plasma radiation in Local Thermodynamic Equilibrium (LTE) within cylindrical geometries is studied with an application towards modeling the radiative transfer inside arc-constrictors, a central component of constricted-arc arc jets. A detailed database of spectral absorption coefficients for LTE air is formulated using the NEQAIR code developed at NASA Ames Research Center. The database stores calculated absorption coefficients for 1,051,755 wavelengths between 0.04 µm and 200 µm over a wide temperature (500K to 15 000K) and pressure (0.1 atm to 10.0 atm) range. The multi-group method for spectral reduction is studied by generating a range of reductions including pure binning and banding reductions from the detailed absorption coefficient database. The accuracy of each reduction is compared to line-by-line calculations for cylindrical temperature profiles resembling typical profiles found in arc-constrictors. It is found that a reduction of only 1000 groups is sufficient to accurately model the LTE air radiation over a large temperature and pressure range. In addition to the reduction comparison, the cylindrical-slab formulation is compared with the finite-volume method for the numerical integration of the radiative flux inside cylinders with varying length. It is determined that cylindrical-slabs can be used to accurately model most arc-constrictors due to their high length to radius ratios.

  17. Integrated Model Reduction and Control of Aircraft with Flexible Wings

    NASA Technical Reports Server (NTRS)

    Swei, Sean Shan-Min; Zhu, Guoming G.; Nguyen, Nhan T.

    2013-01-01

    This paper presents an integrated approach to the modeling and control of aircraft with exible wings. The coupled aircraft rigid body dynamics with a high-order elastic wing model can be represented in a nite dimensional state-space form. Given a set of desired output covariance, a model reduction process is performed by using the weighted Modal Cost Analysis (MCA). A dynamic output feedback controller, which is designed based on the reduced-order model, is developed by utilizing output covariance constraint (OCC) algorithm, and the resulting OCC design weighting matrix is used for the next iteration of the weighted cost analysis. This controller is then validated for full-order evaluation model to ensure that the aircraft's handling qualities are met and the uttering motion of the wings suppressed. An iterative algorithm is developed in CONDUIT environment to realize the integration of model reduction and controller design. The proposed integrated approach is applied to NASA Generic Transport Model (GTM) for demonstration.

  18. UV laser long-path absorption spectroscopy

    NASA Technical Reports Server (NTRS)

    Dorn, Hans-Peter; Brauers, Theo; Neuroth, Rudolf

    1994-01-01

    Long path Differential Optical Absorption Spectroscopy (DOAS) using a picosecond UV laser as a light source was developed in our institute. Tropospheric OH radicals are measured by their rotational absorption lines around 308 nm. The spectra are obtained using a high resolution spectrograph. The detection system has been improved over the formerly used optomechanical scanning device by application of a photodiode array which increased the observed spectral range by a factor of 6 and which utilizes the light much more effectively leading to a considerable reduction of the measurement time. This technique provides direct measurements of OH because the signal is given by the product of the absorption coefficient and the OH concentration along the light path according to Lambert-Beers law. No calibration is needed. Since the integrated absorption coefficient is well known the accuracy of the measurement essentially depends on the extent to which the OH absorption pattern can be detected in the spectra. No interference by self generated OH radicals in the detection lightpath has been observed. The large bandwidth (greater than 0.15 nm) and the high spectral resolution (1.5 pm) allows absolute determination of interferences by other trace gas absorptions. The measurement error is directly accessible from the absorption-signal to baseline-noise ratio in the spectra. The applicability of the method strongly depends on visibility. Elevated concentrations of aerosols lead to considerable attenuation of the laser light which reduces the S/N-ratio. In the moderately polluted air of Julich, where we performed a number of OH measurement spectra. In addition absorption features of unidentified species were frequently detected. A quantitative deconvolution even of the known species is not easy to achieve and can leave residual structures in the spectra. Thus interferences usually increase the noise and deteriorate the OH detection sensitivity. Using diode arrays for sensitive

  19. Genetic Robots: An Integrated Art and Biology Curriculum.

    ERIC Educational Resources Information Center

    Schramm, Susan L.

    2000-01-01

    Describes the design and implementation of an integrated art and science curriculum "Genetic Robotics: A Three-Dimensional Scientific Inquiry" for high school art and biology students at Madeira Junior/Senior High School in Cincinnati, Ohio. States that the project aimed at recognizing individual differences while enabling students to become…

  20. Economic value of biological control in integrated pest management of managed plant systems.

    PubMed

    Naranjo, Steven E; Ellsworth, Peter C; Frisvold, George B

    2015-01-07

    Biological control is an underlying pillar of integrated pest management, yet little focus has been placed on assigning economic value to this key ecosystem service. Setting biological control on a firm economic foundation would help to broaden its utility and adoption for sustainable crop protection. Here we discuss approaches and methods available for valuation of biological control of arthropod pests by arthropod natural enemies and summarize economic evaluations in classical, augmentative, and conservation biological control. Emphasis is placed on valuation of conservation biological control, which has received little attention. We identify some of the challenges of and opportunities for applying economics to biological control to advance integrated pest management. Interaction among diverse scientists and stakeholders will be required to measure the direct and indirect costs and benefits of biological control that will allow farmers and others to internalize the benefits that incentivize and accelerate adoption for private and public good.

  1. BIOLOGICAL INTEGRITY IN MID-ATLANTIC COASTAL PLAINS HEADWATER STREAMS

    EPA Science Inventory

    The objective of this study was to assess the applicability of landscape metrics, in conjunction with stream water quality to estimate the biological integrity of headwater streams in the Mid-Atlantic Coastal Plains using multivariate techniques.

  2. Data Integration and Mining for Synthetic Biology Design.

    PubMed

    Mısırlı, Göksel; Hallinan, Jennifer; Pocock, Matthew; Lord, Phillip; McLaughlin, James Alastair; Sauro, Herbert; Wipat, Anil

    2016-10-21

    One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

  3. Linking sensory biology and fisheries bycatch reduction in elasmobranch fishes: a review with new directions for research

    PubMed Central

    Jordan, Laura K.; Mandelman, John W.; McComb, D. Michelle; Fordham, Sonja V.; Carlson, John K.; Werner, Timothy B.

    2013-01-01

    Incidental capture, or bycatch, in fisheries represents a substantial threat to the sustainability of elasmobranch populations worldwide. Consequently, researchers are increasingly investigating elasmobranch bycatch reduction methods, including some focused on these species' sensory capabilities, particularly their electrosensory systems. To guide this research, we review current knowledge of elasmobranch sensory biology and feeding ecology with respect to fishing gear interactions and include examples of bycatch reduction methods used for elasmobranchs as well as other taxonomic groups. We discuss potential elasmobranch bycatch reduction strategies for various fishing gear types based on the morphological, physiological, and behavioural characteristics of species within this diverse group. In select examples, we indicate how an understanding of the physiology and sensory biology of vulnerable, bycatch-prone, non-target elasmobranch species can help in the identification of promising options for bycatch reduction. We encourage collaboration among researchers studying bycatch reduction across taxa to provide better understanding of the broad effects of bycatch reduction methods. PMID:27293586

  4. The nu sub 9 fundamental of ethane - Integrated intensity and band absorption measurements with application to the atmospheres of the major planets

    NASA Technical Reports Server (NTRS)

    Varanasi, P.; Cess, R. D.; Bangaru, B. R. P.

    1974-01-01

    Measurements of the absolute intensity and integrated band absorption have been performed for the nu sub 9 fundamental band of ethane. The intensity is found to be about 34 per sq cm per atm at STP, and this is significantly higher than previous estimates. It is shown that a Gaussian profile provides an empirical representation of the apparent spectral absorption coefficient. Employing this empirical profile, a simple expression is derived for the integrated band absorption, which is in excellent agreement with experimental values. The band model is then employed to investigate the possible role of ethane as a source of thermal infrared opacity within the atmospheres of Jupiter and Saturn, and to interpret qualitatively observed brightness temperatures for Saturn.

  5. Process integration for biological sulfate reduction in a carbon monoxide fed packed bed reactor.

    PubMed

    Kumar, Manoj; Sinharoy, Arindam; Pakshirajan, Kannan

    2018-08-01

    This study examined immobilized anaerobic biomass for sulfate reduction using carbon monoxide (CO) as the sole carbon source under batch and continuous fed conditions. The immobilized bacteria with beads made of 10% polyvinyl alcohol (PVA) showed best results in terms of sulfate reduction (84 ± 3.52%) and CO utilization (98 ± 1.67%). The effect of hydraulic retention time (HRT), sulfate loading rate and CO loading rate on sulfate and CO removal was investigated employing a 1L packed bed bioreactor containing the immobilized biomass. At 48, 24 and 12 h HRT, the sulfate removal was 94.42 ± 0.15%, 89.75 ± 0.47% and 61.08 ± 0.34%, respectively, along with a CO utilization of more than 90%. The analysis of variance (ANOVA) of the results obtained showed that only the initial CO concentration significantly affected the sulfate reduction process. The reactor effluent sulfate concentrations were 27.41 ± 0.44, 59.16 ± 1.08, 315.83 ± 7.33 mg/L for 250, 500 and 1000 mg/L of influent sulfate concentrations respectively, under the optimum operating conditions. The sulfate reduction rates matched well with low inlet sulfate loading rates, indicating stable performance of the bioreactor system. Overall, this study yielded very high sulfate reduction efficiency by the immobilized anaerobic biomass under high CO loading condition using the packed bed reactor system. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. Integrating biological and social values when prioritizing places for biodiversity conservation.

    PubMed

    Whitehead, Amy L; Kujala, Heini; Ives, Christopher D; Gordon, Ascelin; Lentini, Pia E; Wintle, Brendan A; Nicholson, Emily; Raymond, Christopher M

    2014-08-01

    The consideration of information on social values in conjunction with biological data is critical for achieving both socially acceptable and scientifically defensible conservation planning outcomes. However, the influence of social values on spatial conservation priorities has received limited attention and is poorly understood. We present an approach that incorporates quantitative data on social values for conservation and social preferences for development into spatial conservation planning. We undertook a public participation GIS survey to spatially represent social values and development preferences and used species distribution models for 7 threatened fauna species to represent biological values. These spatially explicit data were simultaneously included in the conservation planning software Zonation to examine how conservation priorities changed with the inclusion of social data. Integrating spatially explicit information about social values and development preferences with biological data produced prioritizations that differed spatially from the solution based on only biological data. However, the integrated solutions protected a similar proportion of the species' distributions, indicating that Zonation effectively combined the biological and social data to produce socially feasible conservation solutions of approximately equivalent biological value. We were able to identify areas of the landscape where synergies and conflicts between different value sets are likely to occur. Identification of these synergies and conflicts will allow decision makers to target communication strategies to specific areas and ensure effective community engagement and positive conservation outcomes. © 2014 Society for Conservation Biology.

  7. Biological Sulfate Reduction Rates in Hydrothermal Recharge Zones

    NASA Astrophysics Data System (ADS)

    Crowell, B.; Lowell, R. P.

    2007-12-01

    We develop a model to determine the rate of removal of seawater sulfate in the recharge regions of deep-sea hydrothermal systems as a result of biogenic sulfate reduction. The rate of sulfate reduction as a function of temperature derived from laboratory measurements on cores from the Guaymas Basin in Mexico [Jorgensen et al., 1992] is incorporated into a steady state 1-D advection-diffusion temperature equation, and a 1-D, steady- state, advection dominated conservation of solute equation. The diffusivity of sulfate in seawater is on the order of ~ 10-10 m2/s, and unless the flow speeds are < 10-12 m/s, the effects of diffusion are negligible, except within thin diffusive boundary layers. This model is then compared with a model that utilizes Gibbs free energy to quantify biogenic sulfate reduction [Bach and Edwards, 2003] in the upper oceanic crust of aging lithosphere. Using the high rates determined by Jorgensen et al. [1992], our model indicates that biological activity would reduce all seawater sulfate transported into the system within the upper 10 meters or less of the crust, which is inconsistent with the estimates of Bach and Edwards [2003]. Sulfate concentrations from ODP borehole Legs 64 and 168, at the sedimented Guaymas Basin and Juan de Fuca Ridge, respectively, show that most of the seawater sulfate is removed in the upper 100 meters. If the sulfate is assumed to all be reduced biogenically, the sulfate reduction rates at the ODP sites are at least 2 orders of magnitude less than the laboratory estimates of Jorgenson et al. [1992]. Finally, we compare the rate of seawater sulfate removal as a result of the precipitation of anhydrite, with the rate of biogenic sulfate reduction. We find that if hydrothermal recharge occurs rapidly through highly permeable faults, that biogenic sulfate reduction is negligible and that anhydrite precipitation would rapidly clog the recharge zone [Lowell and Yao, 2002]. If recharge occurs through broad zones of slow

  8. The role of wind-tunnel studies in integrative research on migration biology.

    PubMed

    Engel, Sophia; Bowlin, Melissa S; Hedenström, Anders

    2010-09-01

    Wind tunnels allow researchers to investigate animals' flight under controlled conditions, and provide easy access to the animals during flight. These increasingly popular devices can benefit integrative migration biology by allowing us to explore the links between aerodynamic theory and migration as well as the links between flight behavior and physiology. Currently, wind tunnels are being used to investigate many different migratory phenomena, including the relationship between metabolic power and flight speed and carry-over effects between different seasons. Although biotelemetry is also becoming increasingly common, it is unlikely that it will be able to completely supplant wind tunnels because of the difficulty of measuring or varying parameters such as flight speed or temperature in the wild. Wind tunnels and swim tunnels will therefore continue to be important tools we can use for studying integrative migration biology. © The Author 2010. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved.

  9. Anion-exchange high-performance liquid chromatography of water-soluble chromium (VI) and chromium (III) complexes in biological materials.

    PubMed

    Suzuki, Y

    1987-04-10

    A high-performance anion-exchange liquid chromatograph coupled to visible-range (370 nm) and UV (280 nm) detectors and an atomic-absorption spectrometer allowed the rapid determination of CrVI and/or complexes of CrIII in rat plasma, erythrocyte lysate and liver supernatant treated with CrVI or CrIII in vitro. CrVI in the eluates was determined using both the visible-range detector and atomic-absorption spectrometer (AAS). The detection limits of CrVI in standard solutions using these methods were 2 and 5 ng (signal-to-noise ratio = 2), respectively. Separations of the biological components and of CrIII complexes were monitored by UV and AAS analyses, respectively. Time-related decreases of CrVI accompanied by increases in CrIII complexes were observed, indicating the reduction of CrVI by some of the biological components. The reduction rates were considerably higher in the liver supernatant and erythrocyte lysate than in the plasma. These results indicate that the anion-exchange high-performance liquid chromatographic system is useful for simultaneous determination of CrVI and CrIII complexes in biological materials.

  10. A Double-Negative Metamaterial-Inspired Mobile Wireless Antenna for Electromagnetic Absorption Reduction

    PubMed Central

    Alam, Touhidul; Faruque, Mohammad Rashed Iqbal; Islam, Mohammad Tariqul

    2015-01-01

    A double-negative metamaterial-inspired antenna is presented for mobile wireless applications. The antenna consists of a semi-circular radiating patch and a 3 × 4 hexagonal shaped metamaterial unit cell array in the ground plane. The antenna is fed with a 50 Ω microstrip feed line. The electric dimensions of the proposed antenna are 0.20λ × 0.26λ × 0.004λ, at the low-end frequency. The proposed antenna achieves a −10 dB impedance with a bandwidth of 2.29 GHz at the lower band and 1.28 GHz at the upper band and can operate for most of the mobile applications such as upper GSM bands, WiMAX, Bluetooth, and wireless local area network (WLAN) frequency bands. The focused novelties of the proposed antenna are its small size, multi-standard operating bands, and electromagnetic absorption reduction at all the operating frequencies using the double-negative metamaterial ground plane. PMID:28793474

  11. A Double-Negative Metamaterial-Inspired Mobile Wireless Antenna for Electromagnetic Absorption Reduction.

    PubMed

    Alam, Touhidul; Faruque, Mohammad Rashed Iqbal; Islam, Mohammad Tariqul

    2015-07-29

    A double-negative metamaterial-inspired antenna is presented for mobile wireless applications. The antenna consists of a semi-circular radiating patch and a 3 × 4 hexagonal shaped metamaterial unit cell array in the ground plane. The antenna is fed with a 50 Ω microstrip feed line. The electric dimensions of the proposed antenna are 0.20λ × 0.26λ × 0.004λ, at the low-end frequency. The proposed antenna achieves a -10 dB impedance with a bandwidth of 2.29 GHz at the lower band and 1.28 GHz at the upper band and can operate for most of the mobile applications such as upper GSM bands, WiMAX, Bluetooth, and wireless local area network (WLAN) frequency bands. The focused novelties of the proposed antenna are its small size, multi-standard operating bands, and electromagnetic absorption reduction at all the operating frequencies using the double-negative metamaterial ground plane.

  12. Microwave generation in an electro-absorption modulator integrated with a DFB laser subject to optical injection.

    PubMed

    Zhu, Ning Hua; Zhang, Hong Guang; Man, Jiang Wei; Zhu, Hong Liang; Ke, Jian Hong; Liu, Yu; Wang, Xin; Yuan, Hai Qing; Xie, Liang; Wang, Wei

    2009-11-23

    This paper presents a new technique to generate microwave signal using an electro-absorption modulator (EAM) integrated with a distributed feedback (DFB) laser subject to optical injection. Experiments show that the frequency of the generated microwave can be tuned by changing the wavelength of the external laser or adjusting the bias voltage of the EAM. The frequency response of the EAM is studied and found to be unsmooth due to packaging parasitic effects and four-wave mixing effect occurring in the active layer of the DFB laser. It is also demonstrated that an EA modulator integrated in between two DFB lasers can be used instead of the EML under optical injection. This integrated chip can be used to realize a monolithically integrated tunable microwave source.

  13. Absorption, accumulation and biological effects of depleted uranium in Peyer's patches of rats.

    PubMed

    Dublineau, I; Grison, S; Grandcolas, L; Baudelin, C; Tessier, C; Suhard, D; Frelon, S; Cossonnet, C; Claraz, M; Ritt, J; Paquet, P; Voisin, P; Gourmelon, P

    2006-10-29

    The digestive tract is the entry route for radionuclides following the ingestion of contaminated food and/or water wells. It was recently characterized that the small intestine was the main area of uranium absorption throughout the gastrointestinal tract. This study was designed to determine the role played by the Peyer's patches in the intestinal absorption of uranium, as well as the possible accumulation of this radionuclide in lymphoid follicles and the toxicological or pathological consequences on the Peyer's patch function subsequent to the passage and/or accumulation of uranium. Results of experiments performed in Ussing chambers indicate that the apparent permeability to uranium in the intestine was higher (10-fold) in the mucosa than in Peyer's patches ((6.21+/-1.21 to 0.55+/-0.35)x10(-6)cm/s, respectively), demonstrating that the small intestinal epithelium was the preferential pathway for the transmucosal passage of uranium. A quantitative analysis of uranium by ICP-MS following chronic contamination with depleted uranium during 3 or 9 months showed a preferential accumulation of uranium in Peyer's patches (1355% and 1266%, respectively, at 3 and 9 months) as compared with epithelium (890% and 747%, respectively, at 3 and 9 months). Uranium was also detected in the mesenteric lymph nodes ( approximately 5-fold after contamination with DU). The biological effects of this accumulation of depleted uranium after chronic contamination were investigated in Peyer's patches. There was no induction of the apoptosis pathway after chronic DU contamination in Peyer's patches. The results indicate no change in the cytokine expression (Il-10, TGF-beta, IFN-gamma, TNF-alpha, MCP-1) in Peyer's patches and in mesenteric lymph nodes, and no modification in the uptake of yeast cells by Peyer's patches. In conclusion, this study shows that the Peyer's patches were a site of retention for uranium following the chronic ingestion of this radionuclide, without any biological

  14. Integration of electro-absorption modulator in a vertical-cavity surface-emitting laser

    NASA Astrophysics Data System (ADS)

    Marigo-Lombart, L.; Calvez, S.; Arnoult, A.; Rumeau, A.; Viallon, C.; Thienpont, H.; Panajotov, K.; Almuneau, G.

    2018-02-01

    VCSELs became dominant laser sources in many short optical link applications such as datacenter, active cables, etc. Actual standards and commercialized VCSEL are providing 25 Gb/s data rates, but new solutions are expected to settle the next device generation enabling 100 Gb/s. Directly modulated VCSEL have been extensively studied and improved to reach bandwidths in the range of 26-32 GHz [Chalmers, TU Berlin], however at the price of increased applied current and thus reduced device lifetime. Furthermore, the relaxation oscillation limit still subsists with this solution. Thus, splitting the emission and the modulation functions as done with DFB lasers is a very promising alternative [TI-Tech, TU Berlin]. Here, we study the vertical integration of an ElectroAbsorption Modulator (EAM) within a VCSEL, where the output light of the VCSEL is modulated through the EAM section. In our original design, we finely optimized the EAM design to maximize the modulation depth by implementing perturbative Quantum Confined Stark Effect (QCSE) calculations, while designing the vertical integration of the EAM without penalty on the VCSEL static performances. We will present the different fabricated vertical structures, as well as the experimental electrical and optical static measurements for those configurations demonstrating a very good agreement with the reflectivity and absorption simulations obtained for both the VCSEL and the EAM-VCSEL structures. Finally, to reach very high frequency modulation we studied the BCB electrical properties up to 110 GHz and investigated coplanar and microstrip lines access to decrease both the parasitic capacitance and the influence of the substrate.

  15. Workshop on Biological Integrity of Coral Reefs August 21-22 ...

    EPA Pesticide Factsheets

    This report summarizes an EPA-sponsored workshop on coral reef biological integrity held at the Caribbean Coral Reef Institute in La Parguera, Puerto Rico on August 21-22, 2012. The goals of this workshop were to:• Identify key qualitative and quantitative ecological characteristics (reef attributes) that determine the condition of linear coral reefs inhabiting shallow waters (<12 m) in southwestern Puerto Rico.• Use those reef attributes to recommend categorical condition rankings for establishing a biological condition gradient.• Ascertain through expert consensus those reef attributes that characterize biological integrity (a natural, fully-functioning system of organisms and communities) for coral reefs. • Develop a conceptual, narrative model that describes how biological attributes of coral reefs change along a gradient of increasing anthropogenic stress.The workshop brought together scientists with expertise in coral reef taxonomic groups (e.g., stony corals, fishes, sponges, gorgonians, algae, seagrasses and macroinvertebrates), as well as community structure, organism condition, ecosystem function and ecosystem connectivity. The experts evaluated photos and videos from 12 stations collected during EPA Coral Reef surveys (2010 & 2011) from Puerto Rico on coral reefs exhibiting a wide range of conditions. The experts individually rated each station as to observed condition (“good”, “fair” or “poor”) and documented their rationale for

  16. Integration of Semiconducting Sulfides for Full-Spectrum Solar Energy Absorption and Efficient Charge Separation.

    PubMed

    Zhuang, Tao-Tao; Liu, Yan; Li, Yi; Zhao, Yuan; Wu, Liang; Jiang, Jun; Yu, Shu-Hong

    2016-05-23

    The full harvest of solar energy by semiconductors requires a material that simultaneously absorbs across the whole solar spectrum and collects photogenerated electrons and holes separately. The stepwise integration of three semiconducting sulfides, namely ZnS, CdS, and Cu2-x S, into a single nanocrystal, led to a unique ternary multi-node sheath ZnS-CdS-Cu2-x S heteronanorod for full-spectrum solar energy absorption. Localized surface plasmon resonance (LSPR) in the nonstoichiometric copper sulfide nanostructures enables effective NIR absorption. More significantly, the construction of pn heterojunctions between Cu2-x S and CdS leads to staggered gaps, as confirmed by first-principles simulations. This band alignment causes effective electron-hole separation in the ternary system and hence enables efficient solar energy conversion. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Solitonic guide and multiphoton absorption processes in photopolymerizable materials for optical integrated circuits

    NASA Astrophysics Data System (ADS)

    Klein, Stephane; Barsella, Alberto; Acker, D.; Sutter, C.; Beyer, N.; Andraud, Chantal; Fort, Alain F.; Dorkenoo, Kokou D.

    2004-09-01

    Up to now, most of the optical integrated devices are realized on glass or III-V substrates and the waveguides are usually obtained by photolithography techniques. We present here a new approach based on the use of photopolymerizable compounds. The conditions of self-written channel creation by solitonic propagation inside the bulk of these photopolymerizable formulations are analyzed. Both experimental and theoretical results of the various stages of self-written guide propagation are presented. A further step has been achieved by using a two-photon absorption process for the polymerization via a confocal microscopy technique. Combined with the solitonic guide creation, this technique allows to draw 3D optical circuits. Finally, by doping the photopolymerizable mixtures with push-pull chromophores having a controlled orientation, it will be possible to create active optical integrated devices.

  18. A reproducible approach to high-throughput biological data acquisition and integration

    PubMed Central

    Rahnavard, Gholamali; Waldron, Levi; McIver, Lauren; Shafquat, Afrah; Franzosa, Eric A.; Miropolsky, Larissa; Sweeney, Christopher

    2015-01-01

    Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa. PMID:26157642

  19. Ethical Responsibility of Governance for Integrating Disaster Risk Reduction with Development

    NASA Astrophysics Data System (ADS)

    Parkash Gupta, Surya

    2015-04-01

    The development in the public as well as the private sectors is controlled and regulated, directly or indirectly by the governments at federal, provincial and local levels. If this development goes haphazard and unplanned, without due considerations to environmental constraints and potential hazards; it is likely to cause disasters or may get affected by disasters. Therefore, it becomes an ethical responsibility of the people involved in governance sector to integrate disaster risk reduction with development in their administrative territories through enforcement of appropriate policies, guidelines and regulatory mechanisms. Such mechanisms should address the social, scientific, economic, environmental, and legal requirements that play significant role in planning, implementation of developmental activities as well as disaster management. The paper focuses on defining the ethical responsibilities for the governance sector for integrating disaster risk reduction with development. It highlights the ethical issues with examples from two case studies, one from the Uttarakhand state and the other Odhisa state in India. The case studies illustrates how does it make a difference in disaster risk reduction if the governments own or do not own ethical responsibilities. The paper considers two major disaster events, flash floods in Uttarakhand state and Cyclone Phailin in Odhisa state, that happened during the year 2013. The study points out that it makes a great difference in terms of consequences and response to disasters when ethical responsibilities are owned by the governance sector. The papers attempts to define these ethical responsibilities for integrating disaster risk reduction with development so that the governments can be held accountable for their acts or non-actions.

  20. Reduction in biomass burning aerosol light absorption upon humidification: roles of inorganically-induced hygroscopicity, particle collapse, and photoacoustic heat and mass transfer

    NASA Astrophysics Data System (ADS)

    Lewis, K. A.; Arnott, W. P.; Moosmüller, H.; Chakrabarty, R. K.; Carrico, C. M.; Kreidenweis, S. M.; Day, D. E.; Malm, W. C.; Laskin, A.; Jimenez, J. L.; Ulbrich, I. M.; Huffman, J. A.; Onasch, T. B.; Trimborn, A.; Liu, L.; Mishchenko, M. I.

    2009-11-01

    Smoke particle emissions from the combustion of biomass fuels typical for the western and southeastern United States were studied and compared under high humidity and ambient conditions in the laboratory. The fuels used were Montana ponderosa pine (Pinus ponderosa), southern California chamise (Adenostoma fasciculatum), and Florida saw palmetto (Serenoa repens). Information on the non-refractory chemical composition of biomass burning aerosol from each fuel was obtained with an aerosol mass spectrometer and through estimation of the black carbon concentration from light absorption measurements at 870 nm. Changes in the optical and physical particle properties under high humidity conditions were observed for hygroscopic smoke particles containing substantial inorganic mass fractions that were emitted from combustion of chamise and palmetto fuels. Light scattering cross sections increased under high humidity for these particles, consistent with the hygroscopic growth measured for 100 nm particles in HTDMA measurements. Photoacoustic measurements of aerosol light absorption coefficients revealed a 20% reduction with increasing relative humidity, contrary to the expectation of light absorption enhancement by the liquid coating taken up by hygroscopic particles. This reduction is hypothesized to arise from two mechanisms: (1) shielding of inner monomers after particle consolidation or collapse with water uptake; (2) the lower case contribution of mass transfer through evaporation and condensation at high relative humidity (RH) to the usual heat transfer pathway for energy release by laser-heated particles in the photoacoustic measurement of aerosol light absorption. The mass transfer contribution is used to evaluate the fraction of aerosol surface covered with liquid water solution as a function of RH.

  1. Reduction in biomass burning aerosol light absorption upon humidification: roles of inorganically-induced hygroscopicity, particle collapse, and photoacoustic heat and mass transfer

    NASA Astrophysics Data System (ADS)

    Lewis, K. A.; Arnott, W. P.; Moosmüller, H.; Chakrabarty, R. K.; Carrico, C. M.; Kreidenweis, S. M.; Day, D. E.; Malm, W. C.; Laskin, A.; Jimenez, J. L.; Ulbrich, I. M.; Huffman, J. A.; Onasch, T. B.; Trimborn, A.; Liu, L.; Mishchenko, M. I.

    2009-07-01

    Smoke particle emissions from the combustion of biomass fuels typical for the western and southeastern United States were studied and compared under high humidity and ambient conditions in the laboratory. The fuels used are Montana ponderosa pine (Pinus ponderosa), southern California chamise (Adenostoma fasciculatum), and Florida saw palmetto (Serenoa repens). Information on the non-refractory chemical composition of biomass burning aerosol from each fuel was obtained with an aerosol mass spectrometer and through estimation of the black carbon concentration from light absorption measurements at 870 nm. Changes in the optical and physical particle properties under high humidity conditions were observed for hygroscopic smoke particles containing substantial inorganic mass fractions that were emitted from combustion of chamise and palmetto fuels. Light scattering cross sections increased under high humidity for these particles, consistent with the hygroscopic growth measured for 100 nm particles in HTDMA measurements. Photoacoustic measurements of aerosol light absorption coefficients reveal a 20% reduction with increasing relative humidity, contrary to the expectation of light absorption enhancement by the liquid coating taken up by hygroscopic particles. This reduction is hypothesized to arise from two mechanisms: 1. Shielding of inner monomers after particle consolidation or collapse with water uptake; 2. The contribution of mass transfer through evaporation and condensation at high relative humidity to the usual heat transfer pathway for energy release by laser-heated particles in the photoacoustic measurement of aerosol light absorption. The mass transfer contribution is used to evaluate the fraction of aerosol surface covered with liquid water solution as a function of RH.

  2. Glutathionylation and Reduction of Methacrolein in Tomato Plants Account for Its Absorption from the Vapor Phase1[OPEN

    PubMed Central

    Muramoto, Shoko; Matsubara, Yayoi; Mwenda, Cynthia Mugo; Koeduka, Takao; Sakami, Takuya; Tani, Akira; Matsui, Kenji

    2015-01-01

    A large portion of the volatile organic compounds emitted by plants are oxygenated to yield reactive carbonyl species, which have a big impact on atmospheric chemistry. Deposition to vegetation driven by the absorption of reactive carbonyl species into plants plays a major role in cleansing the atmosphere, but the mechanisms supporting this absorption have been little examined. Here, we performed model experiments using methacrolein (MACR), one of the major reactive carbonyl species formed from isoprene, and tomato (Solanum lycopersicum) plants. Tomato shoots enclosed in a jar with MACR vapor efficiently absorbed MACR. The absorption efficiency was much higher than expected from the gas/liquid partition coefficient of MACR, indicating that MACR was likely metabolized in leaf tissues. Isobutyraldehyde, isobutyl alcohol, and methallyl alcohol (MAA) were detected in the headspace and inside tomato tissues treated with MACR vapor, suggesting that MACR was enzymatically reduced. Glutathione (GSH) conjugates of MACR (MACR-GSH) and MAA (MAA-GSH) were also detected. MACR-GSH was essentially formed through spontaneous conjugation between endogenous GSH and exogenous MACR, and reduction of MACR-GSH to MAA-GSH was likely catalyzed by an NADPH-dependent enzyme in tomato leaves. Glutathionylation was the metabolic pathway most responsible for the absorption of MACR, but when the amount of MACR exceeded the available GSH, MACR that accumulated reduced photosynthetic capacity. In an experiment simulating the natural environment using gas flow, MACR-GSH and MAA-GSH accumulation accounted for 30% to 40% of the MACR supplied. These results suggest that MACR metabolism, especially spontaneous glutathionylation, is an essential factor supporting MACR absorption from the atmosphere by tomato plants. PMID:26169680

  3. Microfluidic large-scale integration: the evolution of design rules for biological automation.

    PubMed

    Melin, Jessica; Quake, Stephen R

    2007-01-01

    Microfluidic large-scale integration (mLSI) refers to the development of microfluidic chips with thousands of integrated micromechanical valves and control components. This technology is utilized in many areas of biology and chemistry and is a candidate to replace today's conventional automation paradigm, which consists of fluid-handling robots. We review the basic development of mLSI and then discuss design principles of mLSI to assess the capabilities and limitations of the current state of the art and to facilitate the application of mLSI to areas of biology. Many design and practical issues, including economies of scale, parallelization strategies, multiplexing, and multistep biochemical processing, are discussed. Several microfluidic components used as building blocks to create effective, complex, and highly integrated microfluidic networks are also highlighted.

  4. Hub and pylon fairing integration for helicopter drag reduction

    NASA Technical Reports Server (NTRS)

    Martin, D. M.; Mort, R. W.; Squires, P. K.; Young, L. A.

    1991-01-01

    The results of testing hub and pylon fairings mounted on a one-fifth scale helicopter with the goal of reducing parasite drag are presented. Lift, drag, and pitching moment, as well as side force and yawing moment, were measured. The primary objective of the test was to validate the drag reduction capability of integrated hub and pylon configurations in the aerodynamic environment produced by a rotating hub in forward flight. In addition to the baseline helicopter without fairings, three hub fairings and three pylon fairings were tested in various combinations. The three hub fairings tested reflect two different conceptual design approaches to implementing an integrated fairing configuration on an actual aircraft. The design philosophy is discussed in detail and comparisons are made between the wind tunnel models and potential full-scale prototypes. The data show that model drag can be reduced by as much as 20.8 percent by combining a small hub fairing with circular arc upper and flat lower surfaces and a nontapered 34-percent thick pylon fairing. Aerodynamic effects caused by the fairings, which may have a significant impact on static longitudinal and directional stability, were observed. The results support previous research which showed that the greatest reduction in model drag is achieved if the hub and pylon fairings are integrated with minimum gap between the two.

  5. Recording of absorption spectra by a three-beam integral technique with a tunable laser and external cavity

    NASA Astrophysics Data System (ADS)

    Korolenko, P. V.; Nikolaev, I. V.; Ochkin, V. N.; Tskhai, S. N.

    2014-04-01

    An integral method is considered for recording absorption using three laser beams transmitted through and reflected from an external cavity with the absorbing medium (R-ICOS). The method is the elaboration of a known single-beam ICOS method and allows suppression of the influence of radiation phase fluctuations in the resonator on recording weak absorption spectra. First of all, this reduces high-frequency instabilities and gives a possibility to record spectra during short time intervals. In this method, mirrors of the resonator may have moderate reflection coefficients. Capabilities of the method have been demonstrated by the examples of weak absorption spectra of atmospheric methane and natural gas in a spectral range around 1650 nm. With the mirrors having the reflection coefficients of 0.8-0.99, a spectrum can be recorded for 320 μs with the accuracy sufficient for detecting a background concentration of methane in atmosphere. For the acquisition time of 20 s, the absorption coefficients of ~2×10-8 cm-1 can be measured, which corresponds to a 40 times less molecule concentration than the background value.

  6. The Integration of Javanese Indigenous Knowledge in Biology Learning Resources Development

    NASA Astrophysics Data System (ADS)

    Anazifa, D.; Hadi, R. F.

    2017-02-01

    The student’s difficulties in learning and understanding Biology concepts are caused by the adoption of scientific phenomenon that not suitable with the environment they live in. Students who comes from the Javanese background sometimes find the Biology concepts hard to understand. Science content that comes from the West sometimes is not suitable with the student’s background, because the cultural and geographical background that underlining the science development are different. It can potentially cause the clash in constructing knowledge of students. The proportion of western knowledge and indigenous knowledge has to be balanced, in order to give the scientific rationale of the natural phenomenon that faced by students in everyday life. The ethnoscience experienced by student is still in the form of concrete experience as a result of the interaction with the nature. As one of the largest tribe in Indonesia, Javanese has many unique cultures that can be adopted in science classroom especially in Biology class. The role on ethnoscience in the context of developing Biology learning resources is to connect the science concept with the real world situation. By considering indigenous knowledge as one of learning resources, teachers can start to adjust the Javanese indigenous knowledge into the curriculum. This paper is literature review which will present the background, rationale, and procedure in integrating Javanese indigenous knowledge into Biology classroom as learning resources. The integration of Javanese indigenous knowledge in Biology learning resources development is necessary in order to connect the Biology concept into real situation.

  7. Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of heterogeneous catalytic ozonation and biological process.

    PubMed

    Zhuang, Haifeng; Han, Hongjun; Jia, Shengyong; Hou, Baolin; Zhao, Qian

    2014-08-01

    Advanced treatment of biologically pretreated coal gasification wastewater (CGW) was investigated employing heterogeneous catalytic ozonation integrated with anoxic moving bed biofilm reactor (ANMBBR) and biological aerated filter (BAF) process. The results indicated that catalytic ozonation with the prepared catalyst (i.e. MnOx/SBAC, sewage sludge was converted into sludge based activated carbon (SBAC) which loaded manganese oxides) significantly enhanced performance of pollutants removal by generated hydroxyl radicals. The effluent of catalytic ozonation process was more biodegradable and less toxic than that in ozonation alone. Meanwhile, ANMBBR-BAF showed efficient capacity of pollutants removal in treatment of the effluent of catalytic ozonation at a shorter reaction time, allowing the discharge limits to be met. Therefore, the integrated process with efficient, economical and sustainable advantages was suitable for advanced treatment of real biologically pretreated CGW. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Reconstruction of spatial distributions of sound velocity and absorption in soft biological tissues using model ultrasonic tomographic data

    NASA Astrophysics Data System (ADS)

    Burov, V. A.; Zotov, D. I.; Rumyantseva, O. D.

    2014-07-01

    A two-step algorithm is used to reconstruct the spatial distributions of the acoustic characteristics of soft biological tissues-the sound velocity and absorption coefficient. Knowing these distributions is urgent for early detection of benign and malignant neoplasms in biological tissues, primarily in the breast. At the first stage, large-scale distributions are estimated; at the second step, they are refined with a high resolution. Results of reconstruction on the base of model initial data are presented. The principal necessity of preliminary reconstruction of large-scale distributions followed by their being taken into account at the second step is illustrated. The use of CUDA technology for processing makes it possible to obtain final images of 1024 × 1024 samples in only a few minutes.

  9. Reduze - Feynman integral reduction in C++

    NASA Astrophysics Data System (ADS)

    Studerus, C.

    2010-07-01

    Reduze is a computer program for reducing Feynman integrals to master integrals employing a Laporta algorithm. The program is written in C++ and uses classes provided by the GiNaC library to perform the simplifications of the algebraic prefactors in the system of equations. Reduze offers the possibility to run reductions in parallel. Program summaryProgram title:Reduze Catalogue identifier: AEGE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions:: yes No. of lines in distributed program, including test data, etc.: 55 433 No. of bytes in distributed program, including test data, etc.: 554 866 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Unix/Linux Number of processors used: The number of processors is problem dependent. More than one possible but not arbitrary many. RAM: Depends on the complexity of the system. Classification: 4.4, 5 External routines: CLN ( http://www.ginac.de/CLN/), GiNaC ( http://www.ginac.de/) Nature of problem: Solving large systems of linear equations with Feynman integrals as unknowns and rational polynomials as prefactors. Solution method: Using a Gauss/Laporta algorithm to solve the system of equations. Restrictions: Limitations depend on the complexity of the system (number of equations, number of kinematic invariants). Running time: Depends on the complexity of the system.

  10. A reduction for spiking integrate-and-fire network dynamics ranging from homogeneity to synchrony.

    PubMed

    Zhang, J W; Rangan, A V

    2015-04-01

    In this paper we provide a general methodology for systematically reducing the dynamics of a class of integrate-and-fire networks down to an augmented 4-dimensional system of ordinary-differential-equations. The class of integrate-and-fire networks we focus on are homogeneously-structured, strongly coupled, and fluctuation-driven. Our reduction succeeds where most current firing-rate and population-dynamics models fail because we account for the emergence of 'multiple-firing-events' involving the semi-synchronous firing of many neurons. These multiple-firing-events are largely responsible for the fluctuations generated by the network and, as a result, our reduction faithfully describes many dynamic regimes ranging from homogeneous to synchronous. Our reduction is based on first principles, and provides an analyzable link between the integrate-and-fire network parameters and the relatively low-dimensional dynamics underlying the 4-dimensional augmented ODE.

  11. The roles of integration in molecular systems biology.

    PubMed

    O'Malley, Maureen A; Soyer, Orkun S

    2012-03-01

    A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Integrated network analysis and effective tools in plant systems biology

    PubMed Central

    Fukushima, Atsushi; Kanaya, Shigehiko; Nishida, Kozo

    2014-01-01

    One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1) network visualization tools, (2) pathway analyses, (3) genome-scale metabolic reconstruction, and (4) the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms. PMID:25408696

  13. The reduction in the biomass of cyanobacterial N2 fixer and the biological pump in the Northwestern Pacific Ocean

    PubMed Central

    Kim, Dongseon; Jeong, Jin-Hyun; Kim, Tae-Wook; Noh, Jae Hoon; Kim, Hyung Jeek; Choi, Dong Han; Kim, Eung; Jeon, Dongchull

    2017-01-01

    The comparison of sediment trap data with physical and biogeochemical variables in the surface water column of the Tropical Northwestern Pacific Ocean (TNWPO) indicated that the magnitude of the springtime biological pump has reduced with time due to a corresponding decrease in the biomass of cyanobacterial N2 fixer. The decrease in the biomass of N2 fixer likely resulted from a reduction in phosphate concentrations in response to surface water warming and consequent shoaling of the mixed layer depth during the study period (2009−2014). The same reduction in biological pump was also observed during summer. However, the cause of the summer reduction remains uncertain and is worth assessing in future studies. Our findings have major implications for predicting future trends of the biological pump in the TNWPO, where significant warming has occurred. PMID:28155909

  14. Cyber integrated MEMS microhand for biological applications

    NASA Astrophysics Data System (ADS)

    Weissman, Adam; Frazier, Athena; Pepen, Michael; Lu, Yen-Wen; Yang, Shanchieh Jay

    2009-05-01

    Anthropomorphous robotic hands at microscales have been developed to receive information and perform tasks for biological applications. To emulate a human hand's dexterity, the microhand requires a master-slave interface with a wearable controller, force sensors, and perception displays for tele-manipulation. Recognizing the constraints and complexity imposed in developing feedback interface during miniaturization, this project address the need by creating an integrated cyber environment incorporating sensors with a microhand, haptic/visual display, and object model, to emulates human hands' psychophysical perception at microscale.

  15. Campus Eco Tours: An Integrative & Interactive Field Project for Undergraduate Biology Students

    ERIC Educational Resources Information Center

    Boes, Katie E.

    2013-01-01

    Outdoor areas within or near college campuses offer an opportunity for biology students to observe the natural world and apply concepts from class. Here, I describe an engaging and integrative project where undergraduate non-major biology students work in teams to develop and present professional "eco tours." This project takes place over multiple…

  16. Biological X-ray absorption spectroscopy (BioXAS): a valuable tool for the study of trace elements in the life sciences.

    PubMed

    Strange, Richard W; Feiters, Martin C

    2008-10-01

    Using X-ray absorption spectroscopy (XAS) the binding modes (type and number of ligands, distances and geometry) and oxidation states of metals and other trace elements in crystalline as well as non-crystalline samples can be revealed. The method may be applied to biological systems as a 'stand-alone' technique, but it is particularly powerful when used alongside other X-ray and spectroscopic techniques and computational approaches. In this review, we highlight how biological XAS is being used in concert with crystallography, spectroscopy and computational chemistry to study metalloproteins in crystals, and report recent applications on relatively rare trace elements utilised by living organisms and metals involved in neurodegenerative diseases.

  17. A biomimetic functionalization approach to integration of carbon nanoutbes into biological systems

    NASA Astrophysics Data System (ADS)

    Chen, Xing; Tam, Un Chong; Bertozzi, Carolyn; Zettl, Alex

    2006-03-01

    Due to their remarkable structural, electrical, and mechanical properties, carbon nanotubes (CNTs) have potential applications in biology ranging from imaging and tissue engineering. To realize these applications, however, new strategies for controlling the interaction between CNTs and biological systems such as proteins and cells are required. Here we describe a biomimetic approach to functionalize CNTs and therefore render them biocompatibility in order to facilitate their integration into biological systems. CNTs were coated with synthetic gycopolymers that mimic cell surface mucin gycoproteins. The functionalized CNTs were soluble in water, resisted non-specific protein binding and bound specifically to biomolecules. The coated CNTs could then be integrated onto mammalian cell surface by virtue of glycan-receptor interactions. Furthermore, the functionalized CNTs are non-toxic to cells. This strategy offers new opportunities for development of biosensor to probe biological processes. References: 1. X. Chen, G. S. Lee, A. Zettl, C. R. Bertozzi, Angewandte Chemie-International Edition 43, 6111 (2004). 2. X. Chen, U. C. Tam, J. L. Czlapanski, G. S. Lee, D. Rabuka, A. Zettl, C. R. Bertozzi, submitted.

  18. Low-Cost Carbothermal Reduction Preparation of Monodisperse Fe3O4/C Core-Shell Nanosheets for Improved Microwave Absorption.

    PubMed

    Liu, Yun; Fu, Yiwei; Liu, Lin; Li, Wei; Guan, Jianguo; Tong, Guoxiu

    2018-05-16

    This paper demonstrates a facile and low-cost carbothermal reduction preparation of monodisperse Fe 3 O 4 /C core-shell nanosheets (NSs) for greatly improved microwave absorption. In this protocol, the redox reaction between sheet-like hematite (α-Fe 2 O 3 ) precursors and acetone under inert atmosphere and elevated temperature generates Fe 3 O 4 /C core-shell NSs with the morphology inheriting from α-Fe 2 O 3 . Thus, Fe 3 O 4 /C core-shell NSs of different sizes ( a) and Fe 3 O 4 /C core-shell nanopolyhedrons are obtained by using different precursors. Benefited from the high crystallinity of the Fe 3 O 4 core and the thin carbon layer, the resultant NSs exhibit high specific saturation magnetization larger than 82.51 emu·g -1 . Simultaneously, the coercivity enhances with the increase of a, suggesting a strong shape anisotropy effect. Furthermore, because of the anisotropy structure and the complementary behavior between Fe 3 O 4 and C, the as-obtained Fe 3 O 4 /C core-shell NSs exhibit strong natural magnetic resonance at a high frequency, enhanced interfacial polarization, and improved impedance matching, ensuring the enhancement of the microwave absorption. The 250 nm NSs-paraffin composites exhibit reflection loss (RL) lower than -20 dB (corresponding to 99% absorption) in a large frequency ( f) range of 2.08-16.40 GHz with a minimum RL of -43.95 dB at f = 3.92 GHz when the thickness is tuned from 7.0 to 1.4 mm, indicating that the Fe 3 O 4 /C core-shell NSs are a good candidate to manufacture high-performance microwave absorbers. Moreover, the as-developed carbothermal reduction method could be applied for the fabrication of other composites based on ferrites and carbon.

  19. Integrative biology approach identifies cytokine targeting strategies for psoriasis.

    PubMed

    Perera, Gayathri K; Ainali, Chrysanthi; Semenova, Ekaterina; Hundhausen, Christian; Barinaga, Guillermo; Kassen, Deepika; Williams, Andrew E; Mirza, Muddassar M; Balazs, Mercedesz; Wang, Xiaoting; Rodriguez, Robert Sanchez; Alendar, Andrej; Barker, Jonathan; Tsoka, Sophia; Ouyang, Wenjun; Nestle, Frank O

    2014-02-12

    Cytokines are critical checkpoints of inflammation. The treatment of human autoimmune disease has been revolutionized by targeting inflammatory cytokines as key drivers of disease pathogenesis. Despite this, there exist numerous pitfalls when translating preclinical data into the clinic. We developed an integrative biology approach combining human disease transcriptome data sets with clinically relevant in vivo models in an attempt to bridge this translational gap. We chose interleukin-22 (IL-22) as a model cytokine because of its potentially important proinflammatory role in epithelial tissues. Injection of IL-22 into normal human skin grafts produced marked inflammatory skin changes resembling human psoriasis. Injection of anti-IL-22 monoclonal antibody in a human xenotransplant model of psoriasis, developed specifically to test potential therapeutic candidates, efficiently blocked skin inflammation. Bioinformatic analysis integrating both the IL-22 and anti-IL-22 cytokine transcriptomes and mapping them onto a psoriasis disease gene coexpression network identified key cytokine-dependent hub genes. Using knockout mice and small-molecule blockade, we show that one of these hub genes, the so far unexplored serine/threonine kinase PIM1, is a critical checkpoint for human skin inflammation and potential future therapeutic target in psoriasis. Using in silico integration of human data sets and biological models, we were able to identify a new target in the treatment of psoriasis.

  20. Development and Assessment of a Horizontally Integrated Biological Sciences Course Sequence for Pharmacy Education

    PubMed Central

    Wright, Nicholas J.D.; Alston, Gregory L.

    2015-01-01

    Objective. To design and assess a horizontally integrated biological sciences course sequence and to determine its effectiveness in imparting the foundational science knowledge necessary to successfully progress through the pharmacy school curriculum and produce competent pharmacy school graduates. Design. A 2-semester course sequence integrated principles from several basic science disciplines: biochemistry, molecular biology, cellular biology, anatomy, physiology, and pathophysiology. Each is a 5-credit course taught 5 days per week, with 50-minute class periods. Assessment. Achievement of outcomes was determined with course examinations, student lecture, and an annual skills mastery assessment. The North American Pharmacist Licensure Examination (NAPLEX) results were used as an indicator of competency to practice pharmacy. Conclusion. Students achieved course objectives and program level outcomes. The biological sciences integrated course sequence was successful in providing students with foundational basic science knowledge required to progress through the pharmacy program and to pass the NAPLEX. The percentage of the school’s students who passed the NAPLEX was not statistically different from the national percentage. PMID:26430276

  1. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

    PubMed Central

    2013-01-01

    Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

  2. Edge Preserved Speckle Noise Reduction Using Integrated Fuzzy Filters

    PubMed Central

    Dewal, M. L.; Rohit, Manoj Kumar

    2014-01-01

    Echocardiographic images are inherent with speckle noise which makes visual reading and analysis quite difficult. The multiplicative speckle noise masks finer details, necessary for diagnosis of abnormalities. A novel speckle reduction technique based on integration of geometric, wiener, and fuzzy filters is proposed and analyzed in this paper. The denoising applications of fuzzy filters are studied and analyzed along with 26 denoising techniques. It is observed that geometric filter retains noise and, to address this issue, wiener filter is embedded into the geometric filter during iteration process. The performance of geometric-wiener filter is further enhanced using fuzzy filters and the proposed despeckling techniques are called integrated fuzzy filters. Fuzzy filters based on moving average and median value are employed in the integrated fuzzy filters. The performances of integrated fuzzy filters are tested on echocardiographic images and synthetic images in terms of image quality metrics. It is observed that the performance parameters are highest in case of integrated fuzzy filters in comparison to fuzzy and geometric-fuzzy filters. The clinical validation reveals that the output images obtained using geometric-wiener, integrated fuzzy, nonlocal means, and details preserving anisotropic diffusion filters are acceptable. The necessary finer details are retained in the denoised echocardiographic images. PMID:27437499

  3. Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of heterogeneous Fenton oxidation and biological process.

    PubMed

    Xu, Peng; Han, Hongjun; Zhuang, Haifeng; Hou, Baolin; Jia, Shengyong; Xu, Chunyan; Wang, Dexin

    2015-04-01

    Laboratorial scale experiments were conducted in order to investigate a novel system integrating heterogeneous Fenton oxidation (HFO) with anoxic moving bed biofilm reactor (ANMBBR) and biological aerated filter (BAF) process on advanced treatment of biologically pretreated coal gasification wastewater (CGW). The results indicated that HFO with the prepared catalyst (FeOx/SBAC, sewage sludge based activated carbon (SBAC) which loaded Fe oxides) played a key role in eliminating COD and COLOR as well as in improving the biodegradability of raw wastewater. The surface reaction and hydroxyl radicals (OH) oxidation were the mechanisms for FeOx/SBAC catalytic reaction. Compared with ANMBBR-BAF process, the integrated system was more effective in abating COD, BOD5, total phenols (TPs), total nitrogen (TN) and COLOR and could shorten the retention time. Therefore, the integrated system was a promising technology for engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Ex vivo optical characterization of in vivo grown tissues on dummy sensor implants using double integrating spheres measurement

    NASA Astrophysics Data System (ADS)

    Sharma, Sandeep; Goodarzi, Mohammad; Aernouts, Ben; Gellynck, Karolien; Vlaminck, Lieven; Bockstaele, Ronny; Cornelissen, Maria; Ramon, Herman; Saeys, Wouter

    2014-05-01

    Near infrared spectroscopy offers a promising technological platform for continuous glucose monitoring in the human body. NIR measurements can be performed in vivo with an implantable single-chip based optical NIR sensor. However, the application of NIR spectroscopy for accurate estimation of the analyte concentration in highly scattering biological systems still remains a challenge. For instance, a thin tissue layer may grow in the optical path of the sensor. As most biological tissues allow only a small fraction of the collimated light to pass, this might result in a large reduction of the light throughput. To quantify the effect of presence of a thin tissue layer in the optical path, the bulk optical properties of tissue samples grown on sensor dummies which had been implanted for several months in goats were characterized using Double Integrating Spheres and unscattered transmittance measurements. The measured values of diffuse reflectance, diffuse transmittance and collimated transmittance were used as input to Inverse Adding-Doubling algorithm to estimate the bulk optical properties of the samples. The estimates of absorption and scattering coefficients were then used to calculate the light attenuation through a thin tissue layer. Based on the lower reduction in unscattered transmittance and higher absorptivity of glucose molecules, the measurement in the combination band was found to be the better option for the implantable sensor. As the tissues were found to be highly forward scattering with very low unscattered transmittance, the diffuse transmittance measurement based sensor configuration was recommended for the implantable glucose sensor.

  5. Making United States Integrated Ocean Observing System (U.S. IOOS) inclusive of marine biological resources

    USGS Publications Warehouse

    Moustahfid, H.; Potemra, J.; Goldstein, P.; Mendelssohn, R.; Desrochers, A.

    2011-01-01

    An important Data Management and Communication (DMAC) goal is to enable a multi-disciplinary view of the ocean environment by facilitating discovery and integration of data from various sources, projects and scientific domains. United States Integrated Ocean Observing System (U.S. IOOS) DMAC functional requirements are based upon guidelines for standardized data access services, data formats, metadata, controlled vocabularies, and other conventions. So far, the data integration effort has focused on geophysical U.S. IOOS core variables such as temperature, salinity, ocean currents, etc. The IOOS Biological Observations Project is addressing the DMAC requirements that pertain to biological observations standards and interoperability applicable to U.S. IOOS and to various observing systems. Biological observations are highly heterogeneous and the variety of formats, logical structures, and sampling methods create significant challenges. Here we describe an informatics framework for biological observing data (e.g. species presence/absence and abundance data) that will expand information content and reconcile standards for the representation and integration of these biological observations for users to maximize the value of these observing data. We further propose that the approach described can be applied to other datasets generated in scientific observing surveys and will provide a vehicle for wider dissemination of biological observing data. We propose to employ data definition conventions that are well understood in U.S. IOOS and to combine these with ratified terminologies, policies and guidelines. ?? 2011 MTS.

  6. Physical and biological characterization of a seawater ultraviolet radiation sterilizer

    NASA Astrophysics Data System (ADS)

    Torrentera, Laura; Uribe, Roberto M.; Rodríguez, Romana R.; Carrillo, Ricardo E.

    1994-03-01

    The physical and biological characterization of a seawater ultraviolet (UV) sterilizer is described. The physical characterization was performed using radiochromic dye films by evaluating the uniformity of the radiant exposure along each lamp, the effect of the radiation from one lamp on the array of adjacent lamps, and by measuring the UV radiation absorption of seawater with respect to distilled water. The biological characterization was performed by measuring the amount of reduction of bacteria in stored seawater after different filtration and UV treatments. Among the filtration methods tested, differential filtration (5, 3 and 0.45 μm filters connected in series) caused the highest bacterial reduction factor of 60%. UV radiant exposures of 212, 424, 636 and 848 J m -2 yielded bacteria reduction factors of 99.86, 99.969, 99.997 and 100%, respectively, for populations of Vibrio and Pseudomonas bacteria present in stored seawater. It is concluded that the system is useful for water disinfection when 1, 2 or 3 lamps are on; when 4 lamps are used the treated water becomes sterile.

  7. Milkweed Seed Dispersal: A Means for Integrating Biology and Physics.

    ERIC Educational Resources Information Center

    Bisbee, Gregory D.; Kaiser, Cheryl A.

    1997-01-01

    Describes an activity that integrates biology and physics concepts by experimenting with the seed dispersal of common milkweed or similar wind-dispersed seeds. Student teams collect seeds and measure several parameters, review principles of trajectory motion, perform experiments, and graph data. Students examine the ideas of…

  8. [Problems of world outlook and methodology of science integration in biological studies].

    PubMed

    Khododova, Iu D

    1981-01-01

    Problems of worldoutlook and methodology of the natural-science knowledge are considered basing on the analysis of tendencies in the development of the membrane theory of cell processes and the use of principles of biological membrane functioning when solving some scientific and applied problems pertaining to different branches of chemistry and biology. The notion scientific knowledge integration is defined as interpenetration of approaches, methods and ideas of different branches of knowledge and enrichment on this basis of their content resulting in knowledge augmentation in each field taken separately. These processes are accompanied by appearance of new branches of knowledge - sciences "on junction" and their subsequent differentiations. The analysis of some gnoseological situations shows that integration of sciences contributes to coordination and some agreement of thinking styles of different specialists, puts forward keen personality of a scientist demanding, in particular, his high professional mobility. Problems of scientific activity organization are considered, which involve social sciences into the integration processes. The role of philosophy in the integration processes is emphasized.

  9. Ultrafast X-Ray Absorption Spectroscopy of Isochorically Heated Warm Dense Matter

    NASA Astrophysics Data System (ADS)

    Engelhorn, Kyle Craig

    This dissertation will present a series of new tools, together with new techniques, focused on the understanding of warm and dense matter. We report on the development of a high time resolution and high detection efficiency x-ray camera. The camera is integrated with a short pulse laser and an x-ray beamline at the Advanced Light Source synchrotron. This provides an instrument for single shot, broadband x-ray absorption spectroscopy of warm and dense matter with 2 picosecond time resolution. Warm and dense matter is created by isochorically heating samples of known density with an ultrafast optical laser pulse, and X-ray absorption spectroscopy probes the unoccupied electronic density of states before the onset of hydrodynamic expansion and electron-ion equilibrium is reached. Measured spectra from a variety of materials are compared with first principle molecular dynamics and density functional theory calculations. In heated silicon dioxide spectra, two novel pre-edge features are observed, a peak below the band gap and absorption within the band gap, while a reduction was observed in the features above the edge. From consideration of the calculated spectra, the peak below the gap is attributed to valence electrons that have been promoted to the conduction band, the absorption within the gap is attributed to broken Si-O bonds, and the reduction above the edge is attributed to an elevated ionic temperature. In heated copper spectra, a time-dependent shift and broadening of the absorption edge are observed, consistent with and elevated electron temperature. The temporal evolution of the electronic temperature is accurately determined by fitting the measured spectra with calculated spectra. The electron-ion equilibration is studied with a two-temperature model. In heated nickel spectra, a shift of the absorption edge is observed. This shift is found to be inconsistent with calculated spectra and independent of incident laser fluence. A shift of the chemical potential

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

    ERIC Educational Resources Information Center

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

    2016-01-01

    Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory…

  11. The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

    NASA Astrophysics Data System (ADS)

    Faini, Marco; Stengel, Florian; Aebersold, Ruedi

    2016-06-01

    Protein complexes are key catalysts and regulators for the majority of cellular processes. Unveiling their assembly and structure is essential to understanding their function and mechanism of action. Although conventional structural techniques such as X-ray crystallography and NMR have solved the structure of important protein complexes, they cannot consistently deal with dynamic and heterogeneous assemblies, limiting their applications to small scale experiments. A novel methodological paradigm, integrative structural biology, aims at overcoming such limitations by combining complementary data sources into a comprehensive structural model. Recent applications have shown that a range of mass spectrometry (MS) techniques are able to generate interaction and spatial restraints (cross-linking MS) information on native complexes or to study the stoichiometry and connectivity of entire assemblies (native MS) rapidly, reliably, and from small amounts of substrate. Although these techniques by themselves do not solve structures, they do provide invaluable structural information and are thus ideally suited to contribute to integrative modeling efforts. The group of Brian Chait has made seminal contributions in the use of mass spectrometric techniques to study protein complexes. In this perspective, we honor the contributions of the Chait group and discuss concepts and milestones of integrative structural biology. We also review recent examples of integration of structural MS techniques with an emphasis on cross-linking MS. We then speculate on future MS applications that would unravel the dynamic nature of protein complexes upon diverse cellular states.

  12. DNA barcodes for assessment of the biological integrity of aquatic ecosystems

    EPA Science Inventory

    Water quality regulations and aquatic ecosystem monitoring increasingly rely on direct assessments of biological integrity. Because these aquatic “bioassessments” evaluate the incidence and abundance of sensitive aquatic species, they are able to measure cumulative ecosystem eff...

  13. Biosocial Conservation: Integrating Biological and Ethnographic Methods to Study Human-Primate Interactions.

    PubMed

    Setchell, Joanna M; Fairet, Emilie; Shutt, Kathryn; Waters, Siân; Bell, Sandra

    2017-01-01

    Biodiversity conservation is one of the grand challenges facing society. Many people interested in biodiversity conservation have a background in wildlife biology. However, the diverse social, cultural, political, and historical factors that influence the lives of people and wildlife can be investigated fully only by incorporating social science methods, ideally within an interdisciplinary framework. Cultural hierarchies of knowledge and the hegemony of the natural sciences create a barrier to interdisciplinary understandings. Here, we review three different projects that confront this difficulty, integrating biological and ethnographic methods to study conservation problems. The first project involved wildlife foraging on crops around a newly established national park in Gabon. Biological methods revealed the extent of crop loss, the species responsible, and an effect of field isolation, while ethnography revealed institutional and social vulnerability to foraging wildlife. The second project concerned great ape tourism in the Central African Republic. Biological methods revealed that gorilla tourism poses risks to gorillas, while ethnography revealed why people seek close proximity to gorillas. The third project focused on humans and other primates living alongside one another in Morocco. Incorporating shepherds in the coproduction of ecological knowledge about primates built trust and altered attitudes to the primates. These three case studies demonstrate how the integration of biological and social methods can help us to understand the sustainability of human-wildlife interactions, and thus promote coexistence. In each case, an integrated biosocial approach incorporating ethnographic data produced results that would not otherwise have come to light. Research that transcends conventional academic boundaries requires the openness and flexibility to move beyond one's comfort zone to understand and acknowledge the legitimacy of "other" kinds of knowledge. It is

  14. Enhancement of the static extinction ratio by using a dual-section distributed feedback laser integrated with an electro-absorption modulator

    NASA Astrophysics Data System (ADS)

    Cho, Chun-Hyung; Kim, Jongseong; Sung, Hyuk-Kee

    2016-09-01

    We report on the enhancement of the static extinction ratio by using a dual-section distributed feedback laser diode integrated with an electro-absorption modulator. A directly- modulated dual-section laser can provide improved modulation performance under a low bias level ( i.e., below the threshold level) compared with a standard directly-modulated laser. By combining the extinction ratio from a dual-section laser with that from an electro-absorption modulator section, a total extinction ratio of 49.6. dB are successfully achieved.

  15. Reduction of Aerosol Absorption in Beijing Since 2007 from MODIS and AERONET

    NASA Technical Reports Server (NTRS)

    Lyapustin, A.; Smirnov, A.; Holben, B.; Chin, M.; Streets, D. G.; Lu, Z.; Kahn, R.; Slutsker, I.; Laszlo, I.; Kondragunta, S.; hide

    2011-01-01

    An analysis of the time series of MODIS-based and AERONET aerosol records over Beijing reveals two distinct periods, before and after 2007. The MODIS data from both the Terra and Aqua satellites were processed with the new Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm. A comparison of MAIAC and AERONET AOT shows that whereas MAIAC consistently underestimated peak AOT values by 10-20% in the prior period, the bias mostly disappears after mid-2007. Independent analysis of the AERONET dataset reveals little or no change in the effective radii of the fine and coarse fractions and of the Angstrom exponent. At the same time, it shows an increasing trend in the single scattering albedo, by approx.0.02 in 9 years. As MAIAC was using the same aerosol model for the entire 2000-2010 period, the decrease in AOT bias after 2007 can be explained only by a corresponding decrease of aerosol absorption caused by a reduction in local black carbon emissions. The observed changes correlate in time with the Chinese government's broad measures to improve air quality in Beijing during preparations for the Summer Olympics of 2008.

  16. Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

    PubMed Central

    van den Bedem, Henry; Fraser, James S.

    2015-01-01

    Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

  17. Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned

    PubMed Central

    Gabbard, Joseph L.; Shukla, Maulik; Sobral, Bruno

    2010-01-01

    Systems biology and infectious disease (host-pathogen-environment) research and development is becoming increasingly dependent on integrating data from diverse and dynamic sources. Maintaining integrated resources over long periods of time presents distinct challenges. This paper describes experiences and lessons learned from integrating data in two five-year projects focused on pathosystems biology: the Pathosystems Resource Integration Center (PATRIC, http://patric.vbi.vt.edu/), with a goal of developing bioinformatics resources for the research and countermeasures development communities based on genomics data, and the Resource Center for Biodefense Proteomics Research (RCBPR, http://www.proteomicsresource.org/), with a goal of developing resources based on the experiment data such as microarray and proteomics data from diverse sources and technologies. Some challenges include integrating genomic sequence and experiment data, data synchronization, data quality control, and usability engineering. We present examples of a variety of data integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include (1) an approach for addressing discrepancies between experiment results and interpreted results and (2) expanding the range of data integration techniques to include usability engineering at the presentation level. PMID:20491070

  18. Integrative harm reduction psychotherapy: a case of substance use, multiple trauma, and suicidality.

    PubMed

    Tatarsky, Andrew; Kellogg, Scott

    2010-02-01

    Harm reduction is a new paradigm that seeks to reduce the harmful consequences of substance use and other risky behaviors without requiring abstinence. This article discusses integrative harm reduction psychotherapy, one application of harm reduction principles to psychotherapy. Seven therapeutic tasks are described with attention to clinical process, skills, and strategies. A case is presented that illustrates the application of this approach with life-threatening substance use that was related to multiple trauma and suicidal depression. (c) 2010 Wiley Periodicals, Inc.

  19. Analysis of current density and specific absorption rate in biological tissue surrounding transcutaneous transformer for an artificial heart.

    PubMed

    Shiba, Kenji; Nukaya, Masayuki; Tsuji, Toshio; Koshiji, Kohji

    2008-01-01

    This paper reports on the current density and specific absorption rate (SAR) analysis of biological tissue surrounding an air-core transcutaneous transformer for an artificial heart. The electromagnetic field in the biological tissue is analyzed by the transmission line modeling method, and the current density and SAR as a function of frequency, output voltage, output power, and coil dimension are calculated. The biological tissue of the model has three layers including the skin, fat, and muscle. The results of simulation analysis show SARs to be very small at any given transmission conditions, about 2-14 mW/kg, compared to the basic restrictions of the International Commission on nonionizing radiation protection (ICNIRP; 2 W/kg), while the current density divided by the ICNIRP's basic restrictions gets smaller as the frequency rises and the output voltage falls. It is possible to transfer energy below the ICNIRP's basic restrictions when the frequency is over 250 kHz and the output voltage is under 24 V. Also, the parts of the biological tissue that maximized the current density differ by frequencies; in the low frequency is muscle and in the high frequency is skin. The boundary is in the vicinity of the frequency 600-1000 kHz.

  20. Integrating social capacity into risk reduction strategies

    NASA Astrophysics Data System (ADS)

    Schneiderbauer, S.; Pedoth, L.; Zebisch, M.

    2012-04-01

    The reduction of risk to impacts from external stresses and shocks is an important task in communities worldwide at all government levels and independent of the development status. The importance of building social capacity as part of risk reduction strategies is increasingly recognized. However, there is space for improvement to incorporate related activities into a holistic risk governance approach. Starting point for such enhancements is to promote and improve assessments of what is called 'sensitivity' or 'adaptive capacity' in the climate change community and what is named 'vulnerability' or 'resilience' in the hazard risk community. Challenging issues that need to be tackled in this context are the integration of concepts and method as well as the fusion of data. Against this background we introduce a method to assess regional adaptive capacity to climate change focusing on mountain areas accounting for sector specific problems. By considering three levels of specificity as base for the selection of most appropriate indicators the study results have the potential to support decision making regarding most appropriate adaptation actions. Advantages and shortcomings of certain aspects of adaptive capacity assessment in general and of the proposed method in particular are presented.

  1. Validation of double-pulse 1572 nm integrated path differential absorption lidar measurement of carbon dioxide

    NASA Astrophysics Data System (ADS)

    Du, Juan; Liu, Jiqiao; Bi, Decang; Ma, Xiuhua; Hou, Xia; Zhu, Xiaolei; Chen, Weibiao

    2018-04-01

    A ground-based double-pulse 1572 nm integrated path differential absorption (IPDA) lidar was developed for carbon dioxide (CO2) column concentrations measurement. The lidar measured the CO2 concentrations continuously by receiving the scattered echo signal from a building about 1300 m away. The other two instruments of TDLAS and in-situ CO2 analyzer measured the CO2 concentrations on the same time. A CO2 concentration measurement of 430 ppm with 1.637 ppm standard error was achieved.

  2. R3D: Reduction Package for Integral Field Spectroscopy

    NASA Astrophysics Data System (ADS)

    Sánchez, Sebastián. F.

    2011-06-01

    R3D was developed to reduce fiber-based integral field spectroscopy (IFS) data. The package comprises a set of command-line routines adapted for each of these steps, suitable for creating pipelines. The routines have been tested against simulations, and against real data from various integral field spectrographs (PMAS, PPAK, GMOS, VIMOS and INTEGRAL). Particular attention is paid to the treatment of cross-talk. R3D unifies the reduction techniques for the different IFS instruments to a single one, in order to allow the general public to reduce different instruments data in an homogeneus, consistent and simple way. Although still in its prototyping phase, it has been proved to be useful to reduce PMAS (both in the Larr and the PPAK modes), VIMOS and INTEGRAL data. The current version has been coded in Perl, using PDL, in order to speed-up the algorithm testing phase. Most of the time critical algorithms have been translated to C[float=][/float], and it is our intention to translate all of them. However, even in this phase R3D is fast enough to produce valuable science frames in reasonable time.

  3. Gendering Genetics: Biological Contingencies in the Protective Effects of Social Integration for Men and Women.

    PubMed

    Perry, Brea L

    2016-05-01

    Evidence that social and biological processes are intertwined in producing health and human behavior is rapidly accumulating. Using a feminist approach, this research explores how gender moderates the interaction between biological processes and men's and women's behavioral and emotional responses to similar social environments. Using data from the Collaborative Study on the Genetics of Alcoholism, the influence of gender, social integration, and genetic risk on nicotine and alcohol dependence is examined. Three-way interaction models reveal gender-specific moderation of interactions between genetic risk score and social integration. Namely, being currently married and reporting positive social psychological integration are predictive of reduced risk of nicotine dependence among men with genetic susceptibility to strong nicotine cravings in the presence of social cues like stress. In contrast, the protective effects of marital status and social integration are substantially attenuated and absent, respectively, among women with high-risk genotypes. This pattern reflects the dualism (i.e., simultaneous costs and benefits) inherent in social integration for women, which may disproportionately affect those with a genetic sensitivity to stress. These findings contest the notion of genotype as static biological hardwiring that is independent from social and cultural systems of gender difference.

  4. An integrative systems biology approach to understanding pulmonary diseases.

    PubMed

    Auffray, Charles; Adcock, Ian M; Chung, Kian Fan; Djukanovic, Ratko; Pison, Christophe; Sterk, Peter J

    2010-06-01

    Chronic inflammatory pulmonary diseases such as COPD and asthma are highly prevalent and associated with a major health burden worldwide. Despite a wealth of biologic and clinical information on normal and pathologic airway structure and function, the primary causes and mechanisms of disease remain to a large extent unknown, preventing the development of more efficient diagnosis and treatment. We propose to overcome these limitations through an integrative systems biology research strategy designed to identify the functional and regulatory pathways that play central roles in respiratory pathophysiology, starting with severe asthma. This approach relies on global genome, transcriptome, proteome, and metabolome data sets collected in cross-sectional patient cohorts with high-throughput measurement platforms and integrated with biologic and clinical data to inform predictive multiscale models ranging from the molecular to the organ levels. Working hypotheses formulated on the mechanisms and pathways involved in various disease states are tested through perturbation experiments using model simulation combined with targeted and global technologies in cellular and animal models. The responses observed are compared with those predicted by the initial models, which are refined to account better for the results. Novel perturbation experiments are designed and tested both computationally and experimentally to arbitrate between competing hypotheses. The process is iterated until the derived knowledge allows a better classification and subphenotyping of severe asthma using complex biomarkers, which will facilitate the development of novel diagnostic and therapeutic interventions targeting multiple components of the molecular and cellular pathways involved. This can be tested and validated in prospective clinical trials.

  5. Integrated Passive Biological Treatment System/ Mine Waste Technology Program Report #16

    EPA Science Inventory

    This report summarizes the results of the Mine Waste Technology Program (MWTP) Activity III, Project 16, Integrated, Passive Biological Treatment System, funded by the United States Environmental Protection Agency (EPA) and jointly administered by EPA and the United States Depar...

  6. With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology-An Introduction to the Symposium.

    PubMed

    Kohl, Kevin D; Dearing, M Denise

    2017-10-01

    The role that host-associated microbes play in animal biology is gaining attention in comparative biology. Numerous research groups study the roles that microbes play in human health and nutrition, or in enhancing the production of agricultural animals. However, inclusion of host-associated microbes into research questions of integrative and comparative biology has lagged behind. We hosted a symposium to bring together top researchers in the field of host-associated microbes who also incorporate aspects of integrative and comparative biology. In this introduction, we highlight recent research demonstrating the profound roles that host-associated microbes play in many aspects of animal biology, such as immune function, endocrinology, and even behavior. It is our hope that integrative and comparative biologists will begin to include aspects of host-associated microbes into their research programs, enhancing both the fields of comparative biology and host-microbe interactions. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  7. An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology.

    PubMed

    Kohl, Kevin D

    2017-10-01

    Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  8. Studies on Inhibition of Intestinal Absorption of Radioactive Strontium

    PubMed Central

    Skoryna, Stanley C.; Paul, T. M.; Edward, Deirdre Waldron

    1964-01-01

    A method is reported which permits selective suppression of absorption of radioactive strontium from ingested food material, permitting the calcium to be available to the body. Studies were carried out in vivo by injection of Sr89 and Ca45 in the presence of inert carrier into ligated intestinal segments in rats, and the amount of absorption was measured by standard monitoring techniques. The pattern of absorption of both ions is very similar but the rate of absorption is different. It was found that the polyelectrolyte, sodium alginate, obtained from brown algae (Phaeophyceae), injected simultaneously with radiostrontium effectively reduces the absortion of Sr89 from all segments of the intestine by as much as 50-80% of the control values. No significant reduction in absorption of Ca45 was observed in equivalent concentrations. The reduction in blood levels of Sr89 and in bone uptake corresponded to the absorption pattern. The difference in the effect on strontium and calcium absorption may be due to differences in the binding capacity of sodium alginate from the two metal ions under the conditions present in vivo. PMID:14180534

  9. Reactivity of Chromium(III) Nutritional Supplements in Biological Media: An X-Ray Absorption Spectroscopic Study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nguyen, A.; Mulyani, I.; Levina, A.

    2009-05-22

    Chromium(III) nutritional supplements are widely used due to their purported ability to enhance glucose metabolism, despite growing evidence on low activity and the potential genotoxicity of these compounds. Reactivities of Cr(III) complexes used in nutritional formulations, including [Cr3O(OCOEt)6(OH2)3]+ (A), [Cr(pic)3] (pic) = 2-pyridinecarboxylato(-) (B), and trans-[CrCl2(OH2)4]+ (CrCl3 {center_dot} 6H2O; C), in a range of natural and simulated biological media (artificial digestion systems, blood and its components, cell culture media, and intact L6 rat skeletal muscle cells) were studied by X-ray absorption near-edge structure (XANES) spectroscopy. The XANES spectroscopic data were processed by multiple linear-regression analyses with the use of amore » library of model Cr(III) compounds, and the results were corroborated by the results of X-ray absorption fine structure spectroscopy and electrospray mass spectrometry. Complexes A and B underwent extensive ligand-exchange reactions under conditions of combined gastric and intestinal digestion (in the presence of a semisynthetic meal, 3 h at 310 K), as well as in blood serum and in a cell culture medium (1-24 h at 310 K), with the formation of Cr(III) complexes with hydroxo and amino acid/protein ligands. Reactions of compounds A-C with cultured muscle cells led to similar ligand-exchange products, with at least part of Cr(III) bound to the surface of the cells. The reactions of B with serum greatly enhanced its propensity to be converted to Cr(VI) by biological oxidants (H2O2 or glucose oxidase system), which is proposed to be a major cause of both the insulin-enhancing activity and toxicity of Cr(III) compounds (Mulyani, I.; Levina, A.; Lay, P. A. Angew. Chem. Int. Ed. 2004, 43, 4504-4507). This finding enhances the current concern over the safety of consumption of large doses of Cr(III) supplements, particularly [Cr(pic)3].« less

  10. Integrated risk reduction framework to improve railway hazardous materials transportation safety.

    PubMed

    Liu, Xiang; Saat, M Rapik; Barkan, Christopher P L

    2013-09-15

    Rail transportation plays a critical role to safely and efficiently transport hazardous materials. A number of strategies have been implemented or are being developed to reduce the risk of hazardous materials release from train accidents. Each of these risk reduction strategies has its safety benefit and corresponding implementation cost. However, the cost effectiveness of the integration of different risk reduction strategies is not well understood. Meanwhile, there has been growing interest in the U.S. rail industry and government to best allocate resources for improving hazardous materials transportation safety. This paper presents an optimization model that considers the combination of two types of risk reduction strategies, broken rail prevention and tank car safety design enhancement. A Pareto-optimality technique is used to maximize risk reduction at a given level of investment. The framework presented in this paper can be adapted to address a broader set of risk reduction strategies and is intended to assist decision makers for local, regional and system-wide risk management of rail hazardous materials transportation. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Capability for Integrated Systems Risk-Reduction Analysis

    NASA Technical Reports Server (NTRS)

    Mindock, J.; Lumpkins, S.; Shelhamer, M.

    2016-01-01

    NASA's Human Research Program (HRP) is working to increase the likelihoods of human health and performance success during long-duration missions, and subsequent crew long-term health. To achieve these goals, there is a need to develop an integrated understanding of how the complex human physiological-socio-technical mission system behaves in spaceflight. This understanding will allow HRP to provide cross-disciplinary spaceflight countermeasures while minimizing resources such as mass, power, and volume. This understanding will also allow development of tools to assess the state of and enhance the resilience of individual crewmembers, teams, and the integrated mission system. We will discuss a set of risk-reduction questions that has been identified to guide the systems approach necessary to meet these needs. In addition, a framework of factors influencing human health and performance in space, called the Contributing Factor Map (CFM), is being applied as the backbone for incorporating information addressing these questions from sources throughout HRP. Using the common language of the CFM, information from sources such as the Human System Risk Board summaries, Integrated Research Plan, and HRP-funded publications has been combined and visualized in ways that allow insight into cross-disciplinary interconnections in a systematic, standardized fashion. We will show examples of these visualizations. We will also discuss applications of the resulting analysis capability that can inform science portfolio decisions, such as areas in which cross-disciplinary solicitations or countermeasure development will potentially be fruitful.

  12. Merged beam laser design for reduction of gain-saturation and two-photon absorption in high power single mode semiconductor lasers.

    PubMed

    Lysevych, M; Tan, H H; Karouta, F; Fu, L; Jagadish, C

    2013-04-08

    In this paper we report a method to overcome the limitations of gain-saturation and two-photon absorption faced by developers of high power single mode InP-based lasers and semiconductor optical amplifiers (SOA) including those based on wide-waveguide or slab-coupled optical waveguide laser (SCOWL) technology. The method is based on Y-coupling design of the laser cavity. The reduction in gain-saturation and two-photon absorption in the merged beam laser structures (MBL) are obtained by reducing the intensity of electromagnetic field in the laser cavity. Standard ridge-waveguide lasers and MBLs were fabricated, tested and compared. Despite a slightly higher threshold current, the reduced gain-saturation in MBLs results in higher output power. The MBLs also produced a single spatial mode, as well as a strongly dominating single spectral mode which is the inherent feature of MBL-type cavity.

  13. Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

    PubMed

    Narayanasamy, Shaman; Muller, Emilie E L; Sheik, Abdul R; Wilmes, Paul

    2015-05-01

    Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes'. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure-function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  14. Mapping biological ideas: Concept maps as knowledge integration tools for evolution education

    NASA Astrophysics Data System (ADS)

    Schwendimann, Beat Adrian

    Many students leave school with a fragmented understanding of biology that does not allow them to connect their ideas to their everyday lives (Wandersee, 1989; Mintzes, Wandersee, & Novak, 1998; Mintzes, Wandersee, & Novak, 2000a). Understanding evolution ideas is seen as central to building an integrated knowledge of biology (Blackwell, Powell, & Dukes, 2003; Thagard & Findlay, 2010). However, the theory of evolution has been found difficult to understand as it incorporates a wide range of ideas from different areas (Bahar et al., 1999; Tsui & Treagust, 2003) and multiple interacting levels (Wilensky & Resnick, 1999; Duncan & Reiser, 2007; Hmelo-Silver et al., 2007). Research suggests that learners can hold a rich repertoire of co-existing alternative ideas of evolution (for example, Bishop & Anderson, 1990; Demastes, Good, & Peebles, 1996; Evans, 2008), especially of human evolution (for example, Nelson, 1986; Sinatra et al., 2003; Poling & Evans, 2004). Evolution ideas are difficult to understand because they often contradict existing alternative ideas (Mayr, 1982; Wolpert, 1994; Evans, 2008). Research suggests that understanding human evolution is a key to evolution education (for example, Blackwell et al., 2003; Besterman & Baggott la Velle, 2007). This dissertation research investigates how different concept mapping forms embedded in a collaborative technology-enhanced learning environment can support students' integration of evolution ideas using case studies of human evolution. Knowledge Integration (KI) (Linn et al., 2000; Linn et al., 2004) is used as the operational framework to explore concept maps as knowledge integration tools to elicit, add, critically distinguish, group, connect, and sort out alternative evolution ideas. Concept maps are a form of node-link diagram for organizing and representing connections between ideas as a semantic network (Novak & Gowin, 1984). This dissertation research describes the iterative development of a novel biology

  15. Improving integrative searching of systems chemical biology data using semantic annotation.

    PubMed

    Chen, Bin; Ding, Ying; Wild, David J

    2012-03-08

    Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

  16. Integrated vacuum absorption steam cycle gas separation

    DOEpatents

    Chen, Shiaguo [Champaign, IL; Lu, Yonggi [Urbana, IL; Rostam-Abadi, Massoud [Champaign, IL

    2011-11-22

    Methods and systems for separating a targeted gas from a gas stream emitted from a power plant. The gas stream is brought into contact with an absorption solution to preferentially absorb the targeted gas to be separated from the gas stream so that an absorbed gas is present within the absorption solution. This provides a gas-rich solution, which is introduced into a stripper. Low pressure exhaust steam from a low pressure steam turbine of the power plant is injected into the stripper with the gas-rich solution. The absorbed gas from the gas-rich solution is stripped in the stripper using the injected low pressure steam to provide a gas stream containing the targeted gas. The stripper is at or near vacuum. Water vapor in a gas stream from the stripper is condensed in a condenser operating at a pressure lower than the stripper to concentrate the targeted gas. Condensed water is separated from the concentrated targeted gas.

  17. Teacher Perceptions of the Integration of Laptop Computers in Their High School Biology Classrooms

    NASA Astrophysics Data System (ADS)

    Gundy, Morag S.

    2011-12-01

    Studies indicate that teachers, and in particular science teachers in the senior high school grades, do not integrate laptop computers into their instruction to the extent anticipated by researchers. This technology has not spread easily to other teachers even with improved access to hardware and software, increased support, and a paradigm shift from teacher-centred to student-centred education. Although a number of studies have focused on the issues and problems related to the integration of laptops in classroom instruction, these studies, largely quantitative in nature, have tended to bypass the role teachers play in integrating laptop computers into their instruction. This thesis documents and describes the role of Ontario high school science teachers in the integration of laptop computers in the classroom. Ten teachers who have successfully integrated laptop computers into their biology courses participated in this descriptive study. Their perceptions of implementing laptops into their biology courses, key factors about the implementation process, and how the implementation was accomplished are examined. The study also identifies the conditions which they feel would allow this innovation to be implemented by other teachers. Key findings of the study indicate that teachers must initiate, implement and sustain an emergent and still evolving innovation; teacher perceptions change and continue to change with increased experience using laptops in the science classroom; changes in teaching approaches are significant as a result of the introduction of laptop technology; and, the teachers considered the acquisition and use of new teaching materials to be an important aspect of integrating laptop computers into instruction. Ongoing challenges for appropriate professional development, sharing of knowledge, skills and teaching materials are identified. The study provides a body of practical knowledge for biology teachers who are considering the integration of laptops into

  18. Camels, Cormorants, and Kangaroo Rats: Integration and Synthesis in Organismal Biology After World War II.

    PubMed

    Hagen, Joel B

    2015-01-01

    During the decades following World War II diverse groups of American biologists established a variety of distinctive approaches to organismal biology. Rhetorically, organismal biology could be used defensively to distinguish established research traditions from perceived threats from newly emerging fields such as molecular biology. But, organismal biologists were also interested in integrating biological disciplines and using a focus on organisms to synthesize levels of organization from molecules and cells to populations and communities. Part of this broad movement was the development of an area of research variously referred to as physiological ecology, environmental physiology, or ecophysiology. This area of research was distinctive in its self-conscious blend of field and laboratory practices and its explicit integration with other areas of biology such as ecology, animal behavior, and evolution in order to study adaptation. Comparing the intersecting careers of Knut Schmidt-Nielsen and George Bartholomew highlights two strikingly different approaches to physiological ecology. These alternative approaches to studying the interactions of organisms and environments also differed in important ways from the organismal biology championed by leading figures in the modern synthesis.

  19. Mercury in Environmental and Biological Samples Using Online Combustion with Sequential Atomic Absorption and Fluorescence Measurements: A Direct Comparison of Two Fundamental Techniques in Spectrometry

    ERIC Educational Resources Information Center

    Cizdziel, James V.

    2011-01-01

    In this laboratory experiment, students quantitatively determine the concentration of an element (mercury) in an environmental or biological sample while comparing and contrasting the fundamental techniques of atomic absorption spectrometry (AAS) and atomic fluorescence spectrometry (AFS). A mercury analyzer based on sample combustion,…

  20. Objective Integrated Assessment of Functional Outcomes in Reduction Mammaplasty

    PubMed Central

    Passaro, Ilaria; Malovini, Alberto; Faga, Angela; Toffola, Elena Dalla

    2013-01-01

    Background: The aim of our study was an objective integrated assessment of the functional outcomes of reduction mammaplasty. Methods: The study involved 17 women undergoing reduction mammaplasty from March 2009 to June 2011. Each patient was assessed before surgery and 2 months postoperatively with the original association of 4 subjective and objective assessment methods: a physiatric clinical examination, the Roland Morris Disability Questionnaire, the Berg Balance Scale, and a static force platform analysis. Results: All of the tests proved multiple statistically significant associated outcomes demonstrating a significant improvement in the functional status following reduction mammaplasty. Surgical correction of breast hypertrophy could achieve both spinal pain relief and recovery of performance status in everyday life tasks, owing to a muscular postural functional rearrangement with a consistent antigravity muscle activity sparing. Pain reduction in turn could reduce the antalgic stiffness and improved the spinal range of motion. In our sample, the improvement of the spinal range of motion in flexion matched a similar improvement in extension. Recovery of a more favorable postural pattern with reduction of the anterior imbalance was demonstrated by the static force stabilometry. Therefore, postoperatively, all of our patients narrowed the gap between the actual body barycenter and the ideal one. The static force platform assessment also consistently confirmed the effectiveness of an accurate clinical examination of functional impairment from breast hypertrophy. Conclusions: The static force platform assessment might help the clinician to support the diagnosis of functional impairment from a breast hypertrophy with objectively based data. PMID:25289256

  1. Biological assessment for the effluent reduction program, Los Alamos National Laboratory, Los Alamos, New Mexico

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cross, S.P.

    1996-08-01

    This report describes the biological assessment for the effluent recution program proposed to occur within the boundaries of Los Alamos National Laboratory. Potential effects on wetland plants and on threatened and endangered species are discussed, along with a detailed description of the individual outfalls resulting from the effluent reduction program.

  2. Light absorption properties and radiative effects of primary organic aerosol emissions

    DOE PAGES

    Lu, Zifeng; Streets, David G.; Winijkul, Ekbordin; ...

    2015-03-26

    Organic aerosols (OAs) in the atmosphere affect Earth’s energy budget by not only scattering but also absorbing solar radiation due to the presence of the so-called “brown carbon” (BrC) component. However, the absorptivities of OAs are not represented or are poorly represented in current climate and chemical transport models. In this study, we provide a method to constrain the BrC absorptivity at the emission inventory level using recent laboratory and field observations. We review available measurements of the light-absorbing primary OA (POA), and quantify the wavelength-dependent imaginary refractive indices (k OA, the fundamental optical parameter determining the particle’s absorptivity) andmore » their uncertainties for the bulk POA emitted from biomass/biofuel, lignite, propane, and oil combustion sources. In particular, we parametrize the k OA of biomass/biofuel combustion sources as a function of the black carbon (BC)-to-OA ratio, indicating that the absorptive properties of POA depend strongly on burning conditions. The derived fuel-type-based k OA profiles are incorporated into a global carbonaceous aerosol emission inventory, and the integrated k OA values of sectoral and total POA emissions are presented. The results of a simple radiative transfer model show that the POA absorptivity warms the atmosphere significantly and leads to ~27% reduction in the amount of the net global average POA cooling compared to results from the nonabsorbing assumption.« less

  3. Design and Economic Potential of an Integrated High-Temperature Fuel Cell and Absorption Chiller Combined Cooling, Heat, and Power System

    NASA Astrophysics Data System (ADS)

    Hosford, Kyle S.

    Clean distributed generation power plants can provide a much needed balance to our energy infrastructure in the future. A high-temperature fuel cell and an absorption chiller can be integrated to create an ideal combined cooling, heat, and power system that is efficient, quiet, fuel flexible, scalable, and environmentally friendly. With few real-world installations of this type, research remains to identify the best integration and operating strategy and to evaluate the economic viability and market potential of this system. This thesis informs and documents the design of a high-temperature fuel cell and absorption chiller demonstration system at a generic office building on the University of California, Irvine (UCI) campus. This work details the extension of prior theoretical work to a financially-viable power purchase agreement (PPA) with regard to system design, equipment sizing, and operating strategy. This work also addresses the metering and monitoring for the system showcase and research and details the development of a MATLAB code to evaluate the economics associated with different equipment selections, building loads, and economic parameters. The series configuration of a high-temperature fuel cell, heat recovery unit, and absorption chiller with chiller exhaust recirculation was identified as the optimal system design for the installation in terms of efficiency, controls, ducting, and cost. The initial economic results show that high-temperature fuel cell and absorption chiller systems are already economically competitive with utility-purchased generation, and a brief case study of a southern California hospital shows that the systems are scalable and viable for larger stationary power applications.

  4. Biological and Psychosocial Predictors of Postpartum Depression: Systematic Review and Call for Integration

    PubMed Central

    Tanner Stapleton, Lynlee R.; Guardino, Christine M.; Hahn-Holbrook, Jennifer; Schetter, Christine Dunkel

    2017-01-01

    Postpartum depression (PPD) adversely affects the health and well being of many new mothers, their infants, and their families. A comprehensive understanding of biopsychosocial precursors to PPD is needed to solidify the current evidence base for best practices in translation. We conducted a systematic review of research published from 2000 through 2013 on biological and psychosocial factors associated with PPD and postpartum depressive symptoms. Two hundred fourteen publications based on 199 investigations of 151,651 women in the first postpartum year met inclusion criteria. The biological and psychosocial literatures are largely distinct, and few studies provide integrative analyses. The strongest PPD risk predictors among biological processes are hypothalamic-pituitary-adrenal dysregulation, inflammatory processes, and genetic vulnerabilities. Among psychosocial factors, the strongest predictors are severe life events, some forms of chronic strain, relationship quality, and support from partner and mother. Fully integrated biopsychosocial investigations with large samples are needed to advance our knowledge of PPD etiology. PMID:25822344

  5. Optical characterization of tissue mimicking phantoms by a vertical double integrating sphere system

    NASA Astrophysics Data System (ADS)

    Han, Yilin; Jia, Qiumin; Shen, Shuwei; Liu, Guangli; Guo, Yuwei; Zhou, Ximing; Chu, Jiaru; Zhao, Gang; Dong, Erbao; Allen, David W.; Lemaillet, Paul; Xu, Ronald

    2016-03-01

    Accurate characterization of absorption and scattering properties for biologic tissue and tissue-simulating materials enables 3D printing of traceable tissue-simulating phantoms for medical spectral device calibration and standardized medical optical imaging. Conventional double integrating sphere systems have several limitations and are suboptimal for optical characterization of liquid and soft materials used in 3D printing. We propose a vertical double integrating sphere system and the associated reconstruction algorithms for optical characterization of phantom materials that simulate different human tissue components. The system characterizes absorption and scattering properties of liquid and solid phantom materials in an operating wavelength range from 400 nm to 1100 nm. Absorption and scattering properties of the phantoms are adjusted by adding titanium dioxide powder and India ink, respectively. Different material compositions are added in the phantoms and characterized by the vertical double integrating sphere system in order to simulate the human tissue properties. Our test results suggest that the vertical integrating sphere system is able to characterize optical properties of tissue-simulating phantoms without precipitation effect of the liquid samples or wrinkling effect of the soft phantoms during the optical measurement.

  6. Absorption and biological activity of phytochemical-rich extracts from açai (Euterpe oleracea Mart.) pulp and oil in vitro.

    PubMed

    Pacheco-Palencia, Lisbeth A; Talcott, Stephen T; Safe, Stephen; Mertens-Talcott, Susanne

    2008-05-28

    Polyphenolic extracts from various fruits and vegetables have been shown to exert growth inhibitory effects in cell culture studies. Whereas individual polyphenolic compounds have been extensively evaluated, understanding of the biological activity of polyphenolic extracts from natural sources is limited and critical to the understanding of their potential effects on the human body. This study investigated the absorption and antiproliferative effects of phytochemical extracts from acai pulp and a polyphenolic-enriched acai oil obtained from the fruit pulp of the acai berry ( Euterpe oleracea Mart.). Chemical composition, antioxidant properties, and polyphenolic absorption of phytochemical fractions in a Caco-2 monolayer were determined, along with their cytotoxicity in HT-29 human colon adenocarcinoma cells. Standardized extracts were characterized by their predominance of hydroxybenzoic acids, monomeric flavan-3-ols, and procyanidin dimers and trimers. Polyphenolic mixtures (0-12 microg of gallic acid equiv/mL) from both acai pulp and acai oil extracts inhibited cell proliferation by up to 90.7%, which was accompanied by an increase of up to 2.1-fold in reactive oxygen species. Absorption experiments using a Caco-2 intestinal cell monolayer demonstrated that phenolic acids such as p-hydroxybenzoic, vanillic, syringic, and ferulic acids, in the presence of DMSO, were readily transported from the apical to the basolateral side along with monomeric flavanols such as (+)-catechin and (-)-epicatechin. Results from this study provide further evidence for the bioactive properties of acai polyphenolics and offer new insight on their composition and cellular absorption.

  7. A new parameterization for surface ocean light attenuation in Earth System Models: assessing the impact of light absorption by colored detrital material

    NASA Astrophysics Data System (ADS)

    Kim, G. E.; Pradal, M.-A.; Gnanadesikan, A.

    2015-03-01

    Light limitation can affect the distribution of biota and nutrients in the ocean. Light absorption by colored detrital material (CDM) was included in a fully coupled Earth System Model using a new parameterization for shortwave attenuation. Two model runs were conducted, with and without light attenuation by CDM. In a global average sense, greater light limitation associated with CDM increased surface chlorophyll, biomass and nutrients together. These changes can be attributed to the movement of biological productivity higher up the water column, which increased surface chlorophyll and biomass while simultaneously decreasing total biomass. Meanwhile, the reduction in biomass resulted in greater nutrient availability throughout the water column. Similar results were found on a regional scale in an analysis of the oceans by biome. In coastal regions, surface chlorophyll increased by 35% while total integrated phytoplankton biomass diminished by 18%. The largest relative increases in modeled surface chlorophyll and biomass in the open ocean were found in the equatorial biomes, while largest decreases in depth-integrated biomass and chlorophyll were found in the subpolar and polar biomes. This mismatch of surface and subsurface trends and their regional dependence was analyzed by comparing the competing factors of diminished light availability and increased nutrient availability on phytoplankton growth in the upper 200 m. Overall, increases in surface biomass were expected to accompany greater nutrient uptake and therefore diminish surface nutrients, but changes in light limitation decoupled trends between these two variables. Understanding changes in biological productivity requires both surface and depth-resolved information. Surface trends may be minimal or of the opposite sign to depth-integrated amounts, depending on the vertical structure of phytoplankton abundance.

  8. Tunable integration of absorption-membrane-adsorption for efficiently separating low boiling gas mixtures near normal temperature

    PubMed Central

    Liu, Huang; Pan, Yong; Liu, Bei; Sun, Changyu; Guo, Ping; Gao, Xueteng; Yang, Lanying; Ma, Qinglan; Chen, Guangjin

    2016-01-01

    Separation of low boiling gas mixtures is widely concerned in process industries. Now their separations heavily rely upon energy-intensive cryogenic processes. Here, we report a pseudo-absorption process for separating low boiling gas mixtures near normal temperature. In this process, absorption-membrane-adsorption is integrated by suspending suitable porous ZIF material in suitable solvent and forming selectively permeable liquid membrane around ZIF particles. Green solvents like water and glycol were used to form ZIF-8 slurry and tune the permeability of liquid membrane surrounding ZIF-8 particles. We found glycol molecules form tighter membrane while water molecules form looser membrane because of the hydrophobicity of ZIF-8. When using mixing solvents composed of glycol and water, the permeability of liquid membrane becomes tunable. It is shown that ZIF-8/water slurry always manifests remarkable higher separation selectivity than solid ZIF-8 and it could be tuned to further enhance the capture of light hydrocarbons by adding suitable quantity of glycol to water. Because of its lower viscosity and higher sorption/desorption rate, tunable ZIF-8/water-glycol slurry could be readily used as liquid absorbent to separate different kinds of low boiling gas mixtures by applying a multistage separation process in one traditional absorption tower, especially for the capture of light hydrocarbons. PMID:26892255

  9. Integration of coagulation and adsorption for removal of N-nitrosodimethylamine (NDMA) precursors from biologically treated municipal wastewater.

    PubMed

    Wang, Miaomiao; Meng, Yingjie; Ma, Defang; Wang, Yan; Li, Fengli; Xu, Xing; Xia, Chufan; Gao, Baoyu

    2017-05-01

    This study investigated the N-nitrosodimethylamine (NDMA) formation potential of various dissolved organic matter (DOM) fractions in biologically treated municipal wastewater by UF fractionation, XAD-8 resin adsorption isolation, and excitation and emission matrix (EEM) fluorescence spectroscopy. Removal of various NDMA precursor fractions was also analyzed to evaluate the efficiency of traditional water treatment processes (coagulation, adsorption, and coagulation-adsorption). Results showed that NDMA were mainly formed by low molecular weight (MW) fractions (<30 kDa) and hydrophilic fractions (HiS) in biologically treated municipal wastewater. Integrated coagulation-adsorption treatments showed the highest reduction capacity for NDMA formation potential (57%), followed by isolated adsorption treatment (50%) and isolated coagulation treatment (28%). The powdered activated carbon (PAC) adsorption process could reduce the high MW precursors (>30 kDa) by 48%, which was higher than other treatments. In contrast, the highest uptake (66%) of low MW precursors (<30 kDa) was achieved by the coagulation-adsorption process. All treatments preferentially removed the hydrophobic acids (HoA) fraction compared to other fractions. Coagulation could remove more fulvic acid-like substances and adsorption could remove more microbial by-products and aromatic proteins.

  10. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

    PubMed Central

    Waagmeester, Andra; Pico, Alexander R.

    2016-01-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

  11. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

    PubMed

    Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

    2016-06-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

  12. iTools: a framework for classification, categorization and integration of computational biology resources.

    PubMed

    Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

    2008-05-28

    The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management

  13. iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

    PubMed Central

    Dinov, Ivo D.; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H. V.; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D. Stott; Toga, Arthur W.

    2008-01-01

    The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource

  14. Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms.

    PubMed

    Li, Le; Yip, Kevin Y

    2016-12-15

    Currently most terms and term-term relationships in Gene Ontology (GO) are defined manually, which creates cost, consistency and completeness issues. Recent studies have demonstrated the feasibility of inferring GO automatically from biological networks, which represents an important complementary approach to GO construction. These methods (NeXO and CliXO) are unsupervised, which means 1) they cannot use the information contained in existing GO, 2) the way they integrate biological networks may not optimize the accuracy, and 3) they are not customized to infer the three different sub-ontologies of GO. Here we present a semi-supervised method called Unicorn that extends these previous methods to tackle the three problems. Unicorn uses a sub-tree of an existing GO sub-ontology as training part to learn parameters in integrating multiple networks. Cross-validation results show that Unicorn reliably inferred the left-out parts of each specific GO sub-ontology. In addition, by training Unicorn with an old version of GO together with biological networks, it successfully re-discovered some terms and term-term relationships present only in a new version of GO. Unicorn also successfully inferred some novel terms that were not contained in GO but have biological meanings well-supported by the literature. Source code of Unicorn is available at http://yiplab.cse.cuhk.edu.hk/unicorn/.

  15. Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms

    PubMed Central

    Li, Le; Yip, Kevin Y.

    2016-01-01

    Currently most terms and term-term relationships in Gene Ontology (GO) are defined manually, which creates cost, consistency and completeness issues. Recent studies have demonstrated the feasibility of inferring GO automatically from biological networks, which represents an important complementary approach to GO construction. These methods (NeXO and CliXO) are unsupervised, which means 1) they cannot use the information contained in existing GO, 2) the way they integrate biological networks may not optimize the accuracy, and 3) they are not customized to infer the three different sub-ontologies of GO. Here we present a semi-supervised method called Unicorn that extends these previous methods to tackle the three problems. Unicorn uses a sub-tree of an existing GO sub-ontology as training part to learn parameters in integrating multiple networks. Cross-validation results show that Unicorn reliably inferred the left-out parts of each specific GO sub-ontology. In addition, by training Unicorn with an old version of GO together with biological networks, it successfully re-discovered some terms and term-term relationships present only in a new version of GO. Unicorn also successfully inferred some novel terms that were not contained in GO but have biological meanings well-supported by the literature.Availability: Source code of Unicorn is available at http://yiplab.cse.cuhk.edu.hk/unicorn/. PMID:27976738

  16. Double-pulse 1.57  μm integrated path differential absorption lidar ground validation for atmospheric carbon dioxide measurement.

    PubMed

    Du, Juan; Zhu, Yadan; Li, Shiguang; Zhang, Junxuan; Sun, Yanguang; Zang, Huaguo; Liu, Dan; Ma, Xiuhua; Bi, Decang; Liu, Jiqiao; Zhu, Xiaolei; Chen, Weibiao

    2017-09-01

    A ground-based double-pulse integrated path differential absorption (IPDA) instrument for carbon dioxide (CO 2 ) concentration measurements at 1572 nm has been developed. A ground experiment was implemented under different conditions with a known wall located about 1.17 km away acting as the scattering hard target. Off-/offline testing of a laser transmitter was conducted to estimate the instrument systematic and random errors. Results showed a differential absorption optical depth (DAOD) offset of 0.0046 existing in the instrument. On-/offline testing was done to achieve the actual DAOD resulting from the CO 2 absorption. With 18 s pulses average, it demonstrated that a CO 2 concentration measurement of 432.71±2.42  ppm with 0.56% uncertainty was achieved. The IPDA ranging led to a measurement uncertainty of 1.5 m.

  17. Subgap Absorption in Conjugated Polymers

    DOE R&D Accomplishments Database

    Sinclair, M.; Seager, C. H.; McBranch, D.; Heeger, A. J; Baker, G. L.

    1991-01-01

    Along with X{sup (3)}, the magnitude of the optical absorption in the transparent window below the principal absorption edge is an important parameter which will ultimately determine the utility of conjugated polymers in active integrated optical devices. With an absorptance sensitivity of < 10{sup {minus}5}, Photothermal Deflection Spectroscopy (PDS) is ideal for determining the absorption coefficients of thin films of transparent'' materials. We have used PDS to measure the optical absorption spectra of the conjugated polymers poly(1,4-phenylene-vinylene) (and derivitives) and polydiacetylene-4BCMU in the spectral region from 0.55 eV to 3 eV. Our spectra show that the shape of the absorption edge varies considerably from polymer to polymer, with polydiacetylene-4BCMU having the steepest absorption edge. The minimum absorption coefficients measured varied somewhat with sample age and quality, but were typically in the range 1 cm{sup {minus}1} to 10 cm{sup {minus}1}. In the region below 1 eV, overtones of C-H stretching modes were observed, indicating that further improvements in transparency in this spectral region might be achieved via deuteration of fluorination.

  18. Methods of integrating Islamic values in teaching biology for shaping attitude and character

    NASA Astrophysics Data System (ADS)

    Listyono; Supardi, K. I.; Hindarto, N.; Ridlo, S.

    2018-03-01

    Learning is expected to develop the potential of learners to have the spiritual attitude: moral strength, self-control, personality, intelligence, noble character, as well as the skills needed by themselves, society, and nation. Implementation of role and morale in learning is an alternative way which is expected to answer the challenge. The solution offered is to inject student with religious material Islamic in learning biology. The content value of materials teaching biology includes terms of practical value, religious values, daily life value, socio-political value, and the value of art. In Islamic religious values (Qur'an and Hadith) various methods can touch human feelings, souls, and generate motivation. Integrating learning with Islamic value can be done by the deductive or inductive approach. The appropriate method of integration is the amtsal (analog) method, hiwar (dialog) method, targhib & tarhib (encouragement & warning) method, and example method (giving a noble role model / good example). The right strategy in integrating Islamic values is outlined in the design of lesson plan. The integration of Islamic values in lesson plan will facilitate teachers to build students' character because Islamic values can be implemented in every learning steps so students will be accustomed to receiving the character value in this integrated learning.

  19. Strategies for the reduction of Legionella in biological treatment systems.

    PubMed

    Nogueira, R; Utecht, K-U; Exner, M; Verstraete, W; Rosenwinkel, K-H

    A community-wide outbreak of Legionnaire's disease occurred in Warstein, Germany, in August 2013. The epidemic strain, Legionella pneumophila Serogruppe 1, was isolated from an industrial wastewater stream entering the municipal wastewater treatment plant (WWTP) in Wartein, the WWTP itself, the river Wäster and air/water samples from an industrial cooling system 3 km downstream of the WWTP. The present study investigated the effect of physical-chemical disinfection methods on the reduction of the concentration of Legionella in the biological treatment and in the treated effluent entering the river Wäster. Additionally, to gain insight into the factors that promote the growth of Legionella in biological systems, growth experiments were made with different substrates and temperatures. The dosage rates of silver micro-particles, hydrogen peroxide, chlorine dioxide and ozone and pH stress to the activated sludge were not able to decrease the number of culturable Legionella spp. in the effluent. Nevertheless, the UV treatment of secondary treated effluent reduced Legionella spp. on average by 1.6-3.4 log units. Laboratory-scale experiments and full-scale measurements suggested that the aerobic treatment of warm wastewater (30-35 °C) rich in organic nitrogen (protein) is a possible source of Legionella infection.

  20. Modelling biological Cr(VI) reduction in aquifer microcosm column systems.

    PubMed

    Molokwane, Pulane E; Chirwa, Evans M N

    2013-01-01

    Several chrome processing facilities in South Africa release hexavalent chromium (Cr(VI)) into groundwater resources. Pump-and-treat remediation processes have been implemented at some of the sites but have not been successful in reducing contamination levels. The current study is aimed at developing an environmentally friendly, cost-effective and self-sustained biological method to curb the spread of chromium at the contaminated sites. An indigenous Cr(VI)-reducing mixed culture of bacteria was demonstrated to reduce high levels of Cr(VI) in laboratory samples. The effect of Cr(VI) on the removal rate was evaluated at concentrations up to 400 mg/L. Following the detailed evaluation of fundamental processes for biological Cr(VI) reduction, a predictive model for Cr(VI) breakthrough through aquifer microcosm reactors was developed. The reaction rate in batch followed non-competitive rate kinetics with a Cr(VI) inhibition threshold concentration of approximately 99 mg/L. This study evaluates the application of the kinetic parameters determined in the batch reactors to the continuous flow process. The model developed from advection-reaction rate kinetics in a porous media fitted best the effluent Cr(VI) concentration. The model was also used to elucidate the logistic nature of biomass growth in the reactor systems.

  1. Intraparticle reduction of arsenite (As(III)) by nanoscale zerovalent iron (nZVI) investigated with In Situ X-ray absorption spectroscopy.

    PubMed

    Yan, Weile; Vasic, Relja; Frenkel, Anatoly I; Koel, Bruce E

    2012-07-03

    While a high efficiency of contaminant removal by nanoscale zerovalent iron (nZVI) has often been reported for several contaminants of great concern, including aqueous arsenic species, the transformations and translocation of contaminants at and within the nanoparticles are not clearly understood. By analysis using in situ time-dependent X-ray absorption spectroscopy (XAS) of the arsenic core level for nZVI in anoxic As(III) solutions, we have observed that As(III) species underwent two stages of transformation upon adsorption at the nZVI surface. The first stage corresponds to breaking of As-O bonds at the particle surface, and the second stage involves further reduction and diffusion of arsenic across the thin oxide layer enclosing the nanoparticles, which results in arsenic forming an intermetallic phase with the Fe(0) core. Extended X-ray absorption fine-structure (EXAFS) data from experiments conducted at different iron/arsenic ratios indicate that the reduced arsenic species tend to be enriched at the surface of the Fe(0) core region and had limited mobility into the interior of the metal core within the experimental time frame (up to 22 h). Therefore, there was an accumulation of partially reduced arsenic at the Fe(0)/oxide interface when a relatively large arsenic content was present in the solid phase. These results illuminate the role of intraparticle diffusion and reduction in affecting the chemical state and spatial distribution of arsenic in nZVI materials.

  2. Competency-based reforms of the undergraduate biology curriculum: integrating the physical and biological sciences.

    PubMed

    Thompson, Katerina V; Chmielewski, Jean; Gaines, Michael S; Hrycyna, Christine A; LaCourse, William R

    2013-06-01

    The National Experiment in Undergraduate Science Education project funded by the Howard Hughes Medical Institute is a direct response to the Scientific Foundations for Future Physicians report, which urged a shift in premedical student preparation from a narrow list of specific course work to a more flexible curriculum that helps students develop broad scientific competencies. A consortium of four universities is working to create, pilot, and assess modular, competency-based curricular units that require students to use higher-order cognitive skills and reason across traditional disciplinary boundaries. Purdue University; the University of Maryland, Baltimore County; and the University of Miami are each developing modules and case studies that integrate the biological, chemical, physical, and mathematical sciences. The University of Maryland, College Park, is leading the effort to create an introductory physics for life sciences course that is reformed in both content and pedagogy. This course has prerequisites of biology, chemistry, and calculus, allowing students to apply strategies from the physical sciences to solving authentic biological problems. A comprehensive assessment plan is examining students' conceptual knowledge of physics, their attitudes toward interdisciplinary approaches, and the development of specific scientific competencies. Teaching modules developed during this initial phase will be tested on multiple partner campuses in preparation for eventual broad dissemination.

  3. Classical Affine W-Superalgebras via Generalized Drinfeld-Sokolov Reductions and Related Integrable Systems

    NASA Astrophysics Data System (ADS)

    Suh, Uhi Rinn

    2018-02-01

    The purpose of this article is to investigate relations between W-superalgebras and integrable super-Hamiltonian systems. To this end, we introduce the generalized Drinfel'd-Sokolov (D-S) reduction associated to a Lie superalgebra g and its even nilpotent element f, and we find a new definition of the classical affine W-superalgebra W(g,f,k) via the D-S reduction. This new construction allows us to find free generators of W(g,f,k), as a differential superalgebra, and two independent Lie brackets on W(g,f,k)/partial W(g,f,k). Moreover, we describe super-Hamiltonian systems with the Poisson vertex algebras theory. A W-superalgebra with certain properties can be understood as an underlying differential superalgebra of a series of integrable super-Hamiltonian systems.

  4. Determination of total mercury in environmental and biological samples by flow injection cold vapour atomic absorption spectrometry

    NASA Astrophysics Data System (ADS)

    Murphy, James; Jones, Phil; Hill, Steve J.

    1996-12-01

    A simple and accurate method has been developed for the determination of total mercury in environmental and biological samples. The method utilises an off-line microwave digestion stage followed by analysis using a flow injection system with detection by cold vapour atomic absorption spectrometry. The method has been validated using two certified reference materials (DORM-1 dogfish and MESS-2 estuarine sediment) and the results agreed well with the certified values. A detection limit of 0.2 ng g -1 Hg was obtained and no significant interference was observed. The method was finally applied to the determination of mercury in river sediments and canned tuna fish, and gave results in the range 0.1-3.0 mg kg -1.

  5. Nation-Based Occurrence and Endogenous Biological Reduction of Mycotoxins in Medicinal Herbs and Spices.

    PubMed

    Do, Kee Hun; An, Tae Jin; Oh, Sang-Keun; Moon, Yuseok

    2015-10-14

    Medicinal herbs have been increasingly used for therapeutic purposes against a diverse range of human diseases worldwide. Moreover, the health benefits of spices have been extensively recognized in recent studies. However, inevitable contaminants, including mycotoxins, in medicinal herbs and spices can cause serious problems for humans in spite of their health benefits. Along with the different nation-based occurrences of mycotoxins, the ultimate exposure and toxicities can be diversely influenced by the endogenous food components in different commodities of the medicinal herbs and spices. The phytochemicals in these food stuffs can influence mold growth, mycotoxin production and biological action of the mycotoxins in exposed crops, as well as in animal and human bodies. The present review focuses on the occurrence of mycotoxins in medicinal herbs and spices and the biological interaction between mold, mycotoxin and herbal components. These networks will provide insights into the methods of mycotoxin reduction and toxicological risk assessment of mycotoxin-contaminated medicinal food components in the environment and biological organisms.

  6. Nation-Based Occurrence and Endogenous Biological Reduction of Mycotoxins in Medicinal Herbs and Spices

    PubMed Central

    Do, Kee Hun; An, Tae Jin; Oh, Sang-Keun; Moon, Yuseok

    2015-01-01

    Medicinal herbs have been increasingly used for therapeutic purposes against a diverse range of human diseases worldwide. Moreover, the health benefits of spices have been extensively recognized in recent studies. However, inevitable contaminants, including mycotoxins, in medicinal herbs and spices can cause serious problems for humans in spite of their health benefits. Along with the different nation-based occurrences of mycotoxins, the ultimate exposure and toxicities can be diversely influenced by the endogenous food components in different commodities of the medicinal herbs and spices. The phytochemicals in these food stuffs can influence mold growth, mycotoxin production and biological action of the mycotoxins in exposed crops, as well as in animal and human bodies. The present review focuses on the occurrence of mycotoxins in medicinal herbs and spices and the biological interaction between mold, mycotoxin and herbal components. These networks will provide insights into the methods of mycotoxin reduction and toxicological risk assessment of mycotoxin-contaminated medicinal food components in the environment and biological organisms. PMID:26473926

  7. Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends.

    PubMed

    Snowden, Thomas J; van der Graaf, Piet H; Tindall, Marcus J

    2017-07-01

    Complex models of biochemical reaction systems have become increasingly common in the systems biology literature. The complexity of such models can present a number of obstacles for their practical use, often making problems difficult to intuit or computationally intractable. Methods of model reduction can be employed to alleviate the issue of complexity by seeking to eliminate those portions of a reaction network that have little or no effect upon the outcomes of interest, hence yielding simplified systems that retain an accurate predictive capacity. This review paper seeks to provide a brief overview of a range of such methods and their application in the context of biochemical reaction network models. To achieve this, we provide a brief mathematical account of the main methods including timescale exploitation approaches, reduction via sensitivity analysis, optimisation methods, lumping, and singular value decomposition-based approaches. Methods are reviewed in the context of large-scale systems biology type models, and future areas of research are briefly discussed.

  8. ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

    PubMed

    May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

    2009-05-04

    The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

  9. Integrating the Sciences to Investigate Groundwater Pollution

    ERIC Educational Resources Information Center

    Grady, Julie R.; Madden, Andrew S.

    2010-01-01

    Investigations that integrate concepts from geological sciences with biology and chemistry are rare. The authors present an investigation that introduces high school students to microbe-mineral interactions by tying together anaerobic respiration, reduction reactions, metal ion solubility, and groundwater pollution. During the investigation,…

  10. Broadening Participation in the Society for Integrative and Comparative Biology.

    PubMed

    Wilga, Cheryl A D; Nishiguchi, Michele; Tsukimura, Brian

    2017-07-01

    The goal of the Society for Integrative and Comparative Biology's Broadening Participation Committee (SICB BPC) is to increase the number of underrepresented group (URG) members within the society and to expand their capabilities as future researchers and leaders within SICB. Our short-term 10-year goal was to increase the recruitment and retention of URG members in the society by 10%. Our long-term 25-year goal is to increase the membership of URG in the society through recruitment and retention until the membership demographic mirrors that of the US Census. Our plans to accomplish this included establishment of a formal standing committee, establishment of a moderate budget to support BPC activities, hosting professional development workshops, hosting diversity and mentor socials, and obtaining grant funds to supplement our budget. This paper documents broadening participation activities in the society, discusses the effectiveness of these activities, and evaluates BPC goals after 5 years of targeted funded activities. Over the past 5 years, the number of URG members rose by 5.2% to a total of 16.2%, members who report ethnicity and gender increased by 25.2% and 18%, respectively, and the number of members attending BPC activities has increased to 33% by 2016. SICB has made significant advances in broadening participation, not only through increased expenditures, but also with a commitment by its members and leadership to increase diversity. Most members realize that increasing diversity will both improve the Society's ability to develop different approaches to tackling problems within integrative biology, and help solve larger global issues that are evident throughout science and technology fields. In addition, having URG members as part of the executive committee would provide other URG members role models within the society, as well as have a voice in the leadership that represents diversity and inclusion for all scientists. © The Author 2017. Published by

  11. Reductions in finite-dimensional integrable systems and special points of classical r-matrices

    NASA Astrophysics Data System (ADS)

    Skrypnyk, T.

    2016-12-01

    For a given 𝔤 ⊗ 𝔤-valued non-skew-symmetric non-dynamical classical r-matrices r(u, v) with spectral parameters, we construct the general form of 𝔤-valued Lax matrices of finite-dimensional integrable systems satisfying linear r-matrix algebra. We show that the reduction in the corresponding finite-dimensional integrable systems is connected with "the special points" of the classical r-matrices in which they become degenerated. We also propose a systematic way of the construction of additional integrals of the Lax-integrable systems associated with the symmetries of the corresponding r-matrices. We consider examples of the Lax matrices and integrable systems that are obtained in the framework of the general scheme. Among them there are such physically important systems as generalized Gaudin systems in an external magnetic field, ultimate integrable generalization of Toda-type chains (including "modified" or "deformed" Toda chains), generalized integrable Jaynes-Cummings-Dicke models, integrable boson models generalizing Bose-Hubbard dimer models, etc.

  12. Biological and psychological rhythms: an integrative approach to rhythm disturbances in autistic disorder.

    PubMed

    Botbol, Michel; Cabon, Philippe; Kermarrec, Solenn; Tordjman, Sylvie

    2013-09-01

    Biological rhythms are crucial phenomena that are perfect examples of the adaptation of organisms to their environment. A considerable amount of work has described different types of biological rhythms (from circadian to ultradian), individual differences in their patterns and the complexity of their regulation. In particular, the regulation and maturation of the sleep-wake cycle have been thoroughly studied. Its desynchronization, both endogenous and exogenous, is now well understood, as are its consequences for cognitive impairments and health problems. From a completely different perspective, psychoanalysts have shown a growing interest in the rhythms of psychic life. This interest extends beyond the original focus of psychoanalysis on dreams and the sleep-wake cycle, incorporating central theoretical and practical psychoanalytic issues related to the core functioning of the psychic life: the rhythmic structures of drive dynamics, intersubjective developmental processes and psychic containment functions. Psychopathological and biological approaches to the study of infantile autism reveal the importance of specific biological and psychological rhythmic disturbances in this disorder. Considering data and hypotheses from both perspectives, this paper proposes an integrative approach to the study of these rhythmic disturbances and offers an etiopathogenic hypothesis based on this integrative approach. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

    PubMed Central

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

    2016-01-01

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

  14. Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

    PubMed Central

    2010-01-01

    Background Simulation of sophisticated biological models requires considerable computational power. These models typically integrate together numerous biological phenomena such as spatially-explicit heterogeneous cells, cell-cell interactions, cell-environment interactions and intracellular gene networks. The recent advent of programming for graphical processing units (GPU) opens up the possibility of developing more integrative, detailed and predictive biological models while at the same time decreasing the computational cost to simulate those models. Results We construct a 3D model of epidermal development and provide a set of GPU algorithms that executes significantly faster than sequential central processing unit (CPU) code. We provide a parallel implementation of the subcellular element method for individual cells residing in a lattice-free spatial environment. Each cell in our epidermal model includes an internal gene network, which integrates cellular interaction of Notch signaling together with environmental interaction of basement membrane adhesion, to specify cellular state and behaviors such as growth and division. We take a pedagogical approach to describing how modeling methods are efficiently implemented on the GPU including memory layout of data structures and functional decomposition. We discuss various programmatic issues and provide a set of design guidelines for GPU programming that are instructive to avoid common pitfalls as well as to extract performance from the GPU architecture. Conclusions We demonstrate that GPU algorithms represent a significant technological advance for the simulation of complex biological models. We further demonstrate with our epidermal model that the integration of multiple complex modeling methods for heterogeneous multicellular biological processes is both feasible and computationally tractable using this new technology. We hope that the provided algorithms and source code will be a starting point for modelers to

  15. Measurement of the Ecological Integrity of Cerrado Streams Using Biological Metrics and the Index of Habitat Integrity

    PubMed Central

    dos Reis, Deusiano Florêncio; Salazar, Ayala Eduardo; Machado, Mayana Mendes Dias; Couceiro, Sheyla Regina Marques; de Morais, Paula Benevides

    2017-01-01

    Generally, aquatic communities reflect the effects of anthropogenic changes such as deforestation or organic pollution. The Cerrado stands among the most threatened ecosystems by human activities in Brazil. In order to evaluate the ecological integrity of the streams in a preserved watershed in the Northern Cerrado biome corresponding to a mosaic of ecosystems in transition to the Amazonia biome in Brazil, biological metrics related to diversity, structure, and sensitivity of aquatic macroinvertebrates were calculated. Sampling included collections along stretches of 200 m of nine streams and measurements of abiotic variables (temperature, electrical conductivity, pH, total dissolved solids, dissolved oxygen, and discharge) and the Index of Habitat Integrity (HII). The values of the abiotic variables and the HII indicated that most of the streams have good ecological integrity, due to high oxygen levels and low concentrations of dissolved solids and electric conductivity. Two streams showed altered HII scores mainly related to small dams for recreational and domestic use, use of Cerrado natural pasture for cattle raising, and spot deforestation in bathing areas. However, this finding is not reflected in the biological metrics that were used. Considering all nine streams, only two showed satisfactory ecological quality (measured by Biological Monitoring Working Party (BMWP), total richness, and EPT (Ephemeroptera, Plecoptera, and Trichoptera) richness), only one of which had a low HII score. These results indicate that punctual measures of abiotic parameters do not reveal the long-term impacts of anthropic activities in these streams, including related fire management of pasture that annually alters the vegetation matrix and may act as a disturbance for the macroinvertebrate communities. Due to this, biomonitoring of low order streams in Cerrado ecosystems of the Northern Central Brazil by different biotic metrics and also physical attributes of the riparian zone

  16. Measurement of the Ecological Integrity of Cerrado Streams Using Biological Metrics and the Index of Habitat Integrity.

    PubMed

    Reis, Deusiano Florêncio Dos; Salazar, Ayala Eduardo; Machado, Mayana Mendes Dias; Couceiro, Sheyla Regina Marques; Morais, Paula Benevides de

    2017-01-12

    Generally, aquatic communities reflect the effects of anthropogenic changes such as deforestation or organic pollution. The Cerrado stands among the most threatened ecosystems by human activities in Brazil. In order to evaluate the ecological integrity of the streams in a preserved watershed in the Northern Cerrado biome corresponding to a mosaic of ecosystems in transition to the Amazonia biome in Brazil, biological metrics related to diversity, structure, and sensitivity of aquatic macroinvertebrates were calculated. Sampling included collections along stretches of 200 m of nine streams and measurements of abiotic variables (temperature, electrical conductivity, pH, total dissolved solids, dissolved oxygen, and discharge) and the Index of Habitat Integrity (HII). The values of the abiotic variables and the HII indicated that most of the streams have good ecological integrity, due to high oxygen levels and low concentrations of dissolved solids and electric conductivity. Two streams showed altered HII scores mainly related to small dams for recreational and domestic use, use of Cerrado natural pasture for cattle raising, and spot deforestation in bathing areas. However, this finding is not reflected in the biological metrics that were used. Considering all nine streams, only two showed satisfactory ecological quality (measured by Biological Monitoring Working Party (BMWP), total richness, and EPT (Ephemeroptera, Plecoptera, and Trichoptera) richness), only one of which had a low HII score. These results indicate that punctual measures of abiotic parameters do not reveal the long-term impacts of anthropic activities in these streams, including related fire management of pasture that annually alters the vegetation matrix and may act as a disturbance for the macroinvertebrate communities. Due to this, biomonitoring of low order streams in Cerrado ecosystems of the Northern Central Brazil by different biotic metrics and also physical attributes of the riparian zone

  17. Effects of various pretreatments on biological sulfate reduction with waste activated sludge as electron donor and waste activated sludge diminution under biosulfidogenic condition.

    PubMed

    Sheng, Yuxing; Cao, Hongbin; Li, Yuping; Zhang, Yi

    2010-07-15

    The current study focused on the influences of various pretreatments, including alkaline, ultrasonic and thermal pretreatments on biological sulfate reduction with waste activated sludge (WAS) as sole electron donor. Our results showed that thermal and ultrasonic pretreatments increased the sulfate reduction percentage by 14.8% and 7.1%, respectively, compared with experiment with raw WAS, while alkaline pretreatment decreased the sulfate reduction percentage by 46%. By analyzing the WAS structure, particle size distribution, organic component, and enzyme activity after different pretreatments, we studied the effects of these pretreatments on WAS as well as on the mechanisms of how biological sulfate reduction was affected. The reduction of WAS and variation of WAS structure in the process of sulfate reduction were investigated. Our results showed that biosulfidogenesis was an efficient method of diminishing WAS, and various pretreatments could enhance the reduction efficiency of volatile solid in the WAS. 2010 Elsevier B.V. All rights reserved.

  18. Quantifying biological integrity by taxonomic completeness: its utility in regional and global assessments.

    PubMed

    Hawkins, Charles P

    2006-08-01

    Water resources managers and conservation biologists need reliable, quantitative, and directly comparable methods for assessing the biological integrity of the world's aquatic ecosystems. Large-scale assessments are constrained by the lack of consistency in the indicators used to assess biological integrity and our current inability to translate between indicators. In theory, assessments based on estimates of taxonomic completeness, i.e., the proportion of expected taxa that were observed (observed/expected, O/E) are directly comparable to one another and should therefore allow regionally and globally consistent summaries of the biological integrity of freshwater ecosystems. However, we know little about the true comparability of O/E assessments derived from different data sets or how well O/E assessments perform relative to other indicators in use. I compared the performance (precision, bias, and sensitivity to stressors) of O/E assessments based on five different data sets with the performance of the indicators previously applied to these data (three multimetric indices, a biotic index, and a hybrid method used by the state of Maine). Analyses were based on data collected from U.S. stream ecosystems in North Carolina, the Mid-Atlantic Highlands, Maine, and Ohio. O/E assessments resulted in very similar estimates of mean regional conditions compared with most other indicators once these indicators' values were standardized relative to reference-site means. However, other indicators tended to be biased estimators of O/E, a consequence of differences in their response to natural environmental gradients and sensitivity to stressors. These results imply that, in some cases, it may be possible to compare assessments derived from different indicators by standardizing their values (a statistical approach to data harmonization). In situations where it is difficult to standardize or otherwise harmonize two or more indicators, O/E values can easily be derived from existing

  19. Simple method for determination of selenium in biological materials by flameless atomic-absorption spectrometry using a carbon-tube atomizer.

    PubMed

    Ishizaki, M

    1978-03-01

    A method for determination of selenium in biological materials by flameless atomic-absorption spectrometry using a carbon-tube atomizer is described. The sample is burned by an oxygen-flask combustion procedure, the resulting solution is treated with a cation-exchange resin to eliminate interfering cations, the selenium is extracted with dithizone in carbon tetrachloride and the resulting selenium dithizonate is combined with nickel nitrate in the carbon tube to enhance the sensitivity for selenium and avoid volatilization losses. The method measures selenium concentrations as low as 0.01 mug/g with a relative standard deviation of 8%.

  20. BIRD SPECIES ASSEMBLAGES AS INDICATORS OF BIOLOGICAL INTEGRITY IN GREAT BASIN RANGELAND

    EPA Science Inventory

    The study evaluates the potential for bird species assemblages to serve as indicators of biological integrity of rangelands in the Great Basin in much the same way that fish and invertebrate assemblages have been used as indicators in aquatic environments. Our approach was to ide...

  1. Dietary Phospholipids and Intestinal Cholesterol Absorption

    PubMed Central

    Cohn, Jeffrey S.; Kamili, Alvin; Wat, Elaine; Chung, Rosanna W. S.; Tandy, Sally

    2010-01-01

    Experiments carried out with cultured cells and in experimental animals have consistently shown that phospholipids (PLs) can inhibit intestinal cholesterol absorption. Limited evidence from clinical studies suggests that dietary PL supplementation has a similar effect in man. A number of biological mechanisms have been proposed in order to explain how PL in the gut lumen is able to affect cholesterol uptake by the gut mucosa. Further research is however required to establish whether the ability of PLs to inhibit cholesterol absorption is of therapeutic benefit. PMID:22254012

  2. Engaging Non-Science Majors by Integrating Biology and the Liberal Arts

    ERIC Educational Resources Information Center

    Bozzone, Donna M.; Doyle, Mary Beth

    2017-01-01

    We describe a pair of fully integrated courses designed to teach biology to non-majors in a manner that connects authentically to the liberal arts. The co-taught courses were organized around the question: What does it mean to be human? Students investigated this question in the context of three topics: dis/ability, race, and sex and gender. In…

  3. High-purity nano particles ZnS production by a simple coupling reaction process of biological reduction and chemical precipitation mediated with EDTA.

    PubMed

    Xin, Baoping; Huang, Qun; Chen, Shi; Tang, Xuemei

    2008-01-01

    High-purity nanoparticles ZnS has been successfully synthesized using a simple coupling reaction process of biological reduction and chemical precipitation mediated with EDTA referred to as the CRBRCP-EDTA process. This research investigated the optimum conditions of the transformation of SO(4) (2-) into S(2-) by SRB, and the production of ZnS in the CRBRCP-EDTA process. The results showed that the molar ratio of Zn(2+) to EDTA = 1:1 was crucial for SRB growth and ZnS synthesis. At the ratio(n) (Zn2+)/n) (EDTA) = 1:1, lower Zn(2+) concentration enhanced both the growth of SRB and the reduction of SO(4) (2-), leading to higher ZnS production. Although increase in Na(2)SO(4) concentration resulted in decrease in both SRB growth and SO(4) (2-) reduction, it improved the S(2-) and ZnS production. Under the optimum conditions (0.05 mol L(-1) ZnCl(2), 0.05 mol L(-1) EDTA, and 0.1 mol L(-1) Na(2)SO(4)), the synthesized ZnS was characterized by X-ray diffraction (XRD), X-ray energy dispersive spectroscopy (EDS), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The analysis showed that the obtained ZnS were high-purity and well-distributed solid spheres with diameters of about 15 nm for primary particles and around 400 nm for secondary particles. When polyacrylamide (PAM) was incorporated in the CRBRCP-EDTA process, the secondary particle's diameters were reduced to less than 100 nm. The photoluminescence (PL) spectra of produced ZnS centered at 396 nm, the spectrum with PAM added showed the gradual increase in absorption and stronger intensity in PL property. The present simple, low-cost, and safe method may be extended to prepare other metal-sulfide nanocomposites.

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

    PubMed

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

    2016-01-01

    Redesigning undergraduate biology courses to integrate quantitative reasoning and skill development is critical to prepare students for careers in modern medicine and scientific research. In this paper, we report on the development, implementation, and assessment of stand-alone modules that integrate quantitative reasoning into introductory biology courses. Modules are designed to improve skills in quantitative numeracy, interpreting data sets using visual tools, and making inferences about biological phenomena using mathematical/statistical models. We also examine demographic/background data that predict student improvement in these skills through exposure to these modules. We carried out pre/postassessment tests across four semesters and used student interviews in one semester to examine how students at different levels approached quantitative problems. We found that students improved in all skills in most semesters, although there was variation in the degree of improvement among skills from semester to semester. One demographic variable, transfer status, stood out as a major predictor of the degree to which students improved (transfer students achieved much lower gains every semester, despite the fact that pretest scores in each focus area were similar between transfer and nontransfer students). We propose that increased exposure to quantitative skill development in biology courses is effective at building competency in quantitative reasoning. © 2016 K. Hoffman, S. Leupen, et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  5. Enhancing maximum measurable sound reduction index using sound intensity method and strong receiving room absorption.

    PubMed

    Hongisto, V; Lindgren, M; Keränen, J

    2001-01-01

    The sound intensity method is usually recommended instead of the pressure method in the presence of strong flanking transmission. Especially when small and/or heavy specimens are tested, the flanking often causes problems in laboratories practicing only the pressure method. The purpose of this study was to determine experimentally the difference between the maximum sound reduction indices obtained by the intensity method, RI,max, and by the pressure method, Rmax. In addition, the influence of adding room absorption to the receiving room was studied. The experiments were carried out in an ordinary two-room test laboratory. The exact value of RI,max was estimated by applying a fitting equation to the measured data points. The fitting equation involved the dependence of the pressure-intensity indicator on measured acoustical parameters. In an empty receiving room, the difference between RI,max and Rmax was 4-15 dB, depending on frequency. When the average reverberation time was reduced from 3.5 to 0.6 s, the values of RI,max increased by 2-10 dB compared to the results in the empty room. Thus, it is possible to measure wall structures having 9-22 dB better sound reduction index using the intensity method than with the pressure method. This facilitates the measurements of small and/or heavy specimens in the presence of flanking. Moreover, when new laboratories are designed, the intensity method is an alternative to the pressure method which presupposes expensive isolation structures between the rooms.

  6. X-Ray Absorption Near Edge Structure And Extended X-Ray Absorption Fine Structure Analysis of Standards And Biological Samples Containing Mixed Oxidation States of Chromium(III) And Chromium(VI)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Parsons, J.G.; Dokken, K.; Peralta-Videa, J.R.

    For the first time a method has been developed for the extended X-ray absorption fine structure (EXAFS) data analyses of biological samples containing multiple oxidation states of chromium. In this study, the first shell coordination and interatomic distances based on the data analysis of known standards of potassium chromate (Cr(VI)) and chromium nitrate hexahydrate (Cr(III)) were investigated. The standards examined were mixtures of the following molar ratios of Cr(VI):Cr(III), 0:1, 0.25:0.75, 0.5:0.5, 0.75:0.25, and 1:0. It was determined from the calibration data that the fitting error associated with linear combination X-ray absorption near edge structure (LC-XANES) fittings was approximately {+-}10%more » of the total fitting. The peak height of the Cr(VI) pre-edge feature after normalization of the X-ray absorption (XAS) spectra was used to prepare a calibration curve. The EXAFS fittings of the standards were also investigated and fittings to lechuguilla biomass samples laden with different ratios of Cr(III) and Cr(VI) were performed as well. An excellent agreement between the XANES data and the data presented in the EXAFS spectra was observed. The EXFAS data also presented mean coordination numbers directly related to the ratios of the different chromium oxidation states in the sample. The chromium oxygen interactions had two different bond lengths at approximately 1.68 and 1.98 {angstrom} for the Cr(VI) and Cr(III) in the sample, respectively.« less

  7. Informing Biological Design by Integration of Systems and Synthetic Biology

    PubMed Central

    Smolke, Christina D.; Silver, Pamela A.

    2011-01-01

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. PMID:21414477

  8. PathText: a text mining integrator for biological pathway visualizations

    PubMed Central

    Kemper, Brian; Matsuzaki, Takuya; Matsuoka, Yukiko; Tsuruoka, Yoshimasa; Kitano, Hiroaki; Ananiadou, Sophia; Tsujii, Jun'ichi

    2010-01-01

    Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations. Contact: brian@monrovian.com. PMID:20529930

  9. Absorption into fluorescence. A method to sense biologically relevant gas molecules

    NASA Astrophysics Data System (ADS)

    Strianese, Maria; Varriale, Antonio; Staiano, Maria; Pellecchia, Claudio; D'Auria, Sabato

    2011-01-01

    In this work we present an innovative optical sensing methodology based on the use of biomolecules as molecular gating nano-systems. Here, as an example, we report on the detection ofanalytes related to climate change. In particular, we focused our attention on the detection ofnitric oxide (NO) and oxygen (O2). Our methodology builds on the possibility of modulating the excitation intensity of a fluorescent probe used as a transducer and a sensor molecule whose absorption is strongly affected by the binding of an analyte of interest used as a filter. The two simple conditions that have to be fulfilled for the method to work are: (a) the absorption spectrum of the sensor placed inside the cuvette, and acting as the recognition element for the analyte of interest, should strongly change upon the binding of the analyte and (b) the fluorescence dye transducer should exhibit an excitation band which overlaps with one or more absorption bands of the sensor. The absorption band of the sensor affected by the binding of the specific analyte should overlap with the excitation band of the transducer. The high sensitivity of fluorescence detection combined with the use of proteins as highly selective sensors makes this method a powerful basis for the development of a new generation of analytical assays. Proof-of-principle results showing that cytochrome c peroxidase (CcP) for NO detection and myoglobin (Mb) for O2 detection can be successfully used by exploiting our new methodology are reported. The proposed technology can be easily expanded to the determination of different target analytes.

  10. Development of a Coherent Differential Absorption Lidar for Range Resolved Atmospheric CO2 Measurements

    NASA Technical Reports Server (NTRS)

    Yu, Jirong; Petros, Mulgueta; Chen, Songsheng; Bai, Yingxin; Petzar, Paul J.; Trieu, Bo. C.; Koch, Grady J.; Beyon, Jeffery J.; Singh, Upendra N.

    2010-01-01

    A pulsed, 2-m coherent Differential Absorption Lidar (DIAL) / Integrated Path Differential Absorption (IPDA) transceiver, developed under the Laser Risk Reduction Program (LRRP) at NASA, is integrated into a fully functional lidar instrument. This instrument will measure atmospheric CO2 profiles (by DIAL) initially from a ground platform, and then be prepared for aircraft installation to measure the atmospheric CO2 column densities in the atmospheric boundary layer (ABL) and lower troposphere. The airborne prototype CO2 lidar can measure atmospheric CO2 column density in a range bin of 1km with better than 1.5% precision at horizontal resolution of less than 50km. It can provide the image of the pooling of CO2 in lowlying areas and performs nighttime mass balance measurements at landscape scale. This sensor is unique in its capability to study the vertical ABL-free troposphere exchange of CO2 directly. It will allow the investigators to pursue subsequent in science-driven deployments, and provides a unique tool for Active Sensing of CO2 Emissions over Night, Days, and Seasons (ASCENDS) validation that was strongly advocated in the recent ASCENDS Workshop.

  11. Towards Improving the Integration of Undergraduate Biology and Mathematics Education

    PubMed Central

    Bergevin, Christopher

    2010-01-01

    Arguments have recently asserted the need for change in undergraduate biology education, particularly with regard to the role of mathematics. The crux of these protests is that rapidly developing technology is expanding the types of measurements and subsequent data available to biologists. Thus future generations of biologists will require a set of quantitative and analytic skills that will allow them to handle these types of data in order to tackle relevant questions of interest. In this spirit, we describe here strategies (or lessons learned) for undergraduate educators with regard to better preparing undergraduate biology majors for the new types of challenges that lay ahead. The topics covered here span a broad range, from classroom approaches to the administrative level (e.g., fostering inter-departmental communication, student advising) and beyond. A key theme here is the need for an attitude shift with regard to mathematics education by both students and faculty alike. Such a shift will facilitate the development and implementation of new teaching strategies with regard to improving integration of mathematics and biology pedagogy. PMID:23653694

  12. Drag Reduction and Performance Improvement of Hydraulic Torque Converters with Multiple Biological Characteristics.

    PubMed

    Chunbao, Liu; Li, Li; Yulong, Lei; Changsuo, Liu; Yubo, Zhang

    2016-01-01

    Fish-like, dolphin-like, and bionic nonsmooth surfaces were employed in a hydraulic torque converter to achieve drag reduction and performance improvement, which were aimed at reducing profile loss, impacting loss and friction loss, respectively. YJSW335, a twin turbine torque converter, was bionically designed delicately. The biological characteristics consisted of fish-like blades in all four wheels, dolphin-like structure in the first turbine and the stator, and nonsmooth surfaces in the pump. The prediction performance of bionic YJSW335, obtained by computational fluid dynamics simulation, was improved compared with that of the original model, and then it could be proved that drag reduction had been achieved. The mechanism accounting for drag reduction of three factors was also investigated. After bionic design, the torque ratio and the highest efficiencies of YJSW335 were both advanced, which were very difficult to achieve through traditional design method. Moreover, the highest efficiency of the low speed area and high speed area is 85.65% and 86.32%, respectively. By economic matching analysis of the original and bionic powertrains, the latter can significantly reduce the fuel consumption and improve the operating economy of the loader.

  13. Drag Reduction and Performance Improvement of Hydraulic Torque Converters with Multiple Biological Characteristics

    PubMed Central

    Chunbao, Liu; Changsuo, Liu; Yubo, Zhang

    2016-01-01

    Fish-like, dolphin-like, and bionic nonsmooth surfaces were employed in a hydraulic torque converter to achieve drag reduction and performance improvement, which were aimed at reducing profile loss, impacting loss and friction loss, respectively. YJSW335, a twin turbine torque converter, was bionically designed delicately. The biological characteristics consisted of fish-like blades in all four wheels, dolphin-like structure in the first turbine and the stator, and nonsmooth surfaces in the pump. The prediction performance of bionic YJSW335, obtained by computational fluid dynamics simulation, was improved compared with that of the original model, and then it could be proved that drag reduction had been achieved. The mechanism accounting for drag reduction of three factors was also investigated. After bionic design, the torque ratio and the highest efficiencies of YJSW335 were both advanced, which were very difficult to achieve through traditional design method. Moreover, the highest efficiency of the low speed area and high speed area is 85.65% and 86.32%, respectively. By economic matching analysis of the original and bionic powertrains, the latter can significantly reduce the fuel consumption and improve the operating economy of the loader. PMID:27752220

  14. Meat science: From proteomics to integrated omics towards system biology.

    PubMed

    D'Alessandro, Angelo; Zolla, Lello

    2013-01-14

    Since the main ultimate goal of farm animal raising is the production of proteins for human consumption, research tools to investigate proteins play a major role in farm animal and meat science. Indeed, proteomics has been applied to the field of farm animal science to monitor in vivo performances of livestock animals (growth performances, fertility, milk quality etc.), but also to further our understanding of the molecular processes at the basis of meat quality, which are largely dependent on the post mortem biochemistry of the muscle, often in a species-specific way. Post mortem alterations to the muscle proteome reflect the biological complexity of the process of "muscle to meat conversion," a process that, despite decades of advancements, is all but fully understood. This is mainly due to the enormous amounts of variables affecting meat tenderness per se, including biological factors, such as animal species, breed specific-characteristic, muscle under investigation. However, it is rapidly emerging that the tender meat phenotype is not only tied to genetics (livestock breeding selection), but also to extrinsic factors, such as the rearing environment, feeding conditions, physical activity, administration of hormonal growth promotants, pre-slaughter handling and stress, post mortem handling. From this intricate scenario, biochemical approaches and systems-wide integrated investigations (metabolomics, transcriptomics, interactomics, phosphoproteomics, mathematical modeling), which have emerged as complementary tools to proteomics, have helped establishing a few milestones in our understanding of the events leading from muscle to meat conversion. The growing integration of omics disciplines in the field of systems biology will soon contribute to take further steps forward. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Development of a Pulsed 2-Micron Integrated Path Differential Absorption Lidar for CO2 Measurement

    NASA Technical Reports Server (NTRS)

    Singh, Upendra N.; Yu, Jirong; Petros, Mulugeta; Refaat, Tamer; Refaat, Tamer

    2013-01-01

    Atmospheric carbon dioxide (CO2) is an important greenhouse gas that significantly contributes to the carbon cycle and global radiation budget on Earth. Active remote sensing of CO2 is important to address several limitations that contend with passive sensors. A 2-micron double-pulsed, Integrated Path Differential Absorption (IPDA) lidar instrument for ground and airborne atmospheric CO2 concentration measurements via direct detection method is being developed at NASA Langley Research Center. This active remote sensing instrument will provide an alternate approach of measuring atmospheric CO2 concentrations with significant advantages. A high energy pulsed approach provides high-precision measurement capability by having high signal-to-noise ratio level and unambiguously eliminates the contamination from aerosols and clouds that can bias the IPDA measurement. Commercial, on the shelf, components are implemented for the detection system. Instrument integration will be presented in this paper as well as a background for CO2 measurement at NASA Langley research Center

  16. CPICOR{trademark}: Clean power from integrated coal-ore reduction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wintrell, R.; Miller, R.N.; Harbison, E.J.

    1997-12-31

    The US steel industry, in order to maintain its basic iron production, is thus moving to lower coke requirements and to the cokeless or direct production of iron. The US Department of Energy (DOE), in its Clean Coal Technology programs, has encouraged the move to new coal-based technology. The steel industry, in its search for alternative direct iron processes, has been limited to a single process, COREX{reg_sign}. The COREX{reg_sign} process, though offering commercial and environmental acceptance, produces a copious volume of offgas which must be effectively utilized to ensure an economical process. This volume, which normally exceeds the internal needsmore » of a single steel company, offers a highly acceptable fuel for power generation. The utility companies seeking to offset future natural gas cost increases are interested in this clean fuel. The COREX{reg_sign} smelting process, when integrated with a combined cycle power generation facility (CCPG) and a cryogenic air separation unit (ASU), is an outstanding example of a new generation of environmentally compatible and highly energy efficient Clean Coal Technologies. This combination of highly integrated electric power and hot metal coproduction, has been designated CPICOR{trademark}, Clean Power from Integrated Coal/Ore Reduction.« less

  17. Informing biological design by integration of systems and synthetic biology.

    PubMed

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Triple-Pulse Integrated Path Differential Absorption Lidar for Carbon Dioxide Measurement - Novel Lidar Technologies and Techniques with Path to Space

    NASA Technical Reports Server (NTRS)

    Singh, Upendra N.; Refaat, Tamer F.; Petros, Mulugeta

    2017-01-01

    The societal benefits of understanding climate change through identification of global carbon dioxide sources and sinks led to the desired NASA's active sensing of carbon dioxide emissions over nights, days, and seasons (ASCENDS) space-based missions of global carbon dioxide measurements. For more than 15 years, NASA Langley Research Center (LaRC) have developed several carbon dioxide active remote sensors using the differential absorption lidar (DIAL) technique operating at the two-micron wavelength. Currently, an airborne two-micron triple-pulse integrated path differential absorption (IPDA) lidar is under development. This IPDA lidar measures carbon dioxide as well as water vapor, the dominant interfering molecule on carbon dioxide remote sensing. Advancement of this triple-pulse IPDA lidar development is presented.

  19. Aerosol Angstrom Absorption Coefficient Comparisons during MILAGRO.

    NASA Astrophysics Data System (ADS)

    Marley, N. A.; Marchany-Rivera, A.; Kelley, K. L.; Mangu, A.; Gaffney, J. S.

    2007-12-01

    Measurements of aerosol absorption were obtained as part of the MAX-Mex component of the MILAGRO field campaign at site T0 (Instituto Mexicano de Petroleo in Mexico City) by using a 7-channel aethalometer (Thermo- Anderson) during the month of March, 2006. The absorption measurements obtained in the field at 370, 470, 520, 590, 660, 880, and 950 nm were used to determine the aerosol Angstrom absorption exponents by linear regression. Since, unlike other absorbing aerosol species (e.g. humic like substances, nitrated PAHs), black carbon absorption is relatively constant from the ultraviolet to the infrared with an Angstrom absorption exponent of -1 (1), a comparison of the Angstrom exponents can indicate the presence of aerosol components with an enhanced UV absorption over that expected from BC content alone. The Angstrom exponents determined from the aerosol absorption measurements obtained in the field varied from - 0.7 to - 1.3 during the study and was generally lower in the afternoon than the morning hours, indicating an increase in secondary aerosol formation and photochemically generated UV absorbing species in the afternoon. Twelve-hour integrated samples of fine atmospheric aerosols (<0.1micron) were also collected at site T0 and T1 (Universidad Technologica de Tecamac, State of Mexico) from 5 am to 5 pm (day) and from 5 pm to 5 am (night) during the month of March 2006. Samples were collected on quartz fiber filters with high volume impactor samplers. Continuous absorption spectra of these aerosol samples have been obtained in the laboratory from 280 to 900nm with the use of an integrating sphere coupled to a UV spectrometer (Beckman DU with a Labsphere accessory). The integrating sphere allows the detector to collect and spatially integrate the total radiant flux reflected from the sample and therefore allows for the measurement of absorption on highly reflective or diffusely scattering samples. These continuous spectra have also been used to obtain the

  20. Copper increases reductive dehalogenation of haloacetamides by zero-valent iron in drinking water: Reduction efficiency and integrated toxicity risk.

    PubMed

    Chu, Wenhai; Li, Xin; Bond, Tom; Gao, Naiyun; Bin, Xu; Wang, Qiongfang; Ding, Shunke

    2016-12-15

    The haloacetamides (HAcAms), an emerging class of nitrogen-containing disinfection byproducts (N-DBPs), are highly cytotoxic and genotoxic, and typically occur in treated drinking waters at low μg/L concentrations. Since many drinking distribution and storage systems contain unlined cast iron and copper pipes, reactions of HAcAms with zero-valent iron (ZVI) and metallic copper (Cu) may play a role in determining their fate. Moreover, ZVI and/or Cu are potentially effective HAcAm treatment technologies in drinking water supply and storage systems. This study reports that ZVI alone reduces trichloroacetamide (TCAcAm) to sequentially form dichloroacetamide (DCAcAm) and then monochloroacetamide (MCAcAm), whereas Cu alone does not impact HAcAm concentrations. The addition of Cu to ZVI significantly improved the removal of HAcAms, relative to ZVI alone. TCAcAm and their reduction products (DCAcAm and MCAcAm) were all decreased to below detection limits at a molar ratio of ZVI/Cu of 1:1 after 24 h reaction (ZVI/TCAcAm = 0.18 M/5.30 μM). TCAcAm reduction increased with the decreasing pH from 8.0 to 5.0, but values from an integrated toxic risk assessment were minimised at pH 7.0, due to limited removal MCAcAm under weak acid conditions (pH = 5.0 and 6.0). Higher temperatures (40 °C) promoted the reductive dehalogenation of HAcAms. Bromine was preferentially removed over chlorine, thus brominated HAcAms were more easily reduced than chlorinated HAcAms by ZVI/Cu. Although tribromoacetamide was more easily reduced than TCAcAm during ZVI/Cu reduction, treatment of tribromoacetamide resulted in a higher integrated toxicity risk than TCAcAm, due to the formation of monobromoacetamide (MBAcAm). Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Reduction of graphene oxide by resveratrol: a novel and simple biological method for the synthesis of an effective anticancer nanotherapeutic molecule

    PubMed Central

    Gurunathan, Sangiliyandi; Han, Jae Woong; Kim, Eun Su; Park, Jung Hyun; Kim, Jin-Hoi

    2015-01-01

    Objective Graphene represents a monolayer or a few layers of sp2-bonded carbon atoms with a honeycomb lattice structure. Unique physical, chemical, and biological properties of graphene have attracted great interest in various fields including electronics, energy, material industry, and medicine, where it is used for tissue engineering and scaffolding, drug delivery, and as an antibacterial and anticancer agent. However, graphene cytotoxicity for ovarian cancer cells is still not fully investigated. The objective of this study was to synthesize graphene using a natural polyphenol compound resveratrol and to investigate its toxicity for ovarian cancer cells. Methods The successful reduction of graphene oxide (GO) to graphene was confirmed by UV-vis and Fourier transform infrared spectroscopy. Dynamic light scattering and scanning electron microscopy were employed to evaluate particle size and surface morphology of GO and resveratrol-reduced GO (RES-rGO). Raman spectroscopy was used to determine the removal of oxygen-containing functional groups from GO surface and to ensure the formation of graphene. We also performed a comprehensive analysis of GO and RES-rGO cytotoxicity by examining the morphology, viability, membrane integrity, activation of caspase-3, apoptosis, and alkaline phosphatase activity of ovarian cancer cells. Results The results also show that resveratrol effectively reduced GO to graphene and the properties of RES-rGO nanosheets were comparable to those of chemically reduced graphene. Biological experiments showed that GO and RES-rGO caused a dose-dependent membrane leakage and oxidative stress in cancer cells, and reduced their viability via apoptosis confirmed by the upregulation of apoptosis executioner caspase-3. Conclusion Our data demonstrate a single, simple green approach for the synthesis of highly water-dispersible functionalized graphene nanosheets, suggesting a possibility of replacing toxic hydrazine by a natural and safe phenolic

  2. Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy

    PubMed Central

    Beltrà, Aleixandre; Addison, Pia; Ávalos, Juan Antonio; Crochard, Didier; Garcia-Marí, Ferran; Guerrieri, Emilio; Giliomee, Jan H.; Malausa, Thibaut; Navarro-Campos, Cristina; Palero, Ferran; Soto, Antonia

    2015-01-01

    Delottococcus aberiae De Lotto (Hemiptera: Pseudococcidae) is a mealybug of Southern African origin that has recently been introduced into Eastern Spain. It causes severe distortions on young citrus fruits and represents a growing threat to Mediterranean citrus production. So far, biological control has proven unsatisfactory due to the absence of efficient natural enemies in Spain. Hence, the management of this pest currently relies only on chemical control. The introduction of natural enemies of D. aberiae from the native area of the pest represents a sustainable and economically viable alternative to reduce the risks linked to pesticide applications. Since biological control of mealybugs has been traditionally challenged by taxonomic misidentification, an intensive survey of Delottococcus spp. and their associated parasitoids in South Africa was required as a first step towards a classical biological control programme. Combining morphological and molecular characterization (integrative taxonomy) a total of nine mealybug species were identified in this study, including three species of Delottococcus. Different populations of D. aberiae were found on wild olive trees, in citrus orchards and on plants of Chrysanthemoides monilifera, showing intra-specific divergences according to their host plants. Interestingly, the invasive mealybug populations from Spanish orchards clustered together with the population on citrus from Limpopo Province (South Africa), sharing COI haplotypes. This result pointed to an optimum location to collect natural enemies against the invasive mealybug. A total of 14 parasitoid species were recovered from Delottococcus spp. and identified to genus and species level, by integrating morphological and molecular data. A parasitoid belonging to the genus Anagyrus, collected from D. aberiae in citrus orchards in Limpopo, is proposed here as a good biological control agent to be introduced into Spain. PMID:26047349

  3. Personalized genetic testing as a tool for integrating ethics instruction into biology courses.

    PubMed

    Zhang, Tenny R; Anderson, Misti Ault

    2014-12-01

    Personalized genetic testing (PGT) has been used by some educational institutions as a pedagogical tool for teaching human genetics. While work has been done that examines the potential for PGT to improve students' interest and understanding of the science involved in genetic testing, there has been less dialogue about how this method might be useful for integrating ethical and societal issues surrounding genetic testing into classroom discussions. Citing the importance of integrating ethics into the biology classroom, we argue that PGT can be an effective educational tool for integrating ethics and science education, and discuss relevant ethical considerations for instructors using this approach.

  4. Dermal absorption and short-term biological impact in hairless mice from sunscreens containing zinc oxide nano- or larger particles

    PubMed Central

    Oytam, Yalchin; Kirby, Jason K.; Gomez-Fernandez, Laura; Baxter, Brent; McCall, Maxine J.

    2014-01-01

    Previous studies have shown no, or very limited, skin penetration of metal oxide nanoparticles following topical application of sunscreens, yet concerns remain about their safety compared to larger particles. Here, we assessed the comparative dermal absorption of a traceable form of Zn (68Zn) from 68ZnO nano-sized and larger particles in sunscreens. Sunscreens were applied to the backs of virgin or pregnant hairless mice over four days. Control groups received topical applications of the sunscreen formulation containing no ZnO particles, or no treatment. Major organs were assessed for changes in 68Zn/64Zn ratios, 68Zn tracer and total Zn concentrations. Short-term biological impact was assessed by measuring levels of serum amyloid A in blood, and by performing whole-genome transcriptional profiling on livers from each group. Increased concentrations of 68Zn tracer were detected in internal organs of mice receiving topical applications of 68ZnO (nano-sized and larger particles), as well as in fetal livers from treated dams, compared with controls. Furthermore, concentrations of 68Zn in organs of virgin mice treated with sunscreen containing 68ZnO nanoparticles were found to be significantly higher than in mice treated with sunscreen containing larger 68ZnO particles. However, no ZnO-mediated change in total Zn concentration in any of the major organs was observed. Thus, despite 68Zn absorption, which may have been in the form of soluble 68Zn species or 68ZnO particles (not known), Zn homeostasis was largely maintained, and the presence of ZnO particles in sunscreen did not elicit an adverse biological response in the mice following short-term topical applications. PMID:24266363

  5. Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics.

    PubMed

    Nottale, Laurent; Auffray, Charles

    2008-05-01

    In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, which aims at describing the effects of a non-differentiable and fractal (i.e., explicitly scale dependent) geometry of space-time. The first paper of this series was devoted, in this new framework, to the construction from first principles of scale laws of increasing complexity, and to the discussion of some tentative applications of these laws to biological systems. In this second review and perspective paper, we describe the effects induced by the internal fractal structures of trajectories on motion in standard space. Their main consequence is the transformation of classical dynamics into a generalized, quantum-like self-organized dynamics. A Schrödinger-type equation is derived as an integral of the geodesic equation in a fractal space. We then indicate how gauge fields can be constructed from a geometric re-interpretation of gauge transformations as scale transformations in fractal space-time. Finally, we introduce a new tentative development of the theory, in which quantum laws would hold also in scale space, introducing complexergy as a measure of organizational complexity. Initial possible applications of this extended framework to the processes of morphogenesis and the emergence of prokaryotic and eukaryotic cellular structures are discussed. Having founded elements of the evolutionary, developmental, biochemical and cellular theories on the first principles of scale relativity theory, we introduce proposals for the construction of an integrative theory of life and for the design and implementation of novel macroscopic quantum-type experiments and devices, and discuss their potential

  6. Effect of biological and chemical oxidation on the removal of estrogenic compounds (NP and BPA) from wastewater: an integrated assessment procedure.

    PubMed

    Bertanza, Giorgio; Pedrazzani, Roberta; Dal Grande, Mario; Papa, Matteo; Zambarda, Valerio; Montani, Claudia; Steimberg, Nathalie; Mazzoleni, Giovanna; Di Lorenzo, Diego

    2011-04-01

    A major source of the wide presence of EDCs (Endocrine Disrupting Compounds) in water bodies is represented by direct/indirect discharge of sewage. Recent scientific literature reports data about their trace concentration in water, sediments and aquatic organisms, as well as removal efficiencies of different wastewater treatment schemes. Despite the availability of a huge amount of data, some doubts still persist due to the difficulty in evaluating synergistic effects of trace pollutants in complex matrices. In this paper, an integrated assessment procedure was used, based on chemical and biological analyses, in order to compare the performance of two full scale biological wastewater treatment plants (either equipped with conventional settling tanks or with an ultrafiltration membrane unit) and tertiary ozonation (pilot scale). Nonylphenol and bisphenol A were chosen as model EDCs, together with the parent compounds mono- and di-ethoxylated nonylphenol (quantified by means of GC-MS). Water estrogenic activity was evaluated by applying the human breast cancer MCF-7 based reporter gene assay. Process parameters (e.g., sludge age, temperature) and conventional pollutants (e.g., COD, suspended solids) were also measured during monitoring campaigns. Conventional activated sludge achieved satisfactory removal of both analytes and estrogenicity. A further reduction of biological activity was exerted by MBR (Membrane Biological Reactor) as well as ozonation; the latter contributed also to decrease EDC concentrations. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Hybrid integrated biological-solid-state system powered with adenosine triphosphate.

    PubMed

    Roseman, Jared M; Lin, Jianxun; Ramakrishnan, Siddharth; Rosenstein, Jacob K; Shepard, Kenneth L

    2015-12-07

    There is enormous potential in combining the capabilities of the biological and the solid state to create hybrid engineered systems. While there have been recent efforts to harness power from naturally occurring potentials in living systems in plants and animals to power complementary metal-oxide-semiconductor integrated circuits, here we report the first successful effort to isolate the energetics of an electrogenic ion pump in an engineered in vitro environment to power such an artificial system. An integrated circuit is powered by adenosine triphosphate through the action of Na(+)/K(+) adenosine triphosphatases in an integrated in vitro lipid bilayer membrane. The ion pumps (active in the membrane at numbers exceeding 2 × 10(6) mm(-2)) are able to sustain a short-circuit current of 32.6 pA mm(-2) and an open-circuit voltage of 78 mV, providing for a maximum power transfer of 1.27 pW mm(-2) from a single bilayer. Two series-stacked bilayers provide a voltage sufficient to operate an integrated circuit with a conversion efficiency of chemical to electrical energy of 14.9%.

  8. FIMic: design for ultimate 3D-integral microscopy of in-vivo biological samples

    PubMed Central

    Scrofani, G.; Sola-Pikabea, J.; Llavador, A.; Sanchez-Ortiga, E.; Barreiro, J. C.; Saavedra, G.; Garcia-Sucerquia, J.; Martínez-Corral, M.

    2017-01-01

    In this work, Fourier integral microscope (FIMic), an ultimate design of 3D-integral microscopy, is presented. By placing a multiplexing microlens array at the aperture stop of the microscope objective of the host microscope, FIMic shows extended depth of field and enhanced lateral resolution in comparison with regular integral microscopy. As FIMic directly produces a set of orthographic views of the 3D-micrometer-sized sample, it is suitable for real-time imaging. Following regular integral-imaging reconstruction algorithms, a 2.75-fold enhanced depth of field and 2-time better spatial resolution in comparison with conventional integral microscopy is reported. Our claims are supported by theoretical analysis and experimental images of a resolution test target, cotton fibers, and in-vivo 3D-imaging of biological specimens. PMID:29359107

  9. The role of bacillus-based biological control agents in integrated pest management systems: plant diseases.

    PubMed

    Jacobsen, B J; Zidack, N K; Larson, B J

    2004-11-01

    ABSTRACT Bacillus-based biological control agents (BCAs) have great potential in integrated pest management (IPM) systems; however, relatively little work has been published on integration with other IPM management tools. Unfortunately, most research has focused on BCAs as alternatives to synthetic chemical fungicides or bactericides and not as part of an integrated management system. IPM has had many definitions and this review will use the national coalition for IPM definition: "A sustainable approach to managing pests by combining biological, cultural, physical and chemical tools in a way that minimizes economic, health and environmental risks." This review will examine the integrated use of Bacillus-based BCAs with disease management tools, including resistant cultivars, fungicides or bactericides, or other BCAs. This integration is important because the consistency and degree of disease control by Bacillus-based BCAs is rarely equal to the control afforded by the best fungicides or bactericides. In theory, integration of several tools brings stability to disease management programs. Integration of BCAs with other disease management tools often provides broader crop adaptation and both more efficacious and consistent levels of disease control. This review will also discuss the use of Bacillus-based BCAs in fungicide resistance management. Work with Bacillus thuringiensis and insect pest management is the exception to the relative paucity of reports but will not be the focus of this review.

  10. SVS: data and knowledge integration in computational biology.

    PubMed

    Zycinski, Grzegorz; Barla, Annalisa; Verri, Alessandro

    2011-01-01

    In this paper we present a framework for structured variable selection (SVS). The main concept of the proposed schema is to take a step towards the integration of two different aspects of data mining: database and machine learning perspective. The framework is flexible enough to use not only microarray data, but other high-throughput data of choice (e.g. from mass spectrometry, microarray, next generation sequencing). Moreover, the feature selection phase incorporates prior biological knowledge in a modular way from various repositories and is ready to host different statistical learning techniques. We present a proof of concept of SVS, illustrating some implementation details and describing current results on high-throughput microarray data.

  11. A massive Feynman integral and some reduction relations for Appell functions

    NASA Astrophysics Data System (ADS)

    Shpot, M. A.

    2007-12-01

    New explicit expressions are derived for the one-loop two-point Feynman integral with arbitrary external momentum and masses m12 and m22 in D dimensions. The results are given in terms of Appell functions, manifestly symmetric with respect to the masses mi2. Equating our expressions with previously known results in terms of Gauss hypergeometric functions yields reduction relations for the involved Appell functions that are apparently new mathematical results.

  12. PISCES High Contrast Integral Field Spectrograph Simulations and Data Reduction Pipeline

    NASA Technical Reports Server (NTRS)

    Llop Sayson, Jorge Domingo; Memarsadeghi, Nargess; McElwain, Michael W.; Gong, Qian; Perrin, Marshall; Brandt, Timothy; Grammer, Bryan; Greeley, Bradford; Hilton, George; Marx, Catherine

    2015-01-01

    The PISCES (Prototype Imaging Spectrograph for Coronagraphic Exoplanet Studies) is a lenslet array based integral field spectrograph (IFS) designed to advance the technology readiness of the WFIRST (Wide Field Infrared Survey Telescope)-AFTA (Astrophysics Focused Telescope Assets) high contrast Coronagraph Instrument. We present the end to end optical simulator and plans for the data reduction pipeline (DRP). The optical simulator was created with a combination of the IDL (Interactive Data Language)-based PROPER (optical propagation) library and Zemax (a MatLab script), while the data reduction pipeline is a modified version of the Gemini Planet Imager's (GPI) IDL pipeline. The simulations of the propagation of light through the instrument are based on Fourier transform algorithms. The DRP enables transformation of the PISCES IFS data to calibrated spectral data cubes.

  13. Integrating pharmacology topics in high school biology and chemistry classes improves performance

    NASA Astrophysics Data System (ADS)

    Schwartz-Bloom, Rochelle D.; Halpin, Myra J.

    2003-11-01

    Although numerous programs have been developed for Grade Kindergarten through 12 science education, evaluation has been difficult owing to the inherent problems conducting controlled experiments in the typical classroom. Using a rigorous experimental design, we developed and tested a novel program containing a series of pharmacology modules (e.g., drug abuse) to help high school students learn basic principles in biology and chemistry. High school biology and chemistry teachers were recruited for the study and they attended a 1-week workshop to learn how to integrate pharmacology into their teaching. Working with university pharmacology faculty, they also developed classroom activities. The following year, teachers field-tested the pharmacology modules in their classrooms. Students in classrooms using the pharmacology topics scored significantly higher on a multiple choice test of basic biology and chemistry concepts compared with controls. Very large effect sizes (up to 1.27 standard deviations) were obtained when teachers used as many as four modules. In addition, biology students increased performance on chemistry questions and chemistry students increased performance on biology questions. Substantial gains in achievement may be made when high school students are taught science using topics that are interesting and relevant to their own lives.

  14. Bacterial carbonate precipitation improves water absorption of interlocking compressed earth block (ICEB)

    NASA Astrophysics Data System (ADS)

    Zamer, M. M.; Irwan, J. M.; Othman, N.; Faisal, S. K.; Anneza, L. H.; Alshalif, A. F.; Teddy, T.

    2017-11-01

    Interlocking compressed earth blocks (ICEB) are soil based blocks that allows for mortarless construction. The addition of many alternative materials into interlocking block in order to improve the durability has been reported. However there are currently lack of report and evidence on the application of biocalcification or microbiologically induced calcite precipitation (MICP) in improving the engineering properties of ICEB. This paper evaluate the effect of UB in improving the water absorption properties of ICEB. This paper also provide the results on SEM analysis of addition of 1%, 3% and 5% UB in ICEB. The bacteria were added as partial replacement of limestone water in ICEB. The results showed the reduction of 14.72% with 5% UB on initial water absorption followed by the results for water absorption by 24-hour soaking which also indicates reduction of 14.68% with 5% UB on 28th days of testing compared to control specimen. It was expected that the reduction of water absorption was due to the plugging of pores by the bacterial calcite which prevent ingression of water in ICEB samples. Therefore this study hopes that the positive results from the UB as improving in water absorption of ICEB will lead to improve others ICEB properties and others construction materials.

  15. Explanation in Biology: Reduction, Pluralism, and Explanatory Aims

    ERIC Educational Resources Information Center

    Brigandt, Ingo

    2013-01-01

    This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and…

  16. Personalized Genetic Testing as a Tool for Integrating Ethics Instruction into Biology Courses

    PubMed Central

    Zhang, Tenny R.; Anderson, Misti Ault

    2014-01-01

    Personalized genetic testing (PGT) has been used by some educational institutions as a pedagogical tool for teaching human genetics. While work has been done that examines the potential for PGT to improve students’ interest and understanding of the science involved in genetic testing, there has been less dialogue about how this method might be useful for integrating ethical and societal issues surrounding genetic testing into classroom discussions. Citing the importance of integrating ethics into the biology classroom, we argue that PGT can be an effective educational tool for integrating ethics and science education, and discuss relevant ethical considerations for instructors using this approach. PMID:25574278

  17. Water dynamics of Ser-His-Glu-Cys-Asn powder and effects of moisture absorption on its chemical properties.

    PubMed

    Lin, Songyi; Xue, Peiyu; Yang, Shuailing; Li, Xingfang; Dong, Xiuping; Chen, Feng

    2017-08-01

    This study has elucidated moisture dynamics in the soybean peptide, Ser-His-Glu-Cys-Asn (SHECN) powder by using dynamic vapor sorption (DVS) and nuclear magnetic resonance (NMR). We also tried to investigate the effects of moisture absorption on the biological activity and chemical properties of SHECN with some effective methods such as mid-infrared (MIR) spectroscopy and gas chromatography-mass spectrometry (GC-MS). DVS results showed that the moisture absorption of SHECN could reach a maximum of 33%, and the SHECN powder after synthesis actually existed in a trihydrate state of SHECN.3H 2 O. Low-field NMR revealed that three water proportions including strong combined water, binding water and bulk water were involved in SHECN moisture absorption and absored water dominantly existed in the form of combined water. Magnetic resonance imaging (MRI) and MIR spectroscopy results indicated that moisture absorption could change the morphology and structure of SHECN. After moisture absorption at 50% and 75% relative humidity, 19 volatiles were identified by GC-MS analysis. Additionally, this study showed that a part of reductive groups in SHECN was oxidized and its antioxidant ability declined significantly (P < 0.05) after moisture absorption. Water absorbed into SHECN powder can significantly change its microstructure and cause its activity to decrease. We must prevent SHECN from absorbing moisture during storage because the water can accelerate the oxidation of samples and promote microbial reactions. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  18. A Neural Systems-Based Neurobiology and Neuropsychiatry Course: Integrating Biology, Psychodynamics, and Psychology in the Psychiatric Curriculum

    ERIC Educational Resources Information Center

    Lacy, Timothy; Hughes, John D.

    2006-01-01

    Objective: Psychotherapy and biological psychiatry remain divided in psychiatry residency curricula. Behavioral neurobiology and neuropsychiatry provide a systems-level framework that allows teachers to integrate biology, psychodynamics, and psychology. Method: The authors detail the underlying assumptions and outline of a neural systems-based…

  19. Pre-analytic evaluation of volumetric absorptive microsampling and integration in a mass spectrometry-based metabolomics workflow.

    PubMed

    Volani, Chiara; Caprioli, Giulia; Calderisi, Giovanni; Sigurdsson, Baldur B; Rainer, Johannes; Gentilini, Ivo; Hicks, Andrew A; Pramstaller, Peter P; Weiss, Guenter; Smarason, Sigurdur V; Paglia, Giuseppe

    2017-10-01

    Volumetric absorptive microsampling (VAMS) is a novel approach that allows single-drop (10 μL) blood collection. Integration of VAMS with mass spectrometry (MS)-based untargeted metabolomics is an attractive solution for both human and animal studies. However, to boost the use of VAMS in metabolomics, key pre-analytical questions need to be addressed. Therefore, in this work, we integrated VAMS in a MS-based untargeted metabolomics workflow and investigated pre-analytical strategies such as sample extraction procedures and metabolome stability at different storage conditions. We first evaluated the best extraction procedure for the polar metabolome and found that the highest number and amount of metabolites were recovered upon extraction with acetonitrile/water (70:30). In contrast, basic conditions (pH 9) resulted in divergent metabolite profiles mainly resulting from the extraction of intracellular metabolites originating from red blood cells. In addition, the prolonged storage of blood samples at room temperature caused significant changes in metabolome composition, but once the VAMS devices were stored at - 80 °C, the metabolome remained stable for up to 6 months. The time used for drying the sample did also affect the metabolome. In fact, some metabolites were rapidly degraded or accumulated in the sample during the first 48 h at room temperature, indicating that a longer drying step will significantly change the concentration in the sample. Graphical abstract Volumetric absorptive microsampling (VAMS) is a novel technology that allows single-drop blood collection and, in combination with mass spectrometry (MS)-based untargeted metabolomics, represents an attractive solution for both human and animal studies. In this work, we integrated VAMS in a MS-based untargeted metabolomics workflow and investigated pre-analytical strategies such as sample extraction procedures and metabolome stability at different storage conditions. The latter revealed that

  20. Formation of Copper Catalysts for CO 2 Reduction with High Ethylene/Methane Product Ratio Investigated with In Situ X-ray Absorption Spectroscopy

    DOE PAGES

    Eilert, André; Roberts, F. Sloan; Friebel, Daniel; ...

    2016-04-04

    Nanostructured copper cathodes are among the most efficient and selective catalysts to date for making multicarbon products from the electrochemical carbon dioxide reduction reaction (CO 2RR). We report an in situ X-ray absorption spectroscopy investigation of the formation of a copper nanocube CO 2RR catalyst with high activity that highly favors ethylene over methane production. The results show that the precursor for the copper nanocube formation is copper(I)-oxide, not copper(I)-chloride as previously assumed. A second route to an electrochemically similar material via a copper(II)–carbonate/hydroxide is also reported. In conclusion, this study highlights the importance of using oxidized copper precursors formore » constructing selective CO 2 reduction catalysts and shows the precursor oxidation state does not affect the electrocatalyst selectivity toward ethylene formation.« less

  1. On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types

    PubMed Central

    2014-01-01

    Background Integrating and analyzing heterogeneous genome-scale data is a huge algorithmic challenge for modern systems biology. Bipartite graphs can be useful for representing relationships across pairs of disparate data types, with the interpretation of these relationships accomplished through an enumeration of maximal bicliques. Most previously-known techniques are generally ill-suited to this foundational task, because they are relatively inefficient and without effective scaling. In this paper, a powerful new algorithm is described that produces all maximal bicliques in a bipartite graph. Unlike most previous approaches, the new method neither places undue restrictions on its input nor inflates the problem size. Efficiency is achieved through an innovative exploitation of bipartite graph structure, and through computational reductions that rapidly eliminate non-maximal candidates from the search space. An iterative selection of vertices for consideration based on non-decreasing common neighborhood sizes boosts efficiency and leads to more balanced recursion trees. Results The new technique is implemented and compared to previously published approaches from graph theory and data mining. Formal time and space bounds are derived. Experiments are performed on both random graphs and graphs constructed from functional genomics data. It is shown that the new method substantially outperforms the best previous alternatives. Conclusions The new method is streamlined, efficient, and particularly well-suited to the study of huge and diverse biological data. A robust implementation has been incorporated into GeneWeaver, an online tool for integrating and analyzing functional genomics experiments, available at http://geneweaver.org. The enormous increase in scalability it provides empowers users to study complex and previously unassailable gene-set associations between genes and their biological functions in a hierarchical fashion and on a genome-wide scale. This practical

  2. Trace Element Analysis of Biological Samples.

    ERIC Educational Resources Information Center

    Veillon, Claude

    1986-01-01

    Reviews background of atomic absorption spectrometry techniques. Discusses problems encountered and precautions to be taken in determining trace elements in the parts-per-billion concentration range and below. Concentrates on determining chromium in biological samples by graphite furnace atomic absorption. Considers other elements, matrices, and…

  3. Pioneer-Venus radio occultation (ORO) data reduction: Profiles of 13 cm absorptivity

    NASA Technical Reports Server (NTRS)

    Steffes, Paul G.

    1990-01-01

    In order to characterize possible variations in the abundance and distribution of subcloud sulfuric acid vapor, 13 cm radio occultation signals from 23 orbits that occurred in late 1986 and 1987 (Season 10) and 7 orbits that occurred in 1979 (Season 1) were processed. The data were inverted via inverse Abel transform to produce 13 cm absorptivity profiles. Pressure and temperature profiles obtained with the Pioneer-Venus night probe and the northern probe were used along with the absorptivity profiles to infer upper limits for vertical profiles of the abundance of gaseous H2SO4. In addition to inverting the data, error bars were placed on the absorptivity profiles and H2SO4 abundance profiles using the standard propagation of errors. These error bars were developed by considering the effects of statistical errors only. The profiles show a distinct pattern with regard to latitude which is consistent with latitude variations observed in data obtained during the occultation seasons nos. 1 and 2. However, when compared with the earlier data, the recent occultation studies suggest that the amount of sulfuric acid vapor occurring at and below the main cloud layer may have decreased between early 1979 and late 1986.

  4. Excitonic Resonant Emission–Absorption of Surface Plasmons in Transition Metal Dichalcogenides for Chip-Level Electronic–Photonic Integrated Circuits

    DOE PAGES

    Zhu, Zhuan; Yuan, Jiangtan; Zhou, Haiqing; ...

    2016-04-19

    The monolithic integration of electronics and photonics has attracted enormous attention due to its potential applications. A major challenge to this integration is the identification of suitable materials that can emit and absorb light at the same wavelength. In this paper we utilize unique excitonic transitions in WS 2 monolayers and show that WS 2 exhibits a perfect overlap between its absorption and photoluminescence spectra. By coupling WS 2 to Ag nanowires, we then show that WS 2 monolayers are able to excite and absorb surface plasmons of Ag nanowires at the same wavelength of exciton photoluminescence. This resonant absorptionmore » by WS 2 is distinguished from that of the ohmic propagation loss of silver nanowires, resulting in a short propagation length of surface plasmons. Our demonstration of resonant optical generation and detection of surface plasmons enables nanoscale optical communication and paves the way for on-chip electronic–photonic integrated circuits.« less

  5. Middle infrared optoelectronic absorption systems for monitoring physiological glucose solutions

    NASA Astrophysics Data System (ADS)

    Martin, W. Blake

    Tight monitoring of the glucose levels for diabetic individuals is essential to control long-term complications. A definitive diabetes management system has yet to be developed for the diabetic. This research investigates the application of middle infrared absorption frequencies for monitoring glucose levels in biological solutions. Three frequencies were identified using a Fourier transform infrared spectrometer and correlated to changes in glucose concentrations. The 1035 +/- 1 cm-1 frequency was determined to be the best representative frequency. Other biological molecules contributed no significant interference to monitoring glucose absorption. A second frequency at 1193 cm-1 was suggested as a representative background absorption frequency, which could be used for more accurate glucose absorption values. Next, a quantum cascade laser optoelectronic absorption system was designed and developed to monitor glucose. After careful alignment and design, the system was used to monitor physiological glucose concentrations. Correlation at 1036 cm-1 with glucose changes was comparable to the previous results. The use of the background absorption frequency was verified. This frequency essentially acts as a calibrating frequency to adjust in real-time to any changes in the background absorption that may alter the accuracy of the predicted glucose value. An evanescent wave cavity ring-down spectroscopy technique was explored to monitor molecules in a biological solution. Visible light at 425 nm was used to monitor hemoglobin in control urine samples. An adsorption isotherm for hemoglobin was detectable to limit of 5.8 nM. Evanescent wave cavity ring-down spectroscopy would be useful for a glucose solution. Given an equivalent system designed for the middle infrared, the molar extinction coefficient of glucose allows for a detectable limit of 45 mg/dl for a free-floating glucose solution, which is below normal physiological concentrations. The future use of a hydrophobic

  6. Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

    PubMed

    Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

    2016-02-01

    The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

  7. Scramjet Performance Assessment Using Water Absorption Diagnostics (U)

    NASA Technical Reports Server (NTRS)

    Cavolowsky, John A.; Loomis, Mark P.; Deiwert, George

    1995-01-01

    Simultaneous multiple path measurements of temperature and H2O concentration will be presented for the AIMHYE test entries in the NASA Ames 16-Inch Shock Tunnel. Monitoring the progress of high temperature chemical reactions that define scramjet combustor efficiencies is a task uniquely suited to nonintrusive optical diagnostics. One application strategy to overcome the many challenges and limitations of nonintrusive measurements is to use laser absorption spectroscopy coupled with optical fibers. Absorption spectroscopic techniques with rapidly tunable lasers are capable of making simultaneous measurements of mole fraction, temperature, pressure, and velocity. The scramjet water absorption diagnostic was used to measure combustor efficiency and was compared to thrust measurements using a nozzle force balance and integrated nozzle pressures to develop a direct technique for evaluating integrated scramjet performance. Tests were initially performed with a diode laser tuning over a water absorption feature at 1391.7 nm. A second diode laser later became available at a wavelength near 1343.3 nm covering an additional water absorption feature and was incorporated in the system for a two-wavelength technique. Both temperature and mole fraction can be inferred from the lineshape analysis using this approach. Additional high temperature spectroscopy research was conducted to reduce uncertainties in the scramjet application. The lasers are optical fiber coupled to ports at the combustor exit and in the nozzle region. The output from the two diode lasers were combined in a single fiber, and the resultant two-wavelength beam was subsequently split into four legs. Each leg was directed through 60 meters of optical fiber to four combustor exit locations for measurement of beam intensity after absorption by the water within the flow. Absorption results will be compared to 1D combustor analysis using RJPA and nozzle CFD computations as well as to data from a nozzle metric

  8. Integrating bio-inorganic and analytical chemistry into an undergraduate biochemistry laboratory.

    PubMed

    Erasmus, Daniel J; Brewer, Sharon E; Cinel, Bruno

    2015-01-01

    Undergraduate laboratories expose students to a wide variety of topics and techniques in a limited amount of time. This can be a challenge and lead to less exposure to concepts and activities in bio-inorganic chemistry and analytical chemistry that are closely-related to biochemistry. To address this, we incorporated a new iron determination by atomic absorption spectroscopy exercise as part of a five-week long laboratory-based project on the purification of myoglobin from beef. Students were required to prepare samples for chemical analysis, operate an atomic absorption spectrophotometer, critically evaluate their iron data, and integrate these data into a study of myoglobin. © 2015 The International Union of Biochemistry and Molecular Biology.

  9. Förster resonance energy transfer, absorption and emission spectra in multichromophoric systems. III. Exact stochastic path integral evaluation.

    PubMed

    Moix, Jeremy M; Ma, Jian; Cao, Jianshu

    2015-03-07

    A numerically exact path integral treatment of the absorption and emission spectra of open quantum systems is presented that requires only the straightforward solution of a stochastic differential equation. The approach converges rapidly enabling the calculation of spectra of large excitonic systems across the complete range of system parameters and for arbitrary bath spectral densities. With the numerically exact absorption and emission operators, one can also immediately compute energy transfer rates using the multi-chromophoric Förster resonant energy transfer formalism. Benchmark calculations on the emission spectra of two level systems are presented demonstrating the efficacy of the stochastic approach. This is followed by calculations of the energy transfer rates between two weakly coupled dimer systems as a function of temperature and system-bath coupling strength. It is shown that the recently developed hybrid cumulant expansion (see Paper II) is the only perturbative method capable of generating uniformly reliable energy transfer rates and emission spectra across a broad range of system parameters.

  10. SAMI: Sydney-AAO Multi-object Integral field spectrograph pipeline

    NASA Astrophysics Data System (ADS)

    Allen, J. T.; Green, A. W.; Fogarty, L. M. R.; Sharp, R.; Nielsen, J.; Konstantopoulos, I.; Taylor, E. N.; Scott, N.; Cortese, L.; Richards, S. N.; Croom, S.; Owers, M. S.; Bauer, A. E.; Sweet, S. M.; Bryant, J. J.

    2014-07-01

    The SAMI (Sydney-AAO Multi-object Integral field spectrograph) pipeline reduces data from the Sydney-AAO Multi-object Integral field spectrograph (SAMI) for the SAMI Galaxy Survey. The python code organizes SAMI data and, along with the AAO 2dfdr package, carries out all steps in the data reduction, from raw data to fully calibrated datacubes. The principal steps are: data management, use of 2dfdr to produce row-stacked spectra, flux calibration, correction for telluric absorption, removal of atmospheric dispersion, alignment of dithered exposures, and drizzling onto a regular output grid. Variance and covariance information is tracked throughout the pipeline. Some quality control routines are also included.

  11. Insight into the biological effects of acupuncture points by X-ray absorption fine structure.

    PubMed

    Liu, Chenglin; Liu, Qinghua; Zhang, Dongming; Liu, Wei; Yan, Xiaohui; Zhang, Xinyi; Oyanagi, Hiroyuki; Pan, Zhiyun; Hu, Fengchun; Wei, Shiqiang

    2018-06-02

    Exploration of the biological effects of transition metal ions in acupuncture points is essential to clarify the functional mechanism of acupuncture treatment. Here we show that in the SP6 acupuncture point (Sanyinjiao) the Fe ions are in a high-spin state of approximately t 2g 4.5 e g 1.5 in an Fe-N(O) octahedral crystal field. The Fe K-edge synchrotron radiation X-ray absorption fine structure results reveal that the Fe-N and Fe-O bond lengths in the SP6 acupuncture point are 2.05 and 2.13 Å, respectively, and are 0.05-0.10 Å longer than those in the surrounding tissue. The distorted atomic structure reduces the octahedral symmetry and weakens the crystal field around the Fe ions by approximately 0.3 eV, leading to the high-spin configuration of the Fe ions, which is favorable for strengthening the magnetotransport and oxygen transportation properties in the acupuncture point by the enhanced spin coherence. This finding might provide some insight into the microscopic effect of the atomic and electronic interactions of transition metal ions in the acupuncture point. Graphical Abstract ᅟ.

  12. [Construction of research system for processing mechanism of traditional Chinese medicine based on chemical composition transformation combined with intestinal absorption barrier].

    PubMed

    Sun, E; Xu, Feng-Juan; Zhang, Zhen-Hai; Wei, Ying-Jie; Tan, Xiao-Bin; Cheng, Xu-Dong; Jia, Xiao-Bin

    2014-02-01

    Based on practice of Epimedium processing mechanism for many years and integrated multidisciplinary theory and technology, this paper initially constructs the research system for processing mechanism of traditional Chinese medicine based on chemical composition transformation combined with intestinal absorption barrier, which to form an innovative research mode of the " chemical composition changes-biological transformation-metabolism in vitro and in vivo-intestinal absorption-pharmacokinetic combined pharmacodynamic-pharmacodynamic mechanism". Combined with specific examples of Epimedium and other Chinese herbal medicine processing mechanism, this paper also discusses the academic thoughts, research methods and key technologies of this research system, which will be conducive to systematically reveal the modem scientific connotation of traditional Chinese medicine processing, and enrich the theory of Chinese herbal medicine processing.

  13. Bioinformatics for transporter pharmacogenomics and systems biology: data integration and modeling with UML.

    PubMed

    Yan, Qing

    2010-01-01

    Bioinformatics is the rational study at an abstract level that can influence the way we understand biomedical facts and the way we apply the biomedical knowledge. Bioinformatics is facing challenges in helping with finding the relationships between genetic structures and functions, analyzing genotype-phenotype associations, and understanding gene-environment interactions at the systems level. One of the most important issues in bioinformatics is data integration. The data integration methods introduced here can be used to organize and integrate both public and in-house data. With the volume of data and the high complexity, computational decision support is essential for integrative transporter studies in pharmacogenomics, nutrigenomics, epigenetics, and systems biology. For the development of such a decision support system, object-oriented (OO) models can be constructed using the Unified Modeling Language (UML). A methodology is developed to build biomedical models at different system levels and construct corresponding UML diagrams, including use case diagrams, class diagrams, and sequence diagrams. By OO modeling using UML, the problems of transporter pharmacogenomics and systems biology can be approached from different angles with a more complete view, which may greatly enhance the efforts in effective drug discovery and development. Bioinformatics resources of membrane transporters and general bioinformatics databases and tools that are frequently used in transporter studies are also collected here. An informatics decision support system based on the models presented here is available at http://www.pharmtao.com/transporter . The methodology developed here can also be used for other biomedical fields.

  14. Method for the determination of cobalt from biological products with graphite furnace atomic absorption spectrometer

    NASA Astrophysics Data System (ADS)

    Zamfir, Oana-Liliana; Ionicǎ, Mihai; Caragea, Genica; Radu, Simona; Vlǎdescu, Marian

    2016-12-01

    Cobalt is a chemical element with symbol Co and atomic number 27 and atomic weight 58.93. 59 Co is the only stable cobalt isotope and the only isotope to exist naturally on Earth. Cobalt is the active center of coenzymes called cobalamin or cyanocobalamin the most common example of which is vitamin B12. Vitamin B12 deficiency can potentially cause severe and irreversible damage, especially to the brain and nervous system in the form of fatigue, depression and poor memory or even mania and psychosis. In order to study the degree of deficiency of the population with Co or the correctness of treatment with vitamin B12, a modern optoelectronic method for the determination of metals and metalloids from biological samples has been developed, Graphite Furnace - Atomic Absorption Spectrometer (GF- AAS) method is recommended. The technique is based on the fact that free atoms will absorb light at wavelengths characteristic of the element of interest. Free atoms of the chemical element can be produced from samples by the application of high temperatures. The system GF-AAS Varian used as biological samples, blood or urine that followed the digest of the organic matrix. For the investigations was used a high - performance GF-AAS with D2 - background correction system and a transversely heated graphite atomizer. As result of the use of the method are presented the concentration of Co in the blood or urine of a group of patient in Bucharest. The method is sensitive, reproducible relatively easy to apply, with a moderately costs.

  15. Realizing high-rate sulfur reduction under sulfate-rich conditions in a biological sulfide production system to treat metal-laden wastewater deficient in organic matter.

    PubMed

    Sun, Rongrong; Zhang, Liang; Zhang, Zefeng; Chen, Guang-Hao; Jiang, Feng

    2017-12-22

    Biological sulfur reduction can theoretically produce sufficient sulfide to effectively remove and recover heavy metals in the treatment of organics-deficient sulfate-rich metal-laden wastewater such as acid mine drainage and metallurgic wastewater, using 75% less organics than biological sulfate reduction. However, it is still unknown whether sulfur reduction can indeed compete with sulfate reduction, particularly under high-strength sulfate conditions. The aim of this study was to investigate the long-term feasibility of biological sulfur reduction under high sulfate conditions in a lab-scale sulfur-reducing biological sulfide production (BSP) system with sublimed sulfur added. In the 169-day trial, an average sulfide production rate (SPR) as high as 47 ± 9 mg S/L-h was achieved in the absence of sulfate, and the average SPR under sulfate-rich conditions was similar (53 ± 10 mg S/L-h) when 1300 mg S/L sulfate were fed with the influent. Interestingly, sulfate was barely reduced even at such a high strength and contributed to only 1.5% of total sulfide production. Desulfomicrobium was identified as the predominant sulfidogenic bacterium in the bioreactor. Batch tests further revealed that this sulfidogenic bacteria used elemental sulfur as the electron acceptor instead of the highly bioavailable sulfate, during which polysulfide acted as an intermediate, leading to an even higher bioavailability of sulfur than sulfate. The pathway of sulfur to sulfide conversion via polysulfide in the presence of both sulfur and sulfate was discussed. Collectively, when conditions favor polysulfide formation, sulfur reduction can be a promising and attractive technology to realize a high-rate and low-cost BSP process for treating sulfate-rich metal-laden wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

    PubMed

    He, Yongqun

    2014-07-01

    While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ('OneNet') Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

  17. A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

    PubMed Central

    Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

    2011-01-01

    Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug–drug, or drug–metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach. PMID:21483730

  18. Determination of optical absorption coefficient with focusing photoacoustic imaging.

    PubMed

    Li, Zhifang; Li, Hui; Zeng, Zhiping; Xie, Wenming; Chen, Wei R

    2012-06-01

    Absorption coefficient of biological tissue is an important factor for photothermal therapy and photoacoustic imaging. However, its determination remains a challenge. In this paper, we propose a method using focusing photoacoustic imaging technique to quantify the target optical absorption coefficient. It utilizes the ratio of the amplitude of the peak signal from the top boundary of the target to that from the bottom boundary based on wavelet transform. This method is self-calibrating. Factors, such as absolute optical fluence, ultrasound parameters, and Grüneisen parameter, can be canceled by dividing the amplitudes of the two peaks. To demonstrate this method, we quantified the optical absorption coefficient of a target with various concentrations of an absorbing dye. This method is particularly useful to provide accurate absorption coefficient for predicting the outcomes of photothermal interaction for cancer treatment with absorption enhancement.

  19. Super-resolution atomic force photoactivated microscopy of biological samples (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Lee, Seunghyun; Kim, Hyemin; Shin, Seungjun; Doh, Junsang; Kim, Chulhong

    2017-03-01

    Optical microscopy (OM) and photoacoustic microscopy (PAM) have previously been used to image the optical absorption of intercellular features of biological cells. However, the optical diffraction limit ( 200 nm) makes it difficult for these modalities to image nanoscale inner cell structures and the distribution of internal cell components. Although super-resolution fluorescence microscopy, such as stimulated emission depletion microscopy (STED) and stochastic optical reconstruction microscopy (STORM), has successfully performed nanoscale biological imaging, these modalities require the use of exogenous fluorescence agents, which are unfavorable for biological samples. Our newly developed atomic force photoactivated microscopy (AFPM) can provide optical absorption images with nanoscale lateral resolution without any exogenous contrast agents. AFPM combines conventional atomic force microscopy (AFM) and an optical excitation system, and simultaneously provides multiple contrasts, such as the topography and magnitude of optical absorption. AFPM can detect the intrinsic optical absorption of samples with 8 nm lateral resolution, easily overcoming the diffraction limit. Using the label-free AFPM system, we have successfully imaged the optical absorption properties of a single melanoma cell (B16F10) and a rosette leaf epidermal cell of Arabidopsis (ecotype Columbia (Col-0)) with nanoscale lateral resolution. The remarkable images show the melanosome distribution of a melanoma cell and the biological structures of a plant cell. AFPM provides superior imaging of optical absorption with a nanoscale lateral resolution, and it promises to become widely used in biological and chemical research.

  20. Using two classification schemes to develop vegetation indices of biological integrity for wetlands in West Virginia, USA.

    PubMed

    Veselka, Walter; Rentch, James S; Grafton, William N; Kordek, Walter S; Anderson, James T

    2010-11-01

    Bioassessment methods for wetlands, and other bodies of water, have been developed worldwide to measure and quantify changes in "biological integrity." These assessments are based on a classification system, meant to ensure appropriate comparisons between wetland types. Using a local site-specific disturbance gradient, we built vegetation indices of biological integrity (Veg-IBIs) based on two commonly used wetland classification systems in the USA: One based on vegetative structure and the other based on a wetland's position in a landscape and sources of water. The resulting class-specific Veg-IBIs were comprised of 1-5 metrics that varied in their sensitivity to the disturbance gradient (R2=0.14-0.65). Moreover, the sensitivity to the disturbance gradient increased as metrics from each of the two classification schemes were combined (added). Using this information to monitor natural and created wetlands will help natural resource managers track changes in biological integrity of wetlands in response to anthropogenic disturbance and allows the use of vegetative communities to set ecological performance standards for mitigation banks.

  1. Monte Carlo simulation of cutaneous absorption and reflectance for clear, matt and dark biological tissue with varicosities: an investigation for dermatological laser

    NASA Astrophysics Data System (ADS)

    Klouch, Nawel; Riane, Houaria; Hamdache, Fatima; Addi, Djamel

    2013-05-01

    We are interested in modeling the interaction between light and biological tissue from the Monte Carlo method which is an approach used to solve modeling problems in different physical domains. Through the Monte Carlo approach we are going to try to interpret the spectral response absorption, reflectance, transmittance of normal human tissue under its three dominant tints in the visible range (350-700) nm. Then we will focus on the spectral response of the human tissue with varicosities in order to determinate the optimal conditions of operating the semiconductor laser for esthetic aim.

  2. Osteoconductive carriers for integrated bone repair.

    PubMed

    Ganey, Timothy; Hutton, William; Meisel, Hans Jörg

    2009-01-01

    Successful bone repair is judged in achieving restitution of space and mechanical integrity, and in regaining function. When the biology or anatomy are insufficient to attain a full repair, therapeutic use of graft material has been used to omit compliance features such as strain tolerance, reduced stiffness, and attenuated strength, and instead promote primary or membranous-type bone formation within the physical approximation of a graft material. The challenge of most conductive materials is that they emerge from a static platform and in placement force the living system to adapt to placement, dimension, different properties, and eventually are only successful in degradation and replacement, or in integration. The synergy and interdependency between adhesion, ECM, and proteolysis are important concepts that must be understood to engineer scaffolds capable of holding up to standards which are more than cell decoration. Moreover, the reactive specificity to loading, degradation, therapeutic delivery during absorption remains a key aim of both academic and industrial designs. Achieving conductivity comes with challenges of best fit integration, delivery, and in integrated modeling. The more liquid is the delivery, the more modular the components, and adaptive the matrix to meeting the intended application, the more likely that the conductivity will not be excluded by the morphology of the injury site. Considerations for osteoconductive materials for bone repair and replacement have developed conceptually and advanced parallel with a better understanding of not only bone biology but of materials science. First models of material replacements utilized a reductionist-constructionist logic; define the constituents of the material in terms of its morphology and chemical composition, and then engineer material with similar content and properties as a means of accommodating a replacement. Unfortunately for biologic systems, empiric formulation is insufficient to promote

  3. Integrated systems of stroke care and reduction in 30-day mortality

    PubMed Central

    Ganesh, Aravind; Lindsay, Patrice; Fang, Jiming; Kapral, Moira K.; Côté, Robert; Joiner, Ian; Hakim, Antoine M.

    2016-01-01

    Objective: To evaluate the association between the presence of integrated systems of stroke care and stroke case-fatality across Canada. Methods: We used the Canadian Institute of Health Information's Discharge Abstract Database to retrospectively identify a cohort of stroke/TIA patients admitted to all acute care hospitals, excluding the province of Quebec, in 11 fiscal years from 2003/2004 to 2013/2014. We used a modified Poisson regression model to compute the adjusted incidence rate ratio (aIRR) of 30-day in-hospital mortality across time for provinces with stroke systems compared to those without, controlling for age, sex, stroke type, comorbidities, and discharge year. We conducted surveys of stroke care resources in Canadian hospitals in 2009 and 2013, and compared resources in provinces with integrated systems to those without. Results: A total of 319,972 patients were hospitalized for stroke/TIA. The crude 30-day mortality rate decreased from 15.8% in 2003/2004 to 12.7% in 2012/2013 in provinces with stroke systems, while remaining 14.5% in provinces without such systems. Starting with the fiscal year 2009/2010, there was a clear reduction in relative mortality in provinces with stroke systems vs those without, sustained at aIRR of 0.85 (95% confidence interval 0.79–0.92) in the 2011/2012, 2012/2013, and 2013/2014 fiscal years. The surveys indicated that facilities in provinces with such systems were more likely to care for patients on a stroke unit, and have timely access to a stroke prevention clinic and telestroke services. Conclusion: In this retrospective study, the implementation of integrated systems of stroke care was associated with a population-wide reduction in mortality after stroke. PMID:26850979

  4. Variance of transionospheric VLF wave power absorption

    NASA Astrophysics Data System (ADS)

    Tao, X.; Bortnik, J.; Friedrich, M.

    2010-07-01

    To investigate the effects of D-region electron-density variance on wave power absorption, we calculate the power reduction of very low frequency (VLF) waves propagating through the ionosphere with a full wave method using the standard ionospheric model IRI and in situ observational data. We first verify the classic absorption curves of Helliwell's using our full wave code. Then we show that the IRI model gives overall smaller wave absorption compared with Helliwell's. Using D-region electron densities measured by rockets during the past 60 years, we demonstrate that the power absorption of VLF waves is subject to large variance, even though Helliwell's absorption curves are within ±1 standard deviation of absorption values calculated from data. Finally, we use a subset of the rocket data that are more representative of the D region of middle- and low-latitude VLF wave transmitters and show that the average quiet time wave absorption is smaller than that of Helliwell's by up to 100 dB at 20 kHz and 60 dB at 2 kHz, which would make the model-observation discrepancy shown by previous work even larger. This result suggests that additional processes may be needed to explain the discrepancy.

  5. Integration of ecological-biological thresholds in conservation decision making.

    PubMed

    Mavrommati, Georgia; Bithas, Kostas; Borsuk, Mark E; Howarth, Richard B

    2016-12-01

    In the Anthropocene, coupled human and natural systems dominate and only a few natural systems remain relatively unaffected by human influence. On the one hand, conservation criteria based on areas of minimal human impact are not relevant to much of the biosphere. On the other hand, conservation criteria based on economic factors are problematic with respect to their ability to arrive at operational indicators of well-being that can be applied in practice over multiple generations. Coupled human and natural systems are subject to economic development which, under current management structures, tends to affect natural systems and cross planetary boundaries. Hence, designing and applying conservation criteria applicable in real-world systems where human and natural systems need to interact and sustainably coexist is essential. By recognizing the criticality of satisfying basic needs as well as the great uncertainty over the needs and preferences of future generations, we sought to incorporate conservation criteria based on minimal human impact into economic evaluation. These criteria require the conservation of environmental conditions such that the opportunity for intergenerational welfare optimization is maintained. Toward this end, we propose the integration of ecological-biological thresholds into decision making and use as an example the planetary-boundaries approach. Both conservation scientists and economists must be involved in defining operational ecological-biological thresholds that can be incorporated into economic thinking and reflect the objectives of conservation, sustainability, and intergenerational welfare optimization. © 2016 Society for Conservation Biology.

  6. [BIOLOGICAL EFFECTIVENESS OF FISSION SPECTRUM NEUTRONS AND PROTONS WITH ENERGIES OF 60-126 MEV DURING ACUTE AND PROLONGED IRRADIATION].

    PubMed

    Shafirkin, A V

    2015-01-01

    Neutrons of the fission spectrum are characterized by relatively high values of linear energy transfer (LET). Data about their effects on biological objects are used to evaluate the risk of delayed effects of accelerated ions within the same LET range that serve as an experimental model of the nuclei component of galactic cosmic rays (GCR). Additionally, risks of delayed consequences to cosmonaut's health and average lifetime from certain GCR fluxes and secondary neutrons can be also prognosticated. The article deals with comparative analysis of the literature on reduction of average lifespan (ALS) of animals exposed to neutron reactor spectrum, 60-126 MeV protons, and X- and γ-rays in a broad range of radiation intensity and duration. It was shown that a minimal lifespan reduction by 5% occurs due to a brief exposure to neutrons with the absorbed dose of 5 cGy, whereas same lifespan reduction due to hard X- and γ-radiation occurs after absorption of a minimal dose of 100 cGy. Therefore, according to the estimated minimal ALS reduction in mice, neutron effectiveness is 20-fold higher. Biological effectiveness of protons as regards ALS reduction is virtually equal to that of standard types of radiation. Exposure to X- and γ-radiation with decreasing daily doses, and increasing number of fractions and duration gives rise to an apparent trend toward a less dramatic ALS reduction in mice; on the contrary, exposure to neutrons of varying duration had no effect on threshold doses for the specified ALS reductions. Factors of relative biological effectiveness of neutrons reached 40.

  7. Resolution enhancement in integral microscopy by physical interpolation.

    PubMed

    Llavador, Anabel; Sánchez-Ortiga, Emilio; Barreiro, Juan Carlos; Saavedra, Genaro; Martínez-Corral, Manuel

    2015-08-01

    Integral-imaging technology has demonstrated its capability for computing depth images from the microimages recorded after a single shot. This capability has been shown in macroscopic imaging and also in microscopy. Despite the possibility of refocusing different planes from one snap-shot is crucial for the study of some biological processes, the main drawback in integral imaging is the substantial reduction of the spatial resolution. In this contribution we report a technique, which permits to increase the two-dimensional spatial resolution of the computed depth images in integral microscopy by a factor of √2. This is made by a double-shot approach, carried out by means of a rotating glass plate, which shifts the microimages in the sensor plane. We experimentally validate the resolution enhancement as well as we show the benefit of applying the technique to biological specimens.

  8. Resolution enhancement in integral microscopy by physical interpolation

    PubMed Central

    Llavador, Anabel; Sánchez-Ortiga, Emilio; Barreiro, Juan Carlos; Saavedra, Genaro; Martínez-Corral, Manuel

    2015-01-01

    Integral-imaging technology has demonstrated its capability for computing depth images from the microimages recorded after a single shot. This capability has been shown in macroscopic imaging and also in microscopy. Despite the possibility of refocusing different planes from one snap-shot is crucial for the study of some biological processes, the main drawback in integral imaging is the substantial reduction of the spatial resolution. In this contribution we report a technique, which permits to increase the two-dimensional spatial resolution of the computed depth images in integral microscopy by a factor of √2. This is made by a double-shot approach, carried out by means of a rotating glass plate, which shifts the microimages in the sensor plane. We experimentally validate the resolution enhancement as well as we show the benefit of applying the technique to biological specimens. PMID:26309749

  9. Extracellular reduction of uranium via Geobacter conductive pili as a protective cellular mechanism.

    PubMed

    Cologgi, Dena L; Lampa-Pastirk, Sanela; Speers, Allison M; Kelly, Shelly D; Reguera, Gemma

    2011-09-13

    The in situ stimulation of Fe(III) oxide reduction by Geobacter bacteria leads to the concomitant precipitation of hexavalent uranium [U(VI)] from groundwater. Despite its promise for the bioremediation of uranium contaminants, the biological mechanism behind this reaction remains elusive. Because Fe(III) oxide reduction requires the expression of Geobacter's conductive pili, we evaluated their contribution to uranium reduction in Geobacter sulfurreducens grown under pili-inducing or noninducing conditions. A pilin-deficient mutant and a genetically complemented strain with reduced outer membrane c-cytochrome content were used as controls. Pili expression significantly enhanced the rate and extent of uranium immobilization per cell and prevented periplasmic mineralization. As a result, pili expression also preserved the vital respiratory activities of the cell envelope and the cell's viability. Uranium preferentially precipitated along the pili and, to a lesser extent, on outer membrane redox-active foci. In contrast, the pilus-defective strains had different degrees of periplasmic mineralization matching well with their outer membrane c-cytochrome content. X-ray absorption spectroscopy analyses demonstrated the extracellular reduction of U(VI) by the pili to mononuclear tetravalent uranium U(IV) complexed by carbon-containing ligands, consistent with a biological reduction. In contrast, the U(IV) in the pilin-deficient mutant cells also required an additional phosphorous ligand, in agreement with the predominantly periplasmic mineralization of uranium observed in this strain. These findings demonstrate a previously unrecognized role for Geobacter conductive pili in the extracellular reduction of uranium, and highlight its essential function as a catalytic and protective cellular mechanism that is of interest for the bioremediation of uranium-contaminated groundwater.

  10. Airborne 2-Micron Double-Pulsed Integrated Path Differential Absorption Lidar for Column CO2 Measurement

    NASA Technical Reports Server (NTRS)

    Singh, Upendra N.; Yu, Jirong; Petros, Mulugeta; Refaat, Tamer F.; Remus, Ruben G.; Fay, James J.; Reithmaier, Karl

    2014-01-01

    Double-pulse 2-micron lasers have been demonstrated with energy as high as 600 millijouls and up to 10 Hz repetition rate. The two laser pulses are separated by 200 microseconds and can be tuned and locked separately. Applying double-pulse laser in DIAL system enhances the CO2 measurement capability by increasing the overlap of the sampled volume between the on-line and off-line. To avoid detection complicity, integrated path differential absorption (IPDA) lidar provides higher signal-to-noise ratio measurement compared to conventional range-resolved DIAL. Rather than weak atmospheric scattering returns, IPDA rely on the much stronger hard target returns that is best suited for airborne platforms. In addition, the IPDA technique measures the total integrated column content from the instrument to the hard target but with weighting that can be tuned by the transmitter. Therefore, the transmitter could be tuned to weight the column measurement to the surface for optimum CO2 interaction studies or up to the free troposphere for optimum transport studies. Currently, NASA LaRC is developing and integrating a double-Pulsed 2-micron direct detection IPDA lidar for CO2 column measurement from an airborne platform. The presentation will describe the development of the 2-micron IPDA lidar system and present the airborne measurement of column CO2 and will compare to in-situ measurement for various ground target of different reflectivity.

  11. Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach.

    PubMed

    Ng, Clara; Hauptman, Ruth; Zhang, Yinliang; Bourne, Philip E; Xie, Lei

    2014-01-01

    The emergence of multi-drug and extensive drug resistance of microbes to antibiotics poses a great threat to human health. Although drug repurposing is a promising solution for accelerating the drug development process, its application to anti-infectious drug discovery is limited by the scope of existing phenotype-, ligand-, or target-based methods. In this paper we introduce a new computational strategy to determine the genome-wide molecular targets of bioactive compounds in both human and bacterial genomes. Our method is based on the use of a novel algorithm, ligand Enrichment of Network Topological Similarity (ligENTS), to map the chemical universe to its global pharmacological space. ligENTS outperforms the state-of-the-art algorithms in identifying novel drug-target relationships. Furthermore, we integrate ligENTS with our structural systems biology platform to identify drug repurposing opportunities via target similarity profiling. Using this integrated strategy, we have identified novel P. falciparum targets of drug-like active compounds from the Malaria Box, and suggest that a number of approved drugs may be active against malaria. This study demonstrates the potential of an integrative chemical genomics and structural systems biology approach to drug repurposing.

  12. National Aerospace Plane Integrated Fuselage/Cryotank Risk Reduction program

    NASA Astrophysics Data System (ADS)

    Dayton, K. E.

    1993-06-01

    The principal objectives and results of the National Aerospace Plane (NASP) Integrated Risk Reduction program are briefly reviewed. The program demonstrated the feasibility of manufacturing lightweight advanced composite materials for single-stage-to-orbit hypersonic flight vehicle applications. A series of combined load simulation tests (thermal, mechanical, and cryogenic) demonstrated proof of concept performance for an all unlined composite cryogenic fuel tank with flat end bulkheads and a high-temperature thin-shell advanced composite fuselage. Temperatures of the fuselage were as high as 1300 F, with 100 percent bending and shear loads applied to the tank while filled with 850 gallons of cryogenic fluid hydrogen (-425 F). Leak rates measured on and around the cryotank shell and bulkheads were well below acceptable levels.

  13. Method of and apparatus for determining the similarity of a biological analyte from a model constructed from known biological fluids

    DOEpatents

    Robinson, Mark R.; Ward, Kenneth J.; Eaton, Robert P.; Haaland, David M.

    1990-01-01

    The characteristics of a biological fluid sample having an analyte are determined from a model constructed from plural known biological fluid samples. The model is a function of the concentration of materials in the known fluid samples as a function of absorption of wideband infrared energy. The wideband infrared energy is coupled to the analyte containing sample so there is differential absorption of the infrared energy as a function of the wavelength of the wideband infrared energy incident on the analyte containing sample. The differential absorption causes intensity variations of the infrared energy incident on the analyte containing sample as a function of sample wavelength of the energy, and concentration of the unknown analyte is determined from the thus-derived intensity variations of the infrared energy as a function of wavelength from the model absorption versus wavelength function.

  14. Design and manufacture of high absorption metal dielectric coatings for the reduction of straylight

    NASA Astrophysics Data System (ADS)

    Cathelinaud, Michel; Lemarquis, Frédéric; Torchio, Philippe; Amra, Claude

    2017-11-01

    This paper describes the design and manufacture of broadband metal dielectric absorbers. First, we give some design principles to obtain achromatic absorption properties. Then, we describe a new method to determine the complex refractive index of metallic layers. A graded index model is developed to take account of the evolution of the film packing density. Manufacturing is detailed in the last section. Absorption levels higher than 99.9% have been measured over the visible range.

  15. High-performance oxygen reduction and evolution carbon catalysis: From mechanistic studies to device integration

    DOE PAGES

    To, John W. F.; Ng, Jia Wei Desmond; Siahrostami, Samira; ...

    2016-11-30

    The development of high-performance and low-cost oxygen reduction and evolution catalysts that can be easily integrated into existing devices is crucial for the wide deployment of energy storage systems that utilize O 2-H 2O chemistries, such as regenerative fuel cells and metal-air batteries. Herein, we report an NH 3-activated N-doped hierarchical carbon (NHC) catalyst synthesized via a scalable route, and demonstrate its device integration. The NHC catalyst exhibited good performance for both the oxygen reduction reaction (ORR) and the oxygen evolution reaction (OER), as demonstrated by means of electrochemical studies and evaluation when integrated into the oxygen electrode of amore » regenerative fuel cell. The activities observed for both the ORR and the OER were comparable to those achieved by state-of-the-art Pt and Ir catalysts in alkaline environments. We have further identified the critical role of carbon defects as active sites for electrochemical activity through density functional theory calculations and high-resolution TEM visualization. As a result, this work highlights the potential of NHC to replace commercial precious metals in regenerative fuel cells and possibly metal-air batteries for cost-effective storage of intermittent renewable energy.« less

  16. High-performance oxygen reduction and evolution carbon catalysis: From mechanistic studies to device integration

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    To, John W. F.; Ng, Jia Wei Desmond; Siahrostami, Samira

    The development of high-performance and low-cost oxygen reduction and evolution catalysts that can be easily integrated into existing devices is crucial for the wide deployment of energy storage systems that utilize O 2-H 2O chemistries, such as regenerative fuel cells and metal-air batteries. Herein, we report an NH 3-activated N-doped hierarchical carbon (NHC) catalyst synthesized via a scalable route, and demonstrate its device integration. The NHC catalyst exhibited good performance for both the oxygen reduction reaction (ORR) and the oxygen evolution reaction (OER), as demonstrated by means of electrochemical studies and evaluation when integrated into the oxygen electrode of amore » regenerative fuel cell. The activities observed for both the ORR and the OER were comparable to those achieved by state-of-the-art Pt and Ir catalysts in alkaline environments. We have further identified the critical role of carbon defects as active sites for electrochemical activity through density functional theory calculations and high-resolution TEM visualization. As a result, this work highlights the potential of NHC to replace commercial precious metals in regenerative fuel cells and possibly metal-air batteries for cost-effective storage of intermittent renewable energy.« less

  17. Pilot Test of an Integrated Sexual Risk Reduction Intervention for Women with a History of Childhood Sexual Abuse.

    PubMed

    Senn, Theresa E; Braksmajer, Amy; Urban, Marguerite A; Coury-Doniger, Patricia; Carey, Michael P

    2017-11-01

    HIV and childhood sexual abuse (CSA) are intersecting public health problems for women. We pilot tested an integrated sexual risk reduction intervention for women with a history of CSA that addressed both the consequences of CSA [based on the Traumagenic Dynamics (TD) framework] and the antecedents of sexual risk behavior (based on the Information-Motivation-Behavioral Skills [IMB] model). Women with a history of CSA who were attending a public STI clinic (n = 84) were randomly assigned to a five-session integrated TD/IMB (experimental) group intervention or to a time-matched IMB-guided sexual risk reduction (control) group intervention. Preliminary findings indicated that women in the integrated TD/IMB intervention reduced their average number of episodes of unprotected sex with a primary partner, their alcohol use, and their likelihood of being in a violent relationship, relative to women in the IMB-only group. Our findings suggest that sexual risk reduction interventions that address both the consequences of CSA and the antecedents of sexual risk behavior may be efficacious in reducing sexual risk behavior among women who were sexually abused.

  18. Integrated Biological Warfare Technology Platform (IBWTP). Intelligent Software Supporting Situation Awareness, Response, and Operations

    DTIC Science & Technology

    2007-01-01

    15 4.2.3. Users of Systems for Combating Biological Warfare ................................ 16 4.2.4...21 4.3.1. Existing Biosurveillance Systems .............................................................. 22 4.3.2. Automatic Integration...74 6.4.4. Multi-Agent System Management System (MMS).................................... 75 6.4.5. Agent Glossary

  19. The CHARIS Integral Field Spectrograph with SCExAO: Data Reduction and Performance

    NASA Astrophysics Data System (ADS)

    Kasdin, N. Jeremy; Groff, Tyler; Brandt, Timothy; Currie, Thayne; Rizzo, Maxime; Chilcote, Jeffrey K.; Guyon, Olivier; Jovanovic, Nemanja; Lozi, Julien; Norris, Barnaby; Tamura, Motohide

    2018-01-01

    We summarize the data reduction pipeline and on-sky performance of the CHARIS Integral Field Spectrograph behind the SCExAO Adaptive Optics system on the Subaru Telescope. The open-source pipeline produces data cubes from raw detector reads using a Χ^2-based spectral extraction technique. It implements a number of advances, including a fit to the full nonlinear pixel response, suppression of up to a factor of ~2 in read noise, and deconvolution of the spectra with the line-spread function. The CHARIS team is currently developing the calibration and postprocessing software that will comprise the second component of the data reduction pipeline. Here, we show a range of CHARIS images, spectra, and contrast curves produced using provisional routines. CHARIS is now characterizing exoplanets simultaneously across the J, H, and K bands.

  20. Improved determination of particulate absorption from combined filter pad and PSICAM measurements.

    PubMed

    Lefering, Ina; Röttgers, Rüdiger; Weeks, Rebecca; Connor, Derek; Utschig, Christian; Heymann, Kerstin; McKee, David

    2016-10-31

    Filter pad light absorption measurements are subject to two major sources of experimental uncertainty: the so-called pathlength amplification factor, β, and scattering offsets, o, for which previous null-correction approaches are limited by recent observations of non-zero absorption in the near infrared (NIR). A new filter pad absorption correction method is presented here which uses linear regression against point-source integrating cavity absorption meter (PSICAM) absorption data to simultaneously resolve both β and the scattering offset. The PSICAM has previously been shown to provide accurate absorption data, even in highly scattering waters. Comparisons of PSICAM and filter pad particulate absorption data reveal linear relationships that vary on a sample by sample basis. This regression approach provides significantly improved agreement with PSICAM data (3.2% RMS%E) than previously published filter pad absorption corrections. Results show that direct transmittance (T-method) filter pad absorption measurements perform effectively at the same level as more complex geometrical configurations based on integrating cavity measurements (IS-method and QFT-ICAM) because the linear regression correction compensates for the sensitivity to scattering errors in the T-method. This approach produces accurate filter pad particulate absorption data for wavelengths in the blue/UV and in the NIR where sensitivity issues with PSICAM measurements limit performance. The combination of the filter pad absorption and PSICAM is therefore recommended for generating full spectral, best quality particulate absorption data as it enables correction of multiple errors sources across both measurements.

  1. Energy transmission transformer for a wireless capsule endoscope: analysis of specific absorption rate and current density in biological tissue.

    PubMed

    Shiba, Kenji; Nagato, Tomohiro; Tsuji, Toshio; Koshiji, Kohji

    2008-07-01

    This paper reports on the electromagnetic influences on the analysis of biological tissue surrounding a prototype energy transmission system for a wireless capsule endoscope. Specific absorption rate (SAR) and current density were analyzed by electromagnetic simulator in a model consisting of primary coil and a human trunk including the skin, fat, muscle, small intestine, backbone, and blood. First, electric and magnetic strength in the same conditions as the analytical model were measured and compared to the analytical values to confirm the validity of the analysis. Then, SAR and current density as a function of frequency and output power were analyzed. The validity of the analysis was confirmed by comparing the analytical values with the measured ones. The SAR was below the basic restrictions of the International Commission on Nonionizing Radiation Protection (ICNIRP). At the same time, the results for current density show that the influence on biological tissue was lowest in the 300-400 kHz range, indicating that it was possible to transmit energy safely up to 160 mW. In addition, we confirmed that the current density has decreased by reducing the primary coil's current.

  2. Deterministic Integration of Biological and Soft Materials onto 3D Microscale Cellular Frameworks

    PubMed Central

    McCracken, Joselle M.; Xu, Sheng; Badea, Adina; Jang, Kyung-In; Yan, Zheng; Wetzel, David J.; Nan, Kewang; Lin, Qing; Han, Mengdi; Anderson, Mikayla A.; Lee, Jung Woo; Wei, Zijun; Pharr, Matt; Wang, Renhan; Su, Jessica; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2018-01-01

    Complex 3D organizations of materials represent ubiquitous structural motifs found in the most sophisticated forms of matter, the most notable of which are in life-sustaining hierarchical structures found in biology, but where simpler examples also exist as dense multilayered constructs in high-performance electronics. Each class of system evinces specific enabling forms of assembly to establish their functional organization at length scales not dissimilar to tissue-level constructs. This study describes materials and means of assembly that extend and join these disparate systems—schemes for the functional integration of soft and biological materials with synthetic 3D microscale, open frameworks that can leverage the most advanced forms of multilayer electronic technologies, including device-grade semiconductors such as monocrystalline silicon. Cellular migration behaviors, temporal dependencies of their growth, and contact guidance cues provided by the nonplanarity of these frameworks illustrate design criteria useful for their functional integration with living matter (e.g., NIH 3T3 fibroblast and primary rat dorsal root ganglion cell cultures). PMID:29552634

  3. “Turn-on” fluorescence probe integrated polymer nanoparticles for sensing biological thiol molecules

    NASA Astrophysics Data System (ADS)

    Ang, Chung Yen; Tan, Si Yu; Lu, Yunpeng; Bai, Linyi; Li, Menghuan; Li, Peizhou; Zhang, Quan; Selvan, Subramanian Tamil; Zhao, Yanli

    2014-11-01

    A ``turn-on'' thiol-responsive fluorescence probe was synthesized and integrated into polymeric nanoparticles for sensing intracellular thiols. There is a photo-induced electron transfer process in the off state of the probe, and this process is terminated upon the reaction with thiol compounds. Configuration interaction singles (CIS) calculation was performed to confirm the mechanism of this process. A series of sensing studies were carried out, showing that the probe-integrated nanoparticles were highly selective towards biological thiol compounds over non-thiolated amino acids. Kinetic studies were also performed to investigate the relative reaction rate between the probe and the thiolated amino acids. Subsequently, the Gibbs free energy of the reactions was explored by means of the electrochemical method. Finally, the detection system was employed for sensing intracellular thiols in cancer cells, and the sensing selectivity could be further enhanced with the use of a cancer cell-targeting ligand in the nanoparticles. This development paves a path for the sensing and detection of biological thiols, serving as a potential diagnostic tool in the future.

  4. Aqueous glucose measurement using differential absorption-based frequency domain optical coherence tomography at wavelengths of 1310 nm and 1625 nm

    NASA Astrophysics Data System (ADS)

    John, Pauline; Manoj, Murali; Sujatha, N.; Vasa, Nilesh J.; Rao, Suresh R.

    2015-07-01

    This work presents a combination of differential absorption technique and frequency domain optical coherence tomography for detection of glucose, which is an important analyte in medical diagnosis of diabetes. Differential absorption technique is used to detect glucose selectively in the presence of interfering species especially water and frequency domain optical coherence tomography (FDOCT) helps to obtain faster acquisition of depth information. Two broadband super-luminescent diode (SLED) sources with centre wavelengths 1586 nm (wavelength range of 1540 to 1640 nm) and 1312 nm (wavelength range of 1240 to 1380 nm) and a spectral width of ≍ 60 nm (FWHM) are used. Preliminary studies on absorption spectroscopy using various concentrations of aqueous glucose solution gave promising results to distinguish the absorption characteristics of glucose at two wavelengths 1310 nm (outside the absorption band of glucose) and 1625 nm (within the absorption band of glucose). In order to mimic the optical properties of biological skin tissue, 2% and 10% of 20% intralipid with various concentrations of glucose (0 to 4000 mg/dL) was prepared and used as sample. Using OCT technique, interference spectra were obtained using an optical spectrum analyzer with a resolution of 0.5 nm. Further processing of the interference spectra provided information on reflections from the surfaces of the cuvette containing the aqueous glucose sample. Due to the absorption of glucose in the wavelength range of 1540 nm to 1640 nm, a trend of reduction in the intensity of the back reflected light was observed with increase in the concentration of glucose.

  5. Biological reduction of uranium coupled with oxidation of ammonium by Acidimicrobiaceae bacterium A6 under iron reducing conditions.

    PubMed

    Gilson, Emily R; Huang, Shan; Jaffé, Peter R

    2015-11-01

    This study investigated the possibility of links between the biological immobilization of uranium (U) and ammonium oxidation under iron (Fe) reducing conditions. The recently-identified Acidimicrobiaceae bacterium A6 (ATCC, PTA-122488) derives energy from ammonium oxidation coupled with Fe reduction. This bacterium has been found in various soil and wetland environments, including U-contaminated wetland sediments. Incubations of Acidimicrobiaceae bacteria A6 with nontronite, an Fe(III)-rich clay, and approximately 10 µM U indicate that these bacteria can use U(VI) in addition to Fe(III) as an electron acceptor in the presence of ammonium. Measurements of Fe(II) production and ammonium oxidation support this interpretation. Concentrations of approximately 100 µM U were found to entirely inhibit Acidimicrobiaceae bacteria A6 activity. These results suggest that natural sites of active ammonium oxidation under Fe reducing conditions by Acidimicrobiaceae bacteria A6 could be hotspots of U immobilization by bioreduction. This is the first report of biological U reduction that is not coupled to carbon oxidation.

  6. Promoting Student Learning through the Integration of Lab and Lecture: The Seamless Biology Curriculum

    ERIC Educational Resources Information Center

    Burrowes, Patricia; Nazario, Gladys

    2008-01-01

    The authors engaged in an education experiment to determine if the integration of lab and lecture activities in zoology and botany proved beneficial to student learning and motivation toward biology. Their results revealed that this strategy positively influenced students' academic achievement, conceptual understanding, and ability to apply…

  7. Ontology-supported Research on Vaccine Efficacy, Safety, and Integrative Biological Networks

    PubMed Central

    He, Yongqun

    2016-01-01

    Summary While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including the Vaccine Ontology, Ontology of Adverse Events, and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network (“OneNet”) Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms. PMID:24909153

  8. Structurally Integrated Photoluminescent Chemical and Biological Sensors: An Organic Light-Emitting Diode-Based Platform

    NASA Astrophysics Data System (ADS)

    Shinar, J.; Shinar, R.

    The chapter describes the development, advantages, challenges, and potential of an emerging, compact photoluminescence-based sensing platform for chemical and biological analytes, including multiple analytes. In this platform, the excitation source is an array of organic light-emitting device (OLED) pixels that is structurally integrated with the sensing component. Steps towards advanced integration with additionally a thin-film-based photodetector are also described. The performance of the OLED-based sensing platform is examined for gas-phase and dissolved oxygen, glucose, lactate, ethanol, hydrazine, and anthrax lethal factor.

  9. Analysis of current density and specific absorption rate in biological tissue surrounding an air-core type of transcutaneous transformer for an artificial heart.

    PubMed

    Shiba, Kenji; Nukaya, Masayuki; Tsuji, Toshio; Koshiji, Kohji

    2006-01-01

    This paper reports on the specific absorption rate (SAR) and the current density analysis of biological tissue surrounding an air-core type of transcutaneous transformer for an artificial heart. The electromagnetic field in the biological tissue surrounding the transformer was analyzed by the transmission-line modeling method, and the SAR and current density as a function of frequency (200k-1 MHz) for a transcutaneous transmission of 20 W were calculated. The model's biological tissue has three layers including the skin, fat and muscle. As a result, the SAR in the vicinity of the transformer is sufficiently small and the normalized SAR value, which is divided by the ICNIRP's basic restriction, is 7 x 10(-3) or less. On the contrary, the current density is slightly in excess of the ICNIRP's basic restrictions as the frequency falls and the output voltage rises. Normalized current density is from 0.2 to 1.2. In addition, the layer in which the current's density is maximized depends on the frequency, the muscle in the low frequency (<700 kHz) and the skin in the high frequency (>700 kHz). The result shows that precision analysis taking into account the biological properties is very important for developing the transcutaneous transformer for TAH.

  10. Fish gelatin thin film standards for biological application of PIXE

    NASA Astrophysics Data System (ADS)

    Manuel, Jack E.; Rout, Bibhudutta; Szilasi, Szabolcs Z.; Bohara, Gyanendra; Deaton, James; Luyombya, Henry; Briski, Karen P.; Glass, Gary A.

    2014-08-01

    There exists a critical need to understand the flow and accumulation of metallic ions, both naturally occurring and those introduced to biological systems. In this paper the results of fabricating thin film elemental biological standards containing nearly any combination of trace elements in a protein matrix are presented. Because it is capable of high elemental sensitivity, particle induced X-ray emission spectrometry (PIXE) is an excellent candidate for in situ analysis of biological tissues. Additionally, the utilization of microbeam PIXE allows the determination of elemental concentrations in and around biological cells. However, obtaining elemental reference standards with the same matrix constituents as brain tissue is difficult. An excellent choice for simulating brain-like tissue is Norland® photoengraving glue which is derived from fish skin. Fish glue is water soluble, liquid at room temperature, and resistant to dilute acid. It can also be formed into a thin membrane which dries into a durable, self-supporting film. Elements of interest are introduced to the fish glue in precise volumetric additions of well quantified atomic absorption standard solutions. In this study GeoPIXE analysis package is used to quantify elements intrinsic to the fish glue as well as trace amounts of manganese added to the sample. Elastic (non-Rutherford) backscattered spectroscopy (EBS) and the 1.734 MeV proton-on-carbon 12C(p,p)12C resonance is used for a normalization scheme of the PIXE spectra to account for any discrepancies in X-ray production arising from thickness variation of the prepared standards. It is demonstrated that greater additions of the atomic absorption standard cause a viscosity reduction of the liquid fish glue resulting in thinner films but the film thickness can be monitored by using simultaneous PIXE and EBS proton data acquisition.

  11. UV-H2O2 based AOP and its integration with biological activated carbon treatment for DBP reduction in drinking water.

    PubMed

    Toor, Ramn; Mohseni, Madjid

    2007-02-01

    The presence of disinfection byproducts (DBPs) such as trihalomethanes (THMs) and haloacetic acids (HAAs) in drinking water is of great concern due to their adverse effects on human health. Emerging regulation limiting the concentration of DBPs in drinking water has increased demands for technologies and processes which reduce the formation of DBPs in drinking water. In this study, UV-H2O2 based advance oxidation process (AOP) was used to treat raw surface water. Experiments were conducted using low pressure mercury vapor UV lamps in collimated beam and flow-through annular photoreactors. The effect of UV fluence (0-3500 mJ cm(-2)) and hydrogen peroxide concentration (0-23 mg l(-1)) in reducing the concentration of THMs and HAAs was examined. The UV-H2O2 AOP was then coupled with a downstream biological activated carbon (BAC) treatment to assess the synergetic benefits of combining the two treatments. It was observed that UV-H2O2 AOP was only effective at reducing DBPs at UV fluences of more than 1000 mJ cm(-2) and initial H2O2 concentrations of about or greater than 23 mg l(-1). However, the combined AOP-BAC treatment showed significant reductions of 43%, 52%, and 59% relative to untreated raw water for DBPs, TOC, and UV254, respectively.

  12. Impaired absorption of marked oligopeptide Glycine-I Tyrosine-Glycine after successful autologous-allotopic ileal mucosa transplantation in beagles.

    PubMed

    Beiler, H A; Steinorth, J; Witt, A; Mier, W; Mohammed, A; Waag, K L; Zachariou, Z

    2004-10-01

    After establishing a method for ileal mucosa transplantation in an animal model, the authors investigated the absorptive capacity for oligopeptides of the transplanted mucosa. In 14 beagle dogs the authors transplanted ileal mucosa in a vascularized demucosed segment of the transverse colon. The colonic wall-ileal mucosa complex then was integrated in the ileal continuity. Six animals were lost owing to operative complications. Absorptive capacity for oligopeptides was measured in the remaining 8 animals with the iodine 131 (131I)-marked tripeptide glycine-tyrosine-glycine before and 4 weeks after transplantation. The results were compared and analyzed with the Student's t test for matched pairs. Blood concentrations of the marked tripeptide with P value less than .05 were considered as a significant reduction in the absorptive capacity of the transplanted ileal mucosa. After fixation with glutaraldehyd graft, uptake of the colonic wall-ileal mucosa complex was evaluated histologically in 8 animals. In all 8 animals, a 100% graft uptake was verified in all sections. Fifteen minutes after application of 15 MBc Glycine-131I-Tyrosine-Glycine there was no significant difference in the absorption between normal and transplanted ileal mucosa. After 30 minutes, the absorption of the transplanted ileal mucosa showed a tendency (P < .1) for an impaired uptake of the marked tripeptide. However, 60 minutes after application the difference in the absorptive capacity of the transplanted ileal mucosa was significant (P < .05). Autologous allotopic ileal mucosa transplantation is feasible; however, an impaired absorption of oligopeptides of the transplanted mucosa 4 weeks after transplantation could be observed.

  13. [Dosimetric aspects in studying the biological action of nonionizing electromagnetic radiation].

    PubMed

    Karpov, V N; Galkin, A A; Davydov, B I

    1984-01-01

    In order to clarify mechanisms of biological reactions, it is very important to study the absorption and spatial distribution of the absorbed electromagnetic energy. The procedures and methods of calculating the electromagnetic energy absorption of biological specimens exposed to nonionizing electromagnetic irradiation in a wide frequency range (0-300 GHz) are described. Also presented are formulas and plots to be used in calculating the specific absorption of the dose rate by biological specimens, with the inclusion of resonance absorption, polarization of the incident electromagnetic wave, presence of reflecting surfaces and grounding. The extrapolation of the average energy absorption from one animal species to another and to man is discussed, assuming that spatial and energy distributions are equivalent. The notion of the irradiation quality coefficient is introduced. The magnitudes of the coefficients are given as related to the irradiation frequency and polarization type. A mathematical relation is offered to determine the safety of a complex spectrum of electromagnetic irradiation. The relation takes into consideration different dimensionality of the parameters of the electromagnetic field in the low- and high-frequency ranges.

  14. [Integration of clinical and biological data in clinical practice using bioinformatics].

    PubMed

    Coltell, Oscar; Arregui, María; Fabregat, Antonio; Portolés, Olga

    2008-05-01

    The aim of our work is to describe essential aspects of Medical Informatics, Bioinformatics and Biomedical Informatics, that are used in biomedical research and clinical practice. These disciplines have emerged from the need to find new scientific and technical approaches to manage, store, analyze and report data generated in clinical practice and molecular biology and other medical specialties. It can be also useful to integrate research information generated in different areas of health care. Moreover, these disciplines are interdisciplinary and integrative, two key features not shared by other areas of medical knowledge. Finally, when Bioinformatics and Biomedical Informatics approach to medical investigation and practice are applied, a new discipline, called Clinical Bioinformatics, emerges. The latter requires a specific training program to create a new professional profile. We have not been able to find a specific training program in Clinical Bioinformatics in Spain.

  15. Integration and macroevolutionary patterns in the pollination biology of conifers.

    PubMed

    Leslie, Andrew B; Beaulieu, Jeremy M; Crane, Peter R; Knopf, Patrick; Donoghue, Michael J

    2015-06-01

    Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. To explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face downward at pollination, and the production of a liquid droplet that buoyant grains float through to enter the ovule. We use a well-sampled phylogeny of conifers to test correlated evolution among these characters and specific sequences of character change. Using likelihood models of character evolution, we find that pollen morphology and ovule characters evolve in a concerted manner, where the flotation mechanism breaks down irreversibly following changes in orientation or drop production. The breakdown of this functional constraint, which may be facilitated by the lack of developmental integration among the constituent traits, is associated with increased trait variation and more diverse pollination strategies. Although this functional "release" increases diversity in some ways, the irreversible way in which the flotation mechanism is lost may eventually result in its complete disappearance from seed plant reproductive biology. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  16. A semantic web framework to integrate cancer omics data with biological knowledge

    PubMed Central

    2012-01-01

    Background The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. Results For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. Conclusions We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily. PMID:22373303

  17. A semantic web framework to integrate cancer omics data with biological knowledge.

    PubMed

    Holford, Matthew E; McCusker, James P; Cheung, Kei-Hoi; Krauthammer, Michael

    2012-01-25

    The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily.

  18. Topical absorption and toxicity studies of jet fuel hydrocarbons in skin

    NASA Astrophysics Data System (ADS)

    Muhammad, Faqir

    Kerosene-based fuels have been used for many decades. Over 2 million military and civilian personnel each year are occupationally exposed to various jet fuel mixtures. Dermatitis is one of the major health concerns associated with these exposures. In the past, separate absorption and toxicity studies have been conducted to find the etiology of such skin disorders. There was a need for integrated absorption and toxicity studies to define the causative constituents of jet fuel responsible for skin irritation. The focus of this thesis was to study the percutaneous absorption and to identify the hydrocarbons (HC) causing irritation in jet fuels so that preventive measures could be taken in the future. The initial study was conducted to understand the possible mechanism for additive interactions on hydrocarbon absorption/disposition in silastic, porcine skin and isolated perfused porcine skin flap (IPPSF) models. The influence of JP-8 (100) additives (MDA, BHT, 8Q405) on the dermal kinetics of 14C-naphthalene and 14C/3H-dodecane as markers of HC absorption was evaluated. This study indicated that individual and combination of additives influenced marker disposition in different membranes. MDA was a significant suppressor while BHT was a significant enhancer of naphthalene absorption in IPPSF. The 8Q405 significantly reduced naphthalene content in dosed silastic and skin indicating a direct interaction between additive and marker HC. Similarly, the individual MDA and BHT significantly retained naphthalene in the stratum corneum of porcine skin, but the combination of both of these additives statistically decreased the marker retention in the stratum corneum suggesting a potential biological interaction. This study concluded that all components of a chemical mixture should be assessed since the effects of single components administered alone or as pairs may be confounded when all are present in the complete mixture. However, this study indicated that the marker HC

  19. 2-Micron Triple-Pulse Integrated Path Differential Absorption Lidar Development for Simultaneous Airborne Column Measurements of Carbon Dioxide and Water Vapor in the Atmosphere

    NASA Technical Reports Server (NTRS)

    Singh, Upendra N.; Petros, Mulugeta; Refaat, Tamer F.; Yu, Jirong

    2016-01-01

    For more than 15 years, NASA Langley Research Center (LaRC) has contributed in developing several 2-micron carbon dioxide active remote sensors using the DIAL technique. Currently, an airborne 2-micron triple-pulse integrated path differential absorption (IPDA) lidar is under development at NASA LaRC. This paper focuses on the advancement of the 2-micron triple-pulse IPDA lidar development. Updates on the state-of-the-art triple-pulse laser transmitter will be presented including the status of wavelength control, packaging and lidar integration. In addition, receiver development updates will also be presented, including telescope integration, detection systems and data acquisition electronics. Future plan for IPDA lidar system for ground integration, testing and flight validation will be presented.

  20. Recent Progress in Electromagnetic Absorption and Dosimetry in Biological Systems.

    DTIC Science & Technology

    1978-12-21

    AEROSPACE M!DICAL RESEARCH LABORATORY NAVAL AIR STATION PENSACOLA, FLORIDA 32508 L4 oj6L I SUMMARY PAGE Ti9(PROSLEM Dosimetry , as a subset of research In...absonce of sound dosimetry design, lacks credibility. This study provides a usable orientation in present and future dosimetric technology through a...leading experiment; while at other times experimental results lead the way. Progress In absorption and dosimetry Is still urderway, and higher degrees

  1. Non-target time trend screening: a data reduction strategy for detecting emerging contaminants in biological samples.

    PubMed

    Plassmann, Merle M; Tengstrand, Erik; Åberg, K Magnus; Benskin, Jonathan P

    2016-06-01

    Non-targeted mass spectrometry-based approaches for detecting novel xenobiotics in biological samples are hampered by the occurrence of naturally fluctuating endogenous substances, which are difficult to distinguish from environmental contaminants. Here, we investigate a data reduction strategy for datasets derived from a biological time series. The objective is to flag reoccurring peaks in the time series based on increasing peak intensities, thereby reducing peak lists to only those which may be associated with emerging bioaccumulative contaminants. As a result, compounds with increasing concentrations are flagged while compounds displaying random, decreasing, or steady-state time trends are removed. As an initial proof of concept, we created artificial time trends by fortifying human whole blood samples with isotopically labelled standards. Different scenarios were investigated: eight model compounds had a continuously increasing trend in the last two to nine time points, and four model compounds had a trend that reached steady state after an initial increase. Each time series was investigated at three fortification levels and one unfortified series. Following extraction, analysis by ultra performance liquid chromatography high-resolution mass spectrometry, and data processing, a total of 21,700 aligned peaks were obtained. Peaks displaying an increasing trend were filtered from randomly fluctuating peaks using time trend ratios and Spearman's rank correlation coefficients. The first approach was successful in flagging model compounds spiked at only two to three time points, while the latter approach resulted in all model compounds ranking in the top 11 % of the peak lists. Compared to initial peak lists, a combination of both approaches reduced the size of datasets by 80-85 %. Overall, non-target time trend screening represents a promising data reduction strategy for identifying emerging bioaccumulative contaminants in biological samples. Graphical abstract

  2. Drug-nutrient interactions: inhibition of amino acid intestinal absorption by fluoxetine.

    PubMed

    Urdaneta, E; Idoate, I; Larralde, J

    1998-05-01

    Fluoxetine is one of the most widely used antidepressants and nowadays it is also being used to manage obesity problems. In our laboratory we demonstrated that the drug inhibited sugar absorption (Monteiro et al. 1993). The aim of the present work was to determine the effect of fluoxetine on intestinal leucine absorption. Using a procedure of successive absorptions in vivo the drug diminished amino acid absorption by 30% (P < 0.001). Experiments in vitro in isolated jejunum also revealed a reduction in leucine uptake of 37% (P < 0.001). In both cases fluoxetine only affected mediated transport without altering diffusion. In a preparation enriched in basolateral membrane, fluoxetine inhibited the Na+,K(+)-ATPase (EC 3.6.1.37) activity (55%; P < 0.001) in a non-competitive manner with an inhibition constant (Ki) value of 0.92 mM. Leucine uptake by brush-border membrane vesicles was diminished by the drug (a reduction of 48% was observed at 30s, P < 0.001); only the apical Na(+)-dependent transport system of the amino acid was modified and the inhibition was non-competitive. Leucine uptake in the presence of lysine indicated that transporter B was involved. These results suggest that fluoxetine reduces leucine absorption by its action on the basolateral and apical membrane of the enterocyte; the nutritional status of the patients under drug treatment may be affected as neutral amino acid absorption is decreased.

  3. CHOmine: an integrated data warehouse for CHO systems biology and modeling

    PubMed Central

    Hanscho, Michael; Ruckerbauer, David E.; Zanghellini, Jürgen; Borth, Nicole

    2017-01-01

    Abstract The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. Database URL: http://www.chogenome.org PMID:28605771

  4. CHOmine: an integrated data warehouse for CHO systems biology and modeling.

    PubMed

    Gerstl, Matthias P; Hanscho, Michael; Ruckerbauer, David E; Zanghellini, Jürgen; Borth, Nicole

    2017-01-01

    The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. http://www.chogenome.org. © The Author(s) 2017. Published by Oxford University Press.

  5. Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

    PubMed

    Zong, Nobel C; Li, Haomin; Li, Hua; Lam, Maggie P Y; Jimenez, Rafael C; Kim, Christina S; Deng, Ning; Kim, Allen K; Choi, Jeong Ho; Zelaya, Ivette; Liem, David; Meyer, David; Odeberg, Jacob; Fang, Caiyun; Lu, Hao-Jie; Xu, Tao; Weiss, James; Duan, Huilong; Uhlen, Mathias; Yates, John R; Apweiler, Rolf; Ge, Junbo; Hermjakob, Henning; Ping, Peipei

    2013-10-12

    Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

  6. "Integrating Concepts in Biology" Textbook Increases Learning: Assessment Triangulation Using Concept Inventory, Card Sorting, and MCAT Instruments, Followed by Longitudinal Tracking

    ERIC Educational Resources Information Center

    Luckie, Douglas B.; Hoskinson, Anne-Marie; Griffin, Caleigh E.; Hess, Andrea L.; Price, Katrina J.; Tawa, Alex; Thacker, Samantha M.

    2017-01-01

    The purpose of this study was to examine the educational impact of an intervention, the inquiry-focused textbook "Integrating Concepts in Biology" ("ICB"), when used in a yearlong introductory biology course sequence. Student learning was evaluated using three published instruments: 1) The Biology Concept Inventory probed depth…

  7. Phytosterol glycosides reduce cholesterol absorption in humans

    PubMed Central

    Lin, Xiaobo; Ma, Lina; Racette, Susan B.; Anderson Spearie, Catherine L.; Ostlund, Richard E.

    2009-01-01

    Dietary phytosterols inhibit intestinal cholesterol absorption and regulate whole body cholesterol excretion and balance. However, they are biochemically heterogeneous and a portion is glycosylated in some foods with unknown effects on biological activity. We tested the hypothesis that phytosterol glycosides reduce cholesterol absorption in humans. Phytosterol glycosides were extracted and purified from soy lecithin in a novel two-step process. Cholesterol absorption was measured in a series of three single-meal tests given at intervals of 2 wk to each of 11 healthy subjects. In a randomized crossover design, participants received ∼300 mg of added phytosterols in the form of phytosterol glycosides or phytosterol esters, or placebo in a test breakfast also containing 30 mg cholesterol-d7. Cholesterol absorption was estimated by mass spectrometry of plasma cholesterol-d7 enrichment 4–5 days after each test. Compared with the placebo test, phytosterol glycosides reduced cholesterol absorption by 37.6 ± 4.8% (P < 0.0001) and phytosterol esters 30.6 ± 3.9% (P = 0.0001). These results suggest that natural phytosterol glycosides purified from lecithin are bioactive in humans and should be included in methods of phytosterol analysis and tables of food phytosterol content. PMID:19246636

  8. Inelastic losses in X-ray absorption theory

    NASA Astrophysics Data System (ADS)

    Campbell, Luke Whalin

    There is a surprising lack of many body effects observed in XAS (X-ray Absorption Spectroscopy) experiments. While collective excitations and other satellite effects account for between 20% and 40% of the spectral weight of the core hole and photoelectron excitation spectrum, the only commonly observed many body effect is a relatively structureless amplitude reduction to the fine structure, typically no more than a 10% effect. As a result, many particle effects are typically neglected in the XAS codes used to predict and interpret modern experiments. To compensate, the amplitude reduction factor is simply fitted to experimental data. In this work, a quasi-boson model is developed to treat the case of XAS, when the system has both a photoelectron and a core hole. We find that there is a strong interference between the extrinsic and intrinsic losses. The interference reduces the excitation amplitudes at low energies where the core hole and photo electron induced excitations tend to cancel. At high energies, the interference vanishes, and the theory reduces to the sudden approximation. The x-ray absorption spectrum including many-body excitations is represented by a convolution of the one-electron absorption spectrum with an energy dependent spectral function. The latter has an asymmetric quasiparticle peak and broad satellite structure. The net result is a phasor sum, which yields the many body amplitude reduction and phase shift of the fine structure oscillations (EXAFS), and possibly additional satellite structure. Calculations for several cases of interest are found to be in reasonable agreement with experiment. Edge singularity effects and deviations from the final state rule arising from this theory are also discussed. The ab initio XAS code FEFF has been extended for calculations of the many body amplitude reduction and phase shift in x-ray spectroscopies. A new broadened plasmon pole self energy is added. The dipole matrix elements are modified to include a

  9. Characterizing caged molecules through flash photolysis and transient absorption spectroscopy.

    PubMed

    Kao, Joseph P Y; Muralidharan, Sukumaran

    2013-01-01

    Caged molecules are photosensitive molecules with latent biological activity. Upon exposure to light, they are rapidly transformed into bioactive molecules such as neurotransmitters or second messengers. They are thus valuable tools for using light to manipulate biology with exceptional spatial and temporal resolution. Since the temporal performance of the caged molecule depends critically on the rate at which bioactive molecules are generated by light, it is important to characterize the kinetics of the photorelease process. This is accomplished by initiating the photoreaction with a very brief but intense pulse of light (i.e., flash photolysis) and monitoring the course of the ensuing reactions through various means, the most common of which is absorption spectroscopy. Practical guidelines for performing flash photolysis and transient absorption spectroscopy are described in this chapter.

  10. Osteoconductive carriers for integrated bone repair

    PubMed Central

    Ganey, Timothy; Hutton, William; Meisel, Hans Jörg

    2009-01-01

    Successful bone repair is judged in achieving restitution of space and mechanical integrity, and in regaining function. When the biology or anatomy are insufficient to attain a full repair, therapeutic use of graft material has been used to omit compliance features such as strain tolerance, reduced stiffness, and attenuated strength, and instead promote primary or membranous-type bone formation within the physical approximation of a graft material. The challenge of most conductive materials is that they emerge from a static platform and in placement force the living system to adapt to placement, dimension, different properties, and eventually are only successful in degradation and replacement, or in integration. The synergy and interdependency between adhesion, ECM, and proteolysis are important concepts that must be understood to engineer scaffolds capable of holding up to standards which are more than cell decoration. Moreover, the reactive specificity to loading, degradation, therapeutic delivery during absorption remains a key aim of both academic and industrial designs. Achieving conductivity comes with challenges of best fit integration, delivery, and in integrated modeling. The more liquid is the delivery, the more modular the components, and adaptive the matrix to meeting the intended application, the more likely that the conductivity will not be excluded by the morphology of the injury site. Considerations for osteoconductive materials for bone repair and replacement have developed conceptually and advanced parallel with a better understanding of not only bone biology but of materials science. First models of material replacements utilized a reductionist-constructionist logic; define the constituents of the material in terms of its morphology and chemical composition, and then engineer material with similar content and properties as a means of accommodating a replacement. Unfortunately for biologic systems, empiric formulation is insufficient to promote

  11. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Describes laboratory procedures, demonstrations, and classroom activities/materials, including use of dwarf cichlids (fishes) in secondary school biology, teaching edge effects on stomatal diffusion, computer program on effects of selection on gene frequencies, biological oxidation/reduction reactions, short cuts with Drosophila, computer program…

  12. Water metamaterial for ultra-broadband and wide-angle absorption.

    PubMed

    Xie, Jianwen; Zhu, Weiren; Rukhlenko, Ivan D; Xiao, Fajun; He, Chong; Geng, Junping; Liang, Xianling; Jin, Ronghong; Premaratne, Malin

    2018-02-19

    A subwavelength water metamaterial is proposed and analyzed for ultra-broadband perfect absorption at microwave frequencies. We experimentally demonstrate that this metamaterial shows over 90% absorption within almost the entire frequency band of 12-29.6 GHz. It is also shown that the proposed metamaterial exhibits a good thermal stability with its absorption performance almost unchanged for the temperature range from 0 to 100°C. The study of the angular tolerance of the metamaterial absorber shows its ability of working at wide angles of incidence. Given that the proposed water metamaterial absorber is low-cost and easy for manufacture, we envision it may find numerous applications in electromagnetics such as broadband scattering reduction and electromagnetic energy harvesting.

  13. Effect of iron oxide reductive dissolution on the transformation and immobilization of arsenic in soils: New insights from X-ray photoelectron and X-ray absorption spectroscopy.

    PubMed

    Fan, Jian-Xin; Wang, Yu-Jun; Liu, Cun; Wang, Li-Hua; Yang, Ke; Zhou, Dong-Mei; Li, Wei; Sparks, Donald L

    2014-08-30

    The geochemical behavior and speciation of arsenic (As) in paddy soils is strongly controlled by soil redox conditions and the sequestration by soil iron oxyhydroxides. Hence, the effects of iron oxide reductive dissolution on the adsorption, transformation and precipitation of As(III) and As(V) in soils were investigated using batch experiments and synchrotron based techniques to gain a deeper understanding at both macroscopic and microscopic scales. The results of batch sorption experiments revealed that the sorption capacity of As(V) on anoxic soil was much higher than that on control soil. Synchrotron based X-ray fluorescence (μ-XRF) mapping studies indicated that As was heterogeneously distributed and was mainly associated with iron in the soil. X-ray absorption near edge structure (XANES), micro-X-ray absorption near edge structure (μ-XANES) and X-ray photoelectron spectroscopy (XPS) analyses revealed that the primary speciation of As in the soil is As(V). These results further suggested that, when As(V) was introduced into the anoxic soil, the rapid coprecipitation of As(V) with ferric/ferrous ion prevented its reduction to As(III), and was the main mechanism controlling the immobilization of As. This research could improve the current understanding of soil As chemistry in paddy and wetland soils. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Classification of Time Series Gene Expression in Clinical Studies via Integration of Biological Network

    PubMed Central

    Qian, Liwei; Zheng, Haoran; Zhou, Hong; Qin, Ruibin; Li, Jinlong

    2013-01-01

    The increasing availability of time series expression datasets, although promising, raises a number of new computational challenges. Accordingly, the development of suitable classification methods to make reliable and sound predictions is becoming a pressing issue. We propose, here, a new method to classify time series gene expression via integration of biological networks. We evaluated our approach on 2 different datasets and showed that the use of a hidden Markov model/Gaussian mixture models hybrid explores the time-dependence of the expression data, thereby leading to better prediction results. We demonstrated that the biclustering procedure identifies function-related genes as a whole, giving rise to high accordance in prognosis prediction across independent time series datasets. In addition, we showed that integration of biological networks into our method significantly improves prediction performance. Moreover, we compared our approach with several state-of–the-art algorithms and found that our method outperformed previous approaches with regard to various criteria. Finally, our approach achieved better prediction results on early-stage data, implying the potential of our method for practical prediction. PMID:23516469

  15. Measurement of nitrous acid (HONO) by external-cavity quantum cascade laser based quartz-enhanced photoacoustic absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Yi, Hongming; Maamary, Rabih; Gao, Xiaoming; Sigrist, Markus W.; Fertein, Eric; Chen, Weidong

    2016-04-01

    Spectroscopic detection of short-lived gaseous nitrous acid (HONO) at 1254.85 cm-1 was realized by off-beam coupled quartz-enhanced photoacoustic spectroscopy (QEPAS) in conjunction with an external cavity quantum cascade lasers (EC-QCL). High sensitivity monitoring of HONO was performed within a very small gas-sample volume (of ~40 mm3) allowing a significant reduction (of about 4 orders of magnitude) of air sampling residence time which is highly desired for accurate quantification of chemically reactive short-lived species. Calibration of the developed QEPAS-based HONO sensor was carried out by means of lab-generated HONO samples whose concentrations were determined by simultaneous measurements of direct HONO absorption spectra in a 109.5 m multipass cell using a distributed feedback (DBF) QCL. A minimum detection limit (MDL @ SNR=1) of 66 ppbv HONO was achieved at 70 mbar using a laser output power of 50 mW and 1 s integration time, which corresponded to a normalized noise equivalent absorption coefficient of 3.6×10-8 cm-1.W/Hz1/2. This MDL was down to 7 ppbv at the optimal integration time of 150 s. The corresponding minimum detected absorption coefficient (SNR=1) is ~1.1×10-7 cm-1 (MDL: ~3 ppbv) in 1 s and ~1.1×10-8 cm-1 (MDL~330 pptv) in 150 s, respectively, with 1 W laser power. Acknowledgements The authors acknowledge financial supports from the CaPPA project (ANR-10-LABX-005) and the CPER CLIMIBIO program. References H. Yi, R. Maamary, X. Gao, M. W. Sigrist, E. Fertein, W. Chen, "Short-lived species detection of nitrous acid by external-cavity quantum cascade laser based quartz-enhanced photoacoustic absorption spectroscopy", Appl. Phys. Lett. 106 (2015) 101109

  16. Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible.

    PubMed

    McKemmish, Laura K; Reimers, Jeffrey R; McKenzie, Ross H; Mark, Alan E; Hush, Noel S

    2009-08-01

    Penrose and Hameroff have argued that the conventional models of a brain function based on neural networks alone cannot account for human consciousness, claiming that quantum-computation elements are also required. Specifically, in their Orchestrated Objective Reduction (Orch OR) model [R. Penrose and S. R. Hameroff, J. Conscious. Stud. 2, 99 (1995)], it is postulated that microtubules act as quantum processing units, with individual tubulin dimers forming the computational elements. This model requires that the tubulin is able to switch between alternative conformational states in a coherent manner, and that this process be rapid on the physiological time scale. Here, the biological feasibility of the Orch OR proposal is examined in light of recent experimental studies on microtubule assembly and dynamics. It is shown that the tubulins do not possess essential properties required for the Orch OR proposal, as originally proposed, to hold. Further, we consider also recent progress in the understanding of the long-lived coherent motions in biological systems, a feature critical to Orch OR, and show that no reformation of the proposal based on known physical paradigms could lead to quantum computing within microtubules. Hence, the Orch OR model is not a feasible explanation of the origin of consciousness.

  17. Reduction of pollutants and disinfection of industrial wastewater by an integrated system of copper electrocoagulation and electrochemically generated hydrogen peroxide.

    PubMed

    Barrera-Díaz, Carlos E; Frontana-Uribe, Bernardo A; Roa-Morales, Gabriela; Bilyeu, Bryan W

    2015-01-01

    The objective of this study was to evaluate the effect of copper electrocoagulation and hydrogen peroxide on COD, color, turbidity, and bacterial activity in a mixed industry wastewater. The integrated system of copper electrocoagulation and hydrogen peroxide is effective at reducing the organic and bacterial content of industrial wastewater. The copper electrocoagulation alone reduces COD by 56% in 30 min at pH 2.8, but the combined system reduces COD by 78%, biochemical oxygen demand (BOD5) by 81%, and color by 97% under the same conditions. Colloidal particles are flocculated effectively, as shown by the reduction of zeta potential and the 84% reduction in turbidity and 99% reduction in total solids. Additionally, the total coliforms, fecal coliforms, and bacteria are all reduced by 99%. The integrated system is effective and practical for the reduction of both organic and bacterial content in industrial wastewater.

  18. Integral Twist Actuation of Helicopter Rotor Blades for Vibration Reduction

    NASA Technical Reports Server (NTRS)

    Shin, SangJoon; Cesnik, Carlos E. S.

    2001-01-01

    Active integral twist control for vibration reduction of helicopter rotors during forward flight is investigated. The twist deformation is obtained using embedded anisotropic piezocomposite actuators. An analytical framework is developed to examine integrally-twisted blades and their aeroelastic response during different flight conditions: frequency domain analysis for hover, and time domain analysis for forward flight. Both stem from the same three-dimensional electroelastic beam formulation with geometrical-exactness, and axe coupled with a finite-state dynamic inflow aerodynamics model. A prototype Active Twist Rotor blade was designed with this framework using Active Fiber Composites as the actuator. The ATR prototype blade was successfully tested under non-rotating conditions. Hover testing was conducted to evaluate structural integrity and dynamic response. In both conditions, a very good correlation was obtained against the analysis. Finally, a four-bladed ATR system is built and tested to demonstrate its concept in forward flight. This experiment was conducted at NASA Langley Tansonic Dynamics Tunnel and represents the first-of-a-kind Mach-scaled fully-active-twist rotor system to undergo forward flight test. In parallel, the impact upon the fixed- and rotating-system loads is estimated by the analysis. While discrepancies are found in the amplitude of the loads under actuation, the predicted trend of load variation with respect to its control phase correlates well. It was also shown, both experimentally and numerically, that the ATR blade design has the potential for hub vibratory load reduction of up to 90% using individual blade control actuation. Using the numerical framework, system identification is performed to estimate the harmonic transfer functions. The linear time-periodic system can be represented by a linear time-invariant system under the three modes of blade actuation: collective, longitudinal cyclic, and lateral cyclic. A vibration

  19. Scattering and Absorption Properties of Biomaterials for Dental Restorative Applications

    NASA Astrophysics Data System (ADS)

    Fernandez-Oliveras, A.; Rubiño, M.; Pérez, M. M.

    2013-08-01

    The physical understanding of the optical properties of dental biomaterials is mandatory for their final success in restorative applications.Light propagation in biological media is characterized by the absorption coefficient, the scattering coefficient, the scattering phase function,the refractive index, and the surface conditions (roughness). We have employed the inverse adding-doubling (IAD) method to combine transmittance and reflectance measurements performed using an integrating-sphere setup with the results of the previous scattering-anisotropygoniometric measurements. This has led to the determination of the absorption and the scattering coefficients. The aim was to optically characterize two different dental-resin composites (nanocomposite and hybrid) and one type of zirconia ceramic, and comparatively study them. The experimental procedure was conducted under repeatability conditions of measurement in order to determine the uncertainty associated to the optical properties of the biomaterials. Spectral variations of the refraction index and the scattering anisotropy factor were also considered. The whole experimental procedure fulfilled all the necessary requirements to provide optical-property values with lower associated uncertainties. The effective transport coefficient presented a similar spectral behavior for the two composites but completely different for the zirconia ceramic. The results demonstrated that the scattering anisotropy exerted a clearly distinct impact on the optical properties of the zirconia ceramic compared with those of the dental-resin composites.

  20. A novel integration of three-dimensional electro-Fenton and biological activated carbon and its application in the advanced treatment of biologically pretreated Lurgi coal gasification wastewater.

    PubMed

    Hou, Baolin; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Jia, Shengyong; Li, Kun

    2015-11-01

    A novel integrated process with three-dimensional electro-Fenton (3D EF) and biological activated carbon (BAC) was employed in advanced treatment of biologically pretreated Lurgi coal gasification wastewater. SAC-Fe (sludge deserved activated carbon from sewage and iron sludge) and SAC (sludge deserved activated carbon) were used in 3D EF as catalytic particle electrodes (CPEs) and in BAC as carriers respectively. Results indicated that 3D EF with SAC-Fe as CPEs represented excellent pollutants and COLOR removals as well as biodegradability improvement. The efficiency enhancement attributed to generating more H2O2 and OH. The integrated process exhibited efficient performance of COD, BOD5, total phenols, TOC, TN and COLOR removals at a much shorter retention time, with the corresponding concentrations in effluent of 31.18, 6.69, 4.29, 17.82, 13.88mg/L and <20 times, allowing discharge criteria to be met. The integrated system was efficient, cost-effective and ecological sustainable and could be a promising technology for engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. A tiered approach for integrating exposure and dosimetry with ...

    EPA Pesticide Factsheets

    High-throughput (HT) risk screening approaches apply in vitro dose-response data to estimate potential health risks that arise from exposure to chemicals. However, much uncertainty is inherent in relating bioactivities observed in an in vitro system to the perturbations of biological mechanisms that lead to apical adverse health outcomes in living organisms. The chemical-agnostic Adverse Outcome Pathway (AOP) framework addresses this uncertainty by acting as a scaffold onto which pathway-based data can be arranged to aid in the understanding of in vitro toxicity testing results. In addition, risk estimation also requires reconciling chemical concentrations sufficient to produce bioactivity in vitro with concentrations that trigger a molecular initiating event (MIE) at the relevant biological target in vivo. Such target site exposures (TSEs) can be estimated using computational models to integrate exposure information with a chemical’s absorption, distribution, metabolism, and elimination (ADME) processes. In this presentation, the utility of a tiered approach for integrating exposure, ADME, and hazard into risk-based decision making will be demonstrated using several case studies, along with the investigation of how uncertainties in exposure and ADME might impact risk estimates. These case studies involve 1) identifying and prioritizing chemicals capable of altering biological pathways based on their potential to reach an in vivo target; 2) evaluating the infl

  2. An integrated cell-free metabolic platform for protein production and synthetic biology

    PubMed Central

    Jewett, Michael C; Calhoun, Kara A; Voloshin, Alexei; Wuu, Jessica J; Swartz, James R

    2008-01-01

    Cell-free systems offer a unique platform for expanding the capabilities of natural biological systems for useful purposes, i.e. synthetic biology. They reduce complexity, remove structural barriers, and do not require the maintenance of cell viability. Cell-free systems, however, have been limited by their inability to co-activate multiple biochemical networks in a single integrated platform. Here, we report the assessment of biochemical reactions in an Escherichia coli cell-free platform designed to activate natural metabolism, the Cytomim system. We reveal that central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects. In addition, we describe an improved Cytomim system with enhanced protein synthesis yields (up to 1200 mg/l in 2 h) and lower costs to facilitate production of protein therapeutics and biochemicals that are difficult to make in vivo because of their toxicity, complexity, or unusual cofactor requirements. PMID:18854819

  3. Chiral Compounds and Green Chemistry in Undergraduate Organic Laboratories: Reduction of a Ketone by Sodium Borohydride and Baker's Yeast

    NASA Astrophysics Data System (ADS)

    Pohl, Nicola; Clague, Allen; Schwarz, Kimberly

    2002-06-01

    We describe an integrated set of experiments for the undergraduate organic laboratory that allows students to compare and contrast biological and chemical means of introducing chirality into a molecule. The racemic reduction of ethyl acetoacetate with sodium borohydride and the same reduction in the presence of a tartaric acid ligand are described, and a capillary gas chromatography column packed with a chiral material for product analysis is introduced. The results of these two hydride reactions are compared with the results of a common undergraduate experiment, the baker's yeast reduction of ethyl acetoacetate.

  4. Integrating interactive computational modeling in biology curricula.

    PubMed

    Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

    2015-03-01

    While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  5. Vanadium K-edge X-ray absorption spectroscopy of bromoperoxidase from Ascophyllum nodosum

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Arber, J.M.; de Boer, E.; Garner, C.D.

    Bromoperoxidase from Ascophyllum nodusum was the first vanadium-containing enzyme to be isolated. X-ray absorption spectra have now been collected in order to investigate the coordination of vanadium in the native, native plus bromide, native plus hydrogen peroxide, and dithionite-reduced forms of the enzyme. The edge and X-ray absorption near-edge structures show that, in the four samples studied, it is only on reduction of the native enzyme that the metal site is substantially altered. In addition, these data are consistent with the presence of vanadium(IV) in the reduced enzyme and vanadium(V) in the other samples. Extended X-ray absorption fine structure datamore » confirm that there are structural changes at the metal site on reduction of the native enzyme, notably a lengthening of the average inner-shell distance, and the presence of terminal oxygen together with histidine and oxygen-donating residues.« less

  6. Effect of reduction time on third order optical nonlinearity of reduced graphene oxide

    NASA Astrophysics Data System (ADS)

    Sreeja, V. G.; Vinitha, G.; Reshmi, R.; Anila, E. I.; Jayaraj, M. K.

    2017-04-01

    We report the influence of reduction time on structural, linear and nonlinear optical properties of reduced graphene oxide (rGO) thin films synthesized by spin coating method. We observed that the structural, linear and nonlinear optical properties can be tuned with reduction time in GO is due to the increased structural ordering because of the restoration of sp2 carbon atoms with the time of reduction. The nonlinear absorption studies by open aperture Z-scan technique exhibited a saturable absorption. The nonlinear refraction studies showed the self de focusing nature of rGO by closed aperture Z scan technique. The nonlinear absorption coefficient and saturation intensity varies with the time for reduction of GO which is attributed to the depletion of valence band and the conduction band filling effect. Our results emphasize duration for reduction of GO dependent optical nonlinearity of rGO thin films to a great extent and explore its applications Q switched mode locking laser systems for generating ultra short laser pulses and in optical sensors. The rGO coated films were characterized by X-Ray diffraction method (XRD), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, UV-Vis absorption spectroscopy (UV-Vis), Photoluminescence (PL) and Scanning electron microscope (SEM) measurements.

  7. Emphasizing the "Literacy" in "Scientific Literacy": A Concise Blueprint for Integrating Writing into Biology Classes

    ERIC Educational Resources Information Center

    Yule, Jeffrey V.; Wolf, William C.; Young, Nolan L.

    2010-01-01

    Effectively integrating writing into biology classes gives students the opportunity to develop a better understanding of and engagement with course content. Yet many instructors remain reluctant to emphasize writing. Some are concerned about the time commitment writing assessment requires. Others shy away from emphasizing writing in their classes…

  8. Effects of heat transfer and energy absorption in the ablation of biological tissues by pulsetrain-burst (>100 MHz) ultrafast laser processing

    NASA Astrophysics Data System (ADS)

    Forrester, Paul; Bol, Kieran; Lilge, Lothar; Marjoribanks, Robin

    2006-09-01

    Energy absorption and heat transfer are important factors for regulating the effects of ablation of biological tissues. Heat transfer to surrounding material may be desirable when ablating hard tissue, such as teeth or bone, since melting can produce helpful material modifications. However, when ablating soft tissue it is important to minimize heat transfer to avoid damage to healthy tissue - for example, in eye refractive surgery (e.g., Lasik), nanosecond pulses produce gross absorption and heating in tissue, leading to shockwaves, which kill and thin the non-replicating epithelial cells on the inside of the cornea; ultrafast pulses are recognized to reduce this effect. Using a laser system that delivers 1ps pulses in 10μs pulsetrains at 133MHz we have studied a range of heat- and energy-transfer effects on hard and soft tissue. We describe the ablation of tooth dentin and enamel under various conditions to determine the ablation rate and chemical changes that occur. Furthermore, we characterize the impact of pulsetrain-burst treatment of collagen-based tissue to determine more efficient methods of energy transfer to soft tissues. By studying the optical science of laser tissue interaction we hope to be able to make qualitative improvements to medical treatments using lasers.

  9. Energy-gap reduction in heavily doped silicon: Causes and consequences

    NASA Astrophysics Data System (ADS)

    Pantelides, Sokrates T.; Selloni, Annabella; Car, Roberto

    1985-02-01

    The authors review briefly the existing theoretical treatments of the various effects that contribute to the reduction of the energy gap in heavily doped Si, namely electron-electron and electron-impurity interactions and the effect of disorder in the impurity distribution. They then turn to the longstanding question why energy-gap reductions extracted from three different types of experiments have persistently produced values with substantial discrepancies, making it impossible to compare with theoretical values. First, they demonstrate that a meaningful comparison between theory and experiment can indeed be made if theoretical calculations are carried out for actual quantities that experiments measure, e.g. luminescence spectra, as recently done by Selloni and Pantelides. Then, they demonstrate that, independent of any theoretical calculations, the optical absorption spectra are fully consistent with the luminescence spectra and that the discrepancies in the energy-gap reductions extracted from the two sets of spectra are caused entirely by the curve-fitting procedures used in analyzing optical-absorption data. Finally, they show explicitly that, as already believed by many authors, energy-gap reductions extracted from electrical measurements on transistors do not correspond to true gap reductions. They identify two corrections that must be added to the values extracted from the electrical data in order to arrive at the true gap reductions and show that the resulting values are in good overall agreement with luminescence and absorption data. They, therefore, demonstrate that the observed reduction in emitter injection efficiency in bipolar transistors is not strictly due to a gap reduction, as generally believed, but to three very different effects.

  10. Delivering The Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA (ACS Fall meeting)

    EPA Science Inventory

    Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intent...

  11. Kelp, cobbles, and currents: Biologic reduction of coarse grain entrainment stress

    USGS Publications Warehouse

    Masteller, Claire C; Finnegan, Noah J; Warrick, Jonathan; Miller, Ian M.

    2015-01-01

    Models quantifying the onset of sediment motion do not typically account for the effect of biotic processes because they are difficult to isolate and quantify in relation to physical processes. Here we investigate an example of the interaction of kelp (Order Laminariales) and coarse sediment transport in the coastal zone, where it is possible to directly quantify and test its effect. Kelp is ubiquitous along rocky coastlines and the impact on ecosystems has been well studied. We develop a physical model to explore the reduction in critical shear stress of large cobbles colonized by Nereocystis luetkeana, or bull kelp. Observations of coarse sediment motion at a site in the Strait of Juan de Fuca (northwest United States–Canada boundary channel) confirm the model prediction and show that kelp reduces the critical stress required for transport of a given grain size by as much as 92%, enabling annual coarse sediment transport rates comparable to those of fluvial systems. We demonstrate that biology is fundamental to the physical processes that shape the coastal zone in this setting.

  12. Path integral Monte Carlo study on the structure and absorption spectra of alkali atoms (Li, Na, K) attached to superfluid helium clusters

    NASA Astrophysics Data System (ADS)

    Nakayama, Akira; Yamashita, Koichi

    2001-01-01

    Path integral Monte Carlo calculations have been performed to investigate the microscopic structure and thermodynamic properties of the AkṡHeN (Ak=Li, Na, K,N⩽300) clusters at T=0.5 K. Absorption spectra which correspond to the 2P←2S transitions of alkali atoms are also calculated within a pairwise additive model, which employs diatomic Ak-He potential energy curves. The size dependences of the cluster structure and absorption spectra that show the influence of the helium cluster environment are examined in detail. It is found that alkali atoms are trapped in a dimple on the helium cluster's surface and that, from the asymptotic behavior, the AkṡHe300 cluster, at least semiquantitatively, mimics the local structure of experimentally produced large helium clusters in the vicinity of alkali atoms. We have successfully reproduced the overall shapes of the spectra and explained their features from a static and structural point of view. The positions, relative intensities, and line widths of the absorption maxima are calculated to be in moderate agreement with experiments [F. Stienkemeier, J. Higgins, C. Callegari, S. I. Kanorsky, W. E. Ernst, and G. Scoles, Z. Phys. D 38, 253 (1996)].

  13. Impact of Interdisciplinary Undergraduate Research in mathematics and biology on the development of a new course integrating five STEM disciplines.

    PubMed

    Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

    2010-01-01

    Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics.

  14. Triple-Pulsed Two-Micron Integrated Path Differential Absorption Lidar: A New Active Remote Sensing Capability with Path to Space

    NASA Technical Reports Server (NTRS)

    Singh, Upendra N.; Refaat, Tamer F.; Petros, Mulugeta; Yu, Jirong

    2015-01-01

    The two-micron wavelength is suitable for monitoring atmospheric water vapor and carbon dioxide, the two most dominant greenhouse gases. Recent advances in 2-micron laser technology paved the way for constructing state-of-the-art lidar transmitters for active remote sensing applications. In this paper, a new triple-pulsed 2-micron integrated path differential absorption lidar is presented. This lidar is capable of measuring either two species or single specie with two different weighting functions, simultaneously and independently. Development of this instrument is conducted at NASA Langley Research Center. Instrument scaling for projected future space missions will be discussed.

  15. Integrative Approaches for Predicting in vivo Effects of Chemicals from their Structural Descriptors and the Results of Short-term Biological Assays

    PubMed Central

    Low, Yen S.; Sedykh, Alexander; Rusyn, Ivan; Tropsha, Alexander

    2017-01-01

    Cheminformatics approaches such as Quantitative Structure Activity Relationship (QSAR) modeling have been used traditionally for predicting chemical toxicity. In recent years, high throughput biological assays have been increasingly employed to elucidate mechanisms of chemical toxicity and predict toxic effects of chemicals in vivo. The data generated in such assays can be considered as biological descriptors of chemicals that can be combined with molecular descriptors and employed in QSAR modeling to improve the accuracy of toxicity prediction. In this review, we discuss several approaches for integrating chemical and biological data for predicting biological effects of chemicals in vivo and compare their performance across several data sets. We conclude that while no method consistently shows superior performance, the integrative approaches rank consistently among the best yet offer enriched interpretation of models over those built with either chemical or biological data alone. We discuss the outlook for such interdisciplinary methods and offer recommendations to further improve the accuracy and interpretability of computational models that predict chemical toxicity. PMID:24805064

  16. Harnessing the Power of Integrated Mitochondrial Biology and Physiology: A Special Report on the NHLBI Mitochondria in Heart Diseases Initiative

    PubMed Central

    Ping, Peipei; Gustafsson, Åsa B.; Bers, Don M.; Blatter, Lothar; Cai, Hua; Jahangir, Arshad; Kelly, Daniel; Muoio, Deborah; O'Rourke, Brian; Rabinovitch, Peter; Trayanova, Natalia; Van Eyk, Jennifer; Weiss, James N.; Wong, Renee; Longacre, Lisa Schwartz

    2015-01-01

    Summary Mitochondrial biology is the sum of diverse phenomena from molecular profiles to physiological functions. A mechanistic understanding of mitochondria in disease development, and hence the future prospect of clinical translations, relies on a systems-level integration of expertise from multiple fields of investigation. Upon the successful completion of a recent National Institutes of Health, National Heart, Lung, and Blood Institute initiative on integrative mitochondrial biology in cardiovascular diseases, we reflect on the accomplishments made possible by this unique interdisciplinary collaboration effort and exciting new fronts on the study of these remarkable organelles. PMID:26185209

  17. Implications for an Enhanced Biological Pump in the Sea-Ice Reduction Region of the Western Arctic Ocean

    NASA Astrophysics Data System (ADS)

    Nishino, S.; Shimada, K.; Itoh, M.; Yamamoto-Kawai, M.; Chiba, S.

    2009-12-01

    Since the late 1990s, catastrophic sea-ice reduction during summer has been observed in the western Arctic Ocean. Regions of decreasing sea ice might be associated with increased biological production compared to ice-covered ocean areas due to light intensification in the water column. The R/V Mirai field experiments in summer 2004 revealed that the algal biomass (chlorophyll a) in the open water region of the western Canada Basin increased from that observed in summer 1994, when the sea ice covered that area. Under the euphotic zone of the increased algal biomass area, evidence of diatom detritus decomposition was found, while such evidence was not observed in 1994, suggesting an enhancement of biological pump (see figure). The increase of algal biomass was not found throughout the sea-ice reduction region; rather, it was observed western Canada Basin where nutrients are effectively supplied from shelf regions. Further west from the Canada Basin, Russian river water with relatively high nutrients may play an important role in the biogeochemical cycles. Monthly sea-ice concentrations (white = 100%, black = 0%) in September of (a) 1994 and (b) 2004 (National Ice Center), and (c) vertical profiles of silicate obtained from the field experiments of Arctic Ocean Section 94 in 1994 (○) and Mirai04 in 2004 (■). The positions where the profiles were obtained are depicted by dots in (a) and (b), respectively.

  18. Low content Ag-coated poly(acrylonitrile) microspheres and graphene for enhanced microwave absorption performance epoxy composites

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Wang, Jun; Chen, Xiaocheng; Su, Xiaogang; Zou, Yi; Huo, Siqi; Chen, Wei; Wang, Junpeng

    2018-04-01

    Silver nanoparticles was uniformly anchored on the surface of hollow poly(acrylonitrile) microspheres with a facile chemical method using hydrazine hydrate as reductant. Integrating these conducting hollow spheres (PANS@Ag) with chemical reduced graphene oxide (RGO) dispersed in epoxy resin, a lightweight microwave absorber was successfully prepared with enhanced microwave absorption performance. The chemical constitution and surface morphology of as-synthesized RGO and PANS@Ag powders were characterized by XRD, XPS, FE-SEM and SAED, while the electromagnetic properties of these different proportion PANS@Ag-RGO/EP samples were analyzed through vector network analyzer (VNA). The minimum reflection loss (RL) could reach up to ‑28.1 dB at 8.8 GHz with a layer thickness of 2 mm, and the corresponding effective absorption bandwidth (RL values less than ‑10 dB) was from 7.9 GHz to 9.8 GHz. However, the dosage of PANS@Ag and RGO was merely 3 wt% and 1 wt%, respectively. As the content of PANS@Ag powders decreased to 1 wt%, the PANS@Ag-RGO/EP samples still retained effective microwave absorption performance and the optimal RL was ‑14.7 dB. The density of as-prepared absorbers was in the range of 0.49 ∼ 0.87 g cm‑3. The low content, low density and enhanced microwave absorption performance endow the hybrid composites with competitive application prospect in stealth technology field.

  19. Rational Construction of Uniform CoNi-Based Core-Shell Microspheres with Tunable Electromagnetic Wave Absorption Properties.

    PubMed

    Chen, Na; Jiang, Jian-Tang; Xu, Cheng-Yan; Yan, Shao-Jiu; Zhen, Liang

    2018-02-16

    Core-shell particles with integration of ferromagnetic core and dielectric shell are attracting extensive attention for promising microwave absorption applications. In this work, CoNi microspheres with conical bulges were synthesized by a simple and scalable liquid-phase reduction method. Subsequent coating of dielectric materials was conducted to acquire core-shell structured CoNi@TiO 2 composite particles, in which the thickness of TiO 2 is about 40 nm. The coating of TiO 2 enables the absorption band of CoNi to effectively shift from K u to S band, and endows CoNi@TiO 2 microspheres with outstanding electromagnetic wave absorption performance along with a maximum reflection loss of 76.6 dB at 3.3 GHz, much better than that of bare CoNi microspheres (54.4 dB at 17.8 GHz). The enhanced EMA performance is attributed to the unique core-shell structures, which can induce dipole polarization and interfacial polarization, and tune the dielectric properties to achieve good impedance matching. Impressively, TiO 2 coating endows the composites with better microwave absorption capability than CoNi@SiO 2 microspheres. Compared with SiO 2 , TiO 2 dielectric shells could protect CoNi microspheres from merger and agglomeration during annealed. These results indicate that CoNi@TiO 2 core-shell microspheres can serve as high-performance absorbers for electromagnetic wave absorbing application.

  20. A single-vendor and a single-buyer integrated inventory model with ordering cost reduction dependent on lead time

    NASA Astrophysics Data System (ADS)

    Vijayashree, M.; Uthayakumar, R.

    2017-09-01

    Lead time is one of the major limits that affect planning at every stage of the supply chain system. In this paper, we study a continuous review inventory model. This paper investigates the ordering cost reductions are dependent on lead time. This study addressed two-echelon supply chain problem consisting of a single vendor and a single buyer. The main contribution of this study is that the integrated total cost of the single vendor and the single buyer integrated system is analyzed by adopting two different (linear and logarithmic) types ordering cost reductions act dependent on lead time. In both cases, we develop effective solution procedures for finding the optimal solution and then illustrative numerical examples are given to illustrate the results. The solution procedure is to determine the optimal solutions of order quantity, ordering cost, lead time and the number of deliveries from the single vendor and the single buyer in one production run, so that the integrated total cost incurred has the minimum value. Ordering cost reduction is the main aspect of the proposed model. A numerical example is given to validate the model. Numerical example solved by using Matlab software. The mathematical model is solved analytically by minimizing the integrated total cost. Furthermore, the sensitivity analysis is included and the numerical examples are given to illustrate the results. The results obtained in this paper are illustrated with the help of numerical examples. The sensitivity of the proposed model has been checked with respect to the various major parameters of the system. Results reveal that the proposed integrated inventory model is more applicable for the supply chain manufacturing system. For each case, an algorithm procedure of finding the optimal solution is developed. Finally, the graphical representation is presented to illustrate the proposed model and also include the computer flowchart in each model.

  1. A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology.

    PubMed

    Price, S A; Schmitz, L

    2016-04-05

    Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s).

  2. A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

    PubMed Central

    Schmitz, L.

    2016-01-01

    Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. PMID:26977068

  3. Wiring Together Synthetic Bacterial Consortia to Create a Biological Integrated Circuit.

    PubMed

    Perry, Nicolas; Nelson, Edward M; Timp, Gregory

    2016-12-16

    The promise of adapting biology to information processing will not be realized until engineered gene circuits, operating in different cell populations, can be wired together to express a predictable function. Here, elementary biological integrated circuits (BICs), consisting of two sets of transmitter and receiver gene circuit modules with embedded memory placed in separate cell populations, were meticulously assembled using live cell lithography and wired together by the mass transport of quorum-sensing (QS) signal molecules to form two isolated communication links (comlinks). The comlink dynamics were tested by broadcasting "clock" pulses of inducers into the networks and measuring the responses of functionally linked fluorescent reporters, and then modeled through simulations that realistically captured the protein production and molecular transport. These results show that the comlinks were isolated and each mimicked aspects of the synchronous, sequential networks used in digital computing. The observations about the flow conditions, derived from numerical simulations, and the biofilm architectures that foster or silence cell-to-cell communications have implications for everything from decontamination of drinking water to bacterial virulence.

  4. Morphomics: An integral part of systems biology of the human placenta.

    PubMed

    Mayhew, T M

    2015-04-01

    The placenta is a transient organ the functioning of which has health consequences far beyond the embryo/fetus. Understanding the biology of any system (organ, organism, single cell, etc) requires a comprehensive and inclusive approach which embraces all the biomedical disciplines and 'omic' technologies and then integrates information obtained from all of them. Among the latest 'omics' is morphomics. The terms morphome and morphomics have been applied incoherently in biology and biomedicine but, recently, they have been given clear and widescale definitions. Morphomics is placed in the context of other 'omics' and its pertinent technologies and tools for sampling and quantitation are reviewed. Emphasis is accorded to the importance of random sampling principles in systems biology and the value of combining 3D quantification with alternative imaging techniques to advance knowledge and understanding of the human placental morphome. By analogy to other 'omes', the morphome is the totality of morphological features within a system and morphomics is the systematic study of those structures. Information about structure is required at multiple levels of resolution in order to understand better the processes by which a given system alters with time, experimental treatment or environmental insult. Therefore, morphomics research includes all imaging techniques at all levels of achievable resolution from gross anatomy and medical imaging, via optical and electron microscopy, to molecular characterisation. Quantification is an important element of all 'omics' studies and, because biological systems exist and operate in 3-dimensional (3D) space, precise descriptions of form, content and spatial relationships require the quantification of structure in 3D. These considerations are relevant to future study contributions to the Human Placenta Project. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology.

    PubMed

    Blakes, Jonathan; Twycross, Jamie; Romero-Campero, Francisco Jose; Krasnogor, Natalio

    2011-12-01

    The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking. Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3. Natalio.Krasnogor@nottingham.ac.uk.

  6. How to integrate biological research into society and exclude errors in biomedical publications? Progress in theoretical and systems biology releases pressure on experimental research.

    PubMed

    Volkov, Vadim

    2014-01-01

    This brief opinion proposes measures to increase efficiency and exclude errors in biomedical research under the existing dynamic situation. Rapid changes in biology began with the description of the three dimensional structure of DNA 60 years ago; today biology has progressed by interacting with computer science and nanoscience together with the introduction of robotic stations for the acquisition of large-scale arrays of data. These changes have had an increasing influence on the entire research and scientific community. Future advance demands short-term measures to ensure error-proof and efficient development. They can include the fast publishing of negative results, publishing detailed methodical papers and excluding a strict connection between career progression and publication activity, especially for younger researchers. Further development of theoretical and systems biology together with the use of multiple experimental methods for biological experiments could also be helpful in the context of years and decades. With regards to the links between science and society, it is reasonable to compare both these systems, to find and describe specific features for biology and to integrate it into the existing stream of social life and financial fluxes. It will increase the level of scientific research and have mutual positive effects for both biology and society. Several examples are given for further discussion.

  7. A periodic piezoelectric smart structure with the integrated passive/active vibration-reduction performances

    NASA Astrophysics Data System (ADS)

    Wang, Yuxi; Niu, Shengkai; Hu, Yuantai

    2017-06-01

    The paper proposes a new piezoelectric smart structure with the integrated passive/active vibration-reduction performances, which is made of a series of periodic structural units. Every structural unit is made of two layers, one is an array of piezoelectric bimorphs (PBs) and one is an array of metal beams (MBs), both are connected as a whole by a metal plate. Analyses show that such a periodic smart structure possesses two aspects of vibration-reduction performance: one comes from its phonon crystal characteristics which can isolate those vibrations with the driving frequency inside the band gap(s). The other one comes from the electromechanical conversion of bent PBs, which is actively aimed at those vibrations with the driving frequency outside the band gap(s). By adjusting external inductance, the equivalent circuit of the proposed structure can be forced into parallel resonance such that most of the vibration energy is converted into electrical energy for dissipation by a resistance. Thus, an external circuit under the parallel resonance state is equivalent to a strong damping to the interrelated vibrating structure, which is just the action mechanism of the active vibration reduction performance of the proposed smart structure.

  8. Integrating Climate Change Adaptation into Disaster Risk Reduction in Urban Contexts: Perceptions and Practice

    PubMed Central

    Rivera, Claudia

    2014-01-01

    This paper analyses the perceptions of disaster risk reduction (DRR) practitioners concerning the on-going integration of climate change adaptation (CCA) into their practices in urban contexts in Nicaragua. Understanding their perceptions is important as this will provide information on how this integration can be improved. Exploring the perceptions of practitioners in Nicaragua is important as the country has a long history of disasters, and practitioners have been developing the current DRR planning framework for more than a decade. The analysis is based on semi-structured interviews designed to collect information about practitioners’ understanding of: (a) CCA, (b) the current level of integration of CCA into DRR and urban planning, (c) the opportunities and constraints of this integration, and (d) the potential to adapt cities to climate change. The results revealed that practitioners’ perception is that the integration of CCA into their practice is at an early stage, and that they need to improve their understanding of CCA in terms of a development issue. Three main constraints on improved integration were identified: (a) a recognized lack of understanding of CCA, (b) insufficient guidance on how to integrate it, and (c) the limited opportunities to integrate it into urban planning due to a lack of instruments and capacity in this field. Three opportunities were also identified: (a) practitioners’ awareness of the need to integrate CCA into their practices, (b) the robust structure of the DRR planning framework in the country, which provides a suitable channel for facilitating integration, and (c) the fact that CCA is receiving more attention and financial and technical support from the international community. PMID:24475365

  9. An inexpensive, temporally-integrated system for monitoring occurrence and biological effects of aquatic contaminants in the field

    EPA Science Inventory

    Assessment of potential ecological risks of complex contaminant mixtures in the environment requires integrated chemical and biological approaches. Instrumental analysis of environmental samples alone can identify contaminants, but provides only limited insights as to possible a...

  10. Review of Canadian Light Source facilities for biological applications

    NASA Astrophysics Data System (ADS)

    Grochulski, Pawel; Fodje, Michel; Labiuk, Shaun; Wysokinski, Tomasz W.; Belev, George; Korbas, Malgorzata; Rosendahl, Scott M.

    2017-11-01

    The newly-created Biological and Life Sciences Department at the Canadian Light Source (CLS) encompasses four sets of beamlines devoted to biological studies ranging in scope from the atomic scale to cells, tissues and whole organisms. The Canadian Macromolecular Crystallography Facility (CMCF) consists of two beamlines devoted primarily to crystallographic studies of proteins and other macromolecules. The Mid-Infrared Spectromicroscopy (Mid-IR) beamline focusses on using infrared energy to obtain biochemical, structural and dynamical information about biological systems. The Bio-Medical Imaging and Therapy (BMIT) facility consists of two beamlines devoted to advanced imaging and X-ray therapy techniques. The Biological X-ray Absorption Spectroscopy (BioXAS) facility is being commissioned and houses three beamlines devoted to X-ray absorption spectroscopy and multi-mode X-ray fluorescence imaging. Together, these beamlines provide CLS Users with a powerful array of techniques to study today's most pressing biological questions. We describe these beamlines along with their current powerful features and envisioned future capabilities.

  11. Heterogeneous database integration in biomedicine.

    PubMed

    Sujansky, W

    2001-08-01

    The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, making access to and aggregation of data across databases very difficult. The database heterogeneity problem applies equally to clinical data describing individual patients and biological data characterizing our genome. Specifically, databases are highly heterogeneous with respect to the data models they employ, the data schemas they specify, the query languages they support, and the terminologies they recognize. Heterogeneous database systems attempt to unify disparate databases by providing uniform conceptual schemas that resolve representational heterogeneities, and by providing querying capabilities that aggregate and integrate distributed data. Research in this area has applied a variety of database and knowledge-based techniques, including semantic data modeling, ontology definition, query translation, query optimization, and terminology mapping. Existing systems have addressed heterogeneous database integration in the realms of molecular biology, hospital information systems, and application portability.

  12. Calcium absorption is not increased by caseinophosphopeptides.

    PubMed

    Teucher, Birgit; Majsak-Newman, Gosia; Dainty, Jack R; McDonagh, David; FitzGerald, Richard J; Fairweather-Tait, Susan J

    2006-07-01

    One of the suggested health benefits of caseinophosphopeptides (CPPs) is their ability to enhance calcium absorption. This possibility is based on the assumption that they resist proteolysis in the upper gastrointestinal tract and maintain calcium in a soluble form at alkaline pH in the distal ileum. The effects of CPP-enriched preparations (containing candidate functional food ingredients) on calcium absorption from a calcium lactate drink were tested. A randomized crossover trial was undertaken in 15 adults in whom we measured the absorption of calcium from a calcium lactate drink (drink A: 400 mg Ca as lactate) and 2 preparations enriched with forms of CPP (1.7 g each; drinks B and C). Both drinks B and C contained 400 mg Ca as calcium lactate plus approximately 100 mg CPP-derived calcium). Each volunteer received the 3 drinks in random order. Absorption was measured by the dual-label calcium stable-isotope technique. The quantity of calcium absorbed was significantly lower from drink A (103 mg) than from drink B (117 mg; P = 0.012) or drink C (121 mg; P = 0.002), which indicated a positive effect of the CPPs. However, because the CPP preparations contributed additional calcium besides that found in the calcium lactate (drink A), fractional absorption of calcium from drink B (23%) was slightly but significantly (P = 0.015) lower than that from drink A (26%). The differences in calcium absorption are unlikely to have any biological significance. CPPs are unsuitable as candidate ingredients for functional foods that are designed to deliver improved calcium nutrition.

  13. INTEGRATING BIOLOGICAL PRINCIPLES WITH INSTRUCTION IN VOCATIONAL AGRICULTURE, A RESEARCH REPORT OF A GRADUATE STUDY. RESEARCH SERIES IN AGRICULTURAL EDUCATION.

    ERIC Educational Resources Information Center

    BENDER, RALPH E.; STARLING, JOHN T.

    TO DETERMINE THE FEASIBILITY OF INTEGRATING BIOLOGICAL PRINCIPLES WITH INSTRUCTION IN VOCATIONAL AGRICULTURE IN OHIO HIGH SCHOOLS, 15 PILOT SCHOOLS AND 8 CONTROL SCHOOLS WERE STUDIED. PRETESTS ADMINISTERED TO STUDENTS IN OCTOBER 1963 WERE AN AGRICULTURAL ACHIEVEMENT TEST, A BIOLOGICAL PRINCIPLES TEST, THE CALIFORNIA SHORT-FORM TEST OF MENTAL…

  14. Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines

    PubMed Central

    Caudill, Lester; Hill, April; Lipan, Ovidiu

    2010-01-01

    Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics. PMID:20810953

  15. Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Luo, Wensui; Zhou, Jizhong; Wu, Weimin

    2007-01-01

    A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 mM or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonatemore » (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and geoundwater geochemistry alter microbial communities responsible for U(VI) reduction.« less

  16. [Purification of complicated industrial organic waste gas by complex absorption].

    PubMed

    Chen, Ding-Sheng; Cen, Chao-Ping; Tang, Zhi-Xiong; Fang, Ping; Chen, Zhi-Hang

    2011-12-01

    Complicated industrial organic waste gas with the characteristics of low concentration,high wind volume containing inorganic dust and oil was employed the research object by complex absorption. Complex absorption mechanism, process flow, purification equipment and engineering application were studied. Three different surfactants were prepared for the composite absorbent to purify exhaust gas loaded with toluene and butyl acetate, respectively. Results show that the low surface tension of the composite absorbent can improve the removal efficiency of toluene and butyl acetate. With the advantages of the water film, swirl plate and fill absorption device, efficient absorption equipment was developed for the treatment of complicated industrial organic waste gas. It is with superiorities of simple structure, small size, anti-jam and high mass transfer. Based on absorption technology, waste gas treatment process integrated with heating stripping, burning and anaerobic and other processes, so that emissions of waste gas and absorption solution could meet the discharge standards. The technology has been put into practice, such as manufacturing and spraying enterprises.

  17. Root Systems Biology: Integrative Modeling across Scales, from Gene Regulatory Networks to the Rhizosphere1

    PubMed Central

    Hill, Kristine; Porco, Silvana; Lobet, Guillaume; Zappala, Susan; Mooney, Sacha; Draye, Xavier; Bennett, Malcolm J.

    2013-01-01

    Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond the examination of interactions at the genetic network scale and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism, and rhizosphere scales. Understanding the underlying biological mechanisms and the complex interplay between systems at these different scales requires an integrative approach. Here, we describe examples of such approaches and discuss the merits of developing models to span multiple scales, from network to population levels, and to address dynamic interactions between plants and their environment. PMID:24143806

  18. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.

    PubMed

    Sauro, Herbert M; Hucka, Michael; Finney, Andrew; Wellock, Cameron; Bolouri, Hamid; Doyle, John; Kitano, Hiroaki

    2003-01-01

    Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe in this paper the SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities.

  19. Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses.

    PubMed

    Tian, Ye; Wang, Sean S; Zhang, Zhen; Rodriguez, Olga C; Petricoin, Emanuel; Shih, Ie-Ming; Chan, Daniel; Avantaggiati, Maria; Yu, Guoqiang; Ye, Shaozhen; Clarke, Robert; Wang, Chao; Zhang, Bai; Wang, Yue; Albanese, Chris

    2014-01-01

    Ever growing "omics" data and continuously accumulated biological knowledge provide an unprecedented opportunity to identify molecular biomarkers and their interactions that are responsible for cancer phenotypes that can be accurately defined by clinical measurements such as in vivo imaging. Since signaling or regulatory networks are dynamic and context-specific, systematic efforts to characterize such structural alterations must effectively distinguish significant network rewiring from random background fluctuations. Here we introduced a novel integration of network biology and imaging to study cancer phenotypes and responses to treatments at the molecular systems level. Specifically, Differential Dependence Network (DDN) analysis was used to detect statistically significant topological rewiring in molecular networks between two phenotypic conditions, and in vivo Magnetic Resonance Imaging (MRI) was used to more accurately define phenotypic sample groups for such differential analysis. We applied DDN to analyze two distinct phenotypic groups of breast cancer and study how genomic instability affects the molecular network topologies in high-grade ovarian cancer. Further, FDA-approved arsenic trioxide (ATO) and the ND2-SmoA1 mouse model of Medulloblastoma (MB) were used to extend our analyses of combined MRI and Reverse Phase Protein Microarray (RPMA) data to assess tumor responses to ATO and to uncover the complexity of therapeutic molecular biology.

  20. Noninvasive photoacoustic measurement of absorption coefficient using internal light irradiation of cylindrical diffusing fiber

    NASA Astrophysics Data System (ADS)

    Peng, Dong-qing; Zhu, Li-li; Li, Zhi-fang; Li, Hui

    2017-09-01

    Absorption coefficient of biological tissue is an important parameter in biomedicine, but its determination remains a challenge. In this paper, we propose a method using focusing photoacoustic imaging technique and internal light irradiation of cylindrical diffusing fiber (CDF) to quantify the target optical absorption coefficient. Absorption coefficients for ink absorbers are firstly determined through photoacoustic and spectrophotometric measurements at the same excitation, which demonstrates the feasibility of this method. Also, the optical absorption coefficients of ink absorbers with several concentrations are measured. Finally, the two-dimensional scanning photoacoustic image is obtained. Optical absorption coefficient measurement and simultaneous photoacoustic imaging of absorber non-invasively are the typical characteristics of the method. This method can play a significant role for non-invasive determination of blood oxygen saturation, the absorption-based imaging and therapy.

  1. Redox biology of the intestine

    PubMed Central

    Circu, Magdalena L.; Aw, Tak Yee

    2011-01-01

    The intestinal tract, known for its capability for self-renew, represents the first barrier of defense between the organism and its luminal environment. The thiol/disulfide redox systems comprising the glutathione/glutathione disulfide (GSH/GSSG), cysteine/cystine (Cys/CySS) and reduced and oxidized thioredoxin (Trx/TrxSS) redox couples play important roles in preserving tissue redox homeostasis, metabolic functions, and cellular integrity. Control of the thiol-disulfide status at the luminal surface is essential for maintaining mucus fluidity and absorption of nutrients, and protection against chemical-induced oxidant injury. Within intestinal cells, these redox couples preserve an environment that supports physiological processes and orchestrates networks of enzymatic reactions against oxidative stress. In this review, we focus on the intestinal redox and antioxidant systems, their subcellular compartmentation, redox signaling and epithelial turnover, and contribution of luminal microbiota, key aspects that are relevant to understanding redox-dependent processes in gut biology with implications for degenerative digestive disorders, such as inflammation and cancer. PMID:21831010

  2. Efficient control of ultrafast optical nonlinearity of reduced graphene oxide by infrared reduction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bhattachraya, S.; Maiti, R.; Das, A. C.

    Simultaneous occurrence of saturable absorption nonlinearity and two-photon absorption nonlinearity in the same medium is well sought for the devices like optical limiter and laser mode-locker. Pristine graphene sheet consisting entirely of sp{sup 2}-hybridized carbon atoms has already been identified having large optical nonlinearity. However, graphene oxide (GO), a precursor of graphene having both sp{sup 2} and sp{sup 3}-hybridized carbon atom, is increasingly attracting cross-discipline researchers for its controllable properties by reduction of oxygen containing groups. In this work, GO has been prepared by modified Hummers method, and it has been further reduced by infrared (IR) radiation. Characterization of reducedmore » graphene oxide (RGO) by means of Raman spectroscopy, X-ray photoelectron spectroscopy, and UV-Visible absorption measurements confirms an efficient reduction with infrared radiation. Here, we report precise control of non-linear optical properties of RGO in femtosecond regime with increased degrees of IR reduction measured by open aperture z-scan technique. Depending on the intensity, both saturable absorption and two-photon absorption effects are found to contribute to the non-linearity of all the samples. Saturation dominates at low intensity (∼127 GW/cm{sup 2}) while two-photon absorption becomes prominent at higher intensities (from 217 GW/cm{sup 2} to 302 GW/cm{sup 2}). The values of two-photon absorption co-efficient (∼0.0022–0.0037 cm/GW for GO, and ∼0.0128–0.0143 cm/GW for RGO) and the saturation intensity (∼57 GW/cm{sup 2} for GO, and ∼194 GW/cm{sup 2} for RGO) increase with increasing reduction, indicating GO and RGO as novel tunable photonic devices. We have also explained the reason of tunable nonlinear optical properties by using amorphous carbon model.« less

  3. Symmetry Reductions, Integrability and Solitary Wave Solutions to High-Order Modified Boussinesq Equations with Damping Term

    NASA Astrophysics Data System (ADS)

    Yan, Zhen-Ya; Xie, Fu-Ding; Zhang, Hong-Qing

    2001-07-01

    Both the direct method due to Clarkson and Kruskal and the improved direct method due to Lou are extended to reduce the high-order modified Boussinesq equation with the damping term (HMBEDT) arising in the general Fermi-Pasta-Ulam model. As a result, several types of similarity reductions are obtained. It is easy to show that the nonlinear wave equation is not integrable under the sense of Ablowitz's conjecture from the reduction results obtained. In addition, kink-shaped solitary wave solutions, which are of important physical significance, are found for HMBEDT based on the obtained reduction equation. The project supported by National Natural Science Foundation of China under Grant No. 19572022, the National Key Basic Research Development Project Program of China under Grant No. G1998030600 and Doctoral Foundation of China under Grant No. 98014119

  4. Promoting Convergence: The Integrated Graduate Program in Physical and Engineering Biology at Yale University, a New Model for Graduate Education

    ERIC Educational Resources Information Center

    Noble, Dorottya B.; Mochrie, Simon G. J.; O'Hern, Corey S.; Pollard, Thomas D.; Regan, Lynne

    2016-01-01

    In 2008, we established the Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) at Yale University. Our goal was to create a comprehensive graduate program to train a new generation of scientists who possess a sophisticated understanding of biology and who are capable of applying physical and quantitative methodologies to…

  5. A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture.

    PubMed

    Ciaccio, Mark F; Finkle, Justin D; Xue, Albert Y; Bagheri, Neda

    2014-07-01

    An organism's ability to maintain a desired physiological response relies extensively on how cellular and molecular signaling networks interpret and react to environmental cues. The capacity to quantitatively predict how networks respond to a changing environment by modifying signaling regulation and phenotypic responses will help inform and predict the impact of a changing global enivronment on organisms and ecosystems. Many computational strategies have been developed to resolve cue-signal-response networks. However, selecting a strategy that answers a specific biological question requires knowledge both of the type of data being collected, and of the strengths and weaknesses of different computational regimes. We broadly explore several computational approaches, and we evaluate their accuracy in predicting a given response. Specifically, we describe how statistical algorithms can be used in the context of integrative and comparative biology to elucidate the genomic, proteomic, and/or cellular networks responsible for robust physiological response. As a case study, we apply this strategy to a dataset of quantitative levels of protein abundance from the mussel, Mytilus galloprovincialis, to uncover the temperature-dependent signaling network. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  6. 30GHz Ge electro-absorption modulator integrated with 3 μm silicon-on-insulator waveguide.

    PubMed

    Feng, Ning-Ning; Feng, Dazeng; Liao, Shirong; Wang, Xin; Dong, Po; Liang, Hong; Kung, Cheng-Chih; Qian, Wei; Fong, Joan; Shafiiha, Roshanak; Luo, Ying; Cunningham, Jack; Krishnamoorthy, Ashok V; Asghari, Mehdi

    2011-04-11

    We demonstrate a compact waveguide-based high-speed Ge electro-absorption (EA) modulator integrated with a single mode 3 µm silicon-on-isolator (SOI) waveguide. The Ge EA modulator is based on a horizontally-oriented p-i-n structure butt-coupled with a deep-etched silicon waveguide, which transitions adiabatically to a shallow-etched single mode large core SOI waveguide. The demonstrated device has a compact active region of 1.0 × 45 µm(2), a total insertion loss of 2.5-5 dB and an extinction ratio of 4-7.5 dB over a wavelength range of 1610-1640 nm with -4V(pp) bias. The estimated Δα/α value is in the range of 2-3.3. The 3 dB bandwidth measurements show that the device is capable of operating at more than 30 GHz. Clear eye-diagram openings at 12.5 Gbps demonstrates large signal modulation at high transmission rate. © 2011 Optical Society of America

  7. Harnessing the Power of Integrated Mitochondrial Biology and Physiology: A Special Report on the NHLBI Mitochondria in Heart Diseases Initiative.

    PubMed

    Ping, Peipei; Gustafsson, Åsa B; Bers, Don M; Blatter, Lothar A; Cai, Hua; Jahangir, Arshad; Kelly, Daniel; Muoio, Deborah; O'Rourke, Brian; Rabinovitch, Peter; Trayanova, Natalia; Van Eyk, Jennifer; Weiss, James N; Wong, Renee; Schwartz Longacre, Lisa

    2015-07-17

    Mitochondrial biology is the sum of diverse phenomena from molecular profiles to physiological functions. A mechanistic understanding of mitochondria in disease development, and hence the future prospect of clinical translations, relies on a systems-level integration of expertise from multiple fields of investigation. Upon the successful conclusion of a recent National Institutes of Health, National Heart, Lung, and Blood Institute initiative on integrative mitochondrial biology in cardiovascular diseases, we reflect on the accomplishments made possible by this unique interdisciplinary collaboration effort and exciting new fronts on the study of these remarkable organelles. © 2015 American Heart Association, Inc.

  8. Evaluation of a biological wastewater treatment system combining an OSA process with ultrasound for sludge reduction.

    PubMed

    Romero-Pareja, P M; Aragon, C A; Quiroga, J M; Coello, M D

    2017-05-01

    Sludge production is an undesirable by-product of biological wastewater treatment. The oxic-settling-anaerobic (OSA) process constitutes one of the most promising techniques for reducing the sludge produced at the treatment plant without negative consequences for its overall performance. In the present study, the OSA process is applied in combination with ultrasound treatment, a lysis technique, in a lab-scale wastewater treatment plant to assess whether sludge reduction is enhanced as a result of mechanical treatment. Reported sludge reductions of 45.72% and 78.56% were obtained for the two regimes of combined treatment tested in this study during two respective stages: UO1 and UO2. During the UO1 stage, the general performance and nutrient removal improved, obtaining 47.28% TN removal versus 21.95% in the conventional stage. However, the performance of the system was seriously damaged during the UO2 stage. Increases in dehydrogenase and protease activities were observed during both stages. The advantages of the combined process are not necessarily economic, but operational, as US treatment acts as contributing factor in the OSA process, inducing mechanisms that lead to sludge reduction in the OSA process and improving performance parameters. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Biology's response to dieting: the impetus for weight regain

    PubMed Central

    Bergouignan, Audrey; Cornier, Marc-Andre; Jackman, Matthew R.

    2011-01-01

    Dieting is the most common approach to losing weight for the majority of obese and overweight individuals. Restricting intake leads to weight loss in the short term, but, by itself, dieting has a relatively poor success rate for long-term weight reduction. Most obese people eventually regain the weight they have worked so hard to lose. Weight regain has emerged as one of the most significant obstacles for obesity therapeutics, undoubtedly perpetuating the epidemic of excess weight that now affects more than 60% of U.S. adults. In this review, we summarize the evidence of biology's role in the problem of weight regain. Biology's impact is first placed in context with other pressures known to affect body weight. Then, the biological adaptations to an energy-restricted, low-fat diet that are known to occur in the overweight and obese are reviewed, and an integrative picture of energy homeostasis after long-term weight reduction and during weight regain is presented. Finally, a novel model is proposed to explain the persistence of the “energy depletion” signal during the dynamic metabolic state of weight regain, when traditional adiposity signals no longer reflect stored energy in the periphery. The preponderance of evidence would suggest that the biological response to weight loss involves comprehensive, persistent, and redundant adaptations in energy homeostasis and that these adaptations underlie the high recidivism rate in obesity therapeutics. To be successful in the long term, our strategies for preventing weight regain may need to be just as comprehensive, persistent, and redundant, as the biological adaptations they are attempting to counter. PMID:21677272

  10. TRIENNIAL LACTATION SYMPOSIUM: Nutrigenomics in livestock: Systems biology meets nutrition.

    PubMed

    Loor, J J; Vailati-Riboni, M; McCann, J C; Zhou, Z; Bionaz, M

    2015-12-01

    The advent of high-throughput technologies to study an animal's genome, proteome, and metabolome (i.e., "omics" tools) constituted a setback to the use of reductionism in livestock research. More recent development of "next-generation sequencing" tools was instrumental in allowing in-depth studies of the microbiome in the rumen and other sections of the gastrointestinal tract. Omics, along with bioinformatics, constitutes the foundation of modern systems biology, a field of study widely used in model organisms (e.g., rodents, yeast, humans) to enhance understanding of the complex biological interactions occurring within cells and tissues at the gene, protein, and metabolite level. Application of systems biology concepts is ideal for the study of interactions between nutrition and physiological state with tissue and cell metabolism and function during key life stages of livestock species, including the transition from pregnancy to lactation, in utero development, or postnatal growth. Modern bioinformatic tools capable of discerning functional outcomes and biologically meaningful networks complement the ever-increasing ability to generate large molecular, microbial, and metabolite data sets. Simultaneous visualization of the complex intertissue adaptations to physiological state and nutrition can now be discerned. Studies to understand the linkages between the microbiome and the absorptive epithelium using the integrative approach are emerging. We present examples of new knowledge generated through the application of functional analyses of transcriptomic, proteomic, and metabolomic data sets encompassing nutritional management of dairy cows, pigs, and poultry. Published work to date underscores that the integrative approach across and within tissues may prove useful for fine-tuning nutritional management of livestock. An important goal during this process is to uncover key molecular players involved in the organismal adaptations to nutrition.

  11. Atomic-absorption determination of rhodium in chromite concentrates

    USGS Publications Warehouse

    Schnepfe, M.M.; Grimaldi, F.S.

    1969-01-01

    Rhodium is determined in chromite concentrates by atomic absorption after concentration either by co-precipitation with tellurium formed by the reduction of tellurite with tin(II) chloride or by fire assay into a gold bead. Interelement interferences in the atomic-absorption determination are removed by buffering the solutions with lanthanum sulphate (lanthanum concentration 1%). Substantial amounts of Ag, Al, Au, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ho, Hg, K, La, Mg, Mn, Mo, Na, Ni, Pb, Te, Ti, V, Y, Zn and platinum metals can be tolerated. A lower limit of approximately 0.07 ppm Rh can be determined in a 3-g sample. ?? 1969.

  12. Integration of Biological and Physical Sciences to Advance Ecological Understanding of Aquatic Ecosystems

    NASA Astrophysics Data System (ADS)

    Luce, C. H.; Buffington, J. M.; Rieman, B. E.; Dunham, J. B.; McKean, J. A.; Thurow, R. F.; Gutierrez-Teira, B.; Rosenberger, A. E.

    2005-05-01

    Conservation and restoration of freshwater stream and river habitats are important goals for land management and natural resources research. Several examples of research have emerged showing that many species are adapted to temporary habitat disruptions, but that these adaptations are sensitive to the spatial grain and extent of disturbance as well as to its duration. When viewed from this perspective, questions of timing, spatial pattern, and relevant scales emerge as critical issues. In contrast, much regulation, management, and research remains tied to pollutant loading paradigms that are insensitive to either time or space scales. It is becoming clear that research is needed to examine questions and hypotheses about how physical processes affect ecological processes. Two overarching questions concisely frame the scientific issues: 1) How do we quantify physical watershed processes in a way that is meaningful to biological and ecological processes, and 2) how does the answer to that question vary with changing spatial and temporal scales? A joint understanding of scaling characteristics of physical process and the plasticity of aquatic species will be needed to accomplish this research; hence a strong need exists for integrative and collaborative development. Considering conservation biology problems in this fashion can lead to creative and non-obvious solutions because the integrated system has important non-linearities and feedbacks related to a biological system that has responded to substantial natural variability in the past. We propose that research beginning with ecological theories and principles followed with a structured examination of each physical process as related to the specific ecological theories is a strong approach to developing the necessary science, and such an approach may form a basis for development of scaling theories of hydrologic and geomorphic process. We illustrate the approach with several examples.

  13. Classification of small lesions on dynamic breast MRI: Integrating dimension reduction and out-of-sample extension into CADx methodology

    PubMed Central

    Nagarajan, Mahesh B.; Huber, Markus B.; Schlossbauer, Thomas; Leinsinger, Gerda; Krol, Andrzej; Wismüller, Axel

    2014-01-01

    Objective While dimension reduction has been previously explored in computer aided diagnosis (CADx) as an alternative to feature selection, previous implementations of its integration into CADx do not ensure strict separation between training and test data required for the machine learning task. This compromises the integrity of the independent test set, which serves as the basis for evaluating classifier performance. Methods and Materials We propose, implement and evaluate an improved CADx methodology where strict separation is maintained. This is achieved by subjecting the training data alone to dimension reduction; the test data is subsequently processed with out-of-sample extension methods. Our approach is demonstrated in the research context of classifying small diagnostically challenging lesions annotated on dynamic breast magnetic resonance imaging (MRI) studies. The lesions were dynamically characterized through topological feature vectors derived from Minkowski functionals. These feature vectors were then subject to dimension reduction with different linear and non-linear algorithms applied in conjunction with out-of-sample extension techniques. This was followed by classification through supervised learning with support vector regression. Area under the receiver-operating characteristic curve (AUC) was evaluated as the metric of classifier performance. Results Of the feature vectors investigated, the best performance was observed with Minkowski functional ’perimeter’ while comparable performance was observed with ’area’. Of the dimension reduction algorithms tested with ’perimeter’, the best performance was observed with Sammon’s mapping (0.84 ± 0.10) while comparable performance was achieved with exploratory observation machine (0.82 ± 0.09) and principal component analysis (0.80 ± 0.10). Conclusions The results reported in this study with the proposed CADx methodology present a significant improvement over previous results reported with

  14. Decision-Making Under Risk: Integrating Perspectives From Biology, Economics, and Psychology.

    PubMed

    Mishra, Sandeep

    2014-08-01

    Decision-making under risk has been variably characterized and examined in many different disciplines. However, interdisciplinary integration has not been forthcoming. Classic theories of decision-making have not been amply revised in light of greater empirical data on actual patterns of decision-making behavior. Furthermore, the meta-theoretical framework of evolution by natural selection has been largely ignored in theories of decision-making under risk in the human behavioral sciences. In this review, I critically examine four of the most influential theories of decision-making from economics, psychology, and biology: expected utility theory, prospect theory, risk-sensitivity theory, and heuristic approaches. I focus especially on risk-sensitivity theory, which offers a framework for understanding decision-making under risk that explicitly involves evolutionary considerations. I also review robust empirical evidence for individual differences and environmental/situational factors that predict actual risky decision-making that any general theory must account for. Finally, I offer steps toward integrating various theoretical perspectives and empirical findings on risky decision-making. © 2014 by the Society for Personality and Social Psychology, Inc.

  15. Integration of plastids with their hosts: Lessons learned from dinoflagellates

    PubMed Central

    Dorrell, Richard G.; Howe, Christopher J.

    2015-01-01

    After their endosymbiotic acquisition, plastids become intimately connected with the biology of their host. For example, genes essential for plastid function may be relocated from the genomes of plastids to the host nucleus, and pathways may evolve within the host to support the plastid. In this review, we consider the different degrees of integration observed in dinoflagellates and their associated plastids, which have been acquired through multiple different endosymbiotic events. Most dinoflagellate species possess plastids that contain the pigment peridinin and show extreme reduction and integration with the host biology. In some species, these plastids have been replaced through serial endosymbiosis with plastids derived from a different phylogenetic derivation, of which some have become intimately connected with the biology of the host whereas others have not. We discuss in particular the evolution of the fucoxanthin-containing dinoflagellates, which have adapted pathways retained from the ancestral peridinin plastid symbiosis for transcript processing in their current, serially acquired plastids. Finally, we consider why such a diversity of different degrees of integration between host and plastid is observed in different dinoflagellates and how dinoflagellates may thus inform our broader understanding of plastid evolution and function. PMID:25995366

  16. Integration of plastids with their hosts: Lessons learned from dinoflagellates.

    PubMed

    Dorrell, Richard G; Howe, Christopher J

    2015-08-18

    After their endosymbiotic acquisition, plastids become intimately connected with the biology of their host. For example, genes essential for plastid function may be relocated from the genomes of plastids to the host nucleus, and pathways may evolve within the host to support the plastid. In this review, we consider the different degrees of integration observed in dinoflagellates and their associated plastids, which have been acquired through multiple different endosymbiotic events. Most dinoflagellate species possess plastids that contain the pigment peridinin and show extreme reduction and integration with the host biology. In some species, these plastids have been replaced through serial endosymbiosis with plastids derived from a different phylogenetic derivation, of which some have become intimately connected with the biology of the host whereas others have not. We discuss in particular the evolution of the fucoxanthin-containing dinoflagellates, which have adapted pathways retained from the ancestral peridinin plastid symbiosis for transcript processing in their current, serially acquired plastids. Finally, we consider why such a diversity of different degrees of integration between host and plastid is observed in different dinoflagellates and how dinoflagellates may thus inform our broader understanding of plastid evolution and function.

  17. Scale relativity theory and integrative systems biology: 1. Founding principles and scale laws.

    PubMed

    Auffray, Charles; Nottale, Laurent

    2008-05-01

    In these two companion papers, we provide an overview and a brief history of the multiple roots, current developments and recent advances of integrative systems biology and identify multiscale integration as its grand challenge. Then we introduce the fundamental principles and the successive steps that have been followed in the construction of the scale relativity theory, and discuss how scale laws of increasing complexity can be used to model and understand the behaviour of complex biological systems. In scale relativity theory, the geometry of space is considered to be continuous but non-differentiable, therefore fractal (i.e., explicitly scale-dependent). One writes the equations of motion in such a space as geodesics equations, under the constraint of the principle of relativity of all scales in nature. To this purpose, covariant derivatives are constructed that implement the various effects of the non-differentiable and fractal geometry. In this first review paper, the scale laws that describe the new dependence on resolutions of physical quantities are obtained as solutions of differential equations acting in the scale space. This leads to several possible levels of description for these laws, from the simplest scale invariant laws to generalized laws with variable fractal dimensions. Initial applications of these laws to the study of species evolution, embryogenesis and cell confinement are discussed.

  18. An integrative study on biologically recovered polyhydroxyalkanoates (PHAs) and simultaneous assessment of gut microbiome in yellow mealworm.

    PubMed

    Ong, Su Yean; Kho, Hui-Pheng; Riedel, Sebastian L; Kim, Seok-Won; Gan, Chee-Yuen; Taylor, Todd D; Sudesh, Kumar

    2018-01-10

    Polyhydroxyalkanoates (PHAs) are produced in microbes as a source of carbon and energy storage. They are biodegradable and have properties similar to synthetic plastics, which make them an interesting alternative to petroleum-based plastics. In this study, a refined method of recovering PHA from Cupriavidus necator biomass was proposed by incorporating the use of the yellow mealworm (the larval phase of the mealworm beetle, Tenebrio molitor) as partial purification machinery, followed by washing of the fecal pellets with distilled water and sodium hydroxide. The PHA contents of the cells used in this study were 55wt% (produced from palm olein) and 60 wt% (produced from waste animal fats). The treatment of distilled water and NaOH further increased the purity of PHA to 94%. In parallel, analysis of the 16S rRNA metagenomic sequencing of the mealworm gut microbiome has revealed remarkable changes in the bacterial diversity, especially between the mealworms fed with cells produced from palm olein and waste animal fats. This biological recovery of PHA from cells is an attempt to move towards a green and sustainable process with the aim of reducing the use of harmful solvents and strong chemicals during polymer purification. The results obtained show that - purities of >90%, without a reduction in the molecular weight, can be obtained through this integrative biological recovery approach. In addition, this study has successfully shown that the cells, regardless of their origins, were readily consumed by the mealworms, and there is a correlation between the feed type and the mealworm gut microbiome. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Analysis of specific absorption rate and internal electric field in human biological tissues surrounding an air-core coil-type transcutaneous energy transmission transformer.

    PubMed

    Shiba, Kenji; Zulkifli, Nur Elina Binti; Ishioka, Yuji

    2017-06-01

    In this study, we analyzed the internal electric field E and specific absorption rate (SAR) of human biological tissues surrounding an air-core coil transcutaneous energy transmission transformer. Using an electromagnetic simulator, we created a model of human biological tissues consisting of a dry skin, wet skin, fat, muscle, and cortical bone. A primary coil was placed on the surface of the skin, and a secondary coil was located subcutaneously inside the body. The E and SAR values for the model representing a 34-year-old male subject were analyzed using electrical frequencies of 0.3-1.5 MHz. The transmitting power was 15 W, and the load resistance was 38.4 Ω. The results showed that the E values were below the International Commission on Non-ionizing Radiation Protection (ICNIRP) limit for the general public exposure between the frequencies of 0.9 and 1.5 MHz, and SAR values were well below the limit prescribed by the ICNIRP for the general public exposure between the frequencies of 0.3 and 1.2 MHz.

  20. Neurological and Biological Foundations of Children's Social and Emotional Development: An Integrated Literature Review

    ERIC Educational Resources Information Center

    Nelson, Helen Jean; Kendall, Garth Edward; Shields, Linda

    2014-01-01

    This article provides an integrated review of the expert literature on developmental processes that combine social, biological, and neurological pathways, and the mechanisms through which these pathways may influence school success and health. It begins with a historical overview of the current understanding of how attachment relationships and…

  1. Using dual classifications in the development of avian wetland indices of biological integrity for wetlands in West Virginia, USA.

    PubMed

    Veselka, Walter; Anderson, James T; Kordek, Walter S

    2010-05-01

    Considerable resources are being used to develop and implement bioassessment methods for wetlands to ensure that "biological integrity" is maintained under the United States Clean Water Act. Previous research has demonstrated that avian composition is susceptible to human impairments at multiple spatial scales. Using a site-specific disturbance gradient, we built avian wetland indices of biological integrity (AW-IBI) specific to two wetland classification schemes, one based on vegetative structure and the other based on the wetland's position in the landscape and sources of water. The resulting class-specific AW-IBI was comprised of one to four metrics that varied in their sensitivity to the disturbance gradient. Some of these metrics were specific to only one of the classification schemes, whereas others could discriminate varying levels of disturbance regardless of classification scheme. Overall, all of the derived biological indices specific to the vegetative structure-based classes of wetlands had a significant relation with the disturbance gradient; however, the biological index derived for floodplain wetlands exhibited a more consistent response to a local disturbance gradient. We suspect that the consistency of this response is due to the inherent nature of the connectivity of available habitat in floodplain wetlands.

  2. Dose addition models based on biologically-relevant reductions in fetal testosterone accurately predict postnatal reproductive tract alterations by a phthalate mixture in rats

    EPA Science Inventory

    Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the curren...

  3. Computational systems chemical biology.

    PubMed

    Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

  4. Computational Systems Chemical Biology

    PubMed Central

    Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

    2013-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007). The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology / systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology. PMID:20838980

  5. Emerging concepts for management of river ecosystems and challenges to applied integration of physical and biological sciences in the Pacific Northwest, USA

    Treesearch

    Bruce E. Rieman; Jason B. Dunham; James L. Clayton

    2006-01-01

    Integration of biological and physical concepts is necessary to understand and conserve the ecological integrity of river systems. Past attempts at integration have often focused at relatively small scales and on mechanistic models that may not capture the complexity of natural systems leaving substantial uncertainty about ecological responses to management actions....

  6. Integration of computer-assisted fracture reduction system and a hybrid 3-DOF-RPS mechanism for assisting the orthopedic surgery

    NASA Astrophysics Data System (ADS)

    Irwansyah; Sinh, N. P.; Lai, J. Y.; Essomba, T.; Asbar, R.; Lee, P. Y.

    2018-02-01

    In this paper, we present study to integrate virtual fracture bone reduction simulation tool with a novel hybrid 3-DOF-RPS external fixator to relocate back bone fragments into their anatomically original position. A 3D model of fractured bone was reconstructed and manipulated using 3D design and modeling software, PhysiGuide. The virtual reduction system was applied to reduce a bilateral femoral shaft fracture type 32-A3. Measurement data from fracture reduction and fixation stages were implemented to manipulate the manipulator pose in patient’s clinical case. The experimental result presents that by merging both of those techniques will give more possibilities to reduce virtual bone reduction time, improve facial and shortest healing treatment.

  7. Absorption of the laser radiation by the laser plasma with gas microjet targets

    NASA Astrophysics Data System (ADS)

    Borisevichus, D. A.; Zabrodskii, V. V.; Kalmykov, S. G.; Sasin, M. E.; Seisyan, R. P.

    2017-01-01

    An upper limit of absorption of the laser radiation in the plasma produced in a gas jet Xe target with the average density of (3-6) × 1018 cm-3 and the effective diameter of 0.7 mm is found. It is equal to ≈50% and remains constant under any variation in this range of densities. This result contradicts both theoretical assessments that have predicted virtually complete absorption and results of earlier experiments with the laser spark in an unlimited stationary Xe gas with the same density, where the upper limit of absorption was close to 100%. An analysis shows that nonlinearity of absorption and plasma nonequilibrium lead to the reduction of the absorption coefficient that, along with the limited size of plasma, can explain the experimental results.

  8. Fat, oil and grease reduction in commercial kitchen ductwork: A novel biological approach.

    PubMed

    Mudie, S; Vahdati, M

    2017-03-01

    Recent research has characterised emissions upon cooking a variety of foods in a commercial catering environment in terms of volume, particle size and composition. However, there has been limited focus on the deposition of solid grease in commercial kitchen ductwork, the sustainability of these systems and their implications on the heat recovery potential of kitchen ventilation extract air. This paper reviews the literature concerning grease, commonly referred to as Fat, Oils and Grease (FOG) abatement strategies and finds that many of these systems fall short of claimed performances. Furthermore these technologies often add to the energy cost of the operation and reduce the potential application of heat recovery in the ventilation ductwork. The aim of this study was to develop and evaluate a novel FOG removal system, with a focus on low environmental impact. The novel FOG removal system, utilises the biological activity of Bacillus subtilis and associated enzymes. The biological reagent is delivered via a misting system. The temperature, relative humidity and FOG deposit thickness were measured in the ductwork throughout a 3month trial period. FOG deposit thickness was reduced by 47% within 7weeks. The system was found to be effective at reducing the FOG deposit thickness with minimal energy cost and impact upon the kitchen and external environment. Internal ductwork operating temperature was measured with respect to future heat recovery potential and a reduction of 7°C was observed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Assessing Vermont's stream health and biological integrity using artificial neural networks and Bayesian methods

    NASA Astrophysics Data System (ADS)

    Rizzo, D. M.; Fytilis, N.; Stevens, L.

    2012-12-01

    Environmental managers are increasingly required to monitor and forecast long-term effects and vulnerability of biophysical systems to human-generated stresses. Ideally, a study involving both physical and biological assessments conducted concurrently (in space and time) could provide a better understanding of the mechanisms and complex relationships. However, costs and resources associated with monitoring the complex linkages between the physical, geomorphic and habitat conditions and the biological integrity of stream reaches are prohibitive. Researchers have used classification techniques to place individual streams and rivers into a broader spatial context (hydrologic or health condition). Such efforts require environmental managers to gather multiple forms of information - quantitative, qualitative and subjective. We research and develop a novel classification tool that combines self-organizing maps with a Naïve Bayesian classifier to direct resources to stream reaches most in need. The Vermont Agency of Natural Resources has developed and adopted protocols for physical stream geomorphic and habitat assessments throughout the state of Vermont. Separate from these assessments, the Vermont Department of Environmental Conservation monitors the biological communities and the water quality in streams. Our initial hypothesis is that the geomorphic reach assessments and water quality data may be leveraged to reduce error and uncertainty associated with predictions of biological integrity and stream health. We test our hypothesis using over 2500 Vermont stream reaches (~1371 stream miles) assessed by the two agencies. In the development of this work, we combine a Naïve Bayesian classifier with a modified Kohonen Self-Organizing Map (SOM). The SOM is an unsupervised artificial neural network that autonomously analyzes inherent dataset properties using input data only. It is typically used to cluster data into similar categories when a priori classes do not exist. The

  10. Microbial reduction of graphene oxide by Escherichia coli: a green chemistry approach.

    PubMed

    Gurunathan, Sangiliyandi; Han, Jae Woong; Eppakayala, Vasuki; Kim, Jin-Hoi

    2013-02-01

    Graphene and graphene related materials are an important area of research in recent years due to their unique properties. The extensive industrial application of graphene and related compounds has led researchers to devise novel and simple methods for the synthesis of high quality graphene. In this paper, we developed an environment friendly, cost effective, simple method and green approaches for the reduction of graphene oxide (GO) using Escherichia coli biomass. In biological method, we can avoid use of toxic and environmentally harmful reducing agents commonly used in the chemical reduction of GO to obtain graphene. The biomass of E. coli reduces exfoliated GO to graphene at 37°C in an aqueous medium. The E. coli reduced graphene oxide (ERGO) was characterized with UV-visible absorption spectroscopy, particle analyzer, high resolution X-ray diffractometer, scanning electron microscopy and Raman spectroscopy. Besides the reduction potential, the biomass could also play an important role as stabilizing agent, in which synthesized graphene exhibited good stability in water. This method can open up the new avenue for preparing graphene in cost effective and large scale production. Our findings suggest that GO can be reduced by simple eco-friendly method by using E. coli biomass to produce water dispersible graphene. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Gauss-Kronrod-Trapezoidal Integration Scheme for Modeling Biological Tissues with Continuous Fiber Distributions

    PubMed Central

    Hou, Chieh; Ateshian, Gerard A.

    2015-01-01

    Fibrous biological tissues may be modeled using a continuous fiber distribution (CFD) to capture tension-compression nonlinearity, anisotropic fiber distributions, and load-induced anisotropy. The CFD framework requires spherical integration of weighted individual fiber responses, with fibers contributing to the stress response only when they are in tension. The common method for performing this integration employs the discretization of the unit sphere into a polyhedron with nearly uniform triangular faces (finite element integration or FEI scheme). Although FEI has proven to be more accurate and efficient than integration using spherical coordinates, it presents three major drawbacks: First, the number of elements on the unit sphere needed to achieve satisfactory accuracy becomes a significant computational cost in a finite element analysis. Second, fibers may not be in tension in some regions on the unit sphere, where the integration becomes a waste. Third, if tensed fiber bundles span a small region compared to the area of the elements on the sphere, a significant discretization error arises. This study presents an integration scheme specialized to the CFD framework, which significantly mitigates the first drawback of the FEI scheme, while eliminating the second and third completely. Here, integration is performed only over the regions of the unit sphere where fibers are in tension. Gauss-Kronrod quadrature is used across latitudes and the trapezoidal scheme across longitudes. Over a wide range of strain states, fiber material properties, and fiber angular distributions, results demonstrate that this new scheme always outperforms FEI, sometimes by orders of magnitude in the number of computational steps and relative accuracy of the stress calculation. PMID:26291492

  12. A Review of the Integration of Classical Biological Control with other Management Techniques to Manage Invasive Weeds in Natural Areas and Rangelands

    USDA-ARS?s Scientific Manuscript database

    Integrating classical biological control with other management techniques such as herbicide, fire, mechanical control, grazing, or plant competition, can be the most effective way to manage invasive weeds in natural areas and rangelands. Biological control agents can be protected from potential nega...

  13. Flower biology and biologically-based integrated fire blight management

    USDA-ARS?s Scientific Manuscript database

    Fire blight infection is generally initiated in flowers, and thus, research has been directed to the biology and microbial ecology of flowers as related to this disease. In addition to investigations involving apple and pear flowers, Manchurian crab apple (Malus manchurica), closely related to appl...

  14. Biotic and abiotic studies on the biological fate, transport and ecotoxicity of toxic and hazardous waste in the Mississippi River basin

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Abdelghani, A.; Pramar, Y.; Mandal, T.

    1996-05-02

    This project assesses the levels of xenobiotics in Devils Swamp and studies their biological fate, transport, ecotoxicity, and potential toxicity to man. This article reports on the following studies: assessment of the acute toxicity of individual xenobiotics and toxicity of organic compounds hexachlorobutadience (HCB) and hexachlorobenzene (HCBD) on juvenile crayfish; determination of the biotic influence of temperature, salinity, pH, oxidation-reduction potential, and sediment composition on the migration of xenobiotics; development of a pharmacokinetics model for xenobiotic absorption and storage, distribution and excretion by fish and crayfish.

  15. Five-Photon Absorption and Selective Enhancement of Multiphoton Absorption Processes

    PubMed Central

    2015-01-01

    We study one-, two-, three-, four-, and five-photon absorption of three centrosymmetric molecules using density functional theory. These calculations are the first ab initio calculations of five-photon absorption. Even- and odd-order absorption processes show different trends in the absorption cross sections. The behavior of all even- and odd-photon absorption properties shows a semiquantitative similarity, which can be explained using few-state models. This analysis shows that odd-photon absorption processes are largely determined by the one-photon absorption strength, whereas all even-photon absorption strengths are largely dominated by the two-photon absorption strength, in both cases modulated by powers of the polarizability of the final excited state. We demonstrate how to selectively enhance a specific multiphoton absorption process. PMID:26120588

  16. Five-Photon Absorption and Selective Enhancement of Multiphoton Absorption Processes.

    PubMed

    Friese, Daniel H; Bast, Radovan; Ruud, Kenneth

    2015-05-20

    We study one-, two-, three-, four-, and five-photon absorption of three centrosymmetric molecules using density functional theory. These calculations are the first ab initio calculations of five-photon absorption. Even- and odd-order absorption processes show different trends in the absorption cross sections. The behavior of all even- and odd-photon absorption properties shows a semiquantitative similarity, which can be explained using few-state models. This analysis shows that odd-photon absorption processes are largely determined by the one-photon absorption strength, whereas all even-photon absorption strengths are largely dominated by the two-photon absorption strength, in both cases modulated by powers of the polarizability of the final excited state. We demonstrate how to selectively enhance a specific multiphoton absorption process.

  17. Column carbon dioxide and water vapor measurements by an airborne triple-pulse integrated path differential absorption lidar: novel lidar technologies and techniques with path to space

    NASA Astrophysics Data System (ADS)

    Singh, U. N.; Petros, M.; Refaat, T. F.; Yu, J.; Ismail, S.

    2017-09-01

    The 2-micron wavelength region is suitable for atmospheric carbon dioxide (CO2) measurements due to the existence of distinct absorption features for the gas at this wavelength region [1]. For more than 20 years, researchers at NASA Langley Research Center (LaRC) have developed several high-energy and high repetition rate 2-micron pulsed lasers [2]. Currently, LaRC team is engaged in designing, developing and demonstrating a triple-pulsed 2-micron direct detection Integrated Path Differential Absorption (IPDA) lidar to measure the weighted-average column dry-air mixing ratios of carbon dioxide (XCO2) and water vapor (XH2O) from an airborne platform [1, 3-5]. This novel technique allows measurement of the two most dominant greenhouse gases, simultaneously and independently, using a single instrument. This paper will provide status and details of the development of this airborne 2-micron triple-pulse IPDA lidar. The presented work will focus on the advancement of critical IPDA lidar components. Updates on the state-of-the-art triple-pulse laser transmitter will be presented including the status of seed laser locking, wavelength control, receiver and detector upgrades, laser packaging and lidar integration. Future plans for IPDA lidar ground integration, testing and flight validation will also be discussed. This work enables new Earth observation measurements, while reducing risk, cost, size, volume, mass and development time of required instruments.

  18. The Integration of Biology into Calculus Courses

    ERIC Educational Resources Information Center

    Comar, Timothy D.

    2008-01-01

    This article discusses the incorporation of biological content into existing calculus courses without significantly changing the courses. This is exemplified by the common laboratory course taken by students in all first semester calculus courses at Benedictine University. Several biologically oriented projects are implemented in this laboratory…

  19. Intestinal absorption of copper: influence of carbohydrates.

    PubMed

    Wapnir, R A; Balkman, C

    1992-02-01

    Macronutrients can modulate the intestinal absorption of trace elements by binding the metal or altering mucosal function. We investigated whether certain simple and complex carbohydrates modify copper (Cu) absorption, using an in vivo perfusion technique in the rat. Corn syrup solids, which contain a mixture of glucose polymers of diverse length, added at either 20 or 50 mosm/kg enhanced Cu absorption from a 31.5 microM (2 mg/liter) Cu solution (128 +/- 11 and 130 +/- 11 pmol/min x cm, respectively, vs 101 +/- 4 pmol/min x cm, P less than 0.05, in the absence of carbohydrate). This was concomitant with a stimulation of net water absorption (1.05 +/- 0.08 and 0.84 +/- 0.08 microliter/min x cm, respectively, vs 0.63 +/- 0.02 microliter/min x cm with no carbohydrate, P less than 0.05). Glucose, fructose, lactose, or sucrose had no influence on Cu absorption, although they altered water exchanges, an effect attributable to a reduction of the outflow component of fluid recirculation. Low concentrations of lactose resulted in a greater accumulation of Cu in the intestinal mucosa (8.75 +/- 0.71 micrograms/g vs 5.77 +/- 0.68 micrograms/g for controls, P less than 0.05). Hence, solutes that moderately stimulate mucosa-to-serosa fluid influx in a progressive manner, such as glucose polymers, may contribute to functionally increase Cu absorption. Conversely, conditions which tend to reduce water inflow or increase water outflow across the small intestinal mucosa, as may occur with high lactose diets or in cases of chronic diarrhea, may have negative effects.

  20. Model reduction of multiscale chemical langevin equations: a numerical case study.

    PubMed

    Sotiropoulos, Vassilios; Contou-Carrere, Marie-Nathalie; Daoutidis, Prodromos; Kaznessis, Yiannis N

    2009-01-01

    Two very important characteristics of biological reaction networks need to be considered carefully when modeling these systems. First, models must account for the inherent probabilistic nature of systems far from the thermodynamic limit. Often, biological systems cannot be modeled with traditional continuous-deterministic models. Second, models must take into consideration the disparate spectrum of time scales observed in biological phenomena, such as slow transcription events and fast dimerization reactions. In the last decade, significant efforts have been expended on the development of stochastic chemical kinetics models to capture the dynamics of biomolecular systems, and on the development of robust multiscale algorithms, able to handle stiffness. In this paper, the focus is on the dynamics of reaction sets governed by stiff chemical Langevin equations, i.e., stiff stochastic differential equations. These are particularly challenging systems to model, requiring prohibitively small integration step sizes. We describe and illustrate the application of a semianalytical reduction framework for chemical Langevin equations that results in significant gains in computational cost.

  1. Integrating Functional, Developmental and Evolutionary Biology into Biology Curricula

    ERIC Educational Resources Information Center

    Haave, Neil

    2012-01-01

    A complete understanding of life involves how organisms are able to function in their environment and how they arise. Understanding how organisms arise involves both their evolution and development. Thus to completely comprehend living things, biology must study their function, development and evolution. Previous proposals for standardized…

  2. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Describes laboratory procedures, demonstrations, and classroom activities/materials, including chi-square tests on a microcomputer, an integrated biology game, microscope slides of leaf stomata, culturing soil nematodes, technique for watering locust egg-laying tubes, hazards of biological chemicals (such as benzene, benzidene, calchicine,…

  3. Reduction of urogenital schistosomiasis with an integrated control project in Sudan.

    PubMed

    Lee, Young-Ha; Jeong, Hoo Gn; Kong, Woo Hyun; Lee, Soon-Hyung; Cho, Han-Ik; Nam, Hae-Sung; Ismail, Hassan Ahmed Hassan Ahmed; Alla, Gibril Nouman Abd; Oh, Chung Hyeon; Hong, Sung-Tae

    2015-01-01

    Schistosomiasis remains a major public health concern in Sudan, particularly Schistosoma haematobium infection. This study presents the disease-reduction outcomes of an integrated control program for schistosomiasis in Al Jabalain locality of White Nile State, Sudan from 2009 through 2011. The total population of the project sites was 482,902, and the major target group for intervention among them was 78,615 primary school students. For the cross-sectional study of the prevalence, urine and stool specimens were examined using the urine sedimentation method and the Kato cellophane thick smear method, respectively. To assess the impacts of health education for students and a drinking water supply facility at Al Hidaib village, questionnaire survey was done. The overall prevalence for S. haematobium and S. mansoni at baseline was 28.5% and 0.4%, respectively. At follow-up survey after 6-9 months post-treatment, the prevalence of S. haematobium infection was reduced to 13.5% (95% CI = 0.331-0.462). A higher reduction in prevalence was observed among girls, those with moderately infected status (around 20%), and residents in rural areas, than among boys, those with high prevalence (>40%), and residents in urban areas. After health education, increased awareness about schistosomiasis was checked by questionnaire survey. Also, a drinking water facility was constructed at Al Hidaib village, where infection rate was reduced more compared to that in a neighboring village within the same unit. However, we found no significant change in the prevalence of S. mansoni infection between baseline and follow-up survey (95% CI = 0.933-6.891). At the end of the project, the prevalence of S. haematobium infection was reduced by more than 50% in comparison with the baseline rate. Approximately 200,000 subjects had received either praziquantel therapy, health education, or supply of clean water. To consolidate the achievements of this project, the integrated intervention should

  4. Reduction of Urogenital Schistosomiasis with an Integrated Control Project in Sudan

    PubMed Central

    Lee, Young-Ha; Jeong, Hoo Gn; Kong, Woo Hyun; Lee, Soon-Hyung; Cho, Han-Ik; Nam, Hae-Sung; Ismail, Hassan Ahmed Hassan Ahmed; Alla, Gibril Nouman Abd; Oh, Chung Hyeon; Hong, Sung-Tae

    2015-01-01

    Purpose Schistosomiasis remains a major public health concern in Sudan, particularly Schistosoma haematobium infection. This study presents the disease-reduction outcomes of an integrated control program for schistosomiasis in Al Jabalain locality of White Nile State, Sudan from 2009 through 2011. Methods The total population of the project sites was 482,902, and the major target group for intervention among them was 78,615 primary school students. For the cross-sectional study of the prevalence, urine and stool specimens were examined using the urine sedimentation method and the Kato cellophane thick smear method, respectively. To assess the impacts of health education for students and a drinking water supply facility at Al Hidaib village, questionnaire survey was done. Results The overall prevalence for S. haematobium and S. mansoni at baseline was 28.5% and 0.4%, respectively. At follow-up survey after 6–9 months post-treatment, the prevalence of S. haematobium infection was reduced to 13.5% (95% CI = 0.331–0.462). A higher reduction in prevalence was observed among girls, those with moderately infected status (around 20%), and residents in rural areas, than among boys, those with high prevalence (>40%), and residents in urban areas. After health education, increased awareness about schistosomiasis was checked by questionnaire survey. Also, a drinking water facility was constructed at Al Hidaib village, where infection rate was reduced more compared to that in a neighboring village within the same unit. However, we found no significant change in the prevalence of S. mansoni infection between baseline and follow-up survey (95% CI = 0.933–6.891). Conclusions At the end of the project, the prevalence of S. haematobium infection was reduced by more than 50% in comparison with the baseline rate. Approximately 200,000 subjects had received either praziquantel therapy, health education, or supply of clean water. To consolidate the achievements of this

  5. Reduction of B-integral accumulation in lasers

    DOEpatents

    Meyerhofer, David D.; Konoplev, Oleg A.

    2000-01-01

    A pulsed laser is provided wherein the B-integral accumulated in the laser pulse is reduced using a semiconductor wafer. A laser pulse is generated by a laser pulse source. The laser pulse passes through a semiconductor wafer that has a negative nonlinear index of refraction. Thus, the laser pulse accumulates a negative B-integral. The laser pulse is then fed into a laser amplification medium, which has a positive nonlinear index of refraction. The laser pulse may make a plurality of passes through the laser amplification medium and accumulate a positive B-integral during a positive non-linear phase change. The semiconductor and laser pulse wavelength are chosen such that the negative B-integral accumulated in the semiconductor wafer substantially cancels the positive B-integral accumulated in the laser amplification medium. There may be additional accumulation of positive B-integral if the laser pulse passes through additional optical mediums such as a lens or glass plates. Thus, the effects of self-phase modulation in the laser pulse are substantially reduced.

  6. The role of fiber and matrix in crash energy absorption of composite materials

    NASA Technical Reports Server (NTRS)

    Farley, G. L.; Bird, R. K.; Modlin, J. T.

    1986-01-01

    Static crushing tests were conducted on tube specimens fabricated from graphite/epoxy, Kevlar/epoxy and hybrid combinations of graphite-Kevlar/epoxy to examine the influence the fiber and matrix constitutive properties and laminate architecture have on energy absorption. Fiber and matrix ultimate failure strain were determined to significantly effect energy absorption. The energy absorption capability of high ultimate failure strain materials (AS-6/F185 and AS-6/HST-7) was less than materials having lower ultimate failure strain. Lamina stacking sequence had up to a 300 percent change in energy absorption for the materials tested. Hybridizing with graphite and Kevlar reinforcements resulted in materials with high energy absorption capabilities that have postcrushing integrity.

  7. In search of the Golden Fleece: Unraveling principles of morphogenesis by studying the integrative biology of skin appendages

    PubMed Central

    Hughes, Michael W.; Wu, Ping; Jiang, Ting-Xin; Lin, Sung-Jan; Dong, Chen-Yuan; Li, Ang; Hsieh, Fon-Jou; Widelitz, Randall B.; Choung, Cheng Ming

    2013-01-01

    Summary The mythological story of the Golden Fleece symbolizes the magical regenerative power of skin appendages. Similar to the adventurous pursuit of the Golden Fleece by the multi-talented Argonauts, today we also need an integrated multi-disciplined approach to understand the cellular and molecular processes during development, regeneration and evolution of skin appendages. To this end, we have explored several aspects of skin appendage biology that contribute to the Turing activator / inhibitor model in feather pattern formation, the topo-biological arrangement of stem cells in organ shape determination, the macro-environmental regulation of stem cells in regenerative hair waves, and potential novel molecular pathways in the morphological evolution of feathers. Here we show our current integrative biology efforts to unravel the complex cellular behavior in patterning stem cells and the control of regional specificity in skin appendages. We use feather / scale tissue recombination to demonstrate the timing control of competence and inducibility. Feathers from different body regions are used to study skin regional specificity. Bioinformatic analyses of transcriptome microarrays show the potential involvement of candidate molecular pathways. We further show Hox genes exhibit some region specific expression patterns. To visualize real time events, we applied time-lapse movies, confocal microscopy and multiphoton microscopy to analyze the morphogenesis of cultured embryonic chicken skin explants. These modern imaging technologies reveal unexpectedly complex cellular flow and organization of extracellular matrix molecules in three dimensions. While these approaches are in preliminary stages, this perspective highlights the challenges we face and new integrative tools we will use. Future work will follow these leads to develop a systems biology view and understanding in the morphogenetic principles that govern the development and regeneration of ectodermal organs

  8. [Study on lead absorption in pumpkin by atomic absorption spectrophotometry].

    PubMed

    Li, Zhen-Xia; Sun, Yong-Dong; Chen, Bi-Hua; Li, Xin-Zheng

    2008-07-01

    A study was carried out on the characteristic of lead absorption in pumpkin via atomic absorption spectrophotometer. The results showed that lead absorption amount in pumpkin increased with time, but the absorption rate decreased with time; And the lead absorption amount reached the peak in pH 7. Lead and cadmium have similar characteristic of absorption in pumpkin.

  9. Electron transfer in biology

    NASA Astrophysics Data System (ADS)

    Williams, R. J. P.

    Electron transfer is one of the key reactions of biology not just in catalysis of oxidation/reduction reactions but in the conversion of sources of energy such as light to usable form for chemical transformations. There are then two intriguing problems. What is the nature of the matrix in which electrons flow in a biological cell after the initial charge separation due for example to the absorption of light. Here we are examining biological structures similar to man's electronic wires and the construction must be of low resistance in what are apparently insulators - organic polymers. It has been found that the electronic conduction system is largely made from metallo-proteins associated with lipid membranes. We understand much about these biological wires today. The second problem concerns the conversion of the energy captured from the light into usable chemical form. The major synthetic step in the production of biological polymers, including proteins, DNA, RNA, polysaccharides and fats, is condensation, i.e. the removal of water in the formation of amides, esters and so on. Now these condensation reactions are driven in biology by using a drying agent in water, namely the anhydride, pyrophosphate, in a special compound ATP, adenosine triphosphate. The central problem is to discover exactly how the flow of electrons can be related to the synthesis of (bound) pyrophosphate. (In a thermodynamic sense pyrophosphate is a water soluble kinetically stable drying agent comparable with solid P2O5.) In the biological systems the connection between these different classes of reaction, electron transfer and condensation, is known to be via the production of an energized gradient of protons across the biological membrane which arises from the flow of electrons across the same membrane in the electron transport wires of biology. However we do not understand thoroughly the steps which lead from electron flow in a membrane to proton gradients in that membrane, i.e. electron

  10. Measurements of the absorption coefficient of stratospheric aerosols

    NASA Technical Reports Server (NTRS)

    Ogren, J. A.; Ahlquist, N. C.; Clarke, A. D.; Charlson, R. J.

    1981-01-01

    The absorption coefficients of stratospheric aerosols are measured using a variation on the integrating plate method. The technique is based on the decrease in the transparency of a substrate when an absorbing aerosol is deposited on it. A Lambert scatterer is placed behind the substrate to integrate forward scattered light and minimize the effect of scattering on the measurement. The low pressure in the stratosphere is used for the direct impaction of particles onto a narrow strip of opal glass. The eight samples collected had a median value of 4 x 10 to the -9th m with an uncertainty of + or - 5 x 10 to the -9th m. If this absorption is due to graphitic carbon, then its concentration is estimated at about 0.4 ng/cu m, or about 0.25% of the total aerosol mass concentration. Estimates of the aerosol scattering coefficients based on satellite extinction inversions result in an aerosol single-scattering albedo in the range of 0.96-1.0.

  11. Development of a carbonate absorption-based process for post-combustion CO2 capture: The role of biocatalyst to promote CO2 absorption rate

    USGS Publications Warehouse

    Lu, Y.; Ye, X.; Zhang, Z.; Khodayari, A.; Djukadi, T.

    2011-01-01

    An Integrated Vacuum Carbonate Absorption Process (IVCAP) for post-combustion carbon dioxide (CO2) capture is described. IVCAP employs potassium carbonate (PC) as a solvent, uses waste or low quality steam from the power plant for CO2 stripping, and employs a biocatalyst, carbonic anhydrase (CA) enzyme, for promoting the CO2 absorption into PC solution. A series of experiments were performed to evaluate the activity of CA enzyme mixed in PC solutions in a stirred tank reactor system under various temperatures, CA dosages, CO2 loadings, CO2 partial pressures, and the presence of major flue gas contaminants. It was demonstrated that CA enzyme is an effective biocatalyst for CO2 absorption under IVCAP conditions. ?? 2011 Published by Elsevier Ltd.

  12. Integrative structure modeling with the Integrative Modeling Platform.

    PubMed

    Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano; Pellarin, Riccardo; Greenberg, Charles H; Saltzberg, Daniel; Sali, Andrej

    2018-01-01

    Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use. © 2017 The Protein Society.

  13. Stress, stress reduction, and hypertension in African Americans: an updated review.

    PubMed Central

    Barnes, V.; Schneider, R.; Alexander, C.; Staggers, F.

    1997-01-01

    This is a comprehensive and integrative review of multiple factors underlying the greater prevalence of hypertension in African Americans compared with whites. Evidence linking stress with hypertension and cardiovascular disease in African Americans is reviewed. A survey of mechanisms of hypertension in African Americans and existing behavioral strategies for the treatment of hypertension is presented. Given that the excess of hypertension may be mediated in part by behavioral factors operating through biological mechanisms, a case is presented for behavioral stress reduction measures. This review of stress reduction techniques especially the Transcendental Mediation program for the treatment of hypertension in African Americans highlights current issues facing the field. New information is provided to help direct future nonpharmacological research and practice in hypertension to prevent morbidity and premature mortality in this underserved population. PMID:9220696

  14. Stress, stress reduction, and hypertension in African Americans: an updated review.

    PubMed

    Barnes, V; Schneider, R; Alexander, C; Staggers, F

    1997-07-01

    This is a comprehensive and integrative review of multiple factors underlying the greater prevalence of hypertension in African Americans compared with whites. Evidence linking stress with hypertension and cardiovascular disease in African Americans is reviewed. A survey of mechanisms of hypertension in African Americans and existing behavioral strategies for the treatment of hypertension is presented. Given that the excess of hypertension may be mediated in part by behavioral factors operating through biological mechanisms, a case is presented for behavioral stress reduction measures. This review of stress reduction techniques especially the Transcendental Mediation program for the treatment of hypertension in African Americans highlights current issues facing the field. New information is provided to help direct future nonpharmacological research and practice in hypertension to prevent morbidity and premature mortality in this underserved population.

  15. A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes

    PubMed Central

    Dutta, B; Pusztai, L; Qi, Y; André, F; Lazar, V; Bianchini, G; Ueno, N; Agarwal, R; Wang, B; Shiang, C Y; Hortobagyi, G N; Mills, G B; Symmans, W F; Balázsi, G

    2012-01-01

    Background: The rapid collection of diverse genome-scale data raises the urgent need to integrate and utilise these resources for biological discovery or biomedical applications. For example, diverse transcriptomic and gene copy number variation data are currently collected for various cancers, but relatively few current methods are capable to utilise the emerging information. Methods: We developed and tested a data-integration method to identify gene networks that drive the biology of breast cancer clinical subtypes. The method simultaneously overlays gene expression and gene copy number data on protein–protein interaction, transcriptional-regulatory and signalling networks by identifying coincident genomic and transcriptional disturbances in local network neighborhoods. Results: We identified distinct driver-networks for each of the three common clinical breast cancer subtypes: oestrogen receptor (ER)+, human epidermal growth factor receptor 2 (HER2)+, and triple receptor-negative breast cancers (TNBC) from patient and cell line data sets. Driver-networks inferred from independent datasets were significantly reproducible. We also confirmed the functional relevance of a subset of randomly selected driver-network members for TNBC in gene knockdown experiments in vitro. We found that TNBC driver-network members genes have increased functional specificity to TNBC cell lines and higher functional sensitivity compared with genes selected by differential expression alone. Conclusion: Clinical subtype-specific driver-networks identified through data integration are reproducible and functionally important. PMID:22343619

  16. Isothermal absorption of soluble gases by atmospheric nanoaerosols

    NASA Astrophysics Data System (ADS)

    Elperin, T.; Fominykh, A.; Krasovitov, B.; Lushnikov, A.

    2013-01-01

    We investigate mass transfer during the isothermal absorption of atmospheric trace soluble gases by a single droplet whose size is comparable to the molecular mean free path in air at normal conditions. It is assumed that the trace reactant diffuses to the droplet surface and then reacts with the substances inside the droplet according to the first-order rate law. Our analysis applies a flux-matching theory of transport processes in gases and assumes constant thermophysical properties of the gases and liquids. We derive an integral equation of Volterra type for the transient molecular flux density to a liquid droplet and solve it numerically. Numerical calculations are performed for absorption of sulfur dioxide (SO2), dinitrogen trioxide (N2O3), and chlorine (Cl2) by liquid nanoaerosols accompanied by chemical dissociation reaction. It is shown that during gas absorption by nanoaerosols, the kinetic effects play a significant role, and neglecting kinetic effects leads to a significant overestimation of the soluble gas flux into a droplet during the entire period of gas absorption.

  17. Isothermal absorption of soluble gases by atmospheric nanoaerosols.

    PubMed

    Elperin, T; Fominykh, A; Krasovitov, B; Lushnikov, A

    2013-01-01

    We investigate mass transfer during the isothermal absorption of atmospheric trace soluble gases by a single droplet whose size is comparable to the molecular mean free path in air at normal conditions. It is assumed that the trace reactant diffuses to the droplet surface and then reacts with the substances inside the droplet according to the first-order rate law. Our analysis applies a flux-matching theory of transport processes in gases and assumes constant thermophysical properties of the gases and liquids. We derive an integral equation of Volterra type for the transient molecular flux density to a liquid droplet and solve it numerically. Numerical calculations are performed for absorption of sulfur dioxide (SO(2)), dinitrogen trioxide (N(2)O(3)), and chlorine (Cl(2)) by liquid nanoaerosols accompanied by chemical dissociation reaction. It is shown that during gas absorption by nanoaerosols, the kinetic effects play a significant role, and neglecting kinetic effects leads to a significant overestimation of the soluble gas flux into a droplet during the entire period of gas absorption.

  18. Integrating data from biological experiments into metabolic networks with the DBE information system.

    PubMed

    Borisjuk, Ljudmilla; Hajirezaei, Mohammad-Reza; Klukas, Christian; Rolletschek, Hardy; Schreiber, Falk

    2005-01-01

    Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Website as the interface for the system, (4) the DBE-Pictures application for the up- and download of binary (e. g. image) files, and (5) DBE-Gravisto, a network analysis and graph visualisation system. The usability of this approach is demonstrated in two examples.

  19. Determination of the quasi-TE mode (in-plane) graphene linear absorption coefficient via integration with silicon-on-insulator racetrack cavity resonators.

    PubMed

    Crowe, Iain F; Clark, Nicholas; Hussein, Siham; Towlson, Brian; Whittaker, Eric; Milosevic, Milan M; Gardes, Frederic Y; Mashanovich, Goran Z; Halsall, Matthew P; Vijayaraghaven, Aravind

    2014-07-28

    We examine the near-IR light-matter interaction for graphene integrated cavity ring resonators based on silicon-on-insulator (SOI) race-track waveguides. Fitting of the cavity resonances from quasi-TE mode transmission spectra reveal the real part of the effective refractive index for graphene, n(eff) = 2.23 ± 0.02 and linear absorption coefficient, α(gTE) = 0.11 ± 0.01dBμm(-1). The evanescent nature of the guided mode coupling to graphene at resonance depends strongly on the height of the graphene above the cavity, which places limits on the cavity length for optical sensing applications.

  20. Integrative Assessment of Evolutionary Theory Acceptance and Knowledge Levels of Biology Undergraduate Students from a Brazilian University

    ERIC Educational Resources Information Center

    Tavares, Gustavo Medina; Bobrowski, Vera Lucia

    2018-01-01

    The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students'…

  1. Experimental investigation of sound absorption properties of perforated date palm fibers panel

    NASA Astrophysics Data System (ADS)

    Elwaleed, A. K.; Nikabdullah, N.; Nor, M. J. M.; Tahir, M. F. M.; Zulkifli, R.

    2013-06-01

    This paper presents the sound absorption properties of a natural waste of date palm fiber perforated panel. A single layer of the date palm fibers was tested in this study for its sound absorption properties. The experimental measurements were carried out using impedance tube at the acoustic lab, Faculty of Engineering, Universiti Kebangsaan Malaysia. The experiment was conducted for the panel without air gap, with air gap and with perforated plate facing. Three air gap thicknesses of 10 mm, 20 mm and 30 mm were used between the date palm fiber sample and the rigid backing of the impedance tube. The results showed that when facing the palm date fiber sample with perforated plate the sound absorption coefficient improved at the higher and lower frequency ranges. This increase in sound absorption coincided with reduction in medium frequency absorption. However, this could be improved by using different densities or perforated plate with the date palm fiber panel.

  2. Absorption spectroscopy at the ultimate quantum limit from single-photon states

    NASA Astrophysics Data System (ADS)

    Whittaker, R.; Erven, C.; Neville, A.; Berry, M.; O'Brien, J. L.; Cable, H.; Matthews, J. C. F.

    2017-02-01

    Absorption spectroscopy is routinely used to characterise chemical and biological samples. For the state-of-the-art in laser absorption spectroscopy, precision is theoretically limited by shot-noise due to the fundamental Poisson-distribution of photon number in laser radiation. In practice, the shot-noise limit can only be achieved when all other sources of noise are eliminated. Here, we use wavelength-correlated and tuneable photon pairs to demonstrate how absorption spectroscopy can be performed with precision beyond the shot-noise limit and near the ultimate quantum limit by using the optimal probe for absorption measurement—single photons. We present a practically realisable scheme, which we characterise both the precision and accuracy of by measuring the response of a control feature. We demonstrate that the technique can successfully probe liquid samples and using two spectrally similar types of haemoglobin we show that obtaining a given precision in resolution requires fewer heralded single probe photons compared to using an idealised laser.

  3. Sugars: their origin in photosynthesis and subsequent biological interconversions.

    PubMed

    Nevins, D J

    1995-04-01

    Sugar has been valued as a commodity for thousands of years. Despite its long history in commerce, the biological mechanisms accounting for the production of sugar are rather recent discoveries. The reactions are remarkable. Sugar is produced by all green plants and photosynthetic bacteria in a reaction sequence capable of forming carbon-carbon bonds. The very first steps occur independently of solar energy input, but to sustain the reaction, the products of initial fixation are phosphorylated and undergo a reduction in oxidation state. These steps responsible for phosphorylation and reduction are driven by products generated in the chloroplast upon the absorption of light. At this point, after just a few reactions, the products of photosynthesis have already acquired the attributes characteristic of sugars. Once carbon is stabilized as simple sugars in the chloroplast, the products undergo a sequence of rearrangements to sustain a cycle leading to new carbon dioxide acceptor molecules, and with each turn of the cycle a new carbon atom is introduced into the pool. As the process continues some of the carbon is diverted to synthesize starch within the chloroplast. Sucrose is synthesized in the cytoplasm adjacent to the chloroplast from exported carbohydrate as a diversion from the formation of starch. Sucrose represents the principal transport substance in most plants. Storage starch, cellulose, and other complex cell wall polysaccharides are typically derived from the sugar monomers found in sucrose. Sugars supply all the fixed carbon for synthesis of biological compounds and are fundamental for sustaining the energy flow to all food systems.

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  5. Reduction of Mo(VI) by the bacterium Serratia sp. strain DRY5.

    PubMed

    Rahman, M F A; Shukor, M Y; Suhaili, Z; Mustafa, S; Shamaan, N A; Syed, M A

    2009-01-01

    The need to isolate efficient heavy metal reducers for cost effective bioremediation strategy have resulted in the isolation of a potent molybdenum-reducing bacterium. The isolate was tentatively identified as Serratia sp. strain DRY5 based on the Biolog GN carbon utilization profiles and partial 16S rDNA molecular phylogeny. Strain DRY5 produced 2.3 times the amount of Mo-blue than S. marcescens strain Dr.Y6, 23 times more than E. coli K12 and 7 times more than E. cloacae strain 48. Strain DRY5 required 37 degrees C and pH 7.0 for optimum molybdenum reduction. Carbon sources such as sucrose, maltose, glucose and glycerol, supported cellular growth and molybdate reduction after 24 hr of static incubation. The most optimum carbon source that supported reduction was sucrose at 1.0% (w/v). Ammonium sulphate, ammonium chloride, glutamic acid, cysteine, and valine supported growth and molybdate reduction with ammonium sulphate as the optimum nitrogen source at 0. 2% (w/v). Molybdate reduction was optimally supported by 30 mM molybdate. The optimum concentration of phosphate for molybdate reduction was 5 mM when molybdate concentration was fixed at 30 mM and molybdate reduction was totally inhibited at 100 mM phosphate. Mo-blue produced by this strain shows a unique characteristic absorption profile with a maximum peak at 865 nm and a shoulder at 700 nm, Dialysis tubing experiment showed that 95.42% of Mo-blue was found in the dialysis tubing suggesting that the molybdate reduction seen in this bacterium was catalyzed by enzyme(s). The characteristics of isolate DRY5 suggest that it would be useful in the bioremediation ofmolybdenum-containing waste.

  6. Determination of nickel in water, food, and biological samples by electrothermal atomic absorption spectrometry after preconcentration on modified carbon nanotubes.

    PubMed

    Taher, Mohammad Ali; Mazaheri, Lida; Ashkenani, Hamid; Mohadesi, Alireza; Afzali, Daryoush

    2014-01-01

    A new and sensitive SPE method using modified carbon nanotubes for extraction and preconcentration, and electrothermal atomic absorption spectrometric determination of nickel (Ni) in real samples at ng/L levels was investigated. First, multiwalled carbon nanotubes were oxidized with concentrated HNO3, then modified with 2-(5-bormo-2-pyridylazo)-5-diethylaminophenol reagent. The adsorption was achieved quantitatively on a modified carbon nanotubes column in a pH range of 6.5 to 8.5; the adsorbed Ni(II) ions were then desorbed by passing 5.0 mL of 1 M HNO3. The effects of analytical parameters, including pH of the solution, eluent type and volume, sample volume, flow rate of the eluent, and matrix ions, were investigated for optimization of the presented procedure. The enrichment factor was 180, and the LOD for Ni was 4.9 ng/L. The method was applied to the determination of Ni in water, food, and biological samples, and reproducible results were obtained.

  7. Ligandless dispersive liquid--liquid microextraction of iron in biological and foodstuff samples and its determination by Electrothermal atomic absorption spectrometry.

    PubMed

    Madadizadeh, Mohadeseh; Taher, Mohammad Ali; Ashkenani, Hamid

    2013-01-01

    A new, simple, and efficient method comprising ligandless dispersive liquid-liquid microextraction combined with electrothermal atomic absorption spectrometry is reported for the preconcentration and determination of ultratrace amounts of Fe(III). Carbon tetrachloride and acetone were used as the extraction and disperser solvents, respectively. Some effective parameters of the microextraction such as choice of extraction and disperser solvents, their volume, extraction time and temperature, salt and surfactant effect, and pH were optimized. Under the optimum conditions, the calibration curve was linear in the range of 0.02 to 0.46 microg/L of Fe(III), with LOD and LOQ of 5.2 and 17.4 ng/L, respectively. The RSD for seven replicated determinations of Fe(IIl) ion at 0.1 microg/L concentration level was 5.2%. Operational simplicity, rapidity, low cost, good repeatability, and low consumption of extraction solvent are the main advantages of the proposed method. The method was successfully applied to the determination of iron in biological, food, and certified reference samples.

  8. Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

    PubMed

    D'Souza, Mark; Sulakhe, Dinanath; Wang, Sheng; Xie, Bing; Hashemifar, Somaye; Taylor, Andrew; Dubchak, Inna; Conrad Gilliam, T; Maltsev, Natalia

    2017-01-01

    Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.

  9. A shortcut to wide-ranging biological actions of dietary polyphenols: modulation of the nitrate-nitrite-nitric oxide pathway in the gut.

    PubMed

    Rocha, Bárbara S; Nunes, Carla; Pereira, Cassilda; Barbosa, Rui M; Laranjinha, João

    2014-08-01

    Dietary polyphenols are complex, natural compounds with recognized health benefits. Initially attractive to the biomedical area due to their in vitro antioxidant properties, the biological implications of polyphenols are now known to be far from their acute ability to scavenge free radicals but rather to modulate redox signaling pathways. Actually, it is now recognized that dietary polyphenols are extensively metabolized in vivo and that the chemical, biophysical and biological properties of their metabolites are, in most cases, quite different from the ones of the parent molecules. Hence, the study of the metabolic, absorptive and signaling pathways of both phenolics and derivatives has become a major issue. In this paper we propose a short-cut for the systemic effects of polyphenols in connection with nitric oxide (˙NO) biology. This free radical is a ubiquitous signaling molecule with pivotal functions in vivo. It is produced through an enzymatic pathway and also through the reduction of dietary nitrate and nitrite in the human stomach. At acidic gastric pH, dietary polyphenols, in the form they are conveyed in foods and at high concentration, not only promote nitrite reduction to ˙NO but also embark in a complex network of chemical reactions to produce higher nitrogen oxides with signaling functions, namely by inducing post-translational modifications. Modified endogenous molecules, such as nitrated proteins and lipids, acquire important physiological functions. Thus, local and systemic effects of ˙NO such as modulation of vascular tone, mucus production in the gut and protection against ischemia-reperfusion injury are, in this sense, triggered by dietary polyphenols. Evidence to support the signaling and biological effects of polyphenols by modulation of the nitrate-nitrite-NO pathway will be herein provided and discussed. General actions of polyphenols encompassing absorption and metabolism in the intestine/liver are short-cut via the production of

  10. Short-lived species detection of nitrous acid by external-cavity quantum cascade laser based quartz-enhanced photoacoustic absorption spectroscopy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yi, Hongming; Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, P.O. Box 1125, 350 Shushanhu Road, Hefei, Anhui 230031; Maamary, Rabih

    2015-03-09

    Spectroscopic detection of short-lived gaseous nitrous acid (HONO) at 1254.85 cm{sup −1} was realized by off-beam coupled quartz-enhanced photoacoustic spectroscopy (QEPAS) in conjunction with an external cavity quantum cascade lasers (EC-QCL). High sensitivity monitoring of HONO was performed within a very small gas-sample volume (of ∼40 mm{sup 3}) allowing a significant reduction (of about 4 orders of magnitude) of air sampling residence time which is highly desired for accurate quantification of chemically reactive short-lived species. Calibration of the developed QEPAS-based HONO sensor was carried out by means of lab-generated HONO samples whose concentrations were determined by direct absorption spectroscopy involving a ∼109.5 mmore » multipass cell and a distributed feedback QCL. A minimum detection limit (MDL) of 66 ppbv (1 σ) HONO was achieved at 70 mbar using a laser output power of 50 mW and 1 s integration time, which corresponded to a normalized noise equivalent absorption coefficient of 3.6 × 10{sup −8 }cm{sup −1} W/Hz{sup 1/2}. This MDL was down to 7 ppbv at the optimal integration time of 150 s. The corresponding 1σ minimum detected absorption coefficient is ∼1.1 × 10{sup −7 }cm{sup −1} (MDL ∼ 3 ppbv) in 1 s and ∼1.1 × 10{sup −8 }cm{sup −1} (MDL ∼ 330 pptv) in 150 s, respectively, with 1 W laser power.« less

  11. Influence of organic loading rate on integrated bioreactor treating hypersaline mustard wastewater.

    PubMed

    Kang, Wei; Chai, Hongxiang; Yang, Shiwei; Du, Guojun; Zhou, Jian; He, Qiang

    2016-07-01

    Mustard tuber wastewater is characterized by high salinity and high organic content that is potentially detrimental to the biological treatment system and affects the treatment efficiency accordingly. The experiment used the integrated bioreactor to reduce much of the organics in mustard tuber wastewater, and found the influence of organic loading rate on effluent chemical oxygen demand (COD) and phosphate (PO4 (3-) -P). Results showed that under the condition of 10-15 °C, 6 mg/L of dissolved oxygen, the reduction value of COD removal rate in anaerobic and aerobic area was 14.5% and 31.7% when the organic loading rate increased from 2.0 to 4.0 kg COD/m(3) /day. Therefore, an integrated bioreactor should take 2.0 kg COD/m(3) /day organic loading rate in mustard wastewater treatment if the effluent is expected to meet the third level of "Integrated Wastewater Discharge Standard" (GB 8978-1996). © 2015 International Union of Biochemistry and Molecular Biology, Inc.

  12. Hypersonic research engine project. Phase 2: Aerothermodynamic Integration Model (AIM) data reduction computer program, data item no. 54.16

    NASA Technical Reports Server (NTRS)

    Gaede, A. E.; Platte, W. (Editor)

    1975-01-01

    The data reduction program used to analyze the performance of the Aerothermodynamic Integration Model is described. Routines to acquire, calibrate, and interpolate the test data, to calculate the axial components of the pressure area integrals and the skin function coefficients, and to report the raw data in engineering units are included along with routines to calculate flow conditions in the wind tunnel, inlet, combustor, and nozzle, and the overall engine performance. Various subroutines were modified and used to obtain species concentrations and transport properties in chemical equilibrium at each of the internal and external engine stations. It is recommended that future test plans include the configuration, calibration, and channel assignment data on a magnetic tape generated at the test site immediately before or after a test, and that the data reduction program be designed to operate in a batch environment.

  13. Gold nanorods as contrast agents for biological imaging: optical properties, surface conjugation, and photothermal effects†

    PubMed Central

    Tong, Ling; Wei, Qingshan; Wei, Alexander; Cheng, Ji-Xin

    2009-01-01

    Gold nanorods (NRs) have plasmon-resonant absorption and scattering in the near-infrared (NIR) region, making them attractive probes for in vitro and in vivo imaging. In the cellular environment, NRs can provide scattering contrast for darkfield microscopy, or emit a strong two-photon luminescence (TPL) due to plasmon-enhanced two-photon absorption. NRs have also been employed in biomedical imaging modalities such as optical coherence tomography (OCT) or photoacoustic tomography (PAT). Careful control over surface chemistry enhances the capacity of NRs as biological imaging agents by enabling cell-specific targeting, and by increasing their dispersion stability and circulation lifetimes. NRs can also efficiently convert optical energy into heat, and inflict localized damage to tumor cells. Laser-induced heating of NRs can disrupt cell membrane integrity and homeostasis, resulting in Ca2+ influx and the depolymerization of the intracellular actin network. The combination of plasmon-resonant optical properties, intense local photothermal effects, and robust surface chemistry render gold NRs as promising theragnostic agents. PMID:19161395

  14. The next green movement: Plant biology for the environment and sustainability.

    PubMed

    Jez, Joseph M; Lee, Soon Goo; Sherp, Ashley M

    2016-09-16

    From domestication and breeding to the genetic engineering of crops, plants provide food, fuel, fibers, and feedstocks for our civilization. New research and discoveries aim to reduce the inputs needed to grow crops and to develop plants for environmental and sustainability applications. Faced with population growth and changing climate, the next wave of innovation in plant biology integrates technologies and approaches that span from molecular to ecosystem scales. Recent efforts to engineer plants for better nitrogen and phosphorus use, enhanced carbon fixation, and environmental remediation and to understand plant-microbiome interactions showcase exciting future directions for translational plant biology. These advances promise new strategies for the reduction of inputs to limit environmental impacts and improve agricultural sustainability. Copyright © 2016, American Association for the Advancement of Science.

  15. Biologic lung volume reduction in advanced upper lobe emphysema: phase 2 results.

    PubMed

    Criner, Gerard J; Pinto-Plata, Victor; Strange, Charlie; Dransfield, Mark; Gotfried, Mark; Leeds, William; McLennan, Geoffrey; Refaely, Yael; Tewari, Sanjiv; Krasna, Mark; Celli, Bartolome

    2009-05-01

    Biologic lung volume reduction (BioLVR) is a new endobronchial treatment for advanced emphysema that reduces lung volume through tissue remodeling. Assess the safety and therapeutic dose of BioLVR hydrogel in upper lobe predominant emphysema. Open-labeled, multicenter phase 2 dose-ranging studies were performed with BioLVR hydrogel administered to eight subsegmental sites (four in each upper lobe) involving: (1) low-dose treatment (n = 28) with 10 ml per site (LD); and (2) high-dose treatment (n = 22) with 20 ml per site (HD). Safety was assessed by the incidence of serious medical complications. Efficacy was assessed by change from baseline in pulmonary function tests, dyspnea score, 6-minute walk distance, and health-related quality of life. After treatment there were no deaths and four serious treatment-related complications. A reduction in residual volume to TLC ratio at 12 weeks (primary efficacy outcome) was achieved with both LD (-6.4 +/- 9.3%; P = 0.002) and HD (-5.5 +/- 9.4%; P = 0.028) treatments. Improvements in pulmonary function in HD (6 mo: DeltaFEV(1) = +15.6%; P = 0.002; DeltaFVC = +9.1%; P = 0.034) were greater than in LD patients (6 mo: DeltaFEV(1) = +6.7%; P = 0.021; DeltaFVC = +5.1%; P = 0.139). LD- and HD-treated groups both demonstrated improved symptom scores and health-related quality of life. BioLVR improves physiology and functional outcomes up to 6 months with an acceptable safety profile in upper lobe predominant emphysema. Overall improvement was greater and responses more durable with 20 ml per site than 10 ml per site dosing. Clinical trial registered with www.clinicaltrials.gov (NCT 00435253 and NCT 00515164).

  16. Double-pulse 2-μm integrated path differential absorption lidar airborne validation for atmospheric carbon dioxide measurement.

    PubMed

    Refaat, Tamer F; Singh, Upendra N; Yu, Jirong; Petros, Mulugeta; Remus, Ruben; Ismail, Syed

    2016-05-20

    Field experiments were conducted to test and evaluate the initial atmospheric carbon dioxide (CO2) measurement capability of airborne, high-energy, double-pulsed, 2-μm integrated path differential absorption (IPDA) lidar. This IPDA was designed, integrated, and operated at the NASA Langley Research Center on-board the NASA B-200 aircraft. The IPDA was tuned to the CO2 strong absorption line at 2050.9670 nm, which is the optimum for lower tropospheric weighted column measurements. Flights were conducted over land and ocean under different conditions. The first validation experiments of the IPDA for atmospheric CO2 remote sensing, focusing on low surface reflectivity oceanic surface returns during full day background conditions, are presented. In these experiments, the IPDA measurements were validated by comparison to airborne flask air-sampling measurements conducted by the NOAA Earth System Research Laboratory. IPDA performance modeling was conducted to evaluate measurement sensitivity and bias errors. The IPDA signals and their variation with altitude compare well with predicted model results. In addition, off-off-line testing was conducted, with fixed instrument settings, to evaluate the IPDA systematic and random errors. Analysis shows an altitude-independent differential optical depth offset of 0.0769. Optical depth measurement uncertainty of 0.0918 compares well with the predicted value of 0.0761. IPDA CO2 column measurement compares well with model-driven, near-simultaneous air-sampling measurements from the NOAA aircraft at different altitudes. With a 10-s shot average, CO2 differential optical depth measurement of 1.0054±0.0103 was retrieved from a 6-km altitude and a 4-GHz on-line operation. As compared to CO2 weighted-average column dry-air volume mixing ratio of 404.08 ppm, derived from air sampling, IPDA measurement resulted in a value of 405.22±4.15  ppm with 1.02% uncertainty and

  17. Integrating chemical and biological control

    Treesearch

    Scott Salom; Albert Mayfield; Tom McAvoy

    2011-01-01

    Research and management efforts to establish an effective biological control program against HWA has received significant support by the U.S. Forest Service over the past 17 years. Other federal and state agencies, universities, and private entities have also contributed to this overall research and management effort. Although a number of HWA-specific predator species...

  18. Dynamic absorption and scattering of water and hydrogel during high-repetition-rate (>100 MHz) burst-mode ultrafast-pulse laser ablation.

    PubMed

    Qian, Zuoming; Covarrubias, Andrés; Grindal, Alexander W; Akens, Margarete K; Lilge, Lothar; Marjoribanks, Robin S

    2016-06-01

    High-repetition-rate burst-mode ultrafast-laser ablation and disruption of biological tissues depends on interaction of each pulse with the sample, but under those particular conditions which persist from previous pulses. This work characterizes and compares the dynamics of absorption and scattering of a 133-MHz repetition-rate, burst-mode ultrafast-pulse laser, in agar hydrogel targets and distilled water. The differences in energy partition are quantified, pulse-by-pulse, using a time-resolving integrating-sphere-based device. These measurements reveal that high-repetition-rate burst-mode ultrafast-laser ablation is a highly dynamical process affected by the persistence of ionization, dissipation of plasma plume, neutral material flow, tissue tensile strength, and the hydrodynamic oscillation of cavitation bubbles.

  19. Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors.

    PubMed

    Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

    2013-05-01

    In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors are absorbed in sufficient quantity, and then reach target organs while maintaining beneficial effects. These are the reasons why the bioavailability of functional food factors has been well investigated using rodent models. Recently, many of the biological processes have been reported to follow diurnal rhythms recurring every 24 h. Therefore, absorption and metabolism of functional food factors influenced by the biological processes may vary with time of day. Consequently, the evaluation of the bioavailability of functional food factors using rodent models should take into consideration the timing of consumption. In this review, we provide a perspective overview of the diurnal rhythm of biological processes involved in the bioavailability of functional food factors, particularly flavonoids.

  20. MULTIMAGNON ABSORPTION IN MNF2-OPTICAL ABSORPTION SPECTRUM.

    DTIC Science & Technology

    The absorption spectrum of MnF2 at 4.2K in the 3900A region was measured in zero external fields and in high fields. Exciton lines with magnon ...sidebands are observed, accompanied by a large number of weak satellite lines. Results on the exciton and magnon absorptions are similar to those of...McClure et al. The satellite lines are interpreted as being multi- magnon absorptions, and it is possible to fit the energy of all the absorptions with