Science.gov

Sample records for acid signature analysis

  1. Simulating realistic predator signatures in quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.

    2015-01-01

    Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

  2. Distance measures and optimization spaces in quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.; Rode, Karyn D.; Budge, Suzanne M.; Thiemann, Gregory W.

    2015-01-01

    Quantitative fatty acid signature analysis has become an important method of diet estimation in ecology, especially marine ecology. Controlled feeding trials to validate the method and estimate the calibration coefficients necessary to account for differential metabolism of individual fatty acids have been conducted with several species from diverse taxa. However, research into potential refinements of the estimation method has been limited. We compared the performance of the original method of estimating diet composition with that of five variants based on different combinations of distance measures and calibration-coefficient transformations between prey and predator fatty acid signature spaces. Fatty acid signatures of pseudopredators were constructed using known diet mixtures of two prey data sets previously used to estimate the diets of polar bears Ursus maritimus and gray seals Halichoerus grypus, and their diets were then estimated using all six variants. In addition, previously published diets of Chukchi Sea polar bears were re-estimated using all six methods. Our findings reveal that the selection of an estimation method can meaningfully influence estimates of diet composition. Among the pseudopredator results, which allowed evaluation of bias and precision, differences in estimator performance were rarely large, and no one estimator was universally preferred, although estimators based on the Aitchison distance measure tended to have modestly superior properties compared to estimators based on the Kullback-Leibler distance measure. However, greater differences were observed among estimated polar bear diets, most likely due to differential estimator sensitivity to assumption violations. Our results, particularly the polar bear example, suggest that additional research into estimator performance and model diagnostics is warranted.

  3. Distance measures and optimization spaces in quantitative fatty acid signature analysis

    PubMed Central

    Bromaghin, Jeffrey F; Rode, Karyn D; Budge, Suzanne M; Thiemann, Gregory W

    2015-01-01

    Quantitative fatty acid signature analysis has become an important method of diet estimation in ecology, especially marine ecology. Controlled feeding trials to validate the method and estimate the calibration coefficients necessary to account for differential metabolism of individual fatty acids have been conducted with several species from diverse taxa. However, research into potential refinements of the estimation method has been limited. We compared the performance of the original method of estimating diet composition with that of five variants based on different combinations of distance measures and calibration-coefficient transformations between prey and predator fatty acid signature spaces. Fatty acid signatures of pseudopredators were constructed using known diet mixtures of two prey data sets previously used to estimate the diets of polar bears Ursus maritimus and gray seals Halichoerus grypus, and their diets were then estimated using all six variants. In addition, previously published diets of Chukchi Sea polar bears were re-estimated using all six methods. Our findings reveal that the selection of an estimation method can meaningfully influence estimates of diet composition. Among the pseudopredator results, which allowed evaluation of bias and precision, differences in estimator performance were rarely large, and no one estimator was universally preferred, although estimators based on the Aitchison distance measure tended to have modestly superior properties compared to estimators based on the Kullback–Leibler distance measure. However, greater differences were observed among estimated polar bear diets, most likely due to differential estimator sensitivity to assumption violations. Our results, particularly the polar bear example, suggest that additional research into estimator performance and model diagnostics is warranted. PMID:25859330

  4. Distance measures and optimization spaces in quantitative fatty acid signature analysis.

    PubMed

    Bromaghin, Jeffrey F; Rode, Karyn D; Budge, Suzanne M; Thiemann, Gregory W

    2015-03-01

    Quantitative fatty acid signature analysis has become an important method of diet estimation in ecology, especially marine ecology. Controlled feeding trials to validate the method and estimate the calibration coefficients necessary to account for differential metabolism of individual fatty acids have been conducted with several species from diverse taxa. However, research into potential refinements of the estimation method has been limited. We compared the performance of the original method of estimating diet composition with that of five variants based on different combinations of distance measures and calibration-coefficient transformations between prey and predator fatty acid signature spaces. Fatty acid signatures of pseudopredators were constructed using known diet mixtures of two prey data sets previously used to estimate the diets of polar bears Ursus maritimus and gray seals Halichoerus grypus, and their diets were then estimated using all six variants. In addition, previously published diets of Chukchi Sea polar bears were re-estimated using all six methods. Our findings reveal that the selection of an estimation method can meaningfully influence estimates of diet composition. Among the pseudopredator results, which allowed evaluation of bias and precision, differences in estimator performance were rarely large, and no one estimator was universally preferred, although estimators based on the Aitchison distance measure tended to have modestly superior properties compared to estimators based on the Kullback-Leibler distance measure. However, greater differences were observed among estimated polar bear diets, most likely due to differential estimator sensitivity to assumption violations. Our results, particularly the polar bear example, suggest that additional research into estimator performance and model diagnostics is warranted. PMID:25859330

  5. Water O-H stretching Raman signature for strong acid monitoring via multivariate analysis.

    PubMed

    Casella, Amanda J; Levitskaia, Tatiana G; Peterson, James M; Bryan, Samuel A

    2013-04-16

    A distinct need exists for real time information on an acid concentration of industrial aqueous streams. Acid strength affects efficiency and selectivity of many separation processes, including nuclear fuel reprocessing. Despite the seeming simplicity of the problem, no practical solution has been offered yet, particularly for the large-scale schemes involving toxic streams such as highly radioactive nuclear wastes. The classic potentiometric technique is not amiable for online measurements due to the requirements of frequent calibration/maintenance and poor long-term stability in aggressive chemical and radiation environments. Therefore, an alternative analytical method is needed. In this work, the potential of using Raman spectroscopic measurements for online monitoring of strong acid concentration in solutions relevant to dissolved used nuclear fuel was investigated. The Raman water signature was monitored for solution systems containing nitric and hydrochloric acids and their sodium salts of systematically varied composition, ionic strength, and temperature. The trivalent neodymium ion simulated the presence of multivalent f metals. The gaussian deconvolution analysis was used to interpret observed effects of the solution nature on the Raman water O-H stretching spectrum. The generated Raman spectroscopic database was used to develop predictive multivariate regression models for the quantification of the acid and other solution components, as well as selected physicochemical properties. This method was validated using independent experiments conducted in a flow solvent extraction system. PMID:23472939

  6. Water O–H Stretching Raman Signature for Strong Acid Monitoring via Multivariate Analysis

    SciTech Connect

    Casella, Amanda J.; Levitskaia, Tatiana G.; Peterson, James M.; Bryan, Samuel A.

    2013-04-16

    Spectroscopic techniques have been applied extensively for quantification and analysis of solution compositions. In addition to static measurements, these techniques have been implemented in flow systems providing real-time solution information. A distinct need exists for information regarding acid concentration as it affects extraction efficiency and selectivity of many separation processes. Despite of the seeming simplicity of the problem, no practical solution has been offered yet particularly for the large-scale schemes involving toxic streams such as highly radioactive nuclear wastes. Classic potentiometric technique is not amiable for on-line measurements in nuclear fuel reprocessing due to requirements of frequent calibration/maintenance and poor long-term stability in the aggressive chemical and radiation environments. In this work, the potential of using Raman spectroscopic measurements for on-line monitoring of strong acid concentration in the solutions relevant to the dissolved used fuel was investigated. The Raman water signature was monitored and recorded for nitric and hydrochloric acid solution systems of systematically varied chemical composition, ionic strength, and temperature. The generated Raman spectroscopic database was used to develop predictive chemometric models for the quantification of the acid concentration (H+), neodymium concentration (Nd3+), nitrate concentration (NO3-), density, and ionic strength. This approach was validated using a flow solvent extraction system.

  7. Trophic relationships in an estuarine environment: A quantitative fatty acid analysis signature approach

    NASA Astrophysics Data System (ADS)

    Magnone, Larisa; Bessonart, Martin; Gadea, Juan; Salhi, María

    2015-12-01

    In order to better understand the functioning of aquatic environments, it is necessary to obtain accurate diet estimations in food webs. Their description should incorporate information about energy flow and the relative importance of trophic pathways. Fatty acids have been extensively used in qualitative studies on trophic relationships in food webs. Recently a new method to estimate quantitatively single predator diet has been developed. In this study, a model of aquatic food web through quantitative fatty acid signature analysis was generated to identify the trophic interactions among the species in the Rocha Lagoon. The biological sampling over two consecutive annual periods was comprehensive enough to identify all functional groups in the aquatic food web (except birds and mammals). Heleobia australis seemed to play a central role in this estuarine ecosystem. As both, a grazer and a prey to several other species, probably H. australis is transferring a great amount of energy to upper trophic levels. Most of the species at Rocha Lagoon have a wide range of prey items in their diet reflecting a complex food web, which is characteristic of extremely dynamic environment as estuarine ecosystems. QFASA is a model in tracing and quantitative estimate trophic pathways among species in an estuarine food web. The results obtained in the present work are a valuable contribution in the understanding of trophic relationships in Rocha Lagoon.

  8. Assessing the robustness of quantitative fatty acid signature analysis to assumption violations

    USGS Publications Warehouse

    Bromaghin, Jeffrey; Budge, Suzanne M.; Thiemann, Gregory W.; Rode, Karyn D.

    2016-01-01

    In most QFASA applications, investigators will generally have some knowledge of the prey available to predators and be able to assess the completeness of prey signature data and sample additional prey as necessary. Conversely, because calibration coefficients are derived from feeding trials with captive animals and their values may be sensitive to consumer physiology and nutritional status, their applicability to free-ranging animals is difficult to establish. We therefore recommend that investigators first make any improvements to the prey signature data that seem warranted and then base estimation on the Aitchison distance measure, as it appears to minimize risk from violations of the assumption that is most difficult to verify.

  9. New insights into the diets of harbor seals in the Salish Sea revealed by quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.; Lance, Monique M.; Elliott, Elizabeth W.; Jeffries, Steven J.; Acevedo-Gutiérrez, Alejandro; Kennish, John M.

    2012-01-01

    Harbor seals (Phoca vitulina) are an abundant predator along the west coast of North America, and there is considerable interest in their diet composition, especially in regard to predation on valued fish stocks. Available information on harbor seal diets, primarily derived from scat analysis, suggests that adult salmon (Oncorhynchus spp.), Pacific Herring (Clupea pallasii), and gadids predominate. Because diet assessments based on scat analysis may be biased, we investigated diet composition through quantitative analysis of fatty acid signatures. Blubber samples from 49 harbor seals captured in western North America from haul-outs within the area of the San Juan Islands and southern Strait of Georgia in the Salish Sea were analyzed for fatty acid composition, along with 269 fish and squid specimens representing 27 potential prey classes. Diet estimates varied spatially, demographically, and among individual harbor seals. Findings confirmed the prevalence of previously identified prey species in harbor seal diets, but other species also contributed significantly. In particular, Black (Sebastes melanops) and Yellowtail (S. flavidus) Rockfish were estimated to compose up to 50% of some individual seal diets. Specialization and high predation rates on Black and Yellowtail Rockfish by a subset of harbor seals may play a role in the population dynamics of these regional rockfish stocks that is greater than previously realized.

  10. Fatty acid signatures of stomach oil and adipose tissue of northern fulmars (Fulmarus glacialis) in Alaska: Implications for diet analysis of Procellariiform birds

    USGS Publications Warehouse

    Wang, S.W.; Iverson, S.J.; Springer, A.M.; Hatch, Shyla A.

    2007-01-01

    Procellariiforms are unique among seabirds in storing dietary lipids in both adipose tissue and stomach oil. Thus, both lipid sources are potentially useful for trophic studies using fatty acid (FA) signatures. However, little is known about the relationship between FA signatures in stomach oil and adipose tissue of individuals or whether these signatures provide similar information about diet and physiology. We compared the FA composition of stomach oil and adipose tissue biopsies of individual northern fulmars (N = 101) breeding at three major colonies in Alaska. Fatty acid signatures differed significantly between the two lipid sources, reflecting differences in dietary time scales, metabolic processing, or both. However, these signatures exhibited a relatively consistent relationship between individuals, such that the two lipid sources provided a similar ability to distinguish foraging differences among individuals and colonies. Our results, including the exclusive presence of dietary wax esters in stomach oil but not adipose tissue, are consistent with the notion that stomach oil FA signatures represent lipids retained from prey consumed during recent foraging and reflect little metabolic processing, whereas adipose tissue FA signatures represent a longer-term integration of dietary intake. Our study illustrates the potential for elucidating short- versus longer-term diet information in Procellariiform birds using different lipid sources. ?? 2007 Springer-Verlag.

  11. Block truncation signature coding for hyperspectral analysis

    NASA Astrophysics Data System (ADS)

    Chakravarty, Sumit; Chang, Chein-I.

    2008-08-01

    This paper introduces a new signature coding which is designed based on the well-known Block Truncation Coding (BTC). It comprises of bit-maps of the signature blocks generated by different threshold criteria. Two new BTC-based algorithms are developed for signature coding, to be called Block Truncation Signature Coding (BTSC) and 2-level BTSC (2BTSC). In order to compare the developed BTC based algorithms with current binary signature coding schemes such as Spectral Program Analysis Manager (SPAM) developed by Mazer et al. and Spectral Feature-based Binary Coding (SFBC) by Qian et al., three different thresholding functions, local block mean, local block gradient, local block correlation are derived to improve the BTSC performance where the combined bit-maps generated by these thresholds can provide better spectral signature characterization. Experimental results reveal that the new BTC-based signature coding performs more effectively in characterizing spectral variations than currently available binary signature coding methods.

  12. An Analysis of Diet Quality, How It Controls Fatty Acid Profiles, Isotope Signatures and Stoichiometry in the Malaria Mosquito Anopheles arabiensis

    PubMed Central

    Hood-Nowotny, Rebecca; Schwarzinger, Bettina; Schwarzinger, Clemens; Soliban, Sharon; Madakacherry, Odessa; Aigner, Martina; Watzka, Margarete; Gilles, Jeremie

    2012-01-01

    Background Knowing the underlying mechanisms of mosquito ecology will ensure effective vector management and contribute to the overall goal of malaria control. Mosquito populations show a high degree of population plasticity in response to environmental variability. However, the principle factors controlling population size and fecundity are for the most part unknown. Larval habitat and diet play a crucial role in subsequent mosquito fitness. Developing the most competitive insects for sterile insect technique programmes requires a “production” orientated perspective, to deduce the most effective larval diet formulation; the information gained from this process offers us some insight into the mechanisms and processes taking place in natural native mosquito habitats. Methodology/Principal Findings Fatty acid profiles and de-novo or direct assimilation pathways, of whole-individual mosquitoes reared on a range of larval diets were determined using pyrolysis gas chromatograph/mass spectrometry. We used elemental analysis and isotope ratio mass spectrometry to measure individual-whole-body carbon, nitrogen and phosphorous values and to assess the impact of dietary quality on subsequent population stoichiometry, size, quality and isotopic signature. Diet had the greatest impact on fatty acid (FA) profiles of the mosquitoes, which exhibited a high degree of dietary routing, characteristic of generalist feeders. De-novo synthesis of a number of important FAs was observed. Mosquito C:N stoichiometry was fixed in the teneral stage. Dietary N content had significant influence on mosquito size, and P was shown to be a flexible pool which limited overall population size. Conclusions/Significance Direct routing of FAs was evident but there was ubiquitous de-novo synthesis suggesting mosquito larvae are competent generalist feeders capable of survival on diet with varying characteristics. It was concluded that nitrogen availability in the larval diet controlled teneral

  13. Infrared ship signature analysis and optimisation

    NASA Astrophysics Data System (ADS)

    Neele, Filip

    2005-05-01

    The last decade has seen an increase in the awareness of the infrared signature of naval ships. New ship designs show that infrared signature reduction measures are being incorporated, such as exhaust gas cooling systems, relocation of the exhausts and surface cooling systems. Hull and superstructure are cooled with dedicated spray systems, in addition to special paint systems that are being developed for optimum stealth. This paper presents a method to develop requirements for the emissivity of a ship's coating that reduces the contrast of the ship against its background in the wavelength band or bands of threat sensors. As this contrast strongly depends on the atmospheric environment, these requirements must follow from a detailed analysis of the infrared signature of the ship in its expected areas of operation. Weather statistics for a large number of areas have been collected to produce a series of 'standard environments'. These environments have been used to demonstrate the method of specifying coating emissivity requirements. Results are presented to show that the optimised coatings reduce the temperature contrast. The use of the standard environments yields a complete, yet concise, description of the signature of the ship over its areas of operation. The signature results illustrate the strong dependence of the infrared signature on the atmospheric environment and can be used to identify those conditions where signature reduction is most effective in reducing the ship's susceptibility to detection by IR sensors.

  14. Should fatty acid signature proportions sum to 1 for diet estimation?

    USGS Publications Warehouse

    Bromaghin, Jeffrey; Budge, Suzanne M.; Thiemann, Gregory W.

    2016-01-01

    Knowledge of predator diets, including how diets might change through time or differ among predators, provides essential insights into their ecology. Diet estimation therefore remains an active area of research within quantitative ecology. Quantitative fatty acid signature analysis (QFASA) is an increasingly common method of diet estimation. QFASA is based on a data library of prey signatures, which are vectors of proportions summarizing the fatty acid composition of lipids, and diet is estimated as the mixture of prey signatures that most closely approximates a predator’s signature. Diets are typically estimated using proportions from a subset of all fatty acids that are known to be solely or largely influenced by diet. Given the subset of fatty acids selected, the current practice is to scale their proportions to sum to 1.0. However, scaling signature proportions has the potential to distort the structural relationships within a prey library and between predators and prey. To investigate that possibility, we compared the practice of scaling proportions with two alternatives and found that the traditional scaling can meaningfully bias diet estimators under some conditions. Two aspects of the prey types that contributed to a predator’s diet influenced the magnitude of the bias: the degree to which the sums of unscaled proportions differed among prey types and the identifiability of prey types within the prey library. We caution investigators against the routine scaling of signature proportions in QFASA.

  15. Vibration signature analysis of multistage gear transmission

    NASA Technical Reports Server (NTRS)

    Choy, F. K.; Tu, Y. K.; Savage, M.; Townsend, D. P.

    1989-01-01

    An analysis is presented for multistage multimesh gear transmission systems. The analysis predicts the overall system dynamics and the transmissibility to the gear box or the enclosed structure. The modal synthesis approach of the analysis treats the uncoupled lateral/torsional model characteristics of each stage or component independently. The vibration signature analysis evaluates the global dynamics coupling in the system. The method synthesizes the interaction of each modal component or stage with the nonlinear gear mesh dynamics and the modal support geometry characteristics. The analysis simulates transient and steady state vibration events to determine the resulting torque variations, speeds, changes, rotor imbalances, and support gear box motion excitations. A vibration signature analysis examines the overall dynamic characteristics of the system, and the individual model component responses. The gear box vibration analysis also examines the spectral characteristics of the support system.

  16. Phosphorus Effects on the Mycelium and Storage Structures of an Arbuscular Mycorrhizal Fungus as Studied in the Soil and Roots by Analysis of Fatty Acid Signatures

    PubMed Central

    Olsson, P. A.; Baath, E.; Jakobsen, I.

    1997-01-01

    The distribution of an arbuscular mycorrhizal (AM) fungus between soil and roots, and between mycelial and storage structures, was studied by use of the fatty acid signature 16:1(omega)5. Increasing the soil phosphorus level resulted in a decrease in the level of the fatty acid 16:1(omega)5 in the soil and roots. A similar decrease was detected by microscopic measurements of root colonization and of the length of AM fungal hyphae in the soil. The fatty acid 16:1(omega)5 was estimated from two types of lipids, phospholipids and neutral lipids, which mainly represent membrane lipids and storage lipids, respectively. The numbers of spores of the AM fungus formed in the soil correlated most closely with neutral lipid fatty acid 16:1(omega)5, whereas the hyphal length in the soil correlated most closely with phospholipid fatty acid 16:1(omega)5. The fungal neutral lipid/phospholipid ratio in the extraradical mycelium was positively correlated with the level of root infection and thus decreased with increasing applications of P. The neutral lipid/phospholipid ratio indicated that at high P levels, less carbon was allocated to storage structures. At all levels of P applied, the major part of the AM fungus was found to be present outside the roots, as estimated from phospholipid fatty acid 16:1(omega)5. The ratio of extraradical biomass/intraradical biomass was not affected by the application of P, except for a decrease at the highest level of P applied. PMID:16535691

  17. Hyperspectral signature analysis of skin parameters

    NASA Astrophysics Data System (ADS)

    Vyas, Saurabh; Banerjee, Amit; Garza, Luis; Kang, Sewon; Burlina, Philippe

    2013-02-01

    The temporal analysis of changes in biological skin parameters, including melanosome concentration, collagen concentration and blood oxygenation, may serve as a valuable tool in diagnosing the progression of malignant skin cancers and in understanding the pathophysiology of cancerous tumors. Quantitative knowledge of these parameters can also be useful in applications such as wound assessment, and point-of-care diagnostics, amongst others. We propose an approach to estimate in vivo skin parameters using a forward computational model based on Kubelka-Munk theory and the Fresnel Equations. We use this model to map the skin parameters to their corresponding hyperspectral signature. We then use machine learning based regression to develop an inverse map from hyperspectral signatures to skin parameters. In particular, we employ support vector machine based regression to estimate the in vivo skin parameters given their corresponding hyperspectral signature. We build on our work from SPIE 2012, and validate our methodology on an in vivo dataset. This dataset consists of 241 signatures collected from in vivo hyperspectral imaging of patients of both genders and Caucasian, Asian and African American ethnicities. In addition, we also extend our methodology past the visible region and through the short-wave infrared region of the electromagnetic spectrum. We find promising results when comparing the estimated skin parameters to the ground truth, demonstrating good agreement with well-established physiological precepts. This methodology can have potential use in non-invasive skin anomaly detection and for developing minimally invasive pre-screening tools.

  18. Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness*

    PubMed Central

    Liu, Yansheng; Chen, Jing; Sethi, Atul; Li, Qing K.; Chen, Lijun; Collins, Ben; Gillet, Ludovic C. J.; Wollscheid, Bernd; Zhang, Hui; Aebersold, Ruedi

    2014-01-01

    The identification of biomarkers indicating the level of aggressiveness of prostate cancer (PCa) will address the urgent clinical need to minimize the general overtreatment of patients with non-aggressive PCa, who account for the majority of PCa cases. Here, we isolated formerly N-linked glycopeptides from normal prostate (n = 10) and from non-aggressive (n = 24), aggressive (n = 16), and metastatic (n = 25) PCa tumor tissues and analyzed the samples using SWATH mass spectrometry, an emerging data-independent acquisition method that generates a single file containing fragment ion spectra of all ionized species of a sample. The resulting datasets were searched using a targeted data analysis strategy in which an a priori spectral reference library representing known N-glycosites of the human proteome was used to identify groups of signals in the SWATH mass spectrometry data. On average we identified 1430 N-glycosites from each sample. Out of those, 220 glycoproteins showed significant quantitative changes associated with diverse biological processes involved in PCa aggressiveness and metastasis and indicated functional relationships. Two glycoproteins, N-acylethanolamine acid amidase and protein tyrosine kinase 7, that were significantly associated with aggressive PCa in the initial sample cohort were further validated in an independent set of patient tissues using tissue microarray analysis. The results suggest that N-acylethanolamine acid amidase and protein tyrosine kinase 7 may be used as potential tissue biomarkers to avoid overtreatment of non-aggressive PCa. PMID:24741114

  19. Seismic signature analysis for discrimination of people from animals

    NASA Astrophysics Data System (ADS)

    Damarla, Thyagaraju; Mehmood, Asif; Sabatier, James M.

    2013-05-01

    Cadence analysis has been the main focus for discriminating between the seismic signatures of people and animals. However, cadence analysis fails when multiple targets are generating the signatures. We analyze the mechanism of human walking and the signature generated by a human walker, and compare it with the signature generated by a quadruped. We develop Fourier-based analysis to differentiate the human signatures from the animal signatures. We extract a set of basis vectors to represent the human and animal signatures using non-negative matrix factorization, and use them to separate and classify both the targets. Grazing animals such as deer, cows, etc., often produce sporadic signals as they move around from patch to patch of grass and one must characterize them so as to differentiate their signatures from signatures generated by a horse steadily walking along a path. These differences in the signatures are used in developing a robust algorithm to distinguish the signatures of animals from humans. The algorithm is tested on real data collected in a remote area.

  20. Characteristic vector analysis as a technique for signature extraction of remote ocean color data

    NASA Technical Reports Server (NTRS)

    Grew, G. W.

    1977-01-01

    Characteristic vector analysis is being used to extract spectral signatures of suspended matter in the ocean from remote ocean color data collected with MOCS (Multichannel Ocean Color Sensor), a multispectral scanner. Spectral signatures appear to be obtainable either directly from characteristic vectors or through a transformation of these eigenvectors. Quantification of the suspended matter associated with each resulting signature seems feasible using associated coefficients generated by the technique. This paper presents eigenvectors associated with algae, 'sediment', acid waste, sewage sludge, and oil. The results suggest an efficient method of transmitting from satellites multispectral data of pollution in our oceans.

  1. Temporal shape analysis via the spectral signature.

    PubMed

    Bernardis, Elena; Konukoglu, Ender; Ou, Yangming; Metaxas, Dimitris N; Desjardins, Benoit; Pohl, Kilian M

    2012-01-01

    In this paper, we adapt spectral signatures for capturing morphological changes over time. Advanced techniques for capturing temporal shape changes frequently rely on first registering the sequence of shapes and then analyzing the corresponding set of high dimensional deformation maps. Instead, we propose a simple encoding motivated by the observation that small shape deformations lead to minor refinements in the spectral signature composed of the eigenvalues of the Laplace operator. The proposed encoding does not require registration, since spectral signatures are invariant to pose changes. We apply our representation to the shapes of the ventricles extracted from 22 cine MR scans of healthy controls and Tetralogy of Fallot patients. We then measure the accuracy score of our encoding by training a linear classifier, which outperforms the same classifier based on volumetric measurements. PMID:23286031

  2. Remotely sensed and laboratory spectral signatures of an ocean-dumped acid waste

    NASA Technical Reports Server (NTRS)

    Lewis, B. W.; Collins, V. G.

    1977-01-01

    An ocean-dumped acid waste plume was studied by using a rapid scanning spectrometer to remotely measure ocean radiance from a helicopter. The results of these studies are presented and compared with results from sea truth samples and laboratory experiments. An ocean spectral reflectance signature and a laboratory spectral transmission signature were established for the iron-acid waste pollutant. The spectrally and chemically significant component of the acid waste pollutant was determined to be ferric iron.

  3. Spectral Signature Analysis - BIST for RF Front-Ends

    NASA Astrophysics Data System (ADS)

    Lupea, D.; Pursche, U.; Jentschel, H.-J.

    2003-05-01

    In this paper, the Spectral Signature Analysis is presented as a concept for an integrable self-test system (Built-In Self-Test - BIST) for RF front-ends is presented. It is based on modelling the whole RF front-end (transmitter and receiver) on system level, on generating of a Spectral Signature and of evaluating of the Signature Response. Because of using multi-carrier signal as the test signature, the concept is especially useful for tests of linearity and frequency response of front-ends. Due to the presented method of signature response evaluation, this concept can be used for Built-In Self-Correction (BISC) at critical building blocks.

  4. An integrated spatial signature analysis and automatic defect classification system

    SciTech Connect

    Gleason, S.S.; Tobin, K.W.; Karnowski, T.P.

    1997-08-01

    An integrated Spatial Signature Analysis (SSA) and automatic defect classification (ADC) system for improved automatic semiconductor wafer manufacturing characterization is presented. Both concepts of SSA and ADC methodologies are reviewed and then the benefits of an integrated system are described, namely, focused ADC and signature-level sampling. Focused ADC involves the use of SSA information on a defect signature to reduce the number of possible classes that an ADC system must consider, thus improving the ADC system performance. Signature-level sampling improved the ADC system throughput and accuracy by intelligently sampling defects within a given spatial signature for subsequent off-line, high-resolution ADC. A complete example of wafermap characterization via an integrated SSA/ADC system is presented where a wafer with 3274 defects is completely characterized by revisiting only 25 defects on an off-line ADC review station. 13 refs., 7 figs.

  5. Discrimination of prey species of juvenile swordfish Xiphias gladius (Linnaeus, 1758) using signature fatty acid analyses

    NASA Astrophysics Data System (ADS)

    Young, Jock W.; Guest, Michaela A.; Lansdell, Matt; Phleger, Charles F.; Nichols, Peter D.

    2010-07-01

    Signature lipid and fatty acid analysis were used to discriminate the diet of swordfish ( Xiphias gladius, orbital fork length: 60-203 cm) from waters off eastern Australia. The fatty acid (FA) composition of a range of known prey (squid, myctophids, and other fishes) of swordfish, taken from stomach samples and from net tows, was compared with that of the white muscle tissue (WMT) of swordfish from the same region. Swordfish muscle was lipid rich (average 24-42% dry weight), as was the skeleton (28-41%). The robustness of the approach was also tested by comparison against a key squid prey species that was collected and stored using different protocols: (i) fresh frozen, (ii) fresh frozen, then thawed, and (iii) stomach content collection. The FA profiles were generally similar, with the ratio of docosahexaenoic acid (DHA) and palmitic acid (16:0) in particular showing no significant difference. Major fatty acids in swordfish WMT were 18:1ω9c, 16:0, 22:6ω3, and 18:0. Multidimensional scaling showed that the swordfish WMT grouped closely with small fish prey including myctophids, and not with squid. Squid contained markedly higher 22:6ω3 than swordfish. Individual prey species of the myctophidae could also be separated by the same technique. These results were supported by traditional stomach content analyses (SCA) that showed fish were the dominant prey for small swordfish sampled from southern waters whereas squid were the main prey in more northern waters, matching the FA patterns we found for the two regions. We propose that where general diet patterns are established, signature FA analysis has good potential to compliment or in some cases, replace temporal and spatial monitoring of trophic pathways for swordfish and other marine species.

  6. CRISPR Spacer Arrays for Detection of Viral Signatures from Acidic Hot Springs

    NASA Astrophysics Data System (ADS)

    Snyder, J. C.; Bateson, M. M.; Suciu, D.; Young, M. J.

    2010-04-01

    Viruses are the most abundant life-like entities on the planet Earth. Using CRISPR spacer sequences, we have developed a microarray-based approach to detecting viral signatures in the acidic hot springs of Yellowstone.

  7. Tracking diet preferences of bats using stable isotope and fatty acid signatures of faeces.

    PubMed

    Lam, Monika My-Y; Martin-Creuzburg, Dominik; Rothhaupt, Karl-Otto; Safi, Kamran; Yohannes, Elizabeth; Salvarina, Ioanna

    2013-01-01

    Stable isotope and fatty acid signatures of biomaterials can provide important information about the dietary niche of animals. Stable isotope and fatty acid signatures differ between aquatic and terrestrial food webs, and therefore can be used to assess the aquatic and terrestrial contributions to the diets of species. We studied faecal samples of three co-occurring bat species with known differences in feeding preferences. The aim was to assess whether stable isotope and fatty acid signatures of faeces can be used to determine feeding preferences. We used bat faeces because they can be easily and non-invasively collected. We hypothesised that faeces stable isotope and fatty acid signatures will reveal the terrestrial, aquatic and mixed feeding niches of Myotis myotis, M. daubentonii, and M. mystacinus, respectively. As predicted, the faeces of M. myotis were characterized by higher δ(13)C values and higher concentrations of linoleic acid and total ω6 polyunsaturated fatty acids (PUFAs), which are typically higher in terrestrial food webs. The faeces of M. daubentonii had higher δ(15)Ν values and higher concentrations of docosahexaenoic acid and total ω3 PUFAs, characteristic features of aquatic systems. Myotis mystacinus faeces had intermediate δ(15)Ν values and concentrations of both types of fatty acids. Our results show that analysing stable isotope and/or fatty acid signatures of faeces provides a promising, non-invasive tool to study the feeding ecology of bats and to assess aquatic-terrestrial interactions. PMID:24376703

  8. Tracking Diet Preferences of Bats Using Stable Isotope and Fatty Acid Signatures of Faeces

    PubMed Central

    Lam, Monika My-Y; Martin-Creuzburg, Dominik; Rothhaupt, Karl-Otto; Safi, Kamran; Yohannes, Elizabeth; Salvarina, Ioanna

    2013-01-01

    Stable isotope and fatty acid signatures of biomaterials can provide important information about the dietary niche of animals. Stable isotope and fatty acid signatures differ between aquatic and terrestrial food webs, and therefore can be used to assess the aquatic and terrestrial contributions to the diets of species. We studied faecal samples of three co-occurring bat species with known differences in feeding preferences. The aim was to assess whether stable isotope and fatty acid signatures of faeces can be used to determine feeding preferences. We used bat faeces because they can be easily and non-invasively collected. We hypothesised that faeces stable isotope and fatty acid signatures will reveal the terrestrial, aquatic and mixed feeding niches of Myotis myotis, M. daubentonii, and M. mystacinus, respectively. As predicted, the faeces of M. myotis were characterized by higher δ13C values and higher concentrations of linoleic acid and total ω6 polyunsaturated fatty acids (PUFAs), which are typically higher in terrestrial food webs. The faeces of M. daubentonii had higher δ15Ν values and higher concentrations of docosahexaenoic acid and total ω3 PUFAs, characteristic features of aquatic systems. Myotis mystacinus faeces had intermediate δ15Ν values and concentrations of both types of fatty acids. Our results show that analysing stable isotope and/or fatty acid signatures of faeces provides a promising, non-invasive tool to study the feeding ecology of bats and to assess aquatic-terrestrial interactions. PMID:24376703

  9. Motor current signature analysis method for diagnosing motor operated devices

    DOEpatents

    Haynes, Howard D.; Eissenberg, David M.

    1990-01-01

    A motor current noise signature analysis method and apparatus for remotely monitoring the operating characteristics of an electric motor-operated device such as a motor-operated valve. Frequency domain signal analysis techniques are applied to a conditioned motor current signal to distinctly identify various operating parameters of the motor driven device from the motor current signature. The signature may be recorded and compared with subsequent signatures to detect operating abnormalities and degradation of the device. This diagnostic method does not require special equipment to be installed on the motor-operated device, and the current sensing may be performed at remote control locations, e.g., where the motor-operated devices are used in accessible or hostile environments.

  10. Spatial and temporal diet segregation in northern fulmars Fulmarus glacialis breeding in Alaska: Insights from fatty acid signatures

    USGS Publications Warehouse

    Wang, S.W.; Iverson, S.J.; Springer, A.M.; Hatch, Shyla A.

    2009-01-01

    Northern fulmars Fulmarus glacialis in the North Pacific Ocean are opportunistic, generalist predators, yet their diets are poorly described; thus, relationships of fulmars to supporting food webs, their utility as indicators of variability in forage fish abundances, and their sensitivity to ecosystem change are not known. We employed fatty acid (FA) signature analysis of adipose tissue from adults (n = 235) and chicks (n = 33) to compare spatial, temporal, and age-related variation in diets of fulmars breeding at 3 colonies in Alaska. FA signatures of adult fulmars differed between colonies within years, and between seasons at individual colonies. Seasonal and spatial differences in signatures were greater than interannual differences at all colonies. Differences in FA signatures reflect differences in diets, probably because the breeding colonies are located in distinct ecoregions which create unique habitats for prey assemblages, and because interannual variation in the physical environment affects the availability of forage species. Differences between FA signatures of adults and chicks in 2003 and 2004 suggest that adults fed chicks different prey than they consumed themselves. Alternatively, if adults relied on the same prey as those fed to chicks, the differences in signatures could have resulted from partial digestion of prey items by adults before chicks were fed, or direct metabolism of FAs by chicks for tissue synthesis before FAs could be deposited into adipose tissue. ?? Inter-Research 2009.

  11. Transcriptome analysis and molecular signature of human retinal pigment epithelium

    PubMed Central

    Strunnikova, N.V.; Maminishkis, A.; Barb, J.J.; Wang, F.; Zhi, C.; Sergeev, Y.; Chen, W.; Edwards, A.O.; Stambolian, D.; Abecasis, G.; Swaroop, A.; Munson, P.J.; Miller, S.S.

    2010-01-01

    Retinal pigment epithelium (RPE) is a polarized cell layer critical for photoreceptor function and survival. The unique physiology and relationship to the photoreceptors make the RPE a critical determinant of human vision. Therefore, we performed a global expression profiling of native and cultured human fetal and adult RPE and determined a set of highly expressed ‘signature’ genes by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues. Using stringent selection criteria of at least 10-fold higher expression in three distinct preparations, we identified 154 RPE signature genes, which were validated by qRT-PCR analysis in RPE and in an independent set of 11 tissues. Several of the highly expressed signature genes encode proteins involved in visual cycle, melanogenesis and cell adhesion and Gene ontology analysis enabled the assignment of RPE signature genes to epithelial channels and transporters (ClCN4, BEST1, SLCA20) or matrix remodeling (TIMP3, COL8A2). Fifteen RPE signature genes were associated with known ophthalmic diseases, and 25 others were mapped to regions of disease loci. An evaluation of the RPE signature genes in a recently completed AMD genomewide association (GWA) data set revealed that TIMP3, GRAMD3, PITPNA and CHRNA3 signature genes may have potential roles in AMD pathogenesis and deserve further examination. We propose that RPE signature genes are excellent candidates for retinal diseases and for physiological investigations (e.g. dopachrome tautomerase in melanogenesis). The RPE signature gene set should allow the validation of RPE-like cells derived from human embryonic or induced pluripotent stem cells for cell-based therapies of degenerative retinal diseases. PMID:20360305

  12. Gene expression signature of DMBA-induced hamster buccal pouch carcinomas: modulation by chlorophyllin and ellagic acid.

    PubMed

    Vidya Priyadarsini, Ramamurthi; Kumar, Neeraj; Khan, Imran; Thiyagarajan, Paranthaman; Kondaiah, Paturu; Nagini, Siddavaram

    2012-01-01

    Chlorophyllin (CHL), a water-soluble, semi-synthetic derivative of chlorophyll and ellagic acid (EA), a naturally occurring polyphenolic compound in berries, grapes, and nuts have been reported to exert anticancer effects in various human cancer cell lines and in animal tumour models. The present study was undertaken to examine the mechanism underlying chemoprevention and changes in gene expression pattern induced by dietary supplementation of chlorophyllin and ellagic acid in the 7,12-dimethylbenz[a]anthracene (DMBA)-induced hamster buccal pouch (HBP) carcinogenesis model by whole genome profiling using pangenomic microarrays. In hamsters painted with DMBA, the expression of 1,700 genes was found to be altered significantly relative to control. Dietary supplementation of chlorophyllin and ellagic acid modulated the expression profiles of 104 and 37 genes respectively. Microarray analysis also revealed changes in the expression of TGFβ receptors, NF-κB, cyclin D1, and matrix metalloproteinases (MMPs) that may play a crucial role in the transformation of the normal buccal pouch to a malignant phenotype. This gene expression signature was altered on treatment with chlorophyllin and ellagic acid. Our study has also revealed patterns of gene expression signature specific for chlorophyllin and ellagic acid exposure. Thus dietary chlorophyllin and ellagic acid that can reverse gene expression signature associated with carcinogenesis are novel candidates for cancer prevention and therapy. PMID:22485181

  13. Gene Expression Signature of DMBA-Induced Hamster Buccal Pouch Carcinomas: Modulation by Chlorophyllin and Ellagic Acid

    PubMed Central

    Vidya Priyadarsini, Ramamurthi; Kumar, Neeraj; Khan, Imran; Thiyagarajan, Paranthaman; Kondaiah, Paturu; Nagini, Siddavaram

    2012-01-01

    Chlorophyllin (CHL), a water-soluble, semi-synthetic derivative of chlorophyll and ellagic acid (EA), a naturally occurring polyphenolic compound in berries, grapes, and nuts have been reported to exert anticancer effects in various human cancer cell lines and in animal tumour models. The present study was undertaken to examine the mechanism underlying chemoprevention and changes in gene expression pattern induced by dietary supplementation of chlorophyllin and ellagic acid in the 7,12-dimethylbenz[a]anthracene (DMBA)-induced hamster buccal pouch (HBP) carcinogenesis model by whole genome profiling using pangenomic microarrays. In hamsters painted with DMBA, the expression of 1,700 genes was found to be altered significantly relative to control. Dietary supplementation of chlorophyllin and ellagic acid modulated the expression profiles of 104 and 37 genes respectively. Microarray analysis also revealed changes in the expression of TGFβ receptors, NF-κB, cyclin D1, and matrix metalloproteinases (MMPs) that may play a crucial role in the transformation of the normal buccal pouch to a malignant phenotype. This gene expression signature was altered on treatment with chlorophyllin and ellagic acid. Our study has also revealed patterns of gene expression signature specific for chlorophyllin and ellagic acid exposure. Thus dietary chlorophyllin and ellagic acid that can reverse gene expression signature associated with carcinogenesis are novel candidates for cancer prevention and therapy. PMID:22485181

  14. Infrared signature analysis of the thyroid tumors

    NASA Astrophysics Data System (ADS)

    Gavriloaia, Gheorghe; Ghemigian, Adina-Mariana; Gavriloaia, Mariuca-Roxana

    2009-07-01

    Cancer is a leading cause of death worldwide, and about 30% of cancer deaths can be prevented. In the next future, the number of global cancer deaths is projected to increase 45% in the future. A general treatment has not yet been found. The best defense against cancer is early detection, when tumor dimensions are very small. The methods as mammography, ultrasounds, MRI, CT, etc., can detect anatomic or structural changes like tumors and cysts. They are anatomical imaging procedures, consequently, they have the ability to locate the area of the tumor, but they cannot detect a fast-growing cancer in the pre-invasive stage. Thermograms are looking for the physiologic changes in tissue; which may indicate a risk of developing cancer in the future. The results using a new device, operating in infrared band, are described. The paper focuses on thyroid cancer because it allows investigations on larger areas before surgery and on residual, smaller areas following surgery. The experiment results for 24 patients with thyroid nodules are described. Malign tumors have a distinct infrared signature. Only the area affected is thermal registered and that has an irregular shape and a strong nonuniform structure with rapid variations on skin temperature.

  15. Photon signature analysis using template matching

    NASA Astrophysics Data System (ADS)

    Bradley, D. A.; Hashim, S.; Saripan, M. I.; Wells, K.; Dunn, W. L.

    2011-10-01

    We describe an approach to detect improvised explosive devices (IEDs) by using a template matching procedure. This approach relies on the signature due to backstreaming γ photons from various targets. In this work we have simulated cylindrical targets of aluminum, iron, copper, water and ammonium nitrate (nitrogen-rich fertilizer). We simulate 3.5 MeV source photons distributed on a plane inside a shielded area using Monte Carlo N-Particle (MCNP TM) code version 5 (V5). The 3.5 MeV source gamma rays yield 511 keV peaks due to pair production and scattered gamma rays. In this work, we simulate capture of those photons that backstream, after impinging on the target element, toward a NaI detector. The captured backstreamed photons are expected to produce a unique spectrum that will become part of a simple signal processing recognition system based on the template matching method. Different elements were simulated using different sets of random numbers in the Monte Carlo simulation. To date, the sum of absolute differences (SAD) method has been used to match the template. In the examples investigated, template matching was found to detect all elements correctly.

  16. The effects of diet and caloric restriction on adipose tissue fatty acid signatures of tufted puffin (Fratercula cirrhata) nestlings.

    PubMed

    Williams, Cory T; Iverson, Sara J; Buck, C Loren

    2009-08-01

    Fatty acid (FA) signature analysis is a powerful tool to investigate foraging ecology and food web dynamics in marine ecosystems. However, use of FA signatures to qualitatively or quantitatively infer diets is potentially complicated by effects of nutritional state on lipid metabolism. Estimation of diets using the quantitative fatty acid signature analysis (QFASA) model requires the use of calibration coefficients to account for predator metabolism of individual FAs. We conducted a captive feeding experiment to determine the effects of a 50% reduction in food intake on growth rate and adipose tissue FA signatures of tufted puffin (Fratercula cirrhata) nestlings, a species that routinely experiences food restriction during growth. FA signatures of chicks fed low- and high-calorie diets both exhibited a change in composition in response to the dietary shift with the direction of change in the composition of individual FAs matching the direction of change in the dietary FAs. Despite a growth rate in the restricted nestlings that was 38% of those in the well-fed group, rates of FA turnover were not different between high and low-calorie treatments, and turnover was close to, but not entirely complete, after 27 days on both high-calorie and restricted diets. FA signatures of tufted puffin nestlings were significantly affected by caloric restriction, but these effects were much less pronounced than those of dietary turnover, and calibration coefficients of puffins fed low and high-calorie diets were highly correlated. Our results demonstrate that changes in physiological state can affect FA metabolism, but future research is required to better understand whether the size of these effects is sufficient to substantially alter diet estimation using the QFASA model. PMID:19350253

  17. Spectral derivative feature coding for hyperspectral signature analysis

    NASA Astrophysics Data System (ADS)

    Chang, Chein-I.; Chakravarty, Sumit

    2006-08-01

    This paper presents a new approach to hyperspectral signature analysis, called Spectral Derivative Feature Coding (SDFC). It makes use of gradient changes in adjacent bands to characterize spectral variations so as to improve spectral discrimination and identification. In order to evaluate its performance, two binary coding methods, SPectral Analysis Manager (SPAM) and Spectral Feature-based Binary Coding (SFBC) are used to conduct comparative analysis. The experimental results demonstrate the proposed SDFC performs more effectively in capturing spectral characteristics.

  18. A Coincidence Signature Library for Multicoincidence Radionuclide Analysis Systems

    SciTech Connect

    Smith, Leon E.; Ellis, J E.; Valsan, Andrei B.; Aalseth, Craig E.; Miley, Harry S.

    2003-10-01

    Pacific Northwest National Laboratory (PNNL) is currently developing multicoincidence systems to perform trace radionuclide analysis at or near the sample collection point, for applications that include emergency response, nuclear forensics, and environmental monitoring. Quantifying radionuclide concentrations with these systems requires a library of accurate emission intensities for each detected signature, for all candidate radionuclides. To meet this need, a Coincidence Lookup Library (CLL) is being developed to calculate the emission intensities of coincident signatures from a user-specified radionuclide, or conversely, to determine the radionuclides that may be responsible for a specific detected coincident signature. The algorithms used to generate absolute emission intensities and various query modes for our developmental CLL are described.

  19. Amino acid analysis

    NASA Technical Reports Server (NTRS)

    Winitz, M.; Graff, J. (Inventor)

    1974-01-01

    The process and apparatus for qualitative and quantitative analysis of the amino acid content of a biological sample are presented. The sample is deposited on a cation exchange resin and then is washed with suitable solvents. The amino acids and various cations and organic material with a basic function remain on the resin. The resin is eluted with an acid eluant, and the eluate containing the amino acids is transferred to a reaction vessel where the eluant is removed. Final analysis of the purified acylated amino acid esters is accomplished by gas-liquid chromatographic techniques.

  20. Infrared Signature Modeling and Analysis of Aircraft Plume

    NASA Astrophysics Data System (ADS)

    Rao, Arvind G.

    2011-09-01

    In recent years, the survivability of an aircraft has been put to task more than ever before. One of the main reasons is the increase in the usage of Infrared (IR) guided Anti-Aircraft Missiles, especially due to the availability of Man Portable Air Defence System (MANPADS) with some terrorist groups. Thus, aircraft IR signatures are gaining more importance as compared to their radar, visual, acoustic, or any other signatures. The exhaust plume ejected from the aircraft is one of the important sources of IR signature in military aircraft that use low bypass turbofan engines for propulsion. The focus of the present work is modelling of spectral IR radiation emission from the exhaust jet of a typical military aircraft and to evaluate the aircraft susceptibility in terms of the aircraft lock-on range due to its plume emission, for a simple case against a typical Surface to Air Missile (SAM). The IR signature due to the aircraft plume is examined in a holistic manner. A comprehensive methodology of computing IR signatures and its affect on aircraft lock-on range is elaborated. Commercial CFD software has been used to predict the plume thermo-physical properties and subsequently an in-house developed code was used for evaluating the IR radiation emitted by the plume. The LOWTRAN code has been used for modeling the atmospheric IR characteristics. The results obtained from these models are in reasonable agreement with some available experimental data. The analysis carried out in this paper succinctly brings out the intricacy of the radiation emitted by various gaseous species in the plume and the role of atmospheric IR transmissivity in dictating the plume IR signature as perceived by an IR guided SAM.

  1. Gene Expression Signature in Endemic Osteoarthritis by Microarray Analysis

    PubMed Central

    Wang, Xi; Ning, Yujie; Zhang, Feng; Yu, Fangfang; Tan, Wuhong; Lei, Yanxia; Wu, Cuiyan; Zheng, Jingjing; Wang, Sen; Yu, Hanjie; Li, Zheng; Lammi, Mikko J.; Guo, Xiong

    2015-01-01

    Kashin-Beck Disease (KBD) is an endemic osteochondropathy with an unknown pathogenesis. Diagnosis of KBD is effective only in advanced cases, which eliminates the possibility of early treatment and leads to an inevitable exacerbation of symptoms. Therefore, we aim to identify an accurate blood-based gene signature for the detection of KBD. Previously published gene expression profile data on cartilage and peripheral blood mononuclear cells (PBMCs) from adults with KBD were compared to select potential target genes. Microarray analysis was conducted to evaluate the expression of the target genes in a cohort of 100 KBD patients and 100 healthy controls. A gene expression signature was identified using a training set, which was subsequently validated using an independent test set with a minimum redundancy maximum relevance (mRMR) algorithm and support vector machine (SVM) algorithm. Fifty unique genes were differentially expressed between KBD patients and healthy controls. A 20-gene signature was identified that distinguished between KBD patients and controls with 90% accuracy, 85% sensitivity, and 95% specificity. This study identified a 20-gene signature that accurately distinguishes between patients with KBD and controls using peripheral blood samples. These results promote the further development of blood-based genetic biomarkers for detection of KBD. PMID:25997002

  2. Relation of laboratory and remotely sensed spectral signatures of ocean-dumped acid waste

    NASA Technical Reports Server (NTRS)

    Lewis, B. W.

    1978-01-01

    Results of laboratory transmission and remotely sensed ocean upwelled spectral signatures of acid waste ocean water solutions are presented. The studies were performed to establish ocean-dumped acid waste spectral signatures and to relate them to chemical and physical interactions occurring in the dump plume. The remotely sensed field measurements and the laboratory measurements were made using the same rapid-scanning spectrometer viewing a dump plume and with actual acid waste and ocean water samples, respectively. Laboratory studies showed that the signatures were produced by soluble ferric iron being precipitated in situ as ferric hydroxide upon dilution with ocean water. Sea-truth water samples were taken and analyzed for pertinent major components of the acid waste. Relationships were developed between the field and laboratory data both for spectral signatures and color changes with concentration. The relationships allow for the estimation of concentration of the indicator iron from remotely sensed spectral data and the laboratory transmission concentration data without sea-truth samples.

  3. IRMPD signature of protonated pantothenic acid, an ubiquitous nutrient

    NASA Astrophysics Data System (ADS)

    Corinti, Davide; Mannina, Luisa; Chiavarino, Barbara; Steinmetz, Vincent; Fornarini, Simonetta; Crestoni, Maria Elisa

    2016-02-01

    Intrinsic properties of pantothenic acid, an essential nutraceutical, are examined. The effect of protonation on the energetic and geometric features of pantothenic acid, generated as gaseous protonated species, are investigated by infrared multiple photon dissociation (IRMPD) spectroscopy over an extended frequency range (800-2000 cm-1 and 2800-3700 cm-1). DFT calculations are exploited to identify the possible structures and predict the absorption spectra at the B3LYP/6-311++G(d,p) level. Two amide-protonated structures, characterized by the most stable binding motifs, account well for the experimental spectrum, thus revealing structurally diagnostic features of potential benefit for the development of highly sensitive and selective nutrient screening.

  4. Analysis of non-contact acousto-thermal signature data

    NASA Astrophysics Data System (ADS)

    Criner, Amanda K.; Schehl, Norman

    2016-02-01

    The non-contact acousto-thermal signature (NCATS) is a nondestructive evaluation technique with potential to detect fatigue in materials such as noisy titanium and polymer matrix composites. The determination of underlying physical mechanisms and properties may be determined by parameter estimation via nonlinear regression. The nonlinear regression analysis formulation, including the underlying models, is discussed. Several models and associated data analyses are given along with the assumptions implicit in the underlying model. The results of these analyses are discussed.

  5. Oscillation signature from multi-wavelength analysis on solar chromosphere

    SciTech Connect

    Mumpuni, Emanuel Sungging; Herdiwijaya, Dhani; Djamal, Mitra

    2014-03-24

    In this work, we investigate how the solar chromosphere responds to the photospheric dynamics by using tomography study, implementing multiwavelength analysis observations obtained from Dutch Open Telescope. By using high resolution, high-quality, simultaneous image sequences of multi-wavelength data, we try to obtain the oscillation signature that might play important role on chromospheric dynamic by using H-alpha (Hα) as primary diagnostic tool.

  6. Geochemical and sulfur isotope signatures of microbial activity in acidic and sulfuric hot springs, northern Taiwan

    NASA Astrophysics Data System (ADS)

    Wang, P.; Chen, K.; Cheng, T.; Hsieh, H.; Lin, L.

    2009-12-01

    Acidic and sulfuric hot springs are natural habitats for thermophilic sulfur-utilizing microorganisms. Integration of bioenergetic evaluation, molecular analysis and stable isotopic signatures may be able to exhibit a full view of microbial activity in such an extreme environment. Widely distributed hot springs hosted by the Tatung volcano group in northern Taiwan provide a chance to evaluate the interplay between geochemical variation and microbial metabolism especially for sulfur. Several hot spring ponds varying in sizes and geochemical characteristics were studied to reveal the possible control of fluid compositions on microbial metabolisms, and vice versa. Sulfate, sulfide, elemental sulfur and dissolved organic carbon were available in spring water and sediments in the ponds. Dominant microbial metabolisms inferred from the bioenergetic evaluation were aerobic oxidations of various reduced compounds, including elemental sulfur, pyrite, ferrous iron and organic carbon. Sulfate and sulfur reductions were thermodynamically favorable but provided less energy flux, while sulfur disproportionation was thermodynamically incapable. The analyses of 16S rRNA genes extracted from the spring water and sediments indicated that aerobic oxidation of sulfur, hydrogen or organic carbon and anaerobic elemental sulfur reduction were possible metabolisms. Since the major portion of 16S rRNA sequences were affiliated with unclassified environmental sequences, their potential metabolisms remained obscure. Sulfur isotopic compositions of dissolved sulfate, pyrite and elemental sulfur exhibited significant variations among the different hot spring ponds. Apparently, the microbial effects on the sulfur isotopic signatures were various. A disproportionation reaction of volcanic gas was required to account for high sulfur isotope difference between sulfate and reduced sulfur in the large hot ponds. In contrary, abiotic or microbial oxidation of reduced sulfur might be dominant in the

  7. Diagnostic marker signature for esophageal cancer from transcriptome analysis.

    PubMed

    Warnecke-Eberz, Ute; Metzger, Ralf; Hölscher, Arnulf H; Drebber, Uta; Bollschweiler, Elfriede

    2016-05-01

    Esophageal cancer is often diagnosed at an advanced stage. Diagnostic markers are needed for achieving a cure in esophageal cancer detecting and treating tumor cells earlier. In patients with locally advanced squamous cell carcinoma of the esophagus (ESCC), we profiled the gene expression of ESCC compared to corresponding normal biopsies for diagnostic markers by genome microarrays. Profiling of gene expression identified 4844 genes differentially expressed, 2122 upregulated and 2722 downregulated in ESCC. Twenty-three overexpressed candidates with best scores from significance analysis have been selected for further analysis by TaqMan low-density array-technique using a validation cohort of 40 patients. The verification rate was 100 % for ESCC. Twenty-two markers were additionally overexpressed in adenocarcinoma of the esophagus (EAC). The markers significantly overexpressed already in earlier tumor stages (pT1-2) of both histological subtypes (n = 19) have been clustered in a "diagnostic signature": PLA2G7, PRAME, MMP1, MMP3, MMP12, LIlRB2, TREM2, CHST2, IGFBP2, IGFBP7, KCNJ8, EMILIN2, CTHRC1, EMR2, WDR72, LPCAT1, COL4A2, CCL4, and SNX10. The marker signature will be translated to clinical practice to prove its diagnostic impact. This diagnostic signature may contribute to the earlier detection of tumor cells, with the aim to complement clinical techniques resulting in the development of better detection of concepts of esophageal cancer for earlier therapy and more favorite prognosis. PMID:26631031

  8. Analysis of Nozzle Jet Plume Effects on Sonic Boom Signature

    NASA Technical Reports Server (NTRS)

    Bui, Trong

    2010-01-01

    An axisymmetric full Navier-Stokes computational fluid dynamics (CFD) study was conducted to examine nozzle exhaust jet plume effects on the sonic boom signature of a supersonic aircraft. A simplified axisymmetric nozzle geometry, representative of the nozzle on the NASA Dryden NF-15B Lift and Nozzle Change Effects on Tail Shock (LaNCETS) research airplane, was considered. The highly underexpanded nozzle flow is found to provide significantly more reduction in the tail shock strength in the sonic boom N-wave pressure signature than perfectly expanded and overexpanded nozzle flows. A tail shock train in the sonic boom signature, similar to what was observed in the LaNCETS flight data, is observed for the highly underexpanded nozzle flow. The CFD results provide a detailed description of the nozzle flow physics involved in the LaNCETS nozzle at different nozzle expansion conditions and help in interpreting LaNCETS flight data as well as in the eventual CFD analysis of a full LaNCETS aircraft. The current study also provided important information on proper modeling of the LaNCETS aircraft nozzle. The primary objective of the current CFD research effort was to support the LaNCETS flight research data analysis effort by studying the detailed nozzle exhaust jet plume s imperfect expansion effects on the sonic boom signature of a supersonic aircraft. Figure 1 illustrates the primary flow physics present in the interaction between the exhaust jet plume shock and the sonic boom coming off of an axisymmetric body in supersonic flight. The steeper tail shock from highly expanded jet plume reduces the dip of the sonic boom N-wave signature. A structured finite-volume compressible full Navier-Stokes CFD code was used in the current study. This approach is not limited by the simplifying assumptions inherent in previous sonic boom analysis efforts. Also, this study was the first known jet plume sonic boom CFD study in which the full viscous nozzle flow field was modeled, without

  9. Power Signature Analysis of the SPECpower_ssj2008 Benchmark

    SciTech Connect

    Hsu, Chung-Hsing; Poole, Stephen W

    2011-01-01

    As the power consumption of a server system becomes a mainstream concern in enterprise environments, understanding the system's power behavior at varying utilization levels provides us a key to select appropriate energy-efficiency optimizations. In this work, we present an in-depth analysis of 177 SPECpower_ssj2008 results published between 2007--2010 to understand the changes of server's power behavior over time. In particular, we identified simple nonlinear functions appropriate for modeling the power behavior of today's, aggressively power-managed, machines. We consider this work as an important first step towards developing capability for power signature analysis of a high-end computer system.

  10. Unique plasma metabolomic signatures of individuals with inherited disorders of long-chain fatty acid oxidation.

    PubMed

    McCoin, Colin S; Piccolo, Brian D; Knotts, Trina A; Matern, Dietrich; Vockley, Jerry; Gillingham, Melanie B; Adams, Sean H

    2016-05-01

    Blood and urine acylcarnitine profiles are commonly used to diagnose long-chain fatty acid oxidation disorders (FAOD: i.e., long-chain hydroxy-acyl-CoA dehydrogenase [LCHAD] and carnitine palmitoyltransferase 2 [CPT2] deficiency), but the global metabolic impact of long-chain FAOD has not been reported. We utilized untargeted metabolomics to characterize plasma metabolites in 12 overnight-fasted individuals with FAOD (10 LCHAD, two CPT2) and 11 healthy age-, sex-, and body mass index (BMI)-matched controls, with the caveat that individuals with FAOD consume a low-fat diet supplemented with medium-chain triglycerides (MCT) while matched controls consume a typical American diet. In plasma 832 metabolites were identified, and partial least squared-discriminant analysis (PLS-DA) identified 114 non-acylcarnitine variables that discriminated FAOD subjects and controls. FAOD individuals had significantly higher triglycerides and lower specific phosphatidylethanolamines, ceramides, and sphingomyelins. Differences in phosphatidylcholines were also found but the directionality differed by metabolite species. Further, there were few differences in non-lipid metabolites, indicating the metabolic impact of FAOD specifically on lipid pathways. This analysis provides evidence that LCHAD/CPT2 deficiency significantly alters complex lipid pathway flux. This metabolic signature may provide new clinical tools capable of confirming or diagnosing FAOD, even in subjects with a mild phenotype, and may provide clues regarding the biochemical and metabolic impact of FAOD that is relevant to the etiology of FAOD symptoms. PMID:26907176

  11. Stable Isotope and Signature Fatty Acid Analyses Suggest Reef Manta Rays Feed on Demersal Zooplankton

    PubMed Central

    Couturier, Lydie I. E.; Rohner, Christoph A.; Richardson, Anthony J.; Marshall, Andrea D.; Jaine, Fabrice R. A.; Bennett, Michael B.; Townsend, Kathy A.; Weeks, Scarla J.; Nichols, Peter D.

    2013-01-01

    Assessing the trophic role and interaction of an animal is key to understanding its general ecology and dynamics. Conventional techniques used to elucidate diet, such as stomach content analysis, are not suitable for large threatened marine species. Non-lethal sampling combined with biochemical methods provides a practical alternative for investigating the feeding ecology of these species. Stable isotope and signature fatty acid analyses of muscle tissue were used for the first time to examine assimilated diet of the reef manta ray Manta alfredi, and were compared with different zooplankton functional groups (i.e. near-surface zooplankton collected during manta ray feeding events and non-feeding periods, epipelagic zooplankton, demersal zooplankton and several different zooplankton taxa). Stable isotope δ15N values confirmed that the reef manta ray is a secondary consumer. This species had relatively high levels of docosahexaenoic acid (DHA) indicating a flagellate-based food source in the diet, which likely reflects feeding on DHA-rich near-surface and epipelagic zooplankton. However, high levels of ω6 polyunsaturated fatty acids and slightly enriched δ13C values in reef manta ray tissue suggest that they do not feed solely on pelagic zooplankton, but rather obtain part of their diet from another origin. The closest match was with demersal zooplankton, suggesting it is an important component of the reef manta ray diet. The ability to feed on demersal zooplankton is likely linked to the horizontal and vertical movement patterns of this giant planktivore. These new insights into the habitat use and feeding ecology of the reef manta ray will assist in the effective evaluation of its conservation needs. PMID:24167562

  12. Wheat signature modeling and analysis for improved training statistics

    NASA Technical Reports Server (NTRS)

    Nalepka, R. F. (Principal Investigator); Malila, W. A.; Cicone, R. C.; Gleason, J. M.

    1976-01-01

    The author has identified the following significant results. The spectral, spatial, and temporal characteristics of wheat and other signatures in LANDSAT multispectral scanner data were examined through empirical analysis and simulation. Irrigation patterns varied widely within Kansas; 88 percent of wheat acreage in Finney was irrigated and 24 percent in Morton, as opposed to less than 3 percent for western 2/3's of the State. The irrigation practice was definitely correlated with the observed spectral response; wheat variety differences produced observable spectral differences due to leaf coloration and different dates of maturation. Between-field differences were generally greater than within-field differences, and boundary pixels produced spectral features distinct from those within field centers. Multiclass boundary pixels contributed much of the observed bias in proportion estimates. The variability between signatures obtained by different draws of training data decreased as the sample size became larger; also, the resulting signatures became more robust and the particular decision threshold value became less important.

  13. Amino acid analysis.

    PubMed

    Crabb, J W; West, K A; Dodson, W S; Hulmes, J D

    2001-05-01

    Amino acid analysis (AAA) is one of the best methods to quantify peptides and proteins. Two general approaches to quantitative AAA exist, namely, classical postcolumn derivatization following ion-exchange chromatography and precolumn derivatization followed by reversed-phase HPLC (RP-HPLC). Excellent instrumentation and several specific methodologies are available for both approaches, and both have advantages and disadvantages. This unit focuses on picomole-level AAA of peptides and proteins using the most popular precolumn-derivatization method, namely, phenylthiocarbamyl amino acid analysis (PTC-AAA). It is directed primarily toward those interested in establishing the technology with a modest budget. PTC derivatization and analysis conditions are described, and support and alternate protocols describe additional techniques necessary or useful for most any AAA method--e.g., sample preparation, hydrolysis, instrument calibration, data interpretation, and analysis of difficult or unusual residues such as cysteine, tryptophan, phosphoamino acids, and hydroxyproline. PMID:18429107

  14. Sequence analysis of the aminoacylase-1 family. A new proposed signature for metalloexopeptidases.

    PubMed

    Biagini, A; Puigserver, A

    2001-03-01

    The amino acid sequence analysis of the human and porcine aminoacylases-1, the carboxypeptidase S precursor from Saccharomyces cerevisiae, the succinyl-diaminopimelate desuccinylase from Escherichia coli, Haemophilus influenzae and Corynebacterium glutamicum, the acetylornithine deacetylase from Escherichia coli and Dictyostelium discoideum and the carboxypeptidase G(2) precursor from Pseudomonas strain, using the Basic Local Alignment Search Tool (BLAST) and the Position-Specific Iterated BLAST (PSI-BLAST), allowed us to suggest that all these enzymes, which share common functional and biochemical features, belong to the same structural family. The three amino acid blocks which were found to be highly conserved, using the CLUSTAL W program, could be assigned to the catalytic active site, based on the general three-dimensional structure of the carboxypeptidase G(2) from the Pseudomonas strain precursor. Six additional proteins with the same signature have been retrieved after performing two successive PSI-BLAST iterations using the sequence of the conserved motif, namely Lactobacillus delbrueckii aminoacyl-histidine dipeptidase, Streptomyces griseus aminopeptidase, Saccharomyces cerevisiae aminopeptidase Y precursor, two Bacillus stearothermophilus N-carbamyl-L-amino acid amidohydrolases and Pseudomonas sp. hydantoin utilization protein C. The three conserved amino acid motifs corresponded to the following blocks: (i) [S, G, A]-H-x-D-x-V; (ii) G-x-x-D; and (iii) x-E-E. This new sequence signature is clearly different from that commonly reported in the literature for proteins belonging to the ArgE/DapE/CPG2/YscS family. PMID:11250542

  15. Using fractal analysis of thermal signatures for thyroid disease evaluation

    NASA Astrophysics Data System (ADS)

    Gavriloaia, Gheorghe; Sofron, Emil; Gavriloaia, Mariuca-Roxana; Ghemigean, Adina-Mariana

    2010-11-01

    The skin is the largest organ of the body and it protects against heat, light, injury and infection. Skin temperature is an important parameter for diagnosing diseases. Thermal analysis is non-invasive, painless, and relatively inexpensive, showing a great potential research. Since the thyroid regulates metabolic rate it is intimately connected to body temperature, more than, any modification of its function generates a specific thermal image on the neck skin. The shapes of thermal signatures are often irregular in size and shape. Euclidean geometry is not able to evaluate their shape for different thyroid diseases, and fractal geometry is used in this paper. Different thyroid diseases generate different shapes, and their complexity are evaluated by specific mathematical approaches, fractal analysis, in order to the evaluate selfsimilarity and lacunarity. Two kinds of thyroid diseases, hyperthyroidism and papillary cancer are analyzed in this paper. The results are encouraging and show the ability to continue research for thermal signature to be used in early diagnosis of thyroid diseases.

  16. Clustering and classification techniques for the analysis of vibration signatures

    NASA Astrophysics Data System (ADS)

    Alguindigue, Israel E.; Loskiewicz-Buczak, Anna; Uhrig, Robert E.

    1992-09-01

    A methodology is proposed for the clustering and classification of vibration signatures in the frequency domain. The technique is based on the technologies of neural networks and fuzzy clustering and it is especially suited for the problem of vibration analysis because it permits the incorporation of specific knowledge about the domain in a very simple manner, and because the system learns from actual process data. The system uses the backpropagation algorithm for classification of compressed signatures, where compression is used as a mechanism for noise removal and automatic feature extraction. The clustering system uses the Fuzzy C algorithm with a matrix of weights for the calculation of distances between patterns and centroids. The matrix is used to assign factors of importance to frequencies in the spectrum which are known to be related to particular defects. The two aspects of the analysis (clustering and classification) are complementary because in many cases the exact operating state of a machine cannot be assessed, and clustering may unveil classes of operating states that would not be discovered otherwise. Accurate results were obtained from testing the system on rolling element bearing data.

  17. Identifying signatures of sexual selection using genomewide selection components analysis

    PubMed Central

    Flanagan, Sarah P; Jones, Adam G

    2015-01-01

    Sexual selection must affect the genome for it to have an evolutionary impact, yet signatures of selection remain elusive. Here we use an individual-based model to investigate the utility of genome-wide selection components analysis, which compares allele frequencies of individuals at different life history stages within a single population to detect selection without requiring a priori knowledge of traits under selection. We modeled a diploid, sexually reproducing population and introduced strong mate choice on a quantitative trait to simulate sexual selection. Genome-wide allele frequencies in adults and offspring were compared using weighted FST values. The average number of outlier peaks (i.e., those with significantly large FST values) with a quantitative trait locus in close proximity (“real” peaks) represented correct diagnoses of loci under selection, whereas peaks above the FST significance threshold without a quantitative trait locus reflected spurious peaks. We found that, even with moderate sample sizes, signatures of strong sexual selection were detectable, but larger sample sizes improved detection rates. The model was better able to detect selection with more neutral markers, and when quantitative trait loci and neutral markers were distributed across multiple chromosomes. Although environmental variation decreased detection rates, the identification of real peaks nevertheless remained feasible. We also found that detection rates can be improved by sampling multiple populations experiencing similar selection regimes. In short, genome-wide selection components analysis is a challenging but feasible approach for the identification of regions of the genome under selection. PMID:26257884

  18. Dimensionality analysis of facial signatures in visible and thermal spectra

    NASA Astrophysics Data System (ADS)

    Short, Nathan; Hu, Shuowen; Gurram, Prudhvi

    2015-06-01

    Face images are an important source of information for biometric recognition and intelligence gathering. While face recognition research has made significant progress over the past few decades, recognition of faces at extended ranges is still highly problematic. Recognition of a low-resolution probe face image from a gallery database, typically containing high resolution facial imagery, leads to lowered performance than traditional face recognition techniques. Learning and super-resolution based approaches have been proposed to improve face recognition at extended ranges; however, the resolution threshold for face recognition has not been examined extensively. Establishing a threshold resolution corresponding to the theoretical and empirical limitations of low resolution face recognition will allow algorithm developers to avoid focusing on improving performance where no distinguishable information for identification exists in the acquired signal. This work examines the intrinsic dimensionality of facial signatures and seeks to estimate a lower bound for the size of a face image required for recognition. We estimate a lower bound for face signatures in the visible and thermal spectra by conducting eigenanalysis using principal component analysis (PCA) (i.e., eigenfaces approach). We seek to estimate the intrinsic dimensionality of facial signatures, in terms of reconstruction error, by maximizing the amount of variance retained in the reconstructed dataset while minimizing the number of reconstruction components. Extending on this approach, we also examine the identification error to estimate the dimensionality lower bound for low-resolution to high-resolution (LR-to-HR) face recognition performance. Two multimodal face datasets are used for this study to evaluate the effects of dataset size and diversity on the underlying intrinsic dimensionality: 1) 50-subject NVESD face dataset (containing visible, MWIR, LWIR face imagery) and 2) 119-subject WSRI face dataset

  19. Analysis of parameters probability on Zhang-Wang signature scheme

    NASA Astrophysics Data System (ADS)

    Yang, Weiping; Liu, Chenglian

    2014-10-01

    Zhang and Wang proposed an improved signature scheme without using one-way hash functions. In this paper, we analyze the odd and even probability of signature parameters in Zhang-Wang signature scheme, which combined with Boolean algebra, such as bitwise exclusive-or (XOR). Furthermore, it is pointed out that we can use them for attacks.

  20. Mutational signature of aristolochic acid: Clue to the recognition of a global disease.

    PubMed

    Rosenquist, Thomas A; Grollman, Arthur P

    2016-08-01

    Mutational signatures associated with specific forms of DNA damage have been identified in several forms of human cancer. Such signatures provide information regarding mechanisms of tumor induction which, in turn, can reduce exposure to carcinogens by shaping public health policy. Using a molecular epidemiologic approach that takes advantage of recent advances in genome sequencing while applying sensitive and specific analytical methods to characterize DNA damage, it has become increasingly possible to establish causative linkages between certain environmental mutagens and disease risk. In this perspective, we use aristolochic acid, a human carcinogen and nephrotoxin found in Aristolochia herbs, to illustrate the power and effectiveness of this multidisciplinary approach. The genome-wide mutational signature for this toxin, detected initially in cancers of the upper urinary tract, has subsequently been associated with cancers of the liver and kidney. These findings have significant implications for global public health, especially in China, where millions of individuals have used Aristolochia herbal remedies as part of traditional Chinese medicine and, thus, are at risk of developing aristolochic acid nephropathy and/or upper urinary tract carcinomas. The studies reported here set the stage for research into prevention and early detection, both of which will be required to manage a potentially devastating global disease. PMID:27237586

  1. Renal cell carcinomas of chronic kidney disease patients harbor the mutational signature of carcinogenic aristolochic acid.

    PubMed

    Jelaković, Bojan; Castells, Xavier; Tomić, Karla; Ardin, Maude; Karanović, Sandra; Zavadil, Jiri

    2015-06-15

    Aristolochic acid (AA) is a potent dietary cytotoxin and carcinogen, and an established etiological agent underlying severe human nephropathies and associated upper urinary tract urothelial cancers, collectively designated aristolochic acid nephropathy (AAN). Its genome-wide mutational signature, marked by predominant A:T > T:A transversions occurring in the 5'-CpApG-3' trinucleotide context and enriched on the nontranscribed gene strand, has been identified in human upper urinary tract urothelial carcinomas from East Asian patients and in experimental systems. Here we report a whole-exome sequencing screen performed on DNA from formalin-fixed, paraffin-embedded renal cell carcinomas (RCC) arising in chronic renal disease patients from a Balkan endemic nephropathy (EN) region. In the EN regions, the disease results from the consumption of bread made from wheat contaminated by seeds of Aristolochia clematitis, an AA-containing plant. In five of eight (62.5%) tested RCC tumor specimens, we observed the characteristic global mutational signature consistent with the mutagenic effects of AA. This signature was absent in the control RCC samples obtained from patients from a nonendemic, metropolitan region. By identifying a new tumor type associated with the AA-driven genome-wide mutagenic process in the context of renal disease, our results suggest new epidemiological and public health implications for the RCC incidence worldwide, particularly for the high-risk regions with unregulated use of AA-containing traditional herbal medicines. PMID:25403517

  2. Renal cell carcinomas of chronic kidney disease patients harbor the mutational signature of carcinogenic aristolochic acid

    PubMed Central

    Jelaković, Bojan; Castells, Xavier; Tomić, Karla; Ardin, Maude; Karanović, Sandra; Zavadil, Jiri

    2015-01-01

    Aristolochic acid (AA) is a potent dietary cytotoxin and carcinogen, and an established etiological agent underlying severe human nephropathies and associated upper urinary tract urothelial cancers, collectively designated aristolochic acid nephropathy (AAN). Its genome-wide mutational signature, marked by predominant A:T > T:A transversions occurring in the 5′-CpApG-3′ trinucleotide context and enriched on the nontranscribed gene strand, has been identified in human upper urinary tract urothelial carcinomas from East Asian patients and in experimental systems. Here we report a whole-exome sequencing screen performed on DNA from formalin-fixed, paraffin-embedded renal cell carcinomas (RCC) arising in chronic renal disease patients from a Balkan endemic nephropathy (EN) region. In the EN regions, the disease results from the consumption of bread made from wheat contaminated by seeds of Aristolochia clematitis, an AA-containing plant. In five of eight (62.5%) tested RCC tumor specimens, we observed the characteristic global mutational signature consistent with the mutagenic effects of AA. This signature was absent in the control RCC samples obtained from patients from a nonendemic, metropolitan region. By identifying a new tumor type associated with the AA-driven genome-wide mutagenic process in the context of renal disease, our results suggest new epidemiological and public health implications for the RCC incidence worldwide, particularly for the high-risk regions with unregulated use of AA-containing traditional herbal medicines. PMID:25403517

  3. Diffraction signature analysis methods for improving scatterometry precision

    NASA Astrophysics Data System (ADS)

    Littau, Mike; Forman, Darren; Bruce, Josh; Raymond, Christopher J.; Hummel, Steven G.

    2006-03-01

    Scatterometry is a fast, non-destructive critical dimension (CD) optical metrology technique based on the analysis of light scattered from a periodic array of features. With technological advances in manufacturing, semiconductor devices are made in ever shrinking geometries. In recent years, the ability of scatterometry metrology tools to measure these devices at a gage-capable level for parameters such as CD, thickness or profile has become more challenging. The focus of this research is to analyze the acquired diffraction signature and determine an optimum diffraction signature "scan path." An optimized scan path can result in higher precision, reduced development time, smaller pre-generated library databases and faster real-time optimization speeds. In this work, we will first review several methods for scan path selection and optimization. Our results indicate that the method choice can influence the scan path selection, and that some of the methods are complementary to one another. For example, one method, which we term orthogonal sensitivity, uses intelligent algorithms to select optimal scan path points based on enhancing single parameter sensitivity. While the method works well, it neglects parameter correlation effects. Thus, we will also review a method where correlation effects are considered. Finally, we will calculate and summarize the effectiveness of optimal scan path selection techniques using challenging lithography applications.

  4. Condition monitoring of machinery using motor current signature analysis

    SciTech Connect

    Kryter, R.C.; Haynes, H.D.

    1989-01-01

    Motor current signature analysis (MCSA) is a powerful monitoring tool for motor-driven equipment that provides a nonintrusive means for detecting the presence of mechanical and electrical abnormalities in the motor and the driven equipment, including altered conditions in the process ''downstream'' of the motor-driven equipment. It was developed at the Oak Ridge National Laboratory as a means for determining the effects of aging and service wear systems, but it is applicable to a broad range of machinery. MCSA is based on the recognition that an electric motor (ac or dc) driving a mechanical load acts as an efficient and permanently available transducer by sensing mechanical load variations, large and small, long-term and rapid, and converting them into variations in the induced current generated in the motor windings. These motor current variations are carried by the electrical cables processes as desired. Motor current signatures, obtained in both time and over time to provide early indication of degradation. Successful applications of MCSA technology (patent applied for) include not only motor-operated valves but also pumps of various designs, blowers, and air conditioning systems. Examples are presented briefly, and speculation regarding the applicability of MCSA to a broader range of equipment monitoring and production line testing is also given. 1 ref., 13 figs.

  5. Reactor coolant pump testing using motor current signatures analysis

    SciTech Connect

    Burstein, N.; Bellamy, J.

    1996-12-01

    This paper describes reactor coolant pump motor testing carried out at Florida Power Corporation`s Crystal River plant using Framatome Technologies` new EMPATH (Electric Motor Performance Analysis and Trending Hardware) system. EMPATH{trademark} uses an improved form of Motor Current Signature Analysis (MCSA), technology, originally developed at Oak Ridge National Laboratories, for detecting deterioration in the rotors of AC induction motors. Motor Current Signature Analysis (MCSA) is a monitoring tool for motor driven equipment that provides a non-intrusive means for detecting the presence of mechanical and electrical abnormalities in the motor and the driven equipment. The base technology was developed at the Oak Ridge National Laboratory as a means for determining the affects of aging and service wear specifically on motor-operated valves used in nuclear power plant safety systems, but it is applicable to a broad range of electric machinery. MCSA is based on the recognition that an electric motor (ac or dc) driving a mechanical load acts as an efficient and permanently available transducer by sensing mechanical load variations, large and small, long-term and rapid, and converting them into variations in the induced current generated in the motor windings. The motor current variations, resulting from changes in load caused by gears, pulleys, friction, bearings, and other conditions that may change over the life of the motor, are carried by the electrical cables powering the motor and are extracted at any convenient location along the motor lead. These variations modulate the 60 Hz carrier frequency and appear as sidebands in the spectral plot.

  6. Image analysis of weaverbird nests reveals signature weave textures.

    PubMed

    Bailey, Ida E; Backes, André; Walsh, Patrick T; Morgan, Kate V; Meddle, Simone L; Healy, Susan D

    2015-06-01

    In nature, many animals build structures that can be readily measured at the scale of their gross morphology (e.g. length, volume and weight). Capturing individuality as can be done with the structures designed and built by human architects or artists, however, is more challenging. Here, we tested whether computer-aided image texture classification approaches can be used to describe textural variation in the nests of weaverbirds (Ploceus species) in order to attribute nests to the individual weaverbird that built them. We found that a computer-aided texture analysis approach does allow the assignment of a signature to weaverbirds' nests. We suggest that this approach will be a useful tool with which to examine individual variation across a range of animal constructions, not just for nests. PMID:26543586

  7. Image analysis of weaverbird nests reveals signature weave textures

    PubMed Central

    Bailey, Ida E.; Backes, André; Walsh, Patrick T.; Morgan, Kate V.; Meddle, Simone L.; Healy, Susan D.

    2015-01-01

    In nature, many animals build structures that can be readily measured at the scale of their gross morphology (e.g. length, volume and weight). Capturing individuality as can be done with the structures designed and built by human architects or artists, however, is more challenging. Here, we tested whether computer-aided image texture classification approaches can be used to describe textural variation in the nests of weaverbirds (Ploceus species) in order to attribute nests to the individual weaverbird that built them. We found that a computer-aided texture analysis approach does allow the assignment of a signature to weaverbirds' nests. We suggest that this approach will be a useful tool with which to examine individual variation across a range of animal constructions, not just for nests. PMID:26543586

  8. High-vibration detection using motor current signature analysis

    SciTech Connect

    Castleberry, K.N.

    1996-08-01

    Motor current signature analysis (CSA) has been used for several years as a diagnostic tool for electrical problems in ac, induction motors. Personnel at Oak Ridge National Laboratory have found that CSA can also provide information about system vibrations and imbalances similar to the information provided by an accelerometer. As a result, CSA techniques for monitoring the status of the equipment, such as pumps and compressors, driven by induction motors have been developed and used in dedicated monitoring systems. In this work, researchers have found that CSA responds proportionately to imbalances in rotating equipment and can be used to detect the In high-vibration conditions that can result. This report describes how vibration monitoring with CSA can be implemented and presents test data to support that use.

  9. Sensitive quantitative detection/identification of infectious Cryptosporidium parvum oocysts by signature lipid biomarker analysis

    SciTech Connect

    White, D.C. |; Alugupalli, S.; Schrum, D.P.

    1997-08-01

    Unique signature lipid biomarkers were found in the acid-fast oocytes of Cryptosporidium parvum. This makes possible the rapid detection/identification and potential infectivity directly from drinking water membrane filtrates.

  10. Automated defect spatial signature analysis for semiconductor manufacturing process

    DOEpatents

    Tobin, Jr., Kenneth W.; Gleason, Shaun S.; Karnowski, Thomas P.; Sari-Sarraf, Hamed

    1999-01-01

    An apparatus and method for performing automated defect spatial signature alysis on a data set representing defect coordinates and wafer processing information includes categorizing data from the data set into a plurality of high level categories, classifying the categorized data contained in each high level category into user-labeled signature events, and correlating the categorized, classified signature events to a present or incipient anomalous process condition.

  11. Elusive Sulfurous Acid: Gas-Phase Basicity and IR Signature of the Protonated Species.

    PubMed

    Sinha, Rajeev K; Scuderi, Debora; Maitre, Philippe; Chiavarino, Barbara; Crestoni, Maria Elisa; Fornarini, Simonetta

    2015-05-01

    The ion corresponding to protonated sulfurous acid, H3SO3(+), has been successfully delivered into the gas phase by electrospray ionization of the solution of a suitable precursor and an in-source fragmentation process. The neutral acid is a highly elusive molecule. However, its gas-phase basicity has been ascertained by means of a kinetic study of proton-transfer reactivity. The structure of the H3SO3(+) sampled ion has been probed by IRMPD spectroscopy in two complementary IR frequency ranges in conjunction with density functional theory calculations and found to conform to a trihydroxosulfonium ion. The characteristic IR signatures may aid in deciphering the presence of this species in extraterrestrial atmospheres. PMID:26263321

  12. Cannabinoid acids analysis.

    PubMed

    Lercker, G; Bocci, F; Frega, N; Bortolomeazzi, R

    1992-03-01

    The cannabinoid pattern of vegetable preparations from Cannabis sativa (hashish, marijuana) allows to recognize the phenotype of the plants, to be used as drug or for fiber. Cannabinoid determination by analytical point of view has represented some problems caused by the complex composition of the hexane extract. Capillary gas chromatography of the hexane extracts of vegetable samples, shows the presence of rather polar constituents that eluted, with noticeable interactions, only on polar phase. The compounds can be methylated by diazomethane and silanized (TMS) by silylating reagents. The methyl and methyl-TMS derivatives are analyzed by high resolution gas chromatography (HRGC) and by gas chromatography-mass spectrometry (GC-MS). The identification of the compounds shows their nature of cannabinoid acids, which the main by quantitative point of view results the cannabidiolic acid (CBDA). It is known that the cannabinoid acids are thermally unstable and are transformed in the corresponding cannabinoids by decarboxilation. This is of interest in forensic analysis with the aim to establish the total amount of THC in the Cannabis preparations, as the active component. PMID:1503600

  13. Signatures of Autotrophic and Heterotrophic Metabolic Activity in Enrichment Cultures from a Sulphur Oxidizing Acid Mine Site

    NASA Astrophysics Data System (ADS)

    Slater, G. F.; Bernier, L.; Cowie, B. R.; Warren, L. A.

    2006-12-01

    Delineating the role of microorganisms in geochemical processes of interest in natural environments requires the development of tools that provide the ability to distinguish amongst microbial activity associated with different metabolic guilds. The gap between phylogenetic characterization and phenotypic understanding remains, underscoring the need to consider alternative methods. Compound specific analysis of cellular components has the potential to differentiate between active metabolic processes supporting microbial communities and may be especially useful in extreme environments. The goal of this study was to determine whether the phospholipids fatty acid (PLFA) distribution and isotopic signatures associated with autotrophs and heterotrophs enriched from an acid mine drainage (AMD) system differed, and further whether natural consortial autotrophic isolates showed similar signatures to autotrophic pure strains of Acidithiobacillus ferrooxidans and A. thiooxidans. Two distinct initial enrichments with tetrathionate and CO2 yielded primarily autotrophic (95%) Acidithiobaccillus spp. sulphur oxidizing communities. The remaining microbial members of theses enrichments (<5%) were morphologically distinct and heterotrophic, as subculture of the consortial isolates in a medium amended with glucose but without tetrathionate selectively resulted in their visible growth. PLFA profiles and δ13C signatures from autotrophic (1) natural enrichments, pure cultures of (2) A. ferrooxidans and (3) A. thiooxidans were similar, but collectively differed from those of the natural heterotrophic enrichment cultures. The PLFA profiles for the heterotrophic communities were made up of primarily (88-99%) C16:0 and two isomers of C18:1. In contrast, the autotrophic communities had high proportions of C16:1 (up to 18%) as well as cyclo C17 and cyclo C19 PLFA that combined comprised 18 to 58% of the observed PLFA. The δ13C signatures of the PLFA also differed strongly between the two

  14. Modeling ground vehicle acoustic signatures for analysis and synthesis

    SciTech Connect

    Haschke, G.; Stanfield, R.

    1995-07-01

    Security and weapon systems use acoustic sensor signals to classify and identify moving ground vehicles. Developing robust signal processing algorithms for this is expensive, particularly in presence of acoustic clutter or countermeasures. This paper proposes a parametric ground vehicle acoustic signature model to aid the system designer in understanding which signature features are important, developing corresponding feature extraction algorithms and generating low-cost, high-fidelity synthetic signatures for testing. The authors have proposed computer-generated acoustic signatures of armored, tracked ground vehicles to deceive acoustic-sensored smart munitions. They have developed quantitative measures of how accurately a synthetic acoustic signature matches those produced by actual vehicles. This paper describes parameters of the model used to generate these synthetic signatures and suggests methods for extracting these parameters from signatures of valid vehicle encounters. The model incorporates wide-bandwidth and narrow- bandwidth components that are modulated in a pseudo-random fashion to mimic the time dynamics of valid vehicle signatures. Narrow- bandwidth feature extraction techniques estimate frequency, amplitude and phase information contained in a single set of narrow frequency- band harmonics. Wide-bandwidth feature extraction techniques estimate parameters of a correlated-noise-floor model. Finally, the authors propose a method of modeling the time dynamics of the harmonic amplitudes as a means adding necessary time-varying features to the narrow-bandwidth signal components. The authors present results of applying this modeling technique to acoustic signatures recorded during encounters with one armored, tracked vehicle. Similar modeling techniques can be applied to security systems.

  15. Analysis of polarimetric SAR signatures of vegetated areas

    NASA Technical Reports Server (NTRS)

    French, Nancy H. F.; Bourgeau-Chavez, Laura L.; Kasischke, Eric S.; Sheen, Daniel R.

    1991-01-01

    Several techniques to quantitatively analyze the information in the polarimetric signature are discussed, including: (1) a shape (texture) parameter; (2) fractional polarization; (3) the phase difference signature; and (4) the correlation coefficient. These techniques are applied to airborne synthetic aperture radar imagery collected over several different vegetation communities, including a mangrove swamp, a mixed-age loblolly pine forest, and a flooded bald cypress forest.

  16. The Effects of Different Representations on Static Structure Analysis of Computer Malware Signatures

    PubMed Central

    Narayanan, Ajit; Chen, Yi; Pang, Shaoning; Tao, Ban

    2013-01-01

    The continuous growth of malware presents a problem for internet computing due to increasingly sophisticated techniques for disguising malicious code through mutation and the time required to identify signatures for use by antiviral software systems (AVS). Malware modelling has focused primarily on semantics due to the intended actions and behaviours of viral and worm code. The aim of this paper is to evaluate a static structure approach to malware modelling using the growing malware signature databases now available. We show that, if malware signatures are represented as artificial protein sequences, it is possible to apply standard sequence alignment techniques in bioinformatics to improve accuracy of distinguishing between worm and virus signatures. Moreover, aligned signature sequences can be mined through traditional data mining techniques to extract metasignatures that help to distinguish between viral and worm signatures. All bioinformatics and data mining analysis were performed on publicly available tools and Weka. PMID:23983644

  17. The effects of different representations on static structure analysis of computer malware signatures.

    PubMed

    Narayanan, Ajit; Chen, Yi; Pang, Shaoning; Tao, Ban

    2013-01-01

    The continuous growth of malware presents a problem for internet computing due to increasingly sophisticated techniques for disguising malicious code through mutation and the time required to identify signatures for use by antiviral software systems (AVS). Malware modelling has focused primarily on semantics due to the intended actions and behaviours of viral and worm code. The aim of this paper is to evaluate a static structure approach to malware modelling using the growing malware signature databases now available. We show that, if malware signatures are represented as artificial protein sequences, it is possible to apply standard sequence alignment techniques in bioinformatics to improve accuracy of distinguishing between worm and virus signatures. Moreover, aligned signature sequences can be mined through traditional data mining techniques to extract metasignatures that help to distinguish between viral and worm signatures. All bioinformatics and data mining analysis were performed on publicly available tools and Weka. PMID:23983644

  18. LiDAR Vegetation Investigation and Signature Analysis System (LVISA)

    NASA Astrophysics Data System (ADS)

    Höfle, Bernhard; Koenig, Kristina; Griesbaum, Luisa; Kiefer, Andreas; Hämmerle, Martin; Eitel, Jan; Koma, Zsófia

    2015-04-01

    lacks behind. We propose a novel concept, the LiDAR Vegetation Investigation and Signature Analysis System (LVISA), which shall enhance sharing of i) reference datasets of single vegetation objects with rich reference data (e.g., plant species, basic plant morphometric information) and ii) approaches for information extraction (e.g., single tree detection, tree species classification based on waveform LiDAR features). We will build an extensive LiDAR data repository for supporting the development and benchmarking of LiDAR-based object information extraction. The LiDAR Vegetation Investigation and Signature Analysis System (LVISA) uses international web service standards (Open Geospatial Consortium, OGC) for geospatial data access and also analysis (e.g., OGC Web Processing Services). This will allow the research community identifying plant object specific vegetation features from LiDAR data, while accounting for differences in LiDAR systems (e.g., beam divergence), settings (e.g., point spacing), and calibration techniques. It is the goal of LVISA to develop generic 3D information extraction approaches, which can be seamlessly transferred to other datasets, timestamps and also extraction tasks. The current prototype of LVISA can be visited and tested online via http://uni-heidelberg.de/lvisa. Video tutorials provide a quick overview and entry into the functionality of LVISA. We will present the current advances of LVISA and we will highlight future research and extension of LVISA, such as integrating low-cost LiDAR data and datasets acquired by highly temporal scanning of vegetation (e.g., continuous measurements). Everybody is invited to join the LVISA development and share datasets and analysis approaches in an interoperable way via the web-based LVISA geoportal.

  19. A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.

    PubMed

    Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

    2015-04-01

    Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition. PMID:25854683

  20. A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

    PubMed Central

    Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

    2015-01-01

    Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition. PMID:25854683

  1. Bearing defect signature analysis using advanced nonlinear signal analysis in a controlled environment

    NASA Technical Reports Server (NTRS)

    Zoladz, T.; Earhart, E.; Fiorucci, T.

    1995-01-01

    Utilizing high-frequency data from a highly instrumented rotor assembly, seeded bearing defect signatures are characterized using both conventional linear approaches, such as power spectral density analysis, and recently developed nonlinear techniques such as bicoherence analysis. Traditional low-frequency (less than 20 kHz) analysis and high-frequency envelope analysis of both accelerometer and acoustic emission data are used to recover characteristic bearing distress information buried deeply in acquired data. The successful coupling of newly developed nonlinear signal analysis with recovered wideband envelope data from accelerometers and acoustic emission sensors is the innovative focus of this research.

  2. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    McMahon, Ben [LANL

    2013-01-25

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  3. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect

    McMahon, Ben

    2012-06-01

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  4. Lactobacillus acidophilus NCFM affects vitamin E acetate metabolism and intestinal bile acid signature in monocolonized mice

    PubMed Central

    Roager, Henrik M; Sulek, Karolina; Skov, Kasper; Frandsen, Henrik L; Smedsgaard, Jørn; Wilcks, Andrea; Skov, Thomas H; Villas-Boas, Silas G; Licht, Tine R

    2014-01-01

    Monocolonization of germ-free (GF) mice enables the study of specific bacterial species in vivo. Lactobacillus acidophilus NCFMTM (NCFM) is a probiotic strain; however, many of the mechanisms behind its health-promoting effect remain unknown. Here, we studied the effects of NCFM on the metabolome of jejunum, cecum, and colon of NCFM monocolonized (MC) and GF mice using liquid chromatography coupled to mass-spectrometry (LC-MS). The study adds to existing evidence that NCFM in vivo affects the bile acid signature of mice, in particular by deconjugation. Furthermore, we confirmed that carbohydrate metabolism is affected by NCFM in the mouse intestine as especially the digestion of oligosaccharides (penta- and tetrasaccharides) was increased in MC mice. Additionally, levels of α-tocopherol acetate (vitamin E acetate) were higher in the intestine of GF mice than in MC mice, suggesting that NCFM affects the vitamin E acetate metabolism. NCFM did not digest vitamin E acetate in vitro, suggesting that direct bacterial metabolism was not the cause of the altered metabolome in vivo. Taken together, our results suggest that NCFM affects intestinal carbohydrate metabolism, bile acid metabolism and vitamin E metabolism, although it remains to be investigated whether this effect is unique to NCFM. PMID:24717228

  5. [Generation of nalidixic acid-resistant strains and signature-tagged mutants of Actinobacillus pleuropneumoniae].

    PubMed

    Shang, Lin; Li, Wei; Li, Liangjun; Li, Lu; Zhang, Sihua; Li, Tingting; Li, Yaokun; Liu, Lei; Guo, Zhiwei; Zhou, Rui; Chen, Huanchun

    2008-01-01

    Actinobacillus pleuropneumoniae is a very important respiratory pathogen for swine and causes great economic losses in pig industry worldwide. Signature-tagged mutagenesis (STM) is an effective method to identify virulence genes in bacteria. In this study, we selected nalidixic acid-resistant strains of APP serotypes 1 and 3 by in vitro cultivation, and used as receipt strains for constructing transposon mutants by mating with E. coli CC 118 lambdapir or S17-1 lambdapir containing mini-Tn10 tag plasmids pLOF/TAG1-48, with or without the help of E. coli DH5alpha (pRK2073). We screened mutant strains by antibiotics selection, PCR and Southern blot identification. Our data revealed that nalidixic acid-resistance of APP strains could easily be induced in vitro and the resistance was due to the mutation in the DNA gyrase A subunit gene gyrA. In the mating experiments, the bi-parental mating was more effective and easier than tri-parental mating. Different APP strains showed a different mating and transposon efficiency in the bi-parental mating, with the strains of serotype 1 much higher than serotype 3 and the reference strain of serotype 3 higher than the field strains. These data were helpful for the construction of STM mutants and pickup of virulence genes of APP. PMID:18338580

  6. Lactobacillus acidophilus NCFM affects vitamin E acetate metabolism and intestinal bile acid signature in monocolonized mice.

    PubMed

    Roager, Henrik M; Sulek, Karolina; Skov, Kasper; Frandsen, Henrik L; Smedsgaard, Jørn; Wilcks, Andrea; Skov, Thomas H; Villas-Boas, Silas G; Licht, Tine R

    2014-01-01

    Monocolonization of germ-free (GF) mice enables the study of specific bacterial species in vivo. Lactobacillus acidophilus NCFM(TM) (NCFM) is a probiotic strain; however, many of the mechanisms behind its health-promoting effect remain unknown. Here, we studied the effects of NCFM on the metabolome of jejunum, cecum, and colon of NCFM monocolonized (MC) and GF mice using liquid chromatography coupled to mass-spectrometry (LC-MS). The study adds to existing evidence that NCFM in vivo affects the bile acid signature of mice, in particular by deconjugation. Furthermore, we confirmed that carbohydrate metabolism is affected by NCFM in the mouse intestine as especially the digestion of oligosaccharides (penta- and tetrasaccharides) was increased in MC mice. Additionally, levels of α-tocopherol acetate (vitamin E acetate) were higher in the intestine of GF mice than in MC mice, suggesting that NCFM affects the vitamin E acetate metabolism. NCFM did not digest vitamin E acetate in vitro, suggesting that direct bacterial metabolism was not the cause of the altered metabolome in vivo. Taken together, our results suggest that NCFM affects intestinal carbohydrate metabolism, bile acid metabolism and vitamin E metabolism, although it remains to be investigated whether this effect is unique to NCFM. PMID:24717228

  7. Host Restrictions of Avian Influenza Viruses: In Silico Analysis of H13 and H16 Specific Signatures in the Internal Proteins

    PubMed Central

    Tønnessen, Ragnhild; Hauge, Anna G.; Hansen, Elisabeth F.; Rimstad, Espen; Jonassen, Christine M.

    2013-01-01

    Gulls are the primary hosts of H13 and H16 avian influenza viruses (AIVs). The molecular basis for this host restriction is only partially understood. In this study, amino acid sequences from Eurasian gull H13 and H16 AIVs and Eurasian AIVs (non H13 and H16) were compared to determine if specific signatures are present only in the internal proteins of H13 and H16 AIVs, using a bioinformatics approach. Amino acids identified in an initial analysis performed on 15 selected sequences were checked against a comprehensive set of AIV sequences retrieved from Genbank to verify them as H13 and H16 specific signatures. Analysis of protein similarities and prediction of subcellular localization signals were performed to search for possible functions associated with the confirmed signatures. H13 and H16 AIV specific signatures were found in all the internal proteins examined, but most were found in the non-structural protein 1 (NS1) and in the nucleoprotein. A putative functional signature was predicted to be present in the nuclear export protein. Moreover, it was predicted that the NS1 of H13 and H16 AIVs lack one of the nuclear localization signals present in NS1 of other AIV subtypes. These findings suggest that the signatures found in the internal proteins of H13 and H16 viruses are possibly related to host restriction. PMID:23646204

  8. On-line signature verification method by Laplacian spectral analysis and dynamic time warping

    NASA Astrophysics Data System (ADS)

    Li, Changting; Peng, Liangrui; Liu, Changsong; Ding, Xiaoqing

    2013-12-01

    As smartphones and touch screens are more and more popular, on-line signature verification technology can be used as one of personal identification means for mobile computing. In this paper, a novel Laplacian Spectral Analysis (LSA) based on-line signature verification method is presented and an integration framework of LSA and Dynamic Time Warping (DTW) based methods for practical application is proposed. In LSA based method, a Laplacian matrix is constructed by regarding the on-line signature as a graph. The signature's writing speed information is utilized in the Laplacian matrix of the graph. The eigenvalue spectrum of the Laplacian matrix is analyzed and used for signature verification. The framework to integrate LSA and DTW methods is further proposed. DTW is integrated at two stages. First, it is used to provide stroke matching results for the LSA method to construct the corresponding graph better. Second, the on-line signature verification results by DTW are fused with that of the LSA method. Experimental results on public signature database and practical signature data on mobile phones proved the effectiveness of the proposed method.

  9. Analysis of Organic Acids.

    ERIC Educational Resources Information Center

    Griswold, John R.; Rauner, Richard A.

    1990-01-01

    Presented are the procedures and a discussion of the results for an experiment in which students select unknown carboxylic acids, determine their melting points, and investigate their solubility behavior in water and ethanol. A table of selected carboxylic acids is included. (CW)

  10. Analysis of dissolved organic carbon concentration and 13C isotopic signature by TOC-IRMS - assessment of analytical performance

    NASA Astrophysics Data System (ADS)

    Kirkels, Frédérique; Cerli, Chiara; Federherr, Eugen; Kalbitz, Karsten

    2013-04-01

    Stable carbon isotopes provide a powerful tool to assess carbon pools and their dynamics. Dissolved organic carbon (DOC) has been recognized to play an important role in ecosystem functioning and carbon cycling and has therefore gained increased research interest. However, direct measurement of 13C isotopic signature of carbon in the dissolved phase is technically challenging particularly using high temperature combustion. Until recently, mainly custom-made systems existed which were modified for coupling of TOC instruments with IRMS for simultaneous assessment of C content and isotopic signature. The variety of coupled systems showed differences in their analytical performances. For analysis of DOC high temperature combustion is recognized as best performing method, owing to its high efficiency of conversion to CO2 also for highly refractory components (e.g. humic, fulvic acids) present in DOC and soil extracts. Therefore, we tested high temperature combustion TOC coupled to IRMS (developed by Elementar Group) for bulk measurements of DOC concentration and 13C signature. The instruments are coupled via an Interface to exchange the carrier gas from O2 to He and to concentrate the derived CO2 for the isotope measurement. Analytical performance of the system was assessed for a variety of organic compounds characterized by different stability and complexity, including humic acid and DOM. We tested injection volumes between 0.2-3 ml, thereby enabling measurement of broad concentration ranges. With an injection volume of 0.5 ml (n=3, preceded by 1 discarded injection), DOC and 13C signatures for concentrations between 5-150 mg C/L were analyzed with high precision (standard deviation (SD) predominantly <0.1‰), good accuracy and linearity (overall SD <0.9‰). For the same settings, slightly higher variation in precision was observed among the lower concentration range and depending upon specific system conditions. Differences in 13C signatures of about 50‰ among

  11. Analysis of Plume Effects on Sonic Boom Signature for Isolated Nozzle Configurations

    NASA Technical Reports Server (NTRS)

    Castner, Raymond S.

    2008-01-01

    Computational fluid dynamics (CFD) analysis has been performed to study the plume effects on sonic boom signature for isolated nozzle configurations. The objectives of these analyses were to provide comparison to past work using modern CFD analysis tools, to investigate the differences of high aspect ratio nozzles to circular (axisymmetric) nozzles, and to report the effects of underexpanded nozzle operation on boom signature. CFD analysis was used to address the plume effects on sonic boom signature from a baseline exhaust nozzle. Near-field pressure signatures were collected for nozzle pressure ratios (NPRs) between 6 and 10. A computer code was used to extrapolate these signatures to a ground-observed sonic boom N-wave. Trends show that there is a reduction in sonic boom N-wave signature as NPR is increased from 6 to 10. The performance curve for this supersonic nozzle is flat, so there is not a significant loss in thrust coefficient as the NPR is increased. As a result, this benefit could be realized without significant loss of performance. Analyses were also collected for a high aspect ratio nozzle based on the baseline design for comparison. Pressure signatures were collected for nozzle pressure ratios from 8 to 12. Signatures were nearly twice as strong for the two-dimensional case, and trends also show a reduction in sonic boom signature as NPR is increased from 8 to 12. As low boom designs are developed and improved, there will be a need for understanding the interaction between the aircraft boat tail shocks and the exhaust nozzle plume. These CFD analyses will provide a baseline study for future analysis efforts.

  12. Security analysis and improvements of arbitrated quantum signature schemes

    SciTech Connect

    Zou Xiangfu; Qiu Daowen

    2010-10-15

    A digital signature is a mathematical scheme for demonstrating the authenticity of a digital message or document. For signing quantum messages, some arbitrated quantum signature (AQS) schemes have been proposed. It was claimed that these AQS schemes could guarantee unconditional security. However, we show that they can be repudiated by the receiver Bob. To conquer this shortcoming, we construct an AQS scheme using a public board. The AQS scheme not only avoids being disavowed by the receiver but also preserves all merits in the existing schemes. Furthermore, we discover that entanglement is not necessary while all these existing AQS schemes depend on entanglement. Therefore, we present another AQS scheme without utilizing entangled states in the signing phase and the verifying phase. This scheme has three advantages: it does not utilize entangled states and it preserves all merits in the existing schemes; the signature can avoid being disavowed by the receiver; and it provides a higher efficiency in transmission and reduces the complexity of implementation.

  13. Security analysis and improvements of arbitrated quantum signature schemes

    NASA Astrophysics Data System (ADS)

    Zou, Xiangfu; Qiu, Daowen

    2010-10-01

    A digital signature is a mathematical scheme for demonstrating the authenticity of a digital message or document. For signing quantum messages, some arbitrated quantum signature (AQS) schemes have been proposed. It was claimed that these AQS schemes could guarantee unconditional security. However, we show that they can be repudiated by the receiver Bob. To conquer this shortcoming, we construct an AQS scheme using a public board. The AQS scheme not only avoids being disavowed by the receiver but also preserves all merits in the existing schemes. Furthermore, we discover that entanglement is not necessary while all these existing AQS schemes depend on entanglement. Therefore, we present another AQS scheme without utilizing entangled states in the signing phase and the verifying phase. This scheme has three advantages: it does not utilize entangled states and it preserves all merits in the existing schemes; the signature can avoid being disavowed by the receiver; and it provides a higher efficiency in transmission and reduces the complexity of implementation.

  14. Compound-Specific Isotope Analysis of Amino Acids for Stardust-Returned Samples

    NASA Technical Reports Server (NTRS)

    Cook, Jamie; Elsila, Jamie E.; Stern J. C.; Glavin, D. P.; Dworkin, J. P.

    2008-01-01

    Significant portions of the early Earth's prebiotic organic inventory , including amino acids, could have been delivered to the Earth's sur face by comets and their fragments. Analysis of comets via spectrosc opic observations has identified many organic molecules, including me thane, ethane, arnmonia, cyanic acid, formaldehyde, formamide, acetal ehyde, acetonitrile, and methanol. Reactions between these identifie d molecules could allow the formation of more complex organics such a s amino acids. Isotopic analysis could reveal whether an extraterrest rial signature is present in the Stardust-exposed amines and amino ac ids. Although bulk isotopic analysis would be dominated by the EACA contaminant's terrestrial signature, compoundspecific isotope analysi s (CSIA) could determine the signature of each of the other individua l amines. Here, we report on progress made towards CSIA of the amino acids glycine and EACA in Stardustreturned samples.

  15. Amino Acid Signature Enables Proteins to Recognize Modified tRNA

    PubMed Central

    2015-01-01

    Human tRNALys3UUU is the primer for HIV replication. The HIV-1 nucleocapsid protein, NCp7, facilitates htRNALys3UUU recruitment from the host cell by binding to and remodeling the tRNA structure. Human tRNALys3UUU is post-transcriptionally modified, but until recently, the importance of those modifications in tRNA recognition by NCp7 was unknown. Modifications such as the 5-methoxycarbonylmethyl-2-thiouridine at anticodon wobble position-34 and 2-methylthio-N6-threonylcarbamoyladenosine, adjacent to the anticodon at position-37, are important to the recognition of htRNALys3UUU by NCp7. Several short peptides selected from phage display libraries were found to also preferentially recognize these modifications. Evolutionary algorithms (Monte Carlo and self-consistent mean field) and assisted model building with energy refinement were used to optimize the peptide sequence in silico, while fluorescence assays were developed and conducted to verify the in silico results and elucidate a 15-amino acid signature sequence (R-W-Q/N-H-X2-F-Pho-X-G/A-W-R-X2-G, where X can be most amino acids, and Pho is hydrophobic) that recognized the tRNA’s fully modified anticodon stem and loop domain, hASLLys3UUU. Peptides of this sequence specifically recognized and bound modified htRNALys3UUU with an affinity 10-fold higher than that of the starting sequence. Thus, this approach provides an effective means of predicting sequences of RNA binding peptides that have better binding properties. Such peptides can be used in cell and molecular biology as well as biochemistry to explore RNA binding proteins and to inhibit those protein functions. PMID:24483944

  16. Extraction and analysis of the width, gray scale and radian in Chinese signature handwriting.

    PubMed

    Chen, Xiaohong

    2015-10-01

    Forensic handwriting examination is a relevant identification process in forensic science. This research obtained ideas from the process of features detection and analysis in forensic handwriting examination. A Chinese signature database was developed and comprised original signatures, freehand imitation forgeries, random forgeries and tracing imitation forgeries. The features of width, gray scale and radian combined with stroke orders were automatically extracted after image processing. A correlation coefficient was used to precisely characterize and express the similarities between signatures. To validate the differences between writers, a multivariate analysis of the variance was employed. The canonical discriminant analysis was performed between the original and non-original signatures; the cross-validation estimated the discriminating power of the width, gray scale and radian data. It is suggested that the extraction and analysis of these properties in Chinese signatures is reasonable. Meanwhile, forensic handwriting examination using the quantitative feature extraction and statistical analysis methods in this research could be performed with a satisfactory result in the discriminant analysis. PMID:26209129

  17. Exometabolom analysis of breast cancer cell lines: Metabolic signature

    PubMed Central

    Willmann, Lucas; Erbes, Thalia; Halbach, Sebastian; Brummer, Tilman; Jäger, Markus; Hirschfeld, Marc; Fehm, Tanja; Neubauer, Hans; Stickeler, Elmar; Kammerer, Bernd

    2015-01-01

    Cancer cells show characteristic effects on cellular turnover and DNA/RNA modifications leading to elevated levels of excreted modified nucleosides. We investigated the molecular signature of different subtypes of breast cancer cell lines and the breast epithelial cell line MCF-10A. Prepurification of cell culture supernatants was performed by cis-diol specific affinity chromatography using boronate-derivatized polyacrylamide gel. Samples were analyzed by application of reversed phase chromatography coupled to a triple quadrupole mass spectrometer. Collectively, we determined 23 compounds from RNA metabolism, two from purine metabolism, five from polyamine/methionine cycle, one from histidine metabolism and two from nicotinate and nicotinamide metabolism. We observed major differences of metabolite excretion pattern between the breast cancer cell lines and MCF-10A, just as well as between the different breast cancer cell lines themselves. Differences in metabolite excretion resulting from cancerous metabolism can be integrated into altered processes on the cellular level. Modified nucleosides have great potential as biomarkers in due consideration of the heterogeneity of breast cancer that is reflected by the different molecular subtypes of breast cancer. Our data suggests that the metabolic signature of breast cancer cell lines might be a more subtype-specific tool to predict breast cancer, rather than a universal approach. PMID:26293811

  18. Online Handwritten Signature Verification Using Neural Network Classifier Based on Principal Component Analysis

    PubMed Central

    Iranmanesh, Vahab; Ahmad, Sharifah Mumtazah Syed; Adnan, Wan Azizun Wan; Arigbabu, Olasimbo Ayodeji; Malallah, Fahad Layth

    2014-01-01

    One of the main difficulties in designing online signature verification (OSV) system is to find the most distinctive features with high discriminating capabilities for the verification, particularly, with regard to the high variability which is inherent in genuine handwritten signatures, coupled with the possibility of skilled forgeries having close resemblance to the original counterparts. In this paper, we proposed a systematic approach to online signature verification through the use of multilayer perceptron (MLP) on a subset of principal component analysis (PCA) features. The proposed approach illustrates a feature selection technique on the usually discarded information from PCA computation, which can be significant in attaining reduced error rates. The experiment is performed using 4000 signature samples from SIGMA database, which yielded a false acceptance rate (FAR) of 7.4% and a false rejection rate (FRR) of 6.4%. PMID:25133227

  19. Online handwritten signature verification using neural network classifier based on principal component analysis.

    PubMed

    Iranmanesh, Vahab; Ahmad, Sharifah Mumtazah Syed; Adnan, Wan Azizun Wan; Yussof, Salman; Arigbabu, Olasimbo Ayodeji; Malallah, Fahad Layth

    2014-01-01

    One of the main difficulties in designing online signature verification (OSV) system is to find the most distinctive features with high discriminating capabilities for the verification, particularly, with regard to the high variability which is inherent in genuine handwritten signatures, coupled with the possibility of skilled forgeries having close resemblance to the original counterparts. In this paper, we proposed a systematic approach to online signature verification through the use of multilayer perceptron (MLP) on a subset of principal component analysis (PCA) features. The proposed approach illustrates a feature selection technique on the usually discarded information from PCA computation, which can be significant in attaining reduced error rates. The experiment is performed using 4000 signature samples from SIGMA database, which yielded a false acceptance rate (FAR) of 7.4% and a false rejection rate (FRR) of 6.4%. PMID:25133227

  20. Microfluidics in amino acid analysis.

    PubMed

    Pumera, Martin

    2007-07-01

    Microfluidic devices have been widely used to derivatize, separate, and detect amino acids employing many different strategies. Virtually zero-dead volume interconnections and fast mass transfer in small volume microchannels enable dramatic increases in on-chip derivatization reaction speed, while only minute amounts of sample and reagent are needed. Due to short channel path, fast subsecond separations can be carried out. With sophisticated miniaturized detectors, the whole analytical process can be integrated on one platform. This article reviews developments of lab-on-chip technology in amino acid analysis, it shows important design features such as sample preconcentration, precolumn and postcolumn amino acid derivatization, and unlabeled and labeled amino acid detection with focus on advanced designs. The review also describes important biomedical and space exploration applications of amino acid analysis on microfluidic devices. PMID:17542043

  1. Optical Signature Analysis of Tumbling Rocket Bodies via Laboratory Measurements

    NASA Astrophysics Data System (ADS)

    Cowardin, H.; Lederer, S.; Liou, J.-C.; Ojakangas, G.; Mulrooney, M.

    2012-09-01

    The NASA Orbital Debris Program Office has acquired telescopic lightcurve data on massive intact objects, specifically spent rocket bodies (R/Bs), to ascertain tumble rates in support of the Active Debris Removal (ADR) studies to help remediate the LEO environment. Tumble rates are needed to plan and develop proximity and docking operations for potential future ADR operations. To better characterize and model optical data acquired from ground-based telescopes, the Optical Measurements Center (OMC) at NASA/JSC emulates illumination conditions in space using equipment and techniques that parallel telescopic observations and source-target-sensor orientations. The OMC employs a 75-W Xenon arc lamp as a solar simulator, an SBIG CCD camera with standard Johnson/Bessel filters, and a robotic arm to simulate an object's position and rotation. The OMC does not attempt to replicate the rotation rates, but focuses on ascertaining how an object is rotating as seen from multiple phase angles. The two targets studied are scaled (1:48) SL-8 Cosmos 3M second stages. The first target is painted in the standard Russian government "gray" scheme and the second target is white/orange as used for commercial missions. This paper summarizes results of the two scaled rocket bodies, each observed in three independent rotation states: (a) spin-stabilized rotation (about the long axis), (b) end-over-end rotation, and (c) a 10 degree wobble about the center of mass. The first two cases represent simple spin about either primary axis. The third - what we call "wobble" - represents maximum principal axis rotation, with an inertia tensor that is offset from the symmetry axes. By comparing the resultant phase and orientation-dependent laboratory signatures with actual lightcurves derived from telescopic observations of orbiting R/Bs, we intend to assess the intrinsic R/B rotation states. In the simplest case, simulated R/B behavior coincides with principal axis spin states, while more complex R

  2. Trophic interactions in the benthic boundary layer of the Beaufort Sea shelf, Arctic Ocean: Combining bulk stable isotope and fatty acid signatures

    NASA Astrophysics Data System (ADS)

    Connelly, Tara L.; Deibel, Don; Parrish, Christopher C.

    2014-01-01

    The food web structure and diets of 26 taxa of benthic boundary layer (BBL) zooplankton on the Beaufort Sea shelf were studied using carbon and nitrogen stable isotopes and fatty acids. Mean δ15N values ranged from 7.3‰ for the amphipod Melita formosa to 14.9‰ for an unidentified polychaete, suggesting that taxa sampled came from three trophic levels. For 8 taxa, the lightest carbon signature occurred near the mouth of the Mackenzie River. Stable isotope ratios helped clarify the origin of signature fatty acids. Levels of certain polyunsaturated fatty acids (PUFA) were negatively correlated with δ15N, with the exception of 22:6ω3, which was positively correlated with δ15N, suggesting that this essential PUFA was retained through the food web. Discriminant analysis proved to be a powerful tool, predicting taxa from fatty acid profiles with 99% accuracy, and revealing strong phylogenetic trends in fatty acid profiles. The amphipod Arrhis phyllonyx had higher levels of ω6 PUFA, especially 20:4ω6 with several possible sources, than other peracarid crustaceans. The holothurian had high levels of odd numbered and branched chain fatty acids, indicative of bacterial consumption, while fatty acids of phytoplankton origin were important discriminants for Calanus hyperboreus and the chaetognaths Eukrohnia hamata and Parasagitta elegans. This relationship indicates that the conventional phytoplankton-copepod-chaetognath food web found in the water column also exists in the BBL. This observation, as well as generally low δ15N and high levels of certain PUFA in samples with lower δ15N, strongly suggests that BBL zooplankton on the Beaufort Sea shelf have access to fresh material of phytoplankton origin either by feeding on sedimenting matter or by active migration to surface waters.

  3. Classification Aided Analysis of Oscillatory Signatures in Controlled Retrieval

    PubMed Central

    Ketz, Nicholas; O'Reilly, Randal C.; Curran, Tim

    2013-01-01

    Control processes are critical for both facilitating and suppressing memory retrieval, but these processes are not well understood. The current work, inspired by a similar fMRI design (Detre et al., in press), used a modified Think/No-Think(TNT) paradigm to investigate the neural signatures of volition over enhancing and suppressing memory retrieval. Previous studies have shown memory enhancement when well-learned stimulus pairs are restudied in cued recall (“Recall or think of studied pair item”), and degradation when restudied with cued suppression (“Avoid thinking of studied pair item”). We used category-based (faces vs. scenes) multivariate classification of electroencephalography signals to determine if individual target items were successfully retrieved or suppressed. A logistic regression based on classifier output determined that retrieval activation during the cued recall/suppression period was a predictor for subsequent memory. Labeling trials with this internal measure, as opposed to their nominal Think vs. No-Think condition, revealed the classic TNT pattern of enhanced memory for successful cued-retrieval and degraded memory for cued-suppression. This classification process enabled a more selective investigation into the time-frequency signatures of control over retrieval. Comparing controlled retrieval vs. controlled suppression, results showed more prominent Theta oscillations (3 to 8 Hz) in controlled retrieval. Beta oscillations (12 to 30 Hz) were involved in high levels of both controlled retrieval and suppression, suggesting it may have a more general control-related role. These results suggest unique roles for these frequency bands in retrieval processes. PMID:23845425

  4. Post-analysis report on Chesapeake Bay data processing. [spectral analysis and recognition computer signature extension

    NASA Technical Reports Server (NTRS)

    Thomson, F.

    1972-01-01

    The additional processing performed on data collected over the Rhode River Test Site and Forestry Site in November 1970 is reported. The techniques and procedures used to obtain the processed results are described. Thermal data collected over three approximately parallel lines of the site were contoured, and the results color coded, for the purpose of delineating important scene constituents and to identify trees attacked by pine bark beetles. Contouring work and histogram preparation are reviewed and the important conclusions from the spectral analysis and recognition computer (SPARC) signature extension work are summarized. The SPARC setup and processing records are presented and recommendations are made for future data collection over the site.

  5. Characterization of blubber fatty acid signatures in northern elephant seals (Mirounga angustirostris) over the postweaning fast.

    PubMed

    Noren, Dawn P; Budge, Suzanne M; Iverson, Sara J; Goebel, Michael E; Costa, Daniel P; Williams, Terrie M

    2013-12-01

    Phocids routinely fast for extended periods. During these fasts, energetic requirements are met primarily through the catabolism of blubber lipid. To assess whether fatty acid (FA) composition changes during the postweaning fast in northern elephant seals, blubber biopsies were acquired longitudinally from 43 pups at 2.3 ± 1.5 and 55.2 ± 3.7 days postweaning in 1999 and 2000. At weaning, short-chain monounsaturated FA (SC-MUFA, ≤18 carbons) dominated the blubber while saturated FA (SFA) were found in the next highest proportion. The major FA (all ≥1 % by mass) comprised approximately 91 % of total blubber FA. In both years, 18:1n-9 and 16:0 were the most prevalent FA. Major FA mobilized during the fast consisted of polyunsaturated FA (PUFA), SFA, and SC-MUFA. Long-chain MUFA (>18 carbons) tended to be conserved. The fractional mobilization value of 20:5n-3 was the highest, resulting in significant reductions of this PUFA. Although concentrations of some blubber FA changed significantly during the postweaning fast, the general FA signature of blubber was similar at weaning and near the end of the fast. Changes in some FA differed across years. For example, the concentration of 20:4n-6, a minor PUFA, was significantly reduced in 1999 but not in 2000. FA mobilization patterns in northern elephant seal pups are somewhat similar to those reported previously for other fasting phocids and terrestrial mammals, though there are some notable differences. Differences in FA mobilization patterns across mammalian species may be related to differences in diets, geographical distribution, environmental factors, physiological adaptations, and life history stage. PMID:23925408

  6. Signature Based Detection of User Events for Post-mortem Forensic Analysis

    NASA Astrophysics Data System (ADS)

    James, Joshua Isaac; Gladyshev, Pavel; Zhu, Yuandong

    This paper introduces a novel approach to user event reconstruction by showing the practicality of generating and implementing signature-based analysis methods to reconstruct high-level user actions from a collection of low-level traces found during a post-mortem forensic analysis of a system. Traditional forensic analysis and the inferences an investigator normally makes when given digital evidence, are examined. It is then demonstrated that this natural process of inferring high-level events from low-level traces may be encoded using signature-matching techniques. Simple signatures using the defined method are created and applied for three popular Windows-based programs as a proof of concept.

  7. Investigating Population Structure of Sea Lamprey (Petromyzon marinus, L.) in Western Iberian Peninsula Using Morphological Characters and Heart Fatty Acid Signature Analyses

    PubMed Central

    Lança, Maria João; Machado, Maria; Mateus, Catarina S.; Lourenço, Marta; Ferreira, Ana F.; Quintella, Bernardo R.; Almeida, Pedro R.

    2014-01-01

    This study hypothesizes the existence of three groups of sea lamprey Petromyzon marinus L. in Portugal (North/Central group, Tagus group, and Guadiana group), possibly promoted by seabed topography isolation during the oceanic phase of the life cycle. Within this context, our purpose was to analyze the existence of a stock structure on sea lamprey populations sampled in the major Portuguese river basins using both morphological characters and heart tissue fatty acid signature. In both cases, the multiple discriminant analysis revealed statistically significant differences among groups, and the overall corrected classification rate estimated from cross-validation procedure was particularly high for the cardiac muscle fatty acid profiles (i.e. 83.8%). Morphometric characters were much more useful than meristic ones to discriminate stocks, and the most important variables for group differentiation were eye length, second dorsal fin length and branchial length. Fatty acid analysis showed that all lampreys from the southern Guadiana group were correctly classified and not mixing with individuals from any other group, reflecting a typical heart fatty acid signature. Our results revealed that 89.5% and 72.2% of the individuals from the Tagus and North/Central groups, respectively, were also correctly classified, despite some degree of overlap between individuals from these groups. The fatty acids that contributed to the observed segregation were C16:0; C17:0; C18:1ω9; C20:3ω6 and C22:2ω6. Detected differences are probably related with environmental variables to which lampreys may have been exposed, which leaded to different patterns of gene expression. These results suggest the existence of three different sea lamprey stocks in Portugal, with implication in terms of management and conservation. PMID:25259723

  8. Investigating population structure of Sea Lamprey (Petromyzon marinus, L.) in Western Iberian Peninsula using morphological characters and heart fatty acid signature analyses.

    PubMed

    Lança, Maria João; Machado, Maria; Mateus, Catarina S; Lourenço, Marta; Ferreira, Ana F; Quintella, Bernardo R; Almeida, Pedro R

    2014-01-01

    This study hypothesizes the existence of three groups of sea lamprey Petromyzon marinus L. in Portugal (North/Central group, Tagus group, and Guadiana group), possibly promoted by seabed topography isolation during the oceanic phase of the life cycle. Within this context, our purpose was to analyze the existence of a stock structure on sea lamprey populations sampled in the major Portuguese river basins using both morphological characters and heart tissue fatty acid signature. In both cases, the multiple discriminant analysis revealed statistically significant differences among groups, and the overall corrected classification rate estimated from cross-validation procedure was particularly high for the cardiac muscle fatty acid profiles (i.e. 83.8%). Morphometric characters were much more useful than meristic ones to discriminate stocks, and the most important variables for group differentiation were eye length, second dorsal fin length and branchial length. Fatty acid analysis showed that all lampreys from the southern Guadiana group were correctly classified and not mixing with individuals from any other group, reflecting a typical heart fatty acid signature. Our results revealed that 89.5% and 72.2% of the individuals from the Tagus and North/Central groups, respectively, were also correctly classified, despite some degree of overlap between individuals from these groups. The fatty acids that contributed to the observed segregation were C16:0; C17:0; C18:1ω9; C20:3ω6 and C22:2ω6. Detected differences are probably related with environmental variables to which lampreys may have been exposed, which leaded to different patterns of gene expression. These results suggest the existence of three different sea lamprey stocks in Portugal, with implication in terms of management and conservation. PMID:25259723

  9. Analysis of isotope and organic carbon signatures in hillslope hydrographs

    NASA Astrophysics Data System (ADS)

    Dusek, Jaromir; Vogel, Tomas; Dohnal, Michal; Jankovec, Jakub; Sanda, Martin; Votrubova, Jana

    2015-04-01

    Headwater catchments are among the most important areas for investigation of isotope and carbon fluxes because their small sizes best enable separation of above- and below ground compartments for improved understanding of the respective transport mechanisms. So far, only few studies utilized stable isotope information in modeling and even fewer linked dissolved carbon fluxes to mixing or transport models. Stable isotopes of water and dissolved organic carbon provide basis for studying transport processes ranging from soil profile scale to hillslope and catchment scale. In this study, stormflow dynamics of oxygen-18 and dissolved organic carbon was analyzed using a physically based modeling approach. One-dimensional dual-continuum vertical flow and transport model, based on Richards and advection-dispersion equations, was used to simulate the subsurface processes during significant rainfall-runoff episodes of a summer season. Water flow and transport of solutes were assumed to take place in two mutually communicating continua, the soil matrix and the network of preferential pathways. Oxygen-18 and dissolved organic carbon were observed in soil water, stormflow discharge in the experimental hillslope trench, and stream discharge at the catchment outlet. In the present study, we analyzed the transformation of input solute signals into signatures observed in the stormflow discharge. The research was supported by the Czech Science Foundation Project No. 14-15201J.

  10. The Application of Spatial Signature Analysis to Electrical Test Data: Validation Study

    SciTech Connect

    Gleason, S.S.; Karnowski, T.P.; Lakhani, F.; Tobin, K.W.

    1999-03-15

    This paper presents the results of the Spatial Signature Analysis (SSA) Electrical-test (e-test) validation study that was conducted between February and June, 1998. SSA is an automated procedure developed by researchers at the Oak Ridge National Laboratory to address the issue of intelligent data reduction while providing feedback on current manufacturing processes. SSA was initially developed to automate the analysis of optical defect data. Optical defects can form groups, or clusters, which may have a distinct shape. These patterns can reveal information about the manufacturing process. Optical defect SSA uses image processing algorithms and a classifier system to interpret and identify these patterns, or signatures. SSA has been extended to analyze and interpret electrical test data. The algorithms used for optical defect SSA have been adapted and applied to e-test binmaps. An image of the binmap is created, and features such as geometric and invariant moments are extracted and presented to a pair-wise, fuzzy, k-NN classifier. The classifier itself was prepared by manually training, which consists of storing example signatures of interest in a library, then executing an automated process which treats the examples as prototype signatures. The training process includes a procedure for automatically determining which features are most relevant to each class. The evaluation was performed by installing the SSA software as a batch process at three SEMATECH member company sites. Feedback from member company representatives was incorporated and classifiers were built to automatically assign labels to the binmap signatures. The three sites produced memory devices (DRAM) and microprocessors in a mature process fabrication environment. For all of these products, 5,620 signatures that encompassed approximately 552 wafers were human-classified and analyzed. The performance of the SSA E-test system indicates that the approach was successful in reliably classifying binmap

  11. A measurement approach based on micro-Doppler maps for signature and motion analysis

    NASA Astrophysics Data System (ADS)

    Ricci, R.; Sona, A.

    2013-05-01

    In this paper, a novel and comprehensive measurement approach is proposed for the detection and analysis of human motion signature. The approach combines theoretical concepts and tools of micro-Doppler theory, image processing, and human modeling, in a original way. The attention is primarily focused on the description of the most meaningful parameters influencing the accuracy of the obtained signature. The ultimate purpose is to provide a framework through which organizing, comparing, and merging future research activities, ideas and results in the field of human motion signature analysis for security, health and disaster recovery purposes. Some simulation and experimental results underlying the feasibility and effectiveness of the measurement approach are also summarized and analyzed.

  12. Optical Signature Analysis of Tumbling Rocket Bodies via Laboratory Measurements

    NASA Technical Reports Server (NTRS)

    Cowardin, H.; Lederer, S.; Liou, J.-C.

    2012-01-01

    The NASA Orbital Debris Program Office has acquired telescopic lightcurve data on massive intact objects, specifically spent rocket bodies, in order to ascertain tumble rates in support of the Active Debris Removal (ADR) task to help remediate the LEO environment. Rotation rates are needed to plan and develop proximity operations for potential future ADR operations. To better characterize and model optical data acquired from ground-based telescopes, the Optical Measurements Center (OMC) at NASA/JSC emulates illumination conditions in space using equipment and techniques that parallel telescopic observations and source-target-sensor orientations. The OMC employs a 75-watt Xenon arc lamp as a solar simulator, an SBIG CCD camera with standard Johnson/Bessel filters, and a robotic arm to simulate an object's position and rotation. The light source is mounted on a rotary arm, allowing access any phase angle between 0 -- 360 degrees. The OMC does not attempt to replicate the rotation rates, but focuses on how an object is rotating as seen from multiple phase angles. The two targets studied are scaled (1:48), SL-8 Cosmos 3M second stages. The first target is painted in the standard government "gray" scheme and the second target is primary white, as used for commercial missions. This paper summarizes results of the two scaled rocket bodies, each rotated about two primary axes: (a) a spin-stabilized rotation and (b) an end-over-end rotation. The two rotation states are being investigated as a basis for possible spin states of rocket bodies, beginning with simple spin states about the two primary axes. The data will be used to create a database of potential spin states for future works to convolve with more complex spin states. The optical signatures will be presented for specific phase angles for each rocket body and shown in conjunction with acquired optical data from multiple telescope sources.

  13. A reduction in ag/residential signature conflict using principal components analysis of LANDSAT temporal data

    NASA Technical Reports Server (NTRS)

    Williams, D. L.; Borden, F. Y.

    1977-01-01

    Methods to accurately delineate the types of land cover in the urban-rural transition zone of metropolitan areas were considered. The application of principal components analysis to multidate LANDSAT imagery was investigated as a means of reducing the overlap between residential and agricultural spectral signatures. The statistical concepts of principal components analysis were discussed, as well as the results of this analysis when applied to multidate LANDSAT imagery of the Washington, D.C. metropolitan area.

  14. Signatures of positive selection in East African Shorthorn Zebu: a genome-wide SNP analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The small East African Shorthorn Zebu is the main indigenous cattle across East Africa. A recent genome wide SNPs analysis has revealed their ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signature of positive selection in their genome, with the aim...

  15. New Functional Signatures for Understanding Melanoma Biology from Tumor Cell Lineage-Specific Analysis.

    PubMed

    Rambow, Florian; Job, Bastien; Petit, Valérie; Gesbert, Franck; Delmas, Véronique; Seberg, Hannah; Meurice, Guillaume; Van Otterloo, Eric; Dessen, Philippe; Robert, Caroline; Gautheret, Daniel; Cornell, Robert A; Sarasin, Alain; Larue, Lionel

    2015-10-27

    Molecular signatures specific to particular tumor types are required to design treatments for resistant tumors. However, it remains unclear whether tumors and corresponding cell lines used for drug development share such signatures. We developed similarity core analysis (SCA), a universal and unsupervised computational framework for extracting core molecular features common to tumors and cell lines. We applied SCA to mRNA/miRNA expression data from various sources, comparing melanoma cell lines and metastases. The signature obtained was associated with phenotypic characteristics in vitro, and the core genes CAPN3 and TRIM63 were implicated in melanoma cell migration/invasion. About 90% of the melanoma signature genes belong to an intrinsic network of transcription factors governing neural development (TFAP2A, DLX2, ALX1, MITF, PAX3, SOX10, LEF1, and GAS7) and miRNAs (211-5p, 221-3p, and 10a-5p). The SCA signature effectively discriminated between two subpopulations of melanoma patients differing in overall survival, and classified MEKi/BRAFi-resistant and -sensitive melanoma cell lines. PMID:26489459

  16. Trimethylbenzoic acids as metabolite signatures in the biogeochemical evolution of an aquifer contaminated with jet fuel hydrocarbons

    NASA Astrophysics Data System (ADS)

    Namocatcat, J. A.; Fang, J.; Barcelona, M. J.; Quibuyen, A. T. O.; Abrajano, T. A.

    2003-12-01

    Evolution of trimethylbenzoic acids in the KC-135 aquifer at the former Wurtsmith Air Force Base (WAFB), Oscoda, MI was examined to determine the functionality of trimethylbenzoic acids as key metabolite signatures in the biogeochemical evolution of an aquifer contaminated with JP-4 fuel hydrocarbons. Changes in the composition of trimethylbenzoic acids and the distribution and concentration profiles exhibited by 2,4,6- and 2,3,5-trimethylbenzoic acids temporally and between multilevel wells reflect processes indicative of an actively evolving contaminant plume. The concentration levels of trimethylbenzoic acids were 3-10 orders higher than their tetramethylbenzene precursors, a condition attributed to slow metabolite turnover under sulfidogenic conditions. The observed degradation of tetramethylbenzenes into trimethylbenzoic acids obviates the use of these alkylbenzenes as non-labile tracers for other degradable aromatic hydrocarbons, but provides rare field evidence on the range of high molecular weight alkylbenzenes and isomeric assemblages amenable to anaerobic degradation in situ. The coupling of actual tetramethylbenzene loss with trimethylbenzoic acid production and the general decline in the concentrations of these compounds demonstrate the role of microbially mediated processes in the natural attenuation of hydrocarbons and may be a key indicator in the overall rate of hydrocarbon degradation and the biogeochemical evolution of the KC-135 aquifer.

  17. Electrical signature analysis (ESA) developments at the Oak Ridge Diagnostics Applied Research Center

    SciTech Connect

    Haynes, H.D.

    1995-07-01

    Since 1985, researchers at the Oak Ridge National Laboratory (ORNL) have developed and patented several novel signal conditioning and signature analysis methods that have exploited the intrinsic abilities of conventional electric motors and generators to act as transducers. By using simple nonintrusive sensors such as clamp-on current and voltage probes, these new diagnostic techniques provide an improved means of detecting small time-dependent load and speed variations generated anywhere within an electromechanical system and converting them into revealing signatures that can be used to detect equipment degradation and incipient failures. These developments have been grouped under the general name of electrical signature analysis (ESA) and together provide a breakthrough in the ability to detect, analyze, and correct unwanted changes in process conditions or the presence of abnormalities in electrical and electromechanical equipment. Typical diagnostic information provided by ESA is comparable to that provided by conventional vibration analysis in that both time waveform and frequency spectrum signatures may be produced. The primary benefit of ESA is that an extensive range of diagnostic information can be obtained from a single transducer that may be installed several hundred feet or more from the monitored device on its electrical lines supplying input power (e.g., to a motor) or carrying output power (e.g., from a generator); thus, ESA is truly remote and nonintrusive.

  18. Fractal analysis of scatter imaging signatures to distinguish breast pathologies

    NASA Astrophysics Data System (ADS)

    Eguizabal, Alma; Laughney, Ashley M.; Krishnaswamy, Venkataramanan; Wells, Wendy A.; Paulsen, Keith D.; Pogue, Brian W.; López-Higuera, José M.; Conde, Olga M.

    2013-02-01

    Fractal analysis combined with a label-free scattering technique is proposed for describing the pathological architecture of tumors. Clinicians and pathologists are conventionally trained to classify abnormal features such as structural irregularities or high indices of mitosis. The potential of fractal analysis lies in the fact of being a morphometric measure of the irregular structures providing a measure of the object's complexity and self-similarity. As cancer is characterized by disorder and irregularity in tissues, this measure could be related to tumor growth. Fractal analysis has been probed in the understanding of the tumor vasculature network. This work addresses the feasibility of applying fractal analysis to the scattering power map (as a physical modeling) and principal components (as a statistical modeling) provided by a localized reflectance spectroscopic system. Disorder, irregularity and cell size variation in tissue samples is translated into the scattering power and principal components magnitude and its fractal dimension is correlated with the pathologist assessment of the samples. The fractal dimension is computed applying the box-counting technique. Results show that fractal analysis of ex-vivo fresh tissue samples exhibits separated ranges of fractal dimension that could help classifier combining the fractal results with other morphological features. This contrast trend would help in the discrimination of tissues in the intraoperative context and may serve as a useful adjunct to surgeons.

  19. Vibration Signature Analysis of a Faulted Gear Transmission System

    NASA Technical Reports Server (NTRS)

    Choy, F. K.; Huang, S.; Zakrajsek, J. J.; Handschuh, R. F.; Townsend, D. P.

    1996-01-01

    A comprehensive procedure in predicting faults in gear transmission systems under normal operating conditions is presented. Experimental data were obtained from a spiral bevel gear fatigue test rig at NASA/Lewis. Time-synchronous-averaged vibration data were recorded throughout the test as the fault progressed from a small single pit to severe pitting over several teeth, and finally tooth fracture. A numerical procedure based on the Wigner-Ville distribution was used to examine the time-averaged vibration data. Results from the Wigner-Ville procedure are compared to results from a variety of signal analysis techniques that include time-domain analysis methods and frequency analysis methods. Using photographs of the gear tooth at various stages of damage, the limitations and accuracy of the various techniques are compared and discussed. Conclusions are drawn from the comparison of the different approaches as well as the applicability of the Wigner-Ville method in predicting gear faults.

  20. Vibration signature analysis of a faulted gear transmission system

    NASA Astrophysics Data System (ADS)

    Choy, F. K.; Huang, S.; Zakrajsek, J. J.; Handschuh, R. F.; Townsend, D. P.

    1994-06-01

    A comprehensive procedure in predicting faults in gear transmission systems under normal operating conditions is presented. Experimental data was obtained from a spiral bevel gear fatigue test rig at NASA Lewis Research Center. Time synchronous averaged vibration data was recorded throughout the test as the fault progressed from a small single pit to severe pitting over several teeth, and finally tooth fracture. A numerical procedure based on the Winger-Ville distribution was used to examine the time averaged vibration data. Results from the Wigner-Ville procedure are compared to results from a variety of signal analysis techniques which include time domain analysis methods and frequency analysis methods. Using photographs of the gear tooth at various stages of damage, the limitations and accuracy of the various techniques are compared and discussed. Conclusions are drawn from the comparison of the different approaches as well as the applicability of the Wigner-Ville method in predicting gear faults.

  1. Vibration Signature Analysis of a Faulted Gear Transmission System

    NASA Technical Reports Server (NTRS)

    Choy, F. K.; Huang, S.; Zakrajsek, J. J.; Handschuh, R. F.; Townsend, D. P.

    1994-01-01

    A comprehensive procedure in predicting faults in gear transmission systems under normal operating conditions is presented. Experimental data was obtained from a spiral bevel gear fatigue test rig at NASA Lewis Research Center. Time synchronous averaged vibration data was recorded throughout the test as the fault progressed from a small single pit to severe pitting over several teeth, and finally tooth fracture. A numerical procedure based on the Winger-Ville distribution was used to examine the time averaged vibration data. Results from the Wigner-Ville procedure are compared to results from a variety of signal analysis techniques which include time domain analysis methods and frequency analysis methods. Using photographs of the gear tooth at various stages of damage, the limitations and accuracy of the various techniques are compared and discussed. Conclusions are drawn from the comparison of the different approaches as well as the applicability of the Wigner-Ville method in predicting gear faults.

  2. Rub failure signature analysis for large rotating machinery

    NASA Astrophysics Data System (ADS)

    Zhengjia, He; Yudi, Sheng; Liangsheng, Qu

    1990-09-01

    In many cases rub failure in large rotating machinery may produce noise in certain bandwidths known as coloured noise. It is difficult to diagnose rub failure between rotating and stationary parts using only ordinary FFT spectra or autoregressive spectra. In this paper, a new technique combining principal components analysis and autoregressive spectra (PCAT) is introduced. This technique can reasonably estimate the spectra and determine the chief characteristic parameter of the coloured noise. A successful example of rub failure analysis given in this paper shows that PCAT is an efficient method for use with large rotating machinery.

  3. Application of ultrasonic signature analysis for fatigue detection in complex structures

    NASA Technical Reports Server (NTRS)

    Zuckerwar, A. J.

    1974-01-01

    Ultrasonic signature analysis shows promise of being a singularly well-suited method for detecting fatigue in structures as complex as aircraft. The method employs instrumentation centered about a Fourier analyzer system, which features analog-to-digital conversion, digital data processing, and digital display of cross-correlation functions and cross-spectra. These features are essential to the analysis of ultrasonic signatures according to the procedure described here. In order to establish the feasibility of the method, the initial experiments were confined to simple plates with simulated and fatigue-induced defects respectively. In the first test the signature proved sensitive to the size of a small hole drilled into the plate. In the second test, performed on a series of fatigue-loaded plates, the signature proved capable of indicating both the initial appearance and subsequent growth of a fatigue crack. In view of these encouraging results it is concluded that the method has reached a sufficiently advanced stage of development to warrant application to small-scale structures or even actual aircraft.

  4. Micro-Doppler analysis of multiple frequency continuous wave radar signatures

    NASA Astrophysics Data System (ADS)

    Anderson, Michael G.; Rogers, Robert L.

    2007-04-01

    Micro-Doppler refers to Doppler scattering returns produced by non rigid-body motion. Micro-Doppler gives rise to many detailed radar image features in addition to those associated with bulk target motion. Targets of different classes (for example, humans, animals, and vehicles) produce micro-Doppler images that are often distinguishable even by nonexpert observers. Micro-Doppler features have great potential for use in automatic target classification algorithms. Although the potential benefit of using micro-Doppler in classification algorithms is high, relatively little experimental (non-synthetic) micro-Doppler data exists. Much of the existing experimental data comes from highly cooperative targets (human or vehicle targets directly approaching the radar). This research involved field data collection and analysis of micro-Doppler radar signatures from non-cooperative targets. The data was collected using a low cost Xband multiple frequency continuous wave (MFCW) radar with three transmit frequencies. The collected MFCW radar signatures contain data from humans, vehicles, and animals. The presented data includes micro-Doppler signatures previously unavailable in the literature such as crawling humans and various animal species. The animal micro-Doppler signatures include deer, dog, and goat datasets. This research focuses on the analysis of micro-Doppler from noncooperative targets approaching the radar at various angles, maneuvers, and postures.

  5. Selection Signature Analysis Implicates the PC1/PCSK1 Region for Chicken Abdominal Fat Content

    PubMed Central

    Wang, Zhipeng; Zhang, Yuandan; Wang, Shouzhi; Wang, Ning; Ma, Li; Leng, Li; Wang, Shengwen; Wang, Qigui; Wang, Yuxiang; Tang, Zhiquan; Li, Ning; Da, Yang; Li, Hui

    2012-01-01

    We conducted a selection signature analysis using the chicken 60k SNP chip in two chicken lines that had been divergently selected for abdominal fat content (AFC) for 11 generations. The selection signature analysis used multiple signals of selection, including long-range allele frequency differences between the lean and fat lines, long-range heterozygosity changes, linkage disequilibrium, haplotype frequencies, and extended haplotype homozygosity. Multiple signals of selection identified ten signatures on chromosomes 1, 2, 4, 5, 11, 15, 20, 26 and Z. The 0.73 Mb PC1/PCSK1 region of the Z chromosome at 55.43-56.16 Mb was the most heavily selected region. This region had 26 SNP markers and seven genes, Mar-03, SLC12A2, FBN2, ERAP1, CAST, PC1/PCSK1 and ELL2, where PC1/PCSK1 are the chicken/human names for the same gene. The lean and fat lines had two main haplotypes with completely opposite SNP alleles for the 26 SNP markers and were virtually line-specific, and had a recombinant haplotype with nearly equal frequency (0.193 and 0.196) in both lines. Other haplotypes in this region had negligible frequencies. Nine other regions with selection signatures were PAH-IGF1, TRPC4, GJD4-CCNY, NDST4, NOVA1, GALNT9, the ESRP2-GALR1 region with five genes, the SYCP2-CADH4 with six genes, and the TULP1-KIF21B with 14 genes. Genome-wide association analysis showed that nearly all regions with evidence of selection signature had SNP effects with genome-wide significance (P<10–6) on abdominal fat weight and percentage. The results of this study provide specific gene targets for the control of chicken AFC and a potential model of AFC in human obesity. PMID:22792402

  6. Signature analysis of acoustic emission from graphite/epoxy composites

    NASA Technical Reports Server (NTRS)

    Russell, S. S.; Henneke, E. G., II

    1977-01-01

    Acoustic emissions were monitored for crack extension across and parallel to the fibers in a single ply and multiply laminates of graphite epoxy composites. Spectrum analysis was performed on the transient signal to ascertain if the fracture mode can be characterized by a particular spectral pattern. The specimens were loaded to failure quasistatically in a tensile machine. Visual observations were made via either an optical microscope or a television camera. The results indicate that several types of characteristics in the time and frequency domain correspond to different types of failure.

  7. An Analysis of Immunoreactive Signatures in Early Stage Hepatocellular Carcinoma

    PubMed Central

    Hong, Yu; Long, Jiang; Li, Hai; Chen, Shuhong; Liu, Qiqi; Zhang, Bei; He, Xiaomin; Wang, Yan; Li, Hongyi; Li, Yimei; Zhang, Tao; Lu, Chenzhen; Yan, Hao; Zhang, Minli; Li, Qing; Cao, Bangwei; Bai, Zhigang; Wang, Jin; Zhang, Zhongtao; Zhu, Shengtao; Zheng, Jiasheng; Ou, Xiaojuan; Ma, Hong; Jia, Jidong; You, Hong; Wang, Shengqi; Huang, Jian

    2015-01-01

    Background Hepatocellular carcinoma (HCC) is prevalent worldwide and early diagnosis of HCC is critical for effective treatment and optimal prognosis. Methods Serum was screened first by immunoproteomic analysis for HCC-related tumor associated antigens (TAAs). Selected TAAs were clinically evaluated retrospectively in patients with HCC, liver cirrhosis, chronic hepatitis and healthy controls. Levels of autoantibody to the selected TAAs were measured by protein microarrays containing protein antigens of the candidate TAAs. Analyses were done by using receiver operating characteristics (ROC) to calculate diagnostic accuracy. Findings Twenty-two candidate TAAs were assessed by protein microarray analysis in 914 participants with serum α-fetoprotein (AFP) available. Twelve candidate TAAs were statistically different in signal intensity between HCC and controls. Among them, CENPF, HSP60 and IMP-2 showed AUC (area under the curve) values of 0.826, 0.764 and 0.796 respectively for early HCC. The highest prevalence of autoantibody positivity was observed in HCC cases with BCLC tumor stage A, well-differentiated histology and Child-Pugh grade C. Specifically, 73.6% or 79.3% cases of early HCC with negative AFP were positive for autoantibody to CENPF or HSP60. Interpretation Tumor-associated autoimmune reactions may be triggered by early stage HCCs. Measurement of serum autoantibody to TAAs may be complementary to AFP measurements and improve diagnosis of early HCC. PMID:26137588

  8. Genome analysis of the platypus reveals unique signatures of evolution.

    PubMed

    Warren, Wesley C; Hillier, LaDeana W; Marshall Graves, Jennifer A; Birney, Ewan; Ponting, Chris P; Grützner, Frank; Belov, Katherine; Miller, Webb; Clarke, Laura; Chinwalla, Asif T; Yang, Shiaw-Pyng; Heger, Andreas; Locke, Devin P; Miethke, Pat; Waters, Paul D; Veyrunes, Frédéric; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Wallis, John; Puente, Xose S; López-Otín, Carlos; Ordóñez, Gonzalo R; Eichler, Evan E; Chen, Lin; Cheng, Ze; Deakin, Janine E; Alsop, Amber; Thompson, Katherine; Kirby, Patrick; Papenfuss, Anthony T; Wakefield, Matthew J; Olender, Tsviya; Lancet, Doron; Huttley, Gavin A; Smit, Arian F A; Pask, Andrew; Temple-Smith, Peter; Batzer, Mark A; Walker, Jerilyn A; Konkel, Miriam K; Harris, Robert S; Whittington, Camilla M; Wong, Emily S W; Gemmell, Neil J; Buschiazzo, Emmanuel; Vargas Jentzsch, Iris M; Merkel, Angelika; Schmitz, Juergen; Zemann, Anja; Churakov, Gennady; Kriegs, Jan Ole; Brosius, Juergen; Murchison, Elizabeth P; Sachidanandam, Ravi; Smith, Carly; Hannon, Gregory J; Tsend-Ayush, Enkhjargal; McMillan, Daniel; Attenborough, Rosalind; Rens, Willem; Ferguson-Smith, Malcolm; Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R; Ray, David A; Kube, Michael; Reinhardt, Richard; Pringle, Thomas H; Taylor, James; Jones, Russell C; Nixon, Brett; Dacheux, Jean-Louis; Niwa, Hitoshi; Sekita, Yoko; Huang, Xiaoqiu; Stark, Alexander; Kheradpour, Pouya; Kellis, Manolis; Flicek, Paul; Chen, Yuan; Webber, Caleb; Hardison, Ross; Nelson, Joanne; Hallsworth-Pepin, Kym; Delehaunty, Kim; Markovic, Chris; Minx, Pat; Feng, Yucheng; Kremitzki, Colin; Mitreva, Makedonka; Glasscock, Jarret; Wylie, Todd; Wohldmann, Patricia; Thiru, Prathapan; Nhan, Michael N; Pohl, Craig S; Smith, Scott M; Hou, Shunfeng; Nefedov, Mikhail; de Jong, Pieter J; Renfree, Marilyn B; Mardis, Elaine R; Wilson, Richard K

    2008-05-01

    We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation. PMID:18464734

  9. Genome analysis of the platypus reveals unique signatures of evolution

    PubMed Central

    Warren, Wesley C.; Hillier, LaDeana W.; Marshall Graves, Jennifer A.; Birney, Ewan; Ponting, Chris P.; Grützner, Frank; Belov, Katherine; Miller, Webb; Clarke, Laura; Chinwalla, Asif T.; Yang, Shiaw-Pyng; Heger, Andreas; Locke, Devin P.; Miethke, Pat; Waters, Paul D.; Veyrunes, Frédéric; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Wallis, John; Puente, Xose S.; López-Otín, Carlos; Ordóñez, Gonzalo R.; Eichler, Evan E.; Chen, Lin; Cheng, Ze; Deakin, Janine E.; Alsop, Amber; Thompson, Katherine; Kirby, Patrick; Papenfuss, Anthony T.; Wakefield, Matthew J.; Olender, Tsviya; Lancet, Doron; Huttley, Gavin A.; Smit, Arian F. A.; Pask, Andrew; Temple-Smith, Peter; Batzer, Mark A.; Walker, Jerilyn A.; Konkel, Miriam K.; Harris, Robert S.; Whittington, Camilla M.; Wong, Emily S. W.; Gemmell, Neil J.; Buschiazzo, Emmanuel; Vargas Jentzsch, Iris M.; Merkel, Angelika; Schmitz, Juergen; Zemann, Anja; Churakov, Gennady; Kriegs, Jan Ole; Brosius, Juergen; Murchison, Elizabeth P.; Sachidanandam, Ravi; Smith, Carly; Hannon, Gregory J.; Tsend-Ayush, Enkhjargal; McMillan, Daniel; Attenborough, Rosalind; Rens, Willem; Ferguson-Smith, Malcolm; Lefèvre, Christophe M.; Sharp, Julie A.; Nicholas, Kevin R.; Ray, David A.; Kube, Michael; Reinhardt, Richard; Pringle, Thomas H.; Taylor, James; Jones, Russell C.; Nixon, Brett; Dacheux, Jean-Louis; Niwa, Hitoshi; Sekita, Yoko; Huang, Xiaoqiu; Stark, Alexander; Kheradpour, Pouya; Kellis, Manolis; Flicek, Paul; Chen, Yuan; Webber, Caleb; Hardison, Ross; Nelson, Joanne; Hallsworth-Pepin, Kym; Delehaunty, Kim; Markovic, Chris; Minx, Pat; Feng, Yucheng; Kremitzki, Colin; Mitreva, Makedonka; Glasscock, Jarret; Wylie, Todd; Wohldmann, Patricia; Thiru, Prathapan; Nhan, Michael N.; Pohl, Craig S.; Smith, Scott M.; Hou, Shunfeng; Renfree, Marilyn B.; Mardis, Elaine R.; Wilson, Richard K.

    2009-01-01

    We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation. PMID:18464734

  10. Analysis of cirrus cloud spectral signatures in the far infrared

    NASA Astrophysics Data System (ADS)

    Maestri, T.; Rizzi, R.; Tosi, E.; Veglio, P.; Palchetti, L.; Bianchini, G.; Di Girolamo, P.; Masiello, G.; Serio, C.; Summa, D.

    2014-07-01

    This paper analyses high spectral resolution downwelling radiance measurements in the far infrared in the presence of cirrus clouds taken by the REFIR-PAD interferometer, deployed at 3500 m above the sea level at the Testa Grigia station (Italy), during the Earth COoling by WAter vapouR emission (ECOWAR) campaign. Atmospheric state and cloud geometry are characterised by the co-located millimeter-wave spectrometer GBMS and by radiosonde profile data, an interferometer (I-BEST) and a Raman lidar system deployed at a nearby location (Cervinia). Cloud optical depth and effective diameter are retrieved from REFIR-PAD data using a limited number of channels in the 820-960 cm-1 interval. The retrieved cloud parameters are the input data for simulations covering the 250-1100 cm-1 band in order to test our ability to reproduce the REFIR-PAD spectra in the presence of ice clouds. Inverse and forward simulations are based on the same radiative transfer code. A priori information concerning cloud ice vertical distribution is used to better constrain the simulation scheme and an analysis of the degree of approximation of the phase function within the radiative transfer codes is performed to define the accuracy of computations. Simulation-data residuals over the REFIR-PAD spectral interval show an excellent agreement in the window region, but values are larger than total measurement uncertainties in the far infrared. Possible causes are investigated. It is shown that the uncertainties related to the water vapour and temperature profiles are of the same order as the sensitivity to the a priori assumption on particle habits for an up-looking configuration. In case of a down-looking configuration, errors due to possible incorrect description of the water vapour profile would be drastically reduced.

  11. Search for a three lepton and missing transverse energy signature of supersymmetry using a multivariate analysis

    NASA Astrophysics Data System (ADS)

    Lampen, Caleb Parnell

    A search for evidence of supersymmetry with a three lepton and missing transverse energy signature is presented. This signature is a possible final state from the associated production of a chargino and a neutralino, two particles predicted by supersymmetry. The study is performed on 2.06 fb-1 of 7 TeV center of mass energy proton-proton collisions, recorded with the ATLAS experiment at the Large Hadron Collider in 2011. A multivariate analysis is utilized, implementing a boosted decision tree classifier using lepton pT, missing transverse energy, dilepton mass, and the razor variable R as inputs. No significant excess over the Standard Model prediction is observed, and upper limits are placed on the cross section times branching ratio of simplified models across a mass parameter space.

  12. IRLooK: an advanced mobile infrared signature measurement, data reduction, and analysis system

    NASA Astrophysics Data System (ADS)

    Cukur, Tamer; Altug, Yelda; Uzunoglu, Cihan; Kilic, Kayhan; Emir, Erdem

    2007-04-01

    Infrared signature measurement capability has a key role in the electronic warfare (EW) self protection systems' development activities. In this article, the IRLooK System and its capabilities will be introduced. IRLooK is a truly innovative mobile infrared signature measurement system with all its design, manufacturing and integration accomplished by an engineering philosophy peculiar to ASELSAN. IRLooK measures the infrared signatures of military and civil platforms such as fixed/rotary wing aircrafts, tracked/wheeled vehicles and navy vessels. IRLooK has the capabilities of data acquisition, pre-processing, post-processing, analysis, storing and archiving over shortwave, mid-wave and long wave infrared spectrum by means of its high resolution radiometric sensors and highly sophisticated software analysis tools. The sensor suite of IRLooK System includes imaging and non-imaging radiometers and a spectroradiometer. Single or simultaneous multiple in-band measurements as well as high radiant intensity measurements can be performed. The system provides detailed information on the spectral, spatial and temporal infrared signature characteristics of the targets. It also determines IR Decoy characteristics. The system is equipped with a high quality field proven two-axes tracking mount to facilitate target tracking. Manual or automatic tracking is achieved by using a passive imaging tracker. The system also includes a high quality weather station and field-calibration equipment including cavity and extended area blackbodies. The units composing the system are mounted on flat-bed trailers and the complete system is designed to be transportable by large body aircraft.

  13. Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures.

    PubMed

    Nakaya, Helder I; Hagan, Thomas; Duraisingham, Sai S; Lee, Eva K; Kwissa, Marcin; Rouphael, Nadine; Frasca, Daniela; Gersten, Merril; Mehta, Aneesh K; Gaujoux, Renaud; Li, Gui-Mei; Gupta, Shakti; Ahmed, Rafi; Mulligan, Mark J; Shen-Orr, Shai; Blomberg, Bonnie B; Subramaniam, Shankar; Pulendran, Bali

    2015-12-15

    Systems approaches have been used to describe molecular signatures driving immunity to influenza vaccination in humans. Whether such signatures are similar across multiple seasons and in diverse populations is unknown. We applied systems approaches to study immune responses in young, elderly, and diabetic subjects vaccinated with the seasonal influenza vaccine across five consecutive seasons. Signatures of innate immunity and plasmablasts correlated with and predicted influenza antibody titers at 1 month after vaccination with >80% accuracy across multiple seasons but were not associated with the longevity of the response. Baseline signatures of lymphocyte and monocyte inflammation were positively and negatively correlated, respectively, with antibody responses at 1 month. Finally, integrative analysis of microRNAs and transcriptomic profiling revealed potential regulators of vaccine immunity. These results identify shared vaccine-induced signatures across multiple seasons and in diverse populations and might help guide the development of next-generation vaccines that provide persistent immunity against influenza. PMID:26682988

  14. Security analysis of boolean algebra based on Zhang-Wang digital signature scheme

    SciTech Connect

    Zheng, Jinbin

    2014-10-06

    In 2005, Zhang and Wang proposed an improvement signature scheme without using one-way hash function and message redundancy. In this paper, we show that this scheme exits potential safety concerns through the analysis of boolean algebra, such as bitwise exclusive-or, and point out that mapping is not one to one between assembly instructions and machine code actually by means of the analysis of the result of the assembly program segment, and which possibly causes safety problems unknown to the software.

  15. Security analysis of boolean algebra based on Zhang-Wang digital signature scheme

    NASA Astrophysics Data System (ADS)

    Zheng, Jinbin

    2014-10-01

    In 2005, Zhang and Wang proposed an improvement signature scheme without using one-way hash function and message redundancy. In this paper, we show that this scheme exits potential safety concerns through the analysis of boolean algebra, such as bitwise exclusive-or, and point out that mapping is not one to one between assembly instructions and machine code actually by means of the analysis of the result of the assembly program segment, and which possibly causes safety problems unknown to the software.

  16. Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data

    PubMed Central

    Fortney, Kristen; Griesman, Joshua; Kotlyar, Max; Pastrello, Chiara; Angeli, Marc; Sound-Tsao, Ming; Jurisica, Igor

    2015-01-01

    Repurposing FDA-approved drugs with the aid of gene signatures of disease can accelerate the development of new therapeutics. A major challenge to developing reliable drug predictions is heterogeneity. Different gene signatures of the same disease or drug treatment often show poor overlap across studies, as a consequence of both biological and technical variability, and this can affect the quality and reproducibility of computational drug predictions. Existing algorithms for signature-based drug repurposing use only individual signatures as input. But for many diseases, there are dozens of signatures in the public domain. Methods that exploit all available transcriptional knowledge on a disease should produce improved drug predictions. Here, we adapt an established meta-analysis framework to address the problem of drug repurposing using an ensemble of disease signatures. Our computational pipeline takes as input a collection of disease signatures, and outputs a list of drugs predicted to consistently reverse pathological gene changes. We apply our method to conduct the largest and most systematic repurposing study on lung cancer transcriptomes, using 21 signatures. We show that scaling up transcriptional knowledge significantly increases the reproducibility of top drug hits, from 44% to 78%. We extensively characterize drug hits in silico, demonstrating that they slow growth significantly in nine lung cancer cell lines from the NCI-60 collection, and identify CALM1 and PLA2G4A as promising drug targets for lung cancer. Our meta-analysis pipeline is general, and applicable to any disease context; it can be applied to improve the results of signature-based drug repurposing by leveraging the large number of disease signatures in the public domain. PMID:25786242

  17. Texture analysis of radiometric signatures of new sea ice forming in Arctic leads

    NASA Technical Reports Server (NTRS)

    Eppler, Duane T.; Farmer, L. Dennis

    1991-01-01

    Analysis of 33.6-GHz, high-resolution, passive microwave images suggests that new sea ice accumulating in open leads is characterized by a unique textural signature which can be used to discriminate new ice forming in this environment from adjacent surfaces of similar radiometric temperature. Ten training areas were selected from the data set, three of which consisted entirely of first-year ice, four entirely of multilayer ice, and three of new ice in open leads in the process of freezing. A simple gradient operator was used to characterize the radiometric texture in each training region in terms of the degree to which radiometric gradients are oriented. New ice in leads has a sufficiently high proportion of well-oriented features to distinguish it uniquely from first-year ice and multiyear ice. The predominance of well-oriented features probably reflects physical processes by which new ice accumulates in open leads. Banded structures, which are evident in aerial photographs of new ice, apparently give rise to the radiometric signature observed, in which the trend of brightness temperature gradients is aligned parallel to lead trends. First-year ice and multiyear ice, which have been subjected to a more random growth and process history, lack this banded structure and therefore are characterized by signatures in which well-aligned elements are less dominant.

  18. Relative Amino Acid Concentrations as a Signature for Parent Body Processes of Carbonaceous Chondrites

    NASA Technical Reports Server (NTRS)

    Botta, Oliver; Glavin, Daniel P.; Kminek, Gerhard; Bada, Jeffrey L.

    2002-01-01

    Most meteorites are thought to have originated from objects in the asteroid belt. Carbonaceous chondrites, which contain significant amounts of organic carbon including complex organic compounds, have also been suggested to be derived from comets. The current model for the synthesis of organic compounds found in carbonaceous chondrites includes the survival of interstellar organic compounds and the processing of some of these compounds on the meteoritic parent body. The amino acid composition of five CM carbonaceous chondrites, two CIs, one CR, and one CV3 have been measured using hot water extraction-vapor hydrolysis, OPA/NAC derivatization and high-performance liquid chromatography (HPLC). Total amino acid abundances in the bulk meteorites as well as the amino acid concentrations relative to glycine = 1.0 for beta-alanine, alpha-aminoisobutyric acid and D-alanine were determined. Additional data for three Antarctic CM meteorites were obtained from the literature. All CM meteorites analyzed in this study show a complex distribution of amino acids and a high variability in total concentration ranging from approx. 15,300 to approx. 5800 parts per billion (ppb), while the CIs show a total amino acid abundance of approx. 4300 ppb. The relatively (compared to glycine) high AIB content found in all the CMs is a strong indicator that Strecker-cyanohydrin synthesis is the dominant pathway for the formation of amino acids found in these meteorites. The data from the Antarctic CM carbonaceous chondrites are inconsistent with the results from the other CMs, perhaps due to influences from the Antarctic ice that were effective during their residence time. In contrast to CMs, the data from the CI carbonaceous chondrites indicate that the Strecker synthesis was not active on their parent bodies.

  19. Multispectral signature analysis measurements of selected sniper rifles and small arms

    NASA Astrophysics Data System (ADS)

    Law, David B.; Carapezza, Edward M.; Csanadi, Christina J.; Edwards, Gerald D.; Hintz, Todd M.; Tong, Ronald M.

    1997-02-01

    During October 1995 - June 1996, the Naval Command, Control and Ocean Surveillance Center RDT&E Division (NRaD), under sponsorship from Defense Advanced Research Projects Agency (DARPA), conducted an intensive series of multi-spectral signature analyses of typical sniper weapons. Multi-spectral signatures of the muzzle flashes from rifles and pistols and some imagery of the bullets in flight were collected. Multi- spectral signatures of the muzzle flash were collected in the infrared (2.5 - 14.5 microns), visible -- near-IR (400 - 1200 nanometers), and the ultra-violet (185 - 400 nanometers) wavelength regions. These measurements consisted of high spectral resolution (0.0159 micron) measurements of the spectral radiance of the muzzle flash. A time history plot of the muzzle flash as it evolves just forward of the end of the muzzle is provided. These measurements were performed with a CI Systems Model SR5000 IR/Visible spectroradiometer and an Ocean Optics Model PC1000 UV spectroradiometer. Muzzle flash infrared imagery is provided to show the effect that specific muzzle breaks have on the resulting muzzle flash. The following set of sniper weapons were included in this test: AK-47, SKS, M16A2, M-14, FN-FAL, SMLE IIa, 03 Springfield, SVD Dragunov, 50 caliber McMillan, and a 45 caliber ACP pistol. The results of this signature analysis show that important measurable electro-optical differences do exist between all these weapons in terms of spectral radiance of the flash, spectral content of the gun powders, and spectral shapes/geometries of the muzzle flashes. These differences were sufficient such that, after a more complete data base is collected, it will be possible to develop a passive electro-optical weapon and ammunition identifier.

  20. Identification of Stage-Specific Gene Expression Signatures in Response to Retinoic Acid during the Neural Differentiation of Mouse Embryonic Stem Cells

    PubMed Central

    Akanuma, Hiromi; Qin, Xian-Yang; Nagano, Reiko; Win-Shwe, Tin-Tin; Imanishi, Satoshi; Zaha, Hiroko; Yoshinaga, Jun; Fukuda, Tomokazu; Ohsako, Seiichiroh; Sone, Hideko

    2012-01-01

    We have previously established a protocol for the neural differentiation of mouse embryonic stem cells (mESCs) as an efficient tool to evaluate the neurodevelopmental toxicity of environmental chemicals. Here, we described a multivariate bioinformatic approach to identify the stage-specific gene sets associated with neural differentiation of mESCs. We exposed mESCs (B6G-2 cells) to 10−8 or 10−7 M of retinoic acid (RA) for 4 days during embryoid body formation and then performed morphological analysis on day of differentiation (DoD) 8 and 36, or genomic microarray analysis on DoD 0, 2, 8, and 36. Three gene sets, namely a literature-based gene set (set 1), an analysis-based gene set (set 2) using self-organizing map and principal component analysis, and an enrichment gene set (set 3), were selected by the combined use of knowledge from literatures and gene information selected from the microarray data. A gene network analysis for each gene set was then performed using Bayesian statistics to identify stage-specific gene expression signatures in response to RA during mESC neural differentiation. Our results showed that RA significantly increased the size of neurosphere, neuronal cells, and glial cells on DoD 36. In addition, the gene network analysis showed that glial fibrillary acidic protein, a neural marker, remarkably up-regulates the other genes in gene set 1 and 3, and Gbx2, a neural development marker, significantly up-regulates the other genes in gene set 2 on DoD 36 in the presence of RA. These findings suggest that our protocol for identification of developmental stage-specific gene expression and interaction is a useful method for the screening of environmental chemical toxicity during neurodevelopmental periods. PMID:22891073

  1. Technology Gap Analysis for the Detection of Process Signatures Using Less Than Remote Methods

    SciTech Connect

    Hartman, John S.; Atkinson, David A.; Lind, Michael A.; Maughan, A. D.; Kelly, James F.

    2005-01-01

    Although remote sensing methods offer advantages for monitoring important illicit process activities, remote and stand-off technologies cannot successfully detect all important processes with the sensitivity and certainty that is desired. The main scope of the program is observables, with a primary focus on chemical signatures. A number of key process signatures elude remote or stand-off detection for a variety of reasons (e.g., heavy particulate emissions that do not propagate far enough for detection at stand-off distances, semi-volatile chemicals that do not tend to vaporize and remain in the environment near the source, etc.). Some of these compounds can provide persistent, process-specific information that is not available through remote techniques; however, the associated measurement technologies have their own set of advantages, disadvantages and technical challenges that may need to be overcome before additional signature data can be effectively and reliably exploited. The main objective of this report is to describe a process to identify high impact technology gaps for important less-than-remote detection applications. The subsequent analysis focuses on the technology development needed to enable exploitation of important process signatures. The evaluation process that was developed involves three interrelated and often conflicting requirements generation activities: • Identification of target signature chemicals with unique intelligence value and their associated attributes as mitigated by environmentally influenced fate and transport effects (i.e., what can you expect to actually find that has intelligence value, where do you need to look for it and what sensitivity and selectivity do you need to see it) • Identification of end-user deployment scenario possibilities and constraints with a focus on alternative detection requirements, timing issues, logistical consideration, and training requirements for a successful measurement • Identification of

  2. Laser Scanning for 3D Object Characterization: Infrastructure for Exploration and Analysis of Vegetation Signatures

    NASA Astrophysics Data System (ADS)

    Koenig, K.; Höfle, B.

    2012-04-01

    Mapping and characterization of the three-dimensional nature of vegetation is increasingly gaining in importance. Deeper insight is required for e.g. forest management, biodiversity assessment, habitat analysis, precision agriculture, renewable energy production or the analysis of interaction between biosphere and atmosphere. However the potential of 3D vegetation characterization has not been exploited so far and new technologies are needed. Laser scanning has evolved into the state-of-the-art technology for highly accurate 3D data acquisition. By now several studies indicated a high value of 3D vegetation description by using laser data. The laser sensors provide a detailed geometric presentation (geometric information) of scanned objects as well as a full profile of laser energy that was scattered back to the sensor (radiometric information). In order to exploit the full potential of these datasets, profound knowledge on laser scanning technology for data acquisition, geoinformation technology for data analysis and object of interest (e.g. vegetation) for data interpretation have to be joined. A signature database is a collection of signatures of reference vegetation objects acquired under known conditions and sensor parameters and can be used to improve information extraction from unclassified vegetation datasets. Different vegetation elements (leaves, branches, etc.) at different heights above ground with different geometric composition contribute to the overall description (i.e. signature) of the scanned object. The developed tools allow analyzing tree objects according to single features (e.g. echo width and signal amplitude) and to any relation of features and derived statistical values (e.g. ratio of laser point attributes). For example, a single backscatter cross section value does not allow for tree species determination, whereas the average echo width per tree segment can give good estimates. Statistical values and/or distributions (e.g. Gaussian

  3. Unique plasma metabolomic signatures of individuals with inherited disorders of long-chain fatty acid oxidation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Blood and urine acylcarnitine profiles are commonly used to diagnose long-chain fatty acid oxidation disorders (FAOD: i.e., long-chain hydroxy-acyl-CoA dehydrogenase [LCHAD] and carnitine palmitoyltransferase 2 [CPT2] deficiency), but the global metabolic impact of long-chain FAOD has not been repor...

  4. Unique amino acid signatures that are evolutionarily conserved distinguish simple-type, epidermal and hair keratins

    PubMed Central

    Strnad, Pavel; Usachov, Valentyn; Debes, Cedric; Gräter, Frauke; Parry, David A. D.; Omary, M. Bishr

    2011-01-01

    Keratins (Ks) consist of central α-helical rod domains that are flanked by non-α-helical head and tail domains. The cellular abundance of keratins, coupled with their selective cell expression patterns, suggests that they diversified to fulfill tissue-specific functions although the primary structure differences between them have not been comprehensively compared. We analyzed keratin sequences from many species: K1, K2, K5, K9, K10, K14 were studied as representatives of epidermal keratins, and compared with K7, K8, K18, K19, K20 and K31, K35, K81, K85, K86, which represent simple-type (single-layered or glandular) epithelial and hair keratins, respectively. We show that keratin domains have striking differences in their amino acids. There are many cysteines in hair keratins but only a small number in epidermal keratins and rare or none in simple-type keratins. The heads and/or tails of epidermal keratins are glycine and phenylalanine rich but alanine poor, whereas parallel domains of hair keratins are abundant in prolines, and those of simple-type epithelial keratins are enriched in acidic and/or basic residues. The observed differences between simple-type, epidermal and hair keratins are highly conserved throughout evolution. Cysteines and histidines, which are infrequent keratin amino acids, are involved in de novo mutations that are markedly overrepresented in keratins. Hence, keratins have evolutionarily conserved and domain-selectively enriched amino acids including glycine and phenylalanine (epidermal), cysteine and proline (hair), and basic and acidic (simple-type epithelial), which reflect unique functions related to structural flexibility, rigidity and solubility, respectively. Our findings also support the importance of human keratin ‘mutation hotspot’ residues and their wild-type counterparts. PMID:22215855

  5. Regression analysis of non-contact acousto-thermal signature data

    NASA Astrophysics Data System (ADS)

    Criner, Amanda; Schehl, Norman

    2016-05-01

    The non-contact acousto-thermal signature (NCATS) is a nondestructive evaluation technique with potential to detect fatigue in materials such as noisy titanium and polymer matrix composites. The underlying physical mechanisms and properties may be determined by parameter estimation via nonlinear regression. The nonlinear regression analysis formulation, including the underlying models, is discussed. Several models and associated data analyses are given along with the assumptions implicit in the underlying model. The results are anomalous. These anomalous results are evaluated with respect to the accuracy of the implicit assumptions.

  6. Colon Cancer Cells Gene Expression Signature As Response to 5- Fluorouracil, Oxaliplatin, and Folinic Acid Treatment

    PubMed Central

    Negrei, Carolina; Hudita, Ariana; Ginghina, Octav; Galateanu, Bianca; Voicu, Sorina Nicoleta; Stan, Miriana; Costache, Marieta; Fenga, Concettina; Drakoulis, Nikolaos; Tsatsakis, Aristidis M.

    2016-01-01

    5-FU cytotoxicity mechanism has been assigned both to the miss-incorporation of fluoronucleotides into RNA and DNA and to the inhibition of thymidylate synthase. 5-FU is one of the most widely used chemotherapeutic drugs, although it has severe side effects that may vary between patients. Pharmacogenetic studies related to 5-FU have been traditionally focused on the rate-limiting catabolic enzyme, dihydropyrimidine dehydrogenase that breaks 80–85% of 5-FU into its inactive metabolite. Choosing the right dosing scheme and chemotherapy strategy for each individual patient remains challenging for personalized chemotherapy management. In the general effort toward reduction of colorectal cancer mortality, in vitro screening studies play a very important role. To accelerate translation research, increasing interest has been focused on using in vivo-like models such as three-dimensional spheroids. The development of higher throughput assays to quantify phenotypic changes in spheroids is an active research area. Consequently, in this study we used the microarray technology to reveal the HT-29 colorectal adenocarcinoma cells gene expression signature as response to 5-FU/OXP/FA treatment in a state of the art 3D culture system. We report here an increased reactive oxygen species production under treatment, correlated with a decrease in cell viability and proliferation potential. With respect to the HT-29 cells gene expression under the treatment with 5-FU/OXP/FA, we found 15.247 genes that were significantly differentially expressed (p < 0.05) with a fold change higher that two-fold. Among these, 7136 genes were upregulated and 8111 genes were downregulated under experimental conditions as compared to untreated cells. The most relevant and statistic significant (p < 0.01) pathways in the experiment are associated with the genes that displayed significant differential expression and are related to intracellular signaling, oxidative stress, apoptosis, and cancer. PMID

  7. Segregation of acid plume pixels from background water pixels, signatures of background water and dispersed acid plumes, and implications for calculation of iron concentration in dense plumes

    NASA Technical Reports Server (NTRS)

    Bahn, G. S.

    1978-01-01

    Two files of data, obtained with a modular multiband scanner, for an acid waste dump into ocean water, were analyzed intensively. Signatures were derived for background water at different levels of effective sunlight intensity, and for different iron concentrations in the dispersed plume from the dump. The effect of increased sunlight intensity on the calculated iron concentration was found to be relatively important at low iron concentrations and relatively unimportant at high values of iron concentration in dispersed plumes. It was concluded that the basic equation for iron concentration is not applicable to dense plumes, particularly because lower values are indicated at the very core of the plume, than in the surrounding sheath, whereas radiances increase consistently from background water to dispersed plume to inner sheath to innermost core. It was likewise concluded that in the dense plume the iron concentration would probably best be measured by the higher wave length radiances, although the suitable relationship remains unknown.

  8. Discriminating the molecular basis of hepatotoxicity using the large-scale characteristic molecular signatures of toxicants by expression profiling analysis.

    PubMed

    Eun, Jung Woo; Ryu, So Yeon; Noh, Ji Heon; Lee, Min-Jae; Jang, Ja-Jun; Ryu, Jae Chun; Jung, Kwang Hwa; Kim, Jeong Kyu; Bae, Hyun Jin; Xie, Hongjian; Kim, Su Young; Lee, Sug Hyung; Park, Won Sang; Yoo, Nam Jin; Lee, Jung Young; Nam, Suk Woo

    2008-07-30

    Predicting the potential human health risk posed by chemical stressors has long been a major challenge for toxicologists, and the use of microarrays to measure responses to toxicologically relevant genes, and to identify selective, sensitive biomarkers of toxicity is a major application of predictive and discovery toxicology. To investigate this possibility, we investigated whether carcinogens (at doses known to induce liver tumors in chronic exposure bioassays) deregulate characteristic sets of genes in mice. Male C3H/He mice were dosed with two hepatocarcinogens (vinyl chloride (VC, 50-25 mg/kg), aldrin (AD, 0.8-0.4 mg/kg)), or two non-hepatocarcinogens (copper sulfate (CS, 150-60 mg/kg), 2,4,5-trichlorophenoxyacetic acid (2,4,5-T, 150-60 mg/kg)). Large-scale molecular changes elicited by these four hepatotoxicants in liver tissues were analyzed using DNA microarray. Three days after administration, no significant phenotypic changes were induced by these four different hepatotoxicants in terms of histological examination or blood biochemical assay. However, unsupervised hierarchical analysis of gene expressional changes induced by hepatotoxicants resulted in two major gene subclusters on dendrogram, i.e., a carcinogen (VN, AD) and non-carcinogen group (CS, 2,4,5-T), and also revealed that distinct molecular signatures exist. These signatures were founded on well-defined functional gene categories and may differentiate genotoxic and non-genotoxic carcinogens. Furthermore, Venn diagram analysis allowed us to identify carcinogen and non-carcinogen-associated molecular signatures. Using statistical methods, we analyzed outlier genes for four different classes (genotoxic-, non-genotoxic-carcinogen, genotoxic-, non-genotoxic non-carcinogen) in terms of their potential to predict different modes-of-action. In conclusion, the identification of large-scale molecular changes in different hepatocarcinogen exposure models revealed that different types of hepatotoxicants are

  9. A critical evaluation of the principal component analysis detection of polarized signatures using real stellar data

    NASA Astrophysics Data System (ADS)

    Paletou, F.

    2012-08-01

    The general context of this study is the post-processing of multiline spectropolarimetric observations of stars, and in particular the numerical analysis techniques aiming at detecting and characterizing polarized signatures. Using real observational data, we compare and clarify several points concerning various methods of analysis. We applied and compared the results of simple line addition, least-squares deconvolution, and denoising by principal component analysis to polarized stellar spectra available from the TBLegacy database of the Narval spectropolarimeter. This comparison of various approaches of distinct sophistication levels allows us to make a safe choice for the next implementation of on-line post-processing of our unique database for the stellar physics community.

  10. Immune signatures and disorder-specific patterns in a cross-disorder gene expression analysis

    PubMed Central

    de Jong, Simone; Newhouse, Stephen J.; Patel, Hamel; Lee, Sanghyuck; Dempster, David; Curtis, Charles; Paya-Cano, Jose; Murphy, Declan; Wilson, C. Ellie; Horder, Jamie; Mendez, M. Andreina; Asherson, Philip; Rivera, Margarita; Costello, Helen; Maltezos, Stefanos; Whitwell, Susannah; Pitts, Mark; Tye, Charlotte; Ashwood, Karen L.; Bolton, Patrick; Curran, Sarah; McGuffin, Peter; Dobson, Richard; Breen, Gerome

    2016-01-01

    Background Recent studies point to overlap between neuropsychiatric disorders in symptomatology and genetic aetiology. Aims To systematically investigate genomics overlap between childhood and adult attention-deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD) and major depressive disorder (MDD). Method Analysis of whole-genome blood gene expression and genetic risk scores of 318 individuals. Participants included individuals affected with adult ADHD (n = 93), childhood ADHD (n = 17), MDD (n = 63), ASD (n = 51), childhood dual diagnosis of ADHD–ASD (n = 16) and healthy controls (n = 78). Results Weighted gene co-expression analysis results reveal disorder-specific signatures for childhood ADHD and MDD, and also highlight two immune-related gene co-expression modules correlating inversely with MDD and adult ADHD disease status. We find no significant relationship between polygenic risk scores and gene expression signatures. Conclusions Our results reveal disorder overlap and specificity at the genetic and gene expression level. They suggest new pathways contributing to distinct pathophysiology in psychiatric disorders and shed light on potential shared genomic risk factors. PMID:27151072

  11. Signature analysis of ballistic missile warhead with micro-nutation in terahertz band

    NASA Astrophysics Data System (ADS)

    Li, Ming; Jiang, Yue-song

    2013-08-01

    In recent years, the micro-Doppler effect has been proposed as a new technique for signature analysis and extraction of radar targets. The ballistic missile is known as a typical radar target and has been paid many attentions for the complexities of its motions in current researches. The trajectory of a ballistic missile can be generally divided into three stages: boost phase, midcourse phase and terminal phase. The midcourse phase is the most important phase for radar target recognition and interception. In this stage, the warhead forms a typical micro-motion called micro-nutation which consists of three basic micro-motions: spinning, coning and wiggle. This paper addresses the issue of signature analysis of ballistic missile warhead in terahertz band via discussing the micro-Doppler effect. We establish a simplified model (cone-shaped) for the missile warhead followed by the micro-motion models including of spinning, coning and wiggle. Based on the basic formulas of these typical micro-motions, we first derive the theoretical formula of micro-nutation which is the main micro-motion of the missile warhead. Then, we calculate the micro-Doppler frequency in both X band and terahertz band via these micro-Doppler formulas. The simulations are given to show the superiority of our proposed method for the recognition and detection of radar micro targets in terahertz band.

  12. Functional Signatures as the Basis for Hydrologic Similarity: Regional Analysis Across the Continental United States

    NASA Astrophysics Data System (ADS)

    Yaeger, M. A.; Ye, S.; Coopersmith, E. J.; Cheng, L.; Sivapalan, M.

    2011-12-01

    Catchment signatures quantify hydrologic responses to rainfall inputs; by distilling catchment behavior into a few signatures, classification of variable behavior across many different catchments can be made. One such signature, the regime curve (RC), shows the intra-annual variability of monthly or even daily average streamflows. Another, the flow duration curve (FDC), plots daily streamflow magnitude as a function of the probability of its exceedance. Encoded within these signatures are the combined impacts of climate, geology, topography, ecology, and even human activities. In this study we analyze regional variations of the RC and the FDC across the continental United States and interpret these using a simple bucket model in order to better understand the climatic and landscape controls. The four parameter functional model used treats a catchment as a nonlinear, two-stage filter. In the first stage, precipitation events are filtered nonlinearly into fast runoff and wetting (infiltration). In the second stage, the infiltrated water is again filtered, more linearly, governed by a competition between subsurface drainage and evapotranspiration. In this filtering process, the FDC associated with the precipitation itself cascades through the catchment system, transformed first into the FDC of fast runoff, and then into the FDC of slow runoff. The FDC of total runoff is therefore a convolution of the two components. Using this partitioning, both the RC and the FDC can be separated into two components, one for the fast runoff, and one for the slow, subsurface runoff. The analysis is repeated for 200 catchments from the MOPEX long-term dataset, spatially ranged across the entire continental United States. The variations in the FDCs are evaluated on the basis of the model parameters for each filter, enabling assessment of the relative contributions of climate (from the FDCs of precipitation and relative seasonality of precipitation and potential evaporation) and

  13. A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

    PubMed Central

    Liu, Wanting

    2013-01-01

    Genome-wide microarray technology has facilitated the systematic discovery of diagnostic biomarkers of cancers and other pathologies. However, meta-analyses of published arrays often uncover significant inconsistencies that hinder advances in clinical practice. Here we present an integrated microarray analysis framework, based on a genome-wide relative significance (GWRS) and genome-wide global significance (GWGS) model. When applied to five microarray datasets on melanoma published between 2000 and 2011, this method revealed a new signature of 200 genes. When these were linked to so-called ‘melanoma driver’ genes involved in MAPK, Ca2+, and WNT signaling pathways we were able to produce a new 12-gene diagnostic biomarker signature for melanoma (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, TNC, CXCL13, COL11A1, CHP2, SHC4, PPP2R2C, and WNT4). We have begun to experimentally validate a subset of these genes involved in MAPK signaling at the protein level, including CXCL13, COL11A1, PTPRF and SHC4 and found these to be over-expressed in metastatic and primary melanoma cells in vitro and in situ compared to melanocytes cultured from healthy skin epidermis and normal healthy human skin. While SHC4 has been reported previously to be associated to melanoma, this is the first time CXCL13, COL11A1, and PTPRF have been associated with melanoma on experimental validation. Our computational evaluation indicates that this 12-gene biomarker signature achieves excellent diagnostic power in distinguishing metastatic melanoma from normal skin and benign nevus. Further experimental validation of the role of these 12 genes in a new signaling network may provide new insights into the underlying biological mechanisms driving the progression of melanoma. PMID:23638386

  14. Screening of gene signatures for rheumatoid arthritis and osteoarthritis based on bioinformatics analysis.

    PubMed

    He, Peiheng; Zhang, Ziji; Liao, Weiming; Xu, Dongliang; Fu, Ming; Kang, Yan

    2016-08-01

    The current study aimed to identify gene signatures during rheumatoid arthritis (RA) and osteoarthritis (OA), and used these to elucidate the underlying modular mechanisms. Using the Gene Expression Omnibus database, the present study obtained the GSE7669 mRNA expression microarray data from RA and OA synovial fibroblasts (n=6 each). The differentially expressed genes (DEGs) in RA synovial samples compared with OA samples were identified using the Linear Models for Microarray Analysis package. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation Visualization and Integrated Discovery. A protein‑protein interaction network was constructed and the modules were further analyzed using the Molecular Complex Detection plugin of Cytoscape. A total of 181 DEGs were identified by comparing RA and OA synovial samples (96 up‑ and 85 downregulated genes). The significant DEGs in module 1, including collagen, type I, α 1 (COL1A1), COL3A1, COL4A1 and COL11A1, were predominantly enriched in the extracellular matrix (ECM)‑receptor interaction and focal adhesion pathways. Additionally, significant DEGs in module 2, including radical S‑adenosyl methionine domain containing 2 (RSAD2), 2'‑5'‑oligoadenylate synthetase 2 (OAS2), myxovirus (influenza virus) resistance 1 (MX1) and ISG15 ubiquitin‑like modifier (ISG15), were predominantly associated with immune function pathways. In conclusion, the present study indicated that RSAD2, OAS2, MX1 and ISG15 may be notable gene signatures in RA development via regulation of the immune response. COL3A1, COL4A1, COL1A1 and COL11A1 may be important gene signatures in OA development via involvement in the pathways of ECM-receptor interactions and focal adhesions. PMID:27356888

  15. Screening of gene signatures for rheumatoid arthritis and osteoarthritis based on bioinformatics analysis

    PubMed Central

    He, Peiheng; Zhang, Ziji; Liao, Weiming; Xu, Dongliang; Fu, Ming; Kang, Yan

    2016-01-01

    The current study aimed to identify gene signatures during rheumatoid arthritis (RA) and osteoarthritis (OA), and used these to elucidate the underlying modular mechanisms. Using the Gene Expression Omnibus database, the present study obtained the GSE7669 mRNA expression microarray data from RA and OA synovial fibroblasts (n=6 each). The differentially expressed genes (DEGs) in RA synovial samples compared with OA samples were identified using the Linear Models for Microarray Analysis package. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation Visualization and Integrated Discovery. A protein-protein interaction network was constructed and the modules were further analyzed using the Molecular Complex Detection plugin of Cytoscape. A total of 181 DEGs were identified by comparing RA and OA synovial samples (96 up- and 85 downregulated genes). The significant DEGs in module 1, including collagen, type I, α 1 (COL1A1), COL3A1, COL4A1 and COL11A1, were predominantly enriched in the extracellular matrix (ECM)-receptor interaction and focal adhesion pathways. Additionally, significant DEGs in module 2, including radical S-adenosyl methionine domain containing 2 (RSAD2), 2′-5′-oligoadenylate synthetase 2 (OAS2), myxovirus (influenza virus) resistance 1 (MX1) and ISG15 ubiquitin-like modifier (ISG15), were predominantly associated with immune function pathways. In conclusion, the present study indicated that RSAD2, OAS2, MX1 and ISG15 may be notable gene signatures in RA development via regulation of the immune response. COL3A1, COL4A1, COL1A1 and COL11A1 may be important gene signatures in OA development via involvement in the pathways of ECM-receptor interactions and focal adhesions. PMID:27356888

  16. A static acoustic signature system for the analysis of dynamic flight information

    NASA Technical Reports Server (NTRS)

    Ramer, D. J.

    1978-01-01

    The Army family of helicopters was analyzed to measure the polar octave band acoustic signature in various modes of flight. A static array of calibrated microphones was used to simultaneously acquire the signature and differential times required to mathematically position the aircraft in space. The signature was then reconstructed, mathematically normalized to a fixed radius around the aircraft.

  17. Salmonella transcriptional signature in Tetrahymena phagosomes and role of acid tolerance in passage through the protist

    PubMed Central

    Rehfuss, Marc Yi Ming; Parker, Craig Thomas; Brandl, Maria Theresa

    2011-01-01

    Salmonella enterica Typhimurium remains undigested in the food vacuoles of the common protist, Tetrahymena. Contrary to its interaction with Acanthamoeba spp., S. Typhimurium is not cytotoxic to Tetrahymena and is egested as viable cells in its fecal pellets. Through microarray gene expression profiling we investigated the factors in S. Typhimurium that are involved in its resistance to digestion by Tetrahymena. The transcriptome of S. Typhimurium in Tetrahymena phagosomes showed that 989 and 1282 genes were altered in expression compared with that in water and in LB culture medium, respectively. A great proportion of the upregulated genes have a role in anaerobic metabolism and the use of alternate electron acceptors. Many genes required for survival and replication within macrophages and human epithelial cells also had increased expression in Tetrahymena, including mgtC, one of the most highly induced genes in all three cells types. A ΔmgtC mutant of S. Typhimurium did not show decreased viability in Tetrahymena, but paradoxically, was egested at a higher cell density than the wild type. The expression of adiA and adiY, which are involved in arginine-dependent acid resistance, also was increased in the protozoan phagosome. A ΔadiAY mutant had lower viability after passage through Tetrahymena, and a higher proportion of S. Typhimurium wild-type cells within pellets remained viable after exposure to pH 3.4 as compared with uningested cells. Our results provide evidence that acid resistance has a role in the resistance of Salmonella to digestion by Tetrahymena and that passage through the protist confers physiological advantages relevant to its contamination cycle. PMID:20686510

  18. Eddy covariance captures four-phase crassulacean acid metabolism (CAM) gas exchange signature in Agave.

    PubMed

    Owen, Nick A; Choncubhair, Órlaith Ní; Males, Jamie; Del Real Laborde, José Ignacio; Rubio-Cortés, Ramón; Griffiths, Howard; Lanigan, Gary

    2016-02-01

    Mass and energy fluxes were measured over a field of Agave tequilana in Mexico using eddy covariance (EC) methodology. Data were gathered over 252 d, including the transition from wet to dry periods. Net ecosystem exchanges (FN,EC ) displayed a crassulacean acid metabolism (CAM) rhythm that alternated from CO2 sink at night to CO2 source during the day, and partitioned canopy fluxes (FA,EC ) showed a characteristic four-phase CO2 exchange pattern. Results were cross-validated against diel changes in titratable acidity, leaf-unfurling rates, energy exchange fluxes and reported biomass yields. Projected carbon balance (g C m(-2)  year(-1) , mean ± 95% confidence interval) indicated the site was a net sink of -333 ± 24, of which contributions from soil respiration were +692 ± 7, and FA,EC was -1025 ± 25. EC estimated biomass yield was 20.1 Mg (dry) ha(-1)  year(-1) . Average integrated daily FA,EC was -234 ± 5 mmol CO2  m(-2)  d(-1) and persisted almost unchanged after 70 d of drought conditions. Regression analyses were performed on the EC data to identify the best environmental predictors of FA . Results suggest that the carbon acquisition strategy of Agave offers productivity and drought resilience advantages over conventional semi-arid C3 and C4 bioenergy candidates. PMID:26177873

  19. Analysis of Infrared Signature Variation and Robust Filter-Based Supersonic Target Detection

    PubMed Central

    Sun, Sun-Gu; Kim, Kyung-Tae

    2014-01-01

    The difficulty of small infrared target detection originates from the variations of infrared signatures. This paper presents the fundamental physics of infrared target variations and reports the results of variation analysis of infrared images acquired using a long wave infrared camera over a 24-hour period for different types of backgrounds. The detection parameters, such as signal-to-clutter ratio were compared according to the recording time, temperature and humidity. Through variation analysis, robust target detection methodologies are derived by controlling thresholds and designing a temporal contrast filter to achieve high detection rate and low false alarm rate. Experimental results validate the robustness of the proposed scheme by applying it to the synthetic and real infrared sequences. PMID:24672290

  20. Meta-Analysis of Gene Expression Signatures Defining the Epithelial to Mesenchymal Transition during Cancer Progression

    PubMed Central

    Gröger, Christian J.; Grubinger, Markus; Waldhör, Thomas; Vierlinger, Klemens; Mikulits, Wolfgang

    2012-01-01

    The epithelial to mesenchymal transition (EMT) represents a crucial event during cancer progression and dissemination. EMT is the conversion of carcinoma cells from an epithelial to a mesenchymal phenotype that associates with a higher cell motility as well as enhanced chemoresistance and cancer stemness. Notably, EMT has been increasingly recognized as an early event of metastasis. Numerous gene expression studies (GES) have been conducted to obtain transcriptome signatures and marker genes to understand the regulatory mechanisms underlying EMT. Yet, no meta-analysis considering the multitude of GES of EMT has been performed to comprehensively elaborate the core genes in this process. Here we report the meta-analysis of 18 independent and published GES of EMT which focused on different cell types and treatment modalities. Computational analysis revealed clustering of GES according to the type of treatment rather than to cell type. GES of EMT induced via transforming growth factor-β and tumor necrosis factor-α treatment yielded uniformly defined clusters while GES of models with alternative EMT induction clustered in a more complex fashion. In addition, we identified those up- and downregulated genes which were shared between the multitude of GES. This core gene list includes well known EMT markers as well as novel genes so far not described in this process. Furthermore, several genes of the EMT-core gene list significantly correlated with impaired pathological complete response in breast cancer patients. In conclusion, this meta-analysis provides a comprehensive survey of available EMT expression signatures and shows fundamental insights into the mechanisms that are governing carcinoma progression. PMID:23251436

  1. Large-scale phenome analysis defines a behavioral signature for Huntington's disease genotype in mice.

    PubMed

    Alexandrov, Vadim; Brunner, Dani; Menalled, Liliana B; Kudwa, Andrea; Watson-Johnson, Judy; Mazzella, Matthew; Russell, Ian; Ruiz, Melinda C; Torello, Justin; Sabath, Emily; Sanchez, Ana; Gomez, Miguel; Filipov, Igor; Cox, Kimberly; Kwan, Mei; Ghavami, Afshin; Ramboz, Sylvie; Lager, Brenda; Wheeler, Vanessa C; Aaronson, Jeff; Rosinski, Jim; Gusella, James F; MacDonald, Marcy E; Howland, David; Kwak, Seung

    2016-08-01

    Rapid technological advances for the frequent monitoring of health parameters have raised the intriguing possibility that an individual's genotype could be predicted from phenotypic data alone. Here we used a machine learning approach to analyze the phenotypic effects of polymorphic mutations in a mouse model of Huntington's disease that determine disease presentation and age of onset. The resulting model correlated variation across 3,086 behavioral traits with seven different CAG-repeat lengths in the huntingtin gene (Htt). We selected behavioral signatures for age and CAG-repeat length that most robustly distinguished between mouse lines and validated the model by correctly predicting the repeat length of a blinded mouse line. Sufficient discriminatory power to accurately predict genotype required combined analysis of >200 phenotypic features. Our results suggest that autosomal dominant disease-causing mutations could be predicted through the use of subtle behavioral signatures that emerge in large-scale, combinatorial analyses. Our work provides an open data platform that we now share with the research community to aid efforts focused on understanding the pathways that link behavioral consequences to genetic variation in Huntington's disease. PMID:27376585

  2. Population analysis of microsatellite genotypes reveals a signature associated with ovarian cancer.

    PubMed

    Fonville, Natalie C; Vaksman, Zalman; McIver, Lauren J; Garner, Harold R

    2015-05-10

    Ovarian cancer (OV) ranks fifth in cancer deaths among women, yet there remain few informative biomarkers for this disease. Microsatellites are repetitive genomic regions which we hypothesize could be a source of novel biomarkers for OV and have traditionally been under-appreciated relative to Single Nucleotide Polymorphisms (SNPs). In this study, we explore microsatellite variation as a potential novel source of genomic variation associated with OV. Exomes from 305 OV patient germline samples and 54 tumors, sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation and compared to healthy females sequenced as part of the 1,000 Genomes Project. We identified a subset of 60 microsatellite loci with genotypes that varied significantly between the OV and healthy female populations. Using these loci as a signature set, we classified germline genomes as 'at risk' for OV with a sensitivity of 90.1% and a specificity of 87.6%. Cross-analysis with a similar set of breast cancer associated loci identified individuals 'at risk' for both diseases. This study revealed a genotype-based microsatellite signature present in the germlines of individuals diagnosed with OV, and provides the basis for a potential novel risk assessment diagnostic for OV and new personal genomics targets in tumors. PMID:25779658

  3. Positioning of the α-subunit isoforms confers a functional signature to γ-aminobutyric acid type A receptors

    PubMed Central

    Minier, Frédéric; Sigel, Erwin

    2004-01-01

    Fast synaptic inhibitory transmission in the CNS is mediated by γ-aminobutyric acid type A (GABAA) receptors. They belong to the ligand-gated ion channel receptor superfamily, and are constituted of five subunits surrounding a chloride channel. Their clinical interest is highlighted by the number of therapeutic drugs that act on them. It is well established that the subunit composition of a receptor subtype determines its pharmacological properties. We have investigated positional effects of two different α-subunit isoforms, α1 and α6, in a single pentamer. For this purpose, we used concatenated subunit receptors in which subunit arrangement is predefined. The resulting receptors were expressed in Xenopus oocytes and analyzed by using the two-electrode voltage-clamp technique. Thus, we have characterized γ2β2α1β2α1, γ2β2α6β2α6, γ2β2α1β2α6, and γ2β2α6β2α1 GABAA receptors. We investigated their response to the agonist GABA, to the partial agonist piperidine-4-sulfonic acid, to the noncompetitive inhibitor furosemide and to the positive allosteric modulator diazepam. Each receptor isoform is characterized by a specific set of properties. In this case, subunit positioning provides a functional signature to the receptor. We furthermore show that a single α6-subunit is sufficient to confer high furosemide sensitivity, and that the diazepam efficacy is determined exclusively by the α-subunit neighboring the γ2-subunit. By using this diagnostic tool, it should become possible to determine the subunit arrangement of receptors expressed in vivo that contain α1- and α6-subunits. This method may also be applied to the study of other ion channels. PMID:15136735

  4. Acousto-optic signature analysis for inspection of the orbiter thermal protection tile bonds

    NASA Technical Reports Server (NTRS)

    Rodriguez, Julio G.; Tow, D. M.; Barna, B. A.

    1990-01-01

    The goal of this research is to develop a viable NDE technique for the inspection of orbiter thermal protection system (TPS) tile bonds. Phase 2, discussed here, concentrated on developing an empirical understanding of the bonded and unbonded vibration signatures of acreage tiles. Controlled experiments in the laboratory have provided useful information on the dynamic response of TPS tiles. It has been shown that several signatures are common to all the pedigree tiles. This degree of consistency in the tile-SIP (strain isolation pad) dynamic response proves that an unbond can be detected for a known tile and establish the basis for extending the analysis capability to arbitrary tiles for which there are no historical data. The field tests of the noncontacting laser acoustic sensor system, conducted at the Kennedy Space Center (KSC), investigated the vibrational environment of the Orbiter Processing Facility (OPF) and its effect on the measurement and analysis techniques being developed. The data collected showed that for orbiter locations, such as the body flap and elevon, the data analysis scheme, and/or the sensor, will require modification to accommodate the ambient motion. Several methods were identified for accomplishing this, and a solution is seen as readily achievable. It was established that the tile response was similar to that observed in the laboratory. Of most importance, however, is that the field environment will not affect the physics of the dynamic response that is related to bond condition. All of this information is fundamental to any future design and development of a prototype system.

  5. Acousto-optic signature analysis for inspection of the orbiter thermal protection tile bonds

    SciTech Connect

    Rodriguez, J.G.; Tow, D.M.; Barna, B.A.

    1989-01-01

    The goal of this research is to develop a viable, on contacting NDE technique for the inspection of orbiter thermal protection system (TPS) tile bonds. Phase 2, discussed here, concentrated on developing an empirical understanding of the b onded and unbonded vibration signatures of acreage tiles. Controlled experiments in the laboratory have provided useful information on the dynamic response of TPS tiles. It has been shown that several signatures are common to all the pedigree'' tiles. This degree of consistency in the tile-SIP (strain isolation pad) dynamic response proves that an unbond can be detected for a known tile and established the basis for extending the analysis capability to arbitrary tiles for which there are no historical data. The field tests of the noncontacting laser acoustic sensor system, conducted at Kennedy Space Center (KSC), investigated the vibrational environment of the Orbiter Processing Facility (OPF) and its effect on the measurement and analysis techniques being developed. The data collected showed that for orbiter locations, such as the body flap and elevon, the data analysis scheme, and/or the sensor, will require modification to accommodate the ambient motion. Several methods have been identified for accomplishing this, and a solution is seen as readily achievable. It was established that the tile response was similar to that observed in the laboratory. Of most importance, however, is that the field environment will not affect the physics of the dynamic response that is related to bond condition. All of this information is fundamental to any future design and development of a prototype system. 2 refs., 9 figs.

  6. Possible signatures of dissipation from time-series analysis techniques using a turbulent laboratory magnetohydrodynamic plasma

    NASA Astrophysics Data System (ADS)

    Schaffner, D. A.; Brown, M. R.; Rock, A. B.

    2016-05-01

    The frequency spectrum of magnetic fluctuations as measured on the Swarthmore Spheromak Experiment is broadband and exhibits a nearly Kolmogorov 5/3 scaling. It features a steepening region which is indicative of dissipation of magnetic fluctuation energy similar to that observed in fluid and magnetohydrodynamic turbulence systems. Two non-spectrum based time-series analysis techniques are implemented on this data set in order to seek other possible signatures of turbulent dissipation beyond just the steepening of fluctuation spectra. Presented here are results for the flatness, permutation entropy, and statistical complexity, each of which exhibits a particular character at spectral steepening scales which can then be compared to the behavior of the frequency spectrum.

  7. Genome-wide analysis of microRNA and mRNA expression signatures in cancer

    PubMed Central

    Li, Ming-hui; Fu, Sheng-bo; Xiao, Hua-sheng

    2015-01-01

    Cancer is an extremely diverse and complex disease that results from various genetic and epigenetic changes such as DNA copy-number variations, mutations, and aberrant mRNA and/or protein expression caused by abnormal transcriptional regulation. The expression profiles of certain microRNAs (miRNAs) and messenger RNAs (mRNAs) are closely related to cancer progression stages. In the past few decades, DNA microarray and next-generation sequencing techniques have been widely applied to identify miRNA and mRNA signatures for cancers on a genome-wide scale and have provided meaningful insights into cancer diagnosis, prognosis and personalized medicine. In this review, we summarize the progress in genome-wide analysis of miRNAs and mRNAs as cancer biomarkers, highlighting their diagnostic and prognostic roles. PMID:26299954

  8. Illumination analysis of the digital pattern recognition system by Bessel masks and one-dimensional signatures

    NASA Astrophysics Data System (ADS)

    Solorza, S.; Álvarez-Borrego, J.

    2013-11-01

    The effects of illumination variations in digital images are a trend topic of the pattern recognition field. The luminance information of the objects help to classify them, however the environment illumination could cause a lot of problem if the system is not illumination invariant. Some applications of this topic include image and video quality, biometrics classification, etc. In this work an illumination analysis for a digital system invariant to position and rotation based on Fourier transform, Bessel masks, one-dimensional signatures and linear correlations are presented. The digital system was tested using a reference database of 21 fossil diatoms images of gray-scale and 307 x 307 pixels. The digital system has shown an excellent performance in the classification of 60,480 problem images which have different non-homogeneous illumination.

  9. Simultaneous analysis of biologically active aminoalkanephosphonic acids.

    PubMed

    Kudzin, Zbigniew H; Gralak, Dorota K; Andrijewski, Grzegorz; Drabowicz, Józef; Luczak, Jerzy

    2003-05-23

    A new approach for simultaneous analysis of biologically active aminoalkanephosphonic acids, namely glyphosate, phosphonoglycine, phosphonosarcosine, phosphonoalanine, phosphono-beta-alanine, phosphonohomoalanine, phosphono-gamma-homoalanine and glufosinate, is presented. This includes a preliminary 31p NMR analysis of these amino acids, their further derivatization to volatile phosphonates (phosphinates) by means of trifluoroacetic acid-trifluoroacetic anhydride-trimethyl orthoacetate reagent and subsequent analysis of derivatization products using MS and/or GC-MS (chemical ionization and/or electron impact ionization). PMID:12862383

  10. Genome-wide analysis of antiviral signature genes in porcine macrophages at different activation statuses.

    PubMed

    Sang, Yongming; Brichalli, Wyatt; Rowland, Raymond R R; Blecha, Frank

    2014-01-01

    Macrophages (MФs) can be polarized to various activation statuses, including classical (M1), alternative (M2), and antiviral states. To study the antiviral activation status of porcine MФs during porcine reproductive and respiratory syndrome virus (PRRSV) infection, we used RNA Sequencing (RNA-Seq) for transcriptomic analysis of differentially expressed genes (DEGs). Sequencing assessment and quality evaluation showed that our RNA-Seq data met the criteria for genome-wide transcriptomic analysis. Comparisons of any two activation statuses revealed more than 20,000 DEGs that were normalized to filter out 153-5,303 significant DEGs [false discovery rate (FDR) ≤0.001, fold change ≥2] in each comparison. The highest 5,303 significant DEGs were found between lipopolysaccharide- (LPS) and interferon (IFN)γ-stimulated M1 cells, whereas only 153 significant DEGs were detected between interleukin (IL)-10-polarized M2 cells and control mock-activated cells. To identify signature genes for antiviral regulation pertaining to each activation status, we identified a set of DEGs that showed significant up-regulation in only one activation state. In addition, pathway analyses defined the top 20-50 significantly regulated pathways at each activation status, and we further analyzed DEGs pertinent to pathways mediated by AMP kinase (AMPK) and epigenetic mechanisms. For the first time in porcine macrophages, our transcriptomic analyses not only compared family-wide differential expression of most known immune genes at different activation statuses, but also revealed transcription evidence of multiple gene families. These findings show that using RNA-Seq transcriptomic analyses in virus-infected and status-synchronized macrophages effectively profiled signature genes and gene response pathways for antiviral regulation, which may provide a framework for optimizing antiviral immunity and immune homeostasis. PMID:24505295

  11. Genome-Wide Analysis of Antiviral Signature Genes in Porcine Macrophages at Different Activation Statuses

    PubMed Central

    Sang, Yongming; Brichalli, Wyatt; Rowland, Raymond R. R.; Blecha, Frank

    2014-01-01

    Macrophages (MФs) can be polarized to various activation statuses, including classical (M1), alternative (M2), and antiviral states. To study the antiviral activation status of porcine MФs during porcine reproductive and respiratory syndrome virus (PRRSV) infection, we used RNA Sequencing (RNA-Seq) for transcriptomic analysis of differentially expressed genes (DEGs). Sequencing assessment and quality evaluation showed that our RNA-Seq data met the criteria for genome-wide transcriptomic analysis. Comparisons of any two activation statuses revealed more than 20,000 DEGs that were normalized to filter out 153–5,303 significant DEGs [false discovery rate (FDR) ≤0.001, fold change ≥2] in each comparison. The highest 5,303 significant DEGs were found between lipopolysaccharide- (LPS) and interferon (IFN)γ-stimulated M1 cells, whereas only 153 significant DEGs were detected between interleukin (IL)-10-polarized M2 cells and control mock-activated cells. To identify signature genes for antiviral regulation pertaining to each activation status, we identified a set of DEGs that showed significant up-regulation in only one activation state. In addition, pathway analyses defined the top 20–50 significantly regulated pathways at each activation status, and we further analyzed DEGs pertinent to pathways mediated by AMP kinase (AMPK) and epigenetic mechanisms. For the first time in porcine macrophages, our transcriptomic analyses not only compared family-wide differential expression of most known immune genes at different activation statuses, but also revealed transcription evidence of multiple gene families. These findings show that using RNA-Seq transcriptomic analyses in virus-infected and status-synchronized macrophages effectively profiled signature genes and gene response pathways for antiviral regulation, which may provide a framework for optimizing antiviral immunity and immune homeostasis. PMID:24505295

  12. Security Analysis of the Unrestricted Identity-Based Aggregate Signature Scheme

    PubMed Central

    Lee, Kwangsu; Lee, Dong Hoon

    2015-01-01

    Aggregate signatures allow anyone to combine different signatures signed by different signers on different messages into a short signature. An ideal aggregate signature scheme is an identity-based aggregate signature (IBAS) scheme that supports full aggregation since it can reduce the total transmitted data by using an identity string as a public key and anyone can freely aggregate different signatures. Constructing a secure IBAS scheme that supports full aggregation in bilinear maps is an important open problem. Recently, Yuan et al. proposed such a scheme and claimed its security in the random oracle model under the computational Diffie-Hellman assumption. In this paper, we show that there is an efficient forgery on their IBAS scheme and that their security proof has a serious flaw. PMID:25993247

  13. Signature analysis of satellite derived SSHa, SST and chlorophyll concentration and their linkage with marine fishery resources

    NASA Astrophysics Data System (ADS)

    Solanki, H. U.; Bhatpuria, Dhyey; Chauhan, Prakash

    2015-10-01

    This study aims to understand patterns, persistence and interrelationship between satellite derived oceanic variables. Time series near-synchronous sea surface height anomaly (SSHa), chlorophyll-a concentration (CC) and sea surface temperature (SST) derived from Topex/Poseidon altimeter, Oceansat-OCM and NOAA-AVHRR, respectively, were used for integrative signature analysis. Three dimensional surface and two dimensional spatial profiles of these variables were generated to understand the spatio-temporal variability. SST and SSHa were co-varying and CC shows an inverse correlation. The time series data analysis indicated bio-physical closely coupled processes. The patterns of variability in CC signatures were found to be associated with SSHa and SST signatures. High fish catch in terms of CPUE (catch-per-unit-effort) were found in low SSHa and corresponding high chlorophyll concentration area during the year 1998-2004 in the Northern Arabian Sea. SSHa signatures were detected earlier than CC and SST. Lower SSHa signatures were inferred as advanced information of the occurrence of productive sites in near future. This study would be useful to understand large scale bio-physical coupled processes for fishery resources exploration.

  14. Principal component analysis of phenolic acid spectra

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenolic acids are common plant metabolites that exhibit bioactive properties and have applications in functional food and animal feed formulations. The ultraviolet (UV) and infrared (IR) spectra of four closely related phenolic acid structures were evaluated by principal component analysis (PCA) to...

  15. Amino acid isotopic analysis in agricultural systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A relatively new approach to stable isotopic analysis—referred to as compound-specific isotopic analysis (CSIA)—has emerged, centering on the measurement of 15N:14N ratios in amino acids (glutamic acid and phenylalanine). CSIA has recently been used to generate trophic position estimates among anima...

  16. Boric Acid in Kjeldahl Analysis

    ERIC Educational Resources Information Center

    Cruz, Gregorio

    2013-01-01

    The use of boric acid in the Kjeldahl determination of nitrogen is a variant of the original method widely applied in many laboratories all over the world. Its use is recommended by control organizations such as ISO, IDF, and EPA because it yields reliable and accurate results. However, the chemical principles the method is based on are not…

  17. Optimal design and evaluation criteria for acoustic emission pulse signature analysis

    NASA Technical Reports Server (NTRS)

    Houghton, J. R.; Townsend, M. A.; Packman, P. F.

    1977-01-01

    Successful pulse recording and evaluation is strongly dependent on the instrumentation system selected and the method of analyzing the pulse signature. The paper studies system design, signal analysis techniques, and interdependences with a view toward defining optimal approaches to pulse signal analysis. For this purpose, the instrumentation system is modeled, and analytical pulses, representative of the types of acoustic emissions to be distinguished are passed through the system. Particular attention is given to comparing frequency spectrum analysis and deconvolution referred to as time domain reconstruction of the pulse or pulse train. The possibility of optimal transducer-filter system parameters is investigated. Deconvolution of a pulse is shown to be a superior approach for transient pulse analysis. Reshaping of a transducer output back to the original input pulse is possible and gives an accurate representation of the generating pulse in the time domain. Any definable transducer and filter system can be used for measurement of pulses by means of the deconvolution method. Selection of design variables for general usage is discussed.

  18. Feature analysis and classification of manufacturing signatures based on semiconductor wafermaps

    SciTech Connect

    Tobin, K.W.; Gleason, S.S.; Karnowski, T.P.; Cohen, S.L.

    1997-02-01

    Automated tools for semiconductor wafer defect analysis are becoming more necessary as device densities and wafer sizes continue to increase. Trends towards larger wafer formats and smaller critical dimensions have caused an exponential increase in the volume of defect data which must be analyzed and stored. To accommodate these changing factors, automatic analysis tools are required that can efficiently and robustly process the increasing amounts of data, and thus quickly characterize manufacturing processes and accelerate yield learning. During the first year of this cooperative research project between SEMATECH and the Oak Ridge National Laboratory, a robust methodology for segmenting signature events prior to feature analysis and classification was developed. Based on the results of this segmentation procedure, a feature measurement strategy has been designed based on interviews with process engineers coupled with the analysis of approximately 1500 electronic wafermap files. In this paper, the authors represent an automated procedure to rank and select relevant features for use with a fuzzy pair-wise classifier and give examples of the efficacy of the approach taken. Results of the feature selection process are given for two uniquely different types of class data to demonstrate a general improvement in classifier performance.

  19. Plasma amino acid and metabolite signatures tracking diabetes progression in the UCD-T2DM rat model.

    PubMed

    Piccolo, Brian D; Graham, James L; Stanhope, Kimber L; Fiehn, Oliver; Havel, Peter J; Adams, Sean H

    2016-06-01

    Elevations of plasma concentrations of branched-chain amino acids (BCAAs) are observed in human insulin resistance and type 2 diabetes mellitus (T2DM); however, there has been some controversy with respect to the passive or causative nature of the BCAA phenotype. Using untargeted metabolomics, plasma BCAA and other metabolites were assessed in lean control Sprague-Dawley rats (LC) and temporally during diabetes development in the UCD-T2DM rat model, i.e., prediabetic (PD) and 2 wk (D2W), 3 mo (D3M), and 6 mo (D6M) post-onset of diabetes. Plasma leucine, isoleucine, and valine concentrations were elevated only in D6M rats compared with D2W rats (by 28, 29, and 30%, respectively). This was in contrast to decreased plasma concentrations of several other amino acids in D3M and/or D6M relative to LC rats (Ala, Arg, Glu, Gln, Met, Ser, Thr, and Trp). BCAAs were positively correlated with fasting glucose and negatively correlated with plasma insulin, total body weight, total adipose tissue weight, and gastrocnemius muscle weight in the D3M and D6M groups. Multivariate analysis revealed that D3M and D6M UCD-T2DM rats had lower concentrations of amino acids, amino acid derivatives, 1,5-anhydroglucitol, and conduritol-β-opoxide and higher concentrations of uronic acids, pantothenic acids, aconitate, benzoic acid, lactate, and monopalmitin-2-glyceride relative to PD and D2W UCD-T2DM rats. The UCD-T2DM rat does not display elevated plasma BCAA concentrations until 6 mo post-onset of diabetes. With the acknowledgement that this is a rodent model of T2DM, the results indicate that elevated plasma BCAA concentrations are not necessary or sufficient to elicit an insulin resistance or T2DM onset. PMID:27094034

  20. How wide is a stream? Spatial extent of the potential "stream signature" in terrestrial food webs using meta-analysis.

    PubMed

    Muehlbauer, Jeffrey D; Collins, Scott F; Doyle, Martin W; Tockner, Klement

    2014-01-01

    The magnitude of cross-ecosystem resource subsidies is increasingly well recognized; however, less is known about the distance these subsidies travel into the recipient landscape. In streams and rivers, this distance can delimit the "biological stream width," complementary to hydro-geomorphic measures (e.g., channel banks) that have typically defined stream ecosystem boundaries. In this study we used meta-analysis to define a "stream signature" on land that relates the stream-to-land subsidy to distance. The 50% stream signature, for example, identifies the point on the landscape where subsidy resources are still at half of their maximum (in- or near-stream) level. The decay curve for these data was best fit by a negative power function in which the 50% stream signature was concentrated near stream banks (1.5 m), but a non-trivial (10%) portion of the maximum subsidy level was still found > 0.5 km from the water's edge. The meta-analysis also identified explanatory variables that affect the stream signature. This improves our understanding of ecosystem conditions that permit spatially extensive subsidy transmission, such as in highly productive, middle-order streams and rivers. Resultant multivariate models from this analysis may be useful to managers implementing buffer rules and conservation strategies for stream and riparian function, as they facilitate prediction of the extent of subsidies. Our results stress that much of the subsidy remains near the stream, but also that subsidies (and aquatic organisms) are capable of long-distance dispersal into adjacent environments, and that the effective "biological stream width" of stream and river ecosystems is often much larger than has been defined by hydro-geomorphic metrics alone. Limited data available from marine and lake sources overlap well with the stream signature data, indicating that the "signature" approach may also be applicable to subsidy spatial dynamics across other ecosystems. PMID:24649645

  1. Identification of Molecular Signatures from Different Vaccine Adjuvants in Chicken by Integrative Analysis of Microarray Data

    PubMed Central

    Kim, Duk Kyung; Won, Kyeong Hye; Moon, Seung Hyun; Lee, Hak-Kyo

    2016-01-01

    The present study compared the differential functions of two groups of adjuvants, Montanide incomplete Seppic adjuvant (ISA) series and Quil A, cholesterol, dimethyl dioctadecyl ammonium bromide, and Carbopol (QCDC) formulations, in chicken by analyzing published microarray data associated with each type of vaccine adjuvants. In the biological function analysis for differentially expressed genes altered by two different adjuvant groups, ISA series and QCDC formulations showed differential effects when chickens were immunized with a recombinant immunogenic protein of Eimeria. Among the biological functions, six categories were modified in both adjuvant types. However, with respect to “Response to stimulus”, no biological process was modified by the two adjuvant groups at the same time. The QCDC adjuvants showed effects on the biological processes (BPs) including the innate immune response and the immune response to the external stimulus such as toxin and bacterium, while the ISA adjuvants modified the BPs to regulate cell movement and the response to stress. In pathway analysis, ISA adjuvants altered the genes involved in the functions related with cell junctions and the elimination of exogenous and endogenous macromolecules. The analysis in the present study could contribute to the development of precise adjuvants based on molecular signatures related with their immunological functions. PMID:26954188

  2. Identification of Molecular Signatures from Different Vaccine Adjuvants in Chicken by Integrative Analysis of Microarray Data.

    PubMed

    Kim, Duk Kyung; Won, Kyeong Hye; Moon, Seung Hyun; Lee, Hak-Kyo

    2016-07-01

    The present study compared the differential functions of two groups of adjuvants, Montanide incomplete Seppic adjuvant (ISA) series and Quil A, cholesterol, dimethyl dioctadecyl ammonium bromide, and Carbopol (QCDC) formulations, in chicken by analyzing published microarray data associated with each type of vaccine adjuvants. In the biological function analysis for differentially expressed genes altered by two different adjuvant groups, ISA series and QCDC formulations showed differential effects when chickens were immunized with a recombinant immunogenic protein of Eimeria. Among the biological functions, six categories were modified in both adjuvant types. However, with respect to "Response to stimulus", no biological process was modified by the two adjuvant groups at the same time. The QCDC adjuvants showed effects on the biological processes (BPs) including the innate immune response and the immune response to the external stimulus such as toxin and bacterium, while the ISA adjuvants modified the BPs to regulate cell movement and the response to stress. In pathway analysis, ISA adjuvants altered the genes involved in the functions related with cell junctions and the elimination of exogenous and endogenous macromolecules. The analysis in the present study could contribute to the development of precise adjuvants based on molecular signatures related with their immunological functions. PMID:26954188

  3. Analysis of Forgery Attack on One-Time Proxy Signature and the Improvement

    NASA Astrophysics Data System (ADS)

    Wang, Tian-Yin; Wei, Zong-Li

    2016-02-01

    In a recent paper, Yang et al. (Quant. Inf. Process. 13(9), 2007-2016, 2014) analyzed the security of one-time proxy signature scheme Wang and Wei (Quant. Inf. Process. 11(2), 455-463, 2012) and pointed out that it cannot satisfy the security requirements of unforgeability and undeniability because an eavesdropper Eve can forge a valid proxy signature on a message chosen by herself. However, we find that the so-called proxy message-signature pair forged by Eve is issued by the proxy signer in fact, and anybody can obtain it as a requester, which means that the forgery attack is not considered as a successful attack. Therefore, the conclusion that this scheme cannot satisfy the security requirements of proxy signature against forging and denying is not appropriate in this sense. Finally, we study the reason for the misunderstanding and clarify the security requirements for proxy signatures.

  4. An Analysis of Measured Pressure Signatures From Two Theory-Validation Low-Boom Models

    NASA Technical Reports Server (NTRS)

    Mack, Robert J.

    2003-01-01

    Two wing/fuselage/nacelle/fin concepts were designed to check the validity and the applicability of sonic-boom minimization theory, sonic-boom analysis methods, and low-boom design methodology in use at the end of the 1980is. Models of these concepts were built, and the pressure signatures they generated were measured in the wind-tunnel. The results of these measurements lead to three conclusions: (1) the existing methods could adequately predict sonic-boom characteristics of wing/fuselage/fin(s) configurations if the equivalent area distributions of each component were smooth and continuous; (2) these methods needed revision so the engine-nacelle volume and the nacelle-wing interference lift disturbances could be accurately predicted; and (3) current nacelle-configuration integration methods had to be updated. With these changes in place, the existing sonic-boom analysis and minimization methods could be effectively applied to supersonic-cruise concepts for acceptable/tolerable sonic-boom overpressures during cruise.

  5. Multi-Tissue Microarray Analysis Identifies a Molecular Signature of Regeneration

    PubMed Central

    Mercer, Sarah E.; Cheng, Chia-Ho; Atkinson, Donald L.; Krcmery, Jennifer; Guzman, Claudia E.; Kent, David T.; Zukor, Katherine; Marx, Kenneth A.; Odelberg, Shannon J.; Simon, Hans-Georg

    2012-01-01

    The inability to functionally repair tissues that are lost as a consequence of disease or injury remains a significant challenge for regenerative medicine. The molecular and cellular processes involved in complete restoration of tissue architecture and function are expected to be complex and remain largely unknown. Unlike humans, certain salamanders can completely regenerate injured tissues and lost appendages without scar formation. A parsimonious hypothesis would predict that all of these regenerative activities are regulated, at least in part, by a common set of genes. To test this hypothesis and identify genes that might control conserved regenerative processes, we performed a comprehensive microarray analysis of the early regenerative response in five regeneration-competent tissues from the newt Notophthalmus viridescens. Consistent with this hypothesis, we established a molecular signature for regeneration that consists of common genes or gene family members that exhibit dynamic differential regulation during regeneration in multiple tissue types. These genes include members of the matrix metalloproteinase family and its regulators, extracellular matrix components, genes involved in controlling cytoskeleton dynamics, and a variety of immune response factors. Gene Ontology term enrichment analysis validated and supported their functional activities in conserved regenerative processes. Surprisingly, dendrogram clustering and RadViz classification also revealed that each regenerative tissue had its own unique temporal expression profile, pointing to an inherent tissue-specific regenerative gene program. These new findings demand a reconsideration of how we conceptualize regenerative processes and how we devise new strategies for regenerative medicine. PMID:23300656

  6. Vemurafenib resistance signature by proteome analysis offers new strategies and rational therapeutic concepts.

    PubMed

    Paulitschke, Verena; Berger, Walter; Paulitschke, Philipp; Hofstätter, Elisabeth; Knapp, Bernhard; Dingelmaier-Hovorka, Ruth; Födinger, Dagmar; Jäger, Walter; Szekeres, Thomas; Meshcheryakova, Anastasia; Bileck, Andrea; Pirker, Christine; Pehamberger, Hubert; Gerner, Christopher; Kunstfeld, Rainer

    2015-03-01

    The FDA-approved BRAF inhibitor vemurafenib achieves outstanding clinical response rates in patients with melanoma, but early resistance is common. Understanding the pathologic mechanisms of drug resistance and identification of effective therapeutic alternatives are key scientific challenges in the melanoma setting. Using proteomic techniques, including shotgun analysis and 2D-gel electrophoresis, we identified a comprehensive signature of the vemurafenib-resistant M24met in comparison with the vemurafenib-sensitive A375 melanoma cell line. The resistant cells were characterized by loss of differentiation, induction of transformation, enhanced expression of the lysosomal compartment, increased potential for metastasis, migration, adherence and Ca2(+) ion binding, enhanced expression of the MAPK pathway and extracellular matrix proteins, and epithelial-mesenchymal transformation. The main features were verified by shotgun analysis with QEXACTIVE orbitrap MS, electron microscopy, lysosomal staining, Western blotting, and adherence assay in a VM-1 melanoma cell line with acquired vemurafenib resistance. On the basis of the resistance profile, we were able to successfully predict that a novel resveratrol-derived COX-2 inhibitor, M8, would be active against the vemurafenib-resistant but not the vemurafenib-sensitive melanoma cells. Using high-throughput methods for cell line and drug characterization may thus offer a new way to identify key features of vemurafenib resistance, facilitating the design of effective rational therapeutic alternatives. PMID:25612618

  7. Uncertainty in hydrological signatures

    NASA Astrophysics Data System (ADS)

    Westerberg, I. K.; McMillan, H. K.

    2015-09-01

    Information about rainfall-runoff processes is essential for hydrological analyses, modelling and water-management applications. A hydrological, or diagnostic, signature quantifies such information from observed data as an index value. Signatures are widely used, e.g. for catchment classification, model calibration and change detection. Uncertainties in the observed data - including measurement inaccuracy and representativeness as well as errors relating to data management - propagate to the signature values and reduce their information content. Subjective choices in the calculation method are a further source of uncertainty. We review the uncertainties relevant to different signatures based on rainfall and flow data. We propose a generally applicable method to calculate these uncertainties based on Monte Carlo sampling and demonstrate it in two catchments for common signatures including rainfall-runoff thresholds, recession analysis and basic descriptive signatures of flow distribution and dynamics. Our intention is to contribute to awareness and knowledge of signature uncertainty, including typical sources, magnitude and methods for its assessment. We found that the uncertainties were often large (i.e. typical intervals of ±10-40 % relative uncertainty) and highly variable between signatures. There was greater uncertainty in signatures that use high-frequency responses, small data subsets, or subsets prone to measurement errors. There was lower uncertainty in signatures that use spatial or temporal averages. Some signatures were sensitive to particular uncertainty types such as rating-curve form. We found that signatures can be designed to be robust to some uncertainty sources. Signature uncertainties of the magnitudes we found have the potential to change the conclusions of hydrological and ecohydrological analyses, such as cross-catchment comparisons or inferences about dominant processes.

  8. Uncertainty in hydrological signatures

    NASA Astrophysics Data System (ADS)

    Westerberg, I. K.; McMillan, H. K.

    2015-04-01

    Information about rainfall-runoff processes is essential for hydrological analyses, modelling and water-management applications. A hydrological, or diagnostic, signature quantifies such information from observed data as an index value. Signatures are widely used, including for catchment classification, model calibration and change detection. Uncertainties in the observed data - including measurement inaccuracy and representativeness as well as errors relating to data management - propagate to the signature values and reduce their information content. Subjective choices in the calculation method are a further source of uncertainty. We review the uncertainties relevant to different signatures based on rainfall and flow data. We propose a generally applicable method to calculate these uncertainties based on Monte Carlo sampling and demonstrate it in two catchments for common signatures including rainfall-runoff thresholds, recession analysis and basic descriptive signatures of flow distribution and dynamics. Our intention is to contribute to awareness and knowledge of signature uncertainty, including typical sources, magnitude and methods for its assessment. We found that the uncertainties were often large (i.e. typical intervals of ±10-40% relative uncertainty) and highly variable between signatures. There was greater uncertainty in signatures that use high-frequency responses, small data subsets, or subsets prone to measurement errors. There was lower uncertainty in signatures that use spatial or temporal averages. Some signatures were sensitive to particular uncertainty types such as rating-curve form. We found that signatures can be designed to be robust to some uncertainty sources. Signature uncertainties of the magnitudes we found have the potential to change the conclusions of hydrological and ecohydrological analyses, such as cross-catchment comparisons or inferences about dominant processes.

  9. Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers

    PubMed Central

    Wang, I-Ming; Zhang, Bin; Yang, Xia; Zhu, Jun; Stepaniants, Serguei; Zhang, Chunsheng; Meng, Qingying; Peters, Mette; He, Yudong; Ni, Chester; Slipetz, Deborah; Crackower, Michael A; Houshyar, Hani; Tan, Christopher M; Asante-Appiah, Ernest; O'Neill, Gary; Jane Luo, Mingjuan; Thieringer, Rolf; Yuan, Jeffrey; Chiu, Chi-Sung; Yee Lum, Pek; Lamb, John; Boie, Yves; Wilkinson, Hilary A; Schadt, Eric E; Dai, Hongyue; Roberts, Christopher

    2012-01-01

    Common inflammatome gene signatures as well as disease-specific signatures were identified by analyzing 12 expression profiling data sets derived from 9 different tissues isolated from 11 rodent inflammatory disease models. The inflammatome signature significantly overlaps with known drug targets and co-expressed gene modules linked to metabolic disorders and cancer. A large proportion of genes in this signature are tightly connected in tissue-specific Bayesian networks (BNs) built from multiple independent mouse and human cohorts. Both the inflammatome signature and the corresponding consensus BNs are highly enriched for immune response-related genes supported as causal for adiposity, adipokine, diabetes, aortic lesion, bone, muscle, and cholesterol traits, suggesting the causal nature of the inflammatome for a variety of diseases. Integration of this inflammatome signature with the BNs uncovered 151 key drivers that appeared to be more biologically important than the non-drivers in terms of their impact on disease phenotypes. The identification of this inflammatome signature, its network architecture, and key drivers not only highlights the shared etiology but also pinpoints potential targets for intervention of various common diseases. PMID:22806142

  10. Analysis of Chiral Carboxylic Acids in Meteorites

    NASA Technical Reports Server (NTRS)

    Burton, A. S.; Elsila, J. E.; Hein, J. E.; Aponte, J. C.; Parker, E. T.; Glavin, D. P.; Dworkin, J. P.

    2015-01-01

    our efforts to develop highly sensitive LC-MS methods for the analysis of chiral carboxylic acids including hydroxy acids.

  11. Amino acid analysis for pharmacopoeial purposes.

    PubMed

    Wahl, Oliver; Holzgrabe, Ulrike

    2016-07-01

    The impurity profile of amino acids depends strongly on the production process. Since there are many different production methods (e.g. fermentation, protein hydrolysis or chemical synthesis) universal, state of the art methods are required to determine the impurity profile of amino acids produced by all relevant competitors. At the moment TLC tests provided by the Ph. Eur. are being replaced by a very specific amino acid analysis procedure possibly missing out on currently unknown process related impurities. Production methods and possible impurities as well as separation and detection methods suitable for said impurities are subject to this review. PMID:27154660

  12. Trophic Hierarchies Illuminated via Amino Acid Isotopic Analysis

    PubMed Central

    Steffan, Shawn A.; Chikaraishi, Yoshito; Horton, David R.; Ohkouchi, Naohiko; Singleton, Merritt E.; Miliczky, Eugene; Hogg, David B.; Jones, Vincent P.

    2013-01-01

    Food web ecologists have long sought to characterize the trophic niches of animals using stable isotopic analysis. However, distilling trophic position from isotopic composition has been difficult, largely because of the variability associated with trophic discrimination factors (inter-trophic isotopic fractionation and routing). We circumvented much of this variability using compound-specific isotopic analysis (CSIA). We examined the 15N signatures of amino acids extracted from organisms reared in pure culture at four discrete trophic levels, across two model communities. We calculated the degree of enrichment at each trophic level and found there was a consistent trophic discrimination factor (~7.6‰). The constancy of the CSIA-derived discrimination factor permitted unprecedented accuracy in the measurement of animal trophic position. Conversely, trophic position estimates generated via bulk-15N analysis significantly underestimated trophic position, particularly among higher-order consumers. We then examined the trophic hierarchy of a free-roaming arthropod community, revealing the highest trophic position (5.07) and longest food chain ever reported using CSIA. High accuracy in trophic position estimation brings trophic function into sharper focus, providing greater resolution to the analysis of food webs. PMID:24086703

  13. Integrative radiogenomic analysis for genomic signatures in glioblastomas presenting leptomeningeal dissemination.

    PubMed

    You, Hye Jin; Park, Ho-Young; Kim, Jinkuk; Lee, In-Hee; Seol, Ho Jun; Lee, Jung-Il; Kim, Sung Tae; Kong, Doo-Sik; Nam, Do-Hyun

    2016-07-01

    Despite therapeutic advances, the prognosis for glioblastoma (GBM) remains poor. In particular, leptomeningeal dissemination (LMD) has a dismal prognosis. The aim of this study was to identify tumor molecular phenotype, which has a great propensity to develop LMD. Between May 2004 and December 2012, a total of 145 GBM tumor samples were obtained from data registry. A total of 20 of the 145 patients with GBM were found to develop LMD. A specialized radiologist confirmed the diagnosis of LMD on magnetic resonance imaging. To clarify the genomic signatures in GBM with LMD, we performed integrative analysis of whole transcriptome sequencing and copy number alteration in the radiological features indicating LMD phenotypes in GBM. Eleven newly diagnosed patients with GBM with LMD had worse prognosis than those without LMD (median 5.55 vs. 12.94 months, P < 0.0001). Integrating analysis using gene expression based on the change of copy number revealed that SPOCK1, EHD2, SLC2A3, and ANXA11 were highly expressed with the gain of copy number, compared with the gene expression in the non-LMD group. In addition, it was demonstrated that NME2, TMEM100, and SIVA1 were downregulated with the loss of copy number. We also found that mesenchymal subtype accounted for 50% in LMD group, whereas mesenchymal subtype consisted of 29% in non-LMD group, even though there was no statistical significance (P = 0.06). Through this radiogenomic analysis, we suggested the possibility of finding candidate genes associated with LMD and highlighted the significance of integrating approach to clarify the molecular characteristics in LMD. PMID:27399113

  14. Comparative analysis of viral RNA signatures on different RIG-I-like receptors

    PubMed Central

    Sanchez David, Raul Y; Combredet, Chantal; Sismeiro, Odile; Dillies, Marie-Agnès; Jagla, Bernd; Coppée, Jean-Yves; Mura, Marie; Guerbois Galla, Mathilde; Despres, Philippe; Tangy, Frédéric; Komarova, Anastassia V

    2016-01-01

    The RIG-I-like receptors (RLRs) play a major role in sensing RNA virus infection to initiate and modulate antiviral immunity. They interact with particular viral RNAs, most of them being still unknown. To decipher the viral RNA signature on RLRs during viral infection, we tagged RLRs (RIG-I, MDA5, LGP2) and applied tagged protein affinity purification followed by next-generation sequencing (NGS) of associated RNA molecules. Two viruses with negative- and positive-sense RNA genome were used: measles (MV) and chikungunya (CHIKV). NGS analysis revealed that distinct regions of MV genome were specifically recognized by distinct RLRs: RIG-I recognized defective interfering genomes, whereas MDA5 and LGP2 specifically bound MV nucleoprotein-coding region. During CHIKV infection, RIG-I associated specifically to the 3’ untranslated region of viral genome. This study provides the first comparative view of the viral RNA ligands for RIG-I, MDA5 and LGP2 in the presence of infection. DOI: http://dx.doi.org/10.7554/eLife.11275.001 PMID:27011352

  15. Analysis of multispectral signatures and investigation of multi-aspect remote sensing techniques

    NASA Technical Reports Server (NTRS)

    Malila, W. A.; Hieber, R. H.; Sarno, J. E.

    1974-01-01

    Two major aspects of remote sensing with multispectral scanners (MSS) are investigated. The first, multispectral signature analysis, includes the effects on classification performance of systematic variations found in the average signals received from various ground covers as well as the prediction of these variations with theoretical models of physical processes. The foremost effects studied are those associated with the time of day airborne MSS data are collected. Six data collection runs made over the same flight line in a period of five hours are analyzed, it is found that the time span significantly affects classification performance. Variations associated with scan angle also are studied. The second major topic of discussion is multi-aspect remote sensing, a new concept in remote sensing with scanners. Here, data are collected on multiple passes by a scanner that can be tilted to scan forward of the aircraft at different angles on different passes. The use of such spatially registered data to achieve improved classification of agricultural scenes is investigated and found promising. Also considered are the possibilities of extracting from multi-aspect data, information on the condition of corn canopies and the stand characteristics of forests.

  16. Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels.

    PubMed

    Baillon, Lucie; Pierron, Fabien; Coudret, Raphaël; Normendeau, Eric; Caron, Antoine; Peluhet, Laurent; Labadie, Pierre; Budzinski, Hélène; Durrieu, Gilles; Sarraco, Jérôme; Elie, Pierre; Couture, Patrice; Baudrimont, Magalie; Bernatchez, Louis

    2015-01-01

    Identifying specific effects of contaminants in a multi-stress field context remain a challenge in ecotoxicology. In this context, "omics" technologies, by allowing the simultaneous measurement of numerous biological endpoints, could help unravel the in situ toxicity of contaminants. In this study, wild Atlantic eels were sampled in 8 sites presenting a broad contamination gradient in France and Canada. The global hepatic transcriptome of animals was determined by RNA-Seq. In parallel, the contamination level of fish to 8 metals and 25 organic pollutants was determined. Factor analysis for multiple testing was used to identify genes that are most likely to be related to a single factor. Among the variables analyzed, arsenic (As), cadmium (Cd), lindane (γ-HCH) and the hepato-somatic index (HSI) were found to be the main factors affecting eel's transcriptome. Genes associated with As exposure were involved in the mechanisms that have been described during As vasculotoxicity in mammals. Genes correlated with Cd were involved in cell cycle and energy metabolism. For γ-HCH, genes were involved in lipolysis and cell growth. Genes associated with HSI were involved in protein, lipid and iron metabolisms. Our study proposes specific gene signatures of pollutants and their impacts in fish exposed to multi-stress conditions. PMID:25258179

  17. Comparative analysis of viral RNA signatures on different RIG-I-like receptors.

    PubMed

    Sanchez David, Raul Y; Combredet, Chantal; Sismeiro, Odile; Dillies, Marie-Agnès; Jagla, Bernd; Coppée, Jean-Yves; Mura, Marie; Guerbois Galla, Mathilde; Despres, Philippe; Tangy, Frédéric; Komarova, Anastassia V

    2016-01-01

    The RIG-I-like receptors (RLRs) play a major role in sensing RNA virus infection to initiate and modulate antiviral immunity. They interact with particular viral RNAs, most of them being still unknown. To decipher the viral RNA signature on RLRs during viral infection, we tagged RLRs (RIG-I, MDA5, LGP2) and applied tagged protein affinity purification followed by next-generation sequencing (NGS) of associated RNA molecules. Two viruses with negative- and positive-sense RNA genome were used: measles (MV) and chikungunya (CHIKV). NGS analysis revealed that distinct regions of MV genome were specifically recognized by distinct RLRs: RIG-I recognized defective interfering genomes, whereas MDA5 and LGP2 specifically bound MV nucleoprotein-coding region. During CHIKV infection, RIG-I associated specifically to the 3' untranslated region of viral genome. This study provides the first comparative view of the viral RNA ligands for RIG-I, MDA5 and LGP2 in the presence of infection. PMID:27011352

  18. Petrographic correlations and mathematical analysis of log signatures for clay identification

    SciTech Connect

    Sharma, B.

    1992-04-01

    This report presents the results of correlation of log signature with information on distribution of the types and volumes of clays in the sandstone pore spaces determined from detailed CT-scan, XRD, SEM and thin section analyses of core samples from three sandstone reservoirs. The log signatures are then analyzed to determine if suitable mathematical/statistical parameter(s) could be calculated from the logs for identification of types and volumes of clays in sandstone reservoirs.

  19. Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

    PubMed

    Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

    2016-07-01

    Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease. PMID:27060756

  20. A Meta-analysis of Gene Expression Signatures of Blood Pressure and Hypertension

    PubMed Central

    Chen, Brian H.; Liu, Chunyu; Joehanes, Roby; Johnson, Andrew D.; Yao, Chen; Ying, Sai-xia; Courchesne, Paul; Milani, Lili; Raghavachari, Nalini; Wang, Richard; Liu, Poching; Reinmaa, Eva; Dehghan, Abbas; Hofman, Albert; Uitterlinden, André G.; Hernandez, Dena G.; Bandinelli, Stefania; Singleton, Andrew; Melzer, David; Metspalu, Andres; Carstensen, Maren; Grallert, Harald; Herder, Christian; Meitinger, Thomas; Peters, Annette; Roden, Michael; Waldenberger, Melanie; Dörr, Marcus; Felix, Stephan B.; Zeller, Tanja; Vasan, Ramachandran; O'Donnell, Christopher J.; Munson, Peter J.; Yang, Xia; Prokisch, Holger; Völker, Uwe; van Meurs, Joyce B. J.; Ferrucci, Luigi; Levy, Daniel

    2015-01-01

    Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not receiving antihypertensive drug treatment. We identified 34 genes that were differentially expressed in relation to BP (Bonferroni-corrected p<0.05). Among these genes, FOS and PTGS2 have been previously reported to be involved in BP-related processes; the others are novel. The top BP signature genes in aggregate explain 5%–9% of inter-individual variance in BP. Of note, rs3184504 in SH2B3, which was also reported in GWAS to be associated with BP, was found to be a trans regulator of the expression of 6 of the transcripts we found to be associated with BP (FOS, MYADM, PP1R15A, TAGAP, S100A10, and FGBP2). Gene set enrichment analysis suggested that the BP-related global gene expression changes include genes involved in inflammatory response and apoptosis pathways. Our study provides new insights into molecular mechanisms underlying BP regulation, and suggests novel transcriptomic markers for the treatment and prevention of hypertension. PMID:25785607

  1. A meta-analysis of gene expression signatures of blood pressure and hypertension.

    PubMed

    Huan, Tianxiao; Esko, Tõnu; Peters, Marjolein J; Pilling, Luke C; Schramm, Katharina; Schurmann, Claudia; Chen, Brian H; Liu, Chunyu; Joehanes, Roby; Johnson, Andrew D; Yao, Chen; Ying, Sai-Xia; Courchesne, Paul; Milani, Lili; Raghavachari, Nalini; Wang, Richard; Liu, Poching; Reinmaa, Eva; Dehghan, Abbas; Hofman, Albert; Uitterlinden, André G; Hernandez, Dena G; Bandinelli, Stefania; Singleton, Andrew; Melzer, David; Metspalu, Andres; Carstensen, Maren; Grallert, Harald; Herder, Christian; Meitinger, Thomas; Peters, Annette; Roden, Michael; Waldenberger, Melanie; Dörr, Marcus; Felix, Stephan B; Zeller, Tanja; Vasan, Ramachandran; O'Donnell, Christopher J; Munson, Peter J; Yang, Xia; Prokisch, Holger; Völker, Uwe; van Meurs, Joyce B J; Ferrucci, Luigi; Levy, Daniel

    2015-03-01

    Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not receiving antihypertensive drug treatment. We identified 34 genes that were differentially expressed in relation to BP (Bonferroni-corrected p<0.05). Among these genes, FOS and PTGS2 have been previously reported to be involved in BP-related processes; the others are novel. The top BP signature genes in aggregate explain 5%-9% of inter-individual variance in BP. Of note, rs3184504 in SH2B3, which was also reported in GWAS to be associated with BP, was found to be a trans regulator of the expression of 6 of the transcripts we found to be associated with BP (FOS, MYADM, PP1R15A, TAGAP, S100A10, and FGBP2). Gene set enrichment analysis suggested that the BP-related global gene expression changes include genes involved in inflammatory response and apoptosis pathways. Our study provides new insights into molecular mechanisms underlying BP regulation, and suggests novel transcriptomic markers for the treatment and prevention of hypertension. PMID:25785607

  2. Vibrational analysis of α-cyanohydroxycinnamic acid

    NASA Astrophysics Data System (ADS)

    Mojica, Elmer-Rico E.; Vedad, Jayson; Desamero, Ruel Z. B.

    2015-08-01

    In the present study, a comparative Raman vibrational analysis of alpha-cyano-4-hydroxycinnamic acid (4CHCA) and its derivative, alpha-cyano-3-hydroxycinnamic acid (3CHCA), was performed. The Raman spectra of the 4CHCA and 3CHCA in solid form were obtained and analyzed to determine differences between the two structurally similar derivatives. For comparison, the CHCA derivatives cyanocinnamic acid (CCA) and coumaric acid (CA) were also studied. The plausible vibrational assignments were made and matched with those obtained theoretically using density functional theory (DFT) based method employing a 6-31 g basis set. The computational wavenumbers obtained were in good agreement with the observed experimental results. This was the first reported Raman study of CCA, 3CHCA and 4CHCA.

  3. Entropy based analysis of satellite magnetic data for searching possible e.m. signatures due to big earthquakes

    NASA Astrophysics Data System (ADS)

    Cianchini, G.; de Santis, A.; Balasis, G.; Mandea, M.; Qamili, E.

    2009-04-01

    The importance of detecting possible electromagnetic signatures due to big earthquakes is self-evident, signatures which can be either anticipating, simultaneous or subsequent with respect to the main shock. Taking advantage of the present orbiting Champ satellite, we apply two "ad hoc" techniques both based on the Information Theory (after the seminal monography by Shannon, 1948) to the satellite magnetic data with the aim at extracting eventual time anomalies. These techniques have different time-space resolutions: the first technique requires a preliminary spherical harmonic analysis of daily magnetic data and, potentially, detects long-wavelength variations, while the second uses a preliminary wavelet analysis and can detect shorter-wavelength anomalies. Some examples are given for magnetic satellite data taken in correspondence with the two big earthquakes occurred in the Sumatra region on 24 December 2004 (M=9.1) and 28 March 2005 (M=8.6).

  4. Modeling and Analysis of Scatterometry Signatures for Optical Critical Dimension Reference Material Applications

    NASA Astrophysics Data System (ADS)

    Patrick, Heather J.; Germer, Thomas A.; Cresswell, Michael W.; Allen, Richard A.; Dixson, Ronald G.; Bishop, Michael

    2007-09-01

    We use an optical critical dimension (OCD) technique, matching modeled to measured scatterometry signatures, to obtain critical dimension linewidth of lines in grating targets fabricated on SIMOX (separation by implantation of oxygen) substrates using the single-crystal critical dimension reference materials (SCCDRM) process. We first compare experimentally obtained reflectance signatures for areas of the unpatterned substrate with signatures modeled using Fresnel theory, and show that the buried oxide (BOX) layer of the SIMOX is not well described optically by a single homogeneous layer of SiO2, but can be so described if a mixed Si-SiO2 boundary layer is included between the Si wafer and the BOX layer. We then obtain linewidths from OCD measurements on a series of grating targets with a range of design linewidths and pitches, and show that the linewidth obtained from the OCD technique is linearly related to the linewidth obtained from scanning electron microscopy (SEM), with a slope near unity and zero offset. While these results are very promising, further work in improving the fit of the simulated signatures to the measured signatures for some of the targets, reducing the target line roughness, and analyzing the uncertainties for potential optical critical dimension reference materials, is anticipated.

  5. Focused and Steady-State Characteristics of Shaped Sonic Boom Signatures: Prediction and Analysis

    NASA Technical Reports Server (NTRS)

    Maglieri, Domenic J.; Bobbitt, Percy J.; Massey, Steven J.; Plotkin, Kenneth J.; Kandil, Osama A.; Zheng, Xudong

    2011-01-01

    The objective of this study is to examine the effect of flight, at off-design conditions, on the propagated sonic boom pressure signatures of a small "low-boom" supersonic aircraft. The amplification, or focusing, of the low magnitude "shaped" signatures produced by maneuvers such as the accelerations from transonic to supersonic speeds, climbs, turns, pull-up and pushovers is the concern. To analyze these effects, new and/or improved theoretical tools have been developed, in addition to the use of existing methodology. Several shaped signatures are considered in the application of these tools to the study of selected maneuvers and off-design conditions. The results of these applications are reported in this paper as well as the details of the new analytical tools. Finally, the magnitude of the focused boom problem for "low boom" supersonic aircraft designs has been more accurately quantified and potential "mitigations" suggested. In general, "shaped boom" signatures, designed for cruise flight, such as asymmetric and symmetric flat-top and initial-shock ramp waveforms retain their basic shape during transition flight. Complex and asymmetric and symmetric initial shock ramp waveforms provide lower magnitude focus boom levels than N-waves or asymmetric and symmetric flat-top signatures.

  6. Analysis of recombinase A (recA/RecA) in the actinobacterial family Streptosporangiaceae and identification of molecular signatures.

    PubMed

    Meyers, Paul R

    2015-12-01

    The family Streptosporangiaceae (suborder Streptosporangineae) comprises 13 genera and 100 species with validly published names. In a recent study, gyrB gene sequences were obtained for members of the family Streptosporangiaceae and the GyrB amino acid sequences were analysed for molecular signatures. In this study, recA gene sequences (895nt) were determined for the type strains of members of the family Streptosporangiaceae. The sequences used represent 81% of the full-length recA gene of Streptosporangium roseum DSM 43021(T). The recA gene sequences were used for phylogenetic analyses and the trees were compared to the corresponding 16S-rRNA and gyrB gene trees. RecA amino acid alignments (298 amino acids) were generated and inspected for unique amino acid signatures to distinguish the genera in the family from each other. As was observed for the gyrB gene trees, the recA gene trees generally supported the division of the members of the family Streptosporangiaceae into 13 genera. The genus Nonomuraea was not monophyletic in any of the recA gene trees, while the genera Planomonospora and Streptosporangium were not monophyletic in the maximum likelihood and maximum parsimony trees. The gyrB-recA concatenated-gene tree was more robust than the recA gene tree, with 63 nodes in the gyrB-recA tree having bootstrap values ≥95%. The only insertions in the recA gene sequences were inteins identified in the type strains of Acrocarpospora phusangensis, Acrocarpospora pleiomorpha and Microbispora mesophila. Examination of the RecA sequence alignments for genus-specific amino acid sequences showed that the genera Herbidospora, Planobispora, Planomonospora and Streptosporangium contain unique amino acid sequences that distinguish these genera from all other genera in the family Streptosporangiaceae. The results of this investigation extend the results of the GyrB study and will be useful in future taxonomic studies in the family Streptosporangiaceae by providing additional

  7. Signature control

    NASA Astrophysics Data System (ADS)

    Pyati, Vittal P.

    The reduction of vehicle radar signature is accomplished by means of vehicle shaping, the use of microwave frequencies-absorbent materials, and either passive or active cancellation techniques; such techniques are also useful in the reduction of propulsion system-associated IR emissions. In some anticipated scenarios, the objective is not signature-reduction but signature control, for deception, via decoy vehicles that mimic the signature characteristics of actual weapons systems. As the stealthiness of airframes and missiles increases, their propulsion systems' exhaust plumes assume a more important role in detection by an adversary.

  8. Are there molecular signatures?

    SciTech Connect

    Bennett, W.P.

    1995-10-01

    This report describes molecular signatures and mutational spectrum analysis. The mutation spectrum is defined as the type and location of DNA base change. There are currently about five well documented cases. Mutations and radon-associated tumors are discussed.

  9. Ontology based molecular signatures for immune cell types via gene expression analysis

    PubMed Central

    2013-01-01

    Background New technologies are focusing on characterizing cell types to better understand their heterogeneity. With large volumes of cellular data being generated, innovative methods are needed to structure the resulting data analyses. Here, we describe an ‘Ontologically BAsed Molecular Signature’ (OBAMS) method that identifies novel cellular biomarkers and infers biological functions as characteristics of particular cell types. This method finds molecular signatures for immune cell types based on mapping biological samples to the Cell Ontology (CL) and navigating the space of all possible pairwise comparisons between cell types to find genes whose expression is core to a particular cell type’s identity. Results We illustrate this ontological approach by evaluating expression data available from the Immunological Genome project (IGP) to identify unique biomarkers of mature B cell subtypes. We find that using OBAMS, candidate biomarkers can be identified at every strata of cellular identity from broad classifications to very granular. Furthermore, we show that Gene Ontology can be used to cluster cell types by shared biological processes in order to find candidate genes responsible for somatic hypermutation in germinal center B cells. Moreover, through in silico experiments based on this approach, we have identified genes sets that represent genes overexpressed in germinal center B cells and identify genes uniquely expressed in these B cells compared to other B cell types. Conclusions This work demonstrates the utility of incorporating structured ontological knowledge into biological data analysis – providing a new method for defining novel biomarkers and providing an opportunity for new biological insights. PMID:24004649

  10. Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing

    PubMed Central

    Sánchez-León, Nidia; Arteaga-Vázquez, Mario; Alvarez-Mejía, César; Mendiola-Soto, Javier; Durán-Figueroa, Noé; Rodríguez-Leal, Daniel; Rodríguez-Arévalo, Isaac; García-Campayo, Vicenta; García-Aguilar, Marcelina; Olmedo-Monfil, Vianey; Arteaga-Sánchez, Mario; Martínez de la Vega, Octavio; Nobuta, Kan; Vemaraju, Kalyan; Meyers, Blake C.; Vielle-Calzada, Jean-Philippe

    2012-01-01

    The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies. PMID:22442422

  11. Structural Monitoring of a Weapons Test Unit Using Imaging Methods for Dynamic Signature Analysis

    SciTech Connect

    Jensen, S A; Malsbury, T N; Leach Jr., R R; Tsap, L V

    2004-09-23

    A methodology to identify structural changes in weapons systems during environmental tests is being developed at Lawrence Livermore National Laboratory. The method is coherence based and relies on comparing the ''dynamic signature'' response of the test article before and after an environmental test or test series. Physical changes in the test article result in changes in the dynamic signature and are mapped to an image matrix where a color scale represents changes in sensor-to-sensor coherence. This methodology is convenient because it allows an image to represent large amounts of information in a very compact form, where even subtle system changes may be easily and quickly identified. Furthermore, comparison of the dynamic signature response data before and after any test event can be made on a quasi-real-time basis. This approach is particularly useful on large and/or complex test articles where many sensors are present, and large volumes of data are generated.

  12. Paired-end genomic signature tags: a method for the functional analysis of genomes and epigenomes.

    PubMed

    Dunn, John J; McCorkle, Sean R; Everett, Logan; Anderson, Carl W

    2007-01-01

    Because paired-end genomic signature tags are sequenced-based, they have the potential to become an alternate tool to tiled microarray hybridization as a method for genome-wide localization of transcription factors and other sequence-specific DNA binding proteins. As outlined here the method also can be used for global analysis of DNA methylation. One advantage of this approach is the ability to easily switch between different genome types without having to fabricate a new microarray for each and every DNA type. However, the method does have some disadvantages. Among the most rate-limiting steps of our PE-GST protocol are the need to concatemerize the diTAGs, size fractionate them and then clone them prior to sequencing. This is usually followed by additional steps to amplify and size select for long (> or = 500) concatemer inserts prior to sequencing. These time-consuming steps are important for standard DNA sequencing as they increase efficiency approximately 20-30-fold since each amplified concatemer can now provide information on multiple tags; the limitation on data acqui- sition is read length during sequencing. However, the development of new sequencing methods such as Life Sciences' 454 new nanotechnology-based sequencing instrument (41) could increase tag sequencing efficiency by several orders of magnitude (> or = 100,000 diTAG reads/run), which is sufficient to provide in-depth global analysis of all ChIP PE-GSTs in a single run. This is because the lengths of our paired-end diTAGs (approximately 60 bp) fall well within the region of high accuracy for read lengths on this instrument. In principle, sequence analysis of diTAGs could begin as soon as they are generated, thereby completely bypassing the need for the concatemerization, sizing, downstream cloning steps and sequencing template purification. In addition, our protocol places any one of several unique four-base long nucleotide sequences, such as GATC, between each and every diTAG pair, which could

  13. Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis

    PubMed Central

    Zhang, Yuanhao; Rowehl, Leahana; Krumsiek, Julia M.; Orner, Erika P.; Shaikh, Nurmohammad; Tarr, Phillip I.; Sodergren, Erica; Weinstock, George M.; Boedeker, Edgar C.; Xiong, Xuejian; Parkinson, John; Frank, Daniel N.; Li, Ellen; Gathungu, Grace

    2015-01-01

    Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently within mucosal lesions of patients with Crohn’s disease (CD). The AIEC phenotype consists of adherence and invasion of intestinal epithelial cells and survival within macrophages of these bacteria in vitro. Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth. Differential expression analysis of coding sequences (CDS) homologous to both strains demonstrated 224 and 241 genes with increased and decreased expression, respectively, in LF82 relative to HS. Transition metal transport and siderophore metabolism related pathway genes were up-regulated, while glycogen metabolic and oxidation-reduction related pathway genes were down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82 during the exponential phase, but flagellum-dependent motility pathway genes were down-regulated in LF82 during the stationary phase. CDS that mapped only to the LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics approach to identify CDS specific to AIEC by incorporating the genomes of 10 other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 genome and lacked homology to any of the 11 human NIEC strains. We compared these CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci belonging to clustered regularly interspaced short palindromic repeats region (CRISPR)—CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent from all non-pathogenic bacteria. As previously reported, AIEC strains were enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 AIEC strains. Reverse transcription

  14. Determination of spectral signatures of substances in natural waters

    NASA Technical Reports Server (NTRS)

    Klemas, V.; Philpot, W. D.; Davis, G.

    1978-01-01

    Optical remote sensing of water pollution offers the possibility of fast, large scale coverage at a relatively low cost. The possibility of using the spectral characteristics of the upwelling light from water for the purpose of ocean water quality monitoring was explained. The work was broken into several broad tasks as follows: (1) definition of a remotely measured spectral signature of water, (2) collection of field data and testing of the signature analysis, and (3) the possibility of using LANDSAT data for the identification of substances in water. An attempt to extract spectral signatures of acid waste and sediment was successful.

  15. Proteomic Analysis of MG132-Treated Germinating Pollen Reveals Expression Signatures Associated with Proteasome Inhibition

    PubMed Central

    Vannini, Candida; Bracale, Marcella; Crinelli, Rita; Marconi, Valerio; Campomenosi, Paola; Marsoni, Milena; Scoccianti, Valeria

    2014-01-01

    Chemical inhibition of the proteasome has been previously found to effectively impair pollen germination and tube growth in vitro. However, the mediators of these effects at the molecular level are unknown. By performing 2DE proteomic analysis, 24 differentially expressed protein spots, representing 14 unique candidate proteins, were identified in the pollen of kiwifruit (Actinidia deliciosa) germinated in the presence of the MG132 proteasome inhibitor. qPCR analysis revealed that 11 of these proteins are not up-regulated at the mRNA level, but are most likely stabilized by proteasome inhibition. These differentially expressed proteins are predicted to function in various pathways including energy and lipid metabolism, cell wall synthesis, protein synthesis/degradation and stress responses. In line with this evidence, the MG132-induced changes in the proteome were accompanied by an increase in ATP and ROS content and by an alteration in fatty acid composition. PMID:25265451

  16. Application of signature analysis for determining the operational readiness of motor-operated valves under blowdown test conditions

    SciTech Connect

    Haynes, H.D.

    1988-01-01

    In support of the NRC-funded Nuclear Plant Aging Research (NPAR) program, Oak Ridge National Laboratory (ORNL) has carried out a comprehensive aging assessment of Motor-Operated Valves (MOVs). As part of this work, ORNL participated in the Gate Valve Flow Interruption Blowdown (GVFIB) tests carried out in Huntsville, Alabama. The GVFIB tests were intended primarily to determine the behavior of motor-operated gate valves under the temperature, pressure, and flow conditions expected to be experienced by isolation valves in Boiling Water Reactors (BWRs) during a high energy line break (blowdown) outside of containment. In addition, the tests provided an excellent opportunity to evaluate signature analysis methods for determining the operational readiness of the MOVs under those accident conditions. ORNL acquired motor current and torque switch shaft angular position data on two test MOVs during various times of the GVFIB tests. The reduction in operating ''margin'' of both MOVs due to the presence of additional valve running loads imposed by high flow was clearly observed in motor current and torque switch angular position signatures. In addition, the effects of differential pressure, fluid temperature, and line voltage on MOV operations were observed and more clearly understood as a result of utilizing signature analysis techniques. 1 ref.; 16 figs.

  17. Component-Level Electronic-Assembly Repair (CLEAR) Spacecraft Circuit Diagnostics by Analog and Complex Signature Analysis

    NASA Technical Reports Server (NTRS)

    Oeftering, Richard C.; Wade, Raymond P.; Izadnegahdar, Alain

    2011-01-01

    The Component-Level Electronic-Assembly Repair (CLEAR) project at the NASA Glenn Research Center is aimed at developing technologies that will enable space-flight crews to perform in situ component-level repair of electronics on Moon and Mars outposts, where there is no existing infrastructure for logistics spares. These technologies must provide effective repair capabilities yet meet the payload and operational constraints of space facilities. Effective repair depends on a diagnostic capability that is versatile but easy to use by crew members that have limited training in electronics. CLEAR studied two techniques that involve extensive precharacterization of "known good" circuits to produce graphical signatures that provide an easy-to-use comparison method to quickly identify faulty components. Analog Signature Analysis (ASA) allows relatively rapid diagnostics of complex electronics by technicians with limited experience. Because of frequency limits and the growing dependence on broadband technologies, ASA must be augmented with other capabilities. To meet this challenge while preserving ease of use, CLEAR proposed an alternative called Complex Signature Analysis (CSA). Tests of ASA and CSA were used to compare capabilities and to determine if the techniques provided an overlapping or complementary capability. The results showed that the methods are complementary.

  18. Crystal structure analysis of a bacterial aryl acylamidase belonging to the amidase signature enzyme family.

    PubMed

    Lee, Saeyoung; Park, Eun-Hye; Ko, Hyeok-Jin; Bang, Won Gi; Kim, Hye-Yeon; Kim, Kyoung Heon; Choi, In-Geol

    2015-11-13

    The atomic structure of a bacterial aryl acylamidase (EC 3.5.1.13; AAA) is reported and structural features are investigated to better understand the catalytic profile of this enzyme. Structures of AAA were determined in its native form and in complex with the analgesic acetanilide, p-acetaminophenol, at 1.70 Å and 1.73 Å resolutions, respectively. The overall structural fold of AAA was identified as an α/β fold class, exhibiting an open twisted β-sheet core surrounded by α-helices. The asymmetric unit contains one AAA molecule and the monomeric form is functionally active. The core structure enclosing the signature sequence region, including the canonical Ser-cisSer-Lys catalytic triad, is conserved in all members of the Amidase Signature enzyme family. The structure of AAA in a complex with its ligand reveals a unique organization in the substrate-binding pocket. The binding pocket consists of two loops (loop1 and loop2) in the amidase signature sequence and one helix (α10) in the non-amidase signature sequence. We identified two residues (Tyr(136) and Thr(330)) that interact with the ligand via water molecules, and a hydrogen-bonding network that explains the catalytic affinity over various aryl acyl compounds. The optimum activity of AAA at pH > 10 suggests that the reaction mechanism employs Lys(84) as the catalytic base to polarize the Ser(187) nucleophile in the catalytic triad. PMID:26454172

  19. CFD Analysis of Nozzle Jet Plume Effects on Sonic Boom Signature

    NASA Technical Reports Server (NTRS)

    Bui, Trong T.

    2009-01-01

    A computational fluid dynamics study is conducted to examine nozzle exhaust jet plume effects on the Sonic boom signature of a supersonic aircraft. A simplified axisymmetric nozzle geometry, representative of the nozzle on the NASA Dryden NF-15B Lift and Nozzle Change Effects on Tail Shock research airplane, is considered. The computational fluid dynamics code is validated using available wind-tunnel sonic boom experimental data. The effects of grid size, spatial order of accuracy. grid type, and flow viscosity on the accuracy of the predicted sonic boom pressure signature are quantified. Grid lines parallel to the Mach wave direction are found to give the best results. Second-order accurate upwind methods are required as a minimum for accurate sonic boom simulations. The highly underexpanded nozzle flow is found to provide significantly more reduction in the tail shock strength in the sonic boom N-wave pressure signature than perfectly expanded and overexpanded nozzle flows. A tail shock train in the sonic boom signature is observed for the highly underexpanded nozzle flow. Axisymmetric computational fluid dynamics simulations show the flow physics inside the F-15 nozzle to be nonisentropic and complex.

  20. CFD Analysis of Nozzle Jet Plume Effects on Sonic Boom Signature

    NASA Technical Reports Server (NTRS)

    Bui, Trong T.

    2009-01-01

    An axisymmetric full Navier-Stokes computational fluid dynamics study is conducted to examine nozzle exhaust jet plume effects on the sonic boom signature of a supersonic aircraft. A simplified axisymmetric nozzle geometry, representative of the nozzle on the NASA Dryden NF-15B Lift and Nozzle Change Effects on Tail Shock research airplane, is considered. The computational fluid dynamics code is validated using available wind-tunnel sonic boom experimental data. The effects of grid size, spatial order of accuracy, grid type, and flow viscosity on the accuracy of the predicted sonic boom pressure signature are quantified. Grid lines parallel to the Mach wave direction are found to give the best results. Second-order accurate upwind methods are required as a minimum for accurate sonic boom simulations. The highly underexpanded nozzle flow is found to provide significantly more reduction in the tail shock strength in the sonic boom N-wave pressure signature than perfectly expanded and overexpanded nozzle flows. A tail shock train in the sonic boom signature is observed for the highly underexpanded nozzle flow. Axisymmetric computational fluid dynamics simulations show the flow physics inside the F-15 nozzle to be nonisentropic and complex. Although the one-dimensional isentropic nozzle plume results look reasonable, they fail to capture the sonic boom shock train in the highly underexpanded nozzle flow.

  1. Selection signature analysis in Holstein cattle identified genes known to affect reproduction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using direct comparison of 45,878 SNPs between a group of Holstein cattle unselected since 1964 and contemporary Holsteins that on average take 30 days longer for successful conception than the 1964 Holsteins, we conducted selection signature analyses to identify genomic regions associated with dair...

  2. Signature extraction of ocean pollutants by eigenvector transformation of remote spectra

    NASA Technical Reports Server (NTRS)

    Grew, G. W.

    1978-01-01

    Spectral signatures of suspended matter in the ocean are being extracted through characteristic vector analysis of remote ocean color data collected with MOCS (Multichannel Ocean Color Sensor). Spectral signatures appear to be obtainable through analyses of 'linear' clusters that appear on scatter diagrams associated with eigenvectors. Signatures associated with acid waste, sewage sludge, oil, and algae are presented. The application of vector analysis to two acid waste dumps overflown two years apart is examined in some detail. The relationships between eigenvectors and spectral signatures for these examples are analyzed. These cases demonstrate the value of characteristic vector analysis in remotely identifying pollutants in the ocean and in determining the consistency of their spectral signatures.

  3. Multi-dimensional reliability assessment of fractal signature analysis in an outpatient sports medicine population.

    PubMed

    Jarraya, Mohamed; Guermazi, Ali; Niu, Jingbo; Duryea, Jeffrey; Lynch, John A; Roemer, Frank W

    2015-11-01

    The aim of this study has been to test reproducibility of fractal signature analysis (FSA) in a young, active patient population taking into account several parameters including intra- and inter-reader placement of regions of interest (ROIs) as well as various aspects of projection geometry. In total, 685 patients were included (135 athletes and 550 non-athletes, 18-36 years old). Regions of interest (ROI) were situated beneath the medial tibial plateau. The reproducibility of texture parameters was evaluated using intraclass correlation coefficients (ICC). Multi-dimensional assessment included: (1) anterior-posterior (A.P.) vs. posterior-anterior (P.A.) (Lyon-Schuss technique) views on 102 knees; (2) unilateral (single knee) vs. bilateral (both knees) acquisition on 27 knees (acquisition technique otherwise identical; same A.P. or P.A. view); (3) repetition of the same image acquisition on 46 knees (same A.P. or P.A. view, and same unitlateral or bilateral acquisition); and (4) intra- and inter-reader reliability with repeated placement of the ROIs in the subchondral bone area on 99 randomly chosen knees. ICC values on the reproducibility of texture parameters for A.P. vs. P.A. image acquisitions for horizontal and vertical dimensions combined were 0.72 (95% confidence interval (CI) 0.70-0.74) ranging from 0.47 to 0.81 for the different dimensions. For unilateral vs. bilateral image acquisitions, the ICCs were 0.79 (95% CI 0.76-0.82) ranging from 0.55 to 0.88. For the repetition of the identical view, the ICCs were 0.82 (95% CI 0.80-0.84) ranging from 0.67 to 0.85. Intra-reader reliability was 0.93 (95% CI 0.92-0.94) and inter-observer reliability was 0.96 (95% CI 0.88-0.99). A decrease in reliability was observed with increasing voxel sizes. Our study confirms excellent intra- and inter-reader reliability for FSA, however, results seem to be affected by acquisition technique, which has not been previously recognized. PMID:26343866

  4. Temporal measurement and analysis of high-resolution spectral signatures of plants and relationships to biophysical characteristics

    NASA Astrophysics Data System (ADS)

    Bostater, Charles R., Jr.; Rebbman, Jan; Hall, Carlton; Provancha, Mark; Vieglais, David

    1995-11-01

    Measurements of temporal reflectance signatures as a function of growing season for sand live oak (Quercus geminata), myrtle oak (Q. myrtifolia, and saw palmetto (Serenoa repens) were collected during a two year study period. Canopy level spectral reflectance signatures, as a function of 252 channels between 368 and 1115 nm, were collected using near nadir viewing geometry and a consistent sun illumination angle. Leaf level reflectance measurements were made in the laboratory using a halogen light source and an environmental optics chamber with a barium sulfate reflectance coating. Spectral measurements were related to several biophysical measurements utilizing optimal passive ambient correlation spectroscopy (OPACS) technique. Biophysical parameters included percent moisture, water potential (MPa), total chlorophyll, and total Kjeldahl nitrogen. Quantitative data processing techniques were used to determine optimal bands based on the utilization of a second order derivative or inflection estimator. An optical cleanup procedure was then employed that computes the double inflection ratio (DIR) spectra for all possible three band combinations normalized to the previously computed optimal bands. These results demonstrate a unique approach to the analysis of high spectral resolution reflectance signatures for estimation of several biophysical measures of plants at the leaf and canopy level from optimally selected bands or bandwidths.

  5. Māori identity signatures: A latent profile analysis of the types of Māori identity.

    PubMed

    Greaves, Lara M; Houkamau, Carla; Sibley, Chris G

    2015-10-01

    Māori are the indigenous peoples of New Zealand. However, the term 'Māori' can refer to a wide range of people of varying ethnic compositions and cultural identity. We present a statistical model identifying 6 distinct types, or 'Māori Identity Signatures,' and estimate their proportion in the Māori population. The model is tested using a Latent Profile Analysis of a national probability sample of 686 Māori drawn from the New Zealand Attitudes and Values Study. We identify 6 distinct signatures: Traditional Essentialists (22.6%), Traditional Inclusives (16%), High Moderates (31.7%), Low Moderates (18.7%), Spiritually Orientated (4.1%), and Disassociated (6.9%). These distinct Identity Signatures predicted variation in deprivation, age, mixed-ethnic affiliation, and religion. This research presents the first formal statistical model assessing how people's identity as Māori is psychologically structured, documents the relative proportion of these different patterns of structures, and shows that these patterns reliably predict differences in core demographics. We identify a range of patterns of Māori identity far more diverse than has been previously proposed based on qualitative data, and also show that the majority of Māori fit a moderate or traditional identity pattern. The application of our model for studying Māori health and identity development is discussed. PMID:25774895

  6. Design and Signature Analysis of Remote Trace-Gas Identification Methodology Based on Infrared-Terahertz Double-Resonance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Tanner, Elizabeth A.; Phillips, Dane J.; Persons, Christopher M.; De Lucia, Frank C.; Everitt, Henry O.

    2014-11-01

    The practicality of a newly proposed infrared-terahertz (IR-THz) double-resonance (DR) spectroscopic technique for remote trace-gas identification is explored. The strength of the DR signatures depends on known molecular parameters from which a combination of pump-probe transitions may be identified to recognize a specific analyte. Atmospheric pressure broadening of the IR and THz trace-gas spectra relaxes the stringent pump coincidence requirement, allowing many DR signatures to be excited, some of which occur in the favorable atmospheric transmission windows below 500 GHz. By designing the DR spectrometer and performing a detailed signal analysis, the pump-probe power requirements for detecting trace amounts of methyl fluoride, methyl chloride, or methyl bromide may be estimated for distances up to 1 km. The strength of the DR signature increases linearly with pump intensity but only as the square root of the probe power because the received signal is in the Townes noise limit. The concept of a specificity matrix is introduced and used to quantify the recognition specificity and calculate the probability of false positive detection of an interferent.

  7. Developmental and spatial variations in the diet signatures of hyperbenthic shrimp Nauticaris marionis at the Prince Edward Islands based on stable isotope ratios and fatty acid profiles

    NASA Astrophysics Data System (ADS)

    Richoux, Nicole B.; Allan, E. Louise; Froneman, P. William

    2016-04-01

    The caridean shrimp Nauticaris marionis is an ecologically important species in the benthic community around the sub-Antarctic Prince Edward Islands (PEI) as it represents a key prey item for a variety of top predators breeding on the islands. We hypothesized that the diet of N. marionis shifts during its development, and that spatial variability in food availability results in differentiation in the diet signatures of specimens collected from various locations of the shelf waters around the PEI. Specimens were collected from nine stations (depth range 70 to 240 m) around the PEI at inter-island shelf (from west to east: upstream, between and downstream) and nearshore regions during austral autumn 2009. Stable isotope and fatty acid data both revealed spatial and developmental variations in the shrimp diet. Nearshore shrimp were more 13C-enriched than those from the inter-island region, suggesting increased kelp detritus entered the food web in the nearshore regions. The shrimp showed increases in δ13C and δ15N signatures (and trophic position) with an increase in body size, resulting in distinctions between size classes that reflected shifts in their trophic niche through development. The fatty acid profiles similarly indicated distinctions in diet with increased shrimp size (in the deep regions), and spatial variability was evident in relation to region and depth. All shrimp contained large proportions of polyunsaturated and essential fatty acids, indicating that the quality of food consumed was similar between regions despite the diet variability. Our results provide new dietary information about a key species operating near the base of the food web at the highly productive PEI, and show that there were no areas of enhanced nutrition available to the shrimp. As such, there was no nutritional advantage to shrimp inhabiting any specific region around the PEI.

  8. Amino acid binding by the class I aminoacyl-tRNA synthetases: role for a conserved proline in the signature sequence.

    PubMed Central

    Burbaum, J. J.; Schimmel, P.

    1992-01-01

    Although partial or complete three-dimensional structures are known for three Class I aminoacyl-tRNA synthetases, the amino acid-binding sites in these proteins remain poorly characterized. To explore the methionine binding site of Escherichia coli methionyl-tRNA synthetase, we chose to study a specific, randomly generated methionine auxotroph that contains a mutant methionyl-tRNA synthetase whose defect is manifested in an elevated Km for methionine (Barker, D.G., Ebel, J.-P., Jakes, R.C., & Bruton, C.J., 1982, Eur. J. Biochem. 127, 449-457), and employed the polymerase chain reaction to sequence this mutant synthetase directly. We identified a Pro 14 to Ser replacement (P14S), which accounts for a greater than 300-fold elevation in Km for methionine and has little effect on either the Km for ATP or the kcat of the amino acid activation reaction. This mutation destabilizes the protein in vivo, which may partly account for the observed auxotrophy. The altered proline is found in the "signature sequence" of the Class I synthetases and is conserved. This sequence motif is 1 of 2 found in the 10 Class I aminoacyl-tRNA synthetases and, in the known structures, it is in the nucleotide-binding fold as part of a loop between the end of a beta-strand and the start of an alpha-helix. The phenotype of the mutant and the stability and affinity for methionine of the wild-type and mutant enzymes are influenced by the amino acid that is 25 residues beyond the C-terminus of the signature sequence.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1304356

  9. Impact of feeding and short-term temperature stress on the content and isotopic signature of fatty acids, sterols, and alcohols in the scleractinian coral Turbinaria reniformis

    NASA Astrophysics Data System (ADS)

    Tolosa, I.; Treignier, C.; Grover, R.; Ferrier-Pagès, C.

    2011-09-01

    This study assesses the combined effect of feeding and short-term thermal stress on various physiological parameters and on the fatty acid, sterol, and alcohol composition of the scleractinian coral Turbinaria reniformis. The compound-specific carbon isotope composition of the lipids was also measured. Under control conditions (26°C), feeding with Artemia salina significantly increased the symbiont density and chlorophyll content and the growth rates of the corals. It also doubled the concentrations of almost all fatty acid (FA) compounds and increased the n-alcohol and sterol contents. δ13C results showed that the feeding enhancement of FA concentrations occurred either via a direct pathway, for one of the major polyunsaturated fatty acid (PUFA) compounds of the food (18:3n-3 FA), or via an enhancement of photosynthate transfer (indirect pathway), for the other coral FAs. Cholesterol (C27Δ5) was also directly acquired from the food. Thermal stress (31°C) affected corals, but differently according to their feeding status. Chlorophyll, protein content, and maximal photosynthetic efficiency of photosystem II (PSII) decreased to a greater extent in starved corals. In such corals, FA concentrations were reduced by 33%, (especially C16, C18 FAs, and n-3 PUFA) and the sterol content by 27% (especially the C28∆5,22 and C28∆5). The enrichment in the δ13C signature of the storage and structural FAs suggests that they were the main compounds respired during the stress to maintain the coral metabolism. Thermal stress had less effect on the lipid concentrations of fed corals, as only FA levels were reduced by 13%, with no major changes in their isotope carbon signatures. In conclusion, feeding plays an essential role in sustaining T. reniformis metabolism during the thermal stress.

  10. Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif

    PubMed Central

    Gagnon, Keith T.; Zhang, Xinxin; Qu, Guosheng; Biswas, Shyamasri; Suryadi, Jimmy; Brown, Bernard A.; Maxwell, E. Stuart

    2010-01-01

    The archaeal L7Ae and eukaryotic 15.5kD protein homologs are members of the L7Ae/15.5kD protein family that characteristically recognize K-turn motifs found in both archaeal and eukaryotic RNAs. In Archaea, the L7Ae protein uniquely binds the K-loop motif found in box C/D and H/ACA sRNAs, whereas the eukaryotic 15.5kD homolog is unable to recognize this variant K-turn RNA. Comparative sequence and structural analyses, coupled with amino acid replacement experiments, have demonstrated that five amino acids enable the archaeal L7Ae core protein to recognize and bind the K-loop motif. These signature residues are highly conserved in the archaeal L7Ae and eukaryotic 15.5kD homologs, but differ between the two domains of life. Interestingly, loss of K-loop binding by archaeal L7Ae does not disrupt C′/D′ RNP formation or RNA-guided nucleotide modification. L7Ae is still incorporated into the C′/D′ RNP despite its inability to bind the K-loop, thus indicating the importance of protein–protein interactions for RNP assembly and function. Finally, these five signature amino acids are distinct for each of the L7Ae/L30 family members, suggesting an evolutionary continuum of these RNA-binding proteins for recognition of the various K-turn motifs contained in their cognate RNAs. PMID:19926724

  11. An analysis of the structure of Saturn's magnetic field using charged particle absorption signatures

    SciTech Connect

    Chenette, D.L.; Davis, L. Jr.

    1983-06-01

    A technique is derived for determining the structure of Saturn's magnetic field. This technique uses the observed positions of charged particle absorption signatures due to the satellites and rings of Saturn to determine the parameters of an axially symmetric, spherical harmonic model of the magnetic field using the method of least squares. Absorption signatures observed along the Pioneer 11, Voyager 1, and Voyager 2 spacecraft trajectories are used to derive values for the orientation of the magnetic symmetry axis relative to Saturn's axis of rotation, the axial displacement of the center of the magnetic dipole from the center of Saturn, and the magnitude of the external field component. A comparison of these results with the magnetic field model parameters deduced from analyses of magnetometer data supports models which incorporate a northward offset of the dipole center by about 0.05 R(3).

  12. Analysis of the structure of Saturn's magnetic field using charged particle absorption signatures

    SciTech Connect

    Chenette, D.L.; Davis, L. Jr.

    1982-07-01

    A new technique is derived for determining the structure of Saturn's magnetic field. This technique uses the observed positions of charged particle absorption signatures due to the satellites and rings of Saturn to determine the parameters of an axially symmetric, spherical harmonic model of the magnetic field using the method of least squares. Absorption signatures observed along the Pioneer 11, Voyager 1, and Voyager 2 spacecraft trajectories are used to derive values for the orientation of the magnetic symmetry axis relative to Saturn's axis of rotation, the axial displacement of the center of the magnetic dipole from the center of Saturn, and the magnitude of the external field component. Comparing these results with the magnetic field model parameters deduced from analyses of magnetometer data leads us to prefer models that incorporate a northward offset of the dipole center by about 0.05 R/sub s/.

  13. The spectral signature analysis of inland and coastal water bodies acquired from field spectroradiometric measurements

    NASA Astrophysics Data System (ADS)

    Papoutsa, Christiana; Akylas, Evangelos; Hadjimitsis, Diofantos

    2013-08-01

    The main goal of this research is to examine the optical properties of different water bodies such as coastal water; oligotrophic and eutrophic inland water by observing their spectral signatures. Spectral profiles of sampling points, which correspond to water bodies with different water quality characteristics, are extracted and analyzed. Field spectroscopy is a very important tool giving critical information for the comprehension of spectral signatures of different water bodies. Field spectroradiometric measurements can assist to improve or develop new algorithms and methodology enables to classify several water bodies according to their water quality characteristics using remotely sensed data. Field spectroradiometric data presented at this study were obtained for inland water in Asprokremmos Dam, Paphos District/Cyprus; in Larnaca's Salt Lake, Larnaca District/Cyprus; and in Karla Lake, Volos District/Greece and for coastal water in Zugi-Vasilikos-Old Harbour, Limassol District/Cyprus.

  14. Analysis of microRNA signatures using size-coded ligation-mediated PCR

    PubMed Central

    Arefian, Ehsan; Kiani, Jafar; Soleimani, Masoud; Shariati, S. Ali M.; Aghaee-Bakhtiari, Seyed Hamid; Atashi, Amir; Gheisari, Yousof; Ahmadbeigi, Naser; Banaei-Moghaddam, Ali M.; Naderi, Mahmood; Namvarasl, Nabiolah; Good, Liam; Faridani, Omid R.

    2011-01-01

    The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures in biological samples, we describe here a simple and efficient method to detect multiple miRNAs simultaneously in total RNA. The size-coded ligation-mediated polymerase chain reaction (SL-PCR) method is based on size-coded DNA probe hybridization in solution, followed-by ligation, PCR amplification and gel fractionation. The new method shows quantitative and specific detection of miRNAs. We profiled miRNAs of the let-7 family in a number of organisms, tissues and cell types and the results correspond with their incidence in the genome and reported expression levels. Finally, SL-PCR detected let-7 expression changes in human embryonic stem cells as they differentiate to neuron and also in young and aged mice brain and bone marrow. We conclude that the method can efficiently reveal miRNA signatures in a range of biological samples. PMID:21486750

  15. UV Signature Mutations †

    PubMed Central

    2014-01-01

    Sequencing complete tumor genomes and exomes has sparked the cancer field's interest in mutation signatures for identifying the tumor's carcinogen. This review and meta-analysis discusses signatures and their proper use. We first distinguish between a mutagen's canonical mutations – deviations from a random distribution of base changes to create a pattern typical of that mutagen – and the subset of signature mutations, which are unique to that mutagen and permit inference backward from mutations to mutagen. To verify UV signature mutations, we assembled literature datasets on cells exposed to UVC, UVB, UVA, or solar simulator light (SSL) and tested canonical UV mutation features as criteria for clustering datasets. A confirmed UV signature was: ≥60% of mutations are C→T at a dipyrimidine site, with ≥5% CC→TT. Other canonical features such as a bias for mutations on the non-transcribed strand or at the 3' pyrimidine had limited application. The most robust classifier combined these features with criteria for the rarity of non-UV canonical mutations. In addition, several signatures proposed for specific UV wavelengths were limited to specific genes or species; non-signature mutations induced by UV may cause melanoma BRAF mutations; and the mutagen for sunlight-related skin neoplasms may vary between continents. PMID:25354245

  16. An archaeal genomic signature

    NASA Technical Reports Server (NTRS)

    Graham, D. E.; Overbeek, R.; Olsen, G. J.; Woese, C. R.

    2000-01-01

    Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole. The signature is defined in terms of the set of protein-encoding genes found in at least two diverse members of the euryarchaeal taxa that function uniquely within the Archaea; most signature proteins have no recognizable bacterial or eukaryal homologs. By this definition, 351 clusters of signature proteins have been identified. Functions of most proteins in this signature set are currently unknown. At least 70% of the clusters that contain proteins from all the euryarchaeal genomes also have crenarchaeal homologs. This conservative set, which appears refractory to horizontal gene transfer to the Bacteria or the Eukarya, would seem to reflect the significant innovations that were unique and fundamental to the archaeal "design fabric." Genomic protein signature analysis methods may be extended to characterize the evolution of any phylogenetically defined lineage. The complete set of protein clusters for the archaeal genomic signature is presented as supplementary material (see the PNAS web site, www.pnas.org).

  17. Nucleic Acid Aptamers for Living Cell Analysis

    NASA Astrophysics Data System (ADS)

    Xiong, Xiangling; Lv, Yifan; Chen, Tao; Zhang, Xiaobing; Wang, Kemin; Tan, Weihong

    2014-06-01

    Cells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as “chemical antibodies,” have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.

  18. Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways

    PubMed Central

    Ghosh, Debajyoti; Ding, Lili; Sivaprasad, Umasundari; Geh, Esmond; Biagini Myers, Jocelyn; Bernstein, Jonathan A.; Khurana Hershey, Gurjit K; Mersha, Tesfaye B.

    2015-01-01

    Several studies have identified genes that are differentially expressed in atopic dermatitis (AD) compared to normal skin. However, there is also considerable variation in the list of differentially expressed genes (DEGs) reported by different groups and the exact cause of AD is still not fully understood. Using a rank-based approach, we analyzed gene expression data from five different microarray studies, comprising a total of 127 samples and more than 250,000 transcripts. A total of 89 AD gene expression signatures ‘89ADGES’, including FLG gene, were identified to show dysregulation consistently across these studies. Using a Support Vector Machine, we showed that the ‘89ADGES’ discriminates AD from normal skin with 98% predictive accuracy. Functional annotation of these genes implicated their roles in immune responses (e.g., betadefensin, microseminoprotein), keratinocyte differentiation/epidermal development (e.g., FLG, CORIN, AQP, LOR, KRT16), inflammation (e.g., IL37, IL27RA, CCL18) and lipid metabolism (e.g., AKR1B10, FAD7, FAR2). Subsequently, we validated a subset of signature genes using quantitative PCR in a mouse model. Using a bioinformatic approach, we identified keratinocyte pathway over-represented (P = <0.0006) among the 89 signature genes. Keratinocytes are known to play a major role in barrier function due to their location in the epidermis. Our result suggests that besides immune- mediated pathway, skin barrier pathways such as the keratinocyte differentiation pathway play a key role in AD pathogenesis. A better understanding of the role of keratinocytes in AD will be important for developing novel “barrier therapy” for this disease. PMID:26717000

  19. Use of the Signature Fatty Acid 16:1ω5 as a Tool to Determine the Distribution of Arbuscular Mycorrhizal Fungi in Soil

    PubMed Central

    Ngosong, Christopher; Gabriel, Elke; Ruess, Liliane

    2012-01-01

    Biomass estimation of arbuscular mycorrhiza (AM) fungi, widespread plant root symbionts, commonly employs lipid biomarkers, predominantly the fatty acid 16:1ω5. We briefly reviewed the application of this signature fatty acid, followed by a case study comparing biochemical markers with microscopic techniques in an arable soil following a change to AM non-host plants after 27 years of continuous host crops, that is, two successive cropping seasons with wheat followed by amaranth. After switching to the non-host amaranth, spore biomass estimated by the neutral lipid fatty acid (NLFA) 16:1ω5 decreased to almost nil, whereas microscopic spore counts decreased by about 50% only. In contrast, AM hyphal biomass assessed by the phospholipid (PLFA) 16:1ω5 was greater under amaranth than wheat. The application of PLFA 16:1ω5 as biomarker was hampered by background level derived from bacteria, and further enhanced by its incorporation from degrading spores used as microbial resource. Meanwhile, biochemical and morphological assessments showed negative correlation for spores and none for hyphal biomass. In conclusion, the NLFA 16:1ω5 appears to be a feasible indicator for AM fungi of the Glomales group in the complex field soils, whereas the use of PLFA 16:1ω5 for hyphae is unsuitable and should be restricted to controlled laboratory studies. PMID:22830034

  20. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data

    PubMed Central

    Duforet-Frebourg, Nicolas; Luu, Keurcien; Laval, Guillaume; Bazin, Eric; Blum, Michael G.B.

    2016-01-01

    To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult. PMID:26715629

  1. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data.

    PubMed

    Duforet-Frebourg, Nicolas; Luu, Keurcien; Laval, Guillaume; Bazin, Eric; Blum, Michael G B

    2016-04-01

    To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult. PMID:26715629

  2. Comment on ``Security analysis and improvements of arbitrated quantum signature schemes''

    NASA Astrophysics Data System (ADS)

    Hwang, Tzonelih; Luo, Yi-Ping; Chong, Song-Kong

    2012-05-01

    Recently, Zou, and Qiu [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.82.042325 82, 042325 (2010)] demonstrated that two arbitrated quantum signature (AQS) schemes are not secure because an arbitrator cannot arbitrate the dispute between two users when a receiver repudiates the integrity of a signature. By using a public board, Zou and Qiu's proposed two AQS schemes to solve the problem. This work shows that the same security problem may exist in Zou and Qiu's schemes. Moreover, a malicious verifier, Bob, can actively negate a signed order if he wants to. This attack, a special case of the denial-of-service (DoS) attack mentioned by Cai [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.91.109801 91, 109801 (2003)], is important in quantum cryptography. Bob may get some benefits from this DoS attack since he can actively deny Alice's signed order without being detected. This work also shows that a malicious signer can reveal the verifier's secret key without being detected by using Trojan-horse attacks.

  3. The technique of entropy optimization in motor current signature analysis and its application in the fault diagnosis of gear transmission

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoguang; Liang, Lin; Liu, Fei; Xu, Guanghua; Luo, Ailing; Zhang, Sicong

    2012-05-01

    Nowadays, Motor Current Signature Analysis (MCSA) is widely used in the fault diagnosis and condition monitoring of machine tools. However, although the current signal has lower SNR (Signal Noise Ratio), it is difficult to identify the feature frequencies of machine tools from complex current spectrum that the feature frequencies are often dense and overlapping by traditional signal processing method such as FFT transformation. With the study in the Motor Current Signature Analysis (MCSA), it is found that the entropy is of importance for frequency identification, which is associated with the probability distribution of any random variable. Therefore, it plays an important role in the signal processing. In order to solve the problem that the feature frequencies are difficult to be identified, an entropy optimization technique based on motor current signal is presented in this paper for extracting the typical feature frequencies of machine tools which can effectively suppress the disturbances. Some simulated current signals were made by MATLAB, and a current signal was obtained from a complex gearbox of an iron works made in Luxembourg. In diagnosis the MCSA is combined with entropy optimization. Both simulated and experimental results show that this technique is efficient, accurate and reliable enough to extract the feature frequencies of current signal, which provides a new strategy for the fault diagnosis and the condition monitoring of machine tools.

  4. UV signature mutations.

    PubMed

    Brash, Douglas E

    2015-01-01

    Sequencing complete tumor genomes and exomes has sparked the cancer field's interest in mutation signatures for identifying the tumor's carcinogen. This review and meta-analysis discusses signatures and their proper use. We first distinguish between a mutagen's canonical mutations—deviations from a random distribution of base changes to create a pattern typical of that mutagen—and the subset of signature mutations, which are unique to that mutagen and permit inference backward from mutations to mutagen. To verify UV signature mutations, we assembled literature datasets on cells exposed to UVC, UVB, UVA, or solar simulator light (SSL) and tested canonical UV mutation features as criteria for clustering datasets. A confirmed UV signature was: ≥60% of mutations are C→T at a dipyrimidine site, with ≥5% CC→TT. Other canonical features such as a bias for mutations on the nontranscribed strand or at the 3' pyrimidine had limited application. The most robust classifier combined these features with criteria for the rarity of non-UV canonical mutations. In addition, several signatures proposed for specific UV wavelengths were limited to specific genes or species; UV's nonsignature mutations may cause melanoma BRAF mutations; and the mutagen for sunlight-related skin neoplasms may vary between continents. PMID:25354245

  5. Using Willie's Acid-Base Box for Blood Gas Analysis

    ERIC Educational Resources Information Center

    Dietz, John R.

    2011-01-01

    In this article, the author describes a method developed by Dr. William T. Lipscomb for teaching blood gas analysis of acid-base status and provides three examples using Willie's acid-base box. Willie's acid-base box is constructed using three of the parameters of standard arterial blood gas analysis: (1) pH; (2) bicarbonate; and (3) CO[subscript…

  6. Plasma amino acid and metabolite signatures tracking diabetes progression in the UCD-T2DM rat model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Elevations of plasma concentrations of branched-chain amino acids (BCAAs) are observed in human insulin resistance and type 2 diabetes mellitus (T2DM); however, there has been some controversy with respect to the passive or causative nature of the BCAA phenotype. Using untargeted metabolomics, plasm...

  7. Integrative Pathway Analysis of Metabolic Signature in Bladder Cancer: A Linkage to The Cancer Genome Atlas Project and Prediction of Survival

    PubMed Central

    von Rundstedt, Friedrich-Carl; Rajapakshe, Kimal; Ma, Jing; Arnold, James M.; Gohlke, Jie; Putluri, Vasanta; Krishnapuram, Rashmi; Piyarathna, D. Badrajee; Lotan, Yair; Gödde, Daniel; Roth, Stephan; Störkel, Stephan; Levitt, Jonathan M.; Michailidis, George; Sreekumar, Arun; Lerner, Seth P.; Coarfa, Cristian; Putluri, Nagireddy

    2016-01-01

    Purpose We used targeted mass spectrometry to study the metabolic fingerprint of urothelial cancer and determine whether the biochemical pathway analysis gene signature would have a predictive value in independent cohorts of patients with bladder cancer. Materials and Methods Pathologically evaluated, bladder derived tissues, including benign adjacent tissue from 14 patients and bladder cancer from 46, were analyzed by liquid chromatography based targeted mass spectrometry. Differential metabolites associated with tumor samples in comparison to benign tissue were identified by adjusting the p values for multiple testing at a false discovery rate threshold of 15%. Enrichment of pathways and processes associated with the metabolic signature were determined using the GO (Gene Ontology) Database and MSigDB (Molecular Signature Database). Integration of metabolite alterations with transcriptome data from TCGA (The Cancer Genome Atlas) was done to identify the molecular signature of 30 metabolic genes. Available outcome data from TCGA portal were used to determine the association with survival. Results We identified 145 metabolites, of which analysis revealed 31 differential metabolites when comparing benign and tumor tissue samples. Using the KEGG (Kyoto Encyclopedia of Genes and Genomes) Database we identified a total of 174 genes that correlated with the altered metabolic pathways involved. By integrating these genes with the transcriptomic data from the corresponding TCGA data set we identified a metabolic signature consisting of 30 genes. The signature was significant in its prediction of survival in 95 patients with a low signature score vs 282 with a high signature score (p = 0.0458). Conclusions Targeted mass spectrometry of bladder cancer is highly sensitive for detecting metabolic alterations. Applying transcriptome data allows for integration into larger data sets and identification of relevant metabolic pathways in bladder cancer progression. PMID:26802582

  8. Methyl-CpG island-associated genome signature tags

    DOEpatents

    Dunn, John J

    2014-05-20

    Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.

  9. Analysis of the Effects of Streamwise Lift Distribution on Sonic Boom Signature

    NASA Technical Reports Server (NTRS)

    Yoo, Seung Yeun (Paul)

    2010-01-01

    The streamwise lift distribution of a wing-canard-stabilator-body configuration was varied to study its effect on the near-field sonic boom signature. The investigation was carried out via solving the three-dimensional Euler equation with the OVERFLOW-2 flow solver. The computational meshes were created using the Chimera overset grid topology. The lift distribution was varied by first deflecting the canard then trimming the aircraft with the wing and the stabilator while maintaining constant lift coefficient of 0.05. A validation study using experimental results was also performed to determine required grid resolution and appropriate numerical scheme. A wide range of streamwise lift distribution was simulated. The result shows that the longitudinal wave propagation speed can be controlled through lift distribution thus controlling the shock coalescence.

  10. Security Analysis of an Arbitrated Quantum Signature Scheme with Bell States

    NASA Astrophysics Data System (ADS)

    Xu, Guoliang; Zou, Xiangfu

    2016-09-01

    Recently, to resist attacks using the anticommutativity of nontrivial Pauli operators, an arbitrated quantum signature scheme with Bell states (Int. J. Theor. Phys. 53(5), 1569-1579 2014) was proposed. The scheme randomly adds Hadamard operations to strengthen the quantum one-time pad encryption. Based on this, it claimed that the scheme could resist the receiver's existential forgery and no party had chances to change the message without being discovered. This paper introduces two security issues of the scheme: It can't resist the signer's disavowal and the receiver's existential forgery. Furthermore, we show that the scheme is still vulnerable to the receiver's existential forgery even if the Hadamard operation in the encryption algorithm is replaced with any 2nd-order unitary operation.

  11. Flight measurement and analysis of AAFE RADSCAT wind speed signature of the ocean

    NASA Technical Reports Server (NTRS)

    Schroeder, L. C.; Jones, W. L.; Schaffner, P. R.; Mitchell, J. L.

    1984-01-01

    The advanced aerospace flight experiment radiometer scatterometer (AAFE RADSCAT) which was developed as a research tool to evaluate the use of microwave frequency remote sensors to provide wind speed information at the ocean surface is discussed. The AAFE RADSCAT helped establish the feasibility of the satellite scatterometer for measuring both wind speed and direction. The most important function of the AAFE RADSCAT was to provide a data base of ocean normalized radar cross section (NRCS) measurements as a function of surface wind vector at 13.9 GHz. The NRCS measurements over a wide parametric range of incidence angles, azimuth angles, and winds were obtained in a series of RADSCAT aircraft missions. The obtained data base was used to model the relationship between k sub u band radar signature and ocean surface wind vector. The models developed therefrom are compared with those used for inversion of the SEASAT-A satellite scatterometer (SASS) radar measurements to wind speeds.

  12. Security Analysis of an Arbitrated Quantum Signature Scheme with Bell States

    NASA Astrophysics Data System (ADS)

    Xu, Guoliang; Zou, Xiangfu

    2016-05-01

    Recently, to resist attacks using the anticommutativity of nontrivial Pauli operators, an arbitrated quantum signature scheme with Bell states (Int. J. Theor. Phys. 53(5), 1569-1579 2014) was proposed. The scheme randomly adds Hadamard operations to strengthen the quantum one-time pad encryption. Based on this, it claimed that the scheme could resist the receiver's existential forgery and no party had chances to change the message without being discovered. This paper introduces two security issues of the scheme: It can't resist the signer's disavowal and the receiver's existential forgery. Furthermore, we show that the scheme is still vulnerable to the receiver's existential forgery even if the Hadamard operation in the encryption algorithm is replaced with any 2nd-order unitary operation.

  13. Comparative proteomic analysis of four Bacillus clausii strains: proteomic expression signature distinguishes protein profile of the strains.

    PubMed

    Lippolis, Rosa; Gnoni, Antonio; Abbrescia, Anna; Panelli, Damiano; Maiorano, Stefania; Paternoster, Maria Stefania; Sardanelli, Anna Maria; Papa, Sergio; Gaballo, Antonio

    2011-11-18

    A comparative proteomic approach, using two dimensional gel electrophoresis and mass spectrometry, has been developed to compare and elucidate the differences among the cellular proteomes of four closely related isogenic O/C, SIN, N/R and T, B. clausii strains during both exponential and stationary phases of growth. Image analysis of the electropherograms reveals a high degree of concordance among the four proteomes, some proteins result, however, differently expressed. The proteins spots exhibiting high different expression level were identified, by mass-spectrometry analysis, as alcohol dehydrogenase (ADHA, EC1.2.1.3; ABC0046 isoform) aldehyde dehydrogenase (DHAS, EC 1.2.1.3; ABC0047 isoform) and flagellin-protein of B. clausii KSM-k16. The different expression levels of the two dehydrogenases were confirmed by quantitative RT-PCR and dehydrogenases enzymatic activity. The different patterns of protein expression can be considered as cell proteome signatures of the different strains. PMID:21810490

  14. A Resource for the Transcriptional Signature of Bona Fide Trophoblast Stem Cells and Analysis of Their Embryonic Persistence

    PubMed Central

    Pfeifer, Dietmar; Arnold, Sebastian J.

    2015-01-01

    Trophoblast stem cells (TSCs) represent the multipotent progenitors that give rise to the different cells of the embryonic portion of the placenta. Here, we analysed the expression of key TSC transcription factors Cdx2, Eomes, and Elf5 in the early developing placenta of mouse embryos and in cultured TSCs and reveal surprising heterogeneity in protein levels. We analysed persistence of TSCs in the early placenta and find that TSCs remain in the chorionic hinge until E9.5 and are lost shortly afterwards. To define the transcriptional signature of bona fide TSCs, we used inducible gain- and loss-of-function alleles of Eomes or Cdx2, and EomesGFP, to manipulate and monitor the core maintenance factors of TSCs, followed by genome-wide expression profiling. Combinatorial analysis of resulting expression profiles allowed for defining novel TSC marker genes that might functionally contribute to the maintenance of the TSC state. Analyses by qRT-PCR and in situ hybridisation validated novel TSC- and chorion-specific marker genes, such as Bok/Mtd, Cldn26, Duox2, Duoxa2, Nr0b1, and Sox21. Thus, these expression data provide a valuable resource for the transcriptional signature of bona fide and early differentiating TSCs and may contribute to an increased understanding of the transcriptional circuitries that maintain and/or establish stemness of TSCs. PMID:26783396

  15. DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas.

    PubMed

    Jeyapalan, Jennie N; Doctor, Gabriel T; Jones, Tania A; Alberman, Samuel N; Tep, Alexander; Haria, Chirag M; Schwalbe, Edward C; Morley, Isabel C F; Hill, Alfred A; LeCain, Magdalena; Ottaviani, Diego; Clifford, Steven C; Qaddoumi, Ibrahim; Tatevossian, Ruth G; Ellison, David W; Sheer, Denise

    2016-01-01

    Low-grade gliomas (LGGs) account for about a third of all brain tumours in children. We conducted a detailed study of DNA methylation and gene expression to improve our understanding of the biology of pilocytic and diffuse astrocytomas. Pilocytic astrocytomas were found to have a distinctive signature at 315 CpG sites, of which 312 were hypomethylated and 3 were hypermethylated. Genomic analysis revealed that 182 of these sites are within annotated enhancers. The signature was not present in diffuse astrocytomas, or in published profiles of other brain tumours and normal brain tissue. The AP-1 transcription factor was predicted to bind within 200 bp of a subset of the 315 differentially methylated CpG sites; the AP-1 factors, FOS and FOSL1 were found to be up-regulated in pilocytic astrocytomas. We also analysed splice variants of the AP-1 target gene, CCND1, which encodes cell cycle regulator cyclin D1. CCND1a was found to be highly expressed in both pilocytic and diffuse astrocytomas, but diffuse astrocytomas have far higher expression of the oncogenic variant, CCND1b. These findings highlight novel genetic and epigenetic differences between pilocytic and diffuse astrocytoma, in addition to well-described alterations involving BRAF, MYB and FGFR1. PMID:27229157

  16. A comparative analysis of high-throughput platforms for validation of a circulating microRNA signature in diabetic retinopathy

    PubMed Central

    Farr, Ryan J.; Januszewski, Andrzej S.; Joglekar, Mugdha V.; Liang, Helena; McAulley, Annie K.; Hewitt, Alex W.; Thomas, Helen E.; Loudovaris, Tom; Kay, Thomas W. H.; Jenkins, Alicia; Hardikar, Anandwardhan A.

    2015-01-01

    MicroRNAs are now increasingly recognized as biomarkers of disease progression. Several quantitative real-time PCR (qPCR) platforms have been developed to determine the relative levels of microRNAs in biological fluids. We systematically compared the detection of cellular and circulating microRNA using a standard 96-well platform, a high-content microfluidics platform and two ultra-high content platforms. We used extensive analytical tools to compute inter- and intra-run variability and concordance measured using fidelity scoring, coefficient of variation and cluster analysis. We carried out unprejudiced next generation sequencing to identify a microRNA signature for Diabetic Retinopathy (DR) and systematically assessed the validation of this signature on clinical samples using each of the above four qPCR platforms. The results indicate that sensitivity to measure low copy number microRNAs is inversely related to qPCR reaction volume and that the choice of platform for microRNA biomarker validation should be made based on the abundance of miRNAs of interest. PMID:26035063

  17. Export of pre-aged, labile DOM from a central California coastal upwelling system: Insights from D/L amino acids and Δ14C signatures

    NASA Astrophysics Data System (ADS)

    Walker, B. D.; Shen, Y.; Benner, R. H.; Druffel, E. R. M.

    2014-12-01

    Coastal upwelling zones are among the most productive regions in the world and play a major role in global carbon and nitrogen cycles. Recent research suggests that a substantial fraction of newly fixed organic matter is exported offshore in the form of dissolved organic matter (DOM). However, to date only a few studies have examined DOM composition in the context of production and export from upwelling systems. The ultimate fate and geochemical impact of coastal DOM exported to offshore and mesopelagic ecosystems also remains largely unknown. Between 2007-2009 we conducted a high-resolution biogeochemical time series at the Granite Canyon Marine Pollution Studies Lab in part to evaluate the seasonal production and export of DOM from the Central CA coast. Our previous work demonstrated substantial, albeit disparate, seasonal production of dissolved organic carbon and nitrogen (DOC, DON) - with high DON (and low C:N ratios) produced during upwelling and high DOC produced during summer/fall water column stratification (Walker and McCarthy, 2012). Here we present new total dissolved D/L amino acid (TDAA) and UV-oxidizable DOC radiocarbon (Δ14C) data with the goal of determining the relative sources (heterotrophic vs. autotrophic), bioavailability, microbial processing and 14C-ages of C-rich vs. N-rich DOM exported from this upwelling system. Our results suggest that C-rich DOM produced during water column stratification carries a large microbial signature (i.e. high D/L AA ratios and non-protein AA abundance), whereas N-rich DOM produced during upwelling appears to be fresh, autotrophic DOM (i.e. lowest D/L AA ratios and highest TDAA abundance). DOM Δ14C signatures also did not approximate in situ dissolved inorganic carbon (DIC), and instead were far more negative and highly correlated to water mass density. Together our results indicate a previously unrecognized source of highly labile yet pre-aged DOM potentially impacting offshore and mesopelagic ecosystems.

  18. Carbon-13 natural abundance signatures of long-chain fatty acids to determinate sediment origin: A case study in northeast Austria

    NASA Astrophysics Data System (ADS)

    Mabit, Lionel; Gibbs, Max; Meusburger, Katrin; Toloza, Arsenio; Resch, Christian; Klik, Andreas; Swales, Andrew; Alewell, Christine

    2016-04-01

    - Several recently published information from scientific research have highlighted that compound-specific stable isotope (CSSI) signatures of fatty acids (FAs) based on the measurement of carbon-13 natural abundance signatures showed great promises to identify sediment origin. The authors have used this innovative isotopic approach to investigate the sources of sediment in a three hectares Austrian sub-watershed (i.e. Mistelbach). Through a previous study using the Cs-137 technique, Mabit et al. (Geoderma, 2009) reported a local maximum sedimentation rate reaching 20 to 50 t/ha/yr in the lowest part of this watershed. However, this study did not identify the sources. Subsequently, the deposited sediment at its outlet (i.e. the sediment mixture) and representative soil samples from the four main agricultural fields - expected to be the source soils - of the site were investigated. The bulk delta carbon-13 of the samples and two long-chain FAs (i.e. C22:0 and C24:0) allowed the best statistical discrimination. Using two different mixing models (i.e. IsoSource and CSSIAR v1.00) and the organic carbon content of the soil sources and sediment mixture, the contribution of each source has been established. Results suggested that the grassed waterway contributed to at least 50% of the sediment deposited at the watershed outlet. This study, that will require further validation, highlights that CSSI and Cs-137 techniques are complementary as fingerprints and tracers for establishing land sediment redistribution and could provide meaningful information for optimized decision-making by land managers.

  19. Advanced spectral signature discrimination algorithm

    NASA Astrophysics Data System (ADS)

    Chakravarty, Sumit; Cao, Wenjie; Samat, Alim

    2013-05-01

    This paper presents a novel approach to the task of hyperspectral signature analysis. Hyperspectral signature analysis has been studied a lot in literature and there has been a lot of different algorithms developed which endeavors to discriminate between hyperspectral signatures. There are many approaches for performing the task of hyperspectral signature analysis. Binary coding approaches like SPAM and SFBC use basic statistical thresholding operations to binarize a signature which are then compared using Hamming distance. This framework has been extended to techniques like SDFC wherein a set of primate structures are used to characterize local variations in a signature together with the overall statistical measures like mean. As we see such structures harness only local variations and do not exploit any covariation of spectrally distinct parts of the signature. The approach of this research is to harvest such information by the use of a technique similar to circular convolution. In the approach we consider the signature as cyclic by appending the two ends of it. We then create two copies of the spectral signature. These three signatures can be placed next to each other like the rotating discs of a combination lock. We then find local structures at different circular shifts between the three cyclic spectral signatures. Texture features like in SDFC can be used to study the local structural variation for each circular shift. We can then create different measure by creating histogram from the shifts and thereafter using different techniques for information extraction from the histograms. Depending on the technique used different variant of the proposed algorithm are obtained. Experiments using the proposed technique show the viability of the proposed methods and their performances as compared to current binary signature coding techniques.

  20. Acoustic emission and acousto-ultrasonic signature analysis of failure mechanisms in carbon fiber reinforced polymer materials

    NASA Astrophysics Data System (ADS)

    Carey, Shawn Allen

    Fiber reinforced polymer composite materials, particularly carbon (CFRPs), are being used for primary structural applications, particularly in the aerospace and naval industries. Advantages of CFRP materials, compared to traditional materials such as steel and aluminum, include: light weight, high strength to weight ratio, corrosion resistance, and long life expectancy. A concern with CFRPs is that despite quality control during fabrication, the material can contain many hidden internal flaws. These flaws in combination with unseen damage due to fatigue and low velocity impact have led to catastrophic failure of structures and components. Therefore a large amount of research has been conducted regarding nondestructive testing (NDT) and structural health monitoring (SHM) of CFRP materials. The principal objective of this research program was to develop methods to characterize failure mechanisms in CFRP materials used by the U.S. Army using acoustic emission (AE) and/or acousto-ultrasonic (AU) data. Failure mechanisms addressed include fiber breakage, matrix cracking, and delamination due to shear between layers. CFRP specimens were fabricated and tested in uniaxial tension to obtain AE and AU data. The specimens were designed with carbon fibers in different orientations to produce the different failure mechanisms. Some specimens were impacted with a blunt indenter prior to testing to simulate low-velocity impact. A signature analysis program was developed to characterize the AE data based on data examination using visual pattern recognition techniques. It was determined that it was important to characterize the AE event , using the location of the event as a parameter, rather than just the AE hit (signal recorded by an AE sensor). A back propagation neural network was also trained based on the results of the signature analysis program. Damage observed on the specimens visually with the aid of a scanning electron microscope agreed with the damage type assigned by the

  1. Multifractality of sectoral price indices: Hurst signature analysis of Cantillon effects in disequilibrium factor markets

    NASA Astrophysics Data System (ADS)

    Mulligan, Robert F.

    2014-06-01

    This paper presents Hurst exponent signatures from time series of aggregate price indices for the US over the 1975-2011 time period. Though all highly aggregated, these indices include both broad measures of consumer and producer prices. The constellation of prices evolves as a complex system throughout processes of production and distribution, culminating in the final delivery of output to consumers. Massive feedback characterizes this system, where the demand for consumable output determines the demand for the inputs used to produce it, and supply scarcities for the necessary inputs in turn determine the supply of the final product. Prices in both factor and output markets are jointly determined by interdependent supply and demand conditions. Fractal examination of the interplay among market prices would be of interest regardless, but added interest arises from the consideration of how these markets respond to external shocks over the business cycle, particularly monetary expansion. Because the initial impact of monetary injection is localized in specific sectors, the way the impact on prices diffuses throughout the economy is of special interest.

  2. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.

    PubMed

    Montague, Michael J; Li, Gang; Gandolfi, Barbara; Khan, Razib; Aken, Bronwen L; Searle, Steven M J; Minx, Patrick; Hillier, LaDeana W; Koboldt, Daniel C; Davis, Brian W; Driscoll, Carlos A; Barr, Christina S; Blackistone, Kevin; Quilez, Javier; Lorente-Galdos, Belen; Marques-Bonet, Tomas; Alkan, Can; Thomas, Gregg W C; Hahn, Matthew W; Menotti-Raymond, Marilyn; O'Brien, Stephen J; Wilson, Richard K; Lyons, Leslie A; Murphy, William J; Warren, Wesley C

    2014-12-01

    Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae. PMID:25385592

  3. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

    PubMed Central

    Li, Gang; Gandolfi, Barbara; Khan, Razib; Aken, Bronwen L.; Searle, Steven M. J.; Minx, Patrick; Hillier, LaDeana W.; Koboldt, Daniel C.; Davis, Brian W.; Driscoll, Carlos A.; Barr, Christina S.; Blackistone, Kevin; Quilez, Javier; Lorente-Galdos, Belen; Marques-Bonet, Tomas; Alkan, Can; Thomas, Gregg W. C.; Hahn, Matthew W.; Menotti-Raymond, Marilyn; O’Brien, Stephen J.; Wilson, Richard K.; Lyons, Leslie A.; Murphy, William J.; Warren, Wesley C.

    2014-01-01

    Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae. PMID:25385592

  4. Visualization and analysis for multidimensional gene expressions signature of cigarette smoking

    NASA Astrophysics Data System (ADS)

    Wang, Changbo; Xiao, Zhao; Zhang, Tianlun; Cui, Jin; Pang, Chenming

    2011-11-01

    Biologists often use gene chip to get massive experimental data in the field of bioscience and chemical sciences. Facing a large amount of experimental data, researchers often need to find out a few interesting data or simple regulations. This paper presents a set of methods to visualize and analyze the data for gene expression signatures of people who smoke. We use the latest research data from National Center for Biotechnology Information. Totally, there are more than 400 thousand expressions data. Using these data, we can use parallel coordinates method to visualize the different gene expressions between smokers and nonsmokers and we can distinguish non-smokers, former smokers and current smokers by using the different colors. It can be easy to find out which gene is more important during the lung cancer angiogenesis in the smoking people. In another way, we can use a hierarchical model to visualize the inner relation of different genes. The location of the nodes shows different expression moment and the distance to the root shows the sequence of the expression. We can use the ring layout to represent all the nodes, and connect the different nodes which are related with color lines. Combined with the parallel coordinates method, the visualization result show the important genes and some inner relation obviously, which is useful for examination and prevention of lung cancer.

  5. An analysis of issues concerning acid rain

    SciTech Connect

    Not Available

    1984-01-01

    GAO examines the implications of current scientific knowledge for policy decisions on acid rain and offers a series of observations on the following issues involved in the debate: to what extent has it been scientifically demonstrated that acid rain is resulting in damage to the environment. What are the causes of acid rain and where is it most prevalent. What alternatives exist for controlling acid rain and what are their economic effects.

  6. Recent trends in the advanced analysis of bioactive fatty acids.

    PubMed

    Ruiz-Rodriguez, Alejandro; Reglero, Guillermo; Ibañez, Elena

    2010-01-20

    The consumption of dietary fats have been long associated to chronic diseases such as obesity, diabetes, cancer, arthritis, asthma, and cardiovascular disease; although some controversy still exists in the role of dietary fats in human health, certain fats have demonstrated their positive effect in the modulation of abnormal fatty acid and eicosanoid metabolism, both of them associated to chronic diseases. Among the different fats, some fatty acids can be used as functional ingredients such as alpha-linolenic acid (ALA), arachidonic acid (AA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), gamma-linolenic acid (GLA), stearidonic acid (STA) and conjugated linoleic acid (CLA), among others. The present review is focused on recent developments in FAs analysis, covering sample preparation methods such as extraction, fractionation and derivatization as well as new advances in chromatographic methods such as GC and HPLC. Special attention is paid to trans fatty acids due its increasing interest for the food industry. PMID:19525080

  7. GENETIC ANALYSIS OF ABSCISIC ACID BIOSYNTHESIS

    SciTech Connect

    MCCARTY D R

    2012-01-10

    The carotenoid cleavage dioxygenases (CCD) catalyze synthesis of a variety of apo-carotenoid secondary metabolites in plants, animals and bacteria. In plants, the reaction catalyzed by the 11, 12, 9-cis-epoxy carotenoid dioxygenase (NCED) is the first committed and key regulated step in synthesis of the plant hormone, abscisic acid (ABA). ABA is a key regulator of plant stress responses and has critical functions in normal root and seed development. The molecular mechanisms responsible for developmental control of ABA synthesis in plant tissues are poorly understood. Five of the nine CCD genes present in the Arabidopsis genome encode NCED's involved in control of ABA synthesis in the plant. This project is focused on functional analysis of these five AtNCED genes as a key to understanding developmental regulation of ABA synthesis and dissecting the role of ABA in plant development. For this purpose, the project developed a comprehensive set of gene knockouts in the AtNCED genes that facilitate genetic dissection of ABA synthesis. These mutants were used in combination with key molecular tools to address the following specific objectives: (1) the role of ABA synthesis in root development; (2) developmental control of ABA synthesis in seeds; (3) analysis of ATNCED over-expressers; (4) preliminary crystallography of the maize VP14 protein.

  8. Gamma-Ray Signatures for State-Of-Health Analysis and Monitoring of Widely-Arrayed Radiation Portal Monitor Systems

    SciTech Connect

    Woodring, Mitchell L.; Ely, James H.; Angel, Linda K.; Wright, Ingrid H.; Eslinger, Melany A.; Pospical, A. Jill; Ellis, John E.

    2008-05-15

    Pacific Northwest National Laboratory (PNNL) has deployed a large array of radiation portal monitors for the Department of Homeland Security U.S. Customs and Border Protection. These portal monitors scan incoming vehicles crossing the U.S. border and shipping containers leaving international ports for radioactive material via gamma-ray and neutron detection. Data produced and captured by these systems are recorded for every vehicle related to radiation signature, sensor/system status, and local background, as well as a host of other variables. Within the Radiation Portal Monitor Project at PNNL, state-of-health observation and analysis for the whole RPM system using these data to determine functionality and performance is being developed. (PIET-43741-TM-492)

  9. Spatial changes in fatty acids signatures of the great scallop Pecten maximus across the Bay of Biscay continental shelf

    NASA Astrophysics Data System (ADS)

    Nerot, Caroline; Meziane, Tarik; Schaal, Gauthier; Grall, Jacques; Lorrain, Anne; Paulet, Yves-Marie; Kraffe, Edouard

    2015-10-01

    The spatial variability of food resources along continental margins can strongly influence the physiology and ecology of benthic bivalves. We explored the variability of food sources of the great scallop Pecten maximus, by determining their fatty acid (FA) composition along an inshore-offshore gradient in the Bay of Biscay (from 15 to 190 m depth). The FA composition of the digestive gland showed strong differences between shallow and deep-water habitats. This trend was mainly driven by their content in diatom-characteristic fatty acids, which are abundant near the coast. Scallops collected from the middle of the continental shelf were characterized by higher contents of flagellate markers than scallops from shallow habitats. This could be related to a permanent vertical stratification in the water column, which reduced vertical mixing of waters, thereby enhancing organic matter recycling through the microbial loop. In the deeper water station (190 m), FA compositions were close to the compositions found in scallops from shallow areas, which suggest that scallops could have access to the same resources (i.e. diatoms). Muscle FA composition was more indicative of the physiological state of scallops over this depth range, revealing contrasting reproductive strategies among the two coastal sites and metabolic or physiological adaptation at greater depth (e.g. structural and functional adjustments of membrane composition). This study therefore revealed contrasted patterns between shallow and deeper habitats for both P. maximus muscle and digestive gland tissues. This emphasizes the variability in the diet of this species along its distribution range, and stresses the importance of analyzing different tissues for their FA composition in order to better understand their physiology and ecology.

  10. Trophodynamics of euphausiids in the Amundsen Sea during the austral summer by fatty acid and stable isotopic signatures

    NASA Astrophysics Data System (ADS)

    Ko, Ah-Ra; Yang, Eun Jin; Kim, Min-Seob; Ju, Se-Jong

    2016-01-01

    The Amundsen Sea is characterized by a continental shelf, long-term sea ice, and many coastal polynyas with high biological productivity. Euphausia superba and Euphausia crystallorophias, which are dominant Antarctic krill, are major prey for most predators, such as fishes, birds, and marine mammals. An understanding of the feeding ecology of krill may provide the information for the structure and function of the Amundsen Sea ecosystem. Thus, we applied two biochemical approaches (fatty acids and stable isotopes) to determine the trophodynamics of adult krill in the Amundsen Sea. There were no significant differences in lipid contents between the two species, but the dominant storage lipids were different. Triacylglycerol (TAG) was dominant in E. superba, but wax esters (WE) were dominant in E. crystallorophias due to their different living strategies. Furthermore, the lipid content of E. crystallorophias displayed a spatial variation, being highest on the glacial edge. It was difficult to understand the feeding strategy and food source using only the fatty acid compositions of krill and in situ particulate organic matter. However, we found that specific FA ratios (18:1ω9/18:1ω7 and PUFA/SFA) and the nitrogen isotope ratio (δ15N) provide more insight into the feeding ecology of krill, such as feeding strategy and trophic position. These ratios suggest that E. crystallorophias consistently showed a higher degree of carnivorous feeding than E. superba in the Amundsen Sea during the austral summer. In conclusion, adult E. superba might more directly obtain their energy from in situ primary producers in the open sea, but, in the Amundsen Sea Polynya, adult E. crystallorophias seems to obtain their energy mainly through the microbial loop (microzooplankton). If so, E. crystallolophias would be a key player not only to transfer the energy from microbes to higher trophic levels but also to control the carbon and nitrogen cycle in the Amundsen Sea Polynya.

  11. Transcriptomic and metabolomic signatures of an n-3 polyunsaturated fatty acids supplementation in a normolipidemic/normocholesterolemic Caucasian population.

    PubMed

    Rudkowska, Iwona; Paradis, Ann-Marie; Thifault, Elisabeth; Julien, Pierre; Tchernof, André; Couture, Patrick; Lemieux, Simone; Barbier, Olivier; Vohl, Marie-Claude

    2013-01-01

    OMIC technologies, including transcriptomics and metabolomics, may provide powerful tools for identifying the effects of nutrients on molecular functions and metabolic pathways. The objective was to investigate molecular and metabolic changes following n-3 polyunsaturated fatty acid (PUFA) supplementation in healthy subjects via traditional biomarkers as well as transcriptome and metabolome analyses. Thirteen men and 17 women followed a 2-week run-in period based on Canada's Food Guide and then underwent 6-week supplementation with n-3 PUFA (3 g/day). Traditional biochemical markers such as plasma lipids, inflammatory markers, glycemic parameters and erythrocyte fatty acid concentrations were measured. Changes in gene expression of peripheral blood mononuclear cells were assessed by microarrays, and metabolome profiles were assessed by mass spectrometry assay kit. After supplementation, plasma triglycerides decreased and erythrocyte n-3 PUFA concentrations increased to a similar extent in both genders. Further, plasma high-density lipoprotein cholesterol concentrations and fasting glucose levels increased in women after n-3 PUFA supplementation. N-3 PUFA supplementation changed the expression of 610 genes in men, whereas the expression of 250 genes was altered in women. Pathway analyses indicate changes in gene expression of the nuclear receptor peroxisome proliferator-activated receptor-alpha, nuclear transcription-factor kappaB, oxidative stress and activation of the oxidative stress response mediated by nuclear factor (erythroid-derived 2)-like 2. After n-3 PUFA supplementation, metabolomics profiles demonstrate an increase in acylcarnitines, hexose and leucine in men only and a decrease in saturation of glycerophosphatidylcholine and lysophosphatidylcholine concentrations in all subjects. Overall, traditional and novel biomarkers suggest that n-3 PUFA supplementation exerts cardioprotective effects. PMID:22748805

  12. Trophic spectra under the lens of amino acid isotopic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in compound specific isotopic ratio analysis (CSIRA) have allowed researchers to measure trophic fractionation of 15N in specific amino acids, namely glutamic acid and phenylalanine. These amino acids have proven useful in food web studies because of the wide and consistent disparity...

  13. Exome Analysis Reveals Differentially Mutated Gene Signatures of Stage, Grade and Subtype in Breast Cancers

    PubMed Central

    Li, You; Wang, Xiaosheng; Vural, Suleyman; Mishra, Nitish K.; Cowan, Kenneth H.; Guda, Chittibabu

    2015-01-01

    Breast cancers exhibit highly heterogeneous molecular profiles. Although gene expression profiles have been used to predict the risks and prognostic outcomes of breast cancers, the high variability of gene expression limits its clinical application. In contrast, genetic mutation profiles would be more advantageous than gene expression profiles because genetic mutations can be stably detected and the mutational heterogeneity widely exists in breast cancer genomes. We analyzed 98 breast cancer whole exome samples that were sorted into three subtypes, two grades and two stages. The sum deleterious effect of all mutations in each gene was scored to identify differentially mutated genes (DMGs) for this case-control study. DMGs were corroborated using extensive published knowledge. Functional consequences of deleterious SNVs on protein structure and function were also investigated. Genes such as ERBB2, ESP8, PPP2R4, KIAA0922, SP4, CENPJ, PRCP and SELP that have been experimentally or clinically verified to be tightly associated with breast cancer prognosis are among the DMGs identified in this study. We also identified some genes such as ARL6IP5, RAET1E, and ANO7 that could be crucial for breast cancer development and prognosis. Further, SNVs such as rs1058808, rs2480452, rs61751507, rs79167802, rs11540666, and rs2229437 that potentially influence protein functions are observed at significantly different frequencies in different comparison groups. Protein structure modeling revealed that many non-synonymous SNVs have a deleterious effect on protein stability, structure and function. Mutational profiling at gene- and SNV-level revealed differential patterns within each breast cancer comparison group, and the gene signatures correlate with expected prognostic characteristics of breast cancer classes. Some of the genes and SNVs identified in this study show high promise and are worthy of further investigation by experimental studies. PMID:25803781

  14. Multimodal signature modeling of humans

    NASA Astrophysics Data System (ADS)

    Cathcart, J. Michael; Kocher, Brian; Prussing, Keith; Lane, Sarah; Thomas, Alan

    2010-04-01

    Georgia Tech been investigating method for the detection of covert personnel in traditionally difficult environments (e.g., urban, caves). This program focuses on a detailed phenomenological analysis of human physiology and signatures with the subsequent identification and characterization of potential observables. Both aspects are needed to support the development of personnel detection and tracking algorithms. The difficult nature of these personnel-related problems dictates a multimodal sensing approach. Human signature data of sufficient and accurate quality and quantity do not exist, thus the development of an accurate signature model for a human is needed. This model should also simulate various human activities to allow motion-based observables to be exploited. This paper will describe a multimodal signature modeling approach that incorporates human physiological aspects, thermoregulation, and dynamics into the signature calculation. This approach permits both passive and active signatures to be modeled. The focus of the current effort involved the computation of signatures in urban environments. This paper will discuss the development of a human motion model for use in simulating both electro-optical signatures and radar-based signatures. Video sequences of humans in a simulated urban environment will also be presented; results using these sequences for personnel tracking will be presented.

  15. Analysis of issues concerning acid rain

    SciTech Connect

    Bowsher, C.A.

    1984-12-11

    Although science has largely determined that man-made emissions cause acid rain, there is uncertainty concerning the extent and timing of its anticipated effects. Thus, at the present time scientific information alone does not lead unequivocally to a conclusion on whether it is appropriate to begin control actions now or to await better understanding. Given this uncertainty, decisionmakers must weigh the risks of further, potentially avoidable environmental damage against the risks of economic impacts from acid rain control actions which may ultimately prove to be unwarranted. GAO examines the implications of current scientific knowledge for policy decisions on acid rain and offers a series of observations on the following issues involved in the debate: To what extent has it been scientifically demonstrated that acid rain is resulting in damage to the environment. What are the causes of acid rain and where is it most prevalent. What alternatives exist for controlling acid rain and what are their economic effects. 5 figures, 20 tables.

  16. Source analysis of two unique Microseismic Signature from Hurricanes Katrina (2005) and Ioke (2006)

    NASA Astrophysics Data System (ADS)

    Sim, S.; Laske, G.

    2011-12-01

    Traversing the Pacific Ocean for 19 days, Hurricane Ioke was a long-lived hurricane, reaching category 5 status several times and becoming a super-typhoon after crossing the international dateline. Ioke brushed Wake Island on 31 August 2006 and caused damage on the island estimating 90 million. On the other hand, Hurricane Katrina provides a stark contrast, being much shorter-lived but causing over 1800 fatalities and damage of an estimated 80 billion or more. Here, we compare the seismic signature of these two storm systems and several others in the microseism band (0.1-0.35 Hz). Although there were limited seismic stations for Hurricane Katrina, we could use the large dataset of the Hawaiian Plume-Lithosphere Undersea Mantle Experiment (PLUME) Project (Laske et al. 2009) for Hurricane Ioke. We looked at the seismic data of 70 ocean bottom seismometers (OBS) and 13 temporary and permanent land stations. In the relatively few records of land seismic stations available for Hurricane Katrina, the seismic signal of Katrina clearly peaked when it made landfall in Lousiana. In contrast, the seismic signal of Ioke built up as it developed in the open ocean. It peaked long before it brushed Wake Island. The large number seismic data from the PLUME OBSs allowed us to explore the marked difference in the signal levels across the network, which covered the area around the Hawaiian Islands. With the aid of the significant wave height provided by the Fleet Numerical Meteorology and Oceanography Center, we can identify possible source regions for the signals in our microseism records. We also analyzed the significant wave heights collected by ocean buoys from National Oceanographic and Atmospheric Agency (NOAA), which were active during the time period of the hurricane, to help us with this investigation. There is no strong correlation of the available significant wave height data to the microseismic signals from the OBSs and land seismic station from the PLUME project. However

  17. Tissue and size-related changes in the fatty acid and stable isotope signatures of the deep sea grenadier fish Coryphaenoides armatus from the Charlie-Gibbs Fracture Zone region of the Mid-Atlantic Ridge

    NASA Astrophysics Data System (ADS)

    Mayor, Daniel J.; Sharples, Caroline J.; Webster, Lynda; Walsham, Pamela; Lacaze, Jean-Pierre; Cousins, Nicola J.

    2013-12-01

    Coryphaenoides armatus is a cosmopolitan deep-sea fish that plays a major role in the ecology of abyssal ecosystems. We investigated the trophic ecology and physiology of this species by determining the δ13C, δ15N and fatty acid signatures of muscle, liver and ovary tissues of individuals collected from ∼2700 m to the north and south of the Charlie-Gibbs Fracture Zone (CGFZ) of the Mid-Atlantic Ridge, NE Atlantic. Fatty acid and δ13C data both suggested that C. armatus shows an ontogenetic dietary shift, with the relative contributions of benthic and pelagic prey decreasing and increasing respectively as the animals grow. They also indicated that dietary overlap between animals living to the north and south of the CGFZ increases as they grow, suggesting that larger animals forage over greater distances and are not hindered by the presence of the CGFZ. Comparison of tissue-specific fatty acid signatures with previously published data suggests compositional homeostasis of the fatty acids 20:5(n-3) and 22:6(n-3) in the muscle, and 18:1(n-9) in the liver tissues. We ascribe this primarily to strict physiological requirements for these compounds, rather than simply to their abundance in the diet. We pose several speculative mechanisms to explain the observed trends in tissue-specific δ13C and δ15N values, illustrating some of the numerous processes that can influence the isotopic signatures of bulk tissues.

  18. Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis

    PubMed Central

    Poupin, Nathalie; Mariotti, François; Huneau, Jean-François; Hermier, Dominique; Fouillet, Hélène

    2014-01-01

    Body tissues are generally 15N-enriched over the diet, with a discrimination factor (Δ15N) that varies among tissues and individuals as a function of their nutritional and physiopathological condition. However, both 15N bioaccumulation and intra- and inter-individual Δ15N variations are still poorly understood, so that theoretical models are required to understand their underlying mechanisms. Using experimental Δ15N measurements in rats, we developed a multi-compartmental model that provides the first detailed representation of the complex functioning of the body's Δ15N system, by explicitly linking the sizes and Δ15N values of 21 nitrogen pools to the rates and isotope effects of 49 nitrogen metabolic fluxes. We have shown that (i) besides urea production, several metabolic pathways (e.g., protein synthesis, amino acid intracellular metabolism, urea recycling and intestinal absorption or secretion) are most probably associated with isotope fractionation and together contribute to 15N accumulation in tissues, (ii) the Δ15N of a tissue at steady-state is not affected by variations of its P turnover rate, but can vary according to the relative orientation of tissue free amino acids towards oxidation vs. protein synthesis, (iii) at the whole-body level, Δ15N variations result from variations in the body partitioning of nitrogen fluxes (e.g., urea production, urea recycling and amino acid exchanges), with or without changes in nitrogen balance, (iv) any deviation from the optimal amino acid intake, in terms of both quality and quantity, causes a global rise in tissue Δ15N, and (v) Δ15N variations differ between tissues depending on the metabolic changes involved, which can therefore be identified using simultaneous multi-tissue Δ15N measurements. This work provides proof of concept that Δ15N measurements constitute a new promising tool to investigate how metabolic fluxes are nutritionally or physiopathologically reorganized or altered. The existence of such

  19. Investigation into nitrogen attenuation in groundwater pathways in Irish RBDs through the use of stable isotopic signature analysis

    NASA Astrophysics Data System (ADS)

    Orr, Alison; Ofterdinger, Ulrich; Flynn, Raymond

    2010-05-01

    Nitrogen has been identified by the Water Framework Directive as a major pollutant of concern in terms of water quality. Nitrogen contamination can pose a threat to human health and excessive loading into surface waters can lead to eutrophication. This research aims to investigate groundwater pathways from diffuse sources of nitrogen contamination and attenuation processes in various geological settings in Ireland. As part of the EPA Strive Pathways Project, the overall purpose of this research is to improve the understanding of nitrogen attenuation processes in groundwater for the development of a catchment management tool to assess the risk posed by diffuse contamination to surface and groundwater receptors. This will be undertaken through examining nitrogen attenuation pathways in various geological settings in distinctly different catchments in Ireland. These catchments include Gortinlieve in Co. Donegal and Mattock in Co. Louth which are both poorly drained catchments and Nuenna in Co. Kilkenny which is a well drained limestone catchment. This research will be useful to develop further ongoing research carried out into the natural chemistry of the Gortinlieve catchment. The research will focus mainly on characterising the fractionation of stable nitrogen isotopes in groundwater. The use of the stable isotopes δ15N and δ18O in the study of denitrification has been well documented in literature. In addition, the isotopes δ13C and δ34S have also been shown to be useful in evaluating the influence of sulphur and carbon as electron donors in denitrification. For example FeS2 produced as a result of denitrification has a different isotopic signature than FeS2 produced from other processes. This research aims to apply these established stable isotope signatures to a new context in terms of the catchment geology and the broader integrated approach of the Pathways project. Furthermore factors influencing the rate of attenuation will be explored, such as: strata

  20. Inplementation of an automated signal processing approach for the analysis of chemical spectral signatures collected from FT-IR mounted in an aircraft

    SciTech Connect

    Kroutil, Robert T

    2008-01-01

    The automated detection of chemical spectral signatures using a passive infrared Fourier Transform Infrared (FT-IR) Spectrometer mounted in an aircraft is a difficult challenge due to the small total infrared energy contribution of a particular chemical species compared to the background signature. The detection of spectral signatures is complicated by the fact that a large, widely varying infrared background is present that is coupled with the presence of a number of chemical interferents in the atmosphere. This paper describes a mathematical technique that has been demonstrated to automatically detect specific chemical species in an automated processing environment. The data analysis methodology has been demonstrated to be effective using data of low spectral resolution at low aircraft altitudes. An overview of the implementation and basic concepts of the approach are presented.

  1. Global and Targeted Lipid Analysis of Gemmata obscuriglobus Reveals the Presence of Lipopolysaccharide, a Signature of the Classical Gram-Negative Outer Membrane

    PubMed Central

    Mahat, Rajendra; Seebart, Corrine

    2015-01-01

    ABSTRACT Planctomycete bacteria possess many unusual cellular properties, contributing to a cell plan long considered to be unique among the bacteria. However, data from recent studies are more consistent with a modified Gram-negative cell plan. A key feature of the Gram-negative plan is the presence of an outer membrane (OM), for which lipopolysaccharide (LPS) is a signature molecule. Despite genomic evidence for an OM in planctomycetes, no biochemical verification has been reported. We attempted to detect and characterize LPS in the planctomycete Gemmata obscuriglobus. We obtained direct evidence for LPS and lipid A using electrophoresis and differential staining. Gas chromatography-mass spectrometry (GC-MS) compositional analysis of LPS extracts identified eight different 3-hydroxy fatty acids (3-HOFAs), 2-keto 3-deoxy-d-manno-octulosonic acid (Kdo), glucosamine, and hexose and heptose sugars, a chemical profile unique to Gram-negative LPS. Combined with molecular/structural information collected from matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS analysis of putative intact lipid A, these data led us to propose a heterogeneous hexa-acylated lipid A structure (multiple-lipid A species). We also confirmed previous reports of G. obscuriglobus whole-cell fatty acid (FA) and sterol compositions and detected a novel polyunsaturated FA (PUFA). Our confirmation of LPS, and by implication an OM, in G. obscuriglobus raises the possibility that other planctomycetes possess an OM. The pursuit of this question, together with studies of the structural connections between planctomycete LPS and peptidoglycans, will shed more light on what appears to be a planctomycete variation on the Gram-negative cell plan. IMPORTANCE Bacterial species are classified as Gram positive or negative based on their cell envelope structure. For 25 years, the envelope of planctomycete bacteria has been considered a unique exception, as it lacks peptidoglycan and an

  2. Metabolic Signatures of Adiposity in Young Adults: Mendelian Randomization Analysis and Effects of Weight Change

    PubMed Central

    Würtz, Peter; Wang, Qin; Kangas, Antti J.; Richmond, Rebecca C.; Skarp, Joni; Tiainen, Mika; Tynkkynen, Tuulia; Soininen, Pasi; Havulinna, Aki S.; Kaakinen, Marika; Viikari, Jorma S.; Savolainen, Markku J.; Kähönen, Mika; Lehtimäki, Terho; Männistö, Satu; Blankenberg, Stefan; Zeller, Tanja; Laitinen, Jaana; Pouta, Anneli; Mäntyselkä, Pekka; Vanhala, Mauno; Elliott, Paul; Pietiläinen, Kirsi H.; Ripatti, Samuli; Salomaa, Veikko; Raitakari, Olli T.; Järvelin, Marjo-Riitta; Smith, George Davey; Ala-Korpela, Mika

    2014-01-01

    Background Increased adiposity is linked with higher risk for cardiometabolic diseases. We aimed to determine to what extent elevated body mass index (BMI) within the normal weight range has causal effects on the detailed systemic metabolite profile in early adulthood. Methods and Findings We used Mendelian randomization to estimate causal effects of BMI on 82 metabolic measures in 12,664 adolescents and young adults from four population-based cohorts in Finland (mean age 26 y, range 16–39 y; 51% women; mean ± standard deviation BMI 24±4 kg/m2). Circulating metabolites were quantified by high-throughput nuclear magnetic resonance metabolomics and biochemical assays. In cross-sectional analyses, elevated BMI was adversely associated with cardiometabolic risk markers throughout the systemic metabolite profile, including lipoprotein subclasses, fatty acid composition, amino acids, inflammatory markers, and various hormones (p<0.0005 for 68 measures). Metabolite associations with BMI were generally stronger for men than for women (median 136%, interquartile range 125%–183%). A gene score for predisposition to elevated BMI, composed of 32 established genetic correlates, was used as the instrument to assess causality. Causal effects of elevated BMI closely matched observational estimates (correspondence 87%±3%; R2 = 0.89), suggesting causative influences of adiposity on the levels of numerous metabolites (p<0.0005 for 24 measures), including lipoprotein lipid subclasses and particle size, branched-chain and aromatic amino acids, and inflammation-related glycoprotein acetyls. Causal analyses of certain metabolites and potential sex differences warrant stronger statistical power. Metabolite changes associated with change in BMI during 6 y of follow-up were examined for 1,488 individuals. Change in BMI was accompanied by widespread metabolite changes, which had an association pattern similar to that of the cross-sectional observations, yet with greater metabolic

  3. Remote sensing analysis of the Tiber River sediment plume (Tyrrhenian Sea): spectral signature of erratic vs. persistent events

    NASA Astrophysics Data System (ADS)

    Falcini, Federico; Di Cicco, Annalisa; Pitarch, Jaime; Marullo, Salvatore; Colella, Simone; Volpe, Gianluca; Nardin, William; Margiotta, Francesca; Santoleri, Rosalia

    2016-04-01

    During the last decade, several regions along the western Tyrrhenian coast have been dramatically affected by intense river runoffs, which delivered a significant amount of sediment off and along shore. A crucial question that coastal geomorphologists and marine scientists need to face is about the fate and impact of this impulsive sediment load, especially with respect to the historical trend, seasonal variability, and persistent events. A satellite-based analysis of these sediment discharges is a key ingredient for such a study since it represents the primary dataset for the recognition of coastal patterns of Total Suspended Matter (TSM) that may reflect erosional or depositional processes along the coats. On this regard, we developed and implemented a TSM regional product from remote sensing, which was calibrated and validated by in situ measurements collected in the Tyrrhenian Sea. We discuss spatial patterns and spectral signature of the TSM that we observe during the 2012 high river discharge event of the Tiber River. Our analysis gives some insights on the main differences of the geomorphological impacts related to erratic vs persistent events.

  4. Blind separation of human- and horse-footstep signatures using independent component analysis

    NASA Astrophysics Data System (ADS)

    Mehmood, Asif; Damarla, Thyagaraju

    2012-06-01

    Seismic footstep detection based systems for homeland security applications are important to perimeter protection and other security systems. This paper reports seismic footstep signal separation for a walking horse and a walking human. The well-known Independent Component Analysis (ICA) approach is employed to accomplish this task. ICA techniques have become widely used in audio analysis and source separation. The concept of lCA may actually be seen as an extension of the principal component analysis (PCA), which can only impose independence up to the second order and, consequently, defines directions that are orthogonal. They can also be used in conjunction with a classification method to achieve a high percentage of correct classification and reduce false alarms. In this paper, an ICA based algorithm is developed and implemented on seismic data of human and horse footsteps. The performance of this method is very promising and is demonstrated by the experimental results.

  5. Application of spatial features to satellite land-use analysis. [spectral signature variations

    NASA Technical Reports Server (NTRS)

    Smith, J.; Hornung, R.; Berry, J.

    1975-01-01

    A Level I land-use analysis of selected training areas of the Colorado Front Range was carried out using digital ERTS-A satellite imagery. Level I land-use categories included urban, agriculture (irrigated and dryland farming), rangeland, and forests. The spatial variations in spectral response for these land-use classes were analyzed using discrete two-dimensional Fourier transforms to isolate and extract spatial features. Analysis was performed on ERTS frame 1352-17134 (July 10, 1973) and frame number 1388-17131 (August 15, 1973). On training sets, spatial features yielded 80 to 100 percent classification accuracies with commission errors ranging from 0 to 20 percent.

  6. Extraterrestrial material analysis: loss of amino acids during liquid-phase acid hydrolysis

    NASA Astrophysics Data System (ADS)

    Buch, Arnaud; Brault, Amaury; Szopa, Cyril; Freissinet, Caroline

    2015-04-01

    Searching for building blocks of life in extraterrestrial material is a way to learn more about how life could have appeared on Earth. With this aim, liquid-phase acid hydrolysis has been used, since at least 1970 , in order to extract amino acids and other organic molecules from extraterrestrial materials (e.g. meteorites, lunar fines) or Earth analogues (e.g. Atacama desert soil). This procedure involves drastic conditions such as heating samples in 6N HCl for 24 h, either under inert atmosphere/vacuum, or air. Analysis of the hydrolyzed part of the sample should give its total (free plus bound) amino acid content. The present work deals with the influence of the 6N HCl hydrolysis on amino acid degradation. Our experiments have been performed on a standard solution of 17 amino acids. After liquid-phase acid hydrolysis (6N HCl) under argon atmosphere (24 h at 100°C), the liquid phase was evaporated and the dry residue was derivatized with N-Methyl-N-(t-butyldimethylsilyl)trifluoroacetamide (MTBSTFA) and dimethylformamide (DMF), followed by gas chromatography-mass spectrometry analysis. After comparison with derivatized amino acids from the standard solution, a significant reduction of the chromatographic peak areas was observed for most of the amino acids after liquid-phase acid hydrolysis. Furthermore, the same loss pattern was observed when the amino acids were exposed to cold 6N HCl for a short amount of time. The least affected amino acid, i.e. glycine, was found to be 73,93% percent less abundant compared to the non-hydrolyzed standard, while the most affected, i.e. histidine, was not found in the chromatograms after hydrolysis. Our experiments thereby indicate that liquid-phase acid hydrolysis, even under inert atmosphere, leads to a partial or total loss of all of the 17 amino acids present in the standard solution, and that a quick cold contact with 6N HCl is sufficient to lead to a loss of amino acids. Therefore, in the literature, the reported increase

  7. Combining parallel factor analysis and machine learning for the classification of dissolved organic matter according to source using fluorescence signatures.

    PubMed

    Cuss, C W; McConnell, S M; Guéguen, C

    2016-07-01

    Parallel factor (PARAFAC) analysis of dissolved organic matter (DOM) fluorescence has facilitated a surge of investigation into its biogeochemical cycling. However, rigorous, PARAFAC-based methods for holistically distinguishing DOM sources are lacking. This study classified 1029 PARAFAC-analyzed excitation-emission matrices (EEMs) measured using DOM isolated from 24 different leaf leachates, rivers, and organic matter standards using four machine learning methods (MLM). EEMs were also divided into subsets to assess the impact of experimental treatments (i.e. whole EEMs, size fractionation, mixtures, quenching) and dataset properties (i.e. different numbers of EEMs from each leachate/river) on classification. A split-half validated, 10-component PARAFAC model was extended to 12 components to remove consistent peaks evident in model residuals. The 12-component model performed better than the 10-component model, correctly classifying up to 80 additional EEMs, when the dataset included size-fractionated DOM or several different sources (i.e. many leaf species and rivers); however, the 10-component model performed better for whole-sample EEMs when comparing leaf leachates to rivers. The MLM correctly classified whole EEMs of riverine DOM by source with up to 87.0% accuracy, leachates with up to 92.5% accuracy, and distinguished leachates from rivers with 97.2% accuracy. A difference of up to 17.3% in classification accuracy was observed depending on the MLM method used with the following order: multilayer perceptron = support vector machine > k-nearest neighbours ≫ decision tree; however, performances differed widely depending on the data subset. Classification accuracy for whole and size-fractionated rivers compared to whole and size-fractionated leachates using N-way partial least-squares discriminant analysis (NPLS-DA; 97.7%) was similar to that achieved using MLM. Combining MLM with PARAFAC is an effective method for classifying DOM based on its

  8. Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer

    PubMed Central

    Watanabe, Kazuhide; Biesinger, Jacob; Salmans, Michael L.; Roberts, Brian S.; Arthur, William T.; Cleary, Michele; Andersen, Bogi; Xie, Xiaohui; Dai, Xing

    2014-01-01

    Background Deregulation of canonical Wnt/CTNNB1 (beta-catenin) pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 are highly frequent in colon cancer and cause aberrant stabilization of CTNNB1, which activates the transcription of Wnt target genes by binding to chromatin via the TCF/LEF transcription factors. Here we report an integrative analysis of genome-wide chromatin occupancy of CTNNB1 by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and gene expression profiling by microarray analysis upon RNAi-mediated knockdown of CTNNB1 in colon cancer cells. Results We observed 3629 CTNNB1 binding peaks across the genome and a significant correlation between CTNNB1 binding and knockdown-induced gene expression change. Our integrative analysis led to the discovery of a direct Wnt target signature composed of 162 genes. Gene ontology analysis of this signature revealed a significant enrichment of Wnt pathway genes, suggesting multiple feedback regulations of the pathway. We provide evidence that this gene signature partially overlaps with the Lgr5+ intestinal stem cell signature, and is significantly enriched in normal intestinal stem cells as well as in clinical colorectal cancer samples. Interestingly, while the expression of the CTNNB1 target gene set does not correlate with survival, elevated expression of negative feedback regulators within the signature predicts better prognosis. Conclusion Our data provide a genome-wide view of chromatin occupancy and gene regulation of Wnt/CTNNB1 signaling in colon cancer cells. PMID:24651522

  9. Seeking genetic signature of radiosensitivity - a novel method for data analysis in case of small sample sizes

    PubMed Central

    2014-01-01

    Background The identification of polymorphisms and/or genes responsible for an organism's radiosensitivity increases the knowledge about the cell cycle and the mechanism of the phenomena themselves, possibly providing the researchers with a better understanding of the process of carcinogenesis. Aim The aim of the study was to develop a data analysis strategy capable of discovering the genetic background of radiosensitivity in the case of small sample size studies. Results Among many indirect measures of radiosensitivity known, the level of radiation-induced chromosomal aberrations was used in the study. Mathematical modelling allowed the transformation of the yield-time curve of radiation-induced chromosomal aberrations into the exponential curve with limited number of parameters, while Gaussian mixture models applied to the distributions of these parameters provided the criteria for mouse strain classification. A detailed comparative analysis of genotypes between the obtained subpopulations of mice followed by functional validation provided a set of candidate polymorphisms that might be related to radiosensitivity. Among 1857 candidate relevant SNPs, that cluster in 28 genes, eight SNPs were detected nonsynonymous (nsSNP) on protein function. Two of them, rs48840878 (gene Msh3) and rs5144199 (gene Cc2d2a), were predicted as having increased probability of a deleterious effect. Additionally, rs48840878 is capable of disordering phosphorylation with 14 PKs. In silico analysis of candidate relevant SNP similarity score distribution among 60 CGD mouse strains allowed for the identification of SEA/GnJ and ZALENDE/EiJ mouse strains (95.26% and 86.53% genetic consistency respectively) as the most similar to radiosensitive subpopulation Conclusions A complete step-by-step strategy for seeking the genetic signature of radiosensitivity in the case of small sample size studies conducted on mouse models was proposed. It is shown that the strategy, which is a combination of

  10. Field Tests And Signature Analysis Of An Imaging CO2 Laser Radar

    NASA Astrophysics Data System (ADS)

    Wang, J. Y.; Bartholomew, B. J.; Streiff, M. L.; Starr, E. F.; Pruitt, P. A.

    1983-12-01

    A coherent, imaging CO2 laser radar has been built and tested in the field. This laser radar uses a single-waveguide CO2 laser and heterodyne detection. Two acousto-optic frequency shifters generate the IF frequency. An acousto-optic standing-wave device provides the 15 MHz intensity modulation used for ranging. The sensor includes a two-axis, dual-aperture galvonometer scanner with selectable field of view and depression angles. The optical system fits on an easily transportable 3 ft by 4 ft optical bench. Both reflectance and range images are produced. The range imagery analysis shows a range resolution of approximately one foot. Statistical analysis of the reflectance data from a military truck, the dirt ground, and an asphalt road shows that they are Rayleigh distributed. The reflectivities of these objects are determined to be around two percent through comparison with laboratory reflectometer measurements.

  11. Metabonomic signature analysis of cervical carcinoma and precancerous lesions in women by (1)H NMR spectroscopy.

    PubMed

    Hasim, Ayshamgul; Ali, Mayinuer; Mamtimin, Batur; Ma, Jun-Qi; Li, Qiao-Zhi; Abudula, Abulizi

    2012-06-01

    (1)H nuclear magnetic resonance (NMR)-based metabonomics has been used to characterize the metabolic profiles of cervical intraepithelial neoplasia (CIN) and cervical squamous cell carcinoma (CSCC). Principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) were used to model the systematic variation related to patients with CIN or CSCC with healthy controls. Potential metabolic biomarkers were identified using database comparisons, and the one-way analysis of variance (ANOVA) test was used to examine the significance of the metabolites. Compared with plasma obtained from the healthy controls, plasma from patients with CIN had higher levels of very-low density lipoprotein (VLDL), acetone, unsaturated lipid and carnitine, together with lower levels of creatine, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine, glycine, acetylcysteine, myo-inositol, choline and glycoprotein. Plasma from patients with CSCC had higher levels of acetate and formate, together with lower levels of creatine, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine and tyrosine compared with the plasma of the healthy controls. In addition, compared with the plasma of patients with CIN, the plasma of CSCC patients had higher levels of acetate, formate, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine, tyrosine, acetylcysteine, myo-inositol, glycoprotein, α-glucose and β-glucose, together with lower levels of acetone, unsaturated lipid and carnitine. Moreover, the profiles showed high feasibility and specificity by statistical analysis with OPLS-DA compared to the Thinprep cytology test (TCT) by setting the histopathological outcome as standard. The metabolic profile obtained for cervical cancer is significant, even for the precancerous disease. This suggests a systemic metabolic response to cancer, which may be used to identify potential early diagnostic biomarkers of the cancer and to establish

  12. Metabonomic signature analysis of cervical carcinoma and precancerous lesions in women by 1H NMR spectroscopy

    PubMed Central

    HASIM, AYSHAMGUL; ALI, MAYINUER; MAMTIMIN, BATUR; MA, JUN-QI; LI, QIAO-ZHI; ABUDULA, ABULIZI

    2012-01-01

    1H nuclear magnetic resonance (NMR)-based metabonomics has been used to characterize the metabolic profiles of cervical intraepithelial neoplasia (CIN) and cervical squamous cell carcinoma (CSCC). Principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) were used to model the systematic variation related to patients with CIN or CSCC with healthy controls. Potential metabolic biomarkers were identified using database comparisons, and the one-way analysis of variance (ANOVA) test was used to examine the significance of the metabolites. Compared with plasma obtained from the healthy controls, plasma from patients with CIN had higher levels of very-low density lipoprotein (VLDL), acetone, unsaturated lipid and carnitine, together with lower levels of creatine, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine, glycine, acetylcysteine, myo-inositol, choline and glycoprotein. Plasma from patients with CSCC had higher levels of acetate and formate, together with lower levels of creatine, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine and tyrosine compared with the plasma of the healthy controls. In addition, compared with the plasma of patients with CIN, the plasma of CSCC patients had higher levels of acetate, formate, lactate, isoleucine, leucine, valine, alanine, glutamine, histidine, tyrosine, acetylcysteine, myo-inositol, glycoprotein, α-glucose and β-glucose, together with lower levels of acetone, unsaturated lipid and carnitine. Moreover, the profiles showed high feasibility and specificity by statistical analysis with OPLS-DA compared to the Thinprep cytology test (TCT) by setting the histopathological outcome as standard. The metabolic profile obtained for cervical cancer is significant, even for the precancerous disease. This suggests a systemic metabolic response to cancer, which may be used to identify potential early diagnostic biomarkers of the cancer and to establish

  13. Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress.

    PubMed

    Chitraju, Chandramohan; Trötzmüller, Martin; Hartler, Jürgen; Wolinski, Heimo; Thallinger, Gerhard G; Lass, Achim; Zechner, Rudolf; Zimmermann, Robert; Köfeler, Harald C; Spener, Friedrich

    2012-10-01

    Liver steatosis can be induced by fasting or high-fat diet. We investigated by lipidomic analysis whether such metabolic states are reflected in the lipidome of hepatocyte lipid droplets (LDs) from mice fed normal chow diet (FED), fasted (FAS), or fed a high-fat diet (HFD). LC-MS/MS at levels of lipid species profiles and of lipid molecular species uncovered a FAS phenotype of LD enriched in triacylglycerol (TG) molecular species with very long-chain (VLC)-PUFA residues and an HFD phenotype with less unsaturated TG species in addition to characteristic lipid marker species. Nutritional stress did not result in dramatic structural alterations in diacylglycerol (DG) and phospholipid (PL) classes. Moreover, molecular species of bulk TG and of DG indicated concomitant de novo TG synthesis and lipase-catalyzed degradation to be active in LDs. DG species with VLC-PUFA residues would be preferred precursors for phosphatidylcholine (PC) species, the others for TG molecular species. In addition, molecular species of PL classes fitted the hepatocyte Kennedy and phosphatidylethanolamine methyltransferase pathways. We demonstrate that lipidomic analysis of LDs enables phenotyping of nutritional stress. TG species are best suited for such phenotyping, whereas structural analysis of TG, DG, and PL molecular species provides metabolic insights. PMID:22872753

  14. Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization

    PubMed Central

    Dequéant, Mary-Lee; Fagegaltier, Delphine; Hu, Yanhui; Spirohn, Kerstin; Simcox, Amanda; Hannon, Gregory J.; Perrimon, Norbert

    2015-01-01

    The use of time series profiling to identify groups of functionally related genes (synexpression groups) is a powerful approach for the discovery of gene function. Here we apply this strategy during RasV12 immortalization of Drosophila embryonic cells, a phenomenon not well characterized. Using high-resolution transcriptional time-series datasets, we generated a gene network based on temporal expression profile similarities. This analysis revealed that common immortalized cells are related to adult muscle precursors (AMPs), a stem cell-like population contributing to adult muscles and sharing properties with vertebrate satellite cells. Remarkably, the immortalized cells retained the capacity for myogenic differentiation when treated with the steroid hormone ecdysone. Further, we validated in vivo the transcription factor CG9650, the ortholog of mammalian Bcl11a/b, as a regulator of AMP proliferation predicted by our analysis. Our study demonstrates the power of time series synexpression analysis to characterize Drosophila embryonic progenitor lines and identify stem/progenitor cell regulators. PMID:26438832

  15. ANALYSIS OF RICIN TOXIN PREPARATIONS FOR CARBOHYDRATE AND FATTY ACID ABUNDANCE AND ISOTOPE RATIO INFORMATION

    SciTech Connect

    Wunschel, David S.; Kreuzer-Martin, Helen W.; Antolick, Kathryn C.; Colburn, Heather A.; Moran, James J.; Melville, Angela M.

    2009-12-01

    This report describes method development and preliminary evaluation for analyzing castor samples for signatures of purifying ricin. Ricin purification from the source castor seeds is essentially a problem of protein purification using common biochemical methods. Indications of protein purification will likely manifest themselves as removal of the non-protein fractions of the seed. Two major, non-protein, types of biochemical constituents in the seed are the castor oil and various carbohydrates. The oil comprises roughly half the seed weight while the carbohydrate component comprises roughly half of the remaining “mash” left after oil and hull removal. Different castor oil and carbohydrate components can serve as indicators of specific toxin processing steps. Ricinoleic acid is a relatively unique fatty acid in nature and is the most abundant component of castor oil. The loss of ricinoleic acid indicates a step to remove oil from the seeds. The relative amounts of carbohydrates and carbohydrate-like compounds, including arabinose, xylose, myo-inositol fucose, rhamnose, glucosamine and mannose detected in the sample can also indicate specific processing steps. For instance, the differential loss of arabinose relative to mannose and N-acetyl glucosamine indicates enrichment for the protein fraction of the seed using protein precipitation. The methods developed in this project center on fatty acid and carbohydrate extraction from castor samples followed by derivatization to permit analysis by gas chromatography-mass spectrometry (GC-MS). Method descriptions herein include: the source and preparation of castor materials used for method evaluation, the equipment and description of procedure required for chemical derivatization, and the instrument parameters used in the analysis. Two types of derivatization methods describe analysis of carbohydrates and one procedure for analysis of fatty acids. Two types of GC-MS analysis is included in the method development, one

  16. Metabolic Signature of Electrosurgical Liver Dissection

    PubMed Central

    von Schönfels, Witigo; von Kampen, Oliver; Patsenker, Eleonora; Stickel, Felix; Schniewind, Bodo; Hinz, Sebastian; Ahrens, Markus; Balschun, Katharina; Egberts, Jan-Hendrik; Richter, Klaus; Landrock, Andreas; Sipos, Bence; Will, Olga; Huebbe, Patrizia; Schreiber, Stefan; Nothnagel, Michael; Röcken, Christoph; Rimbach, Gerald; Becker, Thomas

    2013-01-01

    Background and Aims High frequency electrosurgery has a key role in the broadening application of liver surgery. Its molecular signature, i.e. the metabolites evolving from electrocauterization which may inhibit hepatic wound healing, have not been systematically studied. Methods Human liver samples were thus obtained during surgery before and after electrosurgical dissection and subjected to a two-stage metabolomic screening experiment (discovery sample: N = 18, replication sample: N = 20) using gas chromatography/mass spectrometry. Results In a set of 208 chemically defined metabolites, electrosurgical dissection lead to a distinct metabolic signature resulting in a separation in the first two dimensions of a principal components analysis. Six metabolites including glycolic acid, azelaic acid, 2-n-pentylfuran, dihydroactinidiolide, 2-butenal and n-pentanal were consistently increased after electrosurgery meeting the discovery (p<2.0×10−4) and the replication thresholds (p<3.5×10−3). Azelaic acid, a lipid peroxidation product from the fragmentation of abundant sn-2 linoleoyl residues, was most abundant and increased 8.1-fold after electrosurgical liver dissection (preplication = 1.6×10−4). The corresponding phospholipid hexadecyl azelaoyl glycerophosphocholine inhibited wound healing and tissue remodelling in scratch- and proliferation assays of hepatic stellate cells and cholangiocytes, and caused apoptosis dose-dependently in vitro, which may explain in part the tissue damage due to electrosurgery. Conclusion Hepatic electrosurgery generates a metabolic signature with characteristic lipid peroxidation products. Among these, azelaic acid shows a dose-dependent toxicity in liver cells and inhibits wound healing. These observations potentially pave the way for pharmacological intervention prior liver surgery to modify the metabolic response and prevent postoperative complications. PMID:24058442

  17. Hair sterol signatures coupled to multivariate data analysis reveal an increased 7β-hydroxycholesterol production in cognitive impairment.

    PubMed

    Son, Hyun-Hwa; Lee, Do-Yup; Seo, Hong Seog; Jeong, Jihyeon; Moon, Ju-Yeon; Lee, Jung-Eun; Chung, Bong Chul; Kim, Eosu; Choi, Man Ho

    2016-01-01

    Altered cholesterol metabolism could be associated with cognitive impairment. The quantitative profiling of 19 hair sterols was developed using gas chromatography-mass spectrometry coupled to multivariate data analysis. The limit of quantification of all sterols ranged from 5 to 20 ng/g, while the calibration linearity was higher than 0.98. The precision (% CV) and accuracy (% bias) ranged from 3.2% to 9.8% and from 83.2% to 119.4%, respectively. Among the sterols examined, 8 were quantitatively detected from two strands of 3-cm-long scalp hair samples of female participants, including mild cognitive impairment (MCI, n=15), Alzheimer's disease (AD, n=31), and healthy controls (HC, n=36). The cognitive impairment (MCI or AD) was correlated with a higher metabolic rate than that of HCs based on 7β-hydroxycholesterol (P<0.005). Significant negative correlations (r=-0.822) were detected between Mini-Mental State Examination (MMSE) scores and hair sample metabolic ratios of 7β-hydroxycholesterol to cholesterol, which is an accepted, sensitive, and specific tool for discriminating HCs from individuals with MCI or AD. In conclusion, improved diagnostic values can be obtained using hair sterol signatures coupled with MMSE scores. This method may prove useful for predictive diagnosis in population screening of cognitive impairment. PMID:26385606

  18. Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis

    PubMed Central

    Bahbahani, Hussain; Clifford, Harry; Wragg, David; Mbole-Kariuki, Mary N; Van Tassell, Curtis; Sonstegard, Tad; Woolhouse, Mark; Hanotte, Olivier

    2015-01-01

    The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and four reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following FST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics. PMID:26130263

  19. Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis.

    PubMed

    Bahbahani, Hussain; Clifford, Harry; Wragg, David; Mbole-Kariuki, Mary N; Van Tassell, Curtis; Sonstegard, Tad; Woolhouse, Mark; Hanotte, Olivier

    2015-01-01

    The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and four reference populations (Holstein-Friesian, Jersey, N'Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following FST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics. PMID:26130263

  20. Cortical signature of patients with HBV-related cirrhosis without overt hepatic encephalopathy: a morphometric analysis.

    PubMed

    Wu, Xiu; Lv, Xiao-Fei; Zhang, Yu-Ling; Wu, Hua-Wang; Cai, Pei-Qiang; Qiu, Ying-Wei; Zhang, Xue-Lin; Jiang, Gui-Hua

    2015-01-01

    Previous studies have shown that patients with hepatitis B virus-related cirrhosis (HBV-RC) without overt hepatic encephalopathy (OHE) are associated with a varying degree of cognitive dysfunction. Several resting-state functional magnetic resonance imaging (fMRI) studies have been conducted to explore the neural correlates of such cognitive deficits, whereas little effort has been made to investigate the cortical integrity in cirrhotic patients without OHE. Here, using cortical thickness, surface area and local gyrification index (lGI), this study performed a comprehensive analysis on the cortical morphometry of patients with HBV-RC without OHE (HBV-RC-NOHE) vs. matched healthy controls. Compared with healthy controls, we found significantly increased cortical thickness in the bilateral lingual and parahippocampal gyrus, right posterior cingulate cortex, precuneus, peri-calcarine sulcus and fusiform gyrus in patient with HBV-RC-NOHE, which may closely relate to be the low-grade brain edema. Cortical gyrification analysis showed significantly increased lGI in the left superior and inferior parietal cortex as well as lateral occipital cortex, which was speculated to be associated with disruptions in white matter connectivity and sub-optimal intra-cortical organization. In addition, the mean cortical thickness/lGI of the regions with structural abnormalities was shown to be negatively correlated with psychometric hepatic encephalopathy score (PHES) of the patients with HBV-RC-NOHE. These morphological changes may serve as potential markers for the preclinical diagnosis and progression of HBV-RC-NOHE. PMID:26106307

  1. Investigating regulatory signatures of human autophagy related gene 5 (ATG5) through functional in silico analysis.

    PubMed

    Vij, Avni; Randhawa, Rohit; Parkash, Jyoti; Changotra, Harish

    2016-09-01

    Autophagy is an essential, homeostatic process which removes damaged cellular proteins and organelles for cellular renewal. ATG5, a part of E3 ubiquitin ligase-like complex (Atg12-Atg5/Atg16L1), is a key regulator involved in autophagosome formation - a crucial phase of autophagy. In this study, we used different in silico methods for comprehensive analysis of ATG5 to investigate its less explored regulatory activity. We have predicted various physico-chemical parameters and two possible transmembrane models that helped in exposing its functional regions. Twenty four PTM sites and 44 TFBS were identified which could be targeted to modulate the autophagy pathway. Furthermore, LD analysis identified 3 blocks of genotyped SNPs and 2 deleterious nsSNPs that may have damaging impact on protein function and thus could be employed for carrying genome-wide association studies. In conclusion, the information obtained in this study could be helpful for better understanding of regulatory roles of ATG5 and provides a base for its implication in population-based studies. PMID:27617225

  2. Cortical signature of patients with HBV-related cirrhosis without overt hepatic encephalopathy: a morphometric analysis

    PubMed Central

    Wu, Xiu; Lv, Xiao-Fei; Zhang, Yu-Ling; Wu, Hua-Wang; Cai, Pei-Qiang; Qiu, Ying-Wei; Zhang, Xue-Lin; Jiang, Gui-Hua

    2015-01-01

    Previous studies have shown that patients with hepatitis B virus-related cirrhosis (HBV-RC) without overt hepatic encephalopathy (OHE) are associated with a varying degree of cognitive dysfunction. Several resting-state functional magnetic resonance imaging (fMRI) studies have been conducted to explore the neural correlates of such cognitive deficits, whereas little effort has been made to investigate the cortical integrity in cirrhotic patients without OHE. Here, using cortical thickness, surface area and local gyrification index (lGI), this study performed a comprehensive analysis on the cortical morphometry of patients with HBV-RC without OHE (HBV-RC-NOHE) vs. matched healthy controls. Compared with healthy controls, we found significantly increased cortical thickness in the bilateral lingual and parahippocampal gyrus, right posterior cingulate cortex, precuneus, peri-calcarine sulcus and fusiform gyrus in patient with HBV-RC-NOHE, which may closely relate to be the low-grade brain edema. Cortical gyrification analysis showed significantly increased lGI in the left superior and inferior parietal cortex as well as lateral occipital cortex, which was speculated to be associated with disruptions in white matter connectivity and sub-optimal intra-cortical organization. In addition, the mean cortical thickness/lGI of the regions with structural abnormalities was shown to be negatively correlated with psychometric hepatic encephalopathy score (PHES) of the patients with HBV-RC-NOHE. These morphological changes may serve as potential markers for the preclinical diagnosis and progression of HBV-RC-NOHE. PMID:26106307

  3. Molecular modeling, spectroscopic signature and NBO analysis of some building blocks of organic conductors.

    PubMed

    Mukherjee, V

    2014-11-11

    Vibrational spectra with IR and Raman intensities in optimum state have been calculated for 2,2'-Bi-1,3-diselenole (commonly known as tetraselenafulvalene) and its halogen derivatives. All these calculations have been done by employing density functional theory (DFT) and second order Moller-Plesset perturbation theory (MP2) methods incorporated with suitable functionals and basis sets. Normal coordinate analysis has also been performed to calculate potential energy distributions (PEDs) to make a conspicuous assignment. The vibrational frequencies of all the four molecules have been assigned using PEDs and the results are compared with available values for the most similar molecules like tetrathiafulvalene. The molecular stability and bond strength have investigated by applying the Natural Bond Orbital (NBO) analysis. The energy gap between HOMO and LUMO is 2.041 eV for tetraselenafulvalene and it is slightly less than 2eV for halogen derivatives which implies that these molecules fall in the wide band gap semiconductor groups. PMID:24858351

  4. Detecting of transient vibration signatures using an improved fast spatial-spectral ensemble kurtosis kurtogram and its applications to mechanical signature analysis of short duration data from rotating machinery

    NASA Astrophysics Data System (ADS)

    Chen, BinQiang; Zhang, ZhouSuo; Zi, YanYang; He, ZhengJia; Sun, Chuang

    2013-10-01

    Detecting transient vibration signatures is of vital importance for vibration-based condition monitoring and fault detection of the rotating machinery. However, raw mechanical signals collected by vibration sensors are generally mixtures of physical vibrations of the multiple mechanical components installed in the examined machinery. Fault-generated incipient vibration signatures masked by interfering contents are difficult to be identified. The fast kurtogram (FK) is a concise and smart gadget for characterizing these vibration features. The multi-rate filter-bank (MRFB) and the spectral kurtosis (SK) indicator of the FK are less powerful when strong interfering vibration contents exist, especially when the FK are applied to vibration signals of short duration. It is encountered that the impulsive interfering contents not authentically induced by mechanical faults complicate the optimal analyzing process and lead to incorrect choosing of the optimal analysis subband, therefore the original FK may leave out the essential fault signatures. To enhance the analyzing performance of FK for industrial applications, an improved version of fast kurtogram, named as "fast spatial-spectral ensemble kurtosis kurtogram", is presented. In the proposed technique, discrete quasi-analytic wavelet tight frame (QAWTF) expansion methods are incorporated as the detection filters. The QAWTF, constructed based on dual tree complex wavelet transform, possesses better vibration transient signature extracting ability and enhanced time-frequency localizability compared with conventional wavelet packet transforms (WPTs). Moreover, in the constructed QAWTF, a non-dyadic ensemble wavelet subband generating strategy is put forward to produce extra wavelet subbands that are capable of identifying fault features located in transition-band of WPT. On the other hand, an enhanced signal impulsiveness evaluating indicator, named "spatial-spectral ensemble kurtosis" (SSEK), is put forward and utilized

  5. Biogeochemical Signatures of Contaminant Transport at the Watershed Scale: Spectral and Wavelet Analysis (Invited)

    NASA Astrophysics Data System (ADS)

    Guan, K.; Harman, C. J.; Basu, N. B.; Rao, S. S.; Sivapalan, M.; Kalita, P. K.; Packman, A. I.

    2009-12-01

    Agricultural watersheds are intensely managed systems, and consist of a large number of dynamic components that interact non-linearly to create emergent patterns in space and time. These systems can be conceptualized as input signals (“drivers”) that cascade through a hierarchy of non-linear “filters” to create the modulated spatial and temporal responses (“signatures”). The coupling between flow and transport (“hydrologic filter”) and transformations (“biogeochemical filter”) control the cascading processes from precipitation through stream flow, and finally to chemical concentrations and loads, at various nested spatial and temporal scales. To detect important “signatures”, we applied spectral analysis and wavelet coherence to the 10-year dataset (at daily resolution) collected from Little Vermillion River watershed (Illinois, USA), an agricultural watershed (~400 km2), drained by an extensive network of subsurface tiles, surface ditches, and streams. Watershed monitoring data includes hydrologic measurements (flow and stage), and concentrations of chemical constituents (nitrate, phosphate, and pesticides) across different spatial scales, from tile-flow stations (drainage area ~ 0.05 km2) to river stations (drainage area ~400 km2). We find that a power-law scaling behavior exists in all the smoothed power spectra for precipitation, stream flow, nitrate concentration and load. The slopes of power spectra increase from precipitation to stream flow to nitrate concentration, demonstrating the cascading effect of the filters. The spectral analysis further shows that the filters retain the major characteristics of long-term response (annual and sub-annual cycle), but smooth (or filter) the short-term responses. Steeper slopes are observed at larger spatial scales, indicating a stronger filtering effect due to greater averaging (buffering) with increasing residence time. Further data analysis using wavelet coherence suggests that at small spatial

  6. Evaluation of Meterorite Amono Acid Analysis Data Using Multivariate Techniques

    NASA Technical Reports Server (NTRS)

    McDonald, G.; Storrie-Lombardi, M.; Nealson, K.

    1999-01-01

    The amino acid distributions in the Murchison carbonaceous chondrite, Mars meteorite ALH84001, and ice from the Allan Hills region of Antarctica are shown, using a multivariate technique known as Principal Component Analysis (PCA), to be statistically distinct from the average amino acid compostion of 101 terrestrial protein superfamilies.

  7. Acid Rain Analysis by Standard Addition Titration.

    ERIC Educational Resources Information Center

    Ophardt, Charles E.

    1985-01-01

    The standard addition titration is a precise and rapid method for the determination of the acidity in rain or snow samples. The method requires use of a standard buret, a pH meter, and Gran's plot to determine the equivalence point. Experimental procedures used and typical results obtained are presented. (JN)

  8. Vertical stratification of fatty acids in the blubber of southern elephant seals (Mirounga leonina): implications for diet analysis.

    PubMed

    Best, Narelle J; Bradshaw, Corey J A; Hindell, Mark A; Nichols, Peter D

    2003-02-01

    Fatty acid signature analysis (FASA) is a powerful ecological tool that uses essential fatty acids (FA) from the tissues of animals to indicate aspects of diet. However, the presence of vertical stratification in FA distribution throughout blubber complicates the application of FASA to marine mammals. Blubber biopsy samples were collected from adult female southern elephant seals (Mirounga leonina) from Macquarie Island (n=11), and blubber cores were divided into inner and outer sections to determine the degree to which the blubber layer was stratified in FA composition, we found 19 FA from both blubber layers in greater than trace amounts (>0.5%). The inner and outer blubber layers could be separated using principal components analysis based on the relative proportion of FA in each layer. Dietary polyunsaturated fatty acids (PUFA) were also observed in significantly higher proportions in the inner blubber layer. Due to the degree of FA stratification in southern elephant seals, we concur with other marine mammal studies that sampling only the outer blubber layer will result in a loss of recently accumulated information regarding diet structure (as indicated by 'surplus' PUFA from the diet). This finding suggests that differential mobilization/deposition of certain FA may result in a modified signature from prey to predator. Thus, sampling animals to recover the inner blubber layer is important for studies attempting to describe aspects of marine mammal diet. This can be achieved in animals such as pinnipeds where the whole blubber layer can be readily sampled. PMID:12568803

  9. A mitochondrial analysis reveals distinct founder effect signatures in Canarian and Balearic goats.

    PubMed

    Ferrando, A; Manunza, A; Jordana, J; Capote, J; Pons, A; Pais, J; Delgado, T; Atoche, P; Cabrera, B; Martínez, A; Landi, V; Delgado, J V; Argüello, A; Vidal, O; Lalueza-Fox, C; Ramírez, O; Amills, M

    2015-08-01

    In the course of human migrations, domestic animals often have been translocated to islands with the aim of assuring food availability. These founder events are expected to leave a genetic footprint that may be recognised nowadays. Herewith, we have examined the mitochondrial diversity of goat populations living in the Canarian and Balearic archipelagos. Median-joining network analysis produced very distinct network topologies for these two populations. Indeed, a majority of Canarian goats shared a single ancestral haplotype that segregated in all sampled islands, suggesting a single founder effect followed by a stepping-stone pattern of diffusion. This haplotype also was present in samples collected from archaeological assemblies at Gran Canaria and Lanzarote, making evident its widespread distribution in ancient times. In stark contrast, goats from Majorca and Ibiza did not share any mitochondrial haplotypes, indicating the occurrence of two independent founder events. Furthermore, in Majorcan goats, we detected the segregation of the mitochondrial G haplogroup that has only been identified in goats from Egypt, Iran and Turkey. This finding suggests the translocation of Asian and/or African goats to Majorca, possibly as a consequence of the Phoenician and Carthaginian colonisations of this island. PMID:26153924

  10. Analysis of the Effects of Streamwise Lift Distribution on Sonic Boom Signature

    NASA Technical Reports Server (NTRS)

    Yoo, Paul

    2013-01-01

    Investigation of sonic boom has been one of the major areas of study in aeronautics due to the benefits a low-boom aircraft has in both civilian and military applications. This work conducts a numerical analysis of the effects of streamwise lift distribution on the shock coalescence characteristics. A simple wing-canard-stabilator body model is used in the numerical simulation. The streamwise lift distribution is varied by fixing the canard at a deflection angle while trimming the aircraft with the wing and the stabilator at the desired lift coefficient. The lift and the pitching moment coefficients are computed using the Missile DATCOM v. 707. The flow field around the wing-canard- stabilator body model is resolved using the OVERFLOW-2 flow solver. Overset/ chimera grid topology is used to simplify the grid generation of various configurations representing different streamwise lift distributions. The numerical simulations are performed without viscosity unless it is required for numerical stability. All configurations are simulated at Mach 1.4, angle-of-attack of 1.50, lift coefficient of 0.05, and pitching moment coefficient of approximately 0. Four streamwise lift distribution configurations were tested.

  11. Transcriptome analysis reveals a classical interferon signature induced by IFNλ4 in human primary cells.

    PubMed

    Lauber, C; Vieyres, G; Terczyńska-Dyla, E; Anggakusuma; Dijkman, R; Gad, H H; Akhtar, H; Geffers, R; Vondran, F W R; Thiel, V; Kaderali, L; Pietschmann, T; Hartmann, R

    2015-09-01

    The IFNL4 gene is negatively associated with spontaneous and treatment-induced clearance of hepatitis C virus infection. The activity of IFNλ4 has an important causal role in the pathogenesis, but the molecular details are not fully understood. One possible reason for the detrimental effect of IFNλ4 could be a tissue-specific regulation of an unknown subset of genes. To address both tissue and subtype specificity in the interferon response, we treated primary human hepatocytes and airway epithelial cells with IFNα, IFNλ3 or IFNλ4 and assessed interferon mediated gene regulation using transcriptome sequencing. Our data show a surprisingly similar response to all three subtypes of interferon. We also addressed the tissue specificity of the response, and identified a subset of tissue-specific genes. However, the interferon response is robust in both tissues with the majority of the identified genes being regulated in hepatocytes as well as airway epithelial cells. Thus we provide an in-depth analysis of the liver interferon response seen over an array of interferon subtypes and compare it to the response in the lung epithelium. PMID:26066369

  12. Signatures of Steady Heating in Time Lag Analysis of Coronal Emission

    NASA Astrophysics Data System (ADS)

    Viall, Nicholeen M.; Klimchuk, James A.

    2016-09-01

    Among the multitude of methods used to investigate coronal heating, the time lag method of Viall & Klimchuk is becoming increasingly prevalent as an analysis technique that is complementary to those that are traditionally used. The time lag method cross correlates light curves at a given spatial location obtained in spectral bands that sample different temperature plasmas. It has been used most extensively with data from the Atmospheric Imaging Assembly on the Solar Dynamics Observatory. We have previously applied the time lag method to entire active regions and surrounding the quiet Sun and created maps of the results. We find that the majority of time lags are consistent with the cooling of coronal plasma that has been impulsively heated. Additionally, a significant fraction of the map area has a time lag of zero. This does not indicate a lack of variability. Rather, strong variability must be present, and it must occur in phase between the different channels. We have previously shown that these zero time lags are consistent with the transition region response to coronal nanoflares, although other explanations are possible. A common misconception is that the zero time lag indicates steady emission resulting from steady heating. Using simulated and observed light curves, we demonstrate here that highly correlated light curves at zero time lag are not compatible with equilibrium solutions. Such light curves can only be created by evolution.

  13. Septic Shock in Advanced Age: Transcriptome Analysis Reveals Altered Molecular Signatures in Neutrophil Granulocytes

    PubMed Central

    Vieira da Silva Pellegrina, Diogo; Severino, Patricia; Vieira Barbeiro, Hermes; Maziero Andreghetto, Flávia; Tadeu Velasco, Irineu; Possolo de Souza, Heraldo; Machado, Marcel Cerqueira César; Reis, Eduardo Moraes; Pinheiro da Silva, Fabiano

    2015-01-01

    Sepsis is one of the highest causes of mortality in hospitalized people and a common complication in both surgical and clinical patients admitted to hospital for non-infectious reasons. Sepsis is especially common in older people and its incidence is likely to increase substantially as a population ages. Despite its increased prevalence and mortality in older people, immune responses in the elderly during septic shock appear similar to that in younger patients. The purpose of this study was to conduct a genome-wide gene expression analysis of circulating neutrophils from old and young septic patients to better understand how aged individuals respond to severe infectious insult. We detected several genes whose expression could be used to differentiate immune responses of the elderly from those of young people, including genes related to oxidative phosphorylation, mitochondrial dysfunction and TGF-β signaling, among others. Our results identify major molecular pathways that are particularly affected in the elderly during sepsis, which might have a pivotal role in worsening clinical outcomes compared with young people with sepsis. PMID:26047321

  14. Analysis of Transcriptional Signatures in Response to Listeria monocytogenes Infection Reveals Temporal Changes That Result from Type I Interferon Signaling

    PubMed Central

    Potempa, Krzysztof; Graham, Christine M.; Moreira-Teixeira, Lucia; McNab, Finlay W.; Howes, Ashleigh; Stavropoulos, Evangelos; Pascual, Virginia; Banchereau, Jacques; Chaussabel, Damien; O’Garra, Anne

    2016-01-01

    Analysis of the mouse transcriptional response to Listeria monocytogenes infection reveals that a large set of genes are perturbed in both blood and tissue and that these transcriptional responses are enriched for pathways of the immune response. Further we identified enrichment for both type I and type II interferon (IFN) signaling molecules in the blood and tissues upon infection. Since type I IFN signaling has been reported widely to impair bacterial clearance we examined gene expression from blood and tissues of wild type (WT) and type I IFNαβ receptor-deficient (Ifnar1-/-) mice at the basal level and upon infection with L. monocytogenes. Measurement of the fold change response upon infection in the absence of type I IFN signaling demonstrated an upregulation of specific genes at day 1 post infection. A less marked reduction of the global gene expression signature in blood or tissues from infected Ifnar1-/- as compared to WT mice was observed at days 2 and 3 after infection, with marked reduction in key genes such as Oasg1 and Stat2. Moreover, on in depth analysis, changes in gene expression in uninfected mice of key IFN regulatory genes including Irf9, Irf7, Stat1 and others were identified, and although induced by an equivalent degree upon infection this resulted in significantly lower final gene expression levels upon infection of Ifnar1-/- mice. These data highlight how dysregulation of this network in the steady state and temporally upon infection may determine the outcome of this bacterial infection and how basal levels of type I IFN-inducible genes may perturb an optimal host immune response to control intracellular bacterial infections such as L. monocytogenes. PMID:26918359

  15. A Mariner Transposon-Based Signature-Tagged Mutagenesis System for the Analysis of Oral Infection by Listeria monocytogenes

    PubMed Central

    Cummins, Joanne; Casey, Pat G.; Joyce, Susan A.; Gahan, Cormac G. M.

    2013-01-01

    Listeria monocytogenes is a Gram-positive foodborne pathogen and the causative agent of listerosis a disease that manifests predominately as meningitis in the non-pregnant individual or infection of the fetus and spontaneous abortion in pregnant women. Common-source outbreaks of foodborne listeriosis are associated with significant morbidity and mortality. However, relatively little is known concerning the mechanisms that govern infection via the oral route. In order to aid functional genetic analysis of the gastrointestinal phase of infection we designed a novel signature-tagged mutagenesis (STM) system based upon the invasive L. monocytogenes 4b serotype H7858 strain. To overcome the limitations of gastrointestinal infection by L. monocytogenes in the mouse model we created a H7858 strain that is genetically optimised for oral infection in mice. Furthermore our STM system was based upon a mariner transposon to favour numerous and random transposition events throughout the L. monocytogenes genome. Use of the STM bank to investigate oral infection by L. monocytogenes identified 21 insertion mutants that demonstrated significantly reduced potential for infection in our model. The sites of transposon insertion included lmOh7858_0671 (encoding an internalin homologous to Lmo0610), lmOh7858_0898 (encoding a putative surface-expressed LPXTG protein homologous to Lmo0842), lmOh7858_2579 (encoding the HupDGC hemin transport system) and lmOh7858_0399 (encoding a putative fructose specific phosphotransferase system). We propose that this represents an optimised STM system for functional genetic analysis of foodborne/oral infection by L. monocytogenes. PMID:24069416

  16. Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis.

    PubMed

    Lakshmanan, Meiyappan; Lim, Sun-Hyung; Mohanty, Bijayalaxmi; Kim, Jae Kwang; Ha, Sun-Hwa; Lee, Dong-Yup

    2015-12-01

    Light quality is an important signaling component upon which plants orchestrate various morphological processes, including seed germination and seedling photomorphogenesis. However, it is still unclear how plants, especially food crops, sense various light qualities and modulate their cellular growth and other developmental processes. Therefore, in this work, we initially profiled the transcripts of a model crop, rice (Oryza sativa), under four different light treatments (blue, green, red, and white) as well as in the dark. Concurrently, we reconstructed a fully compartmentalized genome-scale metabolic model of rice cells, iOS2164, containing 2,164 unique genes, 2,283 reactions, and 1,999 metabolites. We then combined the model with transcriptome profiles to elucidate the light-specific transcriptional signatures of rice metabolism. Clearly, light signals mediated rice gene expressions, differentially regulating numerous metabolic pathways: photosynthesis and secondary metabolism were up-regulated in blue light, whereas reserve carbohydrates degradation was pronounced in the dark. The topological analysis of gene expression data with the rice genome-scale metabolic model further uncovered that phytohormones, such as abscisate, ethylene, gibberellin, and jasmonate, are the key biomarkers of light-mediated regulation, and subsequent analysis of the associated genes' promoter regions identified several light-specific transcription factors. Finally, the transcriptional control of rice metabolism by red and blue light signals was assessed by integrating the transcriptome and metabolome data with constraint-based modeling. The biological insights gained from this integrative systems biology approach offer several potential applications, such as improving the agronomic traits of food crops and designing light-specific synthetic gene circuits in microbial and mammalian systems. PMID:26453433

  17. Molecular signature of disease onset in granulin mutation carriers: a gene expression analysis study.

    PubMed

    Milanesi, Elena; Bonvicini, Cristian; Alberici, Antonella; Pilotto, Andrea; Cattane, Nadia; Premi, Enrico; Gazzina, Stefano; Archetti, Silvana; Gasparotti, Roberto; Cancelli, Vanessa; Gennarelli, Massimo; Padovani, Alessandro; Borroni, Barbara

    2013-07-01

    Mutations within Granulin (GRN) gene are causative of autosomal dominant frontotemporal lobar degeneration (FTLD). Though GRN mutations are inherited at birth, the disease onset usually occurs in the sixth decade of life. The objective of this study was to identify new genetic pathways linked to inherited GRN disease and involved in the shift from asymptomatic to symptomatic stages. Microarray gene expression analysis on leukocytes was carried out on 15 patients carrying GRN T272SfsX10 mutation, and their asymptomatic siblings with (n = 14) or without (n = 11) GRN mutation. The results were then validated by real-time polymerase chain reaction, and compared with those obtained in a cohort of FTLD without GRN mutation (n = 16). The association between candidate genes and damage of specific brain areas was investigated by voxel-based morphometry on magnetic resonance imaging scans (family-wise error-corrected). Leukocytes mRNA levels of TMEM40 and LY6G6F and other genes mainly involved in inflammation were significantly higher in patients carrying GRN mutations compared with asymptomatic carriers and other FTLD. The higher the levels of TMEM40 the greater is the damage of parietal lobule; the higher the LY6G6F gene expression the greater is the atrophy in superior frontal gyrus. Enhanced inflammation associated with the onset of GRN disease might be either related to disease pathogenetic mechanism leading to neurodegeneration or to a compensatory pathway that counteracts disease progression. The identification of specific molecular targets of GRN-FTLD disease is essential when considering future disease-modifying therapies. PMID:23419701

  18. Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator

    PubMed Central

    Wan, Qiu-Hong; Pan, Sheng-Kai; Hu, Li; Zhu, Ying; Xu, Peng-Wei; Xia, Jin-Quan; Chen, Hui; He, Gen-Yun; He, Jing; Ni, Xiao-Wei; Hou, Hao-Long; Liao, Sheng-Guang; Yang, Hai-Qiong; Chen, Ying; Gao, Shu-Kun; Ge, Yun-Fa; Cao, Chang-Chang; Li, Peng-Fei; Fang, Li-Ming; Liao, Li; Zhang, Shu; Wang, Meng-Zhen; Dong, Wei; Fang, Sheng-Guo

    2013-01-01

    Crocodilians are diving reptiles that can hold their breath under water for long periods of time and are crepuscular animals with excellent sensory abilities. They comprise a sister lineage of birds and have no sex chromosome. Here we report the genome sequence of the endangered Chinese alligator (Alligator sinensis) and describe its unique features. The next-generation sequencing generated 314 Gb of raw sequence, yielding a genome size of 2.3 Gb. A total of 22 200 genes were predicted in Alligator sinensis using a de novo, homology- and RNA-based combined model. The genetic basis of long-diving behavior includes duplication of the bicarbonate-binding hemoglobin gene, co-functioning of routine phosphate-binding and special bicarbonate-binding oxygen transport, and positively selected energy metabolism, ammonium bicarbonate excretion and cardiac muscle contraction. Further, we elucidated the robust Alligator sinensis sensory system, including a significantly expanded olfactory receptor repertoire, rapidly evolving nerve-related cellular components and visual perception, and positive selection of the night vision-related opsin and sound detection-associated otopetrin. We also discovered a well-developed immune system with a considerable number of lineage-specific antigen-presentation genes for adaptive immunity as well as expansion of the tripartite motif-containing C-type lectin and butyrophilin genes for innate immunity and expression of antibacterial peptides. Multifluorescence in situ hybridization showed that alligator chromosome 3, which encodes DMRT1, exhibits significant synteny with chicken chromosome Z. Finally, population history analysis indicated population admixture 0.60-1.05 million years ago, when the Qinghai-Tibetan Plateau was uplifted. PMID:23917531

  19. Transcript Analysis Reveals a Specific HOX Signature Associated with Positional Identity of Human Endothelial Cells

    PubMed Central

    Toshner, Mark; Dunmore, Benjamin J.; McKinney, Eoin F.; Southwood, Mark; Caruso, Paola; Upton, Paul D.; Waters, John P.; Ormiston, Mark L.; Skepper, Jeremy N.; Nash, Gerard; Rana, Amer A.; Morrell, Nicholas W.

    2014-01-01

    The endothelial cell has a remarkable ability for sub-specialisation, adapted to the needs of a variety of vascular beds. The role of developmental programming versus the tissue contextual environment for this specialization is not well understood. Here we describe a hierarchy of expression of HOX genes associated with endothelial cell origin and location. In initial microarray studies, differential gene expression was examined in two endothelial cell lines: blood derived outgrowth endothelial cells (BOECs) and pulmonary artery endothelial cells. This suggested shared and differential patterns of HOX gene expression between the two endothelial lines. For example, this included a cluster on chromosome 2 of HOXD1, HOXD3, HOXD4, HOXD8 and HOXD9 that was expressed at a higher level in BOECs. Quantative PCR confirmed the higher expression of these HOXs in BOECs, a pattern that was shared by a variety of microvascular endothelial cell lines. Subsequently, we analysed publically available microarrays from a variety of adult cell and tissue types using the whole “HOX transcriptome” of all 39 HOX genes. Using hierarchical clustering analysis the HOX transcriptome was able to discriminate endothelial cells from 61 diverse human cell lines of various origins. In a separate publically available microarray dataset of 53 human endothelial cell lines, the HOX transcriptome additionally organized endothelial cells related to their organ or tissue of origin. Human tissue staining for HOXD8 and HOXD9 confirmed endothelial expression and also supported increased microvascular expression of these HOXs. Together these observations suggest a significant involvement of HOX genes in endothelial cell positional identity. PMID:24651450

  20. Infrared signature studies of aerospace vehicles

    NASA Astrophysics Data System (ADS)

    Mahulikar, Shripad P.; Sonawane, Hemant R.; Arvind Rao, G.

    2007-10-01

    Infrared (IR) emissions from aircraft are used to detect, track, and lock-on to the target. MAN Portable Air Defence Systems (MANPADS) have emerged as a major cause of aircraft and helicopter loss. Therefore, IR signature studies are important to counter this threat for survivability enhancement, and are an important aspect of stealth technology. This paper reviews contemporary developments in this discipline, with particular emphasis on IR signature prediction from aerospace vehicles. The role of atmosphere in IR signature analysis, and relation between IR signature level and target susceptibility are illustrated. Also, IR signature suppression systems and countermeasure techniques are discussed, to highlight their effectiveness and implications in terms of penalties.

  1. Analysis of fatty acid content and composition in microalgae.

    PubMed

    Breuer, Guido; Evers, Wendy A C; de Vree, Jeroen H; Kleinegris, Dorinde M M; Martens, Dirk E; Wijffels, René H; Lamers, Packo P

    2013-01-01

    A method to determine the content and composition of total fatty acids present in microalgae is described. Fatty acids are a major constituent of microalgal biomass. These fatty acids can be present in different acyl-lipid classes. Especially the fatty acids present in triacylglycerol (TAG) are of commercial interest, because they can be used for production of transportation fuels, bulk chemicals, nutraceuticals (ω-3 fatty acids), and food commodities. To develop commercial applications, reliable analytical methods for quantification of fatty acid content and composition are needed. Microalgae are single cells surrounded by a rigid cell wall. A fatty acid analysis method should provide sufficient cell disruption to liberate all acyl lipids and the extraction procedure used should be able to extract all acyl lipid classes. With the method presented here all fatty acids present in microalgae can be accurately and reproducibly identified and quantified using small amounts of sample (5 mg) independent of their chain length, degree of unsaturation, or the lipid class they are part of. This method does not provide information about the relative abundance of different lipid classes, but can be extended to separate lipid classes from each other. The method is based on a sequence of mechanical cell disruption, solvent based lipid extraction, transesterification of fatty acids to fatty acid methyl esters (FAMEs), and quantification and identification of FAMEs using gas chromatography (GC-FID). A TAG internal standard (tripentadecanoin) is added prior to the analytical procedure to correct for losses during extraction and incomplete transesterification. PMID:24121679

  2. Analysis of Fatty Acid Content and Composition in Microalgae

    PubMed Central

    Breuer, Guido; Evers, Wendy A. C.; de Vree, Jeroen H.; Kleinegris, Dorinde M. M.; Martens, Dirk E.; Wijffels, René H.; Lamers, Packo P.

    2013-01-01

    A method to determine the content and composition of total fatty acids present in microalgae is described. Fatty acids are a major constituent of microalgal biomass. These fatty acids can be present in different acyl-lipid classes. Especially the fatty acids present in triacylglycerol (TAG) are of commercial interest, because they can be used for production of transportation fuels, bulk chemicals, nutraceuticals (ω-3 fatty acids), and food commodities. To develop commercial applications, reliable analytical methods for quantification of fatty acid content and composition are needed. Microalgae are single cells surrounded by a rigid cell wall. A fatty acid analysis method should provide sufficient cell disruption to liberate all acyl lipids and the extraction procedure used should be able to extract all acyl lipid classes. With the method presented here all fatty acids present in microalgae can be accurately and reproducibly identified and quantified using small amounts of sample (5 mg) independent of their chain length, degree of unsaturation, or the lipid class they are part of. This method does not provide information about the relative abundance of different lipid classes, but can be extended to separate lipid classes from each other. The method is based on a sequence of mechanical cell disruption, solvent based lipid extraction, transesterification of fatty acids to fatty acid methyl esters (FAMEs), and quantification and identification of FAMEs using gas chromatography (GC-FID). A TAG internal standard (tripentadecanoin) is added prior to the analytical procedure to correct for losses during extraction and incomplete transesterification. PMID:24121679

  3. Individual and simultaneous determination of uric acid and ascorbic acid by flow injection analysis.

    PubMed

    Almuaibed, A M; Townshend, A

    1992-11-01

    Flow injection methods for the individual and simultaneous determination of ascorbic acid and uric acid are proposed. A spectrophotometer and a miniamperometric detector are connected in sequence. The calibration graphs for uric acid obtained by measuring its absorbance at 293 nm and its current at +0.6 V are linear up to at least 80 and 70 mug/ml, respectively, with an rsd (n = 10) of 1 % for both methods at mid-range concentrations. The calibration graph for ascorbic acid with amperometric detection is linear up to 80 mg/l. with an rsd (n = 10) of 0.8% at 30 mg/l. The simultaneous determination of uric acid and ascorbic acid is based on measurement of the absorbance of uric acid at 393 nm and amperometric determination of both analytes at +0.6 V. The average relative errors of the analysis of binary mixtures of uric acid and ascorbic acid are 2.2 and 4.2%, respectively. PMID:18965554

  4. Study of medical isotope production facility stack emissions and noble gas isotopic signature using automatic gamma-spectra analysis platform

    NASA Astrophysics Data System (ADS)

    Zhang, Weihua; Hoffmann, Emmy; Ungar, Kurt; Dolinar, George; Miley, Harry; Mekarski, Pawel; Schrom, Brian; Hoffman, Ian; Lawrie, Ryan; Loosz, Tom

    2013-04-01

    The nuclear industry emissions of the four CTBT (Comprehensive Nuclear-Test-Ban Treaty) relevant radioxenon isotopes are unavoidably detected by the IMS along with possible treaty violations. Another civil source of radioxenon emissions which contributes to the global background is radiopharmaceutical production companies. To better understand the source terms of these background emissions, a joint project between HC, ANSTO, PNNL and CRL was formed to install real-time detection systems to support 135Xe, 133Xe, 131mXe and 133mXe measurements at the ANSTO and CRL 99Mo production facility stacks as well as the CANDU (CANada Deuterium Uranium) primary coolant monitoring system at CRL. At each site, high resolution gamma spectra were collected every 15 minutes using a HPGe detector to continuously monitor a bypass feed from the stack or CANDU primary coolant system as it passed through a sampling cell. HC also conducted atmospheric monitoring for radioxenon at approximately 200 km distant from CRL. A program was written to transfer each spectrum into a text file format suitable for the automatic gamma-spectra analysis platform and then email the file to a server. Once the email was received by the server, it was automatically analysed with the gamma-spectrum software UniSampo/Shaman to perform radionuclide identification and activity calculation for a large number of gamma-spectra in a short period of time (less than 10 seconds per spectrum). The results of nuclide activity together with other spectrum parameters were saved into the Linssi database. This database contains a large amount of radionuclide information which is a valuable resource for the analysis of radionuclide distribution within the noble gas fission product emissions. The results could be useful to identify the specific mechanisms of the activity release. The isotopic signatures of the various radioxenon species can be determined as a function of release time. Comparison of 133mXe and 133Xe activity

  5. Chemical Signature of Biomass Burning Emitted PM2.5 by Multi-Element Scanning Thermal Analysis

    NASA Astrophysics Data System (ADS)

    Hsieh, Y.; Bugna, G.; Robertson, K.

    2012-12-01

    Particulate matter (PM) emitted from biomass burning and wild fire has been an air quality concern in affected areas. It is desirable to have a sensitive and convenient method to detect, characterize and identify sources of biomass burning emitted PM in the air. We initiated this research to identify the chemical signature of biomass burning emitted PM2.5 by a CNS multi-element scanning thermal analysis (MESTA) method and study the feasibility of using it as a fingerprint to trace the presence of biomass burning emitted PM2.5 in the air. We collected PM2.5 samples from the prescribed burnings of the pine forest at the Tall Timbers Experimental Station and from the pre- and post burning ambient air and analyzed them with the MESTA method. MESTA is a method developed for characterizing the thermal stability of organic compounds in a solid sample in terms of C, N and S thermograms from 40 oC to 750 oC. The results of the MESTA show that the prescribed burning emitted PM2.5 has a characteristic thermally stable (300-700 oC) component with very high C/N ratio (150-300) and non-detectable S content. In contrast, the PM2.5 of the pre- and post burning ambient air has a characteristic thermally unstable (100-300 oC) component with very low C/N (1-3) and C/S (3-7) ratios. The results of this study suggest that the MESTA thermograms of the biomass burning emitted PM2.5 could be used as a tracer for the presence of biomass burning PM2.5 in the air.

  6. Application Power Signature Analysis

    SciTech Connect

    Hsu, Chung-Hsing; Combs, Jacob; Nazor, Jolie; Santiago, Fabian; Thysell, Rachelle; Rivoire, Suzanne; Poole, Stephen W

    2014-01-01

    The high-performance computing (HPC) community has been greatly concerned about energy efficiency. To address this concern, it is essential to understand and characterize the electrical loads of HPC applications. In this work, we study whether HPC applications can be distinguished by their power-consumption patterns using quantitative measures in an automatic manner. Using a collection of 88 power traces from 4 different systems, we find that basic statistical measures do a surprisingly good job of summarizing applications' distinctive power behavior. Moreover, this study opens up a new area of research in power-aware HPC that has a multitude of potential applications.

  7. Explosives signatures and analysis

    NASA Astrophysics Data System (ADS)

    Fountain, Augustus Way, III; Oyler, Jonathan M.; Ostazeski, Stanley A.

    2008-04-01

    The challenge of sampling explosive materials for various high threat military and civilian operational scenarios requires the community to identify and exploit other chemical compounds within the mixtures that may be available to support stand-off detection techniques. While limited surface and vapor phase characterization of IEDs exist, they are insufficient to guide the future development and evaluation of field deployable explosives detection (proximity and standoff) capabilities. ECBC has conducted a limited investigation of three artillery ammunition types to determine what chemical vapors, if any, are available for sensing; the relative composition of the vapors which includes the more volatile compounds in munitions, i.e., plastersizers and binders; and the sensitivity needed detect these vapors at stand-off. Also in partnership with MIT-Lincoln Laboratory, we performed a background measurement campaign at the National Training Center to determine the baseline ambient amounts and variability of nitrates and nitro-ester compounds as vapors, particulates, and on surfaces; as well as other chemical compounds related to non-energetic explosive additives. Environmental persistence studies in contexts relevant to counter-IED sensing operations, such as surface residues, are still necessary.

  8. A new quantum blind signature with unlinkability

    NASA Astrophysics Data System (ADS)

    Shi, Wei-Min; Zhang, Jian-Biao; Zhou, Yi-Hua; Yang, Yu-Guang

    2015-08-01

    Recently, some quantum blind signature protocols have been proposed. However, the previous schemes cannot satisfy the unlinkability requirement. To overcome the drawback of unlinkability in the previous schemes, we propose a new quantum blind signature based on Bell states with the help of an authentic party. In this paper, we provide a method to inject a randomizing factor into a message when it is signed by the signer and then get rid of the blind factor from the blinded signature when it is verified by the verifier. Even when the message owner publishes the message-signature pair, the signer cannot identify the association between the message-signature pair and the blind signature he generated. Therefore, our scheme really realizes unlinkability property. At last, analysis results show that this scheme satisfies the basis security requirements of a weak signature such as no-counterfeiting, no-disavowing, blindness and traceability, and our total efficiency is not less than the previous schemes.

  9. Quantum proxy signature scheme with public verifiability

    NASA Astrophysics Data System (ADS)

    Zhou, Jingxian; Zhou, Yajian; Niu, Xinxin; Yang, Yixian

    2011-10-01

    In recent years, with the development of quantum cryptography, quantum signature has also made great achievement. However, the effectiveness of all the quantum signature schemes reported in the literature can only be verified by a designated person. Therefore, its wide applications are limited. For solving this problem, a new quantum proxy signature scheme using EPR quantum entanglement state and unitary transformation to generate proxy signature is presented. Proxy signer announces his public key when he generates the final signature. According to the property of unitary transformation and quantum one-way function, everyone can verify whether the signature is effective or not by the public key. So the quantum proxy signature scheme in our paper can be public verified. The quantum key distribution and one-time pad encryption algorithm guarantee the unconditional security of this scheme. Analysis results show that this new scheme satisfies strong non-counterfeit and strong non-disavowal.

  10. Developing composite signatures

    NASA Astrophysics Data System (ADS)

    Hawley, Chadwick T.; Carpenter, Tom; Cappelaere, Patrice G.; Frye, Stu; Lemoigne-Stewart, Jacqueline J.; Mandle, Dan; Montgomery, Sarah; Williams-Bess, Autumn

    2011-06-01

    A composite signature is a group of signatures that are related in such a way to more completely or further define a target or operational endeavor at a higher fidelity. This paper explores the merits of using composite signatures, in lieu of waiting for opportunities for the more elusive diagnostic signatures, to satisfy key essential elements of information Keywords: signature, composite signature, civil disaster (EEI) associated with civil disaster-related problems. It discusses efforts to refine composite signature development methodology and quantify the relative value of composite vs. diagnostic signatures. The objectives are to: 1) investigate and develop innovative composite signatures associated with civil disasters, including physical, chemical and pattern/behavioral; 2) explore the feasibility of collecting representative composite signatures using current and emerging intelligence, surveillance, and reconnaissance (ISR) collection architectures leveraging civilian and commercial architectures; and 3) collaborate extensively with scientists and engineers from U.S. government organizations and laboratories, the defense industry, and academic institutions.

  11. Ion Chromatography Analysis of Dibutyl Phosphoric Acid

    SciTech Connect

    Ray, R.J.

    1998-12-04

    Analysis of dibutyl phosphate (DBP), a degradation product of tributyl phosphate (TBP), has long been a problem analysis by Ion Chromatography at the Savannah River Site. Due to the presence of UO{sub 2}{sup +2} and high NO{sub 3}{sup {minus}1} concentrations, inadequate recovery and separation of DBP on the chromatographic column had rendered the analysis undependable and very inconsistent, thus causing high uncertainties in the data. The method presented here by the Savannah River Technology Center (SRTC)/Analytical Development Section (ADS) addresses the sample preparation problems encountered when analyzing for DBP in the presence of uranium and nitrate. The data presented reflects the improvements made to decrease data uncertainty and increase data accuracy and precision.

  12. Comprehensive analysis of miRNA expression in T-cell subsets of rheumatoid arthritis patients reveals defined signatures of naive and memory Tregs

    PubMed Central

    Smigielska-Czepiel, K; van den Berg, A; Jellema, P; van der Lei, R J; Bijzet, J; Kluiver, J; Boots, A M H; Brouwer, E; Kroesen, B-J

    2014-01-01

    Disturbed expression of microRNAs (miRNAs) in regulatory T cells (Tregs) leads to development of autoimmunity in experimental mouse models. However, the miRNA expression signature characterizing Tregs of autoimmune diseases, such as rheumatoid arthritis (RA) has not been determined yet. In this study, we have used a microarray approach to comprehensively analyze miRNA expression signatures of both naive Tregs (CD4+CD45RO-CD25++) and memory Tregs (CD4+CD45RO+CD25+++), as well as conventional naive (CD4+CD45RO−CD25−) and memory (CD4+CD45RO+CD25−) T cells (Tconvs) derived from peripheral blood of RA patients and matched healthy controls. Differential expression of selected miRNAs was validated by TaqMan-based quantitative reverse transcription-PCR. We found a positive correlation between increased expression of miR-451 in T cells of RA patients and disease activity score (DAS28), erythrocyte sedimentation rate levels and serum levels of interleukin-6. Moreover, we found characteristic, disease- and treatment-independent, global miRNA expression signatures defining naive Tregs, memory Tregs, naive Tconvs and memory Tconvs. The analysis allowed us to define miRNAs characteristic for a general naive phenotype (for example, miR-92a) and a general memory phenotype (for example, miR-21, miR-155). Importantly, the analysis allowed us to define miRNAs that are specifically expressed in both naive and memory Tregs, defining as such miRNA signature characterizing the Treg phenotype (that is, miR-146a, miR-3162, miR-1202, miR-1246 and miR-4281). PMID:24401767

  13. Multidimensional signatures in antimicrobial peptides

    PubMed Central

    Yount, Nannette Y.; Yeaman, Michael R.

    2004-01-01

    Conventional analyses distinguish between antimicrobial peptides by differences in amino acid sequence. Yet structural paradigms common to broader classes of these molecules have not been established. The current analyses examined the potential conservation of structural themes in antimicrobial peptides from evolutionarily diverse organisms. Using proteomics, an antimicrobial peptide signature was discovered to integrate stereospecific sequence patterns and a hallmark three-dimensional motif. This striking multidimensional signature is conserved among disulfide-containing antimicrobial peptides spanning biological kingdoms, and it transcends motifs previously limited to defined peptide subclasses. Experimental data validating this model enabled the identification of previously unrecognized antimicrobial activity in peptides of known identity. The multidimensional signature model provides a unifying structural theme in broad classes of antimicrobial peptides, will facilitate discovery of antimicrobial peptides as yet unknown, and offers insights into the evolution of molecular determinants in these and related host defense effector molecules. PMID:15118082

  14. SEM ANALYSIS OF THE ACID-ETCHED ENAMEL PATTERNS PROMOTED BY ACIDIC MONOMERS AND PHOSPHORIC ACIDS

    PubMed Central

    Shinohara, Mirela Sanae; de Oliveira, Marcelo Tavares; Hipólito, Vinícius Di; Giannin, Marcelo; de Goes, Mario Fernando

    2006-01-01

    Objective: Although self-etching bonding systems (SES) are indicated to prepare dental enamel for bonding, concerns have been expressed regarding their effectiveness. The aim of this study was to analyze the etching pattern (EP) of nine SES in comparison with 35% and 34% phosphoric acid etchants (FA) on intact (IN) and ground (GR) enamel surface. Materials and Methods: Twenty-two human third molars were sectioned in mesial-distal and buccal-lingual directions, and four dental fragments were obtained from each tooth. Half of the fragments were ground using 600-grit SiC paper and the other half remained intact. The fragments were randomly assigned into 22 groups, according to the texture of enamel surface (IN and GR) and the technique to etch the enamel (34% FA, 35% FA, AdheSE primer; Brush & Bond; Clearfil Protect Bond primer; iBond; One-up Bond F; OptiBond Solo Plus primer; Tyrian SPE primer; Unifil Bond primer and Xeno III). Conditioners were applied to IN and GR enamel surfaces, according to the manufacturer's instructions. Specimens etched with phosphoric acids were washed with water, while the surfaces treated with SES were submitted to alternate rinsing with alcohol and acetone. The specimens were dried, sputter-coated and examined under a scanning electron microscope. Results: For both IN and GR enamel surfaces, the EP of 34 and 35% FA was deeper and more homogeneous in comparison to EP of SES, except for Tyrian SPE. The acidic monomer action of self-etching systems was more effective on GR enamel. Conclusion: Most of the SES are less aggressive than phosphoric acid etchants and their etching effects were reduced on intact enamel surfaces. Uniterms: Dental acid etching; Dental enamel; Electron microscopy. PMID:19089243

  15. Typing of Histoplasma capsulatum strains by fatty acid profile analysis

    PubMed Central

    Zarnowski, Robert; Miyazaki, Makoto; Dobrzyn, Agnieszka; Ntambi, James M.; Woods, Jon P.

    2009-01-01

    The performance of fatty acid profiling for strain differentiation of Histoplasma capsulatum was assessed. Total fatty acids were isolated from the yeast-phase cells of seven stock and two previously unreported clinical strains of H. capsulatum var. capsulatum, as well as from one unreported clinical strain and one stock strain of H. capsulatum var. duboisii, and one strain of each of three other dimorphic zoopathogenic fungal species, Blastomyces dermatitidis, Paracoccidioides brasiliensis and Sporothrix schenckii. Different colony morphology and pigmentation types of the H. capsulatum strains were also included. The most frequently occurring fatty acids were oleic, palmitic, stearic and linoleic acids. There were variations in the relative percentage fatty acid contents of H. capsulatum strains that could be used for strain identification and discrimination. Differentiation between H. capsulatum strains was achieved by the comparison of detected fatty acids accompanied by principal component analysis using calculated Varimax-rotated principal component loadings. Statistical analysis yielded three major principal components that explained over 94% of total variance in the data. All the strains of H. capsulatum var. capsulatum RFLP classes II and III were grouped into two distinct clusters: the heterogenic RFLP class I formed a large, but also well-defined group, whereas the outgroup strains of H. capsulatum var. duboisii, B. dermatitidis, P. brasiliensis and S. schenckii were shifted away. These data suggest that fatty acid profiling can be used in H. capsulatum strain classification and epidemiological studies that require strain differentiation at the intraspecies level. PMID:17510264

  16. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect

    States, David J.

    2004-07-28

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  17. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect

    David J. States

    1998-08-01

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  18. Fatty acid oxidation: systems analysis and applications.

    PubMed

    Cintolesi, Angela; Rodríguez-Moyá, María; Gonzalez, Ramon

    2013-01-01

    Fatty acids (FAs) are essential components of cellular structure and energy-generating routes in living organisms. They exist in a variety of chemical configurations and functionalities and are catabolized by different oxidative routes, according to their structure. α- and ω-Oxidation are minor routes that occur only in eukaryotes, while β-oxidation is the major degradation route in eukaroytes and prokaryotes. These pathways have been characterized and engineered from different perspectives for industrial and biomedical applications. The severity of FA oxidation disorders in humans initially guided the study of FA metabolism at a molecular-level. On the other hand, recent advances in metabolic engineering and systems biology have powered the study of FA biosynthetic and catabolic routes in microorganisms at a systems-level. Several studies have proposed these pathways as platforms for the production of fuels and chemicals from biorenewable sources. The lower complexity of microbial systems has allowed a more comprehensive study of FA metabolism and has opened opportunities for a wider range of applications. Still, there is a need for techniques that facilitate the translation of high-throughput data from microorganisms to more complex eukaryotic systems in order to aid the development of diagnostic and treatment strategies for FA oxidation disorders. In addition, further systems biology analyses on human systems could also provide valuable insights on oxidation disorders. This article presents a comparison of the three main FA oxidative routes, systems biology analyses that have been used to study FA metabolism, and engineering efforts performed on microbial systems. PMID:23661533

  19. Digital PCR analysis of circulating nucleic acids.

    PubMed

    Hudecova, Irena

    2015-10-01

    Detection of plasma circulating nucleic acids (CNAs) requires the use of extremely sensitive and precise methods. The commonly used quantitative real-time polymerase chain reaction (PCR) poses certain technical limitations in relation to the precise measurement of CNAs whereas the costs of massively parallel sequencing are still relatively high. Digital PCR (dPCR) now represents an affordable and powerful single molecule counting strategy to detect minute amounts of genetic material with performance surpassing many quantitative methods. Microfluidic (chip) and emulsion (droplet)-based technologies have already been integrated into platforms offering hundreds to millions of nanoliter- or even picoliter-scale reaction partitions. The compelling observations reported in the field of cancer research, prenatal testing, transplantation medicine and virology support translation of this technology into routine use. Extremely sensitive plasma detection of rare mutations originating from tumor or placental cells among a large background of homologous sequences facilitates unraveling of the early stages of cancer or the detection of fetal mutations. Digital measurement of quantitative changes in plasma CNAs associated with cancer or graft rejection provides valuable information on the monitoring of disease burden or the recipient's immune response and subsequent therapy treatment. Furthermore, careful quantitative assessment of the viral load offers great value for effective monitoring of antiviral therapy for immunosuppressed or transplant patients. The present review describes the inherent features of dPCR that make it exceptionally robust in precise and sensitive quantification of CNAs. Moreover, I provide an insight into the types of potential clinical applications that have been developed by researchers to date. PMID:25828047

  20. Analysis of the generating action of the acid from PAG using acid sensitive dyes

    NASA Astrophysics Data System (ADS)

    Sekiguchi, Atsushi; Matsumoto, Yoko; Konishi, Hiroko; Moriyasu, Kengo; Morimoto, Yukihiro

    2011-04-01

    The use of acid sensitive dyes to determine the quantity of acid generated from PAG and in the analysis of acid-generating reaction is currently being studied. The method would allow an easy understanding of the PAG acid-generating reaction simply by adding an acid sensitive dye to the resist. In the conventional method, a resist containing a chromogenic substance is applied to a quartz substrate, which is then exposed. Following the exposure, the absorbance of chromogenic component near 530 nm is measured and evaluated with a spectroscope. The rate constant for acid generation (Dill's C parameter) during the exposure is determined based on the relationship between transmittance at 530 nm and the exposure dose. However, the chromogenic substance used in this method degrades over time (fading reaction) after the exposure, resulting in variations in transmittance measurements due to the effects of time between the completion of the exposure and the measurement of transmittance. We devised a prototype instrument capable of in situ measurements of absorbance at 530 nm while irradiating a 193-nm light beam. Using this instrument, we obtained rate constants for acid generation (Dill's C parameter) and examined the differing results obtained with ArF resist polymers of differing PAG concentrations and structures as well as dependence on the quantity of the chromogenic substance.

  1. A preliminary analysis of trace-elemental signatures in statoliths of different spawning cohorts for Dosidicus gigas off EEZ waters of Chile

    NASA Astrophysics Data System (ADS)

    Liu, Bilin; Chen, Xinjun; Fang, Zhou; Hu, Song; Song, Qian

    2015-12-01

    We applied solution-based ICP-MS method to quantify the trace-elemental signatures in statoliths of jumbo flying squid, Dosidius gigas, which were collected from the waters off northern and central Chile during the scientific surveys carried out by Chinese squid jigging vessels in 2007 and 2008. The age and spawning date of the squid were back-calculated based on daily increments in statoliths. Eight elemental ratios (Sr/Ca, Ba/Ca, Mg/Ca, Mn/Ca, Na/Ca, Fe/Ca, Cu/Ca and Zn/Ca) were analyzed. It was found that Sr is the second most abundant element next to Ca, followed by Na, Fe, Mg, Zn, Cu, Ba and Mn. There was no significant relationship between element/Ca and sea surface temperature (SST) and sea surface salinity (SSS), although weak negative or positive tendency was found. MANOVA analysis showed that multivariate elemental signatures did not differ among the cohorts spawned in spring, autumn and winter, and no significant difference was found between the northern and central sampling locations. Classification results showed that all individuals of each spawned cohorts were correctly classified. This study demonstrates that the elemental signatures in D. gigas statoliths are potentially a useful tool to improve our understanding of its population structure and habitat environment.

  2. Association analysis of a chemo-response signature identified within The Cancer Genome Atlas aimed at predicting genetic risk for chemo-response in ovarian cancer

    PubMed Central

    Salinas, Erin A; Newtson, Andreea M; Leslie, Kimberly K; Gonzalez-Bosquet, Jesus

    2016-01-01

    Background: A gene signature associated with chemo-response in ovarian cancer was created through integration of biological data in The Cancer Genome Atlas (TCGA) and validated in five independent microarray experiments. Our study aimed to determine if single nucleotide polymorphisms (SNPs) within the 422-gene signature were associated with a genetic predisposition to platinum-based chemotherapy response in serous ovarian cancer. Methods: An association analysis between SNPs within the 422-gene signature and chemo-response in serous ovarian cancer was performed under the log-additive genetic model using the ‘SNPassoc’ package within the R environment (p<0.0001). Subsequent validation of statistically significant SNPs was done in the Ovarian Cancer Association Consortium (OCAC) database. Results: 19 SNPs were found to be associated with chemo-response with statistical significance. None of the SNPs found significant in TCGA were validated within OCAC for the outcome of interest, chemo-response. Conclusions: SNPs associated with chemo-response in ovarian cancer within TGCA database were not validated in a larger database of patients and controls from OCAC. New strategies integrating somatic and germline information may help to characterize genetic predictors for treatment response in ovarian cancer. PMID:27186327

  3. Bile acids: analysis in biological fluids and tissues

    PubMed Central

    Griffiths, William J.; Sjövall, Jan

    2010-01-01

    The formation of bile acids/bile alcohols is of major importance for the maintenance of cholesterol homeostasis. Besides their functions in lipid absorption, bile acids/bile alcohols are regulatory molecules for a number of metabolic processes. Their effects are structure-dependent, and numerous metabolic conversions result in a complex mixture of biologically active and inactive forms. Advanced methods are required to characterize and quantify individual bile acids in these mixtures. A combination of such analyses with analyses of the proteome will be required for a better understanding of mechanisms of action and nature of endogenous ligands. Mass spectrometry is the basic detection technique for effluents from chromatographic columns. Capillary liquid chromatography-mass spectrometry with electrospray ionization provides the highest sensitivity in metabolome analysis. Classical gas chromatography-mass spectrometry is less sensitive but offers extensive structure-dependent fragmentation increasing the specificity in analyses of isobaric isomers of unconjugated bile acids. Depending on the nature of the bile acid/bile alcohol mixture and the range of concentration of individuals, different sample preparation sequences, from simple extractions to group separations and derivatizations, are applicable. We review the methods currently available for the analysis of bile acids in biological fluids and tissues, with emphasis on the combination of liquid and gas phase chromatography with mass spectrometry. PMID:20008121

  4. Nanopore sensors for nucleic acid analysis

    NASA Astrophysics Data System (ADS)

    Venkatesan, Bala Murali; Bashir, Rashid

    2011-10-01

    Nanopore analysis is an emerging technique that involves using a voltage to drive molecules through a nanoscale pore in a membrane between two electrolytes, and monitoring how the ionic current through the nanopore changes as single molecules pass through it. This approach allows charged polymers (including single-stranded DNA, double-stranded DNA and RNA) to be analysed with subnanometre resolution and without the need for labels or amplification. Recent advances suggest that nanopore-based sensors could be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000. In this article we review the use of nanopore technology in DNA sequencing, genetics and medical diagnostics.

  5. Computerized image analysis for acetic acid induced intraepithelial lesions

    NASA Astrophysics Data System (ADS)

    Li, Wenjing; Ferris, Daron G.; Lieberman, Rich W.

    2008-03-01

    Cervical Intraepithelial Neoplasia (CIN) exhibits certain morphologic features that can be identified during a visual inspection exam. Immature and dysphasic cervical squamous epithelium turns white after application of acetic acid during the exam. The whitening process occurs visually over several minutes and subjectively discriminates between dysphasic and normal tissue. Digital imaging technologies allow us to assist the physician analyzing the acetic acid induced lesions (acetowhite region) in a fully automatic way. This paper reports a study designed to measure multiple parameters of the acetowhitening process from two images captured with a digital colposcope. One image is captured before the acetic acid application, and the other is captured after the acetic acid application. The spatial change of the acetowhitening is extracted using color and texture information in the post acetic acid image; the temporal change is extracted from the intensity and color changes between the post acetic acid and pre acetic acid images with an automatic alignment. The imaging and data analysis system has been evaluated with a total of 99 human subjects and demonstrate its potential to screening underserved women where access to skilled colposcopists is limited.

  6. Diagnostic value of a plasma microRNA signature in gastric cancer: a microRNA expression analysis

    PubMed Central

    Zhou, Xin; Zhu, Wei; Li, Hai; Wen, Wei; Cheng, Wenfang; Wang, Fang; Wu, Yinxia; Qi, Lianwen; Fan, Yong; Chen, Yan; Ding, Yin; Xu, Jing; Qian, Jiaqi; Huang, Zebo; Wang, Tongshan; Zhu, Danxia; Shu, Yongqian; Liu, Ping

    2015-01-01

    The differential expression of microRNAs (miRNAs) in plasma of gastric cancer (GC) patients may serve as a diagnostic biomarker. A total of 33 miRNAs were identified through the initial screening phase (3 GC pools vs. 1 normal control (NC) pool) using quantitative reverse transcription polymerase chain reaction (qRT-PCR) based Exiqon panel (miRCURY-Ready-to-Use-PCR-Human-panel-I + II-V1.M). By qRT-PCR, these miRNAs were further assessed in training (30 GC VS. 30 NCs) and testing stages (71 GC VS. 61 NCs). We discovered a plasma miRNA signature including five up-regulated miRNAs (miR-185, miR-20a, miR-210, miR-25 and miR-92b), and this signature was evaluated to be a potential diagnostic marker of GC. The areas under the receiver operating characteristic curve of the signature were 0.86, 0.74 and 0.87 for the training, testing and the external validation stages (32 GC VS. 18 NCs), respectively. The five miRNAs were consistently dysregulated in GC tissues (n = 30). Moreover, miR-185 was decreased while miR-20a, miR-210 and miR-92b were increased in arterial plasma (n = 38). However, none of the miRNAs in the exosomes showed different expression between 10 GC patients and 10 NCs. In conclusion, we identified a five-miRNA signature in the peripheral plasma which could serve as a non-invasive biomarker in detection of GC. PMID:26059512

  7. Extraction of human gait signatures: an inverse kinematic approach using Groebner basis theory applied to gait cycle analysis

    NASA Astrophysics Data System (ADS)

    Barki, Anum; Kendricks, Kimberly; Tuttle, Ronald F.; Bunker, David J.; Borel, Christoph C.

    2013-05-01

    This research highlights the results obtained from applying the method of inverse kinematics, using Groebner basis theory, to the human gait cycle to extract and identify lower extremity gait signatures. The increased threat from suicide bombers and the force protection issues of today have motivated a team at Air Force Institute of Technology (AFIT) to research pattern recognition in the human gait cycle. The purpose of this research is to identify gait signatures of human subjects and distinguish between subjects carrying a load to those subjects without a load. These signatures were investigated via a model of the lower extremities based on motion capture observations, in particular, foot placement and the joint angles for subjects affected by carrying extra load on the body. The human gait cycle was captured and analyzed using a developed toolkit consisting of an inverse kinematic motion model of the lower extremity and a graphical user interface. Hip, knee, and ankle angles were analyzed to identify gait angle variance and range of motion. Female subjects exhibited the most knee angle variance and produced a proportional correlation between knee flexion and load carriage.

  8. Gas chromatography/mass spectrometric analysis of methyl esters of N,N-dialkylaminoethane-2-sulfonic acids for verification of the Chemical Weapons Convention.

    PubMed

    Pardasani, Deepak; Gupta, Arvinda K; Palit, Meehir; Shakya, Purushottam; Kanaujia, Pankaj K; Sekhar, K; Dubey, Devendra K

    2005-01-01

    This paper describes the synthesis and gas chromatography/electron ionization mass spectrometric (GC/EI-MS) analysis of methyl esters of N,N-dialkylaminoethane-2-sulfonic acids (DAESAs). These sulfonic acids are important environmental signatures of nerve agent VX and its toxic analogues, hence GC/EI-MS analysis of their methyl esters is of paramount importance for verification of the Chemical Weapons Convention. DAESAs were prepared by condensation of 2-bromoethane sulfonic acid with dialkylamines, and by condensation of dialkylaminoethyl chloride with sodium bisulfite. GC/EI-MS analysis of methyl esters of DAESAs yielded mass spectra; based on these spectra, generalized fragmentation routes are proposed that rationalize most of the characteristic ions. PMID:16196000

  9. Acid retardation method in analysis of strongly acidic solutions by inductively coupled plasma mass-spectrometry.

    PubMed

    Seregina, I F; Perevoznik, O A; Bolshov, M A

    2016-10-01

    Acid retardation on the sorbents as a technique for reduction of the acidity of the solutions prior to their analysis by inductively coupled plasma mass spectrometry was proposed and investigated. The proposed scheme provides substantial separation of the analytes and nitric acid, which allows direct introduction of the eluates in plasma without dilution. Two sorbents were examined - AV-17 anion-exchange resin and the Stirosorb 584 sorbent. Sorption and desorption of 38 elements on these sorbents were investigated. The efficiencies of the REEs' sorption on the anion-exchange and neutral sorbents were compared. The higher efficiency of the REEs and HNO3 separation was revealed for the neutral Stirosorb 584 sorbent. It was also found that most elements come out quantitatively of the column filled with the AV-17 resin after pumping 2-4mL of the solution. Wherein, the concentration of nitric acid decreased by 20 times. The anomalous behaviour of Ag, Pb, Th and U on the AV-17 resin was found. These analytes were eluted only after pumping 4 column volumes of deionized water. Na, K, Fe, Al and Li in concentrations within (50-1000mgL(-1)) range did not affect the recovery of REEs. The potential of ARM technique was demonstrate by the analysis of puriss. HNO3 and silverware. ARM enables to avoid dilution of highly acidic solutions prior to their introduction in ICP-MS. PMID:27474322

  10. Quality Analysis of Chlorogenic Acid and Hyperoside in Crataegi fructus

    PubMed Central

    Weon, Jin Bae; Jung, Youn Sik; Ma, Choong Je

    2016-01-01

    Background: Crataegi fructus is a herbal medicine for strong stomach, sterilization, and alcohol detoxification. Chlorogenic acid and hyperoside are the major compounds in Crataegi fructus. Objective: In this study, we established novel high-performance liquid chromatography (HPLC)-diode array detection analysis method of chlorogenic acid and hyperoside for quality control of Crataegi fructus. Materials and Methods: HPLC analysis was achieved on a reverse-phase C18 column (5 μm, 4.6 mm × 250 mm) using water and acetonitrile as mobile phase with gradient system. The method was validated for linearity, precision, and accuracy. About 31 batches of Crataegi fructus samples collected from Korea and China were analyzed by using HPLC fingerprint of developed HPLC method. Then, the contents of chlorogenic acid and hyperoside were compared for quality evaluation of Crataegi fructus. Results: The results have shown that the average contents (w/w %) of chlorogenic acid and hyperoside in Crataegi fructus collected from Korea were 0.0438% and 0.0416%, respectively, and the average contents (w/w %) of 0.0399% and 0.0325%, respectively. Conclusion: In conclusion, established HPLC analysis method was stable and could provide efficient quality evaluation for monitoring of commercial Crataegi fructus. SUMMARY Quantitative analysis method of chlorogenic acid and hyperoside in Crataegi fructus is developed by high.performance liquid chromatography.(HPLC).diode array detectionEstablished HPLC analysis method is validated with linearity, precision, and accuracyThe developed method was successfully applied for quantitative analysis of Crataegi fructus sample collected from Korea and China. Abbreviations used: HPLC: High-performance liquid chromatography, GC: Gas chromatography, MS: Mass spectrometer, LOD: Limits of detection, LOQ: Limits of quantification, RSD: Relative standard deviation, RRT: Relative retention time, RPA: Relation peak area. PMID:27076744

  11. Integrative Metabolic Signatures for Hepatic Radiation Injury

    PubMed Central

    Su, Gang; Meng, Fan; Liu, Laibin; Mohney, Robert; Kulkarni, Shilpa; Guha, Chandan

    2015-01-01

    Background Radiation-induced liver disease (RILD) is a dose-limiting factor in curative radiation therapy (RT) for liver cancers, making early detection of radiation-associated liver injury absolutely essential for medical intervention. A metabolomic approach was used to determine metabolic signatures that could serve as biomarkers for early detection of RILD in mice. Methods Anesthetized C57BL/6 mice received 0, 10 or 50 Gy Whole Liver Irradiation (WLI) and were contrasted to mice, which received 10 Gy whole body irradiation (WBI). Liver and plasma samples were collected at 24 hours after irradiation. The samples were processed using Gas Chromatography/Mass Spectrometry and Liquid Chromatography/Mass Spectrometry. Results Twenty four hours after WLI, 407 metabolites were detected in liver samples while 347 metabolites were detected in plasma. Plasma metabolites associated with 50 Gy WLI included several amino acids, purine and pyrimidine metabolites, microbial metabolites, and most prominently bradykinin and 3-indoxyl-sulfate. Liver metabolites associated with 50 Gy WLI included pentose phosphate, purine, and pyrimidine metabolites in liver. Plasma biomarkers in common between WLI and WBI were enriched in microbial metabolites such as 3 indoxyl sulfate, indole-3-lactic acid, phenyllactic acid, pipecolic acid, hippuric acid, and markers of DNA damage such as 2-deoxyuridine. Metabolites associated with tryptophan and indoles may reflect radiation-induced gut microbiome effects. Predominant liver biomarkers in common between WBI and WLI were amino acids, sugars, TCA metabolites (fumarate), fatty acids (lineolate, n-hexadecanoic acid) and DNA damage markers (uridine). Conclusions We identified a set of metabolomic markers that may prove useful as plasma biomarkers of RILD and WBI. Pathway analysis also suggested that the unique metabolic changes observed after liver irradiation was an integrative response of the intestine, liver and kidney. PMID:26046990

  12. GENOMIC ANALYSIS OF THE TESTICULAR TOXICITY OF HALOACETIC ACIDS

    EPA Science Inventory

    Genomic analysis of the testicular toxicity of haloacetic acids

    David J. Dix and John C. Rockett
    Reproductive Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, R...

  13. Anonymous Signatures Revisited

    NASA Astrophysics Data System (ADS)

    Saraswat, Vishal; Yun, Aaram

    We revisit the notion of the anonymous signature, first formalized by Yang, Wong, Deng and Wang [10], and then further developed by Fischlin [4] and Zhang and Imai [11]. We present a new formalism of anonymous signature, where instead of the message, a part of the signature is withheld to maintain anonymity. We introduce the notion unpretendability to guarantee infeasibility for someone other than the correct signer to pretend authorship of the message and signature. Our definition retains applicability for all previous applications of the anonymous signature, provides stronger security, and is conceptually simpler. We give a generic construction from any ordinary signature scheme, and also show that the short signature scheme by Boneh and Boyen [2] can be naturally regarded as such a secure anonymous signature scheme according to our formalism.

  14. Signatures support program

    NASA Astrophysics Data System (ADS)

    Hawley, Chadwick T.

    2009-05-01

    The Signatures Support Program (SSP) leverages the full spectrum of signature-related activities (collections, processing, development, storage, maintenance, and dissemination) within the Department of Defense (DOD), the intelligence community (IC), other Federal agencies, and civil institutions. The Enterprise encompasses acoustic, seismic, radio frequency, infrared, radar, nuclear radiation, and electro-optical signatures. The SSP serves the war fighter, the IC, and civil institutions by supporting military operations, intelligence operations, homeland defense, disaster relief, acquisitions, and research and development. Data centers host and maintain signature holdings, collectively forming the national signatures pool. The geographically distributed organizations are the authoritative sources and repositories for signature data; the centers are responsible for data content and quality. The SSP proactively engages DOD, IC, other Federal entities, academia, and industry to locate signatures for inclusion in the distributed national signatures pool and provides world-wide 24/7 access via the SSP application.

  15. Novel Quantum Proxy Signature without Entanglement

    NASA Astrophysics Data System (ADS)

    Xu, Guang-bao

    2015-08-01

    Proxy signature is an important research topic in classic cryptography since it has many application occasions in our real life. But only a few quantum proxy signature schemes have been proposed up to now. In this paper, we propose a quantum proxy signature scheme, which is designed based on quantum one-time pad. Our scheme can be realized easily since it only uses single-particle states. Security analysis shows that it is secure and meets all the properties of a proxy signature, such as verifiability, distinguishability, unforgeability and undeniability.

  16. Dynamics of carbon in deep soils inferred from carbon stable isotopes signatures : a worldwide meta-analysis

    NASA Astrophysics Data System (ADS)

    Balesdent, Jérôme; Basile-Doelsch, Isabelle; Chadoeuf, Joël; Cornu, Sophie; Derrien, Delphine; Fekiacova, Zuzana; Hatté, Christine

    2014-05-01

    The contribution of soil carbon deeper than 30 cm to the atmospheric carbon balance is still poorly understood. A very straightforward quantification of the gross exchange of carbon between the atmosphere and soil organic matter can be obtained at places where the 13C/12C signature of vegetation has been changed for known durations, due to switch of the photosynthetic metabolism (C3 or C4) or to Free Air Carbon Enrichment experiments. We compiled C and 13C profile data of 113 sites of this type, either gahered from the literature or from our own measurements. Each site comprised two profiles : one where the 13C/12C of the vegetation had been changed, and a reference profile with unchanged vegetation 13C/12C. An isotope mixing equation was used, which takes into account the natural isotope enrichments with depth and decay. Three main variables were calculated at any depth from 0 to 100 cm and in a few sites down to 200 cm : the carbon content, the proportion of new carbon (aged less than the duration of change t) and the amount of new carbon. The database concerned 23 countries, various climates (58% intertropical and 42% between 23° to 56° latitude) and various soil types and textures. Landuses and vegetation consisted in 26% of forests and woodlands, 35% of grasslands and 38% of cropped systems. The duration of the natural labelling t ranged from 2 years to ca. 4000 years. Peatlands, boreal, and desert environments were absent from the database. Non-linear regressions with time across the dataset yielded kinetic parameters of the age distribution on one hand and of the flux of new carbon incorporation (kg C m-2 yr-1) on the other, each calculated by 10 cm depth increments. On the average, the median ages of carbon increase from ca. 15 years at 0 cm to more than 1000 years at 100 cm. Turnover is on the average 2 to 3 times slower for the subsoil (30-100 cm) than for the topsoil (0-30 cm). Based on the incorporation of new C in the first decades, the carbon input

  17. Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease

    PubMed Central

    Bouquet, Jerome; Soloski, Mark J.; Swei, Andrea; Cheadle, Chris; Federman, Scot; Billaud, Jean-Noel; Rebman, Alison W.; Kabre, Beniwende; Halpert, Richard; Boorgula, Meher

    2016-01-01

    ABSTRACT Lyme disease is a tick-borne illness caused by the bacterium Borrelia burgdorferi, and approximately 10 to 20% of patients report persistent symptoms lasting months to years despite appropriate treatment with antibiotics. To gain insights into the molecular basis of acute Lyme disease and the ensuing development of post-treatment symptoms, we conducted a longitudinal transcriptome study of 29 Lyme disease patients (and 13 matched controls) enrolled at the time of diagnosis and followed for up to 6 months. The differential gene expression signature of Lyme disease following the acute phase of infection persisted for at least 3 weeks and had fewer than 44% differentially expressed genes (DEGs) in common with other infectious or noninfectious syndromes. Early Lyme disease prior to antibiotic therapy was characterized by marked upregulation of Toll-like receptor signaling but lack of activation of the inflammatory T-cell apoptotic and B-cell developmental pathways seen in other acute infectious syndromes. Six months after completion of therapy, Lyme disease patients were found to have 31 to 60% of their pathways in common with three different immune-mediated chronic diseases. No differential gene expression signature was observed between Lyme disease patients with resolved illness to those with persistent symptoms at 6 months post-treatment. The identification of a sustained differential gene expression signature in Lyme disease suggests that a panel of selected human host-based biomarkers may address the need for sensitive clinical diagnostics during the “window period” of infection prior to the appearance of a detectable antibody response and may also inform the development of new therapeutic targets. PMID:26873097

  18. Loop-Mediated Isothermal Amplification (LAMP) Signature Identification Software

    2009-03-17

    This is an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs.

  19. Ballistic Signature Identification System Study

    NASA Technical Reports Server (NTRS)

    1976-01-01

    The first phase of a research project directed toward development of a high speed automatic process to be used to match gun barrel signatures imparted to fired bullets was documented. An optical projection technique has been devised to produce and photograph a planar image of the entire signature, and the phototransparency produced is subjected to analysis using digital Fourier transform techniques. The success of this approach appears to be limited primarily by the accuracy of the photographic step since no significant processing limitations have been encountered.

  20. Analysis of chlorophenoxy acids and other acidic contaminants in food crops.

    PubMed

    Hajslová, J; Tahtah, W H; Jehlicková, Z; Kocourek, V; Cuhra, P

    1993-04-29

    Several chlorophenoxy acids and chlorinated phenols were determined by means of gas chromatography in contaminated samples of cereals. Extraction of plant matrix with acetone/water mixture followed by alkaline hydrolysis was proved to be suitable for isolation of both free and conjugated residues. The use of pentafluorobenzyl bromide for volatilization of analytes, despite of enhanced ECD response, cannot be recommended for routine analysis. Methylation with either methanol/sulphuric acid or methanol/BF3 reagent can substitute diazomethane-based esterification procedure. Mass fragmentography provided the highest selectivity of detection, moreover good sensitivity--5 ppb--was achieved in this way. Even methyl derivatives of monochlorinated analytes could be, contrary to GC/ECD analysis, quantitated at this level. PMID:8475369

  1. Identification of a novel gene signature of ES cells self-renewal fluctuation through system-wide analysis.

    PubMed

    Cerulo, Luigi; Tagliaferri, Daniela; Marotta, Pina; Zoppoli, Pietro; Russo, Filomena; Mazio, Claudia; DeFelice, Mario; Ceccarelli, Michele; Falco, Geppino

    2014-01-01

    Embryonic Stem cells (ESCs) can be differentiated into ectoderm, endoderm, and mesoderm derivatives, producing the majority of cell types. In regular culture conditions, ESCs' self-renewal is maintained through molecules that inhibit spontaneous differentiation enabling long-term cellular expansion. This undifferentiating condition is characterized by multiple metastable states that fluctuate between self-renewal and differentiation balance. Here, we aim to characterize the high-pluripotent ESC metastate marked by the expression of Zscan4 through a supervised machine learning framework based on an ensemble of support vector machine (SVM) classifiers. Our study revealed a leukaemia inhibitor factor (Lif) dependent not-canonical pluripotency signature (AF067063, BC061212, Dub1, Eif1a, Gm12794, Gm13871, Gm4340, Gm4850, Tcstv1/3, and Zfp352), that specifically marks Zscan4 ESCs' fluctuation. This novel ESC metastate is enhanced by high-pluripotency culture conditions obtained through Extracellular signal Regulated-Kinase (ERK) and Glycogen synthase kinase-3 (Gsk-3) signaling inhibition (2i). Significantly, we reported that the conditional ablation of the novel ESC metastate marked by the expression of Gm12794 is required for ESCs self-renewal maintenance. In conclusion, we extend the comprehension of ESCs biology through the identification of a novel molecular signature associated to pluripotency programming. PMID:24392082

  2. Identification of a Novel Gene Signature of ES Cells Self-Renewal Fluctuation through System-Wide Analysis

    PubMed Central

    Marotta, Pina; Zoppoli, Pietro; Russo, Filomena; Mazio, Claudia; DeFelice, Mario; Ceccarelli, Michele; Falco, Geppino

    2014-01-01

    Embryonic Stem cells (ESCs) can be differentiated into ectoderm, endoderm, and mesoderm derivatives, producing the majority of cell types. In regular culture conditions, ESCs' self-renewal is maintained through molecules that inhibit spontaneous differentiation enabling long-term cellular expansion. This undifferentiating condition is characterized by multiple metastable states that fluctuate between self-renewal and differentiation balance. Here, we aim to characterize the high-pluripotent ESC metastate marked by the expression of Zscan4 through a supervised machine learning framework based on an ensemble of support vector machine (SVM) classifiers. Our study revealed a leukaemia inhibitor factor (Lif) dependent not-canonical pluripotency signature (AF067063, BC061212, Dub1, Eif1a, Gm12794, Gm13871, Gm4340, Gm4850, Tcstv1/3, and Zfp352), that specifically marks Zscan4 ESCs' fluctuation. This novel ESC metastate is enhanced by high-pluripotency culture conditions obtained through Extracellular signal Regulated-Kinase (ERK) and Glycogen synthase kinase-3 (Gsk-3) signaling inhibition (2i). Significantly, we reported that the conditional ablation of the novel ESC metastate marked by the expression of Gm12794 is required for ESCs self-renewal maintenance. In conclusion, we extend the comprehension of ESCs biology through the identification of a novel molecular signature associated to pluripotency programming. PMID:24392082

  3. Structural analysis of DNA interaction with retinol and retinoic acid.

    PubMed

    Mandeville, J S; N'soukpoé-Kossi, C N; Neault, J F; Tajmir-Riahi, H A

    2010-06-01

    Dietary constituents of fresh fruits and vegetables may play a relevant role in DNA adduct formation by inhibiting enzymatic activities. Studies have shown the important role of antioxidant vitamins A, C, and E in the protection against cancer and cardiovascular diseases. The antioxidant activity of vitamin A and beta-carotene may consist of scavenging oxygen radicals and preventing DNA damage. This study was designed to examine the interaction of calf-thymus DNA with retinol and retinoic acid in aqueous solution at physiological conditions using a constant DNA concentration and various retinoid contents. Fourier transform infrared (FTIR), circular dichroism (CD), and fluorescence spectroscopic methods were used to determine retinoid binding mode, the binding constant, and the effects of retinol and retinoic acid complexation on DNA conformation and aggregation. Structural analysis showed that retinol and retinoic acid bind DNA via G-C and A-T base pairs and the backbone phosphate groups with overall binding constants of Kret = 3.0 (+/-0.50) x 10(3) (mol.L(-1))(-1) and Kretac = 1.0 (+/-0.20) x 10(4) (mol.L(-1))(-1). The number of bound retinoids per DNA were 0.84 for retinol and 1.3 for retinoic acid. Hydrophobic interactions were also observed at high retinol and retinoic acid contents. At a high retinoid concentration, major DNA aggregation occurred, while DNA remained in the B-family structure. PMID:20555389

  4. Spatially resolved analysis of plutonium isotopic signatures in environmental particle samples by laser ablation-MC-ICP-MS.

    PubMed

    Konegger-Kappel, Stefanie; Prohaska, Thomas

    2016-01-01

    Laser ablation-multi-collector-inductively coupled plasma mass spectrometry (LA-MC-ICP-MS) was optimized and investigated with respect to its performance for determining spatially resolved Pu isotopic signatures within radioactive fuel particle clusters. Fuel particles had been emitted from the Chernobyl nuclear power plant (ChNPP) where the 1986 accident occurred and were deposited in the surrounding soil, where weathering processes caused their transformation into radioactive clusters, so-called micro-samples. The size of the investigated micro-samples, which showed surface alpha activities below 40 mBq, ranged from about 200 to 1000 μm. Direct single static point ablations allowed to identify variations of Pu isotopic signatures not only between distinct fuel particle clusters but also within individual clusters. The resolution was limited to 100 to 120 μm as a result of the applied laser ablation spot sizes and the resolving power of the nuclear track radiography methodology that was applied for particle pre-selection. The determined (242)Pu/(239)Pu and (240)Pu/(239)Pu isotope ratios showed a variation from low to high Pu isotope ratios, ranging from 0.007(2) to 0.047(8) for (242)Pu/(239)Pu and from 0.183(13) to 0.577(40) for (240)Pu/(239)Pu. In contrast to other studies, the applied methodology allowed for the first time to display the Pu isotopic distribution in the Chernobyl fallout, which reflects the differences in the spent fuel composition over the reactor core. The measured Pu isotopic signatures are in good agreement with the expected Pu isotopic composition distribution that is typical for a RBMK-1000 reactor, indicating that the analyzed samples are originating from the ill-fated Chernobyl reactor. The average Pu isotope ratios [(240)Pu/(239)Pu = 0.388(86), (242)Pu/(239)Pu = 0.028(11)] that were calculated from all investigated samples (n = 48) correspond well to previously published results of Pu analyses in contaminated samples from

  5. A group signature scheme based on quantum teleportation

    NASA Astrophysics Data System (ADS)

    Wen, Xiaojun; Tian, Yuan; Ji, Liping; Niu, Xiamu

    2010-05-01

    In this paper, we present a group signature scheme using quantum teleportation. Different from classical group signature and current quantum signature schemes, which could only deliver either group signature or unconditional security, our scheme guarantees both by adopting quantum key preparation, quantum encryption algorithm and quantum teleportation. Security analysis proved that our scheme has the characteristics of group signature, non-counterfeit, non-disavowal, blindness and traceability. Our quantum group signature scheme has a foreseeable application in the e-payment system, e-government, e-business, etc.

  6. Identification of host response signatures of infection.

    SciTech Connect

    Branda, Steven S.; Sinha, Anupama; Bent, Zachary

    2013-02-01

    Biological weapons of mass destruction and emerging infectious diseases represent a serious and growing threat to our national security. Effective response to a bioattack or disease outbreak critically depends upon efficient and reliable distinguishing between infected vs healthy individuals, to enable rational use of scarce, invasive, and/or costly countermeasures (diagnostics, therapies, quarantine). Screening based on direct detection of the causative pathogen can be problematic, because culture- and probe-based assays are confounded by unanticipated pathogens (e.g., deeply diverged, engineered), and readily-accessible specimens (e.g., blood) often contain little or no pathogen, particularly at pre-symptomatic stages of disease. Thus, in addition to the pathogen itself, one would like to detect infection-specific host response signatures in the specimen, preferably ones comprised of nucleic acids (NA), which can be recovered and amplified from tiny specimens (e.g., fingerstick draws). Proof-of-concept studies have not been definitive, however, largely due to use of sub-optimal sample preparation and detection technologies. For purposes of pathogen detection, Sandia has developed novel molecular biology methods that enable selective isolation of NA unique to, or shared between, complex samples, followed by identification and quantitation via Second Generation Sequencing (SGS). The central hypothesis of the current study is that variations on this approach will support efficient identification and verification of NA-based host response signatures of infectious disease. To test this hypothesis, we re-engineered Sandia's sophisticated sample preparation pipelines, and developed new SGS data analysis tools and strategies, in order to pioneer use of SGS for identification of host NA correlating with infection. Proof-of-concept studies were carried out using specimens drawn from pathogen-infected non-human primates (NHP). This work provides a strong foundation for

  7. The Effect of Point-spread Function Interaction with Radiance from Heterogeneous Scenes on Multitemporal Signature Analysis. [soybean stress

    NASA Technical Reports Server (NTRS)

    Duggin, M. J.; Schoch, L. B.

    1984-01-01

    The point-spread function is an important factor in determining the nature of feature types on the basis of multispectral recorded radiance, particularly from heterogeneous scenes and particularly from scenes which are imaged repetitively, in order to provide thematic characterization by means of multitemporal signature. To demonstrate the effect of the interaction of scene heterogeneity with the point spread function (PSF)1, a template was constructed from the line spread function (LSF) data for the thematic mapper photoflight model. The template was in 0.25 (nominal) pixel increments in the scan line direction across three scenes of different heterogeneity. The sensor output was calculated by considering the calculated scene radiance from each scene element occurring between the contours of the PSF template, plotted on a movable mylar sheet while it was located at a given position.

  8. Persistence of virus lipid signatures upon silicification

    NASA Astrophysics Data System (ADS)

    Kyle, J.; Jahnke, L. L.; Stedman, K. M.

    2011-12-01

    To date there is no known evidence of viruses within the rock record. Their small size and absence of a metabolism has led to the hypothesis that they lack unique biological signatures, and the potential to become preserved. Biosignature research relevant to early Earth has focused on prokaryotic communities; however, the most abundant member of modern ecosystems, viruses, have been ignored. In order to establish a baseline for research on virus biosignatures, we have initiated laboratory research on known lipid-containing viruses. PRD1 is a lipid-containing virus that infects and replicates in Salmonella typhimurium LT2. PRD1 is a 65 nm spherical virus with an internal lipid membrane, which is a few nanometers thick. When the PRD1 virus stock was mixed with a 400 ppm SiO2 (final concentration) solution and incubated for six months. Fourier Transform Infrared Spectroscopy and lipid analysis using gas chromatography revealed that the virus lipids were still detectable despite complete removal of dissolved silica. Free fatty acids were also detected. Titers of infectious PRD1 viruses after six months in the presence of silica decreased 40 times more than without silica. Though virus biosignature research is in its incipient stages, the data suggest that virus lipid signatures are preserved under laboratory conditions and may offer the potential for contribution to the organic geochemical record.

  9. Transcriptome analysis using next generation sequencing reveals molecular signatures of diabetic retinopathy and efficacy of candidate drugs

    PubMed Central

    Rajasimha, Harsha K.; Brooks, Matthew J.; Nellissery, Jacob; Wan, Jun; Qian, Jiang; Kern, Timothy S.; Swaroop, Anand

    2012-01-01

    Purpose To define gene expression changes associated with diabetic retinopathy in a mouse model using next generation sequencing, and to utilize transcriptome signatures to assess molecular pathways by which pharmacological agents inhibit diabetic retinopathy. Methods We applied a high throughput RNA sequencing (RNA-seq) strategy using Illumina GAIIx to characterize the entire retinal transcriptome from nondiabetic and from streptozotocin-treated mice 32 weeks after induction of diabetes. Some of the diabetic mice were treated with inhibitors of receptor for advanced glycation endproducts (RAGE) and p38 mitogen activated protein (MAP) kinase, which have previously been shown to inhibit diabetic retinopathy in rodent models. The transcripts and alternatively spliced variants were determined in all experimental groups. Results Next generation sequencing-based RNA-seq profiles provided comprehensive signatures of transcripts that are altered in early stages of diabetic retinopathy. These transcripts encoded proteins involved in distinct yet physiologically relevant disease-associated pathways such as inflammation, microvasculature formation, apoptosis, glucose metabolism, Wnt signaling, xenobiotic metabolism, and photoreceptor biology. Significant upregulation of crystallin transcripts was observed in diabetic animals, and the diabetes-induced upregulation of these transcripts was inhibited in diabetic animals treated with inhibitors of either RAGE or p38 MAP kinase. These two therapies also showed dissimilar regulation of some subsets of transcripts that included alternatively spliced versions of arrestin, neutral sphingomyelinase activation associated factor (Nsmaf), SH3-domain GRB2-like interacting protein 1 (Sgip1), and axin. Conclusions Diabetes alters many transcripts in the retina, and two therapies that inhibit the vascular pathology similarly inhibit a portion of these changes, pointing to possible molecular mechanisms for their beneficial effects. These

  10. Knowledge Driven Variable Selection (KDVS) – a new approach to enrichment analysis of gene signatures obtained from high–throughput data

    PubMed Central

    2013-01-01

    Background High–throughput (HT) technologies provide huge amount of gene expression data that can be used to identify biomarkers useful in the clinical practice. The most frequently used approaches first select a set of genes (i.e. gene signature) able to characterize differences between two or more phenotypical conditions, and then provide a functional assessment of the selected genes with an a posteriori enrichment analysis, based on biological knowledge. However, this approach comes with some drawbacks. First, gene selection procedure often requires tunable parameters that affect the outcome, typically producing many false hits. Second, a posteriori enrichment analysis is based on mapping between biological concepts and gene expression measurements, which is hard to compute because of constant changes in biological knowledge and genome analysis. Third, such mapping is typically used in the assessment of the coverage of gene signature by biological concepts, that is either score–based or requires tunable parameters as well, limiting its power. Results We present Knowledge Driven Variable Selection (KDVS), a framework that uses a priori biological knowledge in HT data analysis. The expression data matrix is transformed, according to prior knowledge, into smaller matrices, easier to analyze and to interpret from both computational and biological viewpoints. Therefore KDVS, unlike most approaches, does not exclude a priori any function or process potentially relevant for the biological question under investigation. Differently from the standard approach where gene selection and functional assessment are applied independently, KDVS embeds these two steps into a unified statistical framework, decreasing the variability derived from the threshold–dependent selection, the mapping to the biological concepts, and the signature coverage. We present three case studies to assess the usefulness of the method. Conclusions We showed that KDVS not only enables the

  11. Analysis of amino acids and carbohydrates in green coffee.

    PubMed

    Murkovic, Michael; Derler, Karin

    2006-11-30

    The analysis of carbohydrates and amino acids in green coffee is of the utmost importance since these two classes of compounds act as precursors of the Maillard reaction during which the colour and aroma are formed. During the course of the Maillard reaction potentially harmful substances like acrylamide or 5-hydroxymethyl-furfural accrue as well. The carbohydrates were analysed by anion-exchange chromatography with pulsed amperometric detection and the amino acids by reversed phase chromatography after derivatization with 6-amino-quinolyl-N-hydroxysuccinimidyl carbamate and fluorescence detection. Both methods had to be optimized to obtain a sufficient resolution of the analytes for identification and quantification. Sucrose is the dominant carbohydrate in green coffee with a concentration of up to 90 mg/g (mean = 73 mg/g) in arabica beans and significantly lower amounts in robusta beans (mean=45 mg/g). Alanine is the amino acid with the highest concentration (mean = 1200 microg/g) followed by asparagine (mean = 680 microg/g) in robusta and 800 microg/g and 360 microg/g in arabica respectively. In general, the concentration of amino acids is higher in robusta than in arabica. PMID:16563515

  12. Thermodynamic analysis of acetic acid steam reforming for hydrogen production

    NASA Astrophysics Data System (ADS)

    Goicoechea, Saioa; Ehrich, Heike; Arias, Pedro L.; Kockmann, Norbert

    2015-04-01

    A thermodynamic analysis of hydrogen generation by acetic acid steam reforming has been carried out with respect to applications in solid oxide fuel cells. The effect of operating parameters on equilibrium composition has been examined focusing especially on hydrogen and carbon monoxide production, which are the fuels in this type of fuel cell. The temperature, steam to acetic acid ratio, and to a lesser extent pressure affect significantly the equilibrium product distribution due to their influence on steam reforming, thermal decomposition and water-gas shift reaction. The study shows that steam reforming of acetic acid with a steam to acetic acid ratio of 2 to 1 is thermodynamically feasible with hydrogen, carbon monoxide and water as the main products at the equilibrium at temperatures higher than 700 °C, and achieving CO/CO2 ratios higher than 1. Thus, it can be concluded that within the operation temperature range of solid oxide fuel cells - between 700 °C and 1000 °C - the production of a gas rich in hydrogen and carbon monoxide is promoted.

  13. Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids

    NASA Astrophysics Data System (ADS)

    Bonacci, Gustavo; Asciutto, Eliana K.; Woodcock, Steven R.; Salvatore, Sonia R.; Freeman, Bruce A.; Schopfer, Francisco J.

    2011-09-01

    Nitro-fatty acids are electrophilic signaling mediators formed in increased amounts during inflammation by nitric oxide and nitrite-dependent redox reactions. A more rigorous characterization of endogenously-generated species requires additional understanding of their gas-phase induced fragmentation. Thus, collision induced dissociation (CID) of nitroalkane and nitroalkene groups in fatty acids were studied in the negative ion mode to provide mass spectrometric tools for their structural characterization. Fragmentation of nitroalkanes occurred mainly through loss of the NO{2/-} anion or neutral loss of HNO2. The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional γ or δ unsaturation occurred through a multiple step cyclization reaction process, leading to 5 and 6 member ring heterocyclic products and carbon chain fragmentation. Cyclization products were not obtained during nitroalkane fragmentation, highlighting the role of double bond π electrons during NO{2/-} rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of 13C and 15N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples.

  14. Draft versus finished sequence data for DNA and protein diagnostic signature development

    SciTech Connect

    Gardner, S N; Lam, M W; Smith, J R; Torres, C L; Slezak, T R

    2004-10-29

    Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors, or NNs) to sequence. We use SAP to assess whether draft data is sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high quality draft with error rates of 10{sup -3}-10{sup -5} ({approx} 8x coverage) of target organisms is suitable for DNA signature prediction. Low quality draft with error rates of {approx} 1% (3x to 6x coverage) of target isolates is inadequate for DNA signature prediction, although low quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high quality draft of target and low quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures.

  15. Comparative analysis of spread-F signature and GPS scintillation occurrences at Tucumán, Argentina

    NASA Astrophysics Data System (ADS)

    Spogli, L.; Lucilla, A.; Pezzopane, M.; Romano, V.; Zuccheretti, E.; De Franceschi, G.; Cabrera, M.; Ezquer, R. G.

    2013-12-01

    A deep understanding of the temporal and spatial evolution of the ionosphere can be achieved by using a multi-instrument approach which provides complementary information. Bearing this in mind, we analyze data recorded from October 2010 to September 2011, during the ascending phase of the 24th solar cycle, from an Advanced Ionospheric Sounder-Istituto Nazionale di Geofisica e Vulcanologia ionosonde and a GPS Ionospheric Scintillation and Total Electron Content (TEC) monitor receiver, located in the same site at low latitude in the Southern American longitudinal sector (Tucumán, 26.9°S, 294.6°E, magnetic latitude 15.5°S, Argentina). Such site offers the opportunity to perform combined spread-F and GPS scintillation statistics of occurrence under the southern crest of the equatorial ionospheric anomaly. Spread-F signatures, classified into four types (strong range spread-F (SSF), range spread-F, frequency spread-F (FSF), and mixed spread-F), the phase and amplitude scintillation index (σΦ and S4, respectively), the TEC, and the rate of TEC parameter, marker of the TEC gradients, that can cause scintillation, are considered. The seasonal behavior results as follows: the occurrence of all four types of spread-F is higher in summer and lower in winter, while the occurrence of scintillation peaks at equinoxes in the postsunset sector and shows a minimum in winter. The correspondence between SSF and scintillation seems to be systematic, and a possible correlation between S4 and FSF peaks is envisaged at the terminator. Evidence that scintillation, unlike ESF, is recorded all-day long, allows to speculate also on the relationship between the features of the sporadic E irregularities and scintillation patterns. Our results indicate that the daytime amplitude scintillation is in correspondence with the appearance of a dense Es layer, with critical frequency above 4 MHz. The investigation focused also on two particular periods, from 12 to 16 March 2011 and from 23 to 29

  16. Influences of acidic reaction and hydrolytic conditions on monosaccharide composition analysis of acidic, neutral and basic polysaccharides.

    PubMed

    Wang, Qing-Chi; Zhao, Xia; Pu, Jiang-Hua; Luan, Xiao-Hong

    2016-06-01

    Monosaccharide composition analysis is important for structural characterization of polysaccharides. To investigate the influences of acidic reaction and hydrolytic conditions on monosaccharide composition analysis of polysaccharides, we chose alginate, starch, chitosan and chondroitin sulfate as representative of acidic, neutral, basic and complex polysaccharides to compare the release degree of monosaccharides under different hydrolytic conditions. The hydrolysis stability of 10 monosaccharide standards was also explored. Results showed that the basic sugars were hard to release but stable, the acidic sugars (uronic acids) were easy to release but unstable, and the release and stability of neutral sugars were in between acidic and basic sugars. In addition, the hydrolysis process was applied to monosaccharide composition analysis of Hippocampus trimaculatus polysaccharide and the appropriate hydrolytic condition was accorded with that of the above four polysaccharides. Thus, different hydrolytic conditions should be used for the monosaccharide composition analysis of polysaccharides based on their structural characteristics. PMID:27083372

  17. Real time gamma-ray signature identifier

    DOEpatents

    Rowland, Mark; Gosnell, Tom B.; Ham, Cheryl; Perkins, Dwight; Wong, James

    2012-05-15

    A real time gamma-ray signature/source identification method and system using principal components analysis (PCA) for transforming and substantially reducing one or more comprehensive spectral libraries of nuclear materials types and configurations into a corresponding concise representation/signature(s) representing and indexing each individual predetermined spectrum in principal component (PC) space, wherein an unknown gamma-ray signature may be compared against the representative signature to find a match or at least characterize the unknown signature from among all the entries in the library with a single regression or simple projection into the PC space, so as to substantially reduce processing time and computing resources and enable real-time characterization and/or identification.

  18. Security Weaknesses in Arbitrated Quantum Signature Protocols

    NASA Astrophysics Data System (ADS)

    Liu, Feng; Zhang, Kejia; Cao, Tianqing

    2014-01-01

    Arbitrated quantum signature (AQS) is a cryptographic scenario in which the sender (signer), Alice, generates the signature of a message and then a receiver (verifier), Bob, can verify the signature with the help of a trusted arbitrator, Trent. In this paper, we point out there exist some security weaknesses in two AQS protocols. Our analysis shows Alice can successfully disavow any of her signatures by a simple attack in the first protocol. Furthermore, we study the security weaknesses of the second protocol from the aspects of forgery and disavowal. Some potential improvements of this kind of protocols are given. We also design a new method to authenticate a signature or a message, which makes AQS protocols immune to Alice's disavowal attack and Bob's forgery attack effectively.

  19. Eukaryotic signature proteins of Prosthecobacter dejongeii and Gemmata sp. Wa-1 as revealed by in silico analysis.

    PubMed

    Staley, James T; Bouzek, Heather; Jenkins, Cheryl

    2005-02-01

    The genomes of representatives of three bacterial phyla have been compared with the list of 347 eukaryotic signature proteins (ESPs) derived by Hartman and Fedorov [Proc. Natl. Acad. Sci. USA 99 (2002) 1420]. The species included Prosthecobacter dejongeii of the Verrucomicrobia phylum, Gemmata sp. Wa-1 of the Planctomycetes phylum and Caulobacter crescentus of the Proteobacteria. The protist Trypanosoma brucei was used as a eukaryotic control. P. dejongeii had unique ERGO blast matches to alpha-, beta-, and gamma-tubulin, to Set2, a transcriptional factor associated with eukaryotic DNA, and to LAMMER protein kinase for a total of 10 high-scoring ESP matches altogether. Gemmata sp. Wa-1 shared four of its 17 high-scoring ESP matches with P. dejongeii, and that information coupled with other genomic data provides strong support that these two phyla are related to one another. If the ESP list is an accurate listing of unique eukaryotic proteins, then the low number of high-scoring matches between the proteins of these two bacteria with the list raises doubts about these phyla being direct ancestors of the Eucarya. However, this does not rule out the possibility that ancestral members of either the Verrucomicrobia or Planctomycetes may have played an important role in the evolution of a proto-eukaryotic organism. PMID:15667994

  20. Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

    PubMed Central

    Choi, Jung-Woo; Choi, Bong-Hwan; Lee, Seung-Hwan; Lee, Seung-Soo; Kim, Hyeong-Cheol; Yu, Dayeong; Chung, Won-Hyong; Lee, Kyung-Tai; Chai, Han-Ha; Cho, Yong-Min; Lim, Dajeong

    2015-01-01

    Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds. PMID:26018558

  1. Transcriptome Analysis of the Interferon-Signature Defining the Autoimmune Process of Sjögren’s Syndrome

    PubMed Central

    Peck, A. B.; Nguyen, C. Q.

    2015-01-01

    Sjögren’s syndrome (SS) of humans and SS-like (SjS-like) diseases in mouse models are characterized by chronic immune attacks against the salivary and lacrimal glands leading to exocrine dysfunction. One characteristic of SS and SjS-like diseases repeatedly observed is a strong upregulated expression of both the type I (α/β) and type II (γ) interferons (IFNs). In addition, recent global transcriptome studies have identified a variety of IFN-stimulated gene (ISG) transcripts differentially expressed in tissues of SS patients and mouse models exhibiting SjS-like disease. Analyses of these transcriptome databases indicate that the sets of differentially expressed genes are highly restricted, suggesting that there is a unique specificity in ISGs activated (or suppressed) during development and onset of disease. As a result, these observations have led to both SS and SjS-like diseases being designated as ‘interferon-signature’ diseases. While SS and SjS-like diseases may be designated as such, very little effort has been made to determine what an interferon-signature might signify relative to autoinflammation and whether it might point directly to an underlying etiopathological mechanism. Here, we review these limited data and provide a model of how the products of these genes interact molecularly and biologically to define critical details of SS pathology. PMID:22703193

  2. Analysis of normalized radar cross section (sigma-O) signature of Amazon rain forest using SEASAT scatterometer data

    NASA Technical Reports Server (NTRS)

    Bracalente, E. M.; Sweet, J. L.

    1984-01-01

    The normalized radar cross section (NRCS) signature of the Amazon rain forest was SEASAT scatterometer data. Statistics of the measured (NRCS) values were determined from multiple orbit passes for three local time periods. Plots of mean normalized radar cross section, dB against incidence angle as a function of beam and polarization show that less than 0.3 dB relative bias exists between all beams over a range of incidence angle from 30 deg to 53 deg. The backscattered measurements analyzed show the Amazon rain forest to be relatively homogeneous, azimuthally isotropic and insensitive to polarization. The return from the rain forest target appears relatively consistent and stable, except for the small diurnal variation (0.75 dB) that occurs at sunrise. Because of the relative stability of the rain forest target and the scatterometer instrument, the response of versus incidence angle was able to detect errors in the estimated yaw altitude angle. Also, small instrument gain biases in some of the processing channels were detected. This led to the development of an improved NRCS algorithm, which uses a more accurate method for estimating the system noise power.

  3. A Real Quantum Designated Verifier Signature Scheme

    NASA Astrophysics Data System (ADS)

    Shi, Wei-Min; Zhou, Yi-Hua; Yang, Yu-Guang

    2015-09-01

    The effectiveness of most quantum signature schemes reported in the literature can be verified by a designated person, however, those quantum signature schemes aren't the real traditional designated verifier signature schemes, because the designated person hasn't the capability to efficiently simulate a signature which is indistinguishable from a signer, which cannot satisfy the requirements in some special environments such as E-voting, call for tenders and software licensing. For solving this problem, a real quantum designated verifier signature scheme is proposed in this paper. According to the property of unitary transformation and quantum one-way function, only a verifier designated by a signer can verify the "validity of a signature" and the designated verifier cannot prove to a third party that the signature was produced by the signer or by himself through a transcript simulation algorithm. Moreover, the quantum key distribution and quantum encryption algorithm guarantee the unconditional security of this scheme. Analysis results show that this new scheme satisfies the main security requirements of designated verifier signature scheme and the major attack strategies.

  4. Chromatographic analysis of amino and organic acids in physiological fluids to detect inborn errors of metabolism.

    PubMed

    Woontner, Michael; Goodman, Stephen I

    2006-11-01

    This unit describes methods for the preparation of samples for analysis of physiological amino acids and organic acids. Amino acids are analyzed by ion-exchange chromatography using an automated system. Organic acids are analyzed by gas-chromatography/mass spectrometry (GC-MS). Analysis of amino and organic acids is necessary to detect and monitor the treatment of many inborn errors of metabolism. PMID:18428392

  5. Analysis of the mineral acid-base components of acid-neutralizing capacity in Adirondack Lakes

    NASA Astrophysics Data System (ADS)

    Munson, R. K.; Gherini, S. A.

    1993-04-01

    Mineral acids and bases influence pH largely through their effects on acid-neutralizing capacity (ANC). This influence becomes particularly significant as ANC approaches zero. Analysis of data collected by the Adirondack Lakes Survey Corporation (ALSC) from 1469 lakes throughout the Adirondack region indicates that variations in ANC in these lakes correlate well with base cation concentrations (CB), but not with the sum of mineral acid anion concentrations (CA). This is because (CA) is relatively constant across the Adirondacks, whereas CB varies widely. Processes that supply base cations to solution are ion-specific. Sodium and silica concentrations are well correlated, indicating a common source, mineral weathering. Calcium and magnesium also covary but do not correlate well with silica. This indicates that ion exchange is a significant source of these cations in the absence of carbonate minerals. Iron and manganese concentrations are elevated in the lower waters of some lakes due to reducing conditions. This leads to an ephemeral increase in CB and ANC. When the lakes mix and oxic conditions are restored, these ions largely precipitate from solution. Sulfate is the dominant mineral acid anion in ALSC lakes. Sulfate concentrations are lowest in seepage lakes, commonly about 40 μeq/L less than in drainage lakes. This is due in part to the longer hydraulic detention time in seepage lakes, which allows slow sulfate reduction reactions more time to decrease lake sulfate concentration. Nitrate typically influences ANC during events such as snowmelt. Chloride concentrations are generally low, except in lakes impacted by road salt.

  6. Plasma amino acid and metabolite signatures tracking diabetes progression in the UCD-T2DM rat model of type 2 diabetes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Elevations of plasma concentrations of branched-chain amino acids (BCAAs) are observed in human insulin resistance and type 2 diabetes mellitus (T2DM); however, there has been some controversy with respect to the passive or causative nature of the BCAA phenotype. Using untargeted metabolomics, plasm...

  7. Disaster relief through composite signatures

    NASA Astrophysics Data System (ADS)

    Hawley, Chadwick T.; Hyde, Brian; Carpenter, Tom; Nichols, Steve

    2012-06-01

    A composite signature is a group of signatures that are related in such a way to more completely or further define a target or operational endeavor at a higher fidelity. This paper builds on previous work developing innovative composite signatures associated with civil disasters, including physical, chemical and pattern/behavioral. For the composite signature approach to be successful it requires effective data fusion and visualization. This plays a key role in both preparedness and the response and recovery which are critical to saving lives. Visualization tools enhance the overall understanding of the crisis by pulling together and analyzing the data, and providing a clear and complete analysis of the information to the organizations/agencies dependant on it for a successful operation. An example of this, Freedom Web, is an easy-to-use data visualization and collaboration solution for use in homeland security, emergency preparedness, situational awareness, and event management. The solution provides a nationwide common operating picture for all levels of government through a web based, map interface. The tool was designed to be utilized by non-geospatial experts and is easily tailored to the specific needs of the users. Consisting of standard COTS and open source databases and a web server, users can view, edit, share, and highlight information easily and quickly through a standard internet browser.

  8. Investigation of amino acid δ 13C signatures in bone collagen to reconstruct human palaeodiets using liquid chromatography-isotope ratio mass spectrometry

    NASA Astrophysics Data System (ADS)

    Choy, Kyungcheol; Smith, Colin I.; Fuller, Benjamin T.; Richards, Michael P.

    2010-11-01

    This research presents the individual amino acid δ 13C values in bone collagen of humans ( n = 9) and animals ( n = 27) from two prehistoric shell midden sites in Korea. We obtained complete baseline separation of 16 of the 18 amino acids found in bone collagen by using liquid chromatography-isotope ratio mass spectrometry (LC-IRMS). The isotopic results reveal that the humans and animals in the two sites had similar patterns in essential amino acids (EAAs) and non-essential amino acids (NEAAs). The EAA and NEAA δ 13C values in humans are intermediate between those in marine and terrestrial animals. However, the threonine δ 13C values in humans and animals measured in this study are more highly enriched than those of other amino acids. At both sites, all amino acids in marine animals are 13C-enriched relative to those of the terrestrial animals. The isotopic evidence suggests that the Tongsamdong human had EAAs and NEAAs from marine food resources, while the Nukdo humans mainly had EAAs from terrestrial food resources but obtained NEAAs from both terrestrial and marine resources. The δ 13C isotopic differences in amino acids between marine and terrestrial animals were the largest for glycine (NEAA) and histidine (EAA) and the smallest for tyrosine (NEAA) and phenylalanine (EAA). In addition, threonine among the EAAs also had a large difference (˜8‰) in δ 13C values between marine and terrestrial animals, and has the potential to be used as an isotopic marker in palaeodietary studies. Threonine δ 13C values were used in conjunction with the established Δ 13C Glycine-phenylalanine values and produced three distinct dietary groups (terrestrial, omnivorous, and marine). In addition, threonine δ 13C values and Δ 13C Serine-phenylalanine values were discovered to separate between two dietary groups (terrestrial vs. marine), and these δ 13C values may provide a potential new indicator for investigating the distinction between marine and terrestrial protein

  9. Cloning and transcriptional analysis of Crepis alpina fatty acid desaturases affecting the biosynthesis of crepenynic acid.

    PubMed

    Nam, Jeong-Won; Kappock, T Joseph

    2007-01-01

    Crepis alpina acetylenase is a variant FAD2 desaturase that catalyses the insertion of a triple bond at the Delta12 position of linoleic acid, forming crepenynic acid in developing seeds. Seeds contain a high level of crepenynic acid but other tissues contain none. Using reverse transcriptase-coupled PCR (RT-PCR), acetylenase transcripts were identified in non-seed C. alpina tissues, which were highest in flower heads. To understand why functional expression of the acetylenase is limited to seeds, genes that affect acetylenase activity by providing substrate (FAD2) or electrons (cytochrome b5), or that compete for substrate (FAD3), were cloned. RT-PCR analysis indicated that the availability of a preferred cytochrome b5 isoform is not a limiting factor. Developing seeds co-express acetylenase and FAD2 isoform 2 (FAD2-2) at high levels. Flower heads co-express FAD2-3 and FAD3 at high levels, and FAD2-2 and acetylenase at moderate levels. FAD2-3 was not expressed in developing seed. Real-time RT-PCR absolute transcript quantitation showed 10(4)-fold higher acetylenase expression in developing seeds than in flower heads. Collectively, the results show that both the acetylenase expression level and the co-expression of other desaturases may contribute to the tissue specificity of crepenynate production. Helianthus annuus contains a Delta12 acetylenase in a polyacetylene biosynthetic pathway, so does not accumulate crepenynate. Real-time RT-PCR analysis showed relatively strong acetylenase expression in young sunflowers. Acetylenase transcription is observed in both species without accumulation of the enzymatic product, crepenynate. Functional expression of acetylenase appears to be affected by competition and collaboration with other enzymes. PMID:17329262

  10. Structure and function analysis of protein–nucleic acid complexes

    NASA Astrophysics Data System (ADS)

    Kuznetsova, S. A.; Oretskaya, T. S.

    2016-05-01

    The review summarizes published data on the results and achievements in the field of structure and function analysis of protein–nucleic acid complexes by means of main physical and biochemical methods, including X-ray diffraction, nuclear magnetic resonance spectroscopy, electron and atomic force microscopy, small-angle X-ray and neutron scattering, footprinting and cross-linking. Special attention is given to combined approaches. The advantages and limitations of each method are considered, and the prospects of their application for wide-scale structural studies in vivo are discussed. The bibliography includes 145 references.

  11. Digital Signature Management.

    ERIC Educational Resources Information Center

    Hassler, Vesna; Biely, Helmut

    1999-01-01

    Describes the Digital Signature Project that was developed in Austria to establish an infrastructure for applying smart card-based digital signatures in banking and electronic-commerce applications. Discusses the need to conform to international standards, an international certification infrastructure, and security features for a public directory…

  12. Analysis of Amino Acid Isotopomers using FT-ICR MS

    SciTech Connect

    Pingitore, Francesco; Tang, Yinjie; Kruppa, Gary H.; Keasling,Jay D.

    2006-10-08

    Fluxes through known metabolic pathways and the presence ofnovel metabolic reactions are often determined by feedingisotopically-labeled substrate to an organism and then determining theisotopomer distribution in amino acids in proteins. However, commonlyused techniques to measure the isotopomer distributions requirederivatization prior to analysis (gas chromatography-mass spectrometry(GC-MS)) or large sample sizes (nuclear magnetic resonance (NMR)spectroscopy). Here, we demonstrate the use of Fourier Transform-IonCyclotron Resonance Mass Spectrometry (FT-ICR MS) with direct infusionvia electrospray ionization to rapidly measure the amino acid isotopomerdistribution in a biomass hydrolysate of the soil bacterium Desulfovibriovulgaris Hildenborough. By applying high front-end resolution for theprecursor ion selection followed by sustained off-resonance irradiation -collision-induced dissociation (SORI-CID), it was possible to determineexactly and unambiguously the specific locations of the labeled atoms inthe amino acids, which usually requires a combination of 2-D 13C NMRspectroscopy and GC-MS. This method should be generally applicable toallbiomass samples and will allow more accurate determination of metabolicfluxes with less work and less sample.

  13. Differential sensory fMRI signatures in autism and schizophrenia: Analysis of amplitude and trial-to-trial variability.

    PubMed

    Haigh, Sarah M; Gupta, Akshat; Barb, Scott M; Glass, Summer A F; Minshew, Nancy J; Dinstein, Ilan; Heeger, David J; Eack, Shaun M; Behrmann, Marlene

    2016-08-01

    Autism and schizophrenia share multiple phenotypic and genotypic markers, and there is ongoing debate regarding the relationship of these two disorders. To examine whether cortical dynamics are similar across these disorders, we directly compared fMRI responses to visual, somatosensory and auditory stimuli in adults with autism (N=15), with schizophrenia (N=15), and matched controls (N=15). All participants completed a one-back letter detection task presented at fixation (to control attention) while task-irrelevant sensory stimulation was delivered to the different modalities. We focused specifically on the response amplitudes and the variability in sensory fMRI responses of the two groups, given the evidence of greater trial-to-trial variability in adults with autism. Both autism and schizophrenia individuals showed weaker signal-to-noise ratios (SNR) in sensory-evoked responses compared to controls (d>0.42), but for different reasons. For the autism group, the fMRI response amplitudes were indistinguishable from controls but were more variable trial-to-trial (d=0.47). For the schizophrenia group, response amplitudes were smaller compared to autism (d=0.44) and control groups (d=0.74), but were not significantly more variable (d<0.29). These differential group profiles suggest (1) that greater trial-to-trial variability in cortical responses may be specific to autism and is not a defining characteristic of schizophrenia, and (2) that blunted response amplitudes may be characteristic of schizophrenia. The relationship between the amplitude and the variability of cortical activity might serve as a specific signature differentiating these neurodevelopmental disorders. Identifying the neural basis of these responses and their relationship to the underlying genetic bases may substantially enlighten the understanding of both disorders. PMID:27083780

  14. Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics

    SciTech Connect

    Baas, T.; Baskin, C. R.; Diamond, Deborah L.; Garcia-Sastre, A.; Bielefeldt-Ohmann, H.; Tumpey, T. M.; Thomas, M. J.; Carter, V. S.; Teal, T. H.; Van Hoven, N.; Proll, Sean; Jacobs, Jon M.; Caldwell, Z.; Gritsenko, Marina A.; Hukkanen, R.; Camp, David G.; Smith, Richard D.; Katze, Michael G.

    2006-11-01

    Recent outbreaks of avian influenza in humans have stressed the need for an improved non-human primate model of influenza pathogenesis. In order to develop our macaque model, we expanded our in vivo and functional genomics experiments: We focused on the innate immune response at day 2 post-inoculation and on gene expression in affected lung tissue with viral genetic material present; finally, we sought to identify signature genes for early infection in whole blood. For these purposes, we infected six pigtailed macaques with 107 TCID50 of influenza A/Texas/36/91 virus and three control animals with a sham inoculate. We sacrificed one control and two experimental animals at day 2, 4, and 7 and lung tissue was harvested for pathology, gene expression profiling, and proteomics. Additionally, blood was collected for genomics every other day from each animal until its endpoint. Gross and microscopic pathology, immunohistochemistry, viral gene expression by arrays and/or quantitative real-time RT-PCR confirmed successful yet mild infection in all experimental animals. Genomic experiments were performed using second generation macaque-specific oligonucleotide arrays and high-throughput proteomics revealed host response to infection at the protein level. Our data showed dramatic differences in gene expression within the same influenza-induced lesion based on the presence or absence of viral mRNA. We also identified genes tightly co-regulated in peripheral white blood cells and in lung tissue at day 2 post-inoculation. This latter finding opens the possibility of using gene expression arrays on whole blood to detect infection after exposure but prior to onset of symptoms or shedding.

  15. Gas chromatographic organic acid profiling analysis of brandies and whiskeys for pattern recognition analysis.

    PubMed

    Park, Y J; Kim, K R; Kim, J H

    1999-06-01

    An efficient gas chromatographic profiling and pattern recognition method is described for brandy and whiskey samples according to their organic acid contents. It involves solid-phase extraction of organic acids using Chromosorb P with subsequent conversion to stable tert-butyldimethylsilyl derivatives for the direct analysis by capillary column gas chromatography and gas chromatography-mass spectrometry. A total of 12 organic acids were reproducibly identified in liquor samples (1 mL). When the GC profiles were simplified to their retention index spectra, characteristic patterns were obtained for each liquor sample as well as for each group average. Stepwise discriminant analysis provided star symbols characteristic for each liquor sample and group average. As expected, canonical discriminant analysis correctly classified 23 liquor samples studied into two groups of either brandy or whiskey. PMID:10794629

  16. Cystic fibrosis-type mutational analysis in the ATP-binding cassette transporter signature of human P-glycoprotein MDR1.

    PubMed

    Hoof, T; Demmer, A; Hadam, M R; Riordan, J R; Tümmler, B

    1994-08-12

    Members of the ATP-binding cassette transporter superfamily such as the P-glycoproteins (MDR) and the cystic fibrosis transmembrane conductance regulator (CFTR) share conserved sequence motifs in their nucleotide binding fold that are the major targets for CFTR mutations in patients with cystic fibrosis. Cystic fibrosis-type mutations were introduced at analogous positions into the human MDR1 gene. Heterologous expression of wild-type or mutated MDR1 revealed similar mRNA transcript levels in Chinese hamster ovary K1 recipients, but the subsequent processing was defective for all mutations that give rise to severe cystic fibrosis in the case of CFTR. Functional multidrug transporter MDR1, however, was obtained when amino acid substitutions were introduced into a less conserved position of the ATP-binding cassette transporter signature (codon 536 in MDR1). The profile of cross-resistance and chemosensitization was modulated in these codon 536 variants, which suggests that this region is involved in the drug transport function of P-glycoprotein. PMID:7914197

  17. Brain Signature of Chronic Orofacial Pain: A Systematic Review and Meta-Analysis on Neuroimaging Research of Trigeminal Neuropathic Pain and Temporomandibular Joint Disorders

    PubMed Central

    Lin, Chia-shu

    2014-01-01

    Brain neuroimaging has been widely used to investigate the bran signature of chronic orofacial pain, including trigeminal neuropathic pain (TNP) and pain related to temporomandibular joint disorders (TMD). We here systematically reviewed the neuroimaging literature regarding the functional and structural changes in the brain of TNP and TMD pain patients, using a computerized search of journal articles via PubMed. Ten TNP studies and 14 TMD studies were reviewed. Study quality and risk of bias were assessed based on the criteria of patient selection, the history of medication, the use of standardized pain/psychological assessments, and the model and statistics of imaging analyses. Qualitative meta-analysis was performed by examining the brain regions which showed significant changes in either brain functions (including the blood-oxygen-level dependent signal, cerebral blood flow and the magnetic resonance spectroscopy signal) or brain structure (including gray matter and white matter anatomy). We hypothesized that the neuroimaging findings would display a common pattern as well as distinct patterns of brain signature in the disorders. This major hypothesis was supported by the following findings: (1) TNP and TMD patients showed consistent functional/structural changes in the thalamus and the primary somatosensory cortex, indicating the thalamocortical pathway as the major site of plasticity. (2) The TNP patients showed more alterations at the thalamocortical pathway, and the two disorders showed distinct patterns of thalamic and insular connectivity. Additionally, functional and structural changes were frequently reported in the prefrontal cortex and the basal ganglia, suggesting the role of cognitive modulation and reward processing in chronic orofacial pain. The findings highlight the potential for brain neuroimaging as an investigating tool for understanding chronic orofacial pain. PMID:24759798

  18. Improved Quantum Signature Scheme with Weak Arbitrator

    NASA Astrophysics Data System (ADS)

    Su, Qi; Li, Wen-Min

    2013-09-01

    In this paper, we find a man-in-the-middle attack on the quantum signature scheme with a weak arbitrator (Luo et al., Int. J. Theor. Phys., 51:2135, 2012). In that scheme, the authors proposed a quantum signature based on quantum one way function which contains both verifying the signer phase and verifying the signed message phase. However, after our analysis we will show that Eve can adopt different strategies in respective phases to forge the signature without being detected. Then we present an improved scheme to increase the security.

  19. Hyperspectral analysis for qualitative and quantitative features related to acid mine drainage at a remediated open-pit mine

    NASA Astrophysics Data System (ADS)

    Davies, G.; Calvin, W. M.

    2015-12-01

    The exposure of pyrite to oxygen and water in mine waste environments is known to generate acidity and the accumulation of secondary iron minerals. Sulfates and secondary iron minerals associated with acid mine drainage (AMD) exhibit diverse spectral properties in the ultraviolet, visible and near-infrared regions of the electromagnetic spectrum. The use of hyperspectral imagery for identification of AMD mineralogy and contamination has been well studied. Fewer studies have examined the impacts of hydrologic variations on mapping AMD or the unique spectral signatures of mine waters. Open-pit mine lakes are an additional environmental hazard which have not been widely studied using imaging spectroscopy. A better understanding of AMD variation related to climate fluctuations and the spectral signatures of contaminated surface waters will aid future assessments of environmental contamination. This study examined the ability of multi-season airborne hyperspectral data to identify the geochemical evolution of substances and contaminant patterns at the Leviathan Mine Superfund site. The mine is located 24 miles southeast of Lake Tahoe and contains remnant tailings piles and several AMD collection ponds. The objectives were to 1) distinguish temporal changes in mineralogy at a the remediated open-pit sulfur mine, 2) identify the absorption features of mine affected waters, and 3) quantitatively link water spectra to known dissolved iron concentrations. Images from NASA's AVIRIS instrument were collected in the spring, summer, and fall seasons for two consecutive years at Leviathan (HyspIRI campaign). Images had a spatial resolution of 15 meters at nadir. Ground-based surveys using the ASD FieldSpecPro spectrometer and laboratory spectral and chemical analysis complemented the remote sensing data. Temporal changes in surface mineralogy were difficult to distinguish. However, seasonal changes in pond water quality were identified. Dissolved ferric iron and chlorophyll

  20. Field enhancement sample stacking for analysis of organic acids in traditional Chinese medicine by capillary electrophoresis.

    PubMed

    Zhu, Qianqian; Xu, Xueqin; Huang, Yuanyuan; Xu, Liangjun; Chen, Guonan

    2012-07-13

    A technique known as field enhancement sample stacking (FESS) and capillary electrophoresis (CE) separation has been developed to analyze and detect organic acids in the three traditional Chinese medicines (such as Portulaca oleracea L., Crataegus pinnatifida and Aloe vera L.). In FESS, a reverse electrode polarity-stacking mode (REPSM) was applied as on-line preconcentration strategy. Under the optimized condition, the baseline separation of eight organic acids (linolenic acid, lauric acid, p-coumaric acid, ascorbic acid, benzoic acid, caffeic acid, succinic acid and fumaric acid) could be achieved within 20 min. Validation parameters of this method (such as detection limits, linearity and precision) were also evaluated. The detection limits ranged from 0.4 to 60 ng/mL. The results indicated that the proposed method was effective for the separation of mixtures of organic acids. Satisfactory recoveries were also obtained in the analysis of these organic acids in the above traditional Chinese medicine samples. PMID:22381886

  1. Analysis of hyperbolic signatures from small discontinuities using an UWB ground-coupled radar: FDTD simulations and field experiments

    NASA Astrophysics Data System (ADS)

    Sagnard, Florence; Tebchrany, Elias; Baltazart, Vincent

    2013-04-01

    Ground penetrating radar (GPR) is a well-known non-destructive technique based on electromagnetic wave propagation that is able to detect by reflection or scattering of waves dielectric discontinuities in the underground. Our application is mainly concerned with civil engineering to perform supervision, inventory, and soil characterization. Because the air-coupled radar suffers from a significant reflection at the ground interface that reduces energy transfer of electromagnetic radiation in the sub-surface and penetration depth, we have developed an ultra-wide band (UWB) ground-coupled radar made of a pair of partially shielded compact planar bowtie slot antennas. As the antenna dimension (36*23 cm2) is close to the A4 sheet size, the maturity of the microstrip technology has allowed to design a particular geometry on the FR4 substrate (h=1.5 mm) which is able to operate at frequencies from 460 MHz to beyond 4 GHz in air. Contrary to a commercial GPR where details on antenna design are not available, it appears here possible to know and control the radiation characteristics and develop full-wave FDTD modeling that can represent field experiments for comparisons and analyses. The objective of this work is to improve, by means of a parametric study, the knowledge of physical phenomena involved in dielectric polarization when waves interact with buried discontinuities and particularly cracks, pipes, delaminations that can be distinguished by their shape, size, dielectric contrast with the surrounding medium, orientation relative to the electric field… Thus, we have first characterized by FDTD modeling and field measurements in a wet sand the radar link in two perpendicular polarizations (parallel and mirror) in the presence of a common soil (epsilon'=5.5, sigma=0.01 S/m) considering variable offsets. Afterwards, we have studied and analyzed the hyperbola signatures generated by the presence of buried canonical objects (pipes, strips) with several dielectric

  2. Comparative 16S rRNA signatures and multilocus sequence analysis for the genus Salinicola and description of Salinicola acroporae sp. nov., isolated from coral Acropora digitifera.

    PubMed

    Lepcha, Rinchen T; Poddar, Abhijit; Schumann, Peter; Das, Subrata K

    2015-07-01

    A novel Gram-negative, aerobic, motile marine bacterium, strain S4-41(T), was isolated from mucus of the coral Acropora digitifera from the Andaman Sea. Heterotrophic growth was observed in 0-25 % NaCl, at 15-45 °C and pH 4.5-9. In phylogenetic trees, strain S4-41(T) was grouped within the genus Salinicola but formed a separate branch distant from a cluster composed of Salinicola salarius M27(T) and Salinicola socius SMB35(T). DNA-DNA relatedness between strain S4-41(T) and these reference strains were well below 70 %. Q-9 was the sole respiratory quinone. The DNA G+C content was determined to be 63.6 mol%. Based on a polyphasic analysis, strain S4-41(T) is concluded to represent a novel species in the genus Salinicola for which the name Salinicola acroporae sp. nov. is proposed. The type strain is S4-41(T) (=JCM 30412(T) = LMG 28587(T)). Comparative 16S rRNA analysis of the genera Salinicola, Kushneria, Chromohalobacter and Cobetia revealed the presence of genus specific sequence signatures. Multilocus sequence analysis based on concatenated sequences of rRNAs (16S and 23S) and four protein coding housekeeping genes (atpA, gyrB, secA, rpoD) was found to be unnecessary for phylogenetic studies of the genus Salinicola. PMID:25944083

  3. Traceable Ring Signature

    NASA Astrophysics Data System (ADS)

    Fujisaki, Eiichiro; Suzuki, Koutarou

    The ring signature allows a signer to leak secrets anonymously, without the risk of identity escrow. At the same time, the ring signature provides great flexibility: No group manager, no special setup, and the dynamics of group choice. The ring signature is, however, vulnerable to malicious or irresponsible signers in some applications, because of its anonymity. In this paper, we propose a traceable ring signature scheme. A traceable ring scheme is a ring signature except that it can restrict “excessive” anonymity. The traceable ring signature has a tag that consists of a list of ring members and an issue that refers to, for instance, a social affair or an election. A ring member can make any signed but anonymous opinion regarding the issue, but only once (per tag). If the member submits another signed opinion, possibly pretending to be another person who supports the first opinion, the identity of the member is immediately revealed. If the member submits the same opinion, for instance, voting “yes” regarding the same issue twice, everyone can see that these two are linked. The traceable ring signature can suit to many applications, such as an anonymous voting on a BBS. We formalize the security definitions for this primitive and show an efficient and simple construction in the random oracle model.

  4. Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by Salicylic Acid (SA) and Jasmonic Acid (JA)

    PubMed Central

    Wu, Guanxun; Li, Guoqiang; Sun, Haifeng; Deng, Suzhen; Shen, Yicheng; Chen, Guoqiang; Zhang, Ruihao; Meng, Chunxiao; Zhang, Xiaowen

    2015-01-01

    Haematococcus pluvialis is an astaxanthin-rich microalga that can increase its astaxanthin production by salicylic acid (SA) or jasmonic acid (JA) induction. The genetic transcriptome details of astaxanthin biosynthesis were analyzed by exposing the algal cells to 25 mg/L of SA and JA for 1, 6 and 24 hours, plus to the control (no stress). Based on the RNA-seq analysis, 56,077 unigenes (51.7%) were identified with functions in response to the hormone stress. The top five identified subcategories were cell, cellular process, intracellular, catalytic activity and cytoplasm, which possessed 5600 (~9.99%), 5302 (~9.45%), 5242 (~9.35%), 4407 (~7.86%) and 4195 (~7.48%) unigenes, respectively. Furthermore, 59 unigenes were identified and assigned to 26 putative transcription factors (TFs), including 12 plant-specific TFs. They were likely associated with astaxanthin biosynthesis in Haematococcus upon SA and JA stress. In comparison, the up-regulation of differential expressed genes occurred much earlier, with higher transcript levels in the JA treatment (about 6 h later) than in the SA treatment (beyond 24 h). These results provide valuable information for directing metabolic engineering efforts to improve astaxanthin biosynthesis in H. pluvialis. PMID:26484871

  5. Transcriptome Analysis in Haematococcus pluvialis: Astaxanthin Induction by Salicylic Acid (SA) and Jasmonic Acid (JA).

    PubMed

    Gao, Zhengquan; Li, Yan; Wu, Guanxun; Li, Guoqiang; Sun, Haifeng; Deng, Suzhen; Shen, Yicheng; Chen, Guoqiang; Zhang, Ruihao; Meng, Chunxiao; Zhang, Xiaowen

    2015-01-01

    Haematococcus pluvialis is an astaxanthin-rich microalga that can increase its astaxanthin production by salicylic acid (SA) or jasmonic acid (JA) induction. The genetic transcriptome details of astaxanthin biosynthesis were analyzed by exposing the algal cells to 25 mg/L of SA and JA for 1, 6 and 24 hours, plus to the control (no stress). Based on the RNA-seq analysis, 56,077 unigenes (51.7%) were identified with functions in response to the hormone stress. The top five identified subcategories were cell, cellular process, intracellular, catalytic activity and cytoplasm, which possessed 5600 (~9.99%), 5302 (~9.45%), 5242 (~9.35%), 4407 (~7.86%) and 4195 (~7.48%) unigenes, respectively. Furthermore, 59 unigenes were identified and assigned to 26 putative transcription factors (TFs), including 12 plant-specific TFs. They were likely associated with astaxanthin biosynthesis in Haematococcus upon SA and JA stress. In comparison, the up-regulation of differential expressed genes occurred much earlier, with higher transcript levels in the JA treatment (about 6 h later) than in the SA treatment (beyond 24 h). These results provide valuable information for directing metabolic engineering efforts to improve astaxanthin biosynthesis in H. pluvialis. PMID:26484871

  6. Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

    SciTech Connect

    Myers, G.; Foley, B.; Korber, B.; Mellors, J.W.; Jeang, K.T.; Wain-Hobson, S.

    1997-04-01

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.

  7. Signature extension studies

    NASA Technical Reports Server (NTRS)

    Vincent, R. K.; Thomas, G. S.; Nalepka, R. F.

    1974-01-01

    The importance of specific spectral regions to signature extension is explored. In the recent past, the signature extension task was focused on the development of new techniques. Tested techniques are now used to investigate this spectral aspect of the large area survey. Sets of channels were sought which, for a given technique, were the least affected by several sources of variation over four data sets and yet provided good object class separation on each individual data set. Using sets of channels determined as part of this study, signature extension was accomplished between data sets collected over a six-day period and over a range of about 400 kilometers.

  8. Australian Acid Playa Lake as a Mars Analog: Results from Sediment Lipid Analysis

    NASA Astrophysics Data System (ADS)

    Graham, H.; Baldridge, A. M.; Stern, J. C.

    2015-12-01

    The ephemeral saline acidic lakes on the Yilgarn Craton of Western Australia have been suggested as geochemical analogues to martian terrains. Both are characterized by interbedded phyllosilicates and hydrated sulfates. On Mars, these areas indicate shifting environmental conditions, from the neutral/alkaline and wet conditions that dominated during the Noachian era to the more familiar dry, acidic conditions that began in the Hesperian. The habitability of such a dynamic environment can be informed by investigation of the Yilgarn Lake system. Previous work has found phospholipid fatty acids (PLFA) evidence of microbial communities in sections of sediment cores taken from Lake Gilmore. These communities include both Gram-positive and -negative bacteria, Actinomycetes, and even methanotrophs. Given recurring detection of methane on the martian surface, evidence of a methane cycling community in an analogous environment is of particular interest. In this study we analyze the carbon isotope composition of bulk organic material as well as extracted lipids from the Lake Gilmore sediment cores at both a near-shore and mid-lake location. These analyses reveal very low accumulations of organic carbon, concentrated primarily in the gypsum-rich near-shore core. The near-shore sediments show a down-core decrease in abundance of organic carbon as well as depletion in the carbon isotope composition (δ13C) with depth. Bulk carbon did not exhibit the unique, highly depleted, diagnostic signature associated with methanotrophic biomass. Compound-specific isotope analysis (CSIA) of carbon in extracted methanotroph PFLAs can confirm the presence of a methane cycling metabolism at depth. Also, additional extractions have isolated lipids associated with lake-edge grasses. These analyses consider both the chain-length distribution and carbon CSIA of these lipids in order to understand the effect of terrestrial detritus on any preserved methanotroph carbon signal, given the very low

  9. Hyperdimensional analysis of amino acid pair distributions in proteins.

    PubMed

    Henriksen, Svend B; Mortensen, Rasmus J; Geertz-Hansen, Henrik M; Neves-Petersen, Maria Teresa; Arnason, Omar; Söring, Jón; Petersen, Steffen B

    2011-01-01

    Our manuscript presents a novel approach to protein structure analyses. We have organized an 8-dimensional data cube with protein 3D-structural information from 8706 high-resolution non-redundant protein-chains with the aim of identifying packing rules at the amino acid pair level. The cube contains information about amino acid type, solvent accessibility, spatial and sequence distance, secondary structure and sequence length. We are able to pose structural queries to the data cube using program ProPack. The response is a 1, 2 or 3D graph. Whereas the response is of a statistical nature, the user can obtain an instant list of all PDB-structures where such pair is found. The user may select a particular structure, which is displayed highlighting the pair in question. The user may pose millions of different queries and for each one he will receive the answer in a few seconds. In order to demonstrate the capabilities of the data cube as well as the programs, we have selected well known structural features, disulphide bridges and salt bridges, where we illustrate how the queries are posed, and how answers are given. Motifs involving cysteines such as disulphide bridges, zinc-fingers and iron-sulfur clusters are clearly identified and differentiated. ProPack also reveals that whereas pairs of Lys residues virtually never appear in close spatial proximity, pairs of Arg are abundant and appear at close spatial distance, contrasting the belief that electrostatic repulsion would prevent this juxtaposition and that Arg-Lys is perceived as a conservative mutation. The presented programs can find and visualize novel packing preferences in proteins structures allowing the user to unravel correlations between pairs of amino acids. The new tools allow the user to view statistical information and visualize instantly the structures that underpin the statistical information, which is far from trivial with most other SW tools for protein structure analysis. PMID:22174733

  10. In-Depth, Label-Free Analysis of the Erythrocyte Cytoplasmic Proteome in Diamond Blackfan Anemia Identifies a Unique Inflammatory Signature

    PubMed Central

    Pesciotta, Esther N.; Lam, Ho-Sun; Kossenkov, Andrew; Ge, Jingping; Showe, Louise C.; Mason, Philip J.; Bessler, Monica; Speicher, David W.

    2015-01-01

    Diamond Blackfan Anemia (DBA) is a rare, congenital erythrocyte aplasia that is usually caused by haploinsufficiency of ribosomal proteins due to diverse mutations in one of several ribosomal genes. A striking feature of this disease is that a range of different mutations in ribosomal proteins results in similar disease phenotypes primarily characterized by erythrocyte abnormalities and macrocytic anemia, while most other cell types in the body are minimally affected. Previously, we analyzed the erythrocyte membrane proteomes of several DBA patients and identified several proteins that are not typically associated with this cell type and that suggested inflammatory mechanisms contribute to the pathogenesis of DBA. In this study, we evaluated the erythrocyte cytosolic proteome of DBA patients through in-depth analysis of hemoglobin-depleted erythrocyte cytosols. Simple, reproducible, hemoglobin depletion using nickel columns enabled in-depth analysis of over 1000 cytosolic erythrocyte proteins with only moderate total analysis time per proteome. Label-free quantitation and statistical analysis identified 29 proteins with significantly altered abundance levels in DBA patients compared to matched healthy control donors. Proteins that were significantly increased in DBA erythrocyte cytoplasms included three proteasome subunit beta proteins that make up the immunoproteasome and proteins induced by interferon-γ such as n-myc interactor and interferon-induced 35 kDa protein [NMI and IFI35 respectively]. Pathway analysis confirmed the presence of an inflammatory signature in erythrocytes of DBA patients and predicted key upstream regulators including mitogen activated kinase 1, interferon-γ, tumor suppressor p53, and tumor necrosis factor. These results show that erythrocytes in DBA patients are intrinsically different from those in healthy controls which may be due to an inflammatory response resulting from the inherent molecular defect of ribosomal protein

  11. In-Depth, Label-Free Analysis of the Erythrocyte Cytoplasmic Proteome in Diamond Blackfan Anemia Identifies a Unique Inflammatory Signature.

    PubMed

    Pesciotta, Esther N; Lam, Ho-Sun; Kossenkov, Andrew; Ge, Jingping; Showe, Louise C; Mason, Philip J; Bessler, Monica; Speicher, David W

    2015-01-01

    Diamond Blackfan Anemia (DBA) is a rare, congenital erythrocyte aplasia that is usually caused by haploinsufficiency of ribosomal proteins due to diverse mutations in one of several ribosomal genes. A striking feature of this disease is that a range of different mutations in ribosomal proteins results in similar disease phenotypes primarily characterized by erythrocyte abnormalities and macrocytic anemia, while most other cell types in the body are minimally affected. Previously, we analyzed the erythrocyte membrane proteomes of several DBA patients and identified several proteins that are not typically associated with this cell type and that suggested inflammatory mechanisms contribute to the pathogenesis of DBA. In this study, we evaluated the erythrocyte cytosolic proteome of DBA patients through in-depth analysis of hemoglobin-depleted erythrocyte cytosols. Simple, reproducible, hemoglobin depletion using nickel columns enabled in-depth analysis of over 1000 cytosolic erythrocyte proteins with only moderate total analysis time per proteome. Label-free quantitation and statistical analysis identified 29 proteins with significantly altered abundance levels in DBA patients compared to matched healthy control donors. Proteins that were significantly increased in DBA erythrocyte cytoplasms included three proteasome subunit beta proteins that make up the immunoproteasome and proteins induced by interferon-γ such as n-myc interactor and interferon-induced 35 kDa protein [NMI and IFI35 respectively]. Pathway analysis confirmed the presence of an inflammatory signature in erythrocytes of DBA patients and predicted key upstream regulators including mitogen activated kinase 1, interferon-γ, tumor suppressor p53, and tumor necrosis factor. These results show that erythrocytes in DBA patients are intrinsically different from those in healthy controls which may be due to an inflammatory response resulting from the inherent molecular defect of ribosomal protein

  12. Infrasound Rocket Signatures

    NASA Astrophysics Data System (ADS)

    Olson, J.

    2012-09-01

    This presentation reviews the work performed by our research group at the Geophysical Institute as we have applied the tools of infrasound research to rocket studies. This report represents one aspect of the effort associated with work done for the National Consortium for MASINT Research (NCMR) program operated by the National MASINT Office (NMO) of the Defense Intelligence Agency (DIA). Infrasound, the study of acoustic signals and their propagation in a frequency band below 15 Hz, enables an investigator to collect and diagnose acoustic signals from distant sources. Absorption of acoustic energy in the atmosphere decreases as the frequency is reduced. In the infrasound band signals can propagate hundreds and thousands of kilometers with little degradation. We will present an overview of signatures from rockets ranging from small sounding rockets such as the Black Brandt and Orion series to larger rockets such as Delta 2,4 and Atlas V. Analysis of the ignition transients provides information that can uniquely identify the motor type. After the rocket ascends infrasound signals can be used to characterize the rocket and identify the various events that take place along a trajectory such as staging and maneuvering. We have also collected information on atmospheric shocks and sonic booms from the passage of supersonic vehicles such as the shuttle. This review is intended to show the richness of the unique signal set that occurs in the low-frequency infrasound band.

  13. Folic acid fortification of grain: an economic analysis.

    PubMed Central

    Romano, P S; Waitzman, N J; Scheffler, R M; Pi, R D

    1995-01-01

    OBJECTIVES. The purpose of this study was to compare the economic costs and benefits of fortifying grain with folic acid to prevent neural tube defects. METHODS. A cost-benefit analysis based on the US population, using the human capital approach to estimate the costs associated with preventable neural tube defects, was conducted. RESULTS. Under a range of assumptions about discount rates, baseline folate intake, the effectiveness of folate in preventing neural tube defects, the threshold dose that minimizes risk, and the cost of surveillance, fortification would likely yield a net economic benefit. The best estimate of this benefit is $94 million with low-level (140 micrograms [mcg] per 100 g grain) fortification and $252 million with high-level (350 mcg/100 g) fortification. The benefit-to-cost ratio is estimated at 4.3:1 for low-level and 6.1:1 for high-level fortification. CONCLUSIONS. By averting costly birth defects, folic acid fortification of grain in the United States may yield a substantial economic benefit. We may have underestimated net benefits because of unmeasured costs of neural tube defects and unmeasured benefits of higher folate intake. We may have overestimated net benefits if the cost of neurologic sequelae related to delayed diagnosis of vitamin B12 deficiency exceeds our projection. PMID:7733427

  14. Comparative analysis of hydrologic signatures in two agricultural watersheds in east-central Illinois: legacies of the past to inform the future

    NASA Astrophysics Data System (ADS)

    Yaeger, M. A.; Sivapalan, M.; McIsaac, G. F.; Cai, X.

    2013-11-01

    Historically, the central Midwestern US has undergone drastic anthropogenic land use change, having been transformed, in part through government policy, from a natural grassland system to an artificially drained agricultural system devoted to row cropping corn and soybeans. Current federal policies are again influencing land use in this region with increased corn acreage and new biomass crops proposed as part of an energy initiative emphasizing biofuels. To better address these present and future challenges it is helpful to understand whether and how the legacies of past changes have shaped the current response of the system. To this end, a comparative analysis of the hydrologic signatures in both spatial and time series data from two central Illinois watersheds was undertaken. The past history of these catchments is reflected in their current hydrologic responses, which are highly heterogeneous due to differences in geologic history, artificial drainage patterns, and reservoir operation, and manifest temporally, from annual to daily timescales, and spatially, both within and between the watersheds. These differences are also apparent from analysis of the summer low flows, where the more tile-drained watershed shows greater variability overall than does the more naturally drained one. In addition, precipitation in this region is also spatially heterogeneous even at small scales, and this, interacting with and filtering through the historical modifications to the system, increases the complexity of the problem of predicting the catchment response to future changes.

  15. Spectroscopic signatures of PETN: Part II. Detection in clay

    NASA Astrophysics Data System (ADS)

    Ballesteros-Rueda, Luz Marina; Herrera-Sandoval, Gloria M.; Mina, Nairmen; Castro-Rosario, Miguel E.; Briano, Julio G.; Hernandez-Rivera, Samuel P.

    2006-05-01

    Infrared Spectroscopy is a well established tool for standoff detection of chemical agents in military applications. Vibrational IR spectroscopic analysis can also be used in Chemical Point Detection mode and to the arena of explosives identification and detection when energetic compounds are in contact with soil. PETN is an important nitroaliphatic explosive for military applications. Due to its intrinsic explosive power, it can be used in laminar form or mixed with RDX to manufacture Semtex plastic explosive and in the fabrication of Improvised Explosive Devices (IEDs). This investigation focused on the study of spectroscopic signatures of PETN in contact with soil. For this study, clay was mixed in different proportions with PETN. Detection of the vibrational signatures of PETN constitutes the central part of the investigation. The mixtures were submitted to the effect of water, acid and alkaline solutions, heat and deep UV light (234 nm) in order to establish the effect on these environmental parameters on the vibrational signatures of the explosive in the mixtures. The results reveal that the characteristic bands of PETN are highly persisted, degraded only by extreme conditions of UV radiation and exposure to high temperature for prolonged time. These results could be used in the development of sensitive sensors for detection of landmines, and improvised explosives devices (IDEs).

  16. Meteor signature interpretation

    SciTech Connect

    Canavan, G.H.

    1997-01-01

    Meteor signatures contain information about the constituents of space debris and present potential false alarms to early warnings systems. Better models could both extract the maximum scientific information possible and reduce their danger. Accurate predictions can be produced by models of modest complexity, which can be inverted to predict the sizes, compositions, and trajectories of object from their signatures for most objects of interest and concern.

  17. Method comparison study for weak acid dissociation cyanide analysis.

    PubMed

    Evans, Joseph D; Thompson, Leslie; Clark, Patrick J; Beckman, Scott W

    2003-02-01

    Method comparison studies of two different methods for the analysis of weak acid dissociable (WAD) cyanide revealed analytical flaws and/or matrix interference problems with both procedures. EPA "draft" method 1677 using a Perstorp 3202 CN analyzer was compared to Standard Method 4500 CN I. It was discovered that the Perstorp analyzer produced more precise and more accurate results once appropriate and necessary procedural steps from the EPA draft method were modified. Comparison of these two methods, was based on "real world" samples collected from a mine-tailing solution. The mine-tailing solution contained high concentrations of cyanide and metals. Inconsistencies in method procedures were traced to sulfide interferences and high concentrations of WAD metals. Conclusions were based upon a large sample base collected from a mine site over a 90-day period. PMID:12630477

  18. Adansonian Analysis and Deoxyribonucleic Acid Base Composition of Serratia marcescens

    PubMed Central

    Colwell, R. R.; Mandel, M.

    1965-01-01

    Colwell, R. R. (Georgetown University, Washington, D.C.), and M. Mandel. Adansonian analysis and deoxyribonucleic acid base composition of Serratia marcescens. J. Bacteriol. 89:454–461. 1965.—A total of 33 strains of Serratia marcescens were subjected to Adansonian analysis for which more than 200 coded features for each of the organisms were included. In addition, the base composition [expressed as moles per cent guanine + cytosine (G + C)] of the deoxyribonucleic acid (DNA) prepared from each of the strains was determined. Except for four strains which were intermediate between Serratia and the Hafnia and Aerobacter group C of Edwards and Ewing, the S. marcescens species group proved to be extremely homogeneous, and the different strains showed high affinities for each other (mean similarity, ¯S = 77%). The G + C ratio of the DNA from the Serratia strains ranged from 56.2 to 58.4% G + C. Many species names have been listed for the genus, but only a single clustering of the strains was obtained at the species level, for which the species name S. marcescens was retained. S. kiliensis, S. indica, S. plymuthica, and S. marinorubra could not be distinguished from S. marcescens; it was concluded, therefore, that there is only a single species in the genus. The variety designation kiliensis does not appear to be valid, since no subspecies clustering of strains with negative Voges-Proskauer reactions could be detected. The characteristics of the species are listed, and a description of S. marcescens is presented. PMID:14255714

  19. Qualitative urinary organic acid analysis: 10 years of quality assurance.

    PubMed

    Peters, Verena; Bonham, James R; Hoffmann, Georg F; Scott, Camilla; Langhans, Claus-Dieter

    2016-09-01

    Over the last 10 years, a total of 90 urine samples from patients with metabolic disorders and controls were circulated to different laboratories in Europe and overseas, starting with 67 laboratories in 2005 and reaching 101 in 2014. The participants were asked to analyse the samples in their usual way and to prepare a report as if to a non-specialist pediatrician. The performance for the detection of fumarase deficiency, glutaric aciduria type I, isovaleric aciduria, methylmalonic aciduria, mevalonic aciduria, phenylketonuria and propionic aciduria was excellent (98-100 %). Over the last few years, detection has clearly improved for tyrosinaemia type I (39 % in 2008 to over 80 % in 2011/2014), maple syrup urine disease (85 % in 2005 to 98 % in 2012), hawkinsinuria (62 % in 2010 to 88 % in 2014), aminoacylase I deficiency (43 % in 2009 to 73 % in 2012) and 3-methylcrotonyl-CoA carboxylase deficiency (60 % in 2005 to 93 % by 2011). Normal urines were mostly considered as normal (83-100 %), but laboratories often made additional diagnostic suggestions. When the findings were unambiguous, the reports were mostly clear. However, when they were less obvious, the content and quality of reports varied greatly. Repetition of organic acid measurements on a fresh sample was rarely suggested, while more complex or invasive diagnostic strategies, including further metabolic screening or biopsy were recommended. Surprisingly very few participants suggested referral from the general paediatrician to a specialist metabolic centre to confirm a diagnosis and, if applicable, to initiate treatment despite evidence suggesting that this improves the outcome for patients with inherited metabolic disorders. The reliability of qualitative organic acid analysis has improved over the last few years. However, several aspects of reporting to non-specialists may need discussion and clinicians need to be aware of the uncertainty inherent in all forms of laboratory diagnostic

  20. Sensitive Amino Acid Composition and Chirality Analysis with the Mars Organic Analyzer (MOA)

    NASA Technical Reports Server (NTRS)

    Skelley, Alison M.; Scherer, James R.; Aubrey, Andrew D.; Grover, William H.; Ivester, Robin H. C.; Ehrenfreund, Pascale; Grunthaner, Frank J.; Bada, Jeffrey L.; Mathies, Richard A.

    2005-01-01

    Detection of life on Mars requires definition of a suitable biomarker and development of sensitive yet compact instrumentation capable of performing in situ analyses. Our studies are focused on amino acid analysis because amino acids are more resistant to decomposition than other biomolecules, and because amino acid chirality is a well-defined biomarker. Amino acid composition and chirality analysis has been previously demonstrated in the lab using microfabricated capillary electrophoresis (CE) chips. To analyze amino acids in the field, we have developed the Mars Organic Analyzer (MOA), a portable analysis system that consists of a compact instrument and a novel multi-layer CE microchip.

  1. Analysis of Post-Traumatic Brain Injury Gene Expression Signature Reveals Tubulins, Nfe2l2, Nfkb, Cd44, and S100a4 as Treatment Targets

    PubMed Central

    Lipponen, Anssi; Paananen, Jussi; Puhakka, Noora; Pitkänen, Asla

    2016-01-01

    We aimed to define the chronically altered gene expression signature of traumatic brain injury (TBI-sig) to discover novel treatments to reverse pathologic gene expression or reinforce the expression of recovery-related genes. Genome-wide RNA-sequencing was performed at 3 months post-TBI induced by lateral fluid-percussion injury in rats. We found 4964 regulated genes in the perilesional cortex and 1966 in the thalamus (FDR < 0.05). TBI-sig was used for a LINCS analysis which identified 11 compounds that showed a strong connectivity with the TBI-sig in neuronal cell lines. Of these, celecoxib and sirolimus were recently reported to have a disease-modifying effect in in vivo animal models of epilepsy. Other compounds revealed by the analysis were BRD-K91844626, BRD-A11009626, NO-ASA, BRD-K55260239, SDZ-NKT-343, STK-661558, BRD-K75971499, ionomycin, and desmethylclomipramine. Network analysis of overlapping genes revealed the effects on tubulins (Tubb2a, Tubb3, Tubb4b), Nfe2l2, S100a4, Cd44, and Nfkb2, all of which are linked to TBI-relevant outcomes, including epileptogenesis and tissue repair. Desmethylclomipramine modulated most of the gene targets considered favorable for TBI outcome. Our data demonstrate long-lasting transcriptomics changes after TBI. LINCS analysis predicted that these changes could be modulated by various compounds, some of which are already in clinical use but never tested in TBI. PMID:27530814

  2. Analysis of Post-Traumatic Brain Injury Gene Expression Signature Reveals Tubulins, Nfe2l2, Nfkb, Cd44, and S100a4 as Treatment Targets.

    PubMed

    Lipponen, Anssi; Paananen, Jussi; Puhakka, Noora; Pitkänen, Asla

    2016-01-01

    We aimed to define the chronically altered gene expression signature of traumatic brain injury (TBI-sig) to discover novel treatments to reverse pathologic gene expression or reinforce the expression of recovery-related genes. Genome-wide RNA-sequencing was performed at 3 months post-TBI induced by lateral fluid-percussion injury in rats. We found 4964 regulated genes in the perilesional cortex and 1966 in the thalamus (FDR < 0.05). TBI-sig was used for a LINCS analysis which identified 11 compounds that showed a strong connectivity with the TBI-sig in neuronal cell lines. Of these, celecoxib and sirolimus were recently reported to have a disease-modifying effect in in vivo animal models of epilepsy. Other compounds revealed by the analysis were BRD-K91844626, BRD-A11009626, NO-ASA, BRD-K55260239, SDZ-NKT-343, STK-661558, BRD-K75971499, ionomycin, and desmethylclomipramine. Network analysis of overlapping genes revealed the effects on tubulins (Tubb2a, Tubb3, Tubb4b), Nfe2l2, S100a4, Cd44, and Nfkb2, all of which are linked to TBI-relevant outcomes, including epileptogenesis and tissue repair. Desmethylclomipramine modulated most of the gene targets considered favorable for TBI outcome. Our data demonstrate long-lasting transcriptomics changes after TBI. LINCS analysis predicted that these changes could be modulated by various compounds, some of which are already in clinical use but never tested in TBI. PMID:27530814

  3. Davydov coupling as a factor influencing the H-bond IR signature: Computational study of the IR spectra of 3-thiopheneacrylic acid crystal

    NASA Astrophysics Data System (ADS)

    Rekik, Najeh; Al-Agel, Faisal A.; Flakus, Henryk T.

    2016-03-01

    In this work, we have studied the role played by Davydov coupling in the evolution of the fine structure of the IR spectra of 3-thiopheneacrylic acid dimer crystal. For this purpose, we took into account the linear dependence of the Davydov coupling on the position coordinate Qi(i = 1, 2) of the slow frequency O←sbnd H …O→ mode of the two H-bond bridges of the cyclic dimer. The Davydov coupling VD term was expanded up to first order with respect to the slow mode coordinate Qi. We have considered: VD (Q1 ,Q2) =VD0 + Θ (Q1 +Q2). That leads to the anharmonic expression of the Davydov coupling parameter VD: VD(Qg) =VD0 +√{ 2} ΘQg within the symmetrized coordinates. The effect of the second order parameter (Θ) of Davydov coupling on to the spectral density was undertaken. The numerical calculations clearly show that the crystal spectral properties of the infrared υOsbnd H stretching band remain in a close relation with the new anharmonic coupling parameter and provide a direct evidence of the increase of the level density and the spectral broadening.

  4. Biomarker Signature Discovery from Mass Spectrometry Data.

    PubMed

    Kong, Ao; Gupta, Chinmaya; Ferrari, Mauro; Agostini, Marco; Bedin, Chiara; Bouamrani, Ali; Tasciotti, Ennio; Azencott, Robert

    2014-01-01

    Mass spectrometry based high throughput proteomics are used for protein analysis and clinical diagnosis. Many machine learning methods have been used to construct classifiers based on mass spectrometry data, for discrimination between cancer stages. However, the classifiers generated by machine learning such as SVM techniques typically lack biological interpretability. We present an innovative technique for automated discovery of signatures optimized to characterize various cancer stages. We validate our signature discovery algorithm on one new colorectal cancer MALDI-TOF data set, and two well-known ovarian cancer SELDI-TOF data sets. In all of these cases, our signature based classifiers performed either better or at least as well as four benchmark machine learning algorithms including SVM and KNN. Moreover, our optimized signatures automatically select smaller sets of key biomarkers than the black-boxes generated by machine learning, and are much easier to interpret. PMID:26356346

  5. Electrical signature analysis to quantify human and animal performance on fitness and therapy equipment such as a treadmill

    SciTech Connect

    Cox, Daryl F.; Hochanadel, Charles D.; Haynes, Howard D.

    2010-05-18

    The invention is a human and animal performance data acquisition, analysis, and diagnostic system for fitness and therapy devices having an interface box removably disposed on incoming power wiring to a fitness and therapy device, at least one current transducer removably disposed on said interface box for sensing current signals to said fitness and therapy device, and a means for analyzing, displaying, and reporting said current signals to determine human and animal performance on said device using measurable parameters.

  6. Modeling the Lexical Morphology of Western Handwritten Signatures

    PubMed Central

    Diaz-Cabrera, Moises; Ferrer, Miguel A.; Morales, Aythami

    2015-01-01

    A handwritten signature is the final response to a complex cognitive and neuromuscular process which is the result of the learning process. Because of the many factors involved in signing, it is possible to study the signature from many points of view: graphologists, forensic experts, neurologists and computer vision experts have all examined them. Researchers study written signatures for psychiatric, penal, health and automatic verification purposes. As a potentially useful, multi-purpose study, this paper is focused on the lexical morphology of handwritten signatures. This we understand to mean the identification, analysis, and description of the signature structures of a given signer. In this work we analyze different public datasets involving 1533 signers from different Western geographical areas. Some relevant characteristics of signature lexical morphology have been selected, examined in terms of their probability distribution functions and modeled through a General Extreme Value distribution. This study suggests some useful models for multi-disciplinary sciences which depend on handwriting signatures. PMID:25860942

  7. Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure.

    PubMed

    Rea, Giuseppina; Lambreva, Maya; Polticelli, Fabio; Bertalan, Ivo; Antonacci, Amina; Pastorelli, Sandro; Damasso, Mario; Johanningmeier, Udo; Giardi, Maria Teresa

    2011-01-01

    Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues more sensitive to

  8. Directed Evolution and In Silico Analysis of Reaction Centre Proteins Reveal Molecular Signatures of Photosynthesis Adaptation to Radiation Pressure

    PubMed Central

    Rea, Giuseppina; Lambreva, Maya; Polticelli, Fabio; Bertalan, Ivo; Antonacci, Amina; Pastorelli, Sandro; Damasso, Mario; Johanningmeier, Udo; Giardi, Maria Teresa

    2011-01-01

    Evolutionary mechanisms adopted by the photosynthetic apparatus to modifications in the Earth's atmosphere on a geological time-scale remain a focus of intense research. The photosynthetic machinery has had to cope with continuously changing environmental conditions and particularly with the complex ionizing radiation emitted by solar flares. The photosynthetic D1 protein, being the site of electron tunneling-mediated charge separation and solar energy transduction, is a hot spot for the generation of radiation-induced radical injuries. We explored the possibility to produce D1 variants tolerant to ionizing radiation in Chlamydomonas reinhardtii and clarified the effect of radiation-induced oxidative damage on the photosynthetic proteins evolution. In vitro directed evolution strategies targeted at the D1 protein were adopted to create libraries of chlamydomonas random mutants, subsequently selected by exposures to radical-generating proton or neutron sources. The common trend observed in the D1 aminoacidic substitutions was the replacement of less polar by more polar amino acids. The applied selection pressure forced replacement of residues more sensitive to oxidative damage with less sensitive ones, suggesting that ionizing radiation may have been one of the driving forces in the evolution of the eukaryotic photosynthetic apparatus. A set of the identified aminoacidic substitutions, close to the secondary plastoquinone binding niche and oxygen evolving complex, were introduced by site-directed mutagenesis in un-transformed strains, and their sensitivity to free radicals attack analyzed. Mutants displayed reduced electron transport efficiency in physiological conditions, and increased photosynthetic performance stability and oxygen evolution capacity in stressful high-light conditions. Finally, comparative in silico analyses of D1 aminoacidic sequences of organisms differently located in the evolution chain, revealed a higher ratio of residues more sensitive to

  9. Invisibly Sanitizable Signature without Pairings

    NASA Astrophysics Data System (ADS)

    Yum, Dae Hyun; Lee, Pil Joong

    Sanitizable signatures allow sanitizers to delete some pre-determined parts of a signed document without invalidating the signature. While ordinary sanitizable signatures allow verifiers to know how many subdocuments have been sanitized, invisibly sanitizable signatures do not leave any clue to the sanitized subdocuments; verifiers do not know whether or not sanitizing has been performed. Previous invisibly sanitizable signature scheme was constructed based on aggregate signature with pairings. In this article, we present the first invisibly sanitizable signature without using pairings. Our proposed scheme is secure under the RSA assumption.

  10. Rapid analysis of acid in etching and pickling solutions

    SciTech Connect

    Tumbina, V.P.; Chinokalov, V.Ya.

    1995-02-01

    A computational method for determining sulfuric and hydrochloric acids in two-component etching solutions has been proposed. The method makes use of linear relationships, assuming that the sum of free and bound acid in solution remains constant.

  11. Selection signatures in Shetland ponies.

    PubMed

    Frischknecht, M; Flury, C; Leeb, T; Rieder, S; Neuditschko, M

    2016-06-01

    Shetland ponies were selected for numerous traits including small stature, strength, hardiness and longevity. Despite the different selection criteria, Shetland ponies are well known for their small stature. We performed a selection signature analysis including genome-wide SNPs of 75 Shetland ponies and 76 large-sized horses. Based upon this dataset, we identified a selection signature on equine chromosome (ECA) 1 between 103.8 Mb and 108.5 Mb. A total of 33 annotated genes are located within this interval including the IGF1R gene at 104.2 Mb and the ADAMTS17 gene at 105.4 Mb. These two genes are well known to have a major impact on body height in numerous species including humans. Homozygosity mapping in the Shetland ponies identified a region with increased homozygosity between 107.4 Mb and 108.5 Mb. None of the annotated genes in this region have so far been associated with height. Thus, we cannot exclude the possibility that the identified selection signature on ECA1 is associated with some trait other than height, for which Shetland ponies were selected. PMID:26857482

  12. [Determination of body fluid based on analysis of nucleic acids].

    PubMed

    Korabečná, Marie

    2015-01-01

    Recent methodological approaches of molecular genetics allow isolation of nucleic acids (DNA and RNA) from negligible forensic samples. Analysis of these molecules may be used not only for individual identification based on DNA profiling but also for the detection of origin of the body fluid which (alone or in mixture with other body fluids) forms the examined biological trace. Such an examination can contribute to the evaluation of procedural, technical and tactical value of the trace. Molecular genetic approaches discussed in the review offer new possibilities in comparison with traditional spectrum of chemical, immunological and spectroscopic tests especially with regard to the interpretation of mixtures of biological fluids and to the confirmatory character of the tests. Approaches based on reverse transcription of tissue specific mRNA and their subsequent polymerase chain reaction (PCR) and fragmentation analysis are applicable on samples containing minimal amounts of biological material. Methods for body fluid discrimination based on examination of microRNA in samples provided so far confusing results therefore further development in this field is needed. The examination of tissue specific methylation of nucleotides in selected gene sequences seems to represent a promising enrichment of the methodological spectrum. The detection of DNA sequences of tissue related bacteria has been established and it provides satisfactory results mainly in combination with above mentioned methodological approaches. PMID:26419517

  13. Meta-Analysis of Public Microarray Datasets Reveals Voltage-Gated Calcium Gene Signatures in Clinical Cancer Patients

    PubMed Central

    Wang, Chih-Yang; Lai, Ming-Derg; Phan, Nam Nhut; Sun, Zhengda; Lin, Yen-Chang

    2015-01-01

    Voltage-gated calcium channels (VGCCs) are well documented to play roles in cell proliferation, migration, and apoptosis; however, whether VGCCs regulate the onset and progression of cancer is still under investigation. The VGCC family consists of five members, which are L-type, N-type, T-type, R-type and P/Q type. To date, no holistic approach has been used to screen VGCC family genes in different types of cancer. We analyzed the transcript expression of VGCCs in clinical cancer tissue samples by accessing ONCOMINE (www.oncomine.org), a web-based microarray database, to perform a systematic analysis. Every member of the VGCCs was examined across 21 different types of cancer by comparing mRNA expression in cancer to that in normal tissue. A previous study showed that altered expression of mRNA in cancer tissue may play an oncogenic role and promote tumor development; therefore, in the present findings, we focus only on the overexpression of VGCCs in different types of cancer. This bioinformatics analysis revealed that different subtypes of VGCCs (CACNA1C, CACNA1D, CACNA1B, CACNA1G, and CACNA1I) are implicated in the development and progression of diverse types of cancer and show dramatic up-regulation in breast cancer. CACNA1F only showed high expression in testis cancer, whereas CACNA1A, CACNA1C, and CACNA1D were highly expressed in most types of cancer. The current analysis revealed that specific VGCCs likely play essential roles in specific types of cancer. Collectively, we identified several VGCC targets and classified them according to different cancer subtypes for prospective studies on the underlying carcinogenic mechanisms. The present findings suggest that VGCCs are possible targets for prospective investigation in cancer treatment. PMID:26147197

  14. Meta-Analysis of Public Microarray Datasets Reveals Voltage-Gated Calcium Gene Signatures in Clinical Cancer Patients.

    PubMed

    Wang, Chih-Yang; Lai, Ming-Derg; Phan, Nam Nhut; Sun, Zhengda; Lin, Yen-Chang

    2015-01-01

    Voltage-gated calcium channels (VGCCs) are well documented to play roles in cell proliferation, migration, and apoptosis; however, whether VGCCs regulate the onset and progression of cancer is still under investigation. The VGCC family consists of five members, which are L-type, N-type, T-type, R-type and P/Q type. To date, no holistic approach has been used to screen VGCC family genes in different types of cancer. We analyzed the transcript expression of VGCCs in clinical cancer tissue samples by accessing ONCOMINE (www.oncomine.org), a web-based microarray database, to perform a systematic analysis. Every member of the VGCCs was examined across 21 different types of cancer by comparing mRNA expression in cancer to that in normal tissue. A previous study showed that altered expression of mRNA in cancer tissue may play an oncogenic role and promote tumor development; therefore, in the present findings, we focus only on the overexpression of VGCCs in different types of cancer. This bioinformatics analysis revealed that different subtypes of VGCCs (CACNA1C, CACNA1D, CACNA1B, CACNA1G, and CACNA1I) are implicated in the development and progression of diverse types of cancer and show dramatic up-regulation in breast cancer. CACNA1F only showed high expression in testis cancer, whereas CACNA1A, CACNA1C, and CACNA1D were highly expressed in most types of cancer. The current analysis revealed that specific VGCCs likely play essential roles in specific types of cancer. Collectively, we identified several VGCC targets and classified them according to different cancer subtypes for prospective studies on the underlying carcinogenic mechanisms. The present findings suggest that VGCCs are possible targets for prospective investigation in cancer treatment. PMID:26147197

  15. Metabolic Signatures of Bacterial Vaginosis

    PubMed Central

    Morgan, Martin T.; Fiedler, Tina L.; Djukovic, Danijel; Hoffman, Noah G.; Raftery, Daniel; Marrazzo, Jeanne M.

    2015-01-01

    ABSTRACT Bacterial vaginosis (BV) is characterized by shifts in the vaginal microbiota from Lactobacillus dominant to a microbiota with diverse anaerobic bacteria. Few studies have linked specific metabolites with bacteria found in the human vagina. Here, we report dramatic differences in metabolite compositions and concentrations associated with BV using a global metabolomics approach. We further validated important metabolites using samples from a second cohort of women and a different platform to measure metabolites. In the primary study, we compared metabolite profiles in cervicovaginal lavage fluid from 40 women with BV and 20 women without BV. Vaginal bacterial representation was determined using broad-range PCR with pyrosequencing and concentrations of bacteria by quantitative PCR. We detected 279 named biochemicals; levels of 62% of metabolites were significantly different in women with BV. Unsupervised clustering of metabolites separated women with and without BV. Women with BV have metabolite profiles marked by lower concentrations of amino acids and dipeptides, concomitant with higher levels of amino acid catabolites and polyamines. Higher levels of the signaling eicosanoid 12-hydroxyeicosatetraenoic acid (12-HETE), a biomarker for inflammation, were noted in BV. Lactobacillus crispatus and Lactobacillus jensenii exhibited similar metabolite correlation patterns, which were distinct from correlation patterns exhibited by BV-associated bacteria. Several metabolites were significantly associated with clinical signs and symptoms (Amsel criteria) used to diagnose BV, and no metabolite was associated with all four clinical criteria. BV has strong metabolic signatures across multiple metabolic pathways, and these signatures are associated with the presence and concentrations of particular bacteria. PMID:25873373

  16. Comparative analysis of hydrologic signatures in two agricultural watersheds in east-central Illinois: legacies of the past to inform the future

    NASA Astrophysics Data System (ADS)

    Yaeger, M. A.; Sivapalan, M.; McIsaac, G. F.; Cai, X.

    2013-05-01

    Historically, the central Midwestern US has undergone drastic anthropogenic land use change, having been transformed, in part through federal government policy, from a natural grassland system to an artificially-drained agricultural system devoted to row cropping corn and soybeans. Current federal policies are again influencing land use change in this region with increased corn acreage and new biomass crops proposed as part of an energy initiative emphasizing biofuels. To better address these present and future challenges it is helpful to understand how the legacies of past changes have shaped the current response of the system. To this end, a comparative analysis of the hydrologic signatures in both spatial and time series data from two central Illinois watersheds was undertaken. The past history of these catchments is reflected in their current hydrologic responses, which are highly heterogeneous, more so in the extensively tile-drained Sangamon watershed. The differences in geologic history, artificial drainage patterns, and to some extent, reservoir construction, manifest at all time scales, from annual to daily, and spatially within the watersheds. These differences can also be seen in the summer low flow patterns, where the more tile-drained watershed shows more variability than does the more naturally drained one. Of interest is the scaling behavior of the low flows; generally as drainage area increases, small-scale heterogeneity decreases. This is not seen in the more tile-drained watershed, thus adding complexity to the problem of predicting the catchment response to future changes.

  17. The lung cancer breath signature: a comparative analysis of exhaled breath and air sampled from inside the lungs

    NASA Astrophysics Data System (ADS)

    Capuano, Rosamaria; Santonico, Marco; Pennazza, Giorgio; Ghezzi, Silvia; Martinelli, Eugenio; Roscioni, Claudio; Lucantoni, Gabriele; Galluccio, Giovanni; Paolesse, Roberto; di Natale, Corrado; D'Amico, Arnaldo

    2015-11-01

    Results collected in more than 20 years of studies suggest a relationship between the volatile organic compounds exhaled in breath and lung cancer. However, the origin of these compounds is still not completely elucidated. In spite of the simplistic vision that cancerous tissues in lungs directly emit the volatile metabolites into the airways, some papers point out that metabolites are collected by the blood and then exchanged at the air-blood interface in the lung. To shed light on this subject we performed an experiment collecting both the breath and the air inside both the lungs with a modified bronchoscopic probe. The samples were measured with a gas chromatography-mass spectrometer (GC-MS) and an electronic nose. We found that the diagnostic capability of the electronic nose does not depend on the presence of cancer in the sampled lung, reaching in both cases an above 90% correct classification rate between cancer and non-cancer samples. On the other hand, multivariate analysis of GC-MS achieved a correct classification rate between the two lungs of only 76%. GC-MS analysis of breath and air sampled from the lungs demonstrates a substantial preservation of the VOCs pattern from inside the lung to the exhaled breath.

  18. Human Amniotic Fluid Mesenchymal Stem Cells from Second- and Third-Trimester Amniocentesis: Differentiation Potential, Molecular Signature, and Proteome Analysis

    PubMed Central

    Savickiene, Jurate; Treigyte, Grazina; Baronaite, Sandra; Valiuliene, Giedre; Kaupinis, Algirdas; Valius, Mindaugas; Arlauskiene, Audrone; Navakauskiene, Ruta

    2015-01-01

    Human amniotic fluid stem cells have become an attractive stem cell source for potential applications in regenerative medicine and tissue engineering. The aim of this study was to characterize amniotic fluid-derived mesenchymal stem cells (AF-MSCs) from second- and third-trimester of gestation. Using two-stage protocol, MSCs were successfully cultured and exhibited typical stem cell morphological, specific cell surface, and pluripotency markers characteristics. AF-MSCs differentiated into adipocytes, osteocytes, chondrocytes, myocytes, and neuronal cells, as determined by morphological changes, cell staining, and RT-qPCR showing the tissue-specific gene presence for differentiated cell lineages. Using SYNAPT G2 High Definition Mass Spectrometry technique approach, we performed for the first time the comparative proteomic analysis between undifferentiated AF-MSCs from late trimester of gestation and differentiated into myogenic, adipogenic, osteogenic, and neurogenic lineages. The analysis of the functional and expression patterns of 250 high abundance proteins selected from more than 1400 demonstrated the similar proteome of cultured and differentiated AF-MSCs but the unique changes in their expression profile during cell differentiation that may help the identification of key markers in differentiated cells. Our results provide evidence that human amniotic fluid of second- and third-trimester contains stem cells with multilineage potential and may be attractive source for clinical applications. PMID:26351462

  19. The lung cancer breath signature: a comparative analysis of exhaled breath and air sampled from inside the lungs

    PubMed Central

    Capuano, Rosamaria; Santonico, Marco; Pennazza, Giorgio; Ghezzi, Silvia; Martinelli, Eugenio; Roscioni, Claudio; Lucantoni, Gabriele; Galluccio, Giovanni; Paolesse, Roberto; Di Natale, Corrado; D’Amico, Arnaldo

    2015-01-01

    Results collected in more than 20 years of studies suggest a relationship between the volatile organic compounds exhaled in breath and lung cancer. However, the origin of these compounds is still not completely elucidated. In spite of the simplistic vision that cancerous tissues in lungs directly emit the volatile metabolites into the airways, some papers point out that metabolites are collected by the blood and then exchanged at the air-blood interface in the lung. To shed light on this subject we performed an experiment collecting both the breath and the air inside both the lungs with a modified bronchoscopic probe. The samples were measured with a gas chromatography-mass spectrometer (GC-MS) and an electronic nose. We found that the diagnostic capability of the electronic nose does not depend on the presence of cancer in the sampled lung, reaching in both cases an above 90% correct classification rate between cancer and non-cancer samples. On the other hand, multivariate analysis of GC-MS achieved a correct classification rate between the two lungs of only 76%. GC-MS analysis of breath and air sampled from the lungs demonstrates a substantial preservation of the VOCs pattern from inside the lung to the exhaled breath. PMID:26559776

  20. Donor-Specific Indirect Pathway Analysis Reveals a B-Cell-Independent Signature Which Reflects Outcomes in Kidney Transplant Recipients

    PubMed Central

    Haynes, L. D.; Jankowska-Gan, E.; Sheka, A.; Keller, M. R.; Hernandez-Fuentes, M. P.; Lechler, R. I.; Seyfert-Margolis, V.; Turka, L. A.; Newell, K. A.; Burlingham, W. J.

    2012-01-01

    To investigate the role of donor-specific indirect pathway T cells in renal transplant tolerance, we analyzed responses in peripheral blood of 45 patients using the trans-vivo delayed-type hypersensitivity assay. Subjects were enrolled into five groups—identical twin, clinically tolerant (TOL), steroid monotherapy (MONO), standard immunosuppression (SI) and chronic rejection (CR)—based on transplant type, posttransplant immunosuppression and graft function. The indirect pathway was active in all groups except twins but distinct intergroup differences were evident, corresponding to clinical status. The antidonor indirect pathway T effector response increased across patient groups (TOL < MONO < SI < CR; p < 0.0001) whereas antidonor indirect pathway T regulatory response decreased (TOL > MONO = SI > CR; p < 0.005). This pattern differed from that seen in circulating naïve B-cell numbers and in a cross-platform biomarker analysis, where patients on monotherapy were not ranked closest to TOL patients, but rather were indistinguishable from chronically rejecting patients. Cross-sectional analysis of the indirect pathway revealed a spectrum in T-regulatory:T-effector balance, ranging from TOL patients having predominantly regulatory responses to CR patients having predominantly effector responses. Therefore, the indirect pathway measurements reflect a distinct aspect of tolerance from the recently reported elevation of circulating naïve B cells, which was apparent only in recipients off immunosuppression. PMID:22151236

  1. Nucleic acid analysis using terminal-phosphate-labeled nucleotides

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2008-04-22

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  2. Mutations in the K+ channel signature sequence.

    PubMed Central

    Heginbotham, L; Lu, Z; Abramson, T; MacKinnon, R

    1994-01-01

    Potassium channels share a highly conserved stretch of eight amino acids, a K+ channel signature sequence. The conserved sequence falls within the previously defined P-region of voltage-activated K+ channels. In this study we investigate the effect of mutations in the signature sequence of the Shaker channel on K+ selectivity determined under bi-ionic conditions. Nonconservative substitutions of two threonine residues and the tyrosine residue leave selectivity intact. In contrast, mutations at some positions render the channel nonselective among monovalent cations. These findings are consistent with a proposal that the signature sequence contributes to a selectivity filter. Furthermore, the results illustrate that the hydroxyl groups at the third and fourth positions, and the aromatic group at position seven, are not essential in determining K+ selectivity. Images FIGURE 1 PMID:8038378

  3. Newborn Urinary Metabolic Signatures of Prematurity and Other Disorders: A Case Control Study.

    PubMed

    Diaz, Sílvia O; Pinto, Joana; Barros, António S; Morais, Elisabete; Duarte, Daniela; Negrão, Fátima; Pita, Cristina; Almeida, Maria do Céu; Carreira, Isabel M; Spraul, Manfred; Gil, Ana M

    2016-01-01

    This work assesses the urinary metabolite signature of prematurity in newborns by nuclear magnetic resonance (NMR) spectroscopy, while establishing the role of possible confounders and signature specificity, through comparison to other disorders. Gender and delivery mode are shown to impact importantly on newborn urine composition, their analysis pointing out at specific metabolite variations requiring consideration in unmatched subject groups. Premature newborns are, however, characterized by a stronger signature of varying metabolites, suggestive of disturbances in nucleotide metabolism, lung surfactants biosynthesis and renal function, along with enhancement of tricarboxylic acid (TCA) cycle activity, fatty acids oxidation, and oxidative stress. Comparison with other abnormal conditions (respiratory depression episode, large for gestational age, malformations, jaundice and premature rupture of membranes) reveals that such signature seems to be largely specific of preterm newborns, showing that NMR metabolomics can retrieve particular disorder effects, as well as general stress effects. These results provide valuable novel information on the metabolic impact of prematurity, contributing to the better understanding of its effects on the newborn's state of health. PMID:26566167

  4. Analysis of fluorotelomer alcohols, fluorotelomer acids, and short- and long-chain perfluorinated acids in water and biota.

    PubMed

    Taniyasu, Sachi; Kannan, Kurunthachalam; So, Man Ka; Gulkowska, Anna; Sinclair, Ewan; Okazawa, Tsuyoshi; Yamashita, Nobuyoshi

    2005-11-01

    Fluorotelomer alcohols and fluorotelomer acids have been proposed as a source of the perfluorinated carboxylic acids found in remote marine locations. To examine the sources and fate of perfluorinated acids in the environment, a method to determine a wide range of poly- and perfluorinated acids in environmental and biological matrices is needed. In this study, a method has been developed to measure a suite of neutral and acidic fluorochemicals including, fluorotelomer alcohols, fluorotelomer acids, and short- and long-chain perfluorinated acids, in water and biological samples. The method involves solid-phase extraction with weak anion exchange (WAX) cartridges, followed by sequential elution with sodium acetate buffer, methanol, and 0.1% NH4OH in methanol. For biological samples, prior to solid-phase extraction, tissues are digested in 0.5N potassium hydroxide/methanol, diluted in water, and passed through the WAX cartridge. Neutral compounds and telomer alcohols are separated from other poly- and perfluorinated acids. The method is robust (i.e., capable of measuring neutral and acidic compounds), and can be applied for the analysis of a range of poly- and perfluorinated acids, including telomer alcohols, telomer acids, perfluoroalkylcarboxylates, and perfluoroalkylsulfonates in water and biota. With the use of high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), a method detection limit in the range of several tens to hundreds of parts-per-quadrillion (pg/L) in water and at a few tens to hundreds of parts-per-trillion (pg/g) levels in biological matrices can be achieved. PMID:16233874

  5. Molecularly Imprinted Polymers for Selective Analysis of Chemical Warfare Surrogate and Nuclear Signature Compounds in Complex Matrices

    SciTech Connect

    Harvey, Scott D.

    2005-08-01

    This paper describes the preparation and evaluation of molecularly imprinted polymers (MIPs) that display specificity toward diisopropyl methylphosphonate (DIMP) and tributyl phosphate (TBP). Polymer activity was assessed by solid-phase extraction and high-performance liquid chromatography experiments. Both DIMP- and TBP-specific MIPs selectively retained their targets relative to a nonimprinted control. Proof-of-principle experiments demonstrated highly selective analysis of the targets from fortified complex matrix samples (diesel fuel, gasoline, and air extract concentrate). The retained MIP fractions gave near quantitative recovery of the target analytes with very low matrix background content. The same fraction from the control sorbent was less pure and recovered only about half of the analyte.

  6. Molecularly imprinted polymers for selective analysis of chemical warfare surrogate and nuclear signature compounds in complex matrices.

    PubMed

    Harvey, Scott D

    2005-07-01

    This paper describes the preparation and evaluation of molecularly imprinted polymers (MIPs) that display specificity toward diisopropyl methylphosphonate (DIMP) and tributyl phosphate (TBP). Polymer activity was assessed by solid-phase extraction and high-performance liquid chromatography experiments. Both DIMP- and TBP-specific vinylpyridine-based MIPs selectively retained their targets relative to a non-imprinted control. Proof-of-principle experiments demonstrated highly selective analysis of the targets from fortified complex matrix samples (diesel fuel, gasoline, and air extract concentrate). The retained MIP fractions gave near quantitative recovery of the target analytes with very low matrix background content. The same fraction from the control sorbent recovered only about half of the analyte and tended to be less pure. PMID:16117000

  7. immunoClust--An automated analysis pipeline for the identification of immunophenotypic signatures in high-dimensional cytometric datasets.

    PubMed

    Sörensen, Till; Baumgart, Sabine; Durek, Pawel; Grützkau, Andreas; Häupl, Thomas

    2015-07-01

    Multiparametric fluorescence and mass cytometry offers new perspectives to disclose and to monitor the high diversity of cell populations in the peripheral blood for biomarker research. While high-end cytometric devices are currently available to detect theoretically up to 120 individual parameters at the single cell level, software tools are needed to analyze these complex datasets automatically in acceptable time and without operator bias or knowledge. We developed an automated analysis pipeline, immunoClust, for uncompensated fluorescence and mass cytometry data, which consists of two parts. First, cell events of each sample are grouped into individual clusters. Subsequently, a classification algorithm assorts these cell event clusters into populations comparable between different samples. The clustering of cell events is designed for datasets with large event counts in high dimensions as a global unsupervised method, sensitive to identify rare cell types even when next to large populations. Both parts use model-based clustering with an iterative expectation maximization algorithm and the integrated classification likelihood to obtain the clusters. A detailed description of both algorithms is presented. Testing and validation was performed using 1) blood cell samples of defined composition that were depleted of particular cell subsets by magnetic cell sorting, 2) datasets of the FlowCAP III challenges to identify populations of rare cell types and 3) high-dimensional fluorescence and mass-cytometry datasets for comparison with conventional manual gating procedures. In conclusion, the immunoClust-algorithm is a promising tool to standardize and automate the analysis of high-dimensional cytometric datasets. As a prerequisite for interpretation of such data, it will support our efforts in developing immunological biomarkers for chronic inflammatory disorders and therapy recommendations in personalized medicine. immunoClust is implemented as an R-package and is

  8. Analysis of cyclic pyrolysis products formed from amino acid monomer.

    PubMed

    Choi, Sung-Seen; Ko, Ji-Eun

    2011-11-18

    Amino acid was mixed with silica and tetramethylammonium hydroxide (TMAH) to favor pyrolysis of amino acid monomer. The pyrolysis products formed from amino acid monomer were using GC/MS and GC. 20 amino acids of alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine were analyzed. The pyrolysis products were divided into cyclic and non-cyclic products. Among the 20 amino acids, arginine, asparagine, glutamic acid, glutamine, histidine, lysine, and phenylalanine generated cyclic pyrolysis products of the monomer. New cyclic pyrolysis products were formed by isolation of amino acid monomers. They commonly had polar side functional groups to 5-, 6-, or 7-membered ring structure. Arginine, asparagine, glutamic acid, glutamine, histidine, and phenylalanine generated only 5- or 6-membered ring products. However, lysine generated both 6- and 7-membered ring compounds. Variations of the relative intensities of the cyclic pyrolysis products with the pyrolysis temperature and amino acid concentration were also investigated. PMID:21993510

  9. Fatty Acid Structure and Degradation Analysis in Fingerprint Residues.

    PubMed

    Pleik, Stefanie; Spengler, Bernhard; Schäfer, Thomas; Urbach, Dieter; Luhn, Steven; Kirsch, Dieter

    2016-09-01

    GC-MS investigations were carried out to elucidate the aging behavior of unsaturated fatty acids in fingerprint residues and to identify their degradation products in aged samples. For this purpose, a new sample preparation technique for fingerprint residues was developed that allows producing N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA) derivatives of the analyzed unsaturated fatty acids and their degradation products. MSTFA derivatization catalyzed by iodotrimethylsilane enables the reliable identification of aldehydes and oxoacids as characteristic MSTFA derivatives in GCMS. The obtained results elucidate the degradation pathway of unsaturated fatty acids. Our study of aged fingerprint residues reveals that decanal is the main degradation product of the observed unsaturated fatty acids. Furthermore, oxoacids with different chain lengths are detected as specific degradation products of the unsaturated fatty acids. The detection of the degradation products and their chain length is a simple and effective method to determine the double bond position in unsaturated compounds. We can show that the hexadecenoic and octadecenoic acids found in fingerprint residues are not the pervasive fatty acids Δ9-hexadecenoic (palmitoleic acid) and Δ9-octadecenoic (oleic acid) acid but Δ6-hexadecenoic acid (sapienic acid) and Δ8-octadecenoic acid. The present study focuses on the structure identification of human sebum-specific unsaturated fatty acids in fingerprint residues based on the identification of their degradation products. These results are discussed for further investigations and method developments for age determination of fingerprints, which is still a tremendous challenge because of several factors affecting the aging behavior of individual compounds in fingerprints. Graphical Abstract ᅟ. PMID:27324649

  10. Fatty Acid Structure and Degradation Analysis in Fingerprint Residues

    NASA Astrophysics Data System (ADS)

    Pleik, Stefanie; Spengler, Bernhard; Schäfer, Thomas; Urbach, Dieter; Luhn, Steven; Kirsch, Dieter

    2016-09-01

    GC-MS investigations were carried out to elucidate the aging behavior of unsaturated fatty acids in fingerprint residues and to identify their degradation products in aged samples. For this purpose, a new sample preparation technique for fingerprint residues was developed that allows producing N-methyl- N-trimethylsilyl-trifluoroacetamide (MSTFA) derivatives of the analyzed unsaturated fatty acids and their degradation products. MSTFA derivatization catalyzed by iodotrimethylsilane enables the reliable identification of aldehydes and oxoacids as characteristic MSTFA derivatives in GCMS. The obtained results elucidate the degradation pathway of unsaturated fatty acids. Our study of aged fingerprint residues reveals that decanal is the main degradation product of the observed unsaturated fatty acids. Furthermore, oxoacids with different chain lengths are detected as specific degradation products of the unsaturated fatty acids. The detection of the degradation products and their chain length is a simple and effective method to determine the double bond position in unsaturated compounds. We can show that the hexadecenoic and octadecenoic acids found in fingerprint residues are not the pervasive fatty acids Δ9-hexadecenoic (palmitoleic acid) and Δ9-octadecenoic (oleic acid) acid but Δ6-hexadecenoic acid (sapienic acid) and Δ8-octadecenoic acid. The present study focuses on the structure identification of human sebum-specific unsaturated fatty acids in fingerprint residues based on the identification of their degradation products. These results are discussed for further investigations and method developments for age determination of fingerprints, which is still a tremendous challenge because of several factors affecting the aging behavior of individual compounds in fingerprints.

  11. Tracing carbon flow in an arctic marine food web using fatty acid-stable isotope analysis.

    PubMed

    Budge, S M; Wooller, M J; Springer, A M; Iverson, S J; McRoy, C P; Divoky, G J

    2008-08-01

    Global warming and the loss of sea ice threaten to alter patterns of productivity in arctic marine ecosystems because of a likely decline in primary productivity by sea ice algae. Estimates of the contribution of ice algae to total primary production range widely, from just 3 to >50%, and the importance of ice algae to higher trophic levels remains unknown. To help answer this question, we investigated a novel approach to food web studies by combining the two established methods of stable isotope analysis and fatty acid (FA) analysis--we determined the C isotopic composition of individual diatom FA and traced these biomarkers in consumers. Samples were collected near Barrow, Alaska and included ice algae, pelagic phytoplankton, zooplankton, fish, seabirds, pinnipeds and cetaceans. Ice algae and pelagic phytoplankton had distinctive overall FA signatures and clear differences in delta(13)C for two specific diatom FA biomarkers: 16:4n-1 (-24.0+/-2.4 and -30.7+/-0.8 per thousand, respectively) and 20:5n-3 (-18.3+/-2.0 and -26.9+/-0.7 per thousand, respectively). Nearly all delta(13)C values of these two FA in consumers fell between the two stable isotopic end members. A mass balance equation indicated that FA material derived from ice algae, compared to pelagic diatoms, averaged 71% (44-107%) in consumers based on delta(13)C values of 16:4n-1, but only 24% (0-61%) based on 20:5n-3. Our estimates derived from 16:4n-1, which is produced only by diatoms, probably best represented the contribution of ice algae relative to pelagic diatoms. However, many types of algae produce 20:5n-3, so the lower value derived from it likely represented a more realistic estimate of the proportion of ice algae material relative to all other types of phytoplankton. These preliminary results demonstrate the potential value of compound-specific isotope analysis of marine lipids to trace C flow through marine food webs and provide a foundation for future work. PMID:18481094

  12. Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand

    PubMed Central

    Coker, Olabisi Oluwabukola; Ngamphiw, Chumpol; Tongsima, Sissades; Regmi, Sanjib Mani; Clark, Taane G.; Ong, Rick Twee Hee; Teo, Yik-Ying; Prammananan, Therdsak; Palittapongarnpim, Prasit

    2016-01-01

    Genome sequencing plays a key role in understanding the genetic diversity of Mycobacterium tuberculosis (M.tb). The genotype-specific character of M. tb contributes to tuberculosis severity and emergence of drug resistance. Strains of M. tb complex can be classified into seven lineages. The Nonthaburi (NB) genotype, belonging to the Indo-Oceanic lineage (lineage 1), has a unique spoligotype and IS6110-RFLP pattern but has not previously undergone a detailed whole genome analysis. In addition, there is not much information available on the whole genome analysis of M. tb isolates from tuberculous meningitis (TBM) patients in public databases. Isolates CSF3053, 46-5069 and 43-13838 of NB genotype were obtained from the cerebrospinal fluids of TBM Thai patients in Siriraj Hospital, Bangkok. The whole genomes were subjected to high throughput sequencing. The sequence data of each isolate were assembled into draft genome. The sequences were also aligned to reference genome, to determine genomic variations. Single nucleotide polymorphisms (SNPs) were obtained and grouped according to the functions of the genes containing them. They were compared with SNPs from 1,601 genomes, representing the seven lineages of M. tb complex, to determine the uniqueness of NB genotype. Susceptibility to first-line, second-line and other antituberculosis drugs were determined and related to the SNPs previously reported in drug-resistant related genes. The assembled genomes have an average size of 4,364,461 bp, 4,154 genes, 48 RNAs and 64 pseudogenes. A 500 base pairs deletion, which includes ppe50, was found in all isolates. RD239, specific for members of Indo Oceanic lineage, and RD147c were identified. A total of 2,202 SNPs were common to the isolates and used to classify the NB strains as members of sublineage 1.2.1. Compared with 1,601 genomes from the seven lineages of M. tb complex, mutation G2342203C was found novel to the isolates in this study. Three mutations (T28910C, C1180580T

  13. Combining random forest and 2D correlation analysis to identify serum spectral signatures for neuro-oncology.

    PubMed

    Smith, Benjamin R; Ashton, Katherine M; Brodbelt, Andrew; Dawson, Timothy; Jenkinson, Michael D; Hunt, Neil T; Palmer, David S; Baker, Matthew J

    2016-06-01

    Fourier transform infrared (FTIR) spectroscopy has long been established as an analytical technique for the measurement of vibrational modes of molecular systems. More recently, FTIR has been used for the analysis of biofluids with the aim of becoming a tool to aid diagnosis. For the clinician, this represents a convenient, fast, non-subjective option for the study of biofluids and the diagnosis of disease states. The patient also benefits from this method, as the procedure for the collection of serum is much less invasive and stressful than traditional biopsy. This is especially true of patients in whom brain cancer is suspected. A brain biopsy is very unpleasant for the patient, potentially dangerous and can occasionally be inconclusive. We therefore present a method for the diagnosis of brain cancer from serum samples using FTIR and machine learning techniques. The scope of the study involved 433 patients from whom were collected 9 spectra each in the range 600-4000 cm(-1). To begin the development of the novel method, various pre-processing steps were investigated and ranked in terms of final accuracy of the diagnosis. Random forest machine learning was utilised as a classifier to separate patients into cancer or non-cancer categories based upon the intensities of wavenumbers present in their spectra. Generalised 2D correlational analysis was then employed to further augment the machine learning, and also to establish spectral features important for the distinction between cancer and non-cancer serum samples. Using these methods, sensitivities of up to 92.8% and specificities of up to 91.5% were possible. Furthermore, ratiometrics were also investigated in order to establish any correlations present in the dataset. We show a rapid, computationally light, accurate, statistically robust methodology for the identification of spectral features present in differing disease states. With current advances in IR technology, such as the development of rapid discrete

  14. RNA-sequencing analysis of high glucose-treated monocytes reveals novel transcriptome signatures and associated epigenetic profiles

    PubMed Central

    Miao, Feng; Chen, Zhuo; Zhang, Lingxiao; Wang, Jinhui; Gao, Harry; Wu, Xiwei

    2013-01-01

    We performed high throughput transcriptomic profiling with RNA sequencing (RNA-Seq) to uncover network responses in human THP-1 monocytes treated with high glucose (HG). Our data analyses revealed that interferon (IFN) signaling, pattern recognition receptors, and activated interferon regulatory factors (IRFs) were enriched among the HG-upregulated genes. Motif analysis identified an HG-responsive IRF-mediated network in which interferon-stimulated genes (ISGs) were enriched. Notably, this network showed strong overlap with a recently discovered IRF7-driven network relevant to Type 1 diabetes. We next examined if the HG-regulated genes possessed any characteristic chromatin features in the basal state by profiling 15 active and repressive chromatin marks under normal glucose conditions using chromatin immunoprecipitation linked to promoter microarrays. Composite profiles revealed higher histone H3 lysine-9-acetylation levels around the promoters of HG-upregulated genes compared with all RefSeq promoters. Interestingly, within the HG-upregulated genes, active chromatin marks were enriched not only at high CpG content promoters, but surprisingly also at low CpG content promoters. Similar results were obtained with peripheral blood monocytes exposed to HG. These new results reveal a novel mechanism by which HG can exercise IFN-α-like effects in monocytes by upregulating a set of ISGs poised for activation with multiple chromatin marks. PMID:23386205

  15. Practical quantum digital signature

    NASA Astrophysics Data System (ADS)

    Yin, Hua-Lei; Fu, Yao; Chen, Zeng-Bing

    2016-03-01

    Guaranteeing nonrepudiation, unforgeability as well as transferability of a signature is one of the most vital safeguards in today's e-commerce era. Based on fundamental laws of quantum physics, quantum digital signature (QDS) aims to provide information-theoretic security for this cryptographic task. However, up to date, the previously proposed QDS protocols are impractical due to various challenging problems and most importantly, the requirement of authenticated (secure) quantum channels between participants. Here, we present the first quantum digital signature protocol that removes the assumption of authenticated quantum channels while remaining secure against the collective attacks. Besides, our QDS protocol can be practically implemented over more than 100 km under current mature technology as used in quantum key distribution.

  16. Uncertainty in hydrological signatures

    NASA Astrophysics Data System (ADS)

    McMillan, Hilary; Westerberg, Ida

    2015-04-01

    Information that summarises the hydrological behaviour or flow regime of a catchment is essential for comparing responses of different catchments to understand catchment organisation and similarity, and for many other modelling and water-management applications. Such information types derived as an index value from observed data are known as hydrological signatures, and can include descriptors of high flows (e.g. mean annual flood), low flows (e.g. mean annual low flow, recession shape), the flow variability, flow duration curve, and runoff ratio. Because the hydrological signatures are calculated from observed data such as rainfall and flow records, they are affected by uncertainty in those data. Subjective choices in the method used to calculate the signatures create a further source of uncertainty. Uncertainties in the signatures may affect our ability to compare different locations, to detect changes, or to compare future water resource management scenarios. The aim of this study was to contribute to the hydrological community's awareness and knowledge of data uncertainty in hydrological signatures, including typical sources, magnitude and methods for its assessment. We proposed a generally applicable method to calculate these uncertainties based on Monte Carlo sampling and demonstrated it for a variety of commonly used signatures. The study was made for two data rich catchments, the 50 km2 Mahurangi catchment in New Zealand and the 135 km2 Brue catchment in the UK. For rainfall data the uncertainty sources included point measurement uncertainty, the number of gauges used in calculation of the catchment spatial average, and uncertainties relating to lack of quality control. For flow data the uncertainty sources included uncertainties in stage/discharge measurement and in the approximation of the true stage-discharge relation by a rating curve. The resulting uncertainties were compared across the different signatures and catchments, to quantify uncertainty

  17. Genetic signatures of heroin addiction

    PubMed Central

    Chen, Shaw-Ji; Liao, Ding-Lieh; Shen, Tsu-Wang; Yang, Hsin-Chou; Chen, Kuang-Chi; Chen, Chia-Hsiang

    2016-01-01

    Abstract Heroin addiction is a complex psychiatric disorder with a chronic course and a high relapse rate, which results from the interaction between genetic and environmental factors. Heroin addiction has a substantial heritability in its etiology; hence, identification of individuals with a high genetic propensity to heroin addiction may help prevent the occurrence and relapse of heroin addiction and its complications. The study aimed to identify a small set of genetic signatures that may reliably predict the individuals with a high genetic propensity to heroin addiction. We first measured the transcript level of 13 genes (RASA1, PRKCB, PDK1, JUN, CEBPG, CD74, CEBPB, AUTS2, ENO2, IMPDH2, HAT1, MBD1, and RGS3) in lymphoblastoid cell lines in a sample of 124 male heroin addicts and 124 male control subjects using real-time quantitative PCR. Seven genes (PRKCB, PDK1, JUN, CEBPG, CEBPB, ENO2, and HAT1) showed significant differential expression between the 2 groups. Further analysis using 3 statistical methods including logistic regression analysis, support vector machine learning analysis, and a computer software BIASLESS revealed that a set of 4 genes (JUN, CEBPB, PRKCB, ENO2, or CEBPG) could predict the diagnosis of heroin addiction with the accuracy rate around 85% in our dataset. Our findings support the idea that it is possible to identify genetic signatures of heroin addiction using a small set of expressed genes. However, the study can only be considered as a proof-of-concept study. As the establishment of lymphoblastoid cell line is a laborious and lengthy process, it would be more practical in clinical settings to identify genetic signatures for heroin addiction directly from peripheral blood cells in the future study. PMID:27495086

  18. Genetic signatures of heroin addiction.

    PubMed

    Chen, Shaw-Ji; Liao, Ding-Lieh; Shen, Tsu-Wang; Yang, Hsin-Chou; Chen, Kuang-Chi; Chen, Chia-Hsiang

    2016-08-01

    Heroin addiction is a complex psychiatric disorder with a chronic course and a high relapse rate, which results from the interaction between genetic and environmental factors. Heroin addiction has a substantial heritability in its etiology; hence, identification of individuals with a high genetic propensity to heroin addiction may help prevent the occurrence and relapse of heroin addiction and its complications. The study aimed to identify a small set of genetic signatures that may reliably predict the individuals with a high genetic propensity to heroin addiction. We first measured the transcript level of 13 genes (RASA1, PRKCB, PDK1, JUN, CEBPG, CD74, CEBPB, AUTS2, ENO2, IMPDH2, HAT1, MBD1, and RGS3) in lymphoblastoid cell lines in a sample of 124 male heroin addicts and 124 male control subjects using real-time quantitative PCR. Seven genes (PRKCB, PDK1, JUN, CEBPG, CEBPB, ENO2, and HAT1) showed significant differential expression between the 2 groups. Further analysis using 3 statistical methods including logistic regression analysis, support vector machine learning analysis, and a computer software BIASLESS revealed that a set of 4 genes (JUN, CEBPB, PRKCB, ENO2, or CEBPG) could predict the diagnosis of heroin addiction with the accuracy rate around 85% in our dataset. Our findings support the idea that it is possible to identify genetic signatures of heroin addiction using a small set of expressed genes. However, the study can only be considered as a proof-of-concept study. As the establishment of lymphoblastoid cell line is a laborious and lengthy process, it would be more practical in clinical settings to identify genetic signatures for heroin addiction directly from peripheral blood cells in the future study. PMID:27495086

  19. Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis1[OPEN

    PubMed Central

    Lim, Sun-Hyung; Kim, Jae Kwang; Ha, Sun-Hwa

    2015-01-01

    Light quality is an important signaling component upon which plants orchestrate various morphological processes, including seed germination and seedling photomorphogenesis. However, it is still unclear how plants, especially food crops, sense various light qualities and modulate their cellular growth and other developmental processes. Therefore, in this work, we initially profiled the transcripts of a model crop, rice (Oryza sativa), under four different light treatments (blue, green, red, and white) as well as in the dark. Concurrently, we reconstructed a fully compartmentalized genome-scale metabolic model of rice cells, iOS2164, containing 2,164 unique genes, 2,283 reactions, and 1,999 metabolites. We then combined the model with transcriptome profiles to elucidate the light-specific transcriptional signatures of rice metabolism. Clearly, light signals mediated rice gene expressions, differentially regulating numerous metabolic pathways: photosynthesis and secondary metabolism were up-regulated in blue light, whereas reserve carbohydrates degradation was pronounced in the dark. The topological analysis of gene expression data with the rice genome-scale metabolic model further uncovered that phytohormones, such as abscisate, ethylene, gibberellin, and jasmonate, are the key biomarkers of light-mediated regulation, and subsequent analysis of the associated genes’ promoter regions identified several light-specific transcription factors. Finally, the transcriptional control of rice metabolism by red and blue light signals was assessed by integrating the transcriptome and metabolome data with constraint-based modeling. The biological insights gained from this integrative systems biology approach offer several potential applications, such as improving the agronomic traits of food crops and designing light-specific synthetic gene circuits in microbial and mammalian systems. PMID:26453433

  20. Macular edema in underserved diabetic patients: Improving detection by enhancing the optical signature and data analysis techniques

    NASA Astrophysics Data System (ADS)

    Alhamami, Mastour Abdullah

    Diabetic retinopathy and diabetic macular edema are chief causes of vision loss in working adults. Thus, retinal screening of patients with diabetes has become standard practice in some countries to prevent visual impairment and blindness from diabetic retinopathy. One goal is to improve techniques currently used to diagnose diabetic retinopathy. Another goal is to probe pathophysiological changes seen with imaging methods. Analysis was performed on a novel dataset from more than 2000 underserved adult diabetic patients, who were recruited for a screening study for diabetic eye disease. Data were collected from four county clinics at Alameda Health, Alameda County, CA. Over 90% of patients self-identified as a racial/ethnic identity other than non-Hispanic white. We investigated the prevalence and optical properties of macular edema. In the first study, a retrospective cohort study was performed to compare macular thickness in diabetic patients with and without macular edema to determine the presence of damage to the external limiting membrane or and the relation of damage to the ELM to damage to photoreceptors. In the second study, we investigated whether the information in red light better visualizes cysts in diabetic macular edema, as compared to green light. In the third study, we investigated whether the demographic and blood glucose information predict diabetic macular edema. Three logistic regression analyses were compared. In the fourth study, we examined how different outcome measures of retinal thickness vary with demographic and blood glucose measures, using a trichotomous variable for retinal thickness. The findings point strongly to large individual differences in the development of macular edema, which is difficult to diagnose with the most common methods in dark eyes. Further, while blood glucose was found to be important, there are additional differences in the potential for macular edema that are associated with ethnic group and gender.

  1. Transcriptome Analysis of Ullrich Congenital Muscular Dystrophy Fibroblasts Reveals a Disease Extracellular Matrix Signature and Key Molecular Regulators

    PubMed Central

    Rodríguez, Maria Angels; Jou, Cristina; Puigdelloses, Montserrat; Ortez, Carlos I.; Diaz-Manera, Jordi; Gallardo, Eduardo; Colomer, Jaume; Nascimento, Andrés; Kalko, Susana G.; Jimenez-Mallebrera, Cecilia

    2015-01-01

    Background Collagen VI related myopathies encompass a range of phenotypes with involvement of skeletal muscle, skin and other connective tissues. They represent a severe and relatively common form of congenital disease for which there is no treatment. Collagen VI in skeletal muscle and skin is produced by fibroblasts. Aims & Methods In order to gain insight into the consequences of collagen VI mutations and identify key disease pathways we performed global gene expression analysis of dermal fibroblasts from patients with Ullrich Congenital Muscular Dystrophy with and without vitamin C treatment. The expression data were integrated using a range of systems biology tools. Results were validated by real-time PCR, western blotting and functional assays. Findings We found significant changes in the expression levels of almost 600 genes between collagen VI deficient and control fibroblasts. Highly regulated genes included extracellular matrix components and surface receptors, including integrins, indicating a shift in the interaction between the cell and its environment. This was accompanied by a significant increase in fibroblasts adhesion to laminin. The observed changes in gene expression profiling may be under the control of two miRNAs, miR-30c and miR-181a, which we found elevated in tissue and serum from patients and which could represent novel biomarkers for muscular dystrophy. Finally, the response to vitamin C of collagen VI mutated fibroblasts significantly differed from healthy fibroblasts. Vitamin C treatment was able to revert the expression of some key genes to levels found in control cells raising the possibility of a beneficial effect of vitamin C as a modulator of some of the pathological aspects of collagen VI related diseases. PMID:26670220

  2. Comprehensive DNA Methylation Analysis Reveals a Common Ten-Gene Methylation Signature in Colorectal Adenomas and Carcinomas

    PubMed Central

    Patai, Árpád V.; Valcz, Gábor; Hollósi, Péter; Kalmár, Alexandra; Péterfia, Bálint; Patai, Árpád; Wichmann, Barnabás; Spisák, Sándor; Barták, Barbara Kinga; Leiszter, Katalin; Tóth, Kinga; Sipos, Ferenc; Kovalszky, Ilona; Péter, Zoltán; Miheller, Pál; Tulassay, Zsolt; Molnár, Béla

    2015-01-01

    Microarray analysis of promoter hypermethylation provides insight into the role and extent of DNA methylation in the development of colorectal cancer (CRC) and may be co-monitored with the appearance of driver mutations. Colonic biopsy samples were obtained endoscopically from 10 normal, 23 adenoma (17 low-grade (LGD) and 6 high-grade dysplasia (HGD)), and 8 ulcerative colitis (UC) patients (4 active and 4 inactive). CRC samples were obtained from 24 patients (17 primary, 7 metastatic (MCRC)), 7 of them with synchronous LGD. Field effects were analyzed in tissues 1 cm (n = 5) and 10 cm (n = 5) from the margin of CRC. Tissue materials were studied for DNA methylation status using a 96 gene panel and for KRAS and BRAF mutations. Expression levels were assayed using whole genomic mRNA arrays. SFRP1 was further examined by immunohistochemistry. HT29 cells were treated with 5-aza-2’ deoxycytidine to analyze the reversal possibility of DNA methylation. More than 85% of tumor samples showed hypermethylation in 10 genes (SFRP1, SST, BNC1, MAL, SLIT2, SFRP2, SLIT3, ALDH1A3, TMEFF2, WIF1), whereas the frequency of examined mutations were below 25%. These genes distinguished precancerous and cancerous lesions from inflamed and healthy tissue. The mRNA alterations that might be caused by systematic methylation could be partly reversed by demethylation treatment. Systematic changes in methylation patterns were observed early in CRC carcinogenesis, occuring in precursor lesions and CRC. Thus we conclude that DNA hypermethylation is an early and systematic event in colorectal carcinogenesis, and it could be potentially reversed by systematic demethylation therapy, but it would need more in vitro and in vivo experiments to support this theory. PMID:26291085

  3. Transcriptome Analysis Reveals a Signature Profile for Tick-Borne Flavivirus Persistence in HEK 293T Cells

    PubMed Central

    Lam, Jennifer; Offerdahl, Danielle K.; Martens, Craig; Sturdevant, Daniel; Turner, Charles V.; Porcella, Stephen F.; Bloom, Marshall E.

    2016-01-01

    ABSTRACT Tick-borne flaviviruses (TBFVs) cause febrile illnesses, which may progress to severe encephalitis and/or death in humans globally. Most people who recover from severe acute disease suffer from debilitating neurological sequelae, which may be due to viral persistence, infection-induced neurological cell damage, host response, or some combination of these. Acute TBFV infection of human embryonic kidney (HEK) 293T cells in vitro results in the death of >95% of infected cells by day 5. However, replacing cell growth medium allows surviving cells to repopulate and become persistently infected for extended periods of time. The mechanisms responsible for initiation and maintenance of viral persistence remain vague. We subjected the HEK 293T cell transcriptome to deep sequencing to identify genes differentially expressed during acute infection and persistent infection. A total of 451 genes showed unique significant differential expression levels in persistently infected cells relative to the acute phase of infection. Ingenuity Pathway Analysis results suggested that the expression of prosurvival oncogenes AKT2 and ERBB2 was upregulated in persistently infected cells, whereas proapoptotic genes, such as Bad and the beta interferon 1 (IFN-β1) gene, were downregulated. Genes encoding antiviral cytokines such as the CCL5, tumor necrosis factor alpha (TNF-α), and CXCL10 genes were upregulated during the acute phase, but the same genes were relatively quiescent in persistently infected cells. Exogenous induction of apoptosis demonstrated that persistently infected cells were resistant to apoptosis in a dose-dependent manner. In summary, the differential transcriptome profiles of acute-phase compared to persistently infected HEK 293T cells demonstrated an evasion of apoptosis, which may be critical for a chronic TBFV infection state. These results provide a basis for further study of the mechanisms of TBFV persistence. PMID:27222466

  4. Current signature sensor

    NASA Technical Reports Server (NTRS)

    Perotti, Jose M. (Inventor); Lucena, Angel (Inventor); Ihlefeld, Curtis (Inventor); Burns, Bradley (Inventor); Bassignani, Karin E. (Inventor)

    2005-01-01

    A solenoid health monitoring system uses a signal conditioner and controller assembly in one embodiment that includes analog circuitry and a DSP controller. The analog circuitry provides signal conditioning to the low-level raw signal coming from a signal acquisition assembly. Software running in a DSP analyzes the incoming data (recorded current signature) and determines the state of the solenoid whether it is energized, de-energized, or in a transitioning state. In one embodiment, the software identifies key features in the current signature during the transition phase and is able to determine the health of the solenoid.

  5. Current Signature Sensor

    NASA Technical Reports Server (NTRS)

    Perotti, Jose M. (Inventor); Lucena, Angel (Inventor); Ihlefeld, Curtis (Inventor); Burns, Bradley (Inventor); Bassignani, Mario (Inventor); Bassignani, Karin E. (Inventor)

    2005-01-01

    A solenoid health monitoring system uses a signal conditioner and controller assembly in one embodiment that includes analog circuitry and a DSP controller. The analog circuitry provides signal conditioning to the low-level raw signal coming from a signal acquisition assembly. Software running in a DSP analyzes the incoming data (recorded current signature) and determines the state of the solenoid whether it is energized, de-energized, or in a transitioning state. In one embodiment, the software identifies key features in the current signature during the transition phase and is able to determine the health of the solenoid.

  6. Quantitative Analysis and In vitro Anti-inflammatory Effects of Gallic Acid, Ellagic Acid, and Quercetin from Radix Sanguisorbae

    PubMed Central

    Seo, Chang-Seob; Jeong, Soo-Jin; Yoo, Sae-Rom; Lee, Na-Ri; Shin, Hyeun-Kyoo

    2016-01-01

    Background: Radix Sanguisorbae has long been used to treat diarrhea, enteritis, duodenal ulcers, and internal hemorrhage. Objective: We investigated the in vitro anti-inflammatory effects of Radix Sanguisorbae and performed quantitative analyses of three marker components, namely gallic acid, ellagic acid, and quercetin, using high-performance liquid chromatography coupled with a photodiode array detector. Materials and Methods: The three marker components were separated using a reversed-phase Gemini C18 analytical column maintained at 40°C by the gradient elution with two solvent systems. We examined the biological effects of the three marker compounds, gallic acid, ellagic acid, and quercetin, by determining their anti-inflammatory activities in the murine macrophage cell line RAW 264.7. Results: All of the marker compounds exhibited inhibitory effects on prostaglandin E2 production in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages, with no cytotoxicity. Particularly, ellagic acid significantly inhibited production of the proinflammatory cytokines tumor necrosis factor alpha and interleukin-6 in LPS-treated RAW 264.7 cells. Conclusion: Our results suggest that ellagic acid is the most potent bioactive phytochemical component of radix Sanguisorbae in the treatment of inflammatory diseases. SUMMARY Established high-performance liquid chromatography method was applied in the quantitative analysis of gallic acid, ellagic acid, and quercetin present in an extract from radix SanguisorbaeAmong the three compounds, the ellagic acid.(7.65.mg/g) is main component in radix SanguisorbaeEllagic acid significantly inhibited production of the proinflammatory cytokines tumor necrosis factor alpha and interleukin-6 in lipopolysaccharide-treated RAW 264.7 cells. Abbreviations used: HPLC: High-performance liquid chromatography, PDA: Photodiode array, TNF-α: Tumor necrosis factor alpha, IL: Interleukin, LPS: Lipopolysaccharide, PGE2: Prostaglandin E2, NSAIDs

  7. Analysis of seasonal variation of stratospheric nitric acid

    NASA Astrophysics Data System (ADS)

    Gruzdev, A. N.

    1998-11-01

    Data from the draft COSPAR reference model for stratospheric nitric acid (HNO3) are analysed. Eight months of LIMS HNO3 measurements allow the analysis of dynamics of regimes associated with the annual HNO3 maximum followed by the HNO3 decrease in the Northern Hemisphere and the annual HNO3 minimum followed by the HNO3 increase in the Southern Hemisphere. The HNO3 minimum is noted earlier (in November) in the Southern Hemisphere subtropical upper stratosphere, from where the regime of minimum HNO3 values propagates to the southern high-latitude middle stratosphere, and then (in Austral summer) the equatorward propagation of the regime is observed, with a persistent downward component. The regime of the HNO3 annual maximum in the Northern Hemisphere propagates from the Arctic lower stratosphere (in autumn) and from the tropical middle stratosphere (in late summer), so that in the mid-latitude middle stratosphere the downward propagation of the regime is observed. Evolution of areas with HNO3 increase and decrease by 1 ppbv against the January HNO3 distribution quantifies intensity of the HNO3 decrease in winter-spring in the Northern Hemisphere and the HNO3 increase in Austral summer-autumn in the Southern Hemisphere.

  8. Blood metabolomics analysis identifies abnormalities in the citric acid cycle, urea cycle, and amino acid metabolism in bipolar disorder

    PubMed Central

    Yoshimi, Noriko; Futamura, Takashi; Kakumoto, Keiji; Salehi, Alireza M.; Sellgren, Carl M.; Holmén-Larsson, Jessica; Jakobsson, Joel; Pålsson, Erik; Landén, Mikael; Hashimoto, Kenji

    2016-01-01

    Background Bipolar disorder (BD) is a severe and debilitating psychiatric disorder. However, the precise biological basis remains unknown, hampering the search for novel biomarkers. We performed a metabolomics analysis to discover novel peripheral biomarkers for BD. Methods We quantified serum levels of 116 metabolites in mood-stabilized male BD patients (n = 54) and age-matched male healthy controls (n = 39). Results After multivariate logistic regression, serum levels of pyruvate, N-acetylglutamic acid, α-ketoglutarate, and arginine were significantly higher in BD patients than in healthy controls. Conversely, serum levels of β-alanine, and serine were significantly lower in BD patients than in healthy controls. Chronic (4-weeks) administration of lithium or valproic acid to adult male rats did not alter serum levels of pyruvate, N-acetylglutamic acid, β-alanine, serine, or arginine, but lithium administration significantly increased serum levels of α-ketoglutarate. Conclusions The metabolomics analysis demonstrated altered serum levels of pyruvate, N-acetylglutamic acid, β-alanine, serine, and arginine in BD patients. General significance The present findings suggest that abnormalities in the citric acid cycle, urea cycle, and amino acid metabolism play a role in the pathogenesis of BD. PMID:27114925

  9. Analysis of amino acids network based on distance matrix

    NASA Astrophysics Data System (ADS)

    Ali, Tazid; Akhtar, Adil; Gohain, Nisha

    2016-06-01

    In this paper we have constructed a distance matrix of the amino acids. The distance is defined based on the relative evolutionary importance of the base position of the corresponding codons. From this distance matrix a network of the amino acids is obtained. We have argued that this network depicts the evolutionary pattern of the amino acids. To examine the relative importance of the amino acids with respect to this network we have discussed different measures of centrality. We have also investigated the correlation coefficients between different measures of centrality. Further we have explored clustering coefficient as well as degree of distribution.

  10. Analysis of amino acid and codon usage in Paramecium bursaria.

    PubMed

    Dohra, Hideo; Fujishima, Masahiro; Suzuki, Haruo

    2015-10-01

    The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis. PMID:26341535

  11. Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry

    PubMed Central

    Beattie, Kirsten E.; De Ferrari, Luna; Mitchell, John B. O.

    2015-01-01

    First, we identify InterPro sequence signatures representing evolutionary relatedness and, second, signatures identifying specific chemical machinery. Thus, we predict the chemical mechanisms of enzyme-catalyzed reactions from catalytic and non-catalytic subsets of InterPro signatures. We first scanned our 249 sequences using InterProScan and then used the MACiE database to identify those amino acid residues that are important for catalysis. The sequences were mutated in silico to replace these catalytic residues with glycine and then again scanned using InterProScan. Those signature matches from the original scan that disappeared on mutation were called catalytic. Mechanism was predicted using all signatures, only the 78 “catalytic” signatures, or only the 519 “non-catalytic” signatures. The non-catalytic signatures gave indistinguishable results from those for the whole feature set, with precision of 0.991 and sensitivity of 0.970. The catalytic signatures alone gave less impressive predictivity, with precision and sensitivity of 0.791 and 0.735, respectively. These results show that our successful prediction of enzyme mechanism is mostly by homology rather than by identifying catalytic machinery. PMID:26740739

  12. Clinical value of integrated-signature miRNAs in colorectal cancer: miRNA expression profiling analysis and experimental validation

    PubMed Central

    Wang, YuQun; Song, Mei; Zhou, Wu; Tu, HongXiang; Lin, Zhuo

    2015-01-01

    MicroRNA (miRNA) expression profiling of colorectal cancer (CRC) are often inconsistent among different studies. To determine candidate miRNA biomarkers for CRC, we performed an integrative analysis of miRNA expression profiling compared CRC tissues and paired neighboring noncancerous colorectal tissues. Using robust rank aggregation method, we identified a miRNA set of 10 integrated-signature miRNAs. In addition, the qRT-PCR validation demonstrated that 9 miRNAs were consistent dysregulated with the integrative analysis in CRC tissues, 4 miRNAs (miR-21-5p, miR-183-5p, miR-17-5p and miR-20a-5p) were up-regulated expression, and 5 miRNAs (miR-145-5p, miR-195-5p, miR-139-5p, miR-378a-5p and miR-143-3p) were down-regulated expression (all p < 0.05). Consistent with the initial analysis, 7 miRNAs were found to be significantly dysregulated in CRC tissues in TCGA data base, 4 miRNAs (miR-21-5p, miR-183-5p, miR-17-5p and miR-20a-5p) were significantly up-regulated expression, and 3 miRNAs (miR-145-5p, miR-139-5p and miR-378a-5p) were significantly down-regulated expression in CRC tissues (all p < 0.001). Furthermore, miR-17-5p (p = 0.011) and miR-20a-5p (p = 0.003) were up-regulated expression in the III/IV tumor stage, miR-145-5p (p = 0.028) and miR-195-5p (p = 0.001) were significantly increased expression with microscopic vascular invasion in CRC tissues, miR-17-5p (p = 0.037) and miR-145-5p (p = 0.023) were significantly increased expression with lymphovascular invasion. Moreover, Cox regression analysis of CRC patients in TCGA data base showed miR-20a-5p was correlated with survival (hazard ratio: 1.875, 95%CI: 1.088–3.232, p = 0.024). Hence, the finding of current study provides a basic implication of these miRNAs for further clinical application in CRC. PMID:26462034

  13. EFFECTS OF NITRIC ACID ON CRITICALITY SAFETY ANALYSIS

    SciTech Connect

    Williamson, B.

    2011-08-18

    As nitric acid molarity is increased, there are two competing phenomena affecting the reactivity of the system. First, there is interaction between each of the 10 wells in the basket-like insert. As the molarity of the nitric acid solution is increased (it moves from 100% water to 100% HNO{sub 3}), the hydrogen atom density decreases by about 80%. However, it remains a relatively efficient moderator. The moderating ratio of nitric acid is about 90% that of water. As the media between the wells is changed from 100% water to 100% nitric acid, the density of the media increases by 50%. A higher density typically leads to a better reflector. However, when the macroscopic scattering cross sections are considered, nitric acid is a much worse reflector than water. The effectiveness of nitric acid as a reflector is about 40% that of water. Since the media between the wells become a worse reflector and still remains an effective moderator, interaction between the wells increases. This phenomenon will cause reactivity to increase as nitric acid molarity increases. The seond phenomenon is due to the moderating ratio changing in the high concentration fissile-nitric acid solution in the 10 wells. Since the wells contain relatively small volumes of high concentration solutions, a small decrease in moderating power has a large effect on reactivity. This is due to the fact that neutrons are more likely to escape the high concentration fissile solution before causing another fission event. The result of this phenomenon is that as nitric acid molarity increases, reactivity decreases. Recent studies have shown that the second phenomenon is indeed the dominating force in determining reactivity changes in relation to nitric acid molarity changes. When considering the system as a whole, as nitric acid molarity increases, reactivity decreases.

  14. Diet of yellow-billed loons (Gavia adamsii) in Arctic lakes during the nesting season inferred from fatty acid analysis

    USGS Publications Warehouse

    Haynes, T B; Schmutz, Joel A.; Bromaghin, Jeffrey; Iverson, S J; Padula, V M; Rosenberger, A E

    2015-01-01

    Understanding the dietary habits of yellow-billed loons (Gavia adamsii) can give important insights into their ecology, however, studying the diet of loons is difficult when direct observation or specimen collection is impractical. We investigate the diet of yellow-billed loons nesting on the Arctic Coastal Plain of Alaska using quantitative fatty acid signature analysis. Tissue analysis from 26 yellow-billed loons and eleven prey groups (nine fish species and two invertebrate groups) from Arctic lakes suggests that yellow-billed loons are eating high proportions of Alaska blackfish (Dallia pectoralis), broad whitefish (Coregonus nasus) and three-spined stickleback (Gasterosteus aculeatus) during late spring and early summer. The prominence of blackfish in diets highlights the widespread availability of blackfish during the early stages of loon nesting, soon after spring thaw. The high proportions of broad whitefish and three-spined stickleback may reflect a residual signal from the coastal staging period prior to establishing nesting territories on lakes, when loons are more likely to encounter these species. Our analyses were sensitive to the choice of calibration coefficient based on data from three different species, indicating the need for development of loon-specific coefficients for future study and confirmation of our results. Regardless, fish that are coastally distributed and that successfully overwinter in lakes are likely key food items for yellow-billed loons early in the nesting season.

  15. In-situ Condition Monitoring of Components in Small Modular Reactors Using Process and Electrical Signature Analysis. Final report, volume 1. Development of experimental flow control loop, data analysis and plant monitoring

    SciTech Connect

    Upadhyaya, Belle; Hines, J. Wesley; Damiano, Brian; Mehta, Chaitanya; Collins, Price; Lish, Matthew; Cady, Brian; Lollar, Victor; de Wet, Dane; Bayram, Duygu

    2015-12-15

    The research and development under this project was focused on the following three major objectives: Objective 1: Identification of critical in-vessel SMR components for remote monitoring and development of their low-order dynamic models, along with a simulation model of an integral pressurized water reactor (iPWR). Objective 2: Development of an experimental flow control loop with motor-driven valves and pumps, incorporating data acquisition and on-line monitoring interface. Objective 3: Development of stationary and transient signal processing methods for electrical signatures, machinery vibration, and for characterizing process variables for equipment monitoring. This objective includes the development of a data analysis toolbox. The following is a summary of the technical accomplishments under this project: - A detailed literature review of various SMR types and electrical signature analysis of motor-driven systems was completed. A bibliography of literature is provided at the end of this report. Assistance was provided by ORNL in identifying some key references. - A review of literature on pump