Sample records for accurately predict isotope

  1. Advances in Multicollector ICPMS for precise and accurate isotope ratio measurements of Uranium isotopes

    NASA Astrophysics Data System (ADS)

    Bouman, C.; Lloyd, N. S.; Schwieters, J.

    2011-12-01

    The accurate and precise determination of uranium isotopes is challenging, because of the large dynamic range posed by the U isotope abundances and the limited available sample material. Various mass spectrometric techniques are used for the measurement of U isotopes, where TIMS is the most accepted and accurate one. Multicollector inductively coupled plasma mass spectrometry (MC-ICPMS) can offer higher productivity compared to TIMS, but is traditionally limited by low efficiency of sample utilisation. This contribution will discuss progress in MC-ICPMS for detecting 234U, 235U, 236U and 238U in various uranium reference materials from IRMM and NBL. The Thermo Scientific NEPTUNE Plus with Jet Interface offers a modified dry plasma ICP interface using a large interface pump combined with a special set of sample and skimmer cones giving ultimate sensitivity for all elements across the mass range. For uranium, an ion yield of > 3 % was reported previously [1]. The NEPTUNE Plus also offers Multi Ion Counting using discrete dynode electron multipliers as well as two high abundance-sensitivity filters to discriminate against peak tailing effects on 234U and 236U originating from the major uranium beams. These improvements in sensitivity and dynamic range allow accurate measurements of 234U, 235U and 236U abundances on very small samples and at low concentration. In our approach, minor U isotopes 234U and 236U were detected on ion counters with high abundance sensitivity filters, whereas 235U and 238U were detected on Faraday Cups using a high gain current amplifier (10e12 Ohm) for 235U. Precisions and accuracies for 234U and 236U were down to ~1%. For 235U, subpermil levels were reached.

  2. Precise and accurate isotope ratio measurements by ICP-MS.

    PubMed

    Becker, J S; Dietze, H J

    2000-09-01

    The precise and accurate determination of isotope ratios by inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS (LA-ICP-MS) is important for quite different application fields (e.g. for isotope ratio measurements of stable isotopes in nature, especially for the investigation of isotope variation in nature or age dating, for determining isotope ratios of radiogenic elements in the nuclear industry, quality assurance of fuel material, for reprocessing plants, nuclear material accounting and radioactive waste control, for tracer experiments using stable isotopes or long-lived radionuclides in biological or medical studies). Thermal ionization mass spectrometry (TIMS), which used to be the dominant analytical technique for precise isotope ratio measurements, is being increasingly replaced for isotope ratio measurements by ICP-MS due to its excellent sensitivity, precision and good accuracy. Instrumental progress in ICP-MS was achieved by the introduction of the collision cell interface in order to dissociate many disturbing argon-based molecular ions, thermalize the ions and neutralize the disturbing argon ions of plasma gas (Ar+). The application of the collision cell in ICP-QMS results in a higher ion transmission, improved sensitivity and better precision of isotope ratio measurements compared to quadrupole ICP-MS without the collision cell [e.g., for 235U/238U approximately 1 (10 microg x L(-1) uranium) 0.07% relative standard deviation (RSD) vs. 0.2% RSD in short-term measurements (n = 5)]. A significant instrumental improvement for ICP-MS is the multicollector device (MC-ICP-MS) in order to obtain a better precision of isotope ratio measurements (with a precision of up to 0.002%, RSD). CE- and HPLC-ICP-MS are used for the separation of isobaric interferences of long-lived radionuclides and stable isotopes by determination of spallation nuclide abundances in an irradiated tantalum target.

  3. Accurate and precise determination of isotopic ratios by MC-ICP-MS: a review.

    PubMed

    Yang, Lu

    2009-01-01

    For many decades the accurate and precise determination of isotope ratios has remained a very strong interest to many researchers due to its important applications in earth, environmental, biological, archeological, and medical sciences. Traditionally, thermal ionization mass spectrometry (TIMS) has been the technique of choice for achieving the highest accuracy and precision. However, recent developments in multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) have brought a new dimension to this field. In addition to its simple and robust sample introduction, high sample throughput, and high mass resolution, the flat-topped peaks generated by this technique provide for accurate and precise determination of isotope ratios with precision reaching 0.001%, comparable to that achieved with TIMS. These features, in combination with the ability of the ICP source to ionize nearly all elements in the periodic table, have resulted in an increased use of MC-ICP-MS for such measurements in various sample matrices. To determine accurate and precise isotope ratios with MC-ICP-MS, utmost care must be exercised during sample preparation, optimization of the instrument, and mass bias corrections. Unfortunately, there are inconsistencies and errors evident in many MC-ICP-MS publications, including errors in mass bias correction models. This review examines "state-of-the-art" methodologies presented in the literature for achievement of precise and accurate determinations of isotope ratios by MC-ICP-MS. Some general rules for such accurate and precise measurements are suggested, and calculations of combined uncertainty of the data using a few common mass bias correction models are outlined.

  4. Mental models accurately predict emotion transitions.

    PubMed

    Thornton, Mark A; Tamir, Diana I

    2017-06-06

    Successful social interactions depend on people's ability to predict others' future actions and emotions. People possess many mechanisms for perceiving others' current emotional states, but how might they use this information to predict others' future states? We hypothesized that people might capitalize on an overlooked aspect of affective experience: current emotions predict future emotions. By attending to regularities in emotion transitions, perceivers might develop accurate mental models of others' emotional dynamics. People could then use these mental models of emotion transitions to predict others' future emotions from currently observable emotions. To test this hypothesis, studies 1-3 used data from three extant experience-sampling datasets to establish the actual rates of emotional transitions. We then collected three parallel datasets in which participants rated the transition likelihoods between the same set of emotions. Participants' ratings of emotion transitions predicted others' experienced transitional likelihoods with high accuracy. Study 4 demonstrated that four conceptual dimensions of mental state representation-valence, social impact, rationality, and human mind-inform participants' mental models. Study 5 used 2 million emotion reports on the Experience Project to replicate both of these findings: again people reported accurate models of emotion transitions, and these models were informed by the same four conceptual dimensions. Importantly, neither these conceptual dimensions nor holistic similarity could fully explain participants' accuracy, suggesting that their mental models contain accurate information about emotion dynamics above and beyond what might be predicted by static emotion knowledge alone.

  5. Mental models accurately predict emotion transitions

    PubMed Central

    Thornton, Mark A.; Tamir, Diana I.

    2017-01-01

    Successful social interactions depend on people’s ability to predict others’ future actions and emotions. People possess many mechanisms for perceiving others’ current emotional states, but how might they use this information to predict others’ future states? We hypothesized that people might capitalize on an overlooked aspect of affective experience: current emotions predict future emotions. By attending to regularities in emotion transitions, perceivers might develop accurate mental models of others’ emotional dynamics. People could then use these mental models of emotion transitions to predict others’ future emotions from currently observable emotions. To test this hypothesis, studies 1–3 used data from three extant experience-sampling datasets to establish the actual rates of emotional transitions. We then collected three parallel datasets in which participants rated the transition likelihoods between the same set of emotions. Participants’ ratings of emotion transitions predicted others’ experienced transitional likelihoods with high accuracy. Study 4 demonstrated that four conceptual dimensions of mental state representation—valence, social impact, rationality, and human mind—inform participants’ mental models. Study 5 used 2 million emotion reports on the Experience Project to replicate both of these findings: again people reported accurate models of emotion transitions, and these models were informed by the same four conceptual dimensions. Importantly, neither these conceptual dimensions nor holistic similarity could fully explain participants’ accuracy, suggesting that their mental models contain accurate information about emotion dynamics above and beyond what might be predicted by static emotion knowledge alone. PMID:28533373

  6. Method to make accurate concentration and isotopic measurements for small gas samples

    NASA Astrophysics Data System (ADS)

    Palmer, M. R.; Wahl, E.; Cunningham, K. L.

    2013-12-01

    Carbon isotopic ratio measurements of CO2 and CH4 provide valuable insight into carbon cycle processes. However, many of these studies, like soil gas, soil flux, and water head space experiments, provide very small gas sample volumes, too small for direct measurement by current constant-flow Cavity Ring-Down (CRDS) isotopic analyzers. Previously, we addressed this issue by developing a sample introduction module which enabled the isotopic ratio measurement of 40ml samples or smaller. However, the system, called the Small Sample Isotope Module (SSIM), does dilute the sample during the delivery with inert carrier gas which causes a ~5% reduction in concentration. The isotopic ratio measurements are not affected by this small dilution, but researchers are naturally interested accurate concentration measurements. We present the accuracy and precision of a new method of using this delivery module which we call 'double injection.' Two portions of the 40ml of the sample (20ml each) are introduced to the analyzer, the first injection of which flushes out the diluting gas and the second injection is measured. The accuracy of this new method is demonstrated by comparing the concentration and isotopic ratio measurements for a gas sampled directly and that same gas measured through the SSIM. The data show that the CO2 concentration measurements were the same within instrument precision. The isotopic ratio precision (1σ) of repeated measurements was 0.16 permil for CO2 and 1.15 permil for CH4 at ambient concentrations. This new method provides a significant enhancement in the information provided by small samples.

  7. Investigation of mass dependence effects for the accurate determination of molybdenum isotope amount ratios by MC-ICP-MS using synthetic isotope mixtures.

    PubMed

    Malinovsky, Dmitry; Dunn, Philip J H; Petrov, Panayot; Goenaga-Infante, Heidi

    2015-01-01

    Methodology for absolute Mo isotope amount ratio measurements by multicollector inductively coupled plasma-mass spectrometry (MC-ICP-MS) using calibration with synthetic isotope mixtures (SIMs) is presented. For the first time, synthetic isotope mixtures prepared from seven commercially available isotopically enriched molybdenum metal powders ((92)Mo, (94)Mo, (95)Mo, (96)Mo, (97)Mo, (98)Mo, and (100)Mo) are used to investigate whether instrumental mass discrimination of Mo isotopes in MC-ICP-MS is consistent with mass-dependent isotope distribution. The parent materials were dissolved and mixed as solutions to obtain mixtures with accurately known isotope amount ratios. The level of elemental impurities in the isotopically enriched molybdenum metal powders was quantified by ICP-MS by using both high-resolution and reaction cell instruments to completely resolve spectral interferences. The Mo isotope amount ratio values with expanded uncertainty (k = 2), determined by MC-ICP-MS for a high-purity Mo rod from Johnson Matthey, were as follows: (92)Mo/(95)Mo = 0.9235(9), (94)Mo/(95)Mo = 0.5785(8), (96)Mo/(95)Mo = 1.0503(9), (97)Mo/(95)Mo = 0.6033(6), (98)Mo/(95)Mo = 1.5291(20), and (100)Mo/(95)Mo = 0.6130(7). A full uncertainty budget for the measurements is presented which shows that the largest contribution to the uncertainty budget comes from correction for elemental impurities (∼51%), followed by the contribution from weighing operations (∼26 %). The atomic weight of molybdenum was calculated to be 95.947(2); the uncertainty in parentheses is expanded uncertainty with the coverage factor of 2. A particular advantage of the developed method is that calibration factors for all six Mo isotope amount ratios, involving the (95)Mo isotope, were experimentally determined. This allows avoiding any assumption on mass-dependent isotope fractions in MC-ICP-MS, inherent to the method of double spike previously used for Mo isotope amount ratio

  8. Biomarker Surrogates Do Not Accurately Predict Sputum Eosinophils and Neutrophils in Asthma

    PubMed Central

    Hastie, Annette T.; Moore, Wendy C.; Li, Huashi; Rector, Brian M.; Ortega, Victor E.; Pascual, Rodolfo M.; Peters, Stephen P.; Meyers, Deborah A.; Bleecker, Eugene R.

    2013-01-01

    Background Sputum eosinophils (Eos) are a strong predictor of airway inflammation, exacerbations, and aid asthma management, whereas sputum neutrophils (Neu) indicate a different severe asthma phenotype, potentially less responsive to TH2-targeted therapy. Variables such as blood Eos, total IgE, fractional exhaled nitric oxide (FeNO) or FEV1% predicted, may predict airway Eos, while age, FEV1%predicted, or blood Neu may predict sputum Neu. Availability and ease of measurement are useful characteristics, but accuracy in predicting airway Eos and Neu, individually or combined, is not established. Objectives To determine whether blood Eos, FeNO, and IgE accurately predict sputum eosinophils, and age, FEV1% predicted, and blood Neu accurately predict sputum neutrophils (Neu). Methods Subjects in the Wake Forest Severe Asthma Research Program (N=328) were characterized by blood and sputum cells, healthcare utilization, lung function, FeNO, and IgE. Multiple analytical techniques were utilized. Results Despite significant association with sputum Eos, blood Eos, FeNO and total IgE did not accurately predict sputum Eos, and combinations of these variables failed to improve prediction. Age, FEV1%predicted and blood Neu were similarly unsatisfactory for prediction of sputum Neu. Factor analysis and stepwise selection found FeNO, IgE and FEV1% predicted, but not blood Eos, correctly predicted 69% of sputum Eospredicted 64% of sputum Neupredict both sputum Eos and Neu accurately assigned only 41% of samples. Conclusion Despite statistically significant associations FeNO, IgE, blood Eos and Neu, FEV1%predicted, and age are poor surrogates, separately and combined, for accurately predicting sputum eosinophils and neutrophils. PMID:23706399

  9. Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'

    PubMed Central

    Draper, John; Enot, David P; Parker, David; Beckmann, Manfred; Snowdon, Stuart; Lin, Wanchang; Zubair, Hassan

    2009-01-01

    Background Metabolomics experiments using Mass Spectrometry (MS) technology measure the mass to charge ratio (m/z) and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensional metabolite 'fingerprint' or metabolite 'profile' data. High resolution MS instruments perform routinely with a mass accuracy of < 5 ppm (parts per million) thus providing potentially a direct method for signal putative annotation using databases containing metabolite mass information. Most database interfaces support only simple queries with the default assumption that molecules either gain or lose a single proton when ionised. In reality the annotation process is confounded by the fact that many ionisation products will be not only molecular isotopes but also salt/solvent adducts and neutral loss fragments of original metabolites. This report describes an annotation strategy that will allow searching based on all potential ionisation products predicted to form during electrospray ionisation (ESI). Results Metabolite 'structures' harvested from publicly accessible databases were converted into a common format to generate a comprehensive archive in MZedDB. 'Rules' were derived from chemical information that allowed MZedDB to generate a list of adducts and neutral loss fragments putatively able to form for each structure and calculate, on the fly, the exact molecular weight of every potential ionisation product to provide targets for annotation searches based on accurate mass. We demonstrate that data matrices representing populations of ionisation products generated from different biological matrices contain a large proportion (sometimes > 50%) of molecular isotopes, salt adducts and neutral loss fragments. Correlation analysis of ESI-MS data features confirmed the predicted relationships of m/z signals. An integrated isotope enumerator in MZedDB allowed verification of exact isotopic pattern distributions to corroborate experimental data

  10. Matrix Effects Originating from Coexisting Minerals and Accurate Determination of Stable Silver Isotopes in Silver Deposits.

    PubMed

    Guo, Qi; Wei, Hai-Zhen; Jiang, Shao-Yong; Hohl, Simon; Lin, Yi-Bo; Wang, Yi-Jing; Li, Yin-Chuan

    2017-12-19

    Except for extensive studies in core formation and volatile-element depletion processes using radiogenic Ag isotopes (i.e., the Pd-Ag chronometer), recent research has revealed that the mass fractionation of silver isotopes is in principle controlled by physicochemical processes (e.g., evaporation, diffusion, chemical exchange, etc.) during magmatic emplacement and hydrothermal alteration. As these geologic processes only produce very minor variations of δ 109 Ag from -0.5 to +1.1‰, more accurate and precise measurements are required. In this work, a robust linear relationship between instrumental mass discrimination of Ag and Pd isotopes was obtained at the Ag/Pd molar ratio of 1:20. In Au-Ag ore deposits, silver minerals have complex paragenetic relationships with other minerals (e.g., chalcopyrite, sphalerite, galena, pyrite, etc.). It is difficult to remove such abundant impurities completely because the other metals are tens to thousands of times richer than silver. Both quantitative evaluation of matrix effects and modification of chemical chromatography were carried out to deal with the problems. Isobaric inferences (e.g., 65 Cu 40 Ar + to 105 Pd, 208 Pb 2+ to 104 Pd, and 67 Zn 40 Ar + to 107 Ag + ) and space charge effects dramatically shift the measured δ 109 Ag values. The selection of alternative Pd isotope pairs is effective in eliminating spectral matrix effects so as to ensure accurate analysis under the largest possible ranges for metal impurities, which are Cu/Ag ≤ 50:1, Fe/Ag ≤ 600:1, Pb/Ag ≤ 10:1, and Zn/Ag ≤ 1:1, respectively. With the modified procedure, we reported silver isotope compositions (δ 109 Ag) in geological standard materials and typical Au-Ag ore deposit samples varying from -0.029 to +0.689 ‰ with external reproducibility of ±0.009-0.084 ‰. A systemic survey of δ 109 Ag (or ε 109 Ag) variations in rocks, ore deposits, and environmental materials in nature is discussed.

  11. Predicting equilibrium uranium isotope fractionation in crystals and solution

    NASA Astrophysics Data System (ADS)

    Schauble, E. A.

    2015-12-01

    Despite the rapidly growing interest in using 238U/235U measurements as a proxy for changes in oxygen abundance in surface and near-surface environments, the present theoretical understanding of uranium isotope fractionation is limited to a few simple gas-phase molecules and analogues of dissolved species (e.g., 1,2,3). Understanding uranium isotope fractionation behavior in more complicated species, such as crystals and adsorption complexes, will help in the design and interpretation of experiments and field studies, and may suggest other uses for 38U/235U measurements. In this study, a recently developed first-principles method for estimating the nuclear volume component of field shift fractionation in crystals and complex molecular species (4) is combined with mass-dependent fractionation theory to predict equilibrium 38U/235U fractionations in aqueous and crystalline uranium compounds, including uraninite (UO2). The nuclear field shift effect, caused by the interaction of electrons with the finite volume of the positive charge distribution in uranium nuclei, is estimated using Density Functional Theory and the Projector Augmented Wave method (DFT-PAW). Tests against relativistic electronic structure calculations and Mössbauer isomer shift data indicate that the DFT-PAW method is reasonably accurate, while being much better suited to models of complex and crystalline species. Initial results confirm previous predictions that the nuclear volume effect overwhelms mass depdendent fractionation in U(VI)-U(IV) exchange reactions, leading to higher 238U/235U in U(IV) species (i.e., for UO2 xtal vs. UO22+aq, ln αNV ≈ +1.8‰ , ln αMD ≈ -0.8‰, ln αTotal ≈ +1.0‰ at 25ºC). UO2 and U(H2O)94+, are within ~0.4‰ of each other, while U(VI) species appear to be more variable. This suggests that speciation is likely to significantly affect natural uranium isotope fractionations, in addition to oxidation state. Tentatively, it appears that uranyl-type (UO22

  12. Accurate Identification of Fear Facial Expressions Predicts Prosocial Behavior

    PubMed Central

    Marsh, Abigail A.; Kozak, Megan N.; Ambady, Nalini

    2009-01-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants’ ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale. PMID:17516803

  13. Accurate identification of fear facial expressions predicts prosocial behavior.

    PubMed

    Marsh, Abigail A; Kozak, Megan N; Ambady, Nalini

    2007-05-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants' ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale.

  14. Oxygen isotope geochemistry of the amphiboles: isotope effects of cation substitutions in minerals

    NASA Astrophysics Data System (ADS)

    Kohn, Matthew J.; Valley, John W.

    1998-06-01

    The occurrence of coexisting amphiboles in rocks and the likelihood of concurrent isotope closure allows equilibrium oxygen isotope fractionations among the amphiboles to be recovered from natural samples. Oxygen isotope analyses of mineral separates using laser fluorination show that coexisting amphiboles increasingly partition 18O in the order: hornblende ≪ gedrite < cummingtonite ≤ anthophyllite. The observed fractionations at ˜575°C are: Δ(Ged-Hbl) = 0.8‰, Δ(Cum-Hbl) = 0.9, Δ(Cum-Ged) = 0.2, Δ(Ath-Ged) = 0.3, and Δ(Ath-Hbl) > 0.9. Previously published data for hornblende, actinolite, glaucophane, and garnet show that Δ(Act-Hbl) ˜ 0.2, Δ(Gln-Grt) ≫ 1, and Δ(Hbl-Grt) ˜ 0. Thus, glaucophane strongly partitions 18O relative to the calcic amphiboles. The fractionation between two amphiboles of arbitrary composition can be predicted from the known fractionations for mica endmembers, pyroxene endmembers, and exchange components such as CaAl(NaSi) -1, NaAl(CaMg) -1, CaMg -1, MgFe -1, FeMn -1, KNa -1, KAl( Si) -1, and Fe 3+Al -1. Applications of the exchange component method reproduce measured amphibole fractionations to within ±0.1 to ±0.2‰, whereas other predictive methods cause misfit for typical metamorphic hornblende of ≥0.5‰ at 575°C. Although the isotope effects of cation exchanges may be small at high-T, they magnify dramatically for minerals formed in surficial, diagenetic, and low-T metamorphic environments. Different composition clays are predicted to have equilibrium δ 18O differences of 2-9‰. If the isotope fractionation can be determined for one mineral endmember, then calibrated exchanges allow accurate prediction of the isotope fractionations for intermediate compositions of most ortho-, ring-, chain-, and sheet-silicates.

  15. Accurate Binding Free Energy Predictions in Fragment Optimization.

    PubMed

    Steinbrecher, Thomas B; Dahlgren, Markus; Cappel, Daniel; Lin, Teng; Wang, Lingle; Krilov, Goran; Abel, Robert; Friesner, Richard; Sherman, Woody

    2015-11-23

    Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods represents a major step toward this goal. Accurately predicting the relative binding free energy changes of modifications to ligands is especially valuable in the field of fragment-based drug design, since fragment screens tend to deliver initial hits of low binding affinity that require multiple rounds of synthesis to gain the requisite potency for a project. In this study, we show that a free energy perturbation protocol, FEP+, which was previously validated on drug-like lead compounds, is suitable for the calculation of relative binding strengths of fragment-sized compounds as well. We study several pharmaceutically relevant targets with a total of more than 90 fragments and find that the FEP+ methodology, which uses explicit solvent molecular dynamics and physics-based scoring with no parameters adjusted, can accurately predict relative fragment binding affinities. The calculations afford R(2)-values on average greater than 0.5 compared to experimental data and RMS errors of ca. 1.1 kcal/mol overall, demonstrating significant improvements over the docking and MM-GBSA methods tested in this work and indicating that FEP+ has the requisite predictive power to impact fragment-based affinity optimization projects.

  16. International challenge to predict the impact of radioxenon releases from medical isotope production on a comprehensive nuclear test ban treaty sampling station.

    PubMed

    Eslinger, Paul W; Bowyer, Ted W; Achim, Pascal; Chai, Tianfeng; Deconninck, Benoit; Freeman, Katie; Generoso, Sylvia; Hayes, Philip; Heidmann, Verena; Hoffman, Ian; Kijima, Yuichi; Krysta, Monika; Malo, Alain; Maurer, Christian; Ngan, Fantine; Robins, Peter; Ross, J Ole; Saunier, Olivier; Schlosser, Clemens; Schöppner, Michael; Schrom, Brian T; Seibert, Petra; Stein, Ariel F; Ungar, Kurt; Yi, Jing

    2016-06-01

    The International Monitoring System (IMS) is part of the verification regime for the Comprehensive Nuclear-Test-Ban-Treaty Organization (CTBTO). At entry-into-force, half of the 80 radionuclide stations will be able to measure concentrations of several radioactive xenon isotopes produced in nuclear explosions, and then the full network may be populated with xenon monitoring afterward. An understanding of natural and man-made radionuclide backgrounds can be used in accordance with the provisions of the treaty (such as event screening criteria in Annex 2 to the Protocol of the Treaty) for the effective implementation of the verification regime. Fission-based production of (99)Mo for medical purposes also generates nuisance radioxenon isotopes that are usually vented to the atmosphere. One of the ways to account for the effect emissions from medical isotope production has on radionuclide samples from the IMS is to use stack monitoring data, if they are available, and atmospheric transport modeling. Recently, individuals from seven nations participated in a challenge exercise that used atmospheric transport modeling to predict the time-history of (133)Xe concentration measurements at the IMS radionuclide station in Germany using stack monitoring data from a medical isotope production facility in Belgium. Participants received only stack monitoring data and used the atmospheric transport model and meteorological data of their choice. Some of the models predicted the highest measured concentrations quite well. A model comparison rank and ensemble analysis suggests that combining multiple models may provide more accurate predicted concentrations than any single model. None of the submissions based only on the stack monitoring data predicted the small measured concentrations very well. Modeling of sources by other nuclear facilities with smaller releases than medical isotope production facilities may be important in understanding how to discriminate those releases from

  17. Predictions and Verification of an Isotope Marine Boundary Layer Model

    NASA Astrophysics Data System (ADS)

    Feng, X.; Posmentier, E. S.; Sonder, L. J.; Fan, N.

    2017-12-01

    A one-dimensional (1D), steady state isotope marine boundary layer (IMBL) model is constructed. The model includes meteorologically important features absent in Craig and Gordon type models, namely height-dependent diffusion/mixing and convergence of subsiding external air. Kinetic isotopic fractionation results from this height-dependent diffusion which starts as pure molecular diffusion at the air-water interface and increases linearly with height due to turbulent mixing. The convergence permits dry, isotopically depleted air subsiding adjacent to the model column to mix into ambient air. In δD-δ18O space, the model results fill a quadrilateral, of which three sides represent 1) vapor in equilibrium with various sea surface temperatures (SSTs) (high d18O boundary of quadrilateral); 2) mixture of vapor in equilibrium with seawater and vapor in the subsiding air (lower boundary depleted in both D and 18O); and 3) vapor that has experienced the maximum possible kinetic fractionation (high δD upper boundary). The results can be plotted in d-excess vs. δ18O space, indicating that these processes all cause variations in d-excess of MBL vapor. In particular, due to relatively high d-excess in the descending air, mixing of this air into the MBL causes an increase in d-excess, even without kinetic isotope fractionation. The model is tested by comparison with seven datasets of marine vapor isotopic ratios, with excellent correspondence; >95% of observational data fall within the quadrilateral area predicted by the model. The distribution of observations also highlights the significant influence of vapor from the nearby converging descending air on isotopic variations in the MBL. At least three factors may explain the <5% of observations that fall slightly outside of the predicted region in both δD-δ18O and d-excess - δ18O space: 1) variations in seawater isotopic ratios, 2) variations in isotopic composition of subsiding air, and 3) influence of sea spray. The model

  18. Can phenological models predict tree phenology accurately under climate change conditions?

    NASA Astrophysics Data System (ADS)

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean Michel; García de Cortázar-Atauri, Inaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2014-05-01

    The onset of the growing season of trees has been globally earlier by 2.3 days/decade during the last 50 years because of global warming and this trend is predicted to continue according to climate forecast. The effect of temperature on plant phenology is however not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud dormancy, and on the other hand higher temperatures are necessary to promote bud cells growth afterwards. Increasing phenological changes in temperate woody species have strong impacts on forest trees distribution and productivity, as well as crops cultivation areas. Accurate predictions of trees phenology are therefore a prerequisite to understand and foresee the impacts of climate change on forests and agrosystems. Different process-based models have been developed in the last two decades to predict the date of budburst or flowering of woody species. They are two main families: (1) one-phase models which consider only the ecodormancy phase and make the assumption that endodormancy is always broken before adequate climatic conditions for cell growth occur; and (2) two-phase models which consider both the endodormancy and ecodormancy phases and predict a date of dormancy break which varies from year to year. So far, one-phase models have been able to predict accurately tree bud break and flowering under historical climate. However, because they do not consider what happens prior to ecodormancy, and especially the possible negative effect of winter temperature warming on dormancy break, it seems unlikely that they can provide accurate predictions in future climate conditions. It is indeed well known that a lack of low temperature results in abnormal pattern of bud break and development in temperate fruit trees. An accurate modelling of the dormancy break date has thus become a major issue in phenology modelling. Two-phases phenological models predict that global warming should delay

  19. Mono-isotope Prediction for Mass Spectra Using Bayes Network.

    PubMed

    Li, Hui; Liu, Chunmei; Rwebangira, Mugizi Robert; Burge, Legand

    2014-12-01

    Mass spectrometry is one of the widely utilized important methods to study protein functions and components. The challenge of mono-isotope pattern recognition from large scale protein mass spectral data needs computational algorithms and tools to speed up the analysis and improve the analytic results. We utilized naïve Bayes network as the classifier with the assumption that the selected features are independent to predict mono-isotope pattern from mass spectrometry. Mono-isotopes detected from validated theoretical spectra were used as prior information in the Bayes method. Three main features extracted from the dataset were employed as independent variables in our model. The application of the proposed algorithm to publicMo dataset demonstrates that our naïve Bayes classifier is advantageous over existing methods in both accuracy and sensitivity.

  20. Predictive Framework and Experimental Tests of the Kinetic Isotope Effect at Redox-Active Interfaces

    NASA Astrophysics Data System (ADS)

    Kavner, A.; John, S.; Black, J. R.

    2013-12-01

    Electrochemical reactions provide a compelling framework to study kinetic isotope effects because redox-related processes are important for a wide variety of geological and environmental processes. In the laboratory, electrochemical reaction rates can be electronically controlled and measured in the laboratory using a potentiostat. This enables variation of redox reactions rates independent of changes in chemistry and, and the resulting isotope compositions of reactants and products can be separated and analyzed. In the past years, a series of experimental studies have demonstrated a large, light, and tunable kinetic isotope effect during electrodeposition of metal Fe, Zn, Li, Cu, and Mo from a variety of solutions (e.g. Black et al., 2009, 2010, 2011). A theoretical framework based on Marcus kinetic theory predicts a voltage-dependent kinetic isotope effect (Kavner et al., 2005, 2008), however while this framework was able to predict the tunable nature of the effect, it was not able to simultaneously predict absolute reaction rates and relative isotope rates. Here we present a more complete development of a statistical mechanical framework for simple interfacial redox reactions, which includes isotopic behavior. The framework is able to predict a kinetic isotope effect as a function of temperature and reaction rate, starting with three input parameters: a single reorganization energy which describes the overall kinetics of the electron transfer reaction, and the equilibrium reduced partition function ratios for heavy and light isotopes in the product and reactant phases. We show the framework, elucidate some of the predictions, and show direct comparisons against isotope fractionation data obtained during laboratory and natural environment redox processes. A. Kavner, A. Shahar, F. Bonet, J. Simon and E. Young (2005) Geochim. Cosmochim. Acta, 69(12), 2971-2979. A. Kavner, S. G. John, S. Sass, and E. A. Boyle (2008), Geochim. Cosmochim. Acta, vol 72, pp. 1731

  1. ASTRAL, DRAGON and SEDAN scores predict stroke outcome more accurately than physicians.

    PubMed

    Ntaios, G; Gioulekas, F; Papavasileiou, V; Strbian, D; Michel, P

    2016-11-01

    ASTRAL, SEDAN and DRAGON scores are three well-validated scores for stroke outcome prediction. Whether these scores predict stroke outcome more accurately compared with physicians interested in stroke was investigated. Physicians interested in stroke were invited to an online anonymous survey to provide outcome estimates in randomly allocated structured scenarios of recent real-life stroke patients. Their estimates were compared to scores' predictions in the same scenarios. An estimate was considered accurate if it was within 95% confidence intervals of actual outcome. In all, 244 participants from 32 different countries responded assessing 720 real scenarios and 2636 outcomes. The majority of physicians' estimates were inaccurate (1422/2636, 53.9%). 400 (56.8%) of physicians' estimates about the percentage probability of 3-month modified Rankin score (mRS) > 2 were accurate compared with 609 (86.5%) of ASTRAL score estimates (P < 0.0001). 394 (61.2%) of physicians' estimates about the percentage probability of post-thrombolysis symptomatic intracranial haemorrhage were accurate compared with 583 (90.5%) of SEDAN score estimates (P < 0.0001). 160 (24.8%) of physicians' estimates about post-thrombolysis 3-month percentage probability of mRS 0-2 were accurate compared with 240 (37.3%) DRAGON score estimates (P < 0.0001). 260 (40.4%) of physicians' estimates about the percentage probability of post-thrombolysis mRS 5-6 were accurate compared with 518 (80.4%) DRAGON score estimates (P < 0.0001). ASTRAL, DRAGON and SEDAN scores predict outcome of acute ischaemic stroke patients with higher accuracy compared to physicians interested in stroke. © 2016 EAN.

  2. Final Progress Report: Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes Feasibility Study

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

    Rawool-Sullivan, Mohini; Bounds, John Alan; Brumby, Steven P.

    2012-04-30

    This is the final report of the project titled, 'Isotope Identification Algorithm for Rapid and Accurate Determination of Radioisotopes,' PMIS project number LA10-HUMANID-PD03. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). It summarizes work performed over the FY10 time period. The goal of the work was to demonstrate principles of emulating a human analysis approach towards the data collected using radiation isotope identification devices (RIIDs). Human analysts begin analyzing a spectrum based on features in the spectrum - lines and shapes that aremore » present in a given spectrum. The proposed work was to carry out a feasibility study that will pick out all gamma ray peaks and other features such as Compton edges, bremsstrahlung, presence/absence of shielding and presence of neutrons and escape peaks. Ultimately success of this feasibility study will allow us to collectively explain identified features and form a realistic scenario that produced a given spectrum in the future. We wanted to develop and demonstrate machine learning algorithms that will qualitatively enhance the automated identification capabilities of portable radiological sensors that are currently being used in the field.« less

  3. International challenge to predict the impact of radioxenon releases from medical isotope production on a comprehensive nuclear test ban treaty sampling station

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

    Eslinger, Paul W.; Bowyer, Ted W.; Achim, Pascal

    Abstract The International Monitoring System (IMS) is part of the verification regime for the Comprehensive Nuclear-Test-Ban-Treaty Organization (CTBTO). At entry-into-force, half of the 80 radionuclide stations will be able to measure concentrations of several radioactive xenon isotopes produced in nuclear explosions, and then the full network may be populated with xenon monitoring afterward (Bowyer et al., 2013). Fission-based production of 99Mo for medical purposes also releases radioxenon isotopes to the atmosphere (Saey, 2009). One of the ways to mitigate the effect of emissions from medical isotope production is the use of stack monitoring data, if it were available, so thatmore » the effect of radioactive xenon emissions could be subtracted from the effect from a presumed nuclear explosion, when detected at an IMS station location. To date, no studies have addressed the impacts the time resolution or data accuracy of stack monitoring data have on predicted concentrations at an IMS station location. Recently, participants from seven nations used atmospheric transport modeling to predict the time-history of 133Xe concentration measurements at an IMS station in Germany using stack monitoring data from a medical isotope production facility in Belgium. Participants received only stack monitoring data and used the atmospheric transport model and meteorological data of their choice. Some of the models predicted the highest measured concentrations quite well (a high composite statistical model comparison rank or a small mean square error with the measured values). The results suggest release data on a 15 min time spacing is best. The model comparison rank and ensemble analysis suggests that combining multiple models may provide more accurate predicted concentrations than any single model. Further research is needed to identify optimal methods for selecting ensemble members and those methods may depend on the specific transport problem. None of the submissions

  4. Application and validation of isotope dilution method (IDM) for predicting bioavailability of hydrophobic organic contaminants in soil.

    PubMed

    Wang, Jie; Taylor, Allison; Schlenk, Daniel; Gan, Jay

    2018-05-01

    Risk assessment of hydrophobic organic contaminants (HOCs) using the total chemical concentration following exhaustive extraction may overestimate the actual availability of HOCs to non-target organisms. Existing methods for estimating HOC bioavailability in soil have various operational limitations. In this study, we explored the application of isotope dilution method (IDM) to quantify the accessible fraction (E) of DDTs and PCBs in both historically-contaminated and freshly-spiked soils. After addition of 13 C or deuterated analogues to a soil sample, the phase distribution of isotope-labeled and native chemicals reached an apparent equilibrium within 48 h of mixing. The derived E values in the three soils ranged from 0.19 to 0.82, depending on the soil properties and also the contact time of HOCs (i.e., aging). The isotope dilution method consistently predicted greater accumulation into earthworm (Eisenia fetida) than that by polyethylene (PE) or solid phase microextraction (SPME) sampler, likely because desorption in the gut enhanced bioavailability of soil-borne HOCs. A highly significant linear regression (R 2  = 0.91) was found between IDM and 24-h Tenax desorption, with a slope statistically identical to 1. The IDM-derived accessible concentration (C e ) was further shown to accurately predict tissue residues in earthworm exposed in the same soils. Given the relatively short duration and simple steps, IDM has the potential to be readily adopted for measuring HOC bioaccessibility in soil and for improving risk assessment and evaluation of remediation efficiency. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Development and Deployment of a Portable Water Isotope Analyzer for Accurate, Continuous and High-Frequency Oxygen and Hydrogen Isotope Measurements in Water Vapor and Liquid Water

    NASA Astrophysics Data System (ADS)

    Dong, Feng; Baer, Douglas

    2010-05-01

    Stable isotopes of water in liquid and vapor samples are powerful tracers to investigate the hydrological cycle and ecological processes. Therefore, continuous, in-situ and accurate measurements of del_18O and del_2H are critical to advance the understanding of water cycle dynamics around the globe. Furthermore, the combination of meteorological techniques and high-frequency isotopic water measurements can provide detailed time-resolved information on the eco-physiological performance of plants and enable improved understanding of water fluxes at ecosystem scales. In this work, we present recent laboratory development and field deployment of a novel Water Vapor Isotope Analyzer (WVIA), based on cavity enhanced laser absorption spectroscopy, capable of simultaneous in-situ measurements of del_18O and del_2H and water mixing ratio with high precision and high frequency (up to 10 Hz measurement rate). In addition, to ensure the accuracy of the water vapor isotope measurements, a novel Water Vapor Isotope Standard Source (WVISS), based on the instantaneous evaporation of micro-droplets of liquid water (with known isotope composition), has been developed to provide the reference water vapor with widely adjustable mixing ratio (500-30,000 ppmv) for real-time calibration of the WVIA. The comprehensive system that includes the WVIA and WVISS has been validated in extensive laboratory and field studies to be insensitive to ambient temperature changes (5-40 C) and to changes in water mixing ratio over a wide range of mixing ratios. In addition, by operating in the dual inlet mode, measurement drift has essentially been eliminated. The system (WVIA+WVISS) has also been deployed for long-term unattended continuous measurements in the field. In addition to water vapor isotope measurements, the new Water Vapor Isotopic Standard Source (WVISS) may be combined with the WVIA to provide continuous isotopic measurements of liquid water samples at rapid data rate. The availability of

  6. Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data

    PubMed Central

    Treutler, Hendrik; Neumann, Steffen

    2016-01-01

    Mass spectrometry is a key analytical platform for metabolomics. The precise quantification and identification of small molecules is a prerequisite for elucidating the metabolism and the detection, validation, and evaluation of isotope clusters in LC-MS data is important for this task. Here, we present an approach for the improved detection of isotope clusters using chemical prior knowledge and the validation of detected isotope clusters depending on the substance mass using database statistics. We find remarkable improvements regarding the number of detected isotope clusters and are able to predict the correct molecular formula in the top three ranks in 92% of the cases. We make our methodology freely available as part of the Bioconductor packages xcms version 1.50.0 and CAMERA version 1.30.0. PMID:27775610

  7. Predicting rates of isotopic turnover across the animal kingdom: a synthesis of existing data.

    PubMed

    Thomas, Stephen M; Crowther, Thomas W

    2015-05-01

    The stable isotopes of carbon ((12)C, (13)C) and nitrogen ((14)N, (15)N) represent powerful tools in food web ecology, providing a wide range of dietary information in animal consumers. However, identifying the temporal window over which a consumer's isotopic signature reflects its diet requires an understanding of elemental incorporation, a process that varies from days to years across species and tissue types. Though theory predicts body size and temperature are likely to control incorporation rates, this has not been tested empirically across a morphologically and phylogenetically diverse range of taxa. Readily available estimates of this relationship would, however, aid in the design of stable isotope food web investigations and improve the interpretation of isotopic data collected from natural systems. Using literature-derived turnover estimates from animal species ranging in size from 1 mg to 2000 kg, we develop a predictive tool for stable isotope ecologists, allowing for estimation of incorporation rates in the structural tissues of entirely novel taxa. In keeping with metabolic scaling theory, we show that isotopic turnover rates of carbon and nitrogen in whole organisms and muscle tissue scale allometrically with body mass raised approximately to the power -0.19, an effect modulated by body temperature. This relationship did not, however, apply to incorporation rates in splanchnic tissues, which were instead dependent on the thermoregulation tactic employed by an organism, being considerably faster in endotherms than ectotherms. We believe the predictive turnover equations we provide can improve the design of experiments and interpretation of results obtained in future stable isotopic food web studies. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

  8. First Principle Predictions of Isotopic Shifts in H2O

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2002-01-01

    We compute isotope independent first and second order corrections to the Born-Oppenheimer approximation for water and use them to predict isotopic shifts. For the diagonal correction, we use icMRCI wavefunctions and derivatives with respect to mass dependent, internal coordinates to generate the mass independent correction functions. For the non-adiabatic correction, we use scaled SCF/CIS wave functions and a generalization of the Handy method to obtain mass independent correction functions. We find that including the non-adiabatic correction gives significantly improved results compared to just including the diagonal correction when the Born-Oppenheimer potential energy surface is optimized for H2O-16. The agreement with experimental results for deuterium and tritium containing isotopes is nearly as good as our best empirical correction, however, the present correction is expected to be more reliable for higher, uncharacterized levels.

  9. FAST TRACK COMMUNICATION Accurate estimate of α variation and isotope shift parameters in Na and Mg+

    NASA Astrophysics Data System (ADS)

    Sahoo, B. K.

    2010-12-01

    We present accurate calculations of fine-structure constant variation coefficients and isotope shifts in Na and Mg+ using the relativistic coupled-cluster method. In our approach, we are able to discover the roles of various correlation effects explicitly to all orders in these calculations. Most of the results, especially for the excited states, are reported for the first time. It is possible to ascertain suitable anchor and probe lines for the studies of possible variation in the fine-structure constant by using the above results in the considered systems.

  10. A Triple-Isotope Approach to Predict the Breeding Origins of European Bats

    PubMed Central

    Popa-Lisseanu, Ana G.; Sörgel, Karin; Luckner, Anja; Wassenaar, Leonard I.; Ibáñez, Carlos; Kramer-Schadt, Stephanie; Ciechanowski, Mateusz; Görföl, Tamás; Niermann, Ivo; Beuneux, Grégory; Mysłajek, Robert W.; Juste, Javier; Fonderflick, Jocelyn; Kelm, Detlev H.; Voigt, Christian C.

    2012-01-01

    Despite a commitment by the European Union to protect its migratory bat populations, conservation efforts are hindered by a poor understanding of bat migratory strategies and connectivity between breeding and wintering grounds. Traditional methods like mark-recapture are ineffective to study broad-scale bat migratory patterns. Stable hydrogen isotopes (δD) have been proven useful in establishing spatial migratory connectivity of animal populations. Before applying this tool, the method was calibrated using bat samples of known origin. Here we established the potential of δD as a robust geographical tracer of breeding origins of European bats by measuring δD in hair of five sedentary bat species from 45 locations throughout Europe. The δD of bat hair strongly correlated with well-established spatial isotopic patterns in mean annual precipitation in Europe, and therefore was highly correlated with latitude. We calculated a linear mixed-effects model, with species as random effect, linking δD of bat hair to precipitation δD of the areas of hair growth. This model can be used to predict breeding origins of European migrating bats. We used δ13C and δ15N to discriminate among potential origins of bats, and found that these isotopes can be used as variables to further refine origin predictions. A triple-isotope approach could thereby pinpoint populations or subpopulations that have distinct origins. Our results further corroborated stable isotope analysis as a powerful method to delineate animal migrations in Europe. PMID:22291947

  11. Accurate Prediction of Motor Failures by Application of Multi CBM Tools: A Case Study

    NASA Astrophysics Data System (ADS)

    Dutta, Rana; Singh, Veerendra Pratap; Dwivedi, Jai Prakash

    2018-02-01

    Motor failures are very difficult to predict accurately with a single condition-monitoring tool as both electrical and the mechanical systems are closely related. Electrical problem, like phase unbalance, stator winding insulation failures can, at times, lead to vibration problem and at the same time mechanical failures like bearing failure, leads to rotor eccentricity. In this case study of a 550 kW blower motor it has been shown that a rotor bar crack was detected by current signature analysis and vibration monitoring confirmed the same. In later months in a similar motor vibration monitoring predicted bearing failure and current signature analysis confirmed the same. In both the cases, after dismantling the motor, the predictions were found to be accurate. In this paper we will be discussing the accurate predictions of motor failures through use of multi condition monitoring tools with two case studies.

  12. Bayesian Integration of Isotope Ratio for Geographic Sourcing of Castor Beans

    PubMed Central

    Webb-Robertson, Bobbie-Jo; Kreuzer, Helen; Hart, Garret; Ehleringer, James; West, Jason; Gill, Gary; Duckworth, Douglas

    2012-01-01

    Recent years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based on the integrated model with a class accuracy of 60.9 ± 2.1% versus 55.9 ± 2.1% and 40.2 ± 1.8% for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model. PMID:22919270

  13. Radiomics biomarkers for accurate tumor progression prediction of oropharyngeal cancer

    NASA Astrophysics Data System (ADS)

    Hadjiiski, Lubomir; Chan, Heang-Ping; Cha, Kenny H.; Srinivasan, Ashok; Wei, Jun; Zhou, Chuan; Prince, Mark; Papagerakis, Silvana

    2017-03-01

    Accurate tumor progression prediction for oropharyngeal cancers is crucial for identifying patients who would best be treated with optimized treatment and therefore minimize the risk of under- or over-treatment. An objective decision support system that can merge the available radiomics, histopathologic and molecular biomarkers in a predictive model based on statistical outcomes of previous cases and machine learning may assist clinicians in making more accurate assessment of oropharyngeal tumor progression. In this study, we evaluated the feasibility of developing individual and combined predictive models based on quantitative image analysis from radiomics, histopathology and molecular biomarkers for oropharyngeal tumor progression prediction. With IRB approval, 31, 84, and 127 patients with head and neck CT (CT-HN), tumor tissue microarrays (TMAs) and molecular biomarker expressions, respectively, were collected. For 8 of the patients all 3 types of biomarkers were available and they were sequestered in a test set. The CT-HN lesions were automatically segmented using our level sets based method. Morphological, texture and molecular based features were extracted from CT-HN and TMA images, and selected features were merged by a neural network. The classification accuracy was quantified using the area under the ROC curve (AUC). Test AUCs of 0.87, 0.74, and 0.71 were obtained with the individual predictive models based on radiomics, histopathologic, and molecular features, respectively. Combining the radiomics and molecular models increased the test AUC to 0.90. Combining all 3 models increased the test AUC further to 0.94. This preliminary study demonstrates that the individual domains of biomarkers are useful and the integrated multi-domain approach is most promising for tumor progression prediction.

  14. Accurate First-Principles Spectra Predictions for Planetological and Astrophysical Applications at Various T-Conditions

    NASA Astrophysics Data System (ADS)

    Rey, M.; Nikitin, A. V.; Tyuterev, V.

    2014-06-01

    Knowledge of near infrared intensities of rovibrational transitions of polyatomic molecules is essential for the modeling of various planetary atmospheres, brown dwarfs and for other astrophysical applications 1,2,3. For example, to analyze exoplanets, atmospheric models have been developed, thus making the need to provide accurate spectroscopic data. Consequently, the spectral characterization of such planetary objects relies on the necessity of having adequate and reliable molecular data in extreme conditions (temperature, optical path length, pressure). On the other hand, in the modeling of astrophysical opacities, millions of lines are generally involved and the line-by-line extraction is clearly not feasible in laboratory measurements. It is thus suggested that this large amount of data could be interpreted only by reliable theoretical predictions. There exists essentially two theoretical approaches for the computation and prediction of spectra. The first one is based on empirically-fitted effective spectroscopic models. Another way for computing energies, line positions and intensities is based on global variational calculations using ab initio surfaces. They do not yet reach the spectroscopic accuracy stricto sensu but implicitly account for all intramolecular interactions including resonance couplings in a wide spectral range. The final aim of this work is to provide reliable predictions which could be quantitatively accurate with respect to the precision of available observations and as complete as possible. All this thus requires extensive first-principles quantum mechanical calculations essentially based on three necessary ingredients which are (i) accurate intramolecular potential energy surface and dipole moment surface components well-defined in a large range of vibrational displacements and (ii) efficient computational methods combined with suitable choices of coordinates to account for molecular symmetry properties and to achieve a good numerical

  15. SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

    PubMed

    Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

    2008-05-01

    Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are

  16. SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

    PubMed Central

    Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

    2008-01-01

    Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of

  17. Accurate isotopic fission yields of electromagnetically induced fission of 238U measured in inverse kinematics at relativistic energies

    NASA Astrophysics Data System (ADS)

    Pellereau, E.; Taïeb, J.; Chatillon, A.; Alvarez-Pol, H.; Audouin, L.; Ayyad, Y.; Bélier, G.; Benlliure, J.; Boutoux, G.; Caamaño, M.; Casarejos, E.; Cortina-Gil, D.; Ebran, A.; Farget, F.; Fernández-Domínguez, B.; Gorbinet, T.; Grente, L.; Heinz, A.; Johansson, H.; Jurado, B.; Kelić-Heil, A.; Kurz, N.; Laurent, B.; Martin, J.-F.; Nociforo, C.; Paradela, C.; Pietri, S.; Rodríguez-Sánchez, J. L.; Schmidt, K.-H.; Simon, H.; Tassan-Got, L.; Vargas, J.; Voss, B.; Weick, H.

    2017-05-01

    SOFIA (Studies On Fission with Aladin) is a novel experimental program, dedicated to accurate measurements of fission-fragment isotopic yields. The setup allows us to fully identify, in nuclear charge and mass, both fission fragments in coincidence for the whole fission-fragment range. It was installed at the GSI facility (Darmstadt), to benefit from the relativistic heavy-ion beams available there, and thus to use inverse kinematics. This paper reports on fission yields obtained in electromagnetically induced fission of 238U.

  18. Accurate experimental determination of the isotope effects on the triple point temperature of water. I. Dependence on the 2H abundance

    NASA Astrophysics Data System (ADS)

    Faghihi, V.; Peruzzi, A.; Aerts-Bijma, A. T.; Jansen, H. G.; Spriensma, J. J.; van Geel, J.; Meijer, H. A. J.

    2015-12-01

    Variation in the isotopic composition of water is one of the major contributors to uncertainty in the realization of the triple point of water (TPW). Although the dependence of the TPW on the isotopic composition of the water has been known for years, there is still a lack of a detailed and accurate experimental determination of the values for the correction constants. This paper is the first of two articles (Part I and Part II) that address quantification of isotope abundance effects on the triple point temperature of water. In this paper, we describe our experimental assessment of the 2H isotope effect. We manufactured five triple point cells with prepared water mixtures with a range of 2H isotopic abundances encompassing widely the natural abundance range, while the 18O and 17O isotopic abundance were kept approximately constant and the 18O  -  17O ratio was close to the Meijer-Li relationship for natural waters. The selected range of 2H isotopic abundances led to cells that realised TPW temperatures between approximately  -140 μK to  +2500 μK with respect to the TPW temperature as realized by VSMOW (Vienna Standard Mean Ocean Water). Our experiment led to determination of the value for the δ2H correction parameter of A2H  =  673 μK / (‰ deviation of δ2H from VSMOW) with a combined uncertainty of 4 μK (k  =  1, or 1σ).

  19. PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

    PubMed Central

    Bendl, Jaroslav; Stourac, Jan; Salanda, Ondrej; Pavelka, Antonin; Wieben, Eric D.; Zendulka, Jaroslav; Brezovsky, Jan; Damborsky, Jiri

    2014-01-01

    Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp. PMID:24453961

  20. Bayesian Integration of Isotope Ratio for Geographic Sourcing of Castor Beans

    DOE PAGES

    Webb-Robertson, Bobbie-Jo; Kreuzer, Helen; Hart, Garret; ...

    2012-01-01

    Recenmore » t years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based on the integrated model with a class accuracy of 60.9 ± 2.1 % versus 55.9 ± 2.1 % and 40.2 ± 1.8 % for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model.« less

  1. Bayesian Integration of Isotope Ratios for Geographic Sourcing of Castor Beans

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

    Webb-Robertson, Bobbie-Jo M.; Kreuzer, Helen W.; Hart, Garret L.

    Recent years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based onmore » the integrated model with a class accuracy of 6 0 . 9 {+-} 2 . 1 % versus 5 5 . 9 {+-} 2 . 1 % and 4 0 . 2 {+-} 1 . 8 % for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model.« less

  2. Bayesian Integration of Isotope Ratio for Geographic Sourcing of Castor Beans

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

    Webb-Robertson, Bobbie-Jo; Kreuzer, Helen; Hart, Garret

    Recenmore » t years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based on the integrated model with a class accuracy of 60.9 ± 2.1 % versus 55.9 ± 2.1 % and 40.2 ± 1.8 % for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model.« less

  3. Heart rate during basketball game play and volleyball drills accurately predicts oxygen uptake and energy expenditure.

    PubMed

    Scribbans, T D; Berg, K; Narazaki, K; Janssen, I; Gurd, B J

    2015-09-01

    There is currently little information regarding the ability of metabolic prediction equations to accurately predict oxygen uptake and exercise intensity from heart rate (HR) during intermittent sport. The purpose of the present study was to develop and, cross-validate equations appropriate for accurately predicting oxygen cost (VO2) and energy expenditure from HR during intermittent sport participation. Eleven healthy adult males (19.9±1.1yrs) were recruited to establish the relationship between %VO2peak and %HRmax during low-intensity steady state endurance (END), moderate-intensity interval (MOD) and high intensity-interval exercise (HI), as performed on a cycle ergometer. Three equations (END, MOD, and HI) for predicting %VO2peak based on %HRmax were developed. HR and VO2 were directly measured during basketball games (6 male, 20.8±1.0 yrs; 6 female, 20.0±1.3yrs) and volleyball drills (12 female; 20.8±1.0yrs). Comparisons were made between measured and predicted VO2 and energy expenditure using the 3 equations developed and 2 previously published equations. The END and MOD equations accurately predicted VO2 and energy expenditure, while the HI equation underestimated, and the previously published equations systematically overestimated VO2 and energy expenditure. Intermittent sport VO2 and energy expenditure can be accurately predicted from heart rate data using either the END (%VO2peak=%HRmax x 1.008-17.17) or MOD (%VO2peak=%HRmax x 1.2-32) equations. These 2 simple equations provide an accessible and cost-effective method for accurate estimation of exercise intensity and energy expenditure during intermittent sport.

  4. Accurate determination of selected pesticides in soya beans by liquid chromatography coupled to isotope dilution mass spectrometry.

    PubMed

    Huertas Pérez, J F; Sejerøe-Olsen, B; Fernández Alba, A R; Schimmel, H; Dabrio, M

    2015-05-01

    A sensitive, accurate and simple liquid chromatography coupled with mass spectrometry method for the determination of 10 selected pesticides in soya beans has been developed and validated. The method is intended for use during the characterization of selected pesticides in a reference material. In this process, high accuracy and appropriate uncertainty levels associated to the analytical measurements are of utmost importance. The analytical procedure is based on sample extraction by the use of a modified QuEChERS (quick, easy, cheap, effective, rugged, safe) extraction and subsequent clean-up of the extract with C18, PSA and Florisil. Analytes were separated on a C18 column using gradient elution with water-methanol/2.5 mM ammonium acetate mobile phase, and finally identified and quantified by triple quadrupole mass spectrometry in the multiple reaction monitoring mode (MRM). Reliable and accurate quantification of the analytes was achieved by means of stable isotope-labelled analogues employed as internal standards (IS) and calibration with pure substance solutions containing both, the isotopically labelled and native compounds. Exceptions were made for thiodicarb and malaoxon where the isotopically labelled congeners were not commercially available at the time of analysis. For the quantification of those compounds methomyl-(13)C2(15)N and malathion-D10 were used respectively. The method was validated according to the general principles covered by DG SANCO guidelines. However, validation criteria were set more stringently. Mean recoveries were in the range of 86-103% with RSDs lower than 8.1%. Repeatability and intermediate precision were in the range of 3.9-7.6% and 1.9-8.7% respectively. LODs were theoretically estimated and experimentally confirmed to be in the range 0.001-0.005 mg kg(-1) in the matrix, while LOQs established as the lowest spiking mass fractionation level were in the range 0.01-0.05 mg kg(-1). The method reliably identifies and quantifies the

  5. Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

    PubMed Central

    Burger, Lukas; van Nimwegen, Erik

    2008-01-01

    Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

  6. A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

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

    Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.

    2004-12-01

    We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, andmore » its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.« less

  7. Modeling Equilibrium Fe Isotope Fractionation in Fe-Organic Complexes: Implications for the use of Fe Isotopes as a Biomarker and Trends Based on the Properties of Bound Ligands

    NASA Astrophysics Data System (ADS)

    Domagal-Goldman, S.; Kubicki, J. D.

    2006-05-01

    Fe Isotopes have been proposed as a useful tracer of biological and geochemical processes. Key to understanding the effects these various processes have on Fe isotopes is accurate modeling of the reactions responsible for the isotope fractionations. In this study, we examined the theoretical basis for the claims that Fe isotopes can be used as a biomarker. This was done by using molecular orbital/density functional theory (MO/DFT) calculations to predict the equilibrium fractionation of Fe isotopes due to changes in the redox state and the bonding environment of Fe. Specifically, we predicted vibrational frequencies for iron desferrioxamine (Fe-DFOB), iron triscatechol (Fe(cat)3), iron trisoxalate (Fe(ox)3), and hexaaquo iron (Fe(H2O)6) for complexes containing both ferrous (Fe2+) and ferric (Fe3+) iron. Using these vibrational frequencies, we then predicted fractionation factors between these six complexes. The predicted fractionation factors resulting from changes in the redox state of Fe fell in the range 2.5- 3.5‰. The fractionation factors resulting from changes in the bonding environment of Fe ranged from 0.2 to 1.4‰. These results indicate that changes in the bonding strength of Fe ligands are less important to Fe isotope fractionation processes than are changes to the redox state of Fe. The implications for use of Fe as a tracer of biological processes is clear: abiological redox changes must be ruled out in a sample before Fe isotopes are considered as a potential biomarker. Furthermore, the use of Fe isotopes to measure the redox state of the Earths surface environment through time is supported by this work, since changes in the redox state of Fe appear to be the more important driver of isotopic fractionations. In addition to the large differences between redox-driven fractionations and ligand-driven fractionations, we will also show general trends in the demand for heavy Fe isotopes as a function of properties of the bound ligand. This will help the

  8. Accurate prediction of energy expenditure using a shoe-based activity monitor.

    PubMed

    Sazonova, Nadezhda; Browning, Raymond C; Sazonov, Edward

    2011-07-01

    The aim of this study was to develop and validate a method for predicting energy expenditure (EE) using a footwear-based system with integrated accelerometer and pressure sensors. We developed a footwear-based device with an embedded accelerometer and insole pressure sensors for the prediction of EE. The data from the device can be used to perform accurate recognition of major postures and activities and to estimate EE using the acceleration, pressure, and posture/activity classification information in a branched algorithm without the need for individual calibration. We measured EE via indirect calorimetry as 16 adults (body mass index=19-39 kg·m) performed various low- to moderate-intensity activities and compared measured versus predicted EE using several models based on the acceleration and pressure signals. Inclusion of pressure data resulted in better accuracy of EE prediction during static postures such as sitting and standing. The activity-based branched model that included predictors from accelerometer and pressure sensors (BACC-PS) achieved the lowest error (e.g., root mean squared error (RMSE)=0.69 METs) compared with the accelerometer-only-based branched model BACC (RMSE=0.77 METs) and nonbranched model (RMSE=0.94-0.99 METs). Comparison of EE prediction models using data from both legs versus models using data from a single leg indicates that only one shoe needs to be equipped with sensors. These results suggest that foot acceleration combined with insole pressure measurement, when used in an activity-specific branched model, can accurately estimate the EE associated with common daily postures and activities. The accuracy and unobtrusiveness of a footwear-based device may make it an effective physical activity monitoring tool.

  9. Are EMS call volume predictions based on demand pattern analysis accurate?

    PubMed

    Brown, Lawrence H; Lerner, E Brooke; Larmon, Baxter; LeGassick, Todd; Taigman, Michael

    2007-01-01

    Most EMS systems determine the number of crews they will deploy in their communities and when those crews will be scheduled based on anticipated call volumes. Many systems use historical data to calculate their anticipated call volumes, a method of prediction known as demand pattern analysis. To evaluate the accuracy of call volume predictions calculated using demand pattern analysis. Seven EMS systems provided 73 consecutive weeks of hourly call volume data. The first 20 weeks of data were used to calculate three common demand pattern analysis constructs for call volume prediction: average peak demand (AP), smoothed average peak demand (SAP), and 90th percentile rank (90%R). The 21st week served as a buffer. Actual call volumes in the last 52 weeks were then compared to the predicted call volumes by using descriptive statistics. There were 61,152 hourly observations in the test period. All three constructs accurately predicted peaks and troughs in call volume but not exact call volume. Predictions were accurate (+/-1 call) 13% of the time using AP, 10% using SAP, and 19% using 90%R. Call volumes were overestimated 83% of the time using AP, 86% using SAP, and 74% using 90%R. When call volumes were overestimated, predictions exceeded actual call volume by a median (Interquartile range) of 4 (2-6) calls for AP, 4 (2-6) for SAP, and 3 (2-5) for 90%R. Call volumes were underestimated 4% of time using AP, 4% using SAP, and 7% using 90%R predictions. When call volumes were underestimated, call volumes exceeded predictions by a median (Interquartile range; maximum under estimation) of 1 (1-2; 18) call for AP, 1 (1-2; 18) for SAP, and 2 (1-3; 20) for 90%R. Results did not vary between systems. Generally, demand pattern analysis estimated or overestimated call volume, making it a reasonable predictor for ambulance staffing patterns. However, it did underestimate call volume between 4% and 7% of the time. Communities need to determine if these rates of over

  10. Rapid and accurate prediction and scoring of water molecules in protein binding sites.

    PubMed

    Ross, Gregory A; Morris, Garrett M; Biggin, Philip C

    2012-01-01

    Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

  11. Kinetics of the reaction of the heaviest hydrogen atom with H2, the 4Heμ + H2 → 4HeμH + H reaction: Experiments, accurate quantal calculations, and variational transition state theory, including kinetic isotope effects for a factor of 36.1 in isotopic mass

    NASA Astrophysics Data System (ADS)

    Fleming, Donald G.; Arseneau, Donald J.; Sukhorukov, Oleksandr; Brewer, Jess H.; Mielke, Steven L.; Truhlar, Donald G.; Schatz, George C.; Garrett, Bruce C.; Peterson, Kirk A.

    2011-11-01

    The neutral muonic helium atom 4Heμ, in which one of the electrons of He is replaced by a negative muon, may be effectively regarded as the heaviest isotope of the hydrogen atom, with a mass of 4.115 amu. We report details of the first muon spin rotation (μSR) measurements of the chemical reaction rate constant of 4Heμ with molecular hydrogen, 4Heμ + H2 → 4HeμH + H, at temperatures of 295.5, 405, and 500 K, as well as a μSR measurement of the hyperfine coupling constant of muonic He at high pressures. The experimental rate constants, kHeμ, are compared with the predictions of accurate quantum mechanical (QM) dynamics calculations carried out on a well converged Born-Huang (BH) potential energy surface, based on complete configuration interaction calculations and including a Born-Oppenheimer diagonal correction. At the two highest measured temperatures the agreement between the quantum theory and experiment is good to excellent, well within experimental uncertainties that include an estimate of possible systematic error, but at 295.5 K the quantum calculations for kHeμ are below the experimental value by 2.1 times the experimental uncertainty estimates. Possible reasons for this discrepancy are discussed. Variational transition state theory calculations with multidimensional tunneling have also been carried out for kHeμ on the BH surface, and they agree with the accurate QM rate constants to within 30% over a wider temperature range of 200-1000 K. Comparisons between theory and experiment are also presented for the rate constants for both the D + H2 and Mu + H2 reactions in a novel study of kinetic isotope effects for the H + H2 reactions over a factor of 36.1 in isotopic mass of the atomic reactant.

  12. Tellurium Stable Isotope Fractionation in Chondritic Meteorites

    NASA Astrophysics Data System (ADS)

    Fehr, M. A.; Hammond, S. J.; Parkinson, I. J.

    2014-09-01

    New Te double spike procedures were set up to obtain high-precision accurate Te stable isotope data. Tellurium stable isotope data for 16 chondrite falls are presented, providing evidence for significant Te stable isotope fractionation.

  13. Integrated carbon and chlorine isotope modeling: applications to chlorinated aliphatic hydrocarbons dechlorination.

    PubMed

    Jin, Biao; Haderlein, Stefan B; Rolle, Massimo

    2013-02-05

    We propose a self-consistent method to predict the evolution of carbon and chlorine isotope ratios during degradation of chlorinated hydrocarbons. The method treats explicitly the cleavage of isotopically different C-Cl bonds and thus considers, simultaneously, combined carbon-chlorine isotopologues. To illustrate the proposed modeling approach we focus on the reductive dehalogenation of chlorinated ethenes. We compare our method with the currently available approach, in which carbon and chlorine isotopologues are treated separately. The new approach provides an accurate description of dual-isotope effects regardless of the extent of the isotope fractionation and physical characteristics of the experimental system. We successfully applied the new approach to published experimental results on dehalogenation of chlorinated ethenes both in well-mixed systems and in situations where mass-transfer limitations control the overall rate of biodegradation. The advantages of our self-consistent dual isotope modeling approach proved to be most evident when isotope fractionation factors of carbon and chlorine differed significantly and for systems with mass-transfer limitations, where both physical and (bio)chemical transformation processes affect the observed isotopic values.

  14. Multi-fidelity machine learning models for accurate bandgap predictions of solids

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

    Pilania, Ghanshyam; Gubernatis, James E.; Lookman, Turab

    Here, we present a multi-fidelity co-kriging statistical learning framework that combines variable-fidelity quantum mechanical calculations of bandgaps to generate a machine-learned model that enables low-cost accurate predictions of the bandgaps at the highest fidelity level. Additionally, the adopted Gaussian process regression formulation allows us to predict the underlying uncertainties as a measure of our confidence in the predictions. In using a set of 600 elpasolite compounds as an example dataset and using semi-local and hybrid exchange correlation functionals within density functional theory as two levels of fidelities, we demonstrate the excellent learning performance of the method against actual high fidelitymore » quantum mechanical calculations of the bandgaps. The presented statistical learning method is not restricted to bandgaps or electronic structure methods and extends the utility of high throughput property predictions in a significant way.« less

  15. Multi-fidelity machine learning models for accurate bandgap predictions of solids

    DOE PAGES

    Pilania, Ghanshyam; Gubernatis, James E.; Lookman, Turab

    2016-12-28

    Here, we present a multi-fidelity co-kriging statistical learning framework that combines variable-fidelity quantum mechanical calculations of bandgaps to generate a machine-learned model that enables low-cost accurate predictions of the bandgaps at the highest fidelity level. Additionally, the adopted Gaussian process regression formulation allows us to predict the underlying uncertainties as a measure of our confidence in the predictions. In using a set of 600 elpasolite compounds as an example dataset and using semi-local and hybrid exchange correlation functionals within density functional theory as two levels of fidelities, we demonstrate the excellent learning performance of the method against actual high fidelitymore » quantum mechanical calculations of the bandgaps. The presented statistical learning method is not restricted to bandgaps or electronic structure methods and extends the utility of high throughput property predictions in a significant way.« less

  16. Measuring the value of accurate link prediction for network seeding.

    PubMed

    Wei, Yijin; Spencer, Gwen

    2017-01-01

    The influence-maximization literature seeks small sets of individuals whose structural placement in the social network can drive large cascades of behavior. Optimization efforts to find the best seed set often assume perfect knowledge of the network topology. Unfortunately, social network links are rarely known in an exact way. When do seeding strategies based on less-than-accurate link prediction provide valuable insight? We introduce optimized-against-a-sample ([Formula: see text]) performance to measure the value of optimizing seeding based on a noisy observation of a network. Our computational study investigates [Formula: see text] under several threshold-spread models in synthetic and real-world networks. Our focus is on measuring the value of imprecise link information. The level of investment in link prediction that is strategic appears to depend closely on spread model: in some parameter ranges investments in improving link prediction can pay substantial premiums in cascade size. For other ranges, such investments would be wasted. Several trends were remarkably consistent across topologies.

  17. Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

    PubMed

    Andersen, Mikael R; Nielsen, Jakob B; Klitgaard, Andreas; Petersen, Lene M; Zachariasen, Mia; Hansen, Tilde J; Blicher, Lene H; Gotfredsen, Charlotte H; Larsen, Thomas O; Nielsen, Kristian F; Mortensen, Uffe H

    2013-01-02

    Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 of 16 known clusters and nearly accurate for the remaining 3 clusters. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (superclusters), and validate this both with legacy data and experimentally by prediction and verification of a supercluster consisting of the synthase AN1242 and the prenyltransferase AN11080, as well as identification of the product compound nidulanin A. We have used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.

  18. Simple prediction scores predict good and devastating outcomes after stroke more accurately than physicians.

    PubMed

    Reid, John Michael; Dai, Dingwei; Delmonte, Susanna; Counsell, Carl; Phillips, Stephen J; MacLeod, Mary Joan

    2017-05-01

    physicians are often asked to prognosticate soon after a patient presents with stroke. This study aimed to compare two outcome prediction scores (Five Simple Variables [FSV] score and the PLAN [Preadmission comorbidities, Level of consciousness, Age, and focal Neurologic deficit]) with informal prediction by physicians. demographic and clinical variables were prospectively collected from consecutive patients hospitalised with acute ischaemic or haemorrhagic stroke (2012-13). In-person or telephone follow-up at 6 months established vital and functional status (modified Rankin score [mRS]). Area under the receiver operating curves (AUC) was used to establish prediction score performance. five hundred and seventy-five patients were included; 46% female, median age 76 years, 88% ischaemic stroke. Six months after stroke, 47% of patients had a good outcome (alive and independent, mRS 0-2) and 26% a devastating outcome (dead or severely dependent, mRS 5-6). The FSV and PLAN scores were superior to physician prediction (AUCs of 0.823-0.863 versus 0.773-0.805, P < 0.0001) for good and devastating outcomes. The FSV score was superior to the PLAN score for predicting good outcomes and vice versa for devastating outcomes (P < 0.001). Outcome prediction was more accurate for those with later presentations (>24 hours from onset). the FSV and PLAN scores are validated in this population for outcome prediction after both ischaemic and haemorrhagic stroke. The FSV score is the least complex of all developed scores and can assist outcome prediction by physicians. © The Author 2016. Published by Oxford University Press on behalf of the British Geriatrics Society. All rights reserved. For permissions, please email: journals.permissions@oup.com

  19. Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins

    PubMed Central

    Li, Bian; Mendenhall, Jeffrey; Nguyen, Elizabeth Dong; Weiner, Brian E.; Fischer, Axel W.; Meiler, Jens

    2017-01-01

    Prediction of the three-dimensional (3D) structures of proteins by computational methods is acknowledged as an unsolved problem. Accurate prediction of important structural characteristics such as contact number is expected to accelerate the otherwise slow progress being made in the prediction of 3D structure of proteins. Here, we present a dropout neural network-based method, TMH-Expo, for predicting the contact number of transmembrane helix (TMH) residues from sequence. Neuronal dropout is a strategy where certain neurons of the network are excluded from back-propagation to prevent co-adaptation of hidden-layer neurons. By using neuronal dropout, overfitting was significantly reduced and performance was noticeably improved. For multi-spanning helical membrane proteins, TMH-Expo achieved a remarkable Pearson correlation coefficient of 0.69 between predicted and experimental values and a mean absolute error of only 1.68. In addition, among those membrane protein–membrane protein interface residues, 76.8% were correctly predicted. Mapping of predicted contact numbers onto structures indicates that contact numbers predicted by TMH-Expo reflect the exposure patterns of TMHs and reveal membrane protein–membrane protein interfaces, reinforcing the potential of predicted contact numbers to be used as restraints for 3D structure prediction and protein–protein docking. TMH-Expo can be accessed via a Web server at www.meilerlab.org. PMID:26804342

  20. Equilibrium properties of dense hydrogen isotope gases based on the theory of simple fluids.

    PubMed

    Kowalczyk, Piotr; MacElroy, J M D

    2006-08-03

    We present a new method for the prediction of the equilibrium properties of dense gases containing hydrogen isotopes. The proposed approach combines the Feynman-Hibbs effective potential method and a deconvolution scheme introduced by Weeks et al. The resulting equations of state and the chemical potentials as functions of pressure for each of the hydrogen isotope gases depend on a single set of Lennard-Jones parameters. In addition to its simplicity, the proposed method with optimized Lennard-Jones potential parameters accurately describes the equilibrium properties of hydrogen isotope fluids in the regime of moderate temperatures and pressures. The present approach should find applications in the nonlocal density functional theory of inhomogeneous quantum fluids and should also be of particular relevance to hydrogen (clean energy) storage and to the separation of quantum isotopes by novel nanomaterials.

  1. Predicting the solubility and lability of Zn, Cd, and Pb in soils from a minespoil-contaminated catchment by stable isotopic exchange

    NASA Astrophysics Data System (ADS)

    Marzouk, E. R.; Chenery, S. R.; Young, S. D.

    2013-12-01

    The Rookhope catchment of Weardale, England, has a diverse legacy of contaminated soils due to extensive lead mining activity over four centuries. We measured the isotopically exchangeable content of Pb, Cd and Zn (E-values) in a large representative subset of the catchment soils (n = 246) using stable isotope dilution. All three metals displayed a wide range of %E-values (c. 1-100%) but relative lability followed the sequence Cd > Pb > Zn. A refinement of the stable isotope dilution approach also enabled detection of non-reactive metal contained within suspended sub-micron (<0.22 μm) colloidal particles (SCP-metal). For most soils, the presence of non-labile SCP-metal caused only minor over-estimation of E-values (<2%) but the effect was greater for soils with particularly large humus or carbonate contents. Approximately 80%, 53% and 66% of the variability in Zn, Cd and Pb %E-values (respectively) could be explained by pH, loss on ignition and total metal content. E-values were affected by the presence of ore minerals at high metal contents leading to an inconsistent trend in the relationship between %E-value and soil metal concentration. Metal solubility, in the soil suspensions used to measure E-values, was predicted using the WHAM geochemical speciation model (versions VI and VII). The use of total and isotopically exchangeable metal as alternative input variables was compared; the latter provided significantly better predictions of solubility, especially in the case of Zn. Lead solubility was less well predicted by either version of WHAM, with over-prediction at low pH and under-prediction at high soil pH values. Quantify the isotopically exchangeable fractions of Zn, Cd and Pb (E-values), and assess their local and regional variability, using multi-element stable isotope dilution, in a diverse range of soil ecosystems within the catchment of an old Pb/Zn mining area. Assess the controlling influences of soil properties on metal lability and develop

  2. Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

    DOE PAGES

    Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

    2013-03-07

    In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

  3. Existing and emerging technologies for measuring stable isotope labelled retinol in biological samples: isotope dilution analysis of body retinol stores.

    PubMed

    Preston, Tom

    2014-01-01

    This paper discusses some of the recent improvements in instrumentation used for stable isotope tracer measurements in the context of measuring retinol stores, in vivo. Tracer costs, together with concerns that larger tracer doses may perturb the parameter under study, demand that ever more sensitive mass spectrometric techniques are developed. GCMS is the most widely used technique. It has high sensitivity in terms of sample amount and uses high resolution GC, yet its ability to detect low isotope ratios is limited by background noise. LCMSMS may become more accessible for tracer studies. Its ability to measure low level stable isotope tracers may prove superior to GCMS, but it is isotope ratio MS (IRMS) that has been designed specifically for low level stable isotope analysis through accurate analysis of tracer:tracee ratios (the tracee being the unlabelled species). Compound-specific isotope analysis, where GC is interfaced to IRMS, is gaining popularity. Here, individual 13C-labelled compounds are separated by GC, combusted to CO2 and transferred on-line for ratiometric analysis by IRMS at the ppm level. However, commercially-available 13C-labelled retinol tracers are 2 - 4 times more expensive than deuterated tracers. For 2H-labelled compounds, GC-pyrolysis-IRMS has now become more generally available as an operating mode on the same IRMS instrument. Here, individual compounds are separated by GC and pyrolysed to H2 at high temperature for analysis by IRMS. It is predicted that GC-pyrolysis-IRMS will facilitate low level tracer procedures to measure body retinol stores, as has been accomplished in the case of fatty acids and amino acids. Sample size requirements for GC-P-IRMS may exceed those of GCMS, but this paper discusses sample preparation procedures and predicts improvements, particularly in the efficiency of sample introduction.

  4. Joint profiling of greenhouse gases, isotopes, thermodynamic variables, and wind from space by combined microwave and IR laser occultation: the ACCURATE concept

    NASA Astrophysics Data System (ADS)

    Kirchengast, G.; Schweitzer, S.

    2008-12-01

    The ACCURATE (Atmospheric Climate and Chemistry in the UTLS Region And climate Trends Explorer) mission was conceived at the Wegener Center in late 2004 and subsequently proposed in 2005 by an international team of more than 20 scientific partners from more than 12 countries to an ESA selection process for next Earth Explorer Missions. While the mission was not selected for formal pre-phase A study, it received very positive evaluation and was recommended for further development and demonstration. ACCURATE employs the occultation measurement principle, known for its unique combination of high vertical resolution, accuracy and long-term stability, in a novel way. It systematically combines use of highly stable signals in the MW 17-23/178-196 GHz bands (LEO-LEO MW crosslink occultation) with laser signals in the SWIR 2-2.5 μm band (LEO-LEO IR laser crosslink occultation) for exploring and monitoring climate and chemistry in the atmosphere with focus on the UTLS region (upper troposphere/lower stratosphere, 5-35 km). The MW occultation is an advanced and at the same time compact version of the LEO-LEO MW occultation concept, studied in 2002-2004 for the ACE+ mission project of ESA for frequencies including the 17-23 GHz band, complemented by U.S. study heritage for frequencies including the 178-196 GHz bands (R. Kursinski et al., Univ. of Arizona, Tucson). The core of ACCURATE is tight synergy of the IR laser crosslinks with the MW crosslinks. The observed parameters, obtained simultaneously and in a self-calibrated manner based on Doppler shift and differential log-transmission profiles, comprise the fundamental thermodynamic variables of the atmosphere (temperature, pressure/geopotential height, humidity) retrieved from the MW bands, complemented by line-of-sight wind, six greenhouse gases (GHGs) and key species of UTLS chemistry (H2O, CO2, CH4, N2O, O3, CO) and four CO2 and H2O isotopes (HDO, H218O, 13CO2, C18OO) from the SWIR band. Furthermore, profiles of

  5. An accurate model for predicting high frequency noise of nanoscale NMOS SOI transistors

    NASA Astrophysics Data System (ADS)

    Shen, Yanfei; Cui, Jie; Mohammadi, Saeed

    2017-05-01

    A nonlinear and scalable model suitable for predicting high frequency noise of N-type Metal Oxide Semiconductor (NMOS) transistors is presented. The model is developed for a commercial 45 nm CMOS SOI technology and its accuracy is validated through comparison with measured performance of a microwave low noise amplifier. The model employs the virtual source nonlinear core and adds parasitic elements to accurately simulate the RF behavior of multi-finger NMOS transistors up to 40 GHz. For the first time, the traditional long-channel thermal noise model is supplemented with an injection noise model to accurately represent the noise behavior of these short-channel transistors up to 26 GHz. The developed model is simple and easy to extract, yet very accurate.

  6. Protein Stable Isotope Fingerprinting (P-SIF): A New Tool to Understand Natural Isotopic Heterogeneity of Mixed Microbial Ecosystems

    NASA Astrophysics Data System (ADS)

    Pearson, A.; Mohr, W.; Tang, T.; Sattin, S.; Bovee, R.

    2014-12-01

    Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determining the ratios of 13C/12C (values of δ13C) for different taxonomic divisions, and (ii) using those values as clues to the metabolic pathways employed by the respective organisms, while (iii) not perturbing the system, i.e., not adding exogenous substrates or isotope labels. To accomplish this, we employ two-dimensional HPLC to resolve a sample containing ca. 5-10 mg of mixed proteins into 960-1440 fractions. Each fraction then is split in two aliquots: The first is digested with trypsin for peptide sequencing, while the second is measured in triplicate using an isotope-ratio mass spectrometer interfaced with a spooling wire microcombustion device. Data from pure cultures show that bacteria have a narrow distribution of protein δ13C values within individual taxa (±0.7-1.2‰, 1σ). This is moderately larger than the mean precision of the triplicate isotope measurements (±0.5‰, 1σ) and may reflect heterogeneous distribution of 13C among the amino acids. When cells from different species are mixed together prior to protein extraction and separation, the results can predict accurately (to within ±1σ) the δ13C values of the original taxa. The number of data points required for this endmember prediction is ≥20/taxon, yielding a theoretical resolution of ca. 10 taxonomic units/sample. Initial tests on environmental samples suggest the approach will be useful to determine the overall trophic breadth of mixed microbial ecosystems.

  7. Fast and Accurate Prediction of Stratified Steel Temperature During Holding Period of Ladle

    NASA Astrophysics Data System (ADS)

    Deodhar, Anirudh; Singh, Umesh; Shukla, Rishabh; Gautham, B. P.; Singh, Amarendra K.

    2017-04-01

    Thermal stratification of liquid steel in a ladle during the holding period and the teeming operation has a direct bearing on the superheat available at the caster and hence on the caster set points such as casting speed and cooling rates. The changes in the caster set points are typically carried out based on temperature measurements at the end of tundish outlet. Thermal prediction models provide advance knowledge of the influence of process and design parameters on the steel temperature at various stages. Therefore, they can be used in making accurate decisions about the caster set points in real time. However, this requires both fast and accurate thermal prediction models. In this work, we develop a surrogate model for the prediction of thermal stratification using data extracted from a set of computational fluid dynamics (CFD) simulations, pre-determined using design of experiments technique. Regression method is used for training the predictor. The model predicts the stratified temperature profile instantaneously, for a given set of process parameters such as initial steel temperature, refractory heat content, slag thickness, and holding time. More than 96 pct of the predicted values are within an error range of ±5 K (±5 °C), when compared against corresponding CFD results. Considering its accuracy and computational efficiency, the model can be extended for thermal control of casting operations. This work also sets a benchmark for developing similar thermal models for downstream processes such as tundish and caster.

  8. Competitive Abilities in Experimental Microcosms Are Accurately Predicted by a Demographic Index for R*

    PubMed Central

    Murrell, Ebony G.; Juliano, Steven A.

    2012-01-01

    Resource competition theory predicts that R*, the equilibrium resource amount yielding zero growth of a consumer population, should predict species' competitive abilities for that resource. This concept has been supported for unicellular organisms, but has not been well-tested for metazoans, probably due to the difficulty of raising experimental populations to equilibrium and measuring population growth rates for species with long or complex life cycles. We developed an index (Rindex) of R* based on demography of one insect cohort, growing from egg to adult in a non-equilibrium setting, and tested whether Rindex yielded accurate predictions of competitive abilities using mosquitoes as a model system. We estimated finite rate of increase (λ′) from demographic data for cohorts of three mosquito species raised with different detritus amounts, and estimated each species' Rindex using nonlinear regressions of λ′ vs. initial detritus amount. All three species' Rindex differed significantly, and accurately predicted competitive hierarchy of the species determined in simultaneous pairwise competition experiments. Our Rindex could provide estimates and rigorous statistical comparisons of competitive ability for organisms for which typical chemostat methods and equilibrium population conditions are impractical. PMID:22970128

  9. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

    PubMed Central

    Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

    2017-01-01

    Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

  10. SIFTER search: a web server for accurate phylogeny-based protein function prediction

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

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

  11. SIFTER search: a web server for accurate phylogeny-based protein function prediction

    DOE PAGES

    Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

    2015-05-15

    We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

  12. XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks.

    PubMed

    Zaretzki, Jed; Matlock, Matthew; Swamidass, S Joshua

    2013-12-23

    Understanding how xenobiotic molecules are metabolized is important because it influences the safety, efficacy, and dose of medicines and how they can be modified to improve these properties. The cytochrome P450s (CYPs) are proteins responsible for metabolizing 90% of drugs on the market, and many computational methods can predict which atomic sites of a molecule--sites of metabolism (SOMs)--are modified during CYP-mediated metabolism. This study improves on prior methods of predicting CYP-mediated SOMs by using new descriptors and machine learning based on neural networks. The new method, XenoSite, is faster to train and more accurate by as much as 4% or 5% for some isozymes. Furthermore, some "incorrect" predictions made by XenoSite were subsequently validated as correct predictions by revaluation of the source literature. Moreover, XenoSite output is interpretable as a probability, which reflects both the confidence of the model that a particular atom is metabolized and the statistical likelihood that its prediction for that atom is correct.

  13. An Investigation into the Relationship Between Distillate Yield and Stable Isotope Fractionation

    NASA Astrophysics Data System (ADS)

    Sowers, T.; Wagner, A. J.

    2016-12-01

    Recent breakthroughs in laser spectrometry have allowed for faster, more efficient analyses of stable isotopic ratios in water samples. Commercially available instruments from Los Gatos Research and Picarro allow users to quickly analyze a wide range of samples, from seawater to groundwater, with accurate isotope ratios of D/H to within ± 0.2 ‰ and 18O/16O to within ± 0.03 ‰. While these instruments have increased the efficiency of stable isotope laboratories, they come with some major limitations, such as not being able to analyze hypersaline waters. The Los Gatos Research Liquid Water Isotope Analyzer (LWIA) can accurately and consistently measure the stable isotope ratios in waters with salinities ranging from 0 to 4 grams per liter (0 to 40 parts per thousand). In order to analyze water samples with salinities greater than 4 grams per liter, however, it was necessary to develop a consistent method through which to reduce salinity while causing as little fractionation as possible. Using a consistent distillation method, predictable fractionation of δ 18O and δ 2 H values was found to occur. This fractionation occurs according to a linear relationship with respect to the percent yield of the water in the sample. Using this method, samples with high salinity can be analyzed using laser spectrometry instruments, thereby enabling laboratories with Los Gatos or Picarro instruments to analyze those samples in house without having to dilute them using labor-intensive in-house standards or expensive premade standards.

  14. Regional prediction of carbon isotopes in soil carbonates for Asian dust source tracer

    NASA Astrophysics Data System (ADS)

    Chen, Bing; Cui, Xinjuan; Wang, Yaqiang

    2016-10-01

    Dust particles emitted from deserts and semi-arid lands in northern China cause particulate pollution that increases the burden of disease particularly for urban population in East Asia. The stable carbon isotopes (δ13C) of carbonates in soils and dust aerosols in northern China were investigated. We found that the δ13C of carbonates in surface soils in northern China showed clearly the negative correlation (R2 = 0.73) with Normalized Difference Vegetation Index (NDVI). Using Moderate Resolution Imaging Spectroradiometer (MODIS) satellite-derived NDVI, we predicted the regional distribution of δ13C of soil carbonates in deserts, sandy lands, and steppe areas. The predictions show the mean δ13C of -0.4 ± 0.7‰ in soil carbonates in Taklimakan Desert and Gobi Deserts, and the isotope values decrease to -3.3 ± 1.1‰ in sandy lands. The increase in vegetation coverage depletes 13C in soil carbonates, thus the steppe areas are predicted by the lowest δ13C levels (-8.1 ± 1.7‰). The measurements of atmospheric dust samples at eight sites showed that the Asian dust sources were well assigned by the 13C mapping in surface soils. Predicting 13C in large geographical areas with fine resolution offers a cost-effective tracer to monitor dust emissions from sandy lands and steppe areas which show an increasing role in Asian dust loading driven by climate change and human activities.

  15. Accurate prediction of personalized olfactory perception from large-scale chemoinformatic features.

    PubMed

    Li, Hongyang; Panwar, Bharat; Omenn, Gilbert S; Guan, Yuanfang

    2018-02-01

    The olfactory stimulus-percept problem has been studied for more than a century, yet it is still hard to precisely predict the odor given the large-scale chemoinformatic features of an odorant molecule. A major challenge is that the perceived qualities vary greatly among individuals due to different genetic and cultural backgrounds. Moreover, the combinatorial interactions between multiple odorant receptors and diverse molecules significantly complicate the olfaction prediction. Many attempts have been made to establish structure-odor relationships for intensity and pleasantness, but no models are available to predict the personalized multi-odor attributes of molecules. In this study, we describe our winning algorithm for predicting individual and population perceptual responses to various odorants in the DREAM Olfaction Prediction Challenge. We find that random forest model consisting of multiple decision trees is well suited to this prediction problem, given the large feature spaces and high variability of perceptual ratings among individuals. Integrating both population and individual perceptions into our model effectively reduces the influence of noise and outliers. By analyzing the importance of each chemical feature, we find that a small set of low- and nondegenerative features is sufficient for accurate prediction. Our random forest model successfully predicts personalized odor attributes of structurally diverse molecules. This model together with the top discriminative features has the potential to extend our understanding of olfactory perception mechanisms and provide an alternative for rational odorant design.

  16. A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).

    PubMed

    Stacey, R Greg; Skinnider, Michael A; Scott, Nichollas E; Foster, Leonard J

    2017-10-23

    An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to assess protein interactions. However, given the vast number of protein complexes, more scalable methods are necessary to accelerate interaction discovery and to construct whole interactomes. We recently developed a complementary technique based on the use of protein correlation profiling (PCP) and stable isotope labeling in amino acids in cell culture (SILAC) to assess chromatographic co-elution as evidence of interacting proteins. Importantly, PCP-SILAC is also capable of measuring protein interactions simultaneously under multiple biological conditions, allowing the detection of treatment-specific changes to an interactome. Given the uniqueness and high dimensionality of co-elution data, new tools are needed to compare protein elution profiles, control false discovery rates, and construct an accurate interactome. Here we describe a freely available bioinformatics pipeline, PrInCE, for the analysis of co-elution data. PrInCE is a modular, open-source library that is computationally inexpensive, able to use label and label-free data, and capable of detecting tens of thousands of protein-protein interactions. Using a machine learning approach, PrInCE offers greatly reduced run time, more predicted interactions at the same stringency, prediction of protein complexes, and greater ease of use over previous bioinformatics tools for co-elution data. PrInCE is implemented in Matlab (version R2017a). Source code and standalone executable programs for Windows and Mac OSX are available at https://github.com/fosterlab/PrInCE , where usage instructions can be found. An example dataset and output are also provided for testing purposes. PrInCE is the first fast and easy

  17. A Critical Review for Developing Accurate and Dynamic Predictive Models Using Machine Learning Methods in Medicine and Health Care.

    PubMed

    Alanazi, Hamdan O; Abdullah, Abdul Hanan; Qureshi, Kashif Naseer

    2017-04-01

    Recently, Artificial Intelligence (AI) has been used widely in medicine and health care sector. In machine learning, the classification or prediction is a major field of AI. Today, the study of existing predictive models based on machine learning methods is extremely active. Doctors need accurate predictions for the outcomes of their patients' diseases. In addition, for accurate predictions, timing is another significant factor that influences treatment decisions. In this paper, existing predictive models in medicine and health care have critically reviewed. Furthermore, the most famous machine learning methods have explained, and the confusion between a statistical approach and machine learning has clarified. A review of related literature reveals that the predictions of existing predictive models differ even when the same dataset is used. Therefore, existing predictive models are essential, and current methods must be improved.

  18. Ensemble predictive model for more accurate soil organic carbon spectroscopic estimation

    NASA Astrophysics Data System (ADS)

    Vašát, Radim; Kodešová, Radka; Borůvka, Luboš

    2017-07-01

    A myriad of signal pre-processing strategies and multivariate calibration techniques has been explored in attempt to improve the spectroscopic prediction of soil organic carbon (SOC) over the last few decades. Therefore, to come up with a novel, more powerful, and accurate predictive approach to beat the rank becomes a challenging task. However, there may be a way, so that combine several individual predictions into a single final one (according to ensemble learning theory). As this approach performs best when combining in nature different predictive algorithms that are calibrated with structurally different predictor variables, we tested predictors of two different kinds: 1) reflectance values (or transforms) at each wavelength and 2) absorption feature parameters. Consequently we applied four different calibration techniques, two per each type of predictors: a) partial least squares regression and support vector machines for type 1, and b) multiple linear regression and random forest for type 2. The weights to be assigned to individual predictions within the ensemble model (constructed as a weighted average) were determined by an automated procedure that ensured the best solution among all possible was selected. The approach was tested at soil samples taken from surface horizon of four sites differing in the prevailing soil units. By employing the ensemble predictive model the prediction accuracy of SOC improved at all four sites. The coefficient of determination in cross-validation (R2cv) increased from 0.849, 0.611, 0.811 and 0.644 (the best individual predictions) to 0.864, 0.650, 0.824 and 0.698 for Site 1, 2, 3 and 4, respectively. Generally, the ensemble model affected the final prediction so that the maximal deviations of predicted vs. observed values of the individual predictions were reduced, and thus the correlation cloud became thinner as desired.

  19. Simulation of dual carbon-bromine stable isotope fractionation during 1,2-dibromoethane degradation.

    PubMed

    Jin, Biao; Nijenhuis, Ivonne; Rolle, Massimo

    2018-06-01

    We performed a model-based investigation to simultaneously predict the evolution of concentration, as well as stable carbon and bromine isotope fractionation during 1,2-dibromoethane (EDB, ethylene dibromide) transformation in a closed system. The modelling approach considers bond-cleavage mechanisms during different reactions and allows evaluating dual carbon-bromine isotopic signals for chemical and biotic reactions, including aerobic and anaerobic biological transformation, dibromoelimination by Zn(0) and alkaline hydrolysis. The proposed model allowed us to accurately simulate the evolution of concentrations and isotope data observed in a previous laboratory study and to successfully identify different reaction pathways. Furthermore, we illustrated the model capabilities in degradation scenarios involving complex reaction systems. Specifically, we examined (i) the case of sequential multistep transformation of EDB and the isotopic evolution of the parent compound, the intermediate and the reaction product and (ii) the case of parallel competing abiotic pathways of EDB transformation in alkaline solution.

  20. A large column analog experiment of stable isotope variations during reactive transport: I. A comprehensive model of sulfur cycling and δ34S fractionation

    NASA Astrophysics Data System (ADS)

    Druhan, Jennifer L.; Steefel, Carl I.; Conrad, Mark E.; DePaolo, Donald J.

    2014-01-01

    This study demonstrates a mechanistic incorporation of the stable isotopes of sulfur within the CrunchFlow reactive transport code to model the range of microbially-mediated redox processes affecting kinetic isotope fractionation. Previous numerical models of microbially mediated sulfate reduction using Monod-type rate expressions have lacked rigorous coupling of individual sulfur isotopologue rates, with the result that they cannot accurately simulate sulfur isotope fractionation over a wide range of substrate concentrations using a constant fractionation factor. Here, we derive a modified version of the dual-Monod or Michaelis-Menten formulation (Maggi and Riley, 2009, 2010) that successfully captures the behavior of the 32S and 34S isotopes over a broad range from high sulfate and organic carbon availability to substrate limitation using a constant fractionation factor. The new model developments are used to simulate a large-scale column study designed to replicate field scale conditions of an organic carbon (acetate) amended biostimulation experiment at the Old Rifle site in western Colorado. Results demonstrate an initial period of iron reduction that transitions to sulfate reduction, in agreement with field-scale behavior observed at the Old Rifle site. At the height of sulfate reduction, effluent sulfate concentrations decreased to 0.5 mM from an influent value of 8.8 mM over the 100 cm flow path, and thus were enriched in sulfate δ34S from 6.3‰ to 39.5‰. The reactive transport model accurately reproduced the measured enrichment in δ34S of both the reactant (sulfate) and product (sulfide) species of the reduction reaction using a single fractionation factor of 0.987 obtained independently from field-scale measurements. The model also accurately simulated the accumulation and δ34S signature of solid phase elemental sulfur over the duration of the experiment, providing a new tool to predict the isotopic signatures associated with reduced mineral pools

  1. Physics of the Isotopic Dependence of Galactic Cosmic Ray Fluence Behind Shielding

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Saganti, Premkumar B.; Hu, Xiao-Dong; Kim, Myung-Hee Y.; Cleghorn, Timothy F.; Wilson, John W.; Tripathi, Ram K.; Zeitlin, Cary J.

    2003-01-01

    For over 25 years, NASA has supported the development of space radiation transport models for shielding applications. The NASA space radiation transport model now predicts dose and dose equivalent in Earth and Mars orbit to an accuracy of plus or minus 20%. However, because larger errors may occur in particle fluence predictions, there is interest in further assessments and improvements in NASA's space radiation transport model. In this paper, we consider the effects of the isotopic composition of the primary galactic cosmic rays (GCR) and the isotopic dependence of nuclear fragmentation cross-sections on the solution to transport models used for shielding studies. Satellite measurements are used to describe the isotopic composition of the GCR. Using NASA's quantum multiple-scattering theory of nuclear fragmentation (QMSFRG) and high-charge and energy (HZETRN) transport code, we study the effect of the isotopic dependence of the primary GCR composition and secondary nuclei on shielding calculations. The QMSFRG is shown to accurately describe the iso-spin dependence of nuclear fragmentation. The principal finding of this study is that large errors (plus or minus 100%) will occur in the mass-fluence spectra when comparing transport models that use a complete isotope grid (approximately 170 ions) to ones that use a reduced isotope grid, for example the 59 ion-grid used in the HZETRN code in the past, however less significant errors (less than 20%) occur in the elemental-fluence spectra. Because a complete isotope grid is readily handled on small computer workstations and is needed for several applications studying GCR propagation and scattering, it is recommended that they be used for future GCR studies.

  2. Towards First Principles-Based Prediction of Highly Accurate Electrochemical Pourbaix Diagrams

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

    Zeng, Zhenhua; Chan, Maria K. Y.; Zhao, Zhi-Jian

    2015-08-13

    Electrochemical potential/pH (Pourbaix) diagrams underpin many aqueous electrochemical processes and are central to the identification of stable phases of metals for processes ranging from electrocatalysis to corrosion. Even though standard DFT calculations are potentially powerful tools for the prediction of such diagrams, inherent errors in the description of transition metal (hydroxy)oxides, together with neglect of van der Waals interactions, have limited the reliability of such predictions for even the simplest pure metal bulk compounds, and corresponding predictions for more complex alloy or surface structures are even more challenging. In the present work, through synergistic use of a Hubbard U correction,more » a state-of-the-art dispersion correction, and a water-based bulk reference state for the calculations, these errors are systematically corrected. The approach describes the weak binding that occurs between hydroxyl-containing functional groups in certain compounds in Pourbaix diagrams, corrects for self-interaction errors in transition metal compounds, and reduces residual errors on oxygen atoms by preserving a consistent oxidation state between the reference state, water, and the relevant bulk phases. The strong performance is illustrated on a series of bulk transition metal (Mn, Fe, Co and Ni) hydroxides, oxyhydroxides, binary, and ternary oxides, where the corresponding thermodynamics of redox and (de)hydration are described with standard errors of 0.04 eV per (reaction) formula unit. The approach further preserves accurate descriptions of the overall thermodynamics of electrochemically-relevant bulk reactions, such as water formation, which is an essential condition for facilitating accurate analysis of reaction energies for electrochemical processes on surfaces. The overall generality and transferability of the scheme suggests that it may find useful application in the construction of a broad array of electrochemical phase diagrams, including

  3. Platinum isotopes in iron meteorites: Galactic cosmic ray effects and nucleosynthetic homogeneity in the p-process isotope 190Pt and the other platinum isotopes

    NASA Astrophysics Data System (ADS)

    Hunt, Alison C.; Ek, Mattias; Schönbächler, Maria

    2017-11-01

    Platinum isotopes are sensitive to the effects of galactic cosmic rays (GCR), which can alter isotope ratios and mask nucleosynthetic isotope variations. Platinum also features one p-process isotope, 190Pt, which is very low abundance and therefore challenging to analyse. Platinum-190 is relevant for early solar-system chronology because of its decay to 186Os. Here, we present new Pt isotope data for five iron meteorite groups (IAB, IIAB, IID, IIIAB and IVA), including high-precision measurements of 190Pt for the IAB, IIAB and IIIAB irons, determined by multi-collector ICPMS. New data are in good agreement with previous studies and display correlations between different Pt isotopes. The slopes of these correlations are well-reproduced by the available GCR models. We report Pt isotope ratios for the IID meteorite Carbo that are consistently higher than the predicted effects from the GCR model. This suggests that the model predictions do not fully account for all the GCR effects on Pt isotopes, but also that the pre-atmospheric radii and exposure times calculated for Carbo may be incorrect. Despite this, the good agreement of relative effects in Pt isotopes with the predicted GCR trends confirms that Pt isotopes are a useful in-situ neutron dosimeter. Once GCR effects are accounted for, our new dataset reveals s- and r-process homogeneity between the iron meteorite groups studied here and the Earth. New 190Pt data for the IAB, IIAB and IIIAB iron meteorites indicate the absence of GCR effects and homogeneity in the p-process isotope between these groups and the Earth. This corresponds well with results from other heavy p-process isotopes and suggests their homogenous distribution in the inner solar system, although it does not exclude that potential p-process isotope variations are too diluted to be currently detectable.

  4. Stable isotope turnover and half-life in animal tissues: a literature synthesis.

    PubMed

    Vander Zanden, M Jake; Clayton, Murray K; Moody, Eric K; Solomon, Christopher T; Weidel, Brian C

    2015-01-01

    Stable isotopes of carbon, nitrogen, and sulfur are used as ecological tracers for a variety of applications, such as studies of animal migrations, energy sources, and food web pathways. Yet uncertainty relating to the time period integrated by isotopic measurement of animal tissues can confound the interpretation of isotopic data. There have been a large number of experimental isotopic diet shift studies aimed at quantifying animal tissue isotopic turnover rate λ (%·day(-1), often expressed as isotopic half-life, ln(2)/λ, days). Yet no studies have evaluated or summarized the many individual half-life estimates in an effort to both seek broad-scale patterns and characterize the degree of variability. Here, we collect previously published half-life estimates, examine how half-life is related to body size, and test for tissue- and taxa-varying allometric relationships. Half-life generally increases with animal body mass, and is longer in muscle and blood compared to plasma and internal organs. Half-life was longest in ecotherms, followed by mammals, and finally birds. For ectotherms, different taxa-tissue combinations had similar allometric slopes that generally matched predictions of metabolic theory. Half-life for ectotherms can be approximated as: ln (half-life) = 0.22*ln (body mass) + group-specific intercept; n = 261, p<0.0001, r2 = 0.63. For endothermic groups, relationships with body mass were weak and model slopes and intercepts were heterogeneous. While isotopic half-life can be approximated using simple allometric relationships for some taxa and tissue types, there is also a high degree of unexplained variation in our models. Our study highlights several strong and general patterns, though accurate prediction of isotopic half-life from readily available variables such as animal body mass remains elusive.

  5. Oxygen isotopes in nitrite: Analysis, calibration, and equilibration

    USGS Publications Warehouse

    Casciotti, K.L.; Böhlke, J.K.; McIlvin, M.R.; Mroczkowski, S.J.; Hannon, J.E.

    2007-01-01

    Nitrite is a central intermediate in the nitrogen cycle and can persist in significant concentrations in ocean waters, sediment pore waters, and terrestrial groundwaters. To fully interpret the effect of microbial processes on nitrate (NO3-), nitrite (NO2-), and nitrous oxide (N2O) cycling in these systems, the nitrite pool must be accessible to isotopic analysis. Furthermore, because nitrite interferes with most methods of nitrate isotopic analysis, accurate isotopic analysis of nitrite is essential for correct measurement of nitrate isotopes in a sample that contains nitrite. In this study, nitrite salts with varying oxygen isotopic compositions were prepared and calibrated and then used to test the denitrifier method for nitrite oxygen isotopic analysis. The oxygen isotopic fractionation during nitrite reduction to N2O by Pseudomonas aureofaciens was lower than for nitrate conversion to N2O, while oxygen isotopic exchange between nitrite and water during the reaction was similar. These results enable the extension of the denitrifier method to oxygen isotopic analysis of nitrite (in the absence of nitrate) and correction of nitrate isotopes for the presence of nitrite in “mixed” samples. We tested storage conditions for seawater and freshwater samples that contain nitrite and provide recommendations for accurate oxygen isotopic analysis of nitrite by any method. Finally, we report preliminary results on the equilibrium isotope effect between nitrite and water, which can play an important role in determining the oxygen isotopic value of nitrite where equilibration with water is significant.

  6. Highly accurate prediction of emotions surrounding the attacks of September 11, 2001 over 1-, 2-, and 7-year prediction intervals.

    PubMed

    Doré, Bruce P; Meksin, Robert; Mather, Mara; Hirst, William; Ochsner, Kevin N

    2016-06-01

    In the aftermath of a national tragedy, important decisions are predicated on judgments of the emotional significance of the tragedy in the present and future. Research in affective forecasting has largely focused on ways in which people fail to make accurate predictions about the nature and duration of feelings experienced in the aftermath of an event. Here we ask a related but understudied question: can people forecast how they will feel in the future about a tragic event that has already occurred? We found that people were strikingly accurate when predicting how they would feel about the September 11 attacks over 1-, 2-, and 7-year prediction intervals. Although people slightly under- or overestimated their future feelings at times, they nonetheless showed high accuracy in forecasting (a) the overall intensity of their future negative emotion, and (b) the relative degree of different types of negative emotion (i.e., sadness, fear, or anger). Using a path model, we found that the relationship between forecasted and actual future emotion was partially mediated by current emotion and remembered emotion. These results extend theories of affective forecasting by showing that emotional responses to an event of ongoing national significance can be predicted with high accuracy, and by identifying current and remembered feelings as independent sources of this accuracy. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  7. Highly accurate prediction of emotions surrounding the attacks of September 11, 2001 over 1-, 2-, and 7-year prediction intervals

    PubMed Central

    Doré, B.P.; Meksin, R.; Mather, M.; Hirst, W.; Ochsner, K.N

    2016-01-01

    In the aftermath of a national tragedy, important decisions are predicated on judgments of the emotional significance of the tragedy in the present and future. Research in affective forecasting has largely focused on ways in which people fail to make accurate predictions about the nature and duration of feelings experienced in the aftermath of an event. Here we ask a related but understudied question: can people forecast how they will feel in the future about a tragic event that has already occurred? We found that people were strikingly accurate when predicting how they would feel about the September 11 attacks over 1-, 2-, and 7-year prediction intervals. Although people slightly under- or overestimated their future feelings at times, they nonetheless showed high accuracy in forecasting 1) the overall intensity of their future negative emotion, and 2) the relative degree of different types of negative emotion (i.e., sadness, fear, or anger). Using a path model, we found that the relationship between forecasted and actual future emotion was partially mediated by current emotion and remembered emotion. These results extend theories of affective forecasting by showing that emotional responses to an event of ongoing national significance can be predicted with high accuracy, and by identifying current and remembered feelings as independent sources of this accuracy. PMID:27100309

  8. Hydrogen and Oxygen Isotope Ratios in Body Water and Hair: Modeling Isotope Dynamics in Nonhuman Primates

    PubMed Central

    O’Grady, Shannon P.; Valenzuela, Luciano O.; Remien, Christopher H.; Enright, Lindsey E.; Jorgensen, Matthew J.; Kaplan, Jay R.; Wagner, Janice D.; Cerling, Thure E.; Ehleringer, James R.

    2012-01-01

    The stable isotopic composition of drinking water, diet, and atmospheric oxygen influence the isotopic composition of body water (2H/1H, 18O/16O expressed as δ2H and δ18O). In turn, body water influences the isotopic composition of organic matter in tissues, such as hair and teeth, which are often used to reconstruct historical dietary and movement patterns of animals and humans. Here, we used a nonhuman primate system (Macaca fascicularis) to test the robustness of two different mechanistic stable isotope models: a model to predict the δ2H and δ18O values of body water and a second model to predict the δ2H and δ18O values of hair. In contrast to previous human-based studies, use of nonhuman primates fed controlled diets allowed us to further constrain model parameter values and evaluate model predictions. Both models reliably predicted the δ2H and δ18O values of body water and of hair. Moreover, the isotope data allowed us to better quantify values for two critical variables in the models: the δ2H and δ18O values of gut water and the 18O isotope fractionation associated with a carbonyl oxygen-water interaction in the gut (αow). Our modeling efforts indicated that better predictions for body water and hair isotope values were achieved by making the isotopic composition of gut water approached that of body water. Additionally, the value of αow was 1.0164, in close agreement with the only other previously measured observation (microbial spore cell walls), suggesting robustness of this fractionation factor across different biological systems. PMID:22553163

  9. pH-dependent equilibrium isotope fractionation associated with the compound specific nitrogen and carbon isotope analysis of substituted anilines by SPME-GC/IRMS.

    PubMed

    Skarpeli-Liati, Marita; Turgeon, Aurora; Garr, Ashley N; Arnold, William A; Cramer, Christopher J; Hofstetter, Thomas B

    2011-03-01

    Solid-phase microextraction (SPME) coupled to gas chromatography/isotope ratio mass spectrometry (GC/IRMS) was used to elucidate the effects of N-atom protonation on the analysis of N and C isotope signatures of selected aromatic amines. Precise and accurate isotope ratios were measured using polydimethylsiloxane/divinylbenzene (PDMS/DVB) as the SPME fiber material at solution pH-values that exceeded the pK(a) of the substituted aniline's conjugate acid by two pH-units. Deviations of δ(15)N and δ(13)C-values from reference measurements by elemental analyzer IRMS were small (<0.9‰) and within the typical uncertainties of isotope ratio measurements by SPME-GC/IRMS. Under these conditions, the detection limits for accurate isotope ratio measurements were between 0.64 and 2.1 mg L(-1) for δ(15)N and between 0.13 and 0.54 mg L(-1) for δ(13)C, respectively. Substantial inverse N isotope fractionation was observed by SPME-GC/IRMS as the fraction of protonated species increased with decreasing pH leading to deviations of -20‰ while the corresponding δ(13)C-values were largely invariant. From isotope ratio analysis at different solution pHs and theoretical calculations by density functional theory, we derived equilibrium isotope effects, EIEs, pertinent to aromatic amine protonation of 0.980 and 1.001 for N and C, respectively, which were very similar for all compounds investigated. Our work shows that N-atom protonation can compromise accurate compound-specific N isotope analysis of aromatic amines.

  10. Ultrahigh thermal conductivity of isotopically enriched silicon

    NASA Astrophysics Data System (ADS)

    Inyushkin, Alexander V.; Taldenkov, Alexander N.; Ager, Joel W.; Haller, Eugene E.; Riemann, Helge; Abrosimov, Nikolay V.; Pohl, Hans-Joachim; Becker, Peter

    2018-03-01

    Most of the stable elements have two and more stable isotopes. The physical properties of materials composed of such elements depend on the isotopic abundance to some extent. A remarkably strong isotope effect is observed in the phonon thermal conductivity, the principal mechanism of heat conduction in nonmetallic crystals. An isotopic disorder due to random distribution of the isotopes in the crystal lattice sites results in a rather strong phonon scattering and, consequently, in a reduction of thermal conductivity. In this paper, we present new results of accurate and precise measurements of thermal conductivity κ(T) for silicon single crystals having three different isotopic compositions at temperatures T from 2.4 to 420 K. The highly enriched crystal containing 99.995% of 28Si, which is one of the most perfect crystals ever synthesized, demonstrates a thermal conductivity of about 450 ± 10 W cm-1 K-1 at 24 K, the highest measured value among bulk dielectrics, which is ten times greater than the one for its counterpart natSi with the natural isotopic constitution. For highly enriched crystal 28Si and crystal natSi, the measurements were performed for two orientations [001] and [011], a magnitude of the phonon focusing effect on thermal conductivity was determined accurately at low temperatures. The anisotropy of thermal conductivity disappears above 31 K. The influence of the boundary scattering on thermal conductivity persists sizable up to much higher temperatures (˜80 K). The κ(T) measured in this work gives the most accurate approximation of the intrinsic thermal conductivity of single crystal silicon which is determined solely by the anharmonic phonon processes and diffusive boundary scattering over a wide temperature range.

  11. High Order Schemes in Bats-R-US for Faster and More Accurate Predictions

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Toth, G.; Gombosi, T. I.

    2014-12-01

    BATS-R-US is a widely used global magnetohydrodynamics model that originally employed second order accurate TVD schemes combined with block based Adaptive Mesh Refinement (AMR) to achieve high resolution in the regions of interest. In the last years we have implemented fifth order accurate finite difference schemes CWENO5 and MP5 for uniform Cartesian grids. Now the high order schemes have been extended to generalized coordinates, including spherical grids and also to the non-uniform AMR grids including dynamic regridding. We present numerical tests that verify the preservation of free-stream solution and high-order accuracy as well as robust oscillation-free behavior near discontinuities. We apply the new high order accurate schemes to both heliospheric and magnetospheric simulations and show that it is robust and can achieve the same accuracy as the second order scheme with much less computational resources. This is especially important for space weather prediction that requires faster than real time code execution.

  12. The Submillimeter Wave Spectrum of Isotopic Methyl Cyanide

    NASA Technical Reports Server (NTRS)

    Pearson, J. C.; Mueller, H. S. P.

    1996-01-01

    The laboratory submillimeter wave rotational spectrum of the 13CH3CN, CH3C13CN, and CH3C15N isotopomers of methyl cyanide has been observed in natural abundance in the 294 to 607 GHz region. The maximum J and K values are 34 and 14, respectively. Fifteen additional CH3CN transitions up to K = 21 were also measured. The transitions of all four species are fitted to a symmetric top Hamiltonian, and the rotation and distortion constants are determined. The 14N quadrupole and spin rotation coupling constants are also calculated and presented. Suggested values for many other parameters, which could not be directly determined from the isotope spectra, are calculated from the normal species values and isotope relationships. The determined and calculated constants should predict the spectrum of the three isotopomers to well over 1 THz accurately enough for astronomical assignments.

  13. Extrinsic labeling method may not accurately measure Fe absorption from cooked pinto beans (Phaseolus vulgaris): comparison of extrinsic and intrinsic labeling of beans.

    PubMed

    Jin, Fuxia; Cheng, Zhiqiang; Rutzke, Michael A; Welch, Ross M; Glahn, Raymond P

    2008-08-27

    Isotopic labeling of food has been widely used for the measurement of Fe absorption in determining requirements and evaluating the factors involved in Fe bioavailability. An extrinsic labeling technique will not accurately predict the total Fe absorption from foods unless complete isotopic exchange takes place between an extrinsically added isotope label and the intrinsic Fe of the food. We examined isotopic exchange in the case of both white beans and colored beans (Phaseolus vulgaris) with an in vitro digestion model. There are significant differences in (58)Fe/(56)Fe ratios between the sample digest supernatant and the pellet of extrinsically labeled pinto bean. The white bean digest shows significantly better equilibration of the extrinsic (58)Fe with the intrinsic (56)Fe. In contrast to the extrinsically labeled samples, both white and red beans labeled intrinsically with (58)Fe demonstrated consistent ratios of (58)Fe/(56)Fe in the bean meal, digest, supernatant, and pellet. It is possible that the polyphenolics in the bean seed coat may bind Fe and thus interfere with extrinsic labeling of the bean meals. These observations raise questions on the accuracy of studies that used extrinsic tags to measure Fe absorption from beans. Intrinsic labeling appears necessary to accurately measure Fe bioavailability from beans.

  14. Accurate high-throughput structure mapping and prediction with transition metal ion FRET

    PubMed Central

    Yu, Xiaozhen; Wu, Xiongwu; Bermejo, Guillermo A.; Brooks, Bernard R.; Taraska, Justin W.

    2013-01-01

    Mapping the landscape of a protein’s conformational space is essential to understanding its functions and regulation. The limitations of many structural methods have made this process challenging for most proteins. Here, we report that transition metal ion FRET (tmFRET) can be used in a rapid, highly parallel screen, to determine distances from multiple locations within a protein at extremely low concentrations. The distances generated through this screen for the protein Maltose Binding Protein (MBP) match distances from the crystal structure to within a few angstroms. Furthermore, energy transfer accurately detects structural changes during ligand binding. Finally, fluorescence-derived distances can be used to guide molecular simulations to find low energy states. Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells. PMID:23273426

  15. A Simple Plasma Retinol Isotope Ratio Method for Estimating β-Carotene Relative Bioefficacy in Humans: Validation with the Use of Model-Based Compartmental Analysis.

    PubMed

    Ford, Jennifer Lynn; Green, Joanne Balmer; Lietz, Georg; Oxley, Anthony; Green, Michael H

    2017-09-01

    Background: Provitamin A carotenoids are an important source of dietary vitamin A for many populations. Thus, accurate and simple methods for estimating carotenoid bioefficacy are needed to evaluate the vitamin A value of test solutions and plant sources. β-Carotene bioefficacy is often estimated from the ratio of the areas under plasma isotope response curves after subjects ingest labeled β-carotene and a labeled retinyl acetate reference dose [isotope reference method (IRM)], but to our knowledge, the method has not yet been evaluated for accuracy. Objectives: Our objectives were to develop and test a physiologically based compartmental model that includes both absorptive and postabsorptive β-carotene bioconversion and to use the model to evaluate the accuracy of the IRM and a simple plasma retinol isotope ratio [(RIR), labeled β-carotene-derived retinol/labeled reference-dose-derived retinol in one plasma sample] for estimating relative bioefficacy. Methods: We used model-based compartmental analysis (Simulation, Analysis and Modeling software) to develop and apply a model that provided known values for β-carotene bioefficacy. Theoretical data for 10 subjects were generated by the model and used to determine bioefficacy by RIR and IRM; predictions were compared with known values. We also applied RIR and IRM to previously published data. Results: Plasma RIR accurately predicted β-carotene relative bioefficacy at 14 d or later. IRM also accurately predicted bioefficacy by 14 d, except that, when there was substantial postabsorptive bioconversion, IRM underestimated bioefficacy. Based on our model, 1-d predictions of relative bioefficacy include absorptive plus a portion of early postabsorptive conversion. Conclusion: The plasma RIR is a simple tracer method that accurately predicts β-carotene relative bioefficacy based on analysis of one blood sample obtained at ≥14 d after co-ingestion of labeled β-carotene and retinyl acetate. The method also provides

  16. Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.

    PubMed

    Lundegaard, Claus; Lund, Ole; Nielsen, Morten

    2008-06-01

    Several accurate prediction systems have been developed for prediction of class I major histocompatibility complex (MHC):peptide binding. Most of these are trained on binding affinity data of primarily 9mer peptides. Here, we show how prediction methods trained on 9mer data can be used for accurate binding affinity prediction of peptides of length 8, 10 and 11. The method gives the opportunity to predict peptides with a different length than nine for MHC alleles where no such peptides have been measured. As validation, the performance of this approach is compared to predictors trained on peptides of the peptide length in question. In this validation, the approximation method has an accuracy that is comparable to or better than methods trained on a peptide length identical to the predicted peptides. The algorithm has been implemented in the web-accessible servers NetMHC-3.0: http://www.cbs.dtu.dk/services/NetMHC-3.0, and NetMHCpan-1.1: http://www.cbs.dtu.dk/services/NetMHCpan-1.1

  17. Hydrogen and oxygen isotope ratios in body water and hair: modeling isotope dynamics in nonhuman primates.

    PubMed

    O'Grady, Shannon P; Valenzuela, Luciano O; Remien, Christopher H; Enright, Lindsey E; Jorgensen, Matthew J; Kaplan, Jay R; Wagner, Janice D; Cerling, Thure E; Ehleringer, James R

    2012-07-01

    The stable isotopic composition of drinking water, diet, and atmospheric oxygen influence the isotopic composition of body water ((2)H/(1)H, (18)O/(16)O expressed as δ(2) H and δ(18)O). In turn, body water influences the isotopic composition of organic matter in tissues, such as hair and teeth, which are often used to reconstruct historical dietary and movement patterns of animals and humans. Here, we used a nonhuman primate system (Macaca fascicularis) to test the robustness of two different mechanistic stable isotope models: a model to predict the δ(2)H and δ(18)O values of body water and a second model to predict the δ(2)H and δ(18)O values of hair. In contrast to previous human-based studies, use of nonhuman primates fed controlled diets allowed us to further constrain model parameter values and evaluate model predictions. Both models reliably predicted the δ(2)H and δ(18)O values of body water and of hair. Moreover, the isotope data allowed us to better quantify values for two critical variables in the models: the δ(2)H and δ(18)O values of gut water and the (18)O isotope fractionation associated with a carbonyl oxygen-water interaction in the gut (α(ow)). Our modeling efforts indicated that better predictions for body water and hair isotope values were achieved by making the isotopic composition of gut water approached that of body water. Additionally, the value of α(ow) was 1.0164, in close agreement with the only other previously measured observation (microbial spore cell walls), suggesting robustness of this fractionation factor across different biological systems. © 2012 Wiley Periodicals, Inc.

  18. Predictions on the modes of decay of even Z superheavy isotopes within the range 104 ≤ Z ≤ 136

    NASA Astrophysics Data System (ADS)

    Santhosh, K. P.; Nithya, C.

    2018-01-01

    The decay modes and half lives of all the even Z isotopes of superheavy elements within the range 104 ≤ Z ≤ 136 have been predicted by comparing the alpha decay half-lives with the spontaneous fission half-lives. The Coulomb and proximity potential model for deformed nuclei (CPPMDN) and the shell-effect-dependent formula of Santhosh et al. are used to calculate the alpha half-lives and spontaneous fission half-lives respectively. For theoretical comparison the alpha decay half-lives are also calculated using Coulomb and proximity potential model (CPPM), the Viola-Seaborg-Sobiczewski semi-empirical (VSS) relation, the universal (UNIV) curve of Poenaru et al., the analytical formula of Royer and the universal decay law (UDL) of Qi et al. Another tool used for the evaluation of spontaneous fission half-lives is the semi-empirical formula of Xu et al. The nuclei with alpha decay half-lives less than spontaneous fission half-lives will survive fission and hence decay through alpha emission. The predicted half lives and decay modes are compared with the available experimental results. The one-proton and two-proton separation energies of all the isotopes are calculated to find nuclei which lie beyond the proton drip line. Among 1119 even Z nuclei within the range 104 ≤ Z ≤ 136, 164 nuclei show sequential alpha emission followed by subsequent spontaneous fission. Since the isotopes decay through alpha decay chain and the half-lives are in measurable range, these isotopes are predicted to be synthesized and detected in laboratory via alpha decay. 2 nuclei will decay by alpha decay followed by proton emission, 54 nuclei show full alpha chains, 642 nuclei will decay through spontaneous fission, 166 nuclei exhibit proton decay and 91 isotopes are found to be stable against alpha decay. All the isotopes are tabulated according to their decay modes. The study is intended to enhance further experimental investigations in superheavy region.

  19. Accurate experimental determination of the isotope effects on the triple point temperature of water. II. Combined dependence on the 18O and 17O abundances

    NASA Astrophysics Data System (ADS)

    Faghihi, V.; Kozicki, M.; Aerts-Bijma, A. T.; Jansen, H. G.; Spriensma, J. J.; Peruzzi, A.; Meijer, H. A. J.

    2015-12-01

    This paper is the second of two articles on the quantification of isotope effects on the triple point temperature of water. In this second article, we address the combined effects of 18O and 17O isotopes. We manufactured five triple point cells with waters with 18O and 17O abundances exceeding widely the natural abundance range while maintaining their natural 18O/17O relationship. The 2H isotopic abundance was kept close to that of VSMOW (Vienna Standard Mean Ocean Water). These cells realized triple point temperatures ranging between  -220 μK to 1420 μK with respect to the temperature realized by a triple point cell filled with VSMOW. Our experiment allowed us to determine an accurate and reliable value for the newly defined combined 18, 17O correction parameter of AO  =  630 μK with a combined uncertainty of 10 μK. To apply this correction, only the 18O abundance of the TPW needs to be known (and the water needs to be of natural origin). Using the results of our two articles, we recommend a correction equation along with the coefficient values for isotopic compositions differing from that of VSMOW and compare the effect of this new equation on a number of triple point cells from the literature and from our own institute. Using our correction equation, the uncertainty in the isotope correction for triple point cell waters used around the world will be  <1 μK.

  20. Can phenological models predict tree phenology accurately in the future? The unrevealed hurdle of endodormancy break.

    PubMed

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean-Michel; García de Cortázar-Atauri, Iñaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2016-10-01

    The onset of the growing season of trees has been earlier by 2.3 days per decade during the last 40 years in temperate Europe because of global warming. The effect of temperature on plant phenology is, however, not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud endodormancy, and, on the other hand, higher temperatures are necessary to promote bud cell growth afterward. Different process-based models have been developed in the last decades to predict the date of budbreak of woody species. They predict that global warming should delay or compromise endodormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budbreak dates only, with no information on the endodormancy break date because this information is very scarce. Here, we evaluated the efficiency of a set of phenological models to accurately predict the endodormancy break dates of three fruit trees. Our results show that models calibrated solely with budbreak dates usually do not accurately predict the endodormancy break date. Providing endodormancy break date for the model parameterization results in much more accurate prediction of this latter, with, however, a higher error than that on budbreak dates. Most importantly, we show that models not calibrated with endodormancy break dates can generate large discrepancies in forecasted budbreak dates when using climate scenarios as compared to models calibrated with endodormancy break dates. This discrepancy increases with mean annual temperature and is therefore the strongest after 2050 in the southernmost regions. Our results claim for the urgent need of massive measurements of endodormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future. © 2016 John Wiley & Sons Ltd.

  1. How accurate is our clinical prediction of "minimal prostate cancer"?

    PubMed

    Leibovici, Dan; Shikanov, Sergey; Gofrit, Ofer N; Zagaja, Gregory P; Shilo, Yaniv; Shalhav, Arieh L

    2013-07-01

    Recommendations for active surveillance versus immediate treatment for low risk prostate cancer are based on biopsy and clinical data, assuming that a low volume of well-differentiated carcinoma will be associated with a low progression risk. However, the accuracy of clinical prediction of minimal prostate cancer (MPC) is unclear. To define preoperative predictors for MPC in prostatectomy specimens and to examine the accuracy of such prediction. Data collected on 1526 consecutive radical prostatectomy patients operated in a single center between 2003 and 2008 included: age, body mass index, preoperative prostate-specific antigen level, biopsy Gleason score, clinical stage, percentage of positive biopsy cores, and maximal core length (MCL) involvement. MPC was defined as < 5% of prostate volume involvement with organ-confined Gleason score < or = 6. Univariate and multivariate logistic regression analyses were used to define independent predictors of minimal disease. Classification and Regression Tree (CART) analysis was used to define cutoff values for the predictors and measure the accuracy of prediction. MPC was found in 241 patients (15.8%). Clinical stage, biopsy Gleason's score, percent of positive biopsy cores, and maximal involved core length were associated with minimal disease (OR 0.42, 0.1, 0.92, and 0.9, respectively). Independent predictors of MPC included: biopsy Gleason score, percent of positive cores and MCL (OR 0.21, 095 and 0.95, respectively). CART showed that when the MCL exceeded 11.5%, the likelihood of MPC was 3.8%. Conversely, when applying the most favorable preoperative conditions (Gleason < or = 6, < 20% positive cores, MCL < or = 11.5%) the chance of minimal disease was 41%. Biopsy Gleason score, the percent of positive cores and MCL are independently associated with MPC. While preoperative prediction of significant prostate cancer was accurate, clinical prediction of MPC was incorrect 59% of the time. Caution is necessary when

  2. Predictive isotopic biogeochemistry: hydrocarbons from anoxic marine basins

    NASA Technical Reports Server (NTRS)

    Freeman, K. H.; Wakeham, S. G.; Hayes, J. M.

    1994-01-01

    Carbon isotopic compositions were determined for individual hydrocarbons in water column and sediment samples from the Cariaco Trench and Black Sea. In order to identify hydrocarbons derived from phytoplankton, the isotopic compositions expected for biomass of autotrophic organisms living in surface waters of both localities were calculated based on the concentrations of CO2(aq) and the isotopic compositions of dissolved inorganic carbon. These calculated values are compared to measured delta values for particulate organic carbon and for individual hydrocarbon compounds. Specifically, we find that lycopane is probably derived from phytoplankton and that diploptene is derived from the lipids of chemoautotrophs living above the oxic/anoxic boundary. Three acyclic isoprenoids that have been considered markers for methanogens, pentamethyleicosane and two hydrogenated squalenes, have different delta values and apparently do not derive from a common source. Based on the concentration profiles and isotopic compositions, the C31 and C33 n-alkanes and n-alkenes have a similar source, and both may have a planktonic origin. If so, previously assigned terrestrial origins of organic matter in some Black Sea sediments may be erroneous.

  3. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

  4. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

    PubMed Central

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

  5. An in-line micro-pyrolysis system to remove contaminating organic species for precise and accurate water isotope analysis by spectroscopic techniques

    NASA Astrophysics Data System (ADS)

    Panetta, R. J.; Hsiao, G.

    2011-12-01

    Trace levels of organic contaminants such as short alcohols and terpenoids have been shown to cause spectral interference in water isotope analysis by spectroscopic techniques. The result is degraded precision and accuracy in both δD and δ18O for samples such as beverages, plant extracts or slightly contaminated waters. An initial approach offered by manufacturers is post-processing software that analyzes spectral features to identify and flag contaminated samples. However, it is impossible for this software to accurately reconstruct the water isotope signature, thus it is primarily a metric for data quality. Here, we describe a novel in-line pyrolysis system (Micro-Pyrolysis Technology, MPT) placed just prior to the inlet of a cavity ring-down spectroscopy (CRDS) analyzer that effectively removes interfering organic molecules without altering the isotope values of the water. Following injection of the water sample, N2 carrier gas passes the sample through a micro-pyrolysis tube heated with multiple high temperature elements in an oxygen-free environment. The temperature is maintained above the thermal decomposition threshold of most organic compounds (≤ 900 oC), but well below that of water (~2000 oC). The main products of the pyrolysis reaction are non-interfering species such as elemental carbon and H2 gas. To test the efficacy and applicability of the system, waters of known isotopic composition were spiked with varying amounts of common interfering alcohols (methanol, ethanol, propanol, hexanol, trans-2-hexenol, cis-3-hexanol up to 5 % v/v) and common soluble plant terpenoids (carveol, linalool, geraniol, prenol). Spiked samples with no treatment to remove the organics show strong interfering absorption peaks that adversely affect the δD and δ18O values. However, with the MPT in place, all interfering absorption peaks are removed and the water absorption spectrum is fully restored. As a consequence, the δD and δ18O values also return to their original

  6. An Approach for Validating Actinide and Fission Product Burnup Credit Criticality Safety Analyses-Isotopic Composition Predictions

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

    Radulescu, Georgeta; Gauld, Ian C; Ilas, Germina

    2011-01-01

    The expanded use of burnup credit in the United States (U.S.) for storage and transport casks, particularly in the acceptance of credit for fission products, has been constrained by the availability of experimental fission product data to support code validation. The U.S. Nuclear Regulatory Commission (NRC) staff has noted that the rationale for restricting the Interim Staff Guidance on burnup credit for storage and transportation casks (ISG-8) to actinide-only is based largely on the lack of clear, definitive experiments that can be used to estimate the bias and uncertainty for computational analyses associated with using burnup credit. To address themore » issues of burnup credit criticality validation, the NRC initiated a project with the Oak Ridge National Laboratory to (1) develop and establish a technically sound validation approach for commercial spent nuclear fuel (SNF) criticality safety evaluations based on best-available data and methods and (2) apply the approach for representative SNF storage and transport configurations/conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The purpose of this paper is to describe the isotopic composition (depletion) validation approach and resulting observations and recommendations. Validation of the criticality calculations is addressed in a companion paper at this conference. For isotopic composition validation, the approach is to determine burnup-dependent bias and uncertainty in the effective neutron multiplication factor (keff) due to bias and uncertainty in isotopic predictions, via comparisons of isotopic composition predictions (calculated) and measured isotopic compositions from destructive radiochemical assay utilizing as much assay data as is available, and a best-estimate Monte Carlo based method. This paper (1) provides a detailed description of the burnup credit isotopic validation approach and its technical bases, (2) describes the application of the

  7. How accurate are resting energy expenditure prediction equations in obese trauma and burn patients?

    PubMed

    Stucky, Chee-Chee H; Moncure, Michael; Hise, Mary; Gossage, Clint M; Northrop, David

    2008-01-01

    While the prevalence of obesity continues to increase in our society, outdated resting energy expenditure (REE) prediction equations may overpredict energy requirements in obese patients. Accurate feeding is essential since overfeeding has been demonstrated to adversely affect outcomes. The first objective was to compare REE calculated by prediction equations to the measured REE in obese trauma and burn patients. Our hypothesis was that an equation using fat-free mass would give a more accurate prediction. The second objective was to consider the effect of a commonly used injury factor on the predicted REE. A retrospective chart review was performed on 28 patients. REE was measured using indirect calorimetry and compared with the Harris-Benedict and Cunningham equations, and an equation using type II diabetes as a factor. Statistical analyses used were paired t test, +/-95% confidence interval, and the Bland-Altman method. Measured average REE in trauma and burn patients was 21.37 +/- 5.26 and 21.81 +/- 3.35 kcal/kg/d, respectively. Harris-Benedict underpredicted REE in trauma and burn patients to the least extent, while the Cunningham equation underpredicted REE in both populations to the greatest extent. Using an injury factor of 1.2, Cunningham continued to underestimate REE in both populations, while the Harris-Benedict and Diabetic equations overpredicted REE in both populations. The measured average REE is significantly less than current guidelines. This finding suggests that a hypocaloric regimen is worth considering for ICU patients. Also, if an injury factor of 1.2 is incorporated in certain equations, patients may be given too many calories.

  8. Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy

    NASA Astrophysics Data System (ADS)

    Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

    2014-01-01

    In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

  9. Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy.

    PubMed

    Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

    2014-01-01

    In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

  10. Toward Predictive Theories of Nuclear Reactions Across the Isotopic Chart: Web Report

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

    Escher, J. E.; Blackmon, J.; Elster, C.

    Recent years have seen exciting new developments and progress in nuclear structure theory, reaction theory, and experimental techniques, that allow us to move towards a description of exotic systems and environments, setting the stage for new discoveries. The purpose of the 5-week program was to bring together physicists from the low-energy nuclear structure and reaction communities to identify avenues for achieving reliable and predictive descriptions of reactions involving nuclei across the isotopic chart. The 4-day embedded workshop focused on connecting theory developments to experimental advances and data needs for astrophysics and other applications. Nuclear theory must address phenomena from laboratorymore » experiments to stellar environments, from stable nuclei to weakly-bound and exotic isotopes. Expanding the reach of theory to these regimes requires a comprehensive understanding of the reaction mechanisms involved as well as detailed knowledge of nuclear structure. A recurring theme throughout the program was the desire to produce reliable predictions rooted in either ab initio or microscopic approaches. At the same time it was recognized that some applications involving heavy nuclei away from stability, e.g. those involving fi ssion fragments, may need to rely on simple parameterizations of incomplete data for the foreseeable future. The goal here, however, is to subsequently improve and refine the descriptions, moving to phenomenological, then microscopic approaches. There was overarching consensus that future work should also focus on reliable estimates of errors in theoretical descriptions.« less

  11. ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers

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

    Visel, Axel; Blow, Matthew J.; Li, Zirong

    2009-02-01

    A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover since they are scattered amongst the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here, we performed chromatin immunoprecipitation with the enhancer-associated protein p300, followed by massively-parallel sequencing, to map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain, and limb tissue. Wemore » tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases revealed reproducible enhancer activity in those tissues predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities and suggest that such datasets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.« less

  12. Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics

    PubMed Central

    Noecker, Cecilia; Schaefer, Krista; Zaccheo, Kelly; Yang, Yiding; Day, Judy; Ganusov, Vitaly V.

    2015-01-01

    Upon infection of a new host, human immunodeficiency virus (HIV) replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV). First, we found that the mode of virus production by infected cells (budding vs. bursting) has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral dose. These results

  13. Improving medical decisions for incapacitated persons: does focusing on "accurate predictions" lead to an inaccurate picture?

    PubMed

    Kim, Scott Y H

    2014-04-01

    The Patient Preference Predictor (PPP) proposal places a high priority on the accuracy of predicting patients' preferences and finds the performance of surrogates inadequate. However, the quest to develop a highly accurate, individualized statistical model has significant obstacles. First, it will be impossible to validate the PPP beyond the limit imposed by 60%-80% reliability of people's preferences for future medical decisions--a figure no better than the known average accuracy of surrogates. Second, evidence supports the view that a sizable minority of persons may not even have preferences to predict. Third, many, perhaps most, people express their autonomy just as much by entrusting their loved ones to exercise their judgment than by desiring to specifically control future decisions. Surrogate decision making faces none of these issues and, in fact, it may be more efficient, accurate, and authoritative than is commonly assumed.

  14. Rapid and accurate prediction of degradant formation rates in pharmaceutical formulations using high-performance liquid chromatography-mass spectrometry.

    PubMed

    Darrington, Richard T; Jiao, Jim

    2004-04-01

    Rapid and accurate stability prediction is essential to pharmaceutical formulation development. Commonly used stability prediction methods include monitoring parent drug loss at intended storage conditions or initial rate determination of degradants under accelerated conditions. Monitoring parent drug loss at the intended storage condition does not provide a rapid and accurate stability assessment because often <0.5% drug loss is all that can be observed in a realistic time frame, while the accelerated initial rate method in conjunction with extrapolation of rate constants using the Arrhenius or Eyring equations often introduces large errors in shelf-life prediction. In this study, the shelf life prediction of a model pharmaceutical preparation utilizing sensitive high-performance liquid chromatography-mass spectrometry (LC/MS) to directly quantitate degradant formation rates at the intended storage condition is proposed. This method was compared to traditional shelf life prediction approaches in terms of time required to predict shelf life and associated error in shelf life estimation. Results demonstrated that the proposed LC/MS method using initial rates analysis provided significantly improved confidence intervals for the predicted shelf life and required less overall time and effort to obtain the stability estimation compared to the other methods evaluated. Copyright 2004 Wiley-Liss, Inc. and the American Pharmacists Association.

  15. Trophic hierarchies revealed via amino acid isotopic analysis

    USDA-ARS?s Scientific Manuscript database

    Despite the potential of isotopic methods to illuminate trophic function, accurate estimates of lifetime feeding tendencies have remained elusive. A relatively new approach—referred to as compound-specific isotopic analysis (CSIA)—has emerged, centering on the measurement of 15N:14N ratios in amino ...

  16. Tissue Turnover Rates and Isotopic Trophic Discrimination Factors in the Endothermic Teleost, Pacific Bluefin Tuna (Thunnus orientalis)

    PubMed Central

    Madigan, Daniel J.; Litvin, Steven Y.; Popp, Brian N.; Carlisle, Aaron B.; Farwell, Charles J.; Block, Barbara A.

    2012-01-01

    Stable isotope analysis (SIA) of highly migratory marine pelagic animals can improve understanding of their migratory patterns and trophic ecology. However, accurate interpretation of isotopic analyses relies on knowledge of isotope turnover rates and tissue-diet isotope discrimination factors. Laboratory-derived turnover rates and discrimination factors have been difficult to obtain due to the challenges of maintaining these species in captivity. We conducted a study to determine tissue- (white muscle and liver) and isotope- (nitrogen and carbon) specific turnover rates and trophic discrimination factors (TDFs) using archived tissues from captive Pacific bluefin tuna (PBFT), Thunnus orientalis, 1–2914 days after a diet shift in captivity. Half-life values for 15N turnover in white muscle and liver were 167 and 86 days, and for 13C were 255 and 162 days, respectively. TDFs for white muscle and liver were 1.9 and 1.1‰ for δ 15N and 1.8 and 1.2‰ for δ 13C, respectively. Our results demonstrate that turnover of 15N and 13C in bluefin tuna tissues is well described by a single compartment first-order kinetics model. We report variability in turnover rates between tissue types and their isotope dynamics, and hypothesize that metabolic processes play a large role in turnover of nitrogen and carbon in PBFT white muscle and liver tissues. 15N in white muscle tissue showed the most predictable change with diet over time, suggesting that white muscle δ 15N data may provide the most reliable inferences for diet and migration studies using stable isotopes in wild fish. These results allow more accurate interpretation of field data and dramatically improve our ability to use stable isotope data from wild tunas to better understand their migration patterns and trophic ecology. PMID:23145128

  17. Kinetic approach to degradation mechanisms in polymer solar cells and their accurate lifetime predictions

    NASA Astrophysics Data System (ADS)

    Arshad, Muhammad Azeem; Maaroufi, AbdelKrim

    2018-07-01

    A beginning has been made in the present study regarding the accurate lifetime predictions of polymer solar cells. Certain reservations about the conventionally employed temperature accelerated lifetime measurements test for its unworthiness of predicting reliable lifetimes of polymer solar cells are brought into light. Critical issues concerning the accelerated lifetime testing include, assuming reaction mechanism instead of determining it, and relying solely on the temperature acceleration of a single property of material. An advanced approach comprising a set of theoretical models to estimate the accurate lifetimes of polymer solar cells is therefore suggested in order to suitably alternate the accelerated lifetime testing. This approach takes into account systematic kinetic modeling of various possible polymer degradation mechanisms under natural weathering conditions. The proposed kinetic approach is substantiated by its applications on experimental aging data-sets of polymer solar materials/solar cells including, P3HT polymer film, bulk heterojunction (MDMO-PPV:PCBM) and dye-sensitized solar cells. Based on the suggested approach, an efficacious lifetime determination formula for polymer solar cells is derived and tested on dye-sensitized solar cells. Some important merits of the proposed method are also pointed out and its prospective applications are discussed.

  18. Water balance model for mean annual hydrogen and oxygen isotope distributions in surface waters of the contiguous United States

    NASA Astrophysics Data System (ADS)

    Bowen, Gabriel J.; Kennedy, Casey D.; Liu, Zhongfang; Stalker, Jeremy

    2011-12-01

    The stable H and O isotope composition of river and stream water records information on runoff sources and land-atmosphere water fluxes within the catchment and is a potentially powerful tool for network-based monitoring of ecohydrological systems. Process-based hydrological models, however, have thus far shown limited power to replicate observed large-scale variation in U.S. surface water isotope ratios. Here we develop a geographic information system-based model to predict long-term annual average surface water isotope ratios across the contiguous United States. We use elevation-explicit, gridded precipitation isotope maps as model input and data from a U.S. Geological Survey monitoring program for validation. We find that models incorporating monthly variation in precipitation-evapotranspiration (P-E) amounts account for the majority (>89%) of isotopic variation and have reduced regional bias relative to models that do not consider intra-annual P-E effects on catchment water balance. Residuals from the water balance model exhibit strong spatial patterning and correlations that suggest model residuals isolate additional hydrological signal. We use interpolated model residuals to generate optimized prediction maps for U.S. surface water δ2H and δ18O values. We show that the modeled surface water values represent a relatively accurate and unbiased proxy for drinking water isotope ratios across the United States, making these data products useful in ecological and criminal forensics applications that require estimates of the local environmental water isotope variation across large geographic regions.

  19. Modeling methodology for the accurate and prompt prediction of symptomatic events in chronic diseases.

    PubMed

    Pagán, Josué; Risco-Martín, José L; Moya, José M; Ayala, José L

    2016-08-01

    Prediction of symptomatic crises in chronic diseases allows to take decisions before the symptoms occur, such as the intake of drugs to avoid the symptoms or the activation of medical alarms. The prediction horizon is in this case an important parameter in order to fulfill the pharmacokinetics of medications, or the time response of medical services. This paper presents a study about the prediction limits of a chronic disease with symptomatic crises: the migraine. For that purpose, this work develops a methodology to build predictive migraine models and to improve these predictions beyond the limits of the initial models. The maximum prediction horizon is analyzed, and its dependency on the selected features is studied. A strategy for model selection is proposed to tackle the trade off between conservative but robust predictive models, with respect to less accurate predictions with higher horizons. The obtained results show a prediction horizon close to 40min, which is in the time range of the drug pharmacokinetics. Experiments have been performed in a realistic scenario where input data have been acquired in an ambulatory clinical study by the deployment of a non-intrusive Wireless Body Sensor Network. Our results provide an effective methodology for the selection of the future horizon in the development of prediction algorithms for diseases experiencing symptomatic crises. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

    PubMed

    Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

    2014-07-01

    With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. © 2013 Wiley Periodicals, Inc.

  1. Do dual-route models accurately predict reading and spelling performance in individuals with acquired alexia and agraphia?

    PubMed

    Rapcsak, Steven Z; Henry, Maya L; Teague, Sommer L; Carnahan, Susan D; Beeson, Pélagie M

    2007-06-18

    Coltheart and co-workers [Castles, A., Bates, T. C., & Coltheart, M. (2006). John Marshall and the developmental dyslexias. Aphasiology, 20, 871-892; Coltheart, M., Rastle, K., Perry, C., Langdon, R., & Ziegler, J. (2001). DRC: A dual route cascaded model of visual word recognition and reading aloud. Psychological Review, 108, 204-256] have demonstrated that an equation derived from dual-route theory accurately predicts reading performance in young normal readers and in children with reading impairment due to developmental dyslexia or stroke. In this paper, we present evidence that the dual-route equation and a related multiple regression model also accurately predict both reading and spelling performance in adult neurological patients with acquired alexia and agraphia. These findings provide empirical support for dual-route theories of written language processing.

  2. A hydrogen gas-water equilibration method produces accurate and precise stable hydrogen isotope ratio measurements in nutrition studies

    USDA-ARS?s Scientific Manuscript database

    Stable hydrogen isotope methodology is used in nutrition studies to measure growth, breast milk intake, and energy requirement. Isotope ratio MS is the best instrumentation to measure the stable hydrogen isotope ratios in physiological fluids. Conventional methods to convert physiological fluids to ...

  3. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

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

    Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys.more » 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.« less

  4. Intramolecular Isotopic Studies: Chemical Enhancements and Alternatives

    NASA Astrophysics Data System (ADS)

    Hayes, J. M.

    2016-12-01

    As mass spectroscopic and NMR-based methods now appropriately flourish, chemical techniques should not be forgotten. First, the methods developed by pioneering intramolecular analysts can be reapplied to new samples. Second, they can be extended. The synthesis of intramolecular isotopic standards is particularly important and straightforward. It requires only that a chemical reaction has no secondary products. An example is provided by the addition of carbon dioxide to a Grignard reagent. The reaction proceeds with an isotope effect. The isotopic composition of the carboxyl group in the acid which is produced is thus not equal to that of the starting carbon dioxide but the unconsumed CO2 can be recovered and analyzed. A simple titration can show that all the rest of the CO2 is in the product acid. The isotopic composition of the carboxyl group can then be calculated by difference. The product is an intramolecular isotopic standard, an organic molecule in which the isotopic composition of a specific carbon position is known accurately. Both analysts and reviewers can thus gain invaluable confidence in the accuracy of instrumental results. A second example: the haloform reaction quantitatively degrades methyl ketones, producing a carboxylic acid which can be decarboxylated to determine the isotopic composition of the parent carbonyl and a haloform (CHI3, for example) that can be combusted to determine the isotopic composition of the methyl group. Ketones thus analyzed can be combined with Grignard reagents to yield carbon skeletons in which the isotopic compositions of internal and terminal -CH2- and -CH3 groups are known accurately. In general, analysts accustomed to demanding quantitative reactions should remember the power of mass balances and recognize that many organic-chemical reactions, while not quantitative, lack side products and can be driven to the total consumption of at least one reactant.

  5. ILT based defect simulation of inspection images accurately predicts mask defect printability on wafer

    NASA Astrophysics Data System (ADS)

    Deep, Prakash; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

    2016-05-01

    At advanced technology nodes mask complexity has been increased because of large-scale use of resolution enhancement technologies (RET) which includes Optical Proximity Correction (OPC), Inverse Lithography Technology (ILT) and Source Mask Optimization (SMO). The number of defects detected during inspection of such mask increased drastically and differentiation of critical and non-critical defects are more challenging, complex and time consuming. Because of significant defectivity of EUVL masks and non-availability of actinic inspection, it is important and also challenging to predict the criticality of defects for printability on wafer. This is one of the significant barriers for the adoption of EUVL for semiconductor manufacturing. Techniques to decide criticality of defects from images captured using non actinic inspection images is desired till actinic inspection is not available. High resolution inspection of photomask images detects many defects which are used for process and mask qualification. Repairing all defects is not practical and probably not required, however it's imperative to know which defects are severe enough to impact wafer before repair. Additionally, wafer printability check is always desired after repairing a defect. AIMSTM review is the industry standard for this, however doing AIMSTM review for all defects is expensive and very time consuming. Fast, accurate and an economical mechanism is desired which can predict defect printability on wafer accurately and quickly from images captured using high resolution inspection machine. Predicting defect printability from such images is challenging due to the fact that the high resolution images do not correlate with actual mask contours. The challenge is increased due to use of different optical condition during inspection other than actual scanner condition, and defects found in such images do not have correlation with actual impact on wafer. Our automated defect simulation tool predicts

  6. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.

    PubMed

    Wang, Sheng; Sun, Siqi; Li, Zhen; Zhang, Renyu; Xu, Jinbo

    2017-01-01

    Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact-assisted models also have

  7. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

    PubMed Central

    Li, Zhen; Zhang, Renyu

    2017-01-01

    Motivation Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. Method This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. Results Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact

  8. Obtaining Accurate Probabilities Using Classifier Calibration

    ERIC Educational Resources Information Center

    Pakdaman Naeini, Mahdi

    2016-01-01

    Learning probabilistic classification and prediction models that generate accurate probabilities is essential in many prediction and decision-making tasks in machine learning and data mining. One way to achieve this goal is to post-process the output of classification models to obtain more accurate probabilities. These post-processing methods are…

  9. Computational prediction of Mg-isotope fractionation between aqueous [Mg(OH2)6]2+ and brucite

    NASA Astrophysics Data System (ADS)

    Colla, Christopher A.; Casey, William H.; Ohlin, C. André

    2018-04-01

    The fractionation factor in the magnesium-isotope fractionation between aqueous solutions of magnesium and brucite changes sign with increasing temperature, as uncovered by recent experiments. To understand this behavior, the Reduced Partition Function Ratios and isotopic fractionation factors (Δ26/24Mgbrucite-Mg(aq)) are calculated using molecular models of aqueous [Mg(OH2)6]2+ and the mineral brucite at increasing levels of density functional theory. The calculations were carried out on the [Mg(OH2)6]2+·12H2O cluster, along with different Pauling-bond-strength-conserving models of the mineral lattice of brucite. Three conclusions were reached: (i) all levels of theory overestimate bond distances in the aqua ion complex relative to Tutton's salts; (ii) the calculations predict that brucite at 298.15 K is always enriched in the heavy isotope, in contrast with experimental observations; (iii) the temperature dependencies of Wimpenny et al. (2014) and Li et al. (2014) could only be achieved by fixing the bond distances in the [Mg(OH2)6]2+·12H2O cluster to values close to those observed in crystals that trap the hydrated ion.

  10. Stable isotope laser spectrometer for exploration of Mars.

    PubMed

    Sauke, T B; Becker, J F

    1998-01-01

    On Earth, measurements of the ratios of stable carbon isotopes have provided much information about geological and biological processes. For example, fractionation of carbon occurs in biotic processes and the retention of a distinctive 2-4% contrast in 13C/12C between organic carbon and carbonates in rocks as old as 3.8 billion years constitutes some of the firmest evidence for the antiquity of life on the Earth. We have developed a prototype tunable diode Laser spectrometer which demonstrates the feasibility of making accurate in situ isotopic ratio measurements on Mars. This miniaturized instrument, with an optical path length of 10 cm, should be capable of making accurate 13C/12C and 15N/14N measurements. Gas samples for measurement are to be produced by pyrolysis using soil samples as small as 50 mg. Measurements of 13C/12C, 18O/16O and 15N/14N have been made to a precision of better than 0.1% and various other isotopes are feasible. This laser technique, which relies on the extremely narrow emission linewidth of tunable diode lasers (<0.001 cm(-1)) has favorable features in comparison to mass spectrometry, the standard method of accurate isotopic ratio measurement. The miniature instrument could be ready to deploy on the 2003 or other Mars lander missions.

  11. Stable isotope dilution HILIC-MS/MS method for accurate quantification of glutamic acid, glutamine, pyroglutamic acid, GABA and theanine in mouse brain tissues.

    PubMed

    Inoue, Koichi; Miyazaki, Yasuto; Unno, Keiko; Min, Jun Zhe; Todoroki, Kenichiro; Toyo'oka, Toshimasa

    2016-01-01

    In this study, we developed the stable isotope dilution hydrophilic interaction liquid chromatography with tandem mass spectrometry (HILIC-MS/MS) technique for the accurate, reasonable and simultaneous quantification of glutamic acid (Glu), glutamine (Gln), pyroglutamic acid (pGlu), γ-aminobutyric acid (GABA) and theanine in mouse brain tissues. The quantification of these analytes was accomplished using stable isotope internal standards and the HILIC separating mode to fully correct the intramolecular cyclization during the electrospray ionization. It was shown that linear calibrations were available with high coefficients of correlation (r(2)  > 0.999, range from 10 pmol/mL to 50 mol/mL). For application of the theanine intake, the determination of Glu, Gln, pGlu, GABA and theanine in the hippocampus and central cortex tissues was performed based on our developed method. In the region of the hippocampus, the concentration levels of Glu and pGlu were significantly reduced during reality-based theanine intake. Conversely, the concentration level of GABA increased. This result showed that transited theanine has an effect on the metabolic balance of Glu analogs in the hippocampus. Copyright © 2015 John Wiley & Sons, Ltd.

  12. Applications of stable isotope analysis in mammalian ecology.

    PubMed

    Walter, W David; Kurle, Carolyn M; Hopkins, John B

    2014-01-01

    In this editorial, we provide a brief introduction and summarize the 10 research articles included in this Special Issue on Applications of stable isotope analysis in mammalian ecology. The first three articles report correction and discrimination factors that can be used to more accurately estimate the diets of extinct and extant mammals using stable isotope analysis. The remaining seven applied research articles use stable isotope analysis to address a variety of wildlife conservation and management questions from the oceans to the mountains.

  13. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb

    DOE PAGES

    Monti, Remo; Barozzi, Iros; Osterwalder, Marco; ...

    2017-08-21

    Epigenomic mapping of enhancer-associated chromatin modifications facilitates the genome-wide discovery of tissue-specific enhancers in vivo. However, reliance on single chromatin marks leads to high rates of false-positive predictions. More sophisticated, integrative methods have been described, but commonly suffer from limited accessibility to the resulting predictions and reduced biological interpretability. Here we present the Limb-Enhancer Genie (LEG), a collection of highly accurate, genome-wide predictions of enhancers in the developing limb, available through a user-friendly online interface. We predict limb enhancers using a combination of > 50 published limb-specific datasets and clusters of evolutionarily conserved transcription factor binding sites, taking advantage ofmore » the patterns observed at previously in vivo validated elements. By combining different statistical models, our approach outperforms current state-of-the-art methods and provides interpretable measures of feature importance. Our results indicate that including a previously unappreciated score that quantifies tissue-specific nuclease accessibility significantly improves prediction performance. We demonstrate the utility of our approach through in vivo validation of newly predicted elements. Moreover, we describe general features that can guide the type of datasets to include when predicting tissue-specific enhancers genome-wide, while providing an accessible resource to the general biological community and facilitating the functional interpretation of genetic studies of limb malformations.« less

  14. Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

    PubMed Central

    Garcia Lopez, Sebastian; Kim, Philip M.

    2014-01-01

    Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT) algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases. PMID:25243403

  15. Accurate analysis of parabens in human urine using isotope-dilution ultrahigh-performance liquid chromatography-high resolution mass spectrometry.

    PubMed

    Zhou, Hui-Ting; Chen, Hsin-Chang; Ding, Wang-Hsien

    2018-02-20

    An analytical method that utilizes isotope-dilution ultrahigh-performance liquid chromatography coupled with hybrid quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS or called UHPLC-HRMS) was developed, and validated to be highly precise and accurate for the detection of nine parabens (methyl-, ethyl-, propyl-, isopropyl-, butyl-, isobutyl-, pentyl-, hexyl-, and benzyl-parabens) in human urine samples. After sample preparation by ultrasound-assisted emulsification microextraction (USAEME), the extract was directly injected into UHPLC-HRMS. By using negative electrospray ionization in the multiple reaction monitoring (MRM) mode and measuring the peak area ratios of both the natural and the labeled-analogues in the samples and calibration standards, the target analytes could be accurately identified and quantified. Another use for the labeled-analogues was to correct for systematic errors associated with the analysis, such as the matrix effect and other variations. The limits of quantitation (LOQs) were ranging from 0.3 to 0.6 ng/mL. High precisions for both repeatability and reproducibility were obtained ranging from 1 to 8%. High trueness (mean extraction recovery, or called accuracy) ranged from 93 to 107% on two concentration levels. According to preliminary results, the total concentrations of four most detected parabens (methyl-, ethyl-, propyl- and butyl-) ranged from 0.5 to 79.1 ng/mL in male urine samples, and from 17 to 237 ng/mL in female urine samples. Interestingly, two infrequently detected pentyl- and hexyl-parabens were found in one of the male samples in this study. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

    PubMed

    Wallace, Jason A; Wang, Yuhang; Shi, Chuanyin; Pastoor, Kevin J; Nguyen, Bao-Linh; Xia, Kai; Shen, Jana K

    2011-12-01

    Proton uptake or release controls many important biological processes, such as energy transduction, virus replication, and catalysis. Accurate pK(a) prediction informs about proton pathways, thereby revealing detailed acid-base mechanisms. Physics-based methods in the framework of molecular dynamics simulations not only offer pK(a) predictions but also inform about the physical origins of pK(a) shifts and provide details of ionization-induced conformational relaxation and large-scale transitions. One such method is the recently developed continuous constant pH molecular dynamics (CPHMD) method, which has been shown to be an accurate and robust pK(a) prediction tool for naturally occurring titratable residues. To further examine the accuracy and limitations of CPHMD, we blindly predicted the pK(a) values for 87 titratable residues introduced in various hydrophobic regions of staphylococcal nuclease and variants. The predictions gave a root-mean-square deviation of 1.69 pK units from experiment, and there were only two pK(a)'s with errors greater than 3.5 pK units. Analysis of the conformational fluctuation of titrating side-chains in the context of the errors of calculated pK(a) values indicate that explicit treatment of conformational flexibility and the associated dielectric relaxation gives CPHMD a distinct advantage. Analysis of the sources of errors suggests that more accurate pK(a) predictions can be obtained for the most deeply buried residues by improving the accuracy in calculating desolvation energies. Furthermore, it is found that the generalized Born implicit-solvent model underlying the current CPHMD implementation slightly distorts the local conformational environment such that the inclusion of an explicit-solvent representation may offer improvement of accuracy. Copyright © 2011 Wiley-Liss, Inc.

  17. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

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

    Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.

    2008-10-20

    One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasetsmore » having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds

  18. Parse, simulation, and prediction of NOx emission across the Midwestern United States

    NASA Astrophysics Data System (ADS)

    Fang, H.; Michalski, G. M.; Spak, S.

    2017-12-01

    Accurately constraining N emissions in space and time has been a challenge for atmospheric scientists. It has been suggested that 15N isotopes may be a way of tracking N emission sources across various spatial and temporal scales. However, the complexity of multiple N sources that can quickly change in intensity has made this a difficult problem. We have used a SMOKE emission model to parse NOx emission across the Midwestern United States for a one-year simulation. An isotope mass balance methods was used to assign 15N values to road, non-road, point, and area sources. The SMOKE emissions and isotope mass balance were then combined to predict the 15N of NOx emissions (Figure 1). This ^15N of NOx emissions model was then incorporated into CMAQ to assess the role of transport and chemistry would impact the 15N value of NOx due to mixing and removal processes. The predicted 15N value of NOx was compared to those in recent measurements of NOx and atmospheric nitrate.

  19. Production of highly-enriched 134Ba for a reference material for isotope dilution mass spectrometry measurements

    DOE PAGES

    Horkley, J. J.; Carney, K. P.; Gantz, E. M.; ...

    2015-03-17

    Isotope dilution mass spectrometry (IDMS) is an analytical technique capable of providing accurate and precise quantitation of trace isotope abundance and assay providing measurement uncertainties below 1 %. To achieve these low uncertainties, the IDMS method ideally utilizes chemically pure “spike” solutions that consist of a single highly enriched isotope that is well-characterized relating to the abundance of companion isotopes and concentration in solution. To address a current demand for accurate 137Cs/137Ba ratio measurements for “age” determination of radioactive 137Cs sources, Idaho National Laboratory (INL) is producing enriched 134Ba isotopes that are tobe used for IDMS spikes to accurately determinemore » 137Ba accumulation from the decay of 137Cs. The final objective of this work it to provide a homogenous set of reference materials that the National Institute of Standards and Technology can certify as standard reference materials used for IDMS. The process that was developed at INL for the separation and isolation of Ba isotopes, chemical purification of the isotopes in solution, and the encapsulation of the materials will be described.« less

  20. Deformation properties of lead isotopes

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

    Tolokonnikov, S. V.; Borzov, I. N.; Lutostansky, Yu. S.

    2016-01-15

    The deformation properties of a long lead isotopic chain up to the neutron drip line are analyzed on the basis of the energy density functional (EDF) in the FaNDF{sup 0} Fayans form. The question of whether the ground state of neutron-deficient lead isotopes can have a stable deformation is studied in detail. The prediction of this deformation is contained in the results obtained on the basis of the HFB-17 and HFB-27 Skyrme EDF versions and reported on Internet. The present analysis reveals that this is at odds with experimental data on charge radii and magnetic moments of odd lead isotopes.more » The Fayans EDF version predicts a spherical ground state for all light lead isotopes, but some of them (for example, {sup 180}Pb and {sup 184}Pb) prove to be very soft—that is, close to the point of a phase transition to a deformed state. Also, the results obtained in our present study are compared with the predictions of some other Skyrme EDF versions, including SKM*, SLy4, SLy6, and UNE1. By and large, their predictions are closer to the results arising upon the application of the Fayans functional. For example, the SLy4 functional predicts, in just the same way as the FaNDF{sup 0} functional, a spherical shape for all nuclei of this region. The remaining three Skyrme EDF versions lead to a deformation of some light lead isotopes, but their number is substantially smaller than that in the case of the HFB-17 and HFB-27 functionals. Moreover, the respective deformation energy is substantially lower, which gives grounds to hope for the restoration of a spherical shape upon going beyond the mean-field approximation, which we use here. Also, the deformation properties of neutron-rich lead isotopes are studied up to the neutron drip line. Here, the results obtained with the FaNDF{sup 0} functional are compared with the predictions of the HFB-17, HFB-27, SKM*, and SLy4 Skyrme EDF versions. All of the EDF versions considered here predict the existence of a region where

  1. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.

    PubMed

    Jones, David T; Singh, Tanya; Kosciolek, Tomasz; Tetchner, Stuart

    2015-04-01

    Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues. Using the original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision of 0.54 for top-L predicted long range contacts-around 60% higher than PSICOV, and around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able to improve the TM-scores of models by a median of 0.05 compared with PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision of 0.69 for the top-L/10 hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV. MetaPSICOV is available as a freely available web server at http://bioinf.cs.ucl.ac.uk/MetaPSICOV. Raw data (predicted contact lists and 3D models) and source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  2. Quasi-closed phase forward-backward linear prediction analysis of speech for accurate formant detection and estimation.

    PubMed

    Gowda, Dhananjaya; Airaksinen, Manu; Alku, Paavo

    2017-09-01

    Recently, a quasi-closed phase (QCP) analysis of speech signals for accurate glottal inverse filtering was proposed. However, the QCP analysis which belongs to the family of temporally weighted linear prediction (WLP) methods uses the conventional forward type of sample prediction. This may not be the best choice especially in computing WLP models with a hard-limiting weighting function. A sample selective minimization of the prediction error in WLP reduces the effective number of samples available within a given window frame. To counter this problem, a modified quasi-closed phase forward-backward (QCP-FB) analysis is proposed, wherein each sample is predicted based on its past as well as future samples thereby utilizing the available number of samples more effectively. Formant detection and estimation experiments on synthetic vowels generated using a physical modeling approach as well as natural speech utterances show that the proposed QCP-FB method yields statistically significant improvements over the conventional linear prediction and QCP methods.

  3. WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms.

    PubMed

    Chi, Sang-Mun; Nam, Dougu

    2012-04-01

    We present an accurate and fast web server, WegoLoc for predicting subcellular localization of proteins based on sequence similarity and weighted Gene Ontology (GO) information. A term weighting method in the text categorization process is applied to GO terms for a support vector machine classifier. As a result, WegoLoc surpasses the state-of-the-art methods for previously used test datasets. WegoLoc supports three eukaryotic kingdoms (animals, fungi and plants) and provides human-specific analysis, and covers several sets of cellular locations. In addition, WegoLoc provides (i) multiple possible localizations of input protein(s) as well as their corresponding probability scores, (ii) weights of GO terms representing the contribution of each GO term in the prediction, and (iii) a BLAST E-value for the best hit with GO terms. If the similarity score does not meet a given threshold, an amino acid composition-based prediction is applied as a backup method. WegoLoc and User's guide are freely available at the website http://www.btool.org/WegoLoc smchiks@ks.ac.kr; dougnam@unist.ac.kr Supplementary data is available at http://www.btool.org/WegoLoc.

  4. Sex-specific lean body mass predictive equations are accurate in the obese paediatric population

    PubMed Central

    Jackson, Lanier B.; Henshaw, Melissa H.; Carter, Janet; Chowdhury, Shahryar M.

    2015-01-01

    Background The clinical assessment of lean body mass (LBM) is challenging in obese children. A sex-specific predictive equation for LBM derived from anthropometric data was recently validated in children. Aim The purpose of this study was to independently validate these predictive equations in the obese paediatric population. Subjects and methods Obese subjects aged 4–21 were analysed retrospectively. Predicted LBM (LBMp) was calculated using equations previously developed in children. Measured LBM (LBMm) was derived from dual-energy x-ray absorptiometry. Agreement was expressed as [(LBMm-LBMp)/LBMm] with 95% limits of agreement. Results Of 310 enrolled patients, 195 (63%) were females. The mean age was 11.8 ± 3.4 years and mean BMI Z-score was 2.3 ± 0.4. The average difference between LBMm and LBMp was −0.6% (−17.0%, 15.8%). Pearson’s correlation revealed a strong linear relationship between LBMm and LBMp (r=0.97, p<0.01). Conclusion This study validates the use of these clinically-derived sex-specific LBM predictive equations in the obese paediatric population. Future studies should use these equations to improve the ability to accurately classify LBM in obese children. PMID:26287383

  5. Accurate prediction of cation-π interaction energy using substituent effects.

    PubMed

    Sayyed, Fareed Bhasha; Suresh, Cherumuttathu H

    2012-06-14

    (M(+))' and ΔV(min). All the Φ-X···M(+) systems showed good agreement between the calculated and predicted E(M(+))() values, suggesting that the ΔV(min) approach to substituent effect is accurate and useful for predicting the interactive behavior of substituted π-systems with cations.

  6. β-decay half-lives of new neutron-rich rare-earth isotopes 159Pm,162Sm, and 166Gd

    NASA Astrophysics Data System (ADS)

    Ichikawa, S.; Asai, M.; Tsukada, K.; Haba, H.; Nagame, Y.; Shibata, M.; Sakama, M.; Kojima, Y.

    2005-06-01

    The new neutron-rich rare-earth isotopes 159Pm, 162Sm, and 166Gd produced in the proton-induced fission of 238U were identified using the JAERI on-line isotope separator (JAERI-ISOL) coupled to a gas-jet transport system. The half-lives of 159Pm, 162Sm, and 166Gd were determined to be 1.5 ± 0.2, 2.4 ± 0.5, and 4.8 ± 1.0 s respectively. The partial decay scheme of 166Gd was constructed from γγ-coincidence data. A more accurate half-life value of 25.6 ± 2.2 s was obtained for the previously identified isotope 166Tb. The half-lives measured in the present study are in good agreement with the theoretical predictions calculated by the second generation of the gross theory with the atomic masses evaluated by Audi and Wapstra.

  7. Changes in hydrogen isotope ratios in sequential plumage stages: an implication for the creation of isotope-base maps for tracking migratory birds.

    PubMed

    Duxbury, J M; Holroyd, G L; Muehlenbachs, K

    2003-09-01

    Accurate reference maps are important in the use of stable-isotopes to track the movements of migratory birds. Reference maps created by the analysis of samples collected from young at the nest site are more accurate than simply referring to naturally occurring patterns of hydrogen isotope ratios created by precipitation cycles. Ratios of hydrogen isotopes in the nutrients incorporated early in the development of young birds can be derived from endogenous, maternal sources. Base-maps should be created with the analysis of tissue samples from hatchlings after local the isotopic signature of exogenous nutrients is dominant. Migratory species such as Peregrine Falcons are known to use endogenous sources in the creation of their eggs, therefore knowledge of what plumage stage best represents the local hydrogen ratios would assist in the planning of nest visits. We conducted diet manipulation experiments involving Japanese Quail and Peregrine Falcons to determine the plumage stage when hydrogen isotope ratios were indicative of a switch in their food source. The natal down of both the quail and falcons reflected the diet of breeding adult females. The hydrogen isotope ratios of a new food source were dominant in the juvenile down of the young falcons, although a further shift was detected in the final juvenile plumage. The juvenile plumage is grown during weeks 3-4 after hatch on Peregrine Falcons. Nest visits for the purpose of collecting feathers for isotope-base-map creation should be made around 4 weeks after the presumed hatch of the young falcons.

  8. Accurate predictions of iron redox state in silicate glasses: A multivariate approach using X-ray absorption spectroscopy

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

    Dyar, M. Darby; McCanta, Molly; Breves, Elly

    2016-03-01

    Pre-edge features in the K absorption edge of X-ray absorption spectra are commonly used to predict Fe3+ valence state in silicate glasses. However, this study shows that using the entire spectral region from the pre-edge into the extended X-ray absorption fine-structure region provides more accurate results when combined with multivariate analysis techniques. The least absolute shrinkage and selection operator (lasso) regression technique yields %Fe3+ values that are accurate to ±3.6% absolute when the full spectral region is employed. This method can be used across a broad range of glass compositions, is easily automated, and is demonstrated to yield accurate resultsmore » from different synchrotrons. It will enable future studies involving X-ray mapping of redox gradients on standard thin sections at 1 × 1 μm pixel sizes.« less

  9. Accurate predictions of iron redox state in silicate glasses: A multivariate approach using X-ray absorption spectroscopy

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

    Dyar, M. Darby; McCanta, Molly; Breves, Elly

    2016-03-01

    Pre-edge features in the K absorption edge of X-ray absorption spectra are commonly used to predict Fe 3+ valence state in silicate glasses. However, this study shows that using the entire spectral region from the pre-edge into the extended X-ray absorption fine-structure region provides more accurate results when combined with multivariate analysis techniques. The least absolute shrinkage and selection operator (lasso) regression technique yields %Fe 3+ values that are accurate to ±3.6% absolute when the full spectral region is employed. This method can be used across a broad range of glass compositions, is easily automated, and is demonstrated to yieldmore » accurate results from different synchrotrons. It will enable future studies involving X-ray mapping of redox gradients on standard thin sections at 1 × 1 μm pixel sizes.« less

  10. Trajectory Calculations for Bergman Cyclization Predict H/D Kinetic Isotope Effects Due to Nonstatistical Dynamics in the Product.

    PubMed

    Doubleday, Charles; Boguslav, Mayla; Howell, Caronae; Korotkin, Scott D; Shaked, David

    2016-06-22

    An unusual H/D kinetic isotope effect (KIE) is described, in which isotopic selectivity arises primarily from nonstatistical dynamics in the product. In DFT-based quasiclassical trajectories of Bergman cyclization of (Z)-3-hexen-1,5-diyne (1) at 470 K, the new CC bond retains its energy, and 28% of nascent p-benzyne recrosses back to the enediyne on a vibrational time scale. The competing process of intramolecular vibrational redistribution (IVR) in p-benzyne is too slow to prevent this. Deuteration increases the rate of IVR, which decreases the fraction of recrossing and increases the yield of statistical (trapable) p-benzyne, 2. Trapable yields for three isotopomers of 2 range from 72% to 86%. The resulting KIEs for Bergman cyclization differ substantially from KIEs predicted by transition state theory, which suggests that IVR in this reaction can be studied by conventional KIEs. Leakage of vibrational zero point energy (ZPE) into the reaction coordinate was probed by trajectories in which initial ZPE in the CH/CD stretching modes was reduced by 25%. This did not change the predicted KIEs.

  11. Accurate indel prediction using paired-end short reads

    PubMed Central

    2013-01-01

    Background One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion. Candidates with a score above a manually defined threshold are then predicted to be true indels. As a consequence, structural variants detected in this manner contain many false positives. Results Here, we present a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate. Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing. We demonstrate the usefulness of our method with paired-end Illumina reads from 80 genomes of the first phase of the 1001 Genomes Project ( http://www.1001genomes.org) in Arabidopsis thaliana. Conclusion In this work we show that indel classification is a necessary step to reduce the number of false positive candidates. We demonstrate that missing classification may lead to spurious biological interpretations. The software is available at: http://agkb.is.tuebingen.mpg.de/Forschung/SV-M/. PMID:23442375

  12. Rate dependent fractionation of sulfur isotopes in through-flowing systems

    NASA Astrophysics Data System (ADS)

    Giannetta, M.; Sanford, R. A.; Druhan, J. L.

    2017-12-01

    The fidelity of reactive transport models in quantifying microbial activity in the subsurface is often improved through the use stable isotopes. However, the accuracy of current predictions for microbially mediated isotope fractionations within open through-flowing systems typically depends on nutrient availability. This disparity arises from the common application of a single `effective' fractionation factor assigned to a given system, despite extensive evidence for variability in the fractionation factor between eutrophic environments and many naturally occurring, nutrient-limited environments. Here, we demonstrate a reactive transport model with the capacity to simulate a variable fractionation factor over a range of microbially mediated reduction rates and constrain the model with experimental data for nutrient limited conditions. Two coupled isotope-specific Monod rate laws for 32S and 34S, constructed to quantify microbial sulfate reduction and predict associated S isotope partitioning, were parameterized using a series of batch reactor experiments designed to minimize microbial growth. In the current study, we implement these parameterized isotope-specific rate laws within an open, through-flowing system to predict variable fractionation with distance as a function of sulfate reduction rate. These predictions are tested through a supporting laboratory experiment consisting of a flow-through column packed with homogenous porous media inoculated with the same species of sulfate reducing bacteria used in the previous batch reactors, Desulfovibrio vulgaris. The collective results of batch reactor and flow-through column experiments support a significant improvement for S isotope predictions in isotope-sensitive multi-component reactive transport models through treatment of rate-dependent fractionation. Such an update to the model will better equip reactive transport software for isotope informed characterization of microbial activity within energy and nutrient

  13. Accurate and robust genomic prediction of celiac disease using statistical learning.

    PubMed

    Abraham, Gad; Tye-Din, Jason A; Bhalala, Oneil G; Kowalczyk, Adam; Zobel, Justin; Inouye, Michael

    2014-02-01

    Practical application of genomic-based risk stratification to clinical diagnosis is appealing yet performance varies widely depending on the disease and genomic risk score (GRS) method. Celiac disease (CD), a common immune-mediated illness, is strongly genetically determined and requires specific HLA haplotypes. HLA testing can exclude diagnosis but has low specificity, providing little information suitable for clinical risk stratification. Using six European cohorts, we provide a proof-of-concept that statistical learning approaches which simultaneously model all SNPs can generate robust and highly accurate predictive models of CD based on genome-wide SNP profiles. The high predictive capacity replicated both in cross-validation within each cohort (AUC of 0.87-0.89) and in independent replication across cohorts (AUC of 0.86-0.9), despite differences in ethnicity. The models explained 30-35% of disease variance and up to ∼43% of heritability. The GRS's utility was assessed in different clinically relevant settings. Comparable to HLA typing, the GRS can be used to identify individuals without CD with ≥99.6% negative predictive value however, unlike HLA typing, fine-scale stratification of individuals into categories of higher-risk for CD can identify those that would benefit from more invasive and costly definitive testing. The GRS is flexible and its performance can be adapted to the clinical situation by adjusting the threshold cut-off. Despite explaining a minority of disease heritability, our findings indicate a genomic risk score provides clinically relevant information to improve upon current diagnostic pathways for CD and support further studies evaluating the clinical utility of this approach in CD and other complex diseases.

  14. Laser ablation molecular isotopic spectrometry of carbon isotopes

    NASA Astrophysics Data System (ADS)

    Bol‧shakov, Alexander A.; Mao, Xianglei; Jain, Jinesh; McIntyre, Dustin L.; Russo, Richard E.

    2015-11-01

    Quantitative determination of carbon isotopes using Laser Ablation Molecular Isotopic Spectrometry (LAMIS) is described. Optical emission of diatomic molecules CN and C2 is used in these measurements. Two quantification approaches are presented: empirical calibration of spectra using a set of reference standards and numerical fitting of a simulated spectrum to the experimental one. Formation mechanisms of C2 and CN in laser ablation plasma are briefly reviewed to provide insights for implementation of LAMIS measurements. A simulated spectrum of the 12C2 Swan system was synthesized using four constituents within 473.5-476.5 nm. Simulation included three branches of 12C2 (1-0), branches R(0-0) and R(1-1), and branch P(9-8) of 12C2. Spectral positions of the tail lines in R(0-0) and R(1-1) were experimentally measured, since they were not accurately known before. The Swan band (1-0) of the isotopologue 13C12C was also simulated. Fitting to the experimental spectrum yielded the ratio 13C/12C = 1.08% in a good agreement with measurements by isotope ratio mass spectrometry. LAMIS promises to be useful in coal, oil and shale exploration, carbon sequestration monitoring, and agronomy studies.

  15. The isotopic effects of electron transfer: an explanation for Fe isotope fractionation in nature

    NASA Astrophysics Data System (ADS)

    Kavner, A.; Shahar, A.; Bonet, F.; Simon, J. I.; Young, E.

    2004-12-01

    Recent developments in mass spectrometry techniques have created opportunities to examine the partitioning behavior of stable isotopes of transition metals with a focus on application to iron isotopes. Iron oxidizing and reducing bacteria have been shown to cause isotope fractionations similar in magnitude to those observed in sedimentary environments and it is believed that biological activity is responsible for the most significant Fe isotope fractionation in natural settings. Debate over the use of Fe isotopes as a biological marker resulted from subsequent measurements of fractionations in a variety of abiotic systems. The accumulated evidence, in both biotic and abiotic systems, points to a connection between redox processes and Fe isotope fractionation, however the exact mechanism for isotope fractionation is not yet well understood. Here, we present both a newly-developed theory based on chemical kinetics and preliminary experimental results that quantitatively delineate the relationship between driving force in a charge transfer reaction and resulting Fe isotope fractionation. The theory, based on R. Marcus's chemical kinetics theory for electron transfer (Ann. Rev. Phys. Chem. 15 (1964), 155), predicts that fractionation increases linearly with driving force with a proportionality related to two factors: the difference between isotopic equilibrium exchange of products and reactants, and the reorganization energy along the reaction coordinate. The theoretical predictions were confirmed by measurements of isotopic fractionation associated with electroplating iron metal from a ferrous chloride solution. Isotope fractionation of Fe electroplated under potentiostatic conditions was measured as a function of applied electrochemical potential. As plating voltage was varied from -50 mV to -2.0 V, the isotopic signature of the electroplated iron became depleted in heavy Fe, with δ 56Fe values ranging from -0.106(±0.01) to -2.290(±±0.006)‰ , and corresponding

  16. Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation

    ERIC Educational Resources Information Center

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-01-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one of…

  17. Transient competitive complexation in biological kinetic isotope fractionation explains non-steady isotopic effects: Theory and application to denitrification in soils

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

    Maggi, F.M.; Riley, W.J.

    2009-06-01

    The theoretical formulation of biological kinetic reactions in isotopic applications often assume first-order or Michaelis-Menten-Monod kinetics under the quasi-steady-state assumption to simplify the system kinetics. However, isotopic e ects have the same order of magnitude as the potential error introduced by these simpli cations. Both formulations lead to a constant fractionation factor which may yield incorrect estimations of the isotopic effect and a misleading interpretation of the isotopic signature of a reaction. We have analyzed the isotopic signature of denitri cation in biogeochemical soil systems by Menyailo and Hungate [2006], where high {sup 15}N{sub 2}O enrichment during N{sub 2}O productionmore » and inverse isotope fractionation during N{sub 2}O consumption could not be explained with first-order kinetics and the Rayleigh equation, or with the quasi-steady-state Michaelis-Menten-Monod kinetics. When the quasi-steady-state assumption was relaxed, transient Michaelis-Menten-Monod kinetics accurately reproduced the observations and aided in interpretation of experimental isotopic signatures. These results may imply a substantial revision in using the Rayleigh equation for interpretation of isotopic signatures and in modeling biological kinetic isotope fractionation with first-order kinetics or quasi-steady-state Michaelis-Menten-Monod kinetics.« less

  18. An Interpretable Machine Learning Model for Accurate Prediction of Sepsis in the ICU.

    PubMed

    Nemati, Shamim; Holder, Andre; Razmi, Fereshteh; Stanley, Matthew D; Clifford, Gari D; Buchman, Timothy G

    2018-04-01

    Sepsis is among the leading causes of morbidity, mortality, and cost overruns in critically ill patients. Early intervention with antibiotics improves survival in septic patients. However, no clinically validated system exists for real-time prediction of sepsis onset. We aimed to develop and validate an Artificial Intelligence Sepsis Expert algorithm for early prediction of sepsis. Observational cohort study. Academic medical center from January 2013 to December 2015. Over 31,000 admissions to the ICUs at two Emory University hospitals (development cohort), in addition to over 52,000 ICU patients from the publicly available Medical Information Mart for Intensive Care-III ICU database (validation cohort). Patients who met the Third International Consensus Definitions for Sepsis (Sepsis-3) prior to or within 4 hours of their ICU admission were excluded, resulting in roughly 27,000 and 42,000 patients within our development and validation cohorts, respectively. None. High-resolution vital signs time series and electronic medical record data were extracted. A set of 65 features (variables) were calculated on hourly basis and passed to the Artificial Intelligence Sepsis Expert algorithm to predict onset of sepsis in the proceeding T hours (where T = 12, 8, 6, or 4). Artificial Intelligence Sepsis Expert was used to predict onset of sepsis in the proceeding T hours and to produce a list of the most significant contributing factors. For the 12-, 8-, 6-, and 4-hour ahead prediction of sepsis, Artificial Intelligence Sepsis Expert achieved area under the receiver operating characteristic in the range of 0.83-0.85. Performance of the Artificial Intelligence Sepsis Expert on the development and validation cohorts was indistinguishable. Using data available in the ICU in real-time, Artificial Intelligence Sepsis Expert can accurately predict the onset of sepsis in an ICU patient 4-12 hours prior to clinical recognition. A prospective study is necessary to determine the

  19. Microbes: Agents of Isotopic Change

    NASA Astrophysics Data System (ADS)

    Fogel, M. L.

    2012-12-01

    Microbes drive many of the important oxidation and reduction reactions on Earth; digest almost all forms of organic matter; and can serve as both primary and secondary producers. Because of their versatile biochemistry and physiology, they impart unique isotopic signatures to organic and inorganic materials, which have proven to be key measurements for understanding elemental cycling now and throughout Earth's history. Understanding microbial isotope fractionations in laboratory experiments has been important for interpreting isotopic patterns measured in natural settings. In fact, the pairing of simple experiment with natural observation has been the pathway for interpreting the fingerprint of microbial processes in ancient sediments and rocks. Examples of how key experiments have explained stable isotope fractionations by microbes and advanced the field of microbial ecology will be presented. Learning the isotopic signatures of Earth's microbes is a valuable exercise for predicting what isotopic signatures could be displayed by possible extant or extinct extraterrestrial life. Given the potential for discovery on Mars, Enceladus, and other solar system bodies, new methods and techniques for pinpointing what is unique about microbial isotope signatures is particularly relevant.

  20. Development and Validation of a Multidisciplinary Tool for Accurate and Efficient Rotorcraft Noise Prediction (MUTE)

    NASA Technical Reports Server (NTRS)

    Liu, Yi; Anusonti-Inthra, Phuriwat; Diskin, Boris

    2011-01-01

    A physics-based, systematically coupled, multidisciplinary prediction tool (MUTE) for rotorcraft noise was developed and validated with a wide range of flight configurations and conditions. MUTE is an aggregation of multidisciplinary computational tools that accurately and efficiently model the physics of the source of rotorcraft noise, and predict the noise at far-field observer locations. It uses systematic coupling approaches among multiple disciplines including Computational Fluid Dynamics (CFD), Computational Structural Dynamics (CSD), and high fidelity acoustics. Within MUTE, advanced high-order CFD tools are used around the rotor blade to predict the transonic flow (shock wave) effects, which generate the high-speed impulsive noise. Predictions of the blade-vortex interaction noise in low speed flight are also improved by using the Particle Vortex Transport Method (PVTM), which preserves the wake flow details required for blade/wake and fuselage/wake interactions. The accuracy of the source noise prediction is further improved by utilizing a coupling approach between CFD and CSD, so that the effects of key structural dynamics, elastic blade deformations, and trim solutions are correctly represented in the analysis. The blade loading information and/or the flow field parameters around the rotor blade predicted by the CFD/CSD coupling approach are used to predict the acoustic signatures at far-field observer locations with a high-fidelity noise propagation code (WOPWOP3). The predicted results from the MUTE tool for rotor blade aerodynamic loading and far-field acoustic signatures are compared and validated with a variation of experimental data sets, such as UH60-A data, DNW test data and HART II test data.

  1. Mass spectrometry in Earth sciences: the precise and accurate measurement of time.

    PubMed

    Schaltegger, Urs; Wotzlaw, Jörn-Frederik; Ovtcharova, Maria; Chiaradia, Massimo; Spikings, Richard

    2014-01-01

    Precise determinations of the isotopic compositions of a variety of elements is a widely applied tool in Earth sciences. Isotope ratios are used to quantify rates of geological processes that occurred during the previous 4.5 billion years, and also at the present time. An outstanding application is geochronology, which utilizes the production of radiogenic daughter isotopes by the radioactive decay of parent isotopes. Geochronological tools, involving isotopic analysis of selected elements from smallest volumes of minerals by thermal ionization mass spectrometry, provide precise and accurate measurements of time throughout the geological history of our planet over nine orders of magnitude, from the accretion of the proto-planetary disk, to the timing of the last glaciation. This article summarizes the recent efforts of the Isotope Geochemistry, Geochronology and Thermochronology research group at the University of Geneva to advance the U-Pb geochronological tool to achieve unprecedented precision and accuracy, and presents two examples of its application to two significant open questions in Earth sciences: what are the triggers and timescales of volcanic supereruptions, and what were the causes of mass extinctions in the geological past, driven by global climatic and environmental deterioration?

  2. Isotopic equilibria in aqueous clusters at low temperatures: Insights from the MB-pol many-body potential

    NASA Astrophysics Data System (ADS)

    Videla, Pablo E.; Rossky, Peter J.; Laria, Daniel

    2018-02-01

    By combining path-integrals molecular dynamics simulations with the accurate MB-pol potential energy surface, we investigate the role of alternative potential models on isotopic fractionation ratios between H and D atoms at dangling positions in water clusters at low temperatures. Our results show clear stabilizations of the lighter isotope at dangling sites, characterized by free energy differences ΔG that become comparable to or larger than kBT for temperatures below ˜75 K. The comparison between these results to those previously reported using the empirical q-TIP4P/F water model [P. E. Videla et al., J. Phys. Chem. Lett. 5, 2375 (2014)] reveals that the latter Hamiltonian overestimates the H stabilization by ˜25%. Moreover, predictions from the MB-pol model are in much better agreement with measured results reported for similar isotope equilibria at ice surfaces. The dissection of the quantum kinetic energies into orthogonal directions shows that the dominant differences between the two models are to be found in the anharmonic characteristics of the potential energy surfaces along OH bond directions involved in hydrogen bonds.

  3. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

    PubMed Central

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K.; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G.; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H.

    2017-01-01

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. PMID:27899623

  4. An optimized method for the accurate determination of patulin in apple products by isotope dilution-liquid chromatography/mass spectrometry.

    PubMed

    Seo, Miyeong; Kim, Byungjoo; Baek, Song-Yee

    2015-07-01

    Patulin, a mycotoxin produced by several molds in fruits, has been frequently detected in apple products. Therefore, regulatory bodies have established recommended maximum permitted patulin concentrations for each type of apple product. Although several analytical methods have been adopted to determine patulin in food, quality control of patulin analysis is not easy, as reliable certified reference materials (CRMs) are not available. In this study, as a part of a project for developing CRMs for patulin analysis, we developed isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC/MS/MS) as a higher-order reference method for the accurate value-assignment of CRMs. (13)C7-patulin was used as internal standard. Samples were extracted with ethyl acetate to improve recovery. For further sample cleanup with solid-phase extraction (SPE), the HLB SPE cartridge was chosen after comparing with several other types of SPE cartridges. High-performance liquid chromatography was performed on a multimode column for proper retention and separation of highly polar and water-soluble patulin from sample interferences. Sample extracts were analyzed by LC/MS/MS with electrospray ionization in negative ion mode with selected reaction monitoring of patulin and (13)C7-patulin at m/z 153→m/z 109 and m/z 160→m/z 115, respectively. The validity of the method was tested by measuring gravimetrically fortified samples of various apple products. In addition, the repeatability and the reproducibility of the method were tested to evaluate the performance of the method. The method was shown to provide accurate measurements in the 3-40 μg/kg range with a relative expanded uncertainty of around 1%.

  5. Accurate prediction of vaccine stability under real storage conditions and during temperature excursions.

    PubMed

    Clénet, Didier

    2018-04-01

    Due to their thermosensitivity, most vaccines must be kept refrigerated from production to use. To successfully carry out global immunization programs, ensuring the stability of vaccines is crucial. In this context, two important issues are critical, namely: (i) predicting vaccine stability and (ii) preventing product damage due to excessive temperature excursions outside of the recommended storage conditions (cold chain break). We applied a combination of advanced kinetics and statistical analyses on vaccine forced degradation data to accurately describe the loss of antigenicity for a multivalent freeze-dried inactivated virus vaccine containing three variants. The screening of large amounts of kinetic models combined with a statistical model selection approach resulted in the identification of two-step kinetic models. Predictions based on kinetic analysis and experimental stability data were in agreement, with approximately five percentage points difference from real values for long-term stability storage conditions, after excursions of temperature and during experimental shipments of freeze-dried products. Results showed that modeling a few months of forced degradation can be used to predict various time and temperature profiles endured by vaccines, i.e. long-term stability, short time excursions outside the labeled storage conditions or shipments at ambient temperature, with high accuracy. Pharmaceutical applications of the presented kinetics-based approach are discussed. Copyright © 2018 The Author. Published by Elsevier B.V. All rights reserved.

  6. In vivo prediction of goat kids body composition from the deuterium oxide dilution space determined by isotope-ratio mass spectrometry.

    PubMed

    Lerch, S; Lastel, M L; Grandclaudon, C; Brechet, C; Rychen, G; Feidt, C

    2015-09-01

    Deuterium oxide dilution space (DOS) determination is one of the most accurate methods for in vivo estimation of ruminant body composition. However, the time-consuming vacuum sublimation of blood preceding infrared spectroscopy analysis, which is traditionally used to determine deuterium oxide (DO) concentration, limits its current use. The use of isotope-ratio mass spectrometry (IRMS) to determine the deuterium enrichment and thus quantify DO in plasma could counteract this limitation by reducing the sample preparation for plasma deproteinisation through centrifugal filters. The aim of this study was to validate the DOS technique using IRMS in growing goat kids to establish in vivo prediction equations of body composition. Seventeen weaned male Alpine goat kids (8.6 wk old) received a hay-based diet supplemented with 2 types of concentrates providing medium ( = 9) or high ( = 8) energy levels. Kids were slaughtered at 14.0 ( = 1, medium-energy diet), 17.2 ( = 4, medium-energy diet, and = 4, high-energy diet), or 21.2 wk of age ( = 4, medium-energy diet, and = 4, high-energy diet). Two days before slaughter, DOS was determined after an intravenous injection of 0.2 g DO/kg body mass (BM) and the resulting study of DO dilution kinetics from 4 plasma samples (+5, +7, +29, and +31 h after injection). The deuterium enrichment was analyzed by IRMS. After slaughter, the gut contents were discarded, the empty body (EB) was minced, and EB water, lipid, protein, ash, and energy contents were measured by chemical analyses. Prediction equations for body components measured postmortem were computed from in vivo BM and DOS. The lack of postmortem variation of fat-free EB composition was confirmed (mean of 75.3% [SD 0.6] of water), and the proportion of lipids in the EB tended ( = 0.06) to be greater for the high-energy diet (13.1%) than for the medium-energy diet (11.1%). There was a close negative relationship (residual CV [rCV] = 3.9%, = 0.957) between EB water and lipid

  7. Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

    DOE PAGES

    Sanchez-Gonzalez, A.; Micaelli, P.; Olivier, C.; ...

    2017-06-05

    Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy,more » we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. Lastly, this opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.« less

  8. Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

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

    Sanchez-Gonzalez, A.; Micaelli, P.; Olivier, C.

    Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy,more » we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. Lastly, this opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.« less

  9. Temperature dependence of carbon kinetic isotope effect for the oxidation reaction of ethane by OH radicals under atmospherically relevant conditions

    NASA Astrophysics Data System (ADS)

    Piansawan, Tammarat; Saccon, Marina; Laumer, Werner; Gensch, Iulia; Kiendler-Scharr, Astrid

    2015-04-01

    Modeling of the global distribution of atmospheric ethane sources and sinks by using the 13C isotopic composition requires accurate knowledge of the carbon kinetic isotope effect (KIE) of its atmospheric removal reactions. The quantum mechanical prediction implies the necessity to elucidate the temperature dependence of KIE within atmospherically relevant temperature range by experiment. In this study, the KIE and its temperature dependence for ethane oxidation by OH radicals was investigated at ambient pressure in a temperature range of 243 K to 303 K. The chemical reactions were carried out in a 15 L PFE reaction chamber, suspended in a thermally controlled oven. The isotope ratios of the gas phase components during the course of the reactions were measured by Thermal Desorption -- Gas Chromatography -- Isotope Ratio Mass Spectrometry (TD-GC-IRMS). For each temperature, the KIE was derived from the temporal evolution of the concentration and stable carbon isotope ratio (δ13C) of ethane using a method adapted from the relative reaction rate concept. The room temperature KIE of the ethane reaction with OH radicals was found to be 6.85 ± 0.32 ‰. This value is in agreement with the previously reported value of 8.57 ± 1.95 ‰ [Anderson et al. 2004] but has a substantially lower uncertainty. The experimental results will be discussed with the KIE temperature dependence predicted by quantum mechanical calculations. Reference: Rebecca S. Anderson, Lin Huang, Richard Iannone, Alexandra E. Thompson, and Jochen Rudolph (2004), Carbon Kinetic Isotope Effects in the Gas Phase Reactions of Light Alkanes and Ethene with the OH Radical at 296 ± 4 K, J. Phys. Chem. A, 108, 11537--11544

  10. Accurate and dynamic predictive model for better prediction in medicine and healthcare.

    PubMed

    Alanazi, H O; Abdullah, A H; Qureshi, K N; Ismail, A S

    2018-05-01

    Information and communication technologies (ICTs) have changed the trend into new integrated operations and methods in all fields of life. The health sector has also adopted new technologies to improve the systems and provide better services to customers. Predictive models in health care are also influenced from new technologies to predict the different disease outcomes. However, still, existing predictive models have suffered from some limitations in terms of predictive outcomes performance. In order to improve predictive model performance, this paper proposed a predictive model by classifying the disease predictions into different categories. To achieve this model performance, this paper uses traumatic brain injury (TBI) datasets. TBI is one of the serious diseases worldwide and needs more attention due to its seriousness and serious impacts on human life. The proposed predictive model improves the predictive performance of TBI. The TBI data set is developed and approved by neurologists to set its features. The experiment results show that the proposed model has achieved significant results including accuracy, sensitivity, and specificity.

  11. Accurate prediction of severe allergic reactions by a small set of environmental parameters (NDVI, temperature).

    PubMed

    Notas, George; Bariotakis, Michail; Kalogrias, Vaios; Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

    2015-01-01

    Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions.

  12. Accurate Prediction of Severe Allergic Reactions by a Small Set of Environmental Parameters (NDVI, Temperature)

    PubMed Central

    Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

    2015-01-01

    Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions. PMID:25794106

  13. A Machine Learned Classifier That Uses Gene Expression Data to Accurately Predict Estrogen Receptor Status

    PubMed Central

    Bastani, Meysam; Vos, Larissa; Asgarian, Nasimeh; Deschenes, Jean; Graham, Kathryn; Mackey, John; Greiner, Russell

    2013-01-01

    Background Selecting the appropriate treatment for breast cancer requires accurately determining the estrogen receptor (ER) status of the tumor. However, the standard for determining this status, immunohistochemical analysis of formalin-fixed paraffin embedded samples, suffers from numerous technical and reproducibility issues. Assessment of ER-status based on RNA expression can provide more objective, quantitative and reproducible test results. Methods To learn a parsimonious RNA-based classifier of hormone receptor status, we applied a machine learning tool to a training dataset of gene expression microarray data obtained from 176 frozen breast tumors, whose ER-status was determined by applying ASCO-CAP guidelines to standardized immunohistochemical testing of formalin fixed tumor. Results This produced a three-gene classifier that can predict the ER-status of a novel tumor, with a cross-validation accuracy of 93.17±2.44%. When applied to an independent validation set and to four other public databases, some on different platforms, this classifier obtained over 90% accuracy in each. In addition, we found that this prediction rule separated the patients' recurrence-free survival curves with a hazard ratio lower than the one based on the IHC analysis of ER-status. Conclusions Our efficient and parsimonious classifier lends itself to high throughput, highly accurate and low-cost RNA-based assessments of ER-status, suitable for routine high-throughput clinical use. This analytic method provides a proof-of-principle that may be applicable to developing effective RNA-based tests for other biomarkers and conditions. PMID:24312637

  14. Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

    PubMed

    Li, Fuyi; Li, Chen; Marquez-Lago, Tatiana T; Leier, André; Akutsu, Tatsuya; Purcell, Anthony W; Smith, A Ian; Lithgow, Trevor; Daly, Roger J; Song, Jiangning; Chou, Kuo-Chen

    2018-06-27

    Kinase-regulated phosphorylation is a ubiquitous type of post-translational modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signalling defects caused by aberrant phosphorylation are highly associated with a variety of human diseases, especially cancers. In light of this, a number of computational methods aiming to accurately predict protein kinase family-specific or kinase-specific phosphorylation sites have been established, thereby facilitating phosphoproteomic data analysis. In this work, we present Quokka, a novel bioinformatics tool that allows users to rapidly and accurately identify human kinase family-regulated phosphorylation sites. Quokka was developed by using a variety of sequence scoring functions combined with an optimized logistic regression algorithm. We evaluated Quokka based on well-prepared up-to-date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively. The independent test demonstrates that Quokka improves the prediction performance compared with state-of-the-art computational tools for phosphorylation prediction. In summary, our tool provides users with high-quality predicted human phosphorylation sites for hypothesis generation and biological validation. The Quokka webserver and datasets are freely available at http://quokka.erc.monash.edu/. Supplementary data are available at Bioinformatics online.

  15. Iron and nickel isotope compositions of presolar silicon carbide grains from supernovae

    NASA Astrophysics Data System (ADS)

    Kodolányi, János; Stephan, Thomas; Trappitsch, Reto; Hoppe, Peter; Pignatari, Marco; Davis, Andrew M.; Pellin, Michael J.

    2018-01-01

    We report the carbon, silicon, iron, and nickel isotope compositions of twenty-five presolar SiC grains of mostly supernova (SN) origin. The iron and nickel isotope compositions were measured with the new Chicago Instrument for Laser Ionization, CHILI, which allows the analysis of all iron and nickel isotopes without the isobaric interferences that plagued previous measurements with the NanoSIMS. Despite terrestrial iron and nickel contamination, significant isotopic anomalies in 54Fe/56Fe, 57Fe/56Fe, 60Ni/58Ni, 61Ni/58Ni, 62Ni/58Ni, and 64Ni/58Ni were detected in nine SN grains (of type X). Combined multi-isotope data of three grains with the largest nickel isotope anomalies (>100‰ or <-100‰ in at least one isotope ratio, when expressed as deviation from the solar value) are compared with the predictions of two SN models, one with and one without hydrogen ingestion in the He shell prior to SN explosion. One grain's carbon-silicon-iron-nickel isotope composition is consistent with the prediction of the model without hydrogen ingestion, whereas the other two grains' isotope anomalies could not be reproduced using either SN models. The discrepancies between the measured isotope compositions and model predictions may indicate element fractionation in the SN ejecta prior to or during grain condensation, and reiterate the need for three-dimensional SN models.

  16. Proton Radii of 4,6,8He Isotopes from High-Precision Nucleon-Nucleon Interactions

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

    Caurier, E; Navratil, P

    2005-11-16

    Recently, precision laser spectroscopy on {sup 6}He atoms determined accurately the isotope shift between {sup 4}He and {sup 6}He and, consequently, the charge radius of {sup 6}He. A similar experiment for {sup 8}He is under way. We have performed large-scale ab initio calculations for {sup 4,6,8}He isotopes using high-precision nucleon-nucleon (NN) interactions within the no-core shell model (NCSM) approach. With the CD-Bonn 2000 NN potential we found point-proton root-mean-square (rms) radii of {sup 4}He and {sup 6}He 1.45(1) fm and 1.89(4), respectively, in agreement with experiment and predict the {sup 8}He point proton rms radius to be 1.88(6) fm. Atmore » the same time, our calculations show that the recently developed nonlocal INOY NN potential gives binding energies closer to experiment, but underestimates the charge radii.« less

  17. Equilibrium isotopic fractionation of copper during oxidation/reduction, aqueous complexation and ore-forming processes: Predictions from hybrid density functional theory

    NASA Astrophysics Data System (ADS)

    Sherman, David M.

    2013-10-01

    Copper exists as two isotopes: 65Cu (∼30.85%) and 63Cu (∼69.15%). The isotopic composition of copper in secondary minerals, surface waters and oxic groundwaters is 1-12‰ heavier than that of copper in primary sulfides. Changes in oxidation state and complexation should yield substantial isotopic fractionation between copper species but it is unclear to what extent the observed Cu isotopic variations reflect equilibrium fractionation. Here, I calculate the reduced partition function ratios for chalcopyrite (CuFeS2), cuprite (Cu2O), tenorite (CuO) and aqueous Cu+, Cu+2 complexes using periodic and molecular hybrid density functional theory to predict the equilibrium isotopic fractionation of Cu resulting from oxidation of Cu+ to Cu+2 and by complexation of dissolved Cu. Among the various copper(II) complexes in aqueous environments, there is a significant (1.3‰) range in the reduced partition function ratios. Oxidation and congruent dissolution of chalcopyrite (CuFeS2) to dissolved Cu+2 (as Cu(H2O)5+2) yields 65-63δ(Cu+2-CuFeS2) = 3.1‰ at 25 °C; however, chalcopyrite oxidation/dissolution is incongruent so that the observed isotopic fractionation will be less. Secondary precipitation of cuprite (Cu2O) would yield further enrichment of dissolved 65Cu since 65-63δ(Cu+2-Cu2O) is 1.2‰ at 25 °C. However, precipitation of tenorite (CuO) will favor the heavy isotope by +1.0‰ making dissolved Cu isotopically lighter. These are upper-limit estimates for equilibrium fractionation. Therefore, the extremely large (9‰) fractionations between dissolved Cu+2 (or Cu+2 minerals) and primary Cu+ sulfides observed in supergene environments must reflect Rayleigh (open-system) or kinetic fractionation. Finally the previously proposed (Asael et al., 2009) use of δ65Cu in chalcopyrite to estimate the oxidation state of fluids that transported Cu in stratiform sediment-hosted copper deposits is refined.

  18. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

    PubMed

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H

    2017-01-09

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  20. Isotopic Resonance Hypothesis: Experimental Verification by Escherichia coli Growth Measurements

    NASA Astrophysics Data System (ADS)

    Xie, Xueshu; Zubarev, Roman A.

    2015-03-01

    Isotopic composition of reactants affects the rates of chemical and biochemical reactions. As a rule, enrichment of heavy stable isotopes leads to progressively slower reactions. But the recent isotopic resonance hypothesis suggests that the dependence of the reaction rate upon the enrichment degree is not monotonous. Instead, at some ``resonance'' isotopic compositions, the kinetics increases, while at ``off-resonance'' compositions the same reactions progress slower. To test the predictions of this hypothesis for the elements C, H, N and O, we designed a precise (standard error +/-0.05%) experiment that measures the parameters of bacterial growth in minimal media with varying isotopic composition. A number of predicted resonance conditions were tested, with significant enhancements in kinetics discovered at these conditions. The combined statistics extremely strongly supports the validity of the isotopic resonance phenomenon (p << 10-15). This phenomenon has numerous implications for the origin of life studies and astrobiology, and possible applications in agriculture, biotechnology, medicine, chemistry and other areas.

  1. An Extrapolation of a Radical Equation More Accurately Predicts Shelf Life of Frozen Biological Matrices.

    PubMed

    De Vore, Karl W; Fatahi, Nadia M; Sass, John E

    2016-08-01

    Arrhenius modeling of analyte recovery at increased temperatures to predict long-term colder storage stability of biological raw materials, reagents, calibrators, and controls is standard practice in the diagnostics industry. Predicting subzero temperature stability using the same practice is frequently criticized but nevertheless heavily relied upon. We compared the ability to predict analyte recovery during frozen storage using 3 separate strategies: traditional accelerated studies with Arrhenius modeling, and extrapolation of recovery at 20% of shelf life using either ordinary least squares or a radical equation y = B1x(0.5) + B0. Computer simulations were performed to establish equivalence of statistical power to discern the expected changes during frozen storage or accelerated stress. This was followed by actual predictive and follow-up confirmatory testing of 12 chemistry and immunoassay analytes. Linear extrapolations tended to be the most conservative in the predicted percent recovery, reducing customer and patient risk. However, the majority of analytes followed a rate of change that slowed over time, which was fit best to a radical equation of the form y = B1x(0.5) + B0. Other evidence strongly suggested that the slowing of the rate was not due to higher-order kinetics, but to changes in the matrix during storage. Predicting shelf life of frozen products through extrapolation of early initial real-time storage analyte recovery should be considered the most accurate method. Although in this study the time required for a prediction was longer than a typical accelerated testing protocol, there are less potential sources of error, reduced costs, and a lower expenditure of resources. © 2016 American Association for Clinical Chemistry.

  2. Computational Replication of the Primary Isotope Dependence of Secondary Kinetic Isotope Effects in Solution Hydride-Transfer Reactions: Supporting the Isotopically Different Tunneling Ready State Conformations.

    PubMed

    Derakhshani-Molayousefi, Mortaza; Kashefolgheta, Sadra; Eilers, James E; Lu, Yun

    2016-06-30

    We recently reported a study of the steric effect on the 1° isotope dependence of 2° KIEs for several hydride-transfer reactions in solution (J. Am. Chem. Soc. 2015, 137, 6653). The unusual 2° KIEs decrease as the 1° isotope changes from H to D, and more in the sterically hindered systems. These were explained in terms of a more crowded tunneling ready state (TRS) conformation in D-tunneling, which has a shorter donor-acceptor distance (DAD) than in H-tunneling. To examine the isotopic DAD difference explanation, in this paper, following an activated motion-assisted H-tunneling model that requires a shorter DAD in a heavier isotope transfer process, we computed the 2° KIEs at various H/D positions at different DADs (2.9 Å to 3.5 Å) for the hydride-transfer reactions from 2-propanol to the xanthylium and thioxanthylium ions (Xn(+) and TXn(+)) and their 9-phenyl substituted derivatives (Ph(T)Xn(+)). The calculated 2° KIEs match the experiments and the calculated DAD effect on the 2° KIEs fits the observed 1° isotope effect on the 2° KIEs. These support the motion-assisted H-tunneling model and the isotopically different TRS conformations. Furthermore, it was found that the TRS of the sterically hindered Ph(T)Xn(+) system does not possess a longer DAD than that of the (T)Xn(+) system. This predicts a no larger 1° KIE in the former system than in the latter. The observed 1° KIE order is, however, contrary to the prediction. This implicates the stronger DAD-compression vibrations coupled to the bulky Ph(T)Xn(+) reaction coordinate.

  3. SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

    PubMed Central

    2014-01-01

    Background Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them. Results SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data. Conclusions SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/. PMID:24980894

  4. {beta}-decay half-lives of new neutron-rich rare-earth isotopes {sup 159}Pm,{sup 162}Sm, and {sup 166}Gd

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

    Ichikawa, S.; Asai, M.; Tsukada, K.

    The new neutron-rich rare-earth isotopes {sup 159}Pm, {sup 162}Sm, and {sup 166}Gd produced in the proton-induced fission of {sup 238}U were identified using the JAERI on-line isotope separator (JAERI-ISOL) coupled to a gas-jet transport system. The half-lives of {sup 159}Pm, {sup 162}Sm, and {sup 166}Gd were determined to be 1.5 {+-} 0.2, 2.4 {+-} 0.5, and 4.8 {+-} 1.0 s respectively. The partial decay scheme of {sup 166}Gd was constructed from {gamma}{gamma}-coincidence data. A more accurate half-life value of 25.6 {+-} 2.2 s was obtained for the previously identified isotope {sup 166}Tb. The half-lives measured in the present study aremore » in good agreement with the theoretical predictions calculated by the second generation of the gross theory with the atomic masses evaluated by Audi and Wapstra.« less

  5. Reassessing the stable isotope composition assigned to methane flux from natural wetlands in isotope-constrained budgets

    NASA Astrophysics Data System (ADS)

    Hornibrook, Edward; Maxfield, Peter; Gauci, Vincent; Stott, Andrew

    2013-04-01

    Stable isotope ratios in CH4 preserve information about its origin and history, and are commonly used to constrain global CH4 budgets. Wetlands are key contributors to the atmospheric burden of CH4 and typically are assigned a stable carbon isotope composition of ~-60 permil in isotope-weighted stable isotope models despite the considerable range of δ13C(CH4) values (~ -100 to -40 permil) known to occur in these diverse ecosystems. Kinetic isotope effects (KIEs) associated with the metabolism of CH4-producing microorganisms generate much of the natural variation but highly negative and positive δ13C(CH4) values generally result from secondary processes (e.g., diffusive transport or oxidation by soil methanotrophs). Despite these complexities, consistent patterns exist in the isotope composition of wetland CH4 that can be linked conclusively to trophic status and consequently, natural succession or human perturbations that impact nutrient levels. Another challenge for accurate representation of wetlands in carbon cycle models is parameterisation of sporadic CH4 emission events. Abrupt release of large volumes of CH4-rich bubbles in short periods of time can account for a significant proportion of the annual CH4 flux from a wetland but such events are difficult to detect using conventional methods. New infrared spectroscopy techniques capable of high temporal resolution measurements of CH4 concentration and stable isotope composition can readily quantify short-lived CH4 pulses. Moreover, the isotope data can be used conclusively to determine shifts in the mode of CH4 transport and provide the potential to link initiation of abrupt emission events to forcing by internal or external factors.

  6. Does the emergency surgery score accurately predict outcomes in emergent laparotomies?

    PubMed

    Peponis, Thomas; Bohnen, Jordan D; Sangji, Naveen F; Nandan, Anirudh R; Han, Kelsey; Lee, Jarone; Yeh, D Dante; de Moya, Marc A; Velmahos, George C; Chang, David C; Kaafarani, Haytham M A

    2017-08-01

    The emergency surgery score is a mortality-risk calculator for emergency general operation patients. We sought to examine whether the emergency surgery score predicts 30-day morbidity and mortality in a high-risk group of patients undergoing emergent laparotomy. Using the 2011-2012 American College of Surgeons National Surgical Quality Improvement Program database, we identified all patients who underwent emergent laparotomy using (1) the American College of Surgeons National Surgical Quality Improvement Program definition of "emergent," and (2) all Current Procedural Terminology codes denoting a laparotomy, excluding aortic aneurysm rupture. Multivariable logistic regression analyses were performed to measure the correlation (c-statistic) between the emergency surgery score and (1) 30-day mortality, and (2) 30-day morbidity after emergent laparotomy. As sensitivity analyses, the correlation between the emergency surgery score and 30-day mortality was also evaluated in prespecified subgroups based on Current Procedural Terminology codes. A total of 26,410 emergent laparotomy patients were included. Thirty-day mortality and morbidity were 10.2% and 43.8%, respectively. The emergency surgery score correlated well with mortality (c-statistic = 0.84); scores of 1, 11, and 22 correlated with mortalities of 0.4%, 39%, and 100%, respectively. Similarly, the emergency surgery score correlated well with morbidity (c-statistic = 0.74); scores of 0, 7, and 11 correlated with complication rates of 13%, 58%, and 79%, respectively. The morbidity rates plateaued for scores higher than 11. Sensitivity analyses demonstrated that the emergency surgery score effectively predicts mortality in patients undergoing emergent (1) splenic, (2) gastroduodenal, (3) intestinal, (4) hepatobiliary, or (5) incarcerated ventral hernia operation. The emergency surgery score accurately predicts outcomes in all types of emergent laparotomy patients and may prove valuable as a bedside decision

  7. Investigation of isotope effects of ozone as a function of temperature

    NASA Astrophysics Data System (ADS)

    McMahon, Daniel J.

    Ozone is an important oxidizer in the atmosphere and plays a crucial role as a cleanser, removing various compounds such NOx and SOx. It also is intriguing to those that study stable isotopes as it has a unique signature found in no other oxygen containing molecule. Ozone is observed to fractionate mass independently, which means it does not follow the typical delta 17O /delta18O = 0.52 ratio expected for molecules enriched with 17O and 18O. The magnitude of ozone's mass independent enrichment has been studied in laboratory experiments and atmospheric observations but its explanation is still incomplete. Symmetry of the isotopically substituted ozone is postulated to be the source of mass independent enrichment and this thesis will build on that explanation to examine the magnitude of isotopic enrichment as a function of temperature. Understanding of the kinetics of ozone formation has come a long way from early predictions of enrichments >200‰ However, while our ability to accurately model ozone's bulk isotopic enrichment has improved to include separate rates for the formation of asymmetric and symmetric ozone, rate experiments are sparse for 17O and of low precision. To improve our understanding of ozone's enrichment, this study presents a temperature dependent enrichment experiment and series of models to predict asymmetric mass independent fractionation. This also served to examine ozone's enrichment in the troposphere by using an open flow experimental setup which is in contrast to previous works examining ozone enrichment in a closed system. Our experimental observations show that under tropospheric conditions, ozone should have delta17O ≈ 75‰, delta18O ≈ 80‰, and delta 17O ≈ 33‰. The models were able to match experimental values, often within 1‰, and with minimal assumptions, predict asymmetric ozone to have delta17O=47.5‰. This value is important as ozone transfers its terminal atom to species it oxidizes and will be the starting point to

  8. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Tracing water sources of terrestrial animal populations with stable isotopes: laboratory tests with crickets and spiders.

    PubMed

    McCluney, Kevin E; Sabo, John L

    2010-12-31

    Fluxes of carbon, nitrogen, and water between ecosystem components and organisms have great impacts across levels of biological organization. Although much progress has been made in tracing carbon and nitrogen, difficulty remains in tracing water sources from the ecosystem to animals and among animals (the "water web"). Naturally occurring, non-radioactive isotopes of hydrogen and oxygen in water provide a potential method for tracing water sources. However, using this approach for terrestrial animals is complicated by a change in water isotopes within the body due to differences in activity of heavy and light isotopes during cuticular and transpiratory water losses. Here we present a technique to use stable water isotopes to estimate the mean mix of water sources in a population by sampling a group of sympatric animals over time. Strong correlations between H and O isotopes in the body water of animals collected over time provide linear patterns of enrichment that can be used to predict a mean mix of water sources useful in standard mixing models to determine relative source contribution. Multiple temperature and humidity treatment levels do not greatly alter these relationships, thus having little effect on our ability to estimate this population-level mix of water sources. We show evidence for the validity of using multiple samples of animal body water, collected across time, to estimate the isotopic mix of water sources in a population and more accurately trace water sources. The ability to use isotopes to document patterns of animal water use should be a great asset to biologists globally, especially those studying drylands, droughts, streamside areas, irrigated landscapes, and the effects of climate change.

  10. Isotopic Dependence of GCR Fluence behind Shielding

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Wilson, John W.; Saganti, Premkumar; Kim, Myung-Hee Y.; Cleghorn, Timothy; Zeitlin, Cary; Tripathi, Ram K.

    2006-01-01

    In this paper we consider the effects of the isotopic composition of the primary galactic cosmic rays (GCR), nuclear fragmentation cross-sections, and isotopic-grid on the solution to transport models used for shielding studies. Satellite measurements are used to describe the isotopic composition of the GCR. For the nuclear interaction data-base and transport solution, we use the quantum multiple-scattering theory of nuclear fragmentation (QMSFRG) and high-charge and energy (HZETRN) transport code, respectively. The QMSFRG model is shown to accurately describe existing fragmentation data including proper description of the odd-even effects as function of the iso-spin dependence on the projectile nucleus. The principle finding of this study is that large errors (+/-100%) will occur in the mass-fluence spectra when comparing transport models that use a complete isotopic-grid (approx.170 ions) to ones that use a reduced isotopic-grid, for example the 59 ion-grid used in the HZETRN code in the past, however less significant errors (<+/-20%) occur in the elemental-fluence spectra. Because a complete isotopic-grid is readily handled on small computer workstations and is needed for several applications studying GCR propagation and scattering, it is recommended that they be used for future GCR studies.

  11. NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data.

    PubMed

    Mao, Wusong; Cong, Peisheng; Wang, Zhiheng; Lu, Longjian; Zhu, Zhongliang; Li, Tonghua

    2013-01-01

    Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 entries), we achieved an accuracy of 75.8% for S8 (the eight states accuracy) and 87.8% for S3 (the three states accuracy). This is higher than only using chemical shifts or sequence data, and confirms that the chemical shift and the structure profile are significant features for shape string prediction and their combination prominently improves the accuracy of the predictor. We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at http://cal.tongji.edu.cn/NMRDSP/index.jsp.

  12. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-07

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  13. Does mesenteric venous imaging assessment accurately predict pathologic invasion in localized pancreatic ductal adenocarcinoma?

    PubMed

    Clanton, Jesse; Oh, Stephen; Kaplan, Stephen J; Johnson, Emily; Ross, Andrew; Kozarek, Richard; Alseidi, Adnan; Biehl, Thomas; Picozzi, Vincent J; Helton, William S; Coy, David; Dorer, Russell; Rocha, Flavio G

    2018-05-09

    Accurate prediction of mesenteric venous involvement in pancreatic ductal adenocarcinoma (PDAC) is necessary for adequate staging and treatment. A retrospective cohort study was conducted in PDAC patients at a single institution. All patients with resected PDAC and staging CT and EUS between 2003 and 2014 were included and sub-divided into "upfront resected" and "neoadjuvant chemotherapy (NAC)" groups. Independent imaging re-review was correlated to venous resection and venous invasion. Sensitivity, specificity, positive and negative predictive values were then calculated. A total of 109 patients underwent analysis, 60 received upfront resection, and 49 NAC. Venous resection (30%) and vein invasion (13%) was less common in patients resected upfront than those who received NAC (53% and 16%, respectively). Both CT and EUS had poor sensitivity (14-44%) but high specificity (75-95%) for detecting venous resection and vein invasion in patients resected upfront, whereas sensitivity was high (84-100%) and specificity was low (27-44%) after NAC. Preoperative CT and EUS in PDAC have similar efficacy but different predictive capacity in assessing mesenteric venous involvement depending on whether patients are resected upfront or received NAC. Both modalities appear to significantly overestimate true vascular involvement and should be interpreted in the appropriate clinical context. Copyright © 2018 International Hepato-Pancreato-Biliary Association Inc. Published by Elsevier Ltd. All rights reserved.

  14. High Resolution Gamma Ray Analysis of Medical Isotopes

    NASA Astrophysics Data System (ADS)

    Chillery, Thomas

    2015-10-01

    Compton-suppressed high-purity Germanium detectors at the University of Massachusetts Lowell have been used to study medical radioisotopes produced at Brookhaven Linac Isotope Producer (BLIP), in particular isotopes such as Pt-191 used for cancer therapy in patients. The ability to precisely analyze the concentrations of such radio-isotopes is essential for both production facilities such as Brookhaven and consumer hospitals across the U.S. Without accurate knowledge of the quantities and strengths of these isotopes, it is possible for doctors to administer incorrect dosages to patients, thus leading to undesired results. Samples have been produced at Brookhaven and shipped to UML, and the advanced electronics and data acquisition capabilities at UML have been used to extract peak areas in the gamma decay spectra. Levels of Pt isotopes in diluted samples have been quantified, and reaction cross-sections deduced from the irradiation parameters. These provide both cross checks with published work, as well as a rigorous quantitative framework with high quality state-of-the-art detection apparatus in use in the experimental nuclear physics community.

  15. Accurate load prediction by BEM with airfoil data from 3D RANS simulations

    NASA Astrophysics Data System (ADS)

    Schneider, Marc S.; Nitzsche, Jens; Hennings, Holger

    2016-09-01

    In this paper, two methods for the extraction of airfoil coefficients from 3D CFD simulations of a wind turbine rotor are investigated, and these coefficients are used to improve the load prediction of a BEM code. The coefficients are extracted from a number of steady RANS simulations, using either averaging of velocities in annular sections, or an inverse BEM approach for determination of the induction factors in the rotor plane. It is shown that these 3D rotor polars are able to capture the rotational augmentation at the inner part of the blade as well as the load reduction by 3D effects close to the blade tip. They are used as input to a simple BEM code and the results of this BEM with 3D rotor polars are compared to the predictions of BEM with 2D airfoil coefficients plus common empirical corrections for stall delay and tip loss. While BEM with 2D airfoil coefficients produces a very different radial distribution of loads than the RANS simulation, the BEM with 3D rotor polars manages to reproduce the loads from RANS very accurately for a variety of load cases, as long as the blade pitch angle is not too different from the cases from which the polars were extracted.

  16. Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

    PubMed Central

    Micsonai, András; Wien, Frank; Kernya, Linda; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

    2015-01-01

    Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. PMID:26038575

  17. Effects of spin crossover on iron isotope fractionation in Earth's mantle

    NASA Astrophysics Data System (ADS)

    Qin, T.; Shukla, G.; Wu, Z.; Wentzcovitch, R.

    2017-12-01

    Recent studies have revealed that the iron isotope composition of mid-ocean ridge basalts (MORBs) is +0.1‰ richer in heavy Fe (56Fe) relative to chondrites, while basalts from Mars and Vesta have similar Fe isotopic composition as chondrites. Several hypotheses could explain these observations. For instance, iron isotope fractionation may have occurred during core formation or Earth may have lost some light Fe isotope during the high temperature event in the early Earth. To better understand what drove these isotopic observations, it is important to obtain accurate Fe isotope fractionation factors among mantle and core phases at the relevant P-T conditions. In bridgmanite, the most voluminous mineral in the lower mantle, Fe can occupy more than one crystalline site, be in ferrous and/or ferric states, and may undergo a spin crossover in the lower mantle. Iron isotopic fractionation properties under spin crossover are poorly constrained, while this may be relevant to differentiation of Earth's magma ocean. In this study we address the effect of these multiple states on the iron isotope fractionation factors between mantle and core phases.

  18. Site-Specific Carbon Isotopes in Organics

    NASA Astrophysics Data System (ADS)

    Piasecki, A.; Eiler, J. M.

    2012-12-01

    propane and labeled propane (13CH3-12CH2-12CH3). Results are consistent with the expected relative fractionations between the two fragments, indicating limited 'scrambling' of carbon positions of less than 2% in the source. The limits of precision of this method are currently ~0.5 ‰, sufficient to resolve known or suspected position-specific isotope effects in propane. We have explored the expected temperature-dependent equilibrium isotopic distributions of propane using density functional theory and quantum mechanical models of vibrational isotope effects. These models predict the homogeneous isotope exchange equilibria among the various isotopologues of propane, which include several of a wide range of effects that should be measurable by our methods. At 300 K we predict that the central carbon site is 15‰ higher in δ13C and 95 ‰ higher in δD than the terminal carbon site; similarly the molecule containing both a 13C and D in the central site is enriched by ~120 ‰ relative to a random isotopic distribution at 300 K. These predictions present targets for future experimental and empirical studies of the temperature dependence of isotopic ordering in propane. More generally, the methods we are developing for the study of intramolecular isotopic distributions in propane will serve as a model for future study of similar effects in other organic compounds. [1]DeNiro, Epstein (1977) Science Volume 197, 261-263.

  19. Pb isotope compositions of modern deep sea turbidites

    NASA Astrophysics Data System (ADS)

    Hemming, S. R.; McLennan, S. M.

    2001-01-01

    Modern deep sea turbidite muds and sands collected from Lamont piston cores represent a large range in age of detrital sources as well as a spectrum of tectonic settings. Pb isotope compositions of all but three of the 66 samples lie to the right of the 4.56 Ga Geochron, and most also lie along a slope consistent with a time-integrated κ ( 232Th/ 238U) between 3.8 and 4.2. Modern deep sea turbidites show a predictable negative correlation between both Pb and Sr isotope ratios and ɛNd and ɛHf, clearly related to the age of continental sources. However, the consistency between Pb and Nd isotopes breaks down for samples with very old provenance ( ɛNd<-20) that are far less radiogenic than predicted by the negative correlation. The correlations among Sr, Nd and Hf isotopes also become more scattered in samples with very old provenance. The unradiogenic Pb isotopic character of modern sediments with Archean Nd model ages is consistent with a model where Th and U abundances of the Archean upper crust are significantly lower than the post-Archean upper crust.

  20. Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles.

    PubMed

    Zou, Lingyun; Nan, Chonghan; Hu, Fuquan

    2013-12-15

    Various human pathogens secret effector proteins into hosts cells via the type IV secretion system (T4SS). These proteins play important roles in the interaction between bacteria and hosts. Computational methods for T4SS effector prediction have been developed for screening experimental targets in several isolated bacterial species; however, widely applicable prediction approaches are still unavailable In this work, four types of distinctive features, namely, amino acid composition, dipeptide composition, .position-specific scoring matrix composition and auto covariance transformation of position-specific scoring matrix, were calculated from primary sequences. A classifier, T4EffPred, was developed using the support vector machine with these features and their different combinations for effector prediction. Various theoretical tests were performed in a newly established dataset, and the results were measured with four indexes. We demonstrated that T4EffPred can discriminate IVA and IVB effectors in benchmark datasets with positive rates of 76.7% and 89.7%, respectively. The overall accuracy of 95.9% shows that the present method is accurate for distinguishing the T4SS effector in unidentified sequences. A classifier ensemble was designed to synthesize all single classifiers. Notable performance improvement was observed using this ensemble system in benchmark tests. To demonstrate the model's application, a genome-scale prediction of effectors was performed in Bartonella henselae, an important zoonotic pathogen. A number of putative candidates were distinguished. A web server implementing the prediction method and the source code are both available at http://bioinfo.tmmu.edu.cn/T4EffPred.

  1. Towards accurate cosmological predictions for rapidly oscillating scalar fields as dark matter

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

    Ureña-López, L. Arturo; Gonzalez-Morales, Alma X., E-mail: lurena@ugto.mx, E-mail: alma.gonzalez@fisica.ugto.mx

    2016-07-01

    As we are entering the era of precision cosmology, it is necessary to count on accurate cosmological predictions from any proposed model of dark matter. In this paper we present a novel approach to the cosmological evolution of scalar fields that eases their analytic and numerical analysis at the background and at the linear order of perturbations. The new method makes use of appropriate angular variables that simplify the writing of the equations of motion, and which also show that the usual field variables play a secondary role in the cosmological dynamics. We apply the method to a scalar fieldmore » endowed with a quadratic potential and revisit its properties as dark matter. Some of the results known in the literature are recovered, and a better understanding of the physical properties of the model is provided. It is confirmed that there exists a Jeans wavenumber k {sub J} , directly related to the suppression of linear perturbations at wavenumbers k > k {sub J} , and which is verified to be k {sub J} = a √ mH . We also discuss some semi-analytical results that are well satisfied by the full numerical solutions obtained from an amended version of the CMB code CLASS. Finally we draw some of the implications that this new treatment of the equations of motion may have in the prediction of cosmological observables from scalar field dark matter models.« less

  2. Stable-isotope fingerprints of biological agents as forensic tools.

    PubMed

    Horita, Juske; Vass, Arpad A

    2003-01-01

    Naturally occurring stable isotopes of light elements in chemical and biological agents may possess unique "stable-isotope fingerprints" depending on their sources and manufacturing processes. To test this hypothesis, two strains of bacteria (Bacillus globigii and Erwinia agglomerans) were grown under controlled laboratory conditions. We observed that cultured bacteria cells faithfully inherited the isotopic composition (hydrogen, carbon, and nitrogen) of media waters and substrates in predictable manners in terms of bacterial metabolism and that even bacterial cells of the same strain, which grew in media water and substrates of different isotopic compositions, have readily distinguishable isotopic signatures. These "stable-isotopic fingerprints" of chemical and biological agents can be used as forensic tools in the event of biochemical terrorist attacks.

  3. Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

    PubMed Central

    Nissley, Daniel A.; Sharma, Ajeet K.; Ahmed, Nabeel; Friedrich, Ulrike A.; Kramer, Günter; Bukau, Bernd; O'Brien, Edward P.

    2016-01-01

    The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. Here we develop a chemical kinetic model that calculates a protein domain's co-translational folding curve during synthesis using only the domain's bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. We then make predictions for a number of different proteins in yeast and find that synonymous codon substitutions, which change translation-elongation rates, can switch some protein domains from folding post-translationally to folding co-translationally—a result consistent with previous experimental studies. Our approach explains essential features of co-translational folding curves and predicts how varying the translation rate at different codon positions along a transcript's coding sequence affects this self-assembly process. PMID:26887592

  4. Isotope fractionation by multicomponent diffusion (Invited)

    NASA Astrophysics Data System (ADS)

    Watkins, J. M.; Liang, Y.; Richter, F. M.; Ryerson, F. J.; DePaolo, D. J.

    2013-12-01

    Isotope fractionation by multicomponent diffusion The isotopic composition of mineral phases can be used to probe the temperatures and rates of mineral formation as well as the degree of post-mineralization alteration. The ability to interpret stable isotope variations is limited by our knowledge of three key parameters and their relative importance in determining the composition of a mineral grain and its surroundings: (1) thermodynamic (equilibrium) partitioning, (2) mass-dependent diffusivities, and (3) mass-dependent reaction rate coefficients. Understanding the mechanisms of diffusion and reaction in geological liquids, and how these mass transport processes discriminate between isotopes, represents an important problem that is receiving considerable attention in the geosciences. Our focus in this presentation will be isotope fractionation by chemical diffusion. Previous studies have documented that diffusive isotope effects vary depending on the cation as well as the liquid composition, but the ability to predict diffusive isotope effects from theory is limited; for example, it is unclear whether the magnitude of diffusive isotopic fractionations might also vary with the direction of diffusion in composition space. To test this hypothesis and to further guide the theoretical treatment of isotope diffusion, two chemical diffusion experiments and one self diffusion experiment were conducted at 1250°C and 0.7 GPa. In one experiment (A-B), CaO and Na2O counter-diffuse rapidly in the presence of a small SiO2 gradient. In the other experiment (D-E), CaO and SiO2 counter-diffuse more slowly in a small Na2O gradient. In both chemical diffusion experiments, Ca isotopes become fractionated by chemical diffusion but by different amounts, documenting for the first time that the magnitude of isotope fractionation by diffusion depends on the direction of diffusion in composition space. The magnitude of Ca isotope fractionation that develops is positively correlated with

  5. Fast-Neutron Activation of Long-Lived Isotopes in Enriched Ge

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

    Elliott, Steven R.; Guiseppe, Vincente; LaRoque, B. H.

    2010-11-16

    We measured the production of 57Co, 54Mn, 68Ge, 65Zn, and 60Co in an sample of Ge enriched in isotope 76 due to high-energy neutron interactions. These isotopes are critical in understanding background in Ge detectors used for double-beta decay experiments. These isotopes are produced by cosmogenic-neutron interactions in the detectors while they reside on the Earth's surface. We compared the measured production to that predicted by cross-section calculations based on CEM03.02. The cross section calculations over-predict our measurements by approximately a factor of 2-3 depending on isotope. We then use the measured cosmic-ray neutron ux and our results to predictmore » the cosmogenic production rate with an accuracy near 15%.« less

  6. Shifts in rotifer life history in response to stable isotope enrichment: testing theories of isotope effects on organismal growth

    PubMed Central

    2017-01-01

    In ecology, stable isotope labelling is commonly used for tracing material transfer in trophic interactions, nutrient budgets and biogeochemical processes. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism growth and metabolism. This assumption is, however, challenged by theoretical considerations and experimental studies on kinetic isotope effects in vivo. Here, I demonstrate profound changes in life histories of the rotifer Brachionus plicatilis fed 15N-enriched algae (0.4–5.0 at%); i.e. at the enrichment levels commonly used in ecological studies. These findings support theoretically predicted effects of heavy isotope enrichment on growth, metabolism and ageing in biological systems and underline the importance of accounting for such effects when using stable isotope labelling in experimental studies. PMID:28405367

  7. Application of zinc isotope tracer technology in tracing soil heavy metal pollution

    NASA Astrophysics Data System (ADS)

    Norbu, Namkha; Wang, Shuguang; Xu, Yan; Yang, Jianqiang; Liu, Qiang

    2017-08-01

    Recent years the soil heavy metal pollution has become increasingly serious, especially the zinc pollution. Due to the complexity of this problem, in order to prevent and treat the soil pollution, it's crucial to accurately and quickly find out the pollution sources and control them. With the development of stable isotope tracer technology, it's able to determine the composition of zinc isotope. Based on the theory of zinc isotope tracer technique, and by means of doing some latest domestic and overseas literature research about the zinc isotope multi-receiving cups of inductively coupled plasma mass spectrometer (MC-ICP-MS) testing technology, this paper summarized the latest research results about the pollution tracer of zinc isotope, and according to the deficiencies and existing problems of previous research, made outlooks of zinc isotope fractionation mechanism, repository establishment and tracer multiple solutions.

  8. Diet-to-female and female-to-pup isotopic discrimination in South American sea lions.

    PubMed

    Drago, Massimiliano; Franco-Trecu, Valentina; Cardona, Luis; Inchausti, Pablo

    2015-08-30

    The use of accurate, species-specific diet-tissue discrimination factors is a critical requirement when applying stable isotope mixing models to predict consumer diet composition. Thus, diet-to-female and female-to-pup isotopic discrimination factors in several tissues for both captive and wild South American sea lions were estimated to provide appropriate values for quantifying feeding preferences at different timescales in the wild populations of this species. Stable carbon and nitrogen isotope ratios in the blood components of two female-pup pairs and females' prey muscle from captive individuals were determined by elemental analyzer/isotope ratio mass spectrometry (EA/IRMS) to calculate the respective isotopic discrimination factors. The same analysis was carried out in both blood components, and skin and hair tissues for eight female-pup pairs from wild individuals. Mean diet-to-female Δ(13) C and Δ(15) N values were higher than the female-to-pup ones. Pup tissues were more (15) N-enriched than their mothers but (13) C-depleted in serum and plasma tissues. In most of the tissue comparisons, we found differences in both Δ(15) N and Δ(13) C values, supporting tissue-specific discrimination. We found no differences between captive and wild female-to-pup discrimination factors either in Δ(13) C or Δ(15) N values of blood components. Only the stable isotope ratios in pup blood are good proxies of the individual lactating females. Thus, we suggest that blood components are more appropriate to quantify the feeding habits of wild individuals of this species. Furthermore, because female-to-pup discrimination factors for blood components did not differ between captive and wild individuals, we suggest that results for captive experiments can be extrapolated to wild South American sea lion populations. Copyright © 2015 John Wiley & Sons, Ltd.

  9. Silicon in Mars' Core: A Prediction Based on Mars Model Using Nitrogen and Oxygen Isotopes in SNC Meteorites

    NASA Technical Reports Server (NTRS)

    Mohapatra, R. K.; Murty, S. V. S.

    2002-01-01

    Chemical and (oxygen) isotopic compositions of SNC meteorites have been used by a number of workers to infer the nature of precursor materials for the accretion of Mars. The idea that chondritic materials played a key role in the formation of Mars has been the central assumption in these works. Wanke and Dreibus have proposed a mixture of two types of chondritic materials, differing in oxygen fugacity but having CI type bulk chemical composition for the nonvolatile elements, for Mars' precursor. But a number of studies based on high pressure and temperature melting experiments do not favor a CI type bulk planet composition for Mars, as it predicts a bulk planet Fe/Si ratio much higher than that reported from the recent Pathfinder data. Oxygen forms the bulk of Mars (approximately 40% by wt.) and might provide clues to the type of materials that formed Mars. But models based on the oxygen isotopic compositions of SNC meteorites predict three different mixtures of precursor materials for Mars: 90% H + 10% CM, 85% H + 11% CV + 4% CI and 45% EH + 55% H. As each of these models has been shown to be consistent with the bulk geophysical properties (such as mean density, and moment of inertia factor) of Mars, the nature of the material that accreted to form Mars remains ambiguous.

  10. A gene expression biomarker accurately predicts estrogen ...

    EPA Pesticide Factsheets

    The EPA’s vision for the Endocrine Disruptor Screening Program (EDSP) in the 21st Century (EDSP21) includes utilization of high-throughput screening (HTS) assays coupled with computational modeling to prioritize chemicals with the goal of eventually replacing current Tier 1 screening tests. The ToxCast program currently includes 18 HTS in vitro assays that evaluate the ability of chemicals to modulate estrogen receptor α (ERα), an important endocrine target. We propose microarray-based gene expression profiling as a complementary approach to predict ERα modulation and have developed computational methods to identify ERα modulators in an existing database of whole-genome microarray data. The ERα biomarker consisted of 46 ERα-regulated genes with consistent expression patterns across 7 known ER agonists and 3 known ER antagonists. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression data sets from experiments in MCF-7 cells. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% or 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) OECD ER reference chemicals including “very weak” agonists and replicated predictions based on 18 in vitro ER-associated HTS assays. For 114 chemicals present in both the HTS data and the MCF-7 c

  11. Capillary absorption spectrometer and process for isotopic analysis of small samples

    DOEpatents

    Alexander, M. Lizabeth; Kelly, James F.; Sams, Robert L.; Moran, James J.; Newburn, Matthew K.; Blake, Thomas A.

    2016-03-29

    A capillary absorption spectrometer and process are described that provide highly sensitive and accurate stable absorption measurements of analytes in a sample gas that may include isotopologues of carbon and oxygen obtained from gas and biological samples. It further provides isotopic images of microbial communities that allow tracking of nutrients at the single cell level. It further targets naturally occurring variations in carbon and oxygen isotopes that avoids need for expensive isotopically labeled mixtures which allows study of samples taken from the field without modification. The method also permits sampling in vivo permitting real-time ambient studies of microbial communities.

  12. Capillary absorption spectrometer and process for isotopic analysis of small samples

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

    Alexander, M. Lizabeth; Kelly, James F.; Sams, Robert L.

    A capillary absorption spectrometer and process are described that provide highly sensitive and accurate stable absorption measurements of analytes in a sample gas that may include isotopologues of carbon and oxygen obtained from gas and biological samples. It further provides isotopic images of microbial communities that allow tracking of nutrients at the single cell level. It further targets naturally occurring variations in carbon and oxygen isotopes that avoids need for expensive isotopically labeled mixtures which allows study of samples taken from the field without modification. The process also permits sampling in vivo permitting real-time ambient studies of microbial communities.

  13. PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides.

    PubMed

    Islam, S M Ashiqul; Sajed, Tanvir; Kearney, Christopher Michel; Baker, Erich J

    2015-07-05

    Numerous organisms have evolved a wide range of toxic peptides for self-defense and predation. Their effective interstitial and macro-environmental use requires energetic and structural stability. One successful group of these peptides includes a tri-disulfide domain arrangement that offers toxicity and high stability. Sequential tri-disulfide connectivity variants create highly compact disulfide folds capable of withstanding a variety of environmental stresses. Their combination of toxicity and stability make these peptides remarkably valuable for their potential as bio-insecticides, antimicrobial peptides and peptide drug candidates. However, the wide sequence variation, sources and modalities of group members impose serious limitations on our ability to rapidly identify potential members. As a result, there is a need for automated high-throughput member classification approaches that leverage their demonstrated tertiary and functional homology. We developed an SVM-based model to predict sequential tri-disulfide peptide (STP) toxins from peptide sequences. One optimized model, called PredSTP, predicted STPs from training set with sensitivity, specificity, precision, accuracy and a Matthews correlation coefficient of 94.86%, 94.11%, 84.31%, 94.30% and 0.86, respectively, using 200 fold cross validation. The same model outperforms existing prediction approaches in three independent out of sample testsets derived from PDB. PredSTP can accurately identify a wide range of cystine stabilized peptide toxins directly from sequences in a species-agnostic fashion. The ability to rapidly filter sequences for potential bioactive peptides can greatly compress the time between peptide identification and testing structural and functional properties for possible antimicrobial and insecticidal candidates. A web interface is freely available to predict STP toxins from http://crick.ecs.baylor.edu/.

  14. PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

    PubMed

    Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets.

  15. Isotopic composition of zinc, copper, and iron in lunar samples

    NASA Astrophysics Data System (ADS)

    Moynier, F.; Albarède, F.; Herzog, G. F.

    2006-12-01

    We determined by ICP-MS the concentrations and isotopic ratios of Fe, Cu, and Zn in the Ti-rich lunar basalt 74275, in the lunar orange glass 74220, and in up to 10 lunar soils, namely, 14163, 15231, 64501, 66041, 68841, 69941, 70011, 72501, 75081, and 76501. Two analyses of zinc in lunar basalt 74275 give δ 66Zn = 0.17‰ and 0.75‰, values within the range of those measured in terrestrial basalts; copper in lunar basalt 74275 has δ 65Cu ˜ +1.4‰, which is isotopically heavier than values observed in terrestrial basalts. In the orange glass, we measured δ 56Fe = -0.24‰, δ 65Cu = -0.42‰, and δ 66Zn ˜ -3.6‰. These values of δ are more negative than those obtained for 74275 and for typical lunar basalts, but for Cu, comparable to those observed in terrestrial sulfides and meteorites. In lunar soils we found 0.11‰ ⩽ δ 56Fe ⩽ 0.51‰, 2.6‰ ⩽ δ 65Cu ⩽ 4.5‰, and 2.2‰ ⩽ δ 66Zn ⩽ 6.4‰. Insofar as we can generalize from a small sample set, S, Fe, Cu, Zn, and Cd show similar trends in isotopic fractionation on the Moon. Lunar basalts have nearly terrestrial isotopic ratios. Relative to the lunar basalt 74275, the pyroclastic glass 74220 is enriched in the lighter isotopes of Fe, Cu, and Zn, and the soils are enriched in the heavier isotopes of Fe, Cu, and Zn. The patterns in the basalts are likely inherited from the source material; the light-isotope enrichments seen in the orange glass originated during lava fountaining or, less probably, during partial condensation of vapor; and the heavy-isotope enrichments in the lunar soils were likely created by a combination of processes that included micrometeorite vaporization and sputtering. In the orange glass, the light-isotope enrichments (relative to lunar basalts) of Zn are larger than those of Cu. If these enrichments reflect accurately the isotopic composition of the gas, they suggest that Cu is more volatile than Zn in the liquid from which the gas derived. A simple model built on

  16. Oxygen isotope thermometry of quartz-Al2SiO5veins in high-grade metamorphic rocks on Naxos island (Greece)

    NASA Astrophysics Data System (ADS)

    Putlitz, Benita; Valley, John; Matthews, Alan; Katzir, Yaron

    2002-04-01

    Diffusion models predict that peak metamorphic temperatures are best recorded by the oxygen isotope fractionation between minerals in a bi-mineralic rock in which a refractory accessory mineral with slow oxygen diffusion rate is modally minor to a mineral with a faster diffusion rate. This premise is demonstrated for high-grade metamorphism on the island of Naxos, Greece, where quartz-kyanite oxygen isotope thermometry from veins in high-grade metamorphic pelites gives temperatures of 635-690 °C. These temperatures are in excellent agreement with independent thermometry for the regional M2 peak metamorphic conditions and show that the vein minerals isotopically equilibrated at the peak of metamorphism. Quartz-sillimanite fractionations in the same veins give similar temperatures (680+/-35 °C) and suggest that the veins grew near to the kyanite-sillimanite boundary, corresponding to pressures of 6.5 to 7.5 kbar for temperatures of 635-685 °C. By contrast, quartz-kyanite and quartz-biotite pairs in the host rocks yield lower temperature estimates than the veins (590-600 and 350-550 °C, respectively). These lower apparent temperatures are also predicted from calculations of diffusional resetting in the polyphase host-rock system. The data demonstrate that bimineralic vein assemblages can be used as accurate thermometers in high-temperature rocks whereas retrograde exchange remains a major problem in many polymineralic rocks.

  17. Isotopic Effects in Nuclear Fragmentation and GCR Transport Problems

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.

    2002-01-01

    Improving the accuracy of the galactic cosmic ray (GCR) environment and transport models is an important goal in preparing for studies of the projected risks and the efficiency of potential mitigations methods for space exploration. In this paper we consider the effects of the isotopic composition of the primary cosmic rays and the isotopic dependence of nuclear fragmentation cross sections on GCR transport models. Measurements are used to describe the isotopic composition of the GCR including their modulation throughout the solar cycle. The quantum multiple-scattering approach to nuclear fragmentation (QMSFRG) is used as the data base generator in order to accurately describe the odd-even effect in fragment production. Using the Badhwar and O'Neill GCR model, the QMSFRG model and the HZETRN transport code, the effects of the isotopic dependence of the primary GCR composition and on fragment production for transport problems is described for a complete GCR isotopic-grid. The principle finding of this study is that large errors ( 100%) will occur in the mass-flux spectra when comparing the complete isotopic-grid (141 ions) to a reduced isotopic-grid (59 ions), however less significant errors 30%) occur in the elemental-flux spectra. Because the full isotopic-grid is readily handled on small computer work-stations, it is recommended that they be used for future GCR studies.

  18. Device and method for accurately measuring concentrations of airborne transuranic isotopes

    DOEpatents

    McIsaac, Charles V.; Killian, E. Wayne; Grafwallner, Ervin G.; Kynaston, Ronnie L.; Johnson, Larry O.; Randolph, Peter D.

    1996-01-01

    An alpha continuous air monitor (CAM) with two silicon alpha detectors and three sample collection filters is described. This alpha CAM design provides continuous sampling and also measures the cumulative transuranic (TRU), i.e., plutonium and americium, activity on the filter, and thus provides a more accurate measurement of airborne TRU concentrations than can be accomplished using a single fixed sample collection filter and a single silicon alpha detector.

  19. Device and method for accurately measuring concentrations of airborne transuranic isotopes

    DOEpatents

    McIsaac, C.V.; Killian, E.W.; Grafwallner, E.G.; Kynaston, R.L.; Johnson, L.O.; Randolph, P.D.

    1996-09-03

    An alpha continuous air monitor (CAM) with two silicon alpha detectors and three sample collection filters is described. This alpha CAM design provides continuous sampling and also measures the cumulative transuranic (TRU), i.e., plutonium and americium, activity on the filter, and thus provides a more accurate measurement of airborne TRU concentrations than can be accomplished using a single fixed sample collection filter and a single silicon alpha detector. 7 figs.

  20. Accurate multimodal probabilistic prediction of conversion to Alzheimer's disease in patients with mild cognitive impairment.

    PubMed

    Young, Jonathan; Modat, Marc; Cardoso, Manuel J; Mendelson, Alex; Cash, Dave; Ourselin, Sebastien

    2013-01-01

    Accurately identifying the patients that have mild cognitive impairment (MCI) who will go on to develop Alzheimer's disease (AD) will become essential as new treatments will require identification of AD patients at earlier stages in the disease process. Most previous work in this area has centred around the same automated techniques used to diagnose AD patients from healthy controls, by coupling high dimensional brain image data or other relevant biomarker data to modern machine learning techniques. Such studies can now distinguish between AD patients and controls as accurately as an experienced clinician. Models trained on patients with AD and control subjects can also distinguish between MCI patients that will convert to AD within a given timeframe (MCI-c) and those that remain stable (MCI-s), although differences between these groups are smaller and thus, the corresponding accuracy is lower. The most common type of classifier used in these studies is the support vector machine, which gives categorical class decisions. In this paper, we introduce Gaussian process (GP) classification to the problem. This fully Bayesian method produces naturally probabilistic predictions, which we show correlate well with the actual chances of converting to AD within 3 years in a population of 96 MCI-s and 47 MCI-c subjects. Furthermore, we show that GPs can integrate multimodal data (in this study volumetric MRI, FDG-PET, cerebrospinal fluid, and APOE genotype with the classification process through the use of a mixed kernel). The GP approach aids combination of different data sources by learning parameters automatically from training data via type-II maximum likelihood, which we compare to a more conventional method based on cross validation and an SVM classifier. When the resulting probabilities from the GP are dichotomised to produce a binary classification, the results for predicting MCI conversion based on the combination of all three types of data show a balanced accuracy

  1. A Test of Carbon and Oxygen Stable Isotope Ratio Process Models in Tree Rings.

    NASA Astrophysics Data System (ADS)

    Roden, J. S.; Farquhar, G. D.

    2008-12-01

    Stable isotopes ratios of carbon and oxygen in tree ring cellulose have been used to infer environmental change. Process-based models have been developed to clarify the potential of historic tree ring records for meaningful paleoclimatic reconstructions. However, isotopic variation can be influenced by multiple environmental factors making simplistic interpretations problematic. Recently, the dual isotope approach, where the variation in one stable isotope ratio (e.g. oxygen) is used to constrain the interpretation of variation in another (e.g. carbon), has been shown to have the potential to de-convolute isotopic analysis. However, this approach requires further testing to determine its applicability for paleo-reconstructions using tree-ring time series. We present a study where the information needed to parameterize mechanistic models for both carbon and oxygen stable isotope ratios were collected in controlled environment chambers for two species (Pinus radiata and Eucalyptus globulus). The seedlings were exposed to treatments designed to modify leaf temperature, transpiration rates, stomatal conductance and photosynthetic capacity. Both species were grown for over 100 days under two humidity regimes that differed by 20%. Stomatal conductance was significantly different between species and for seedlings under drought conditions but not between other treatments or humidity regimes. The treatments produced large differences in transpiration rate and photosynthesis. Treatments that effected photosynthetic rates but not stomatal conductance influenced carbon isotope discrimination more than those that influenced primarily conductance. The various treatments produced a range in oxygen isotope ratios of 7 ‰. Process models predicted greater oxygen isotope enrichment in tree ring cellulose than observed. The oxygen isotope ratios of bulk leaf water were reasonably well predicted by current steady-state models. However, the fractional difference between models that

  2. Isotope dilution ICP-MS with laser-assisted sample introduction for direct determination of sulfur in petroleum products.

    PubMed

    Boulyga, Sergei F; Heilmann, Jens; Heumann, Klaus G

    2005-08-01

    Inductively coupled plasma isotope dilution mass spectrometry (ICP-IDMS) with direct laser-assisted introduction of isotope-diluted samples into the plasma, using a laser ablation system with high ablation rates, was developed for accurate sulfur determinations in different petroleum products such as 'sulfur-free' premium gasoline, diesel fuel, and heating oil. Two certified gas oil reference materials were analyzed for method validation. Two different 34S-enriched spike compounds, namely, elementary sulfur dissolved in xylene and dibenzothiophene in hexane, were synthesized and tested for their usefulness in this isotope dilution technique. The isotope-diluted sample was adsorbed on a filter-paper-like material, which was fixed in a special holder for irradiation by the laser beam. Under these conditions no time-dependent spike/analyte fractionation was only observed for the dibenzothiophene spike during the laser ablation process, which means that the measured 34S/32S isotope ratio of the isotope-diluted sample remained constant-a necessary precondition for accurate results with the isotope dilution technique. A comparison of LA-ICP-IDMS results with the certified values of the gas oil reference materials and with results obtained from ICP-IDMS analyses with wet sample digestion demonstrated the accuracy of the new LA-ICP-IDMS method in the concentration range of 9.2 microg g(-1) ('sulfur-free' premium gasoline) to 10.4 mg g(-1) (gas oil reference material BCR 107). The detection limit for sulfur by LA-ICP-IDMS is 0.04 microg g(-1) and the analysis time is only about 10 min, which therefore also qualifies this method for accurate determinations of low sulfur contents in petroleum products on a routine level.

  3. Accurate determination of sulfur in gasoline and related fuel samples using isotope dilution ICP-MS with direct sample injection and microwave-assisted digestion.

    PubMed

    Heilmann, Jens; Boulyga, Sergei F; Heumann, Klaus G

    2004-09-01

    Inductively coupled plasma isotope-dilution mass spectrometry (ICP-IDMS) with direct injection of isotope-diluted samples into the plasma, using a direct injection high-efficiency nebulizer (DIHEN), was applied for accurate sulfur determinations in sulfur-free premium gasoline, gas oil, diesel fuel, and heating oil. For direct injection a micro-emulsion consisting of the corresponding organic sample and an aqueous 34S-enriched spike solution with additions of tetrahydronaphthalene and Triton X-100, was prepared. The ICP-MS parameters were optimized with respect to high sulfur ion intensities, low mass-bias values, and high precision of 32S/34S ratio measurements. For validation of the DIHEN-ICP-IDMS method two certified gas oil reference materials (BCR 107 and BCR 672) were analyzed. For comparison a wet-chemical ICP-IDMS method was applied with microwave-assisted digestion using decomposition of samples in a closed quartz vessel inserted into a normal microwave system. The results from both ICP-IDMS methods agree well with the certified values of the reference materials and also with each other for analyses of other samples. However, the standard deviation of DIHEN-ICP-IDMS was about a factor of two higher (5-6% RSD at concentration levels above 100 mircog g(-1)) compared with those of wet-chemical ICP-IDMS, mainly due to inhomogeneities of the micro-emulsion, which causes additional plasma instabilities. Detection limits of 4 and 18 microg g(-1) were obtained for ICP-IDMS in connection with microwave-assisted digestion and DIHEN-ICP-IDMS, respectively, with a sulfur background of the used Milli-Q water as the main limiting factor for both methods.

  4. Improvements in Precise and Accurate Isotope Ratio Determination via LA-MC-ICP-MS by Application of an Alternative Data Reduction Protocol

    NASA Astrophysics Data System (ADS)

    Fietzke, J.; Liebetrau, V.; Guenther, D.; Frische, M.; Zumholz, K.; Hansteen, T. H.; Eisenhauer, A.

    2008-12-01

    An alternative approach for the evaluation of isotope ratio data using LA-MC-ICP-MS will be presented. In contrast to previously applied methods it is based on the simultaneous responses of all analyte isotopes of interest and the relevant interferences without performing a conventional background correction. Significant improvements in precision and accuracy can be achieved when applying this new method and will be discussed based on the results of two first methodical applications: a) radiogenic and stable Sr isotopes in carbonates b) stable chlorine isotopes of pyrohydrolytic extracts. In carbonates an external reproducibility of the 87Sr/86Sr ratios of about 19 ppm (RSD) was achieved, an improvement of about a factor of 5. For recent and sub-recent marine carbonates a mean radiogenic strontium isotope ratio 87Sr/86Sr of 0.709170±0.000007 (2SE) was determined, which agrees well with the value of 0.7091741±0.0000024 (2SE) reported for modern sea water [1,2]. Stable chlorine isotope ratios were determined ablating pyrohydrolytic extracts with a reproducibility of about 0.05‰ (RSD). For basaltic reference material JB1a and JB2 chlorine isotope ratios were determined relative to SMOC (standard mean ocean chlorinity) δ37ClJB-1a = (-0.99±0.06) ‰ and δ37ClJB-1a = (-0.60±0.03) ‰ (SD), respectively, in accordance with published data [3]. The described strategies for data reduction are considered to be generally applicable for all isotope ratio measurements using LA-MC-ICP-MS. [1] J.M. McArthur, D. Rio, F. Massari, D. Castradori, T.R. Bailey, M. Thirlwall, S. Houghton, Palaeogeo. Palaeoclim. Palaeoeco., 2006, 242 (126), doi: 10.1016/j.palaeo.2006.06.004 [2] J. Fietzke, V. Liebetrau, D. Guenther, K. Guers, K. Hametner, K. Zumholz, T.H. Hansteen and A. Eisenhauer, J. Anal. At. Spectrom., 2008, 23, 955-961, doi:10.1039/B717706B [3] J. Fietzke, M. Frische, T.H. Hansteen and A. Eisenhauer, J. Anal. At. Spectrom., 2008, 23, 769-772, doi:10.1039/B718597A

  5. A novel fibrosis index comprising a non-cholesterol sterol accurately predicts HCV-related liver cirrhosis.

    PubMed

    Ydreborg, Magdalena; Lisovskaja, Vera; Lagging, Martin; Brehm Christensen, Peer; Langeland, Nina; Buhl, Mads Rauning; Pedersen, Court; Mørch, Kristine; Wejstål, Rune; Norkrans, Gunnar; Lindh, Magnus; Färkkilä, Martti; Westin, Johan

    2014-01-01

    Diagnosis of liver cirrhosis is essential in the management of chronic hepatitis C virus (HCV) infection. Liver biopsy is invasive and thus entails a risk of complications as well as a potential risk of sampling error. Therefore, non-invasive diagnostic tools are preferential. The aim of the present study was to create a model for accurate prediction of liver cirrhosis based on patient characteristics and biomarkers of liver fibrosis, including a panel of non-cholesterol sterols reflecting cholesterol synthesis and absorption and secretion. We evaluated variables with potential predictive significance for liver fibrosis in 278 patients originally included in a multicenter phase III treatment trial for chronic HCV infection. A stepwise multivariate logistic model selection was performed with liver cirrhosis, defined as Ishak fibrosis stage 5-6, as the outcome variable. A new index, referred to as Nordic Liver Index (NoLI) in the paper, was based on the model: Log-odds (predicting cirrhosis) = -12.17+ (age × 0.11) + (BMI (kg/m(2)) × 0.23) + (D7-lathosterol (μg/100 mg cholesterol)×(-0.013)) + (Platelet count (x10(9)/L) × (-0.018)) + (Prothrombin-INR × 3.69). The area under the ROC curve (AUROC) for prediction of cirrhosis was 0.91 (95% CI 0.86-0.96). The index was validated in a separate cohort of 83 patients and the AUROC for this cohort was similar (0.90; 95% CI: 0.82-0.98). In conclusion, the new index may complement other methods in diagnosing cirrhosis in patients with chronic HCV infection.

  6. Molecular controls on Cu and Zn isotopic fractionation in Fe-Mn crusts

    NASA Astrophysics Data System (ADS)

    Little, S. H.; Sherman, D. M.; Vance, D.; Hein, J. R.

    2014-06-01

    The isotopic systems of the transition metals are increasingly being developed as oceanic tracers, due to their tendency to be fractionated by biological and/or redox-related processes. However, for many of these promising isotope systems the molecular level controls on their isotopic fractionations are only just beginning to be explored. Here we investigate the relative roles of abiotic and biotic fractionation processes in controlling modern seawater Cu and Zn isotopic compositions. Scavenging to Fe-Mn oxides represents the principal output for Cu and Zn to sediments deposited under normal marine (oxic) conditions. Using Fe-Mn crusts as an analogue for these dispersed phases, we investigate the phase association and crystal chemistry of Cu and Zn in such sediments. We present the results of an EXAFS study that demonstrate unequivocally that Cu and Zn are predominantly associated with the birnessite (δ-MnO2) phase in Fe-Mn crusts, as previously predicted from sequential leaching experiments (e.g., Koschinsky and Hein, 2003). The crystal chemistry of Cu and Zn in the crusts implies a reduction in coordination number in the sorbed phase relative to the free metal ion in seawater. Thus, theory would predict equilibrium fractionations that enrich the heavy isotope in the sorbed phase (e.g., Schauble, 2004). In natural samples, Fe-Mn crusts and nodules are indeed isotopically heavy in Zn isotopes (at ∼1‰) compared to deep seawater (at ∼0.5‰), consistent with the predicted direction of equilibrium isotopic fractionation based on our observations of the coordination environment of sorbed Zn. Further, ∼50% of inorganic Zn‧ is chloro-complexed (the other ∼50% is present as the free Zn2+ ion), and complexation by Cl- is also predicted to favour equilibrium partitioning of light Zn isotopes into the dissolved phase. The heavy Zn isotopic composition of Fe-Mn crusts and nodules relative to seawater can therefore be explained by an inorganic fractionation during

  7. Towards more accurate vegetation mortality predictions

    DOE PAGES

    Sevanto, Sanna Annika; Xu, Chonggang

    2016-09-26

    Predicting the fate of vegetation under changing climate is one of the major challenges of the climate modeling community. Here, terrestrial vegetation dominates the carbon and water cycles over land areas, and dramatic changes in vegetation cover resulting from stressful environmental conditions such as drought feed directly back to local and regional climate, potentially leading to a vicious cycle where vegetation recovery after a disturbance is delayed or impossible.

  8. Stable isotope deltas: Tiny, yet robust signatures in nature

    USGS Publications Warehouse

    Brand, Willi A.; Coplen, Tyler B.

    2012-01-01

    Although most of them are relatively small, stable isotope deltas of naturally occurring substances are robust and enable workers in anthropology, atmospheric sciences, biology, chemistry, environmental sciences, food and drug authentication, forensic science, geochemistry, geology, oceanography, and paleoclimatology to study a variety of topics. Two fundamental processes explain the stable isotope deltas measured in most terrestrial systems: isotopic fractionation and isotope mixing. Isotopic fractionation is the result of equilibrium or kinetic physicochemical processes that fractionate isotopes because of small differences in physical or chemical properties of molecular species having different isotopes. It is shown that the mixing of radioactive and stable isotope end members can be modelled to provide information on many natural processes, including 14C abundances in the modern atmosphere and the stable hydrogen and oxygen isotopic compositions of the oceans during glacial and interglacial times. The calculation of mixing fractions using isotope balance equations with isotope deltas can be substantially in error when substances with high concentrations of heavy isotopes (e.g. 13C, 2H, and 18O ) are mixed. In such cases, calculations using mole fractions are preferred as they produce accurate mixing fractions. Isotope deltas are dimensionless quantities. In the International System of Units (SI), these quantities have the unit 1 and the usual list of prefixes is not applicable. To overcome traditional limitations with expressing orders of magnitude differences in isotope deltas, we propose the term urey (symbol Ur), after Harold C. Urey, for the unit 1. In such a manner, an isotope delta value expressed traditionally as−25 per mil can be written as−25 mUr (or−2.5 cUr or−0.25 dUr; the use of any SI prefix is possible). Likewise, very small isotopic differences often expressed in per meg ‘units’ are easily included (e.g. either+0.015 ‰ or+15 per meg

  9. Using stable isotopes to associate migratory shorebirds with their wintering locations in Argentina

    USGS Publications Warehouse

    Farmer, A.H.; Abril, M.; Fernandez, M.; Torres, J.; Kester, C.; Bern, C.

    2004-01-01

    We are evaluating the use of stable isotopes to identify the wintering areas of Neotropical migratory shorebirds in Argentina. Our goal is to associate individual birds, captured on the breeding grounds or in migration with specific winter sites, thereby helping to identify distinct areas used by different subpopulations. In January and February 2002 and 2003, we collected flight feathers from shorebirds at 23 wintering sites distributed across seven province s in Argentina (n = 170). Feathers samples were pre- pared and analyzed for δ13C, δ15N, δ34S, δ18O and δD by continuous flow methods. A discriminant function based on deuterium alone was not an accurate predictor of a shorebird’s province of origin, ranging from 8% correct (Santiago del Estero) to 80% correct (San ta Cruz). When other isotopes were included, the prediction accuracy increased substantially (from 56% in Buenos Aires to 100% in Tucumán). The improvement in accuracy was due to C/N, which separated D-depleted sites in the Andes from those in the south, and the inclusion of S separated sites with respect to their distance from the Atlantic. We also were able to correctly discriminate shorebirds from among two closely spaced sites within the province of Tierra del Fuego. These results suggest the feasibility of identifying the origin of a shorebird at a provincial level of accuracy, as well as uniquely identifying birds from some closely spaced sites. There is a high degree of intra- and inter-bird variability, especially in the Pampas region, where there is wide variety of wetland/water conditions. In that important shorebird region, the variability itself may in fact be the “signature.” Future addition of trace elements to the analyses may improve predictions based solely on stable isotopes.

  10. A high order accurate finite element algorithm for high Reynolds number flow prediction

    NASA Technical Reports Server (NTRS)

    Baker, A. J.

    1978-01-01

    A Galerkin-weighted residuals formulation is employed to establish an implicit finite element solution algorithm for generally nonlinear initial-boundary value problems. Solution accuracy, and convergence rate with discretization refinement, are quantized in several error norms, by a systematic study of numerical solutions to several nonlinear parabolic and a hyperbolic partial differential equation characteristic of the equations governing fluid flows. Solutions are generated using selective linear, quadratic and cubic basis functions. Richardson extrapolation is employed to generate a higher-order accurate solution to facilitate isolation of truncation error in all norms. Extension of the mathematical theory underlying accuracy and convergence concepts for linear elliptic equations is predicted for equations characteristic of laminar and turbulent fluid flows at nonmodest Reynolds number. The nondiagonal initial-value matrix structure introduced by the finite element theory is determined intrinsic to improved solution accuracy and convergence. A factored Jacobian iteration algorithm is derived and evaluated to yield a consequential reduction in both computer storage and execution CPU requirements while retaining solution accuracy.

  11. Reliable and accurate point-based prediction of cumulative infiltration using soil readily available characteristics: A comparison between GMDH, ANN, and MLR

    NASA Astrophysics Data System (ADS)

    Rahmati, Mehdi

    2017-08-01

    Developing accurate and reliable pedo-transfer functions (PTFs) to predict soil non-readily available characteristics is one of the most concerned topic in soil science and selecting more appropriate predictors is a crucial factor in PTFs' development. Group method of data handling (GMDH), which finds an approximate relationship between a set of input and output variables, not only provide an explicit procedure to select the most essential PTF input variables, but also results in more accurate and reliable estimates than other mostly applied methodologies. Therefore, the current research was aimed to apply GMDH in comparison with multivariate linear regression (MLR) and artificial neural network (ANN) to develop several PTFs to predict soil cumulative infiltration point-basely at specific time intervals (0.5-45 min) using soil readily available characteristics (RACs). In this regard, soil infiltration curves as well as several soil RACs including soil primary particles (clay (CC), silt (Si), and sand (Sa)), saturated hydraulic conductivity (Ks), bulk (Db) and particle (Dp) densities, organic carbon (OC), wet-aggregate stability (WAS), electrical conductivity (EC), and soil antecedent (θi) and field saturated (θfs) water contents were measured at 134 different points in Lighvan watershed, northwest of Iran. Then, applying GMDH, MLR, and ANN methodologies, several PTFs have been developed to predict cumulative infiltrations using two sets of selected soil RACs including and excluding Ks. According to the test data, results showed that developed PTFs by GMDH and MLR procedures using all soil RACs including Ks resulted in more accurate (with E values of 0.673-0.963) and reliable (with CV values lower than 11 percent) predictions of cumulative infiltrations at different specific time steps. In contrast, ANN procedure had lower accuracy (with E values of 0.356-0.890) and reliability (with CV values up to 50 percent) compared to GMDH and MLR. The results also revealed

  12. Perceived Physician-informed Weight Status Predicts Accurate Weight Self-Perception and Weight Self-Regulation in Low-income, African American Women.

    PubMed

    Harris, Charlie L; Strayhorn, Gregory; Moore, Sandra; Goldman, Brian; Martin, Michelle Y

    2016-01-01

    Obese African American women under-appraise their body mass index (BMI) classification and report fewer weight loss attempts than women who accurately appraise their weight status. This cross-sectional study examined whether physician-informed weight status could predict weight self-perception and weight self-regulation strategies in obese women. A convenience sample of 118 low-income women completed a survey assessing demographic characteristics, comorbidities, weight self-perception, and weight self-regulation strategies. BMI was calculated during nurse triage. Binary logistic regression models were performed to test hypotheses. The odds of obese accurate appraisers having been informed about their weight status were six times greater than those of under-appraisers. The odds of those using an "approach" self-regulation strategy having been physician-informed were four times greater compared with those using an "avoidance" strategy. Physicians are uniquely positioned to influence accurate weight self-perception and adaptive weight self-regulation strategies in underserved women, reducing their risk for obesity-related morbidity.

  13. Paleoproxies: Heavy Stable Isotope Perspectives

    NASA Astrophysics Data System (ADS)

    Nagler, T. F.; Hippler, D.; Siebert, C.; Kramers, J. D.

    2002-12-01

    potential to solve this problem for a given set of samples and thus to model the ocean system more accurately in different scales. Besides all complications some important applications of heavy stable isotopes as paleoproxies already emerge. Pilot studies indicate that Mo isotopes may present a proxy for the extend of anoxic condition in past oceans. On a finer scale the same system appears to provide a measure of (bio)-chemical redox-changes related to diagenesis. The Ca isotope system may complement more classical sea surface temperature proxies in particular environments. Promising results exist for polar waters (N. pachy left), as well as indications on the seasonality under global greenhouse conditions ~110-50 Ma ago. However, the heavily species dependent Ca isotope fractionation can not be interpreted by just adopting concepts and findings from the oxygen system. While a complication to the ease of use as SST proxy, this species dependence offers pathways to unravel different modes of bio-calcifications. Given the complexity of the matter, collaboration of specialists of different fields will be needed to develop successful process-related hypotheses and diagnostic tools.

  14. The Carbon Isotope Ratio in Local Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Goto, Miwa; Usuda, Tomonori; Takato, Naruhisa; Masahiko, Hayashi; Sakamoto, Seiichi; Mitchell, George

    We report the carbon isotope ratio in nearby molecular clouds LkHα 101, AFGL 490, and Mon R2 IRS 3. The vibrational transition bands of 12CO ν = 2 ← 0 and 13CO ν = 1 ← 0 were observed with high resolution near-infrared spectroscopy (R = 23,000) to measure the relative abundance of 13CO to 12CO. The isotopic ratios are 12CO/13CO = 1379 (LkHα 101), 8649 (AFGL 490), and 158 (Mon R2 IRS 3), which is twice higher than in the solar neighborhood. The molecular clouds are with high visible extinction (AV = 10 70 mag), well shielded from destructive FUV field. It is questionable that the selective photo-destruction of 13CO plays a major role in biasing isotope ratio. Uncertainty in the Doppler parameters of the unresolved absorption lines, and possible emission filling of fundamental transitions are suspected to account for the high 12CO/13CO ratio. Higher resolution spectroscopy (R ~ 100,000) is the key to go for the accurate measurement of isotope ratio.

  15. A Hydrogen and He Isotope Nanoprobe

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

    Doyle, Barney L.; Van Deusen, Stuart B.

    Materials that incorporate hydrogen and helium isotopes are of great interest at Sandia and throughout the NNSA and DOE. The Ion Beam Lab at SNL-NM has invented techniques using micron to mm-size MeV ion beams to recoil these light isotopes (Elastic Recoil Detection or ERD) that can very accurately make such measurements. However, there are many measurements that would benefit NW and DOE that require much better resolution, such as the distribution of H isotopes (and 3He) in individual grains of materials relevant to TPBARs, H and He-embrittlement of weapon components important to Tritium Sustainment Programs, issues with GTSs, batteries…more » Higher resolution would also benefit the field of materials science in general. To address these and many other issues, nm-scale lateral resolution is required. This LDRD demonstrated that neutral H atoms could be recoiled through a thin film by 70 keV electrons and detected with a Channeltron electron multiplier (CEM). The electrons were steered away from the CEM by strong permanent magnets. This proved the feasibility that the high energy electrons from a transmissionelectron- microscope-TEM can potentially be used to recoil and subsequently detect (e-ERD), quantify and map the concentration of H and He isotopes with nm resolution. This discovery could lead to a TEM-based H/He-isotope nanoprobe with 1000x higher resolution than currently available.« less

  16. Zinc isotope anomalies in Allende meteorite inclusions

    NASA Technical Reports Server (NTRS)

    Loss, R. D.; Lugmair, G. W.

    1990-01-01

    The isotopic compositions of Zn, Cr, Ti, and Ca have been measured in a number of CAIs from the Allende meteorite. The aim was to test astrophysical models which predict large excesses of Zn-66 to accompany excesses in the neutron-rich isotopes of Ca, Ti, Cr, and Ni. Some of the CAIs show clearly resolved but small excesses for Zn-66 which are at least an order of magnitude smaller than predicted. This result may simply reflect the volatility and chemical behavior of Zn as compared to the other (more refractory) anomalous elements found in these samples. Alternatively, revision of parameters and assumptions used for the model calculations may be required.

  17. Evaluation strategies for isotope ratio measurements of single particles by LA-MC-ICPMS.

    PubMed

    Kappel, S; Boulyga, S F; Dorta, L; Günther, D; Hattendorf, B; Koffler, D; Laaha, G; Leisch, F; Prohaska, T

    2013-03-01

    Data evaluation is a crucial step when it comes to the determination of accurate and precise isotope ratios computed from transient signals measured by multi-collector-inductively coupled plasma mass spectrometry (MC-ICPMS) coupled to, for example, laser ablation (LA). In the present study, the applicability of different data evaluation strategies (i.e. 'point-by-point', 'integration' and 'linear regression slope' method) for the computation of (235)U/(238)U isotope ratios measured in single particles by LA-MC-ICPMS was investigated. The analyzed uranium oxide particles (i.e. 9073-01-B, CRM U010 and NUSIMEP-7 test samples), having sizes down to the sub-micrometre range, are certified with respect to their (235)U/(238)U isotopic signature, which enabled evaluation of the applied strategies with respect to precision and accuracy. The different strategies were also compared with respect to their expanded uncertainties. Even though the 'point-by-point' method proved to be superior, the other methods are advantageous, as they take weighted signal intensities into account. For the first time, the use of a 'finite mixture model' is presented for the determination of an unknown number of different U isotopic compositions of single particles present on the same planchet. The model uses an algorithm that determines the number of isotopic signatures by attributing individual data points to computed clusters. The (235)U/(238)U isotope ratios are then determined by means of the slopes of linear regressions estimated for each cluster. The model was successfully applied for the accurate determination of different (235)U/(238)U isotope ratios of particles deposited on the NUSIMEP-7 test samples.

  18. Predicted osteotomy planes are accurate when using patient-specific instrumentation for total knee arthroplasty in cadavers: a descriptive analysis.

    PubMed

    Kievit, A J; Dobbe, J G G; Streekstra, G J; Blankevoort, L; Schafroth, M U

    2018-06-01

    Malalignment of implants is a major source of failure during total knee arthroplasty. To achieve more accurate 3D planning and execution of the osteotomy cuts during surgery, the Signature (Biomet, Warsaw) patient-specific instrumentation (PSI) was used to produce pin guides for the positioning of the osteotomy blocks by means of computer-aided manufacture based on CT scan images. The research question of this study is: what is the transfer accuracy of osteotomy planes predicted by the Signature PSI system for preoperative 3D planning and intraoperative block-guided pin placement to perform total knee arthroplasty procedures? The transfer accuracy achieved by using the Signature PSI system was evaluated by comparing the osteotomy planes predicted preoperatively with the osteotomy planes seen intraoperatively in human cadaveric legs. Outcomes were measured in terms of translational and rotational errors (varus, valgus, flexion, extension and axial rotation) for both tibia and femur osteotomies. Average translational errors between the osteotomy planes predicted using the Signature system and the actual osteotomy planes achieved was 0.8 mm (± 0.5 mm) for the tibia and 0.7 mm (± 4.0 mm) for the femur. Average rotational errors in relation to predicted and achieved osteotomy planes were 0.1° (± 1.2°) of varus and 0.4° (± 1.7°) of anterior slope (extension) for the tibia, and 2.8° (± 2.0°) of varus and 0.9° (± 2.7°) of flexion and 1.4° (± 2.2°) of external rotation for the femur. The similarity between osteotomy planes predicted using the Signature system and osteotomy planes actually achieved was excellent for the tibia although some discrepancies were seen for the femur. The use of 3D system techniques in TKA surgery can provide accurate intraoperative guidance, especially for patients with deformed bone, tailored to individual patients and ensure better placement of the implant.

  19. Using vegetation cover type to predict and scale peatland methane dynamics.

    NASA Astrophysics Data System (ADS)

    McArthur, K. J.; McCalley, C. K.; Palace, M. W.; Varner, R. K.; Herrick, C.; DelGreco, J. L.

    2015-12-01

    Permafrost ecosystems contain about 50% of the global soil carbon. As these northern ecosystems experience warmer temperature, permafrost thaws and may result in an increase in atmospheric methane. We examined a thawing and discontinuous permafrost boundary at Stordalen Mire, in Northern Sweden, in an effort to better understand methane emissions. Stable isotope analysis of methane in peatland porewater can give insights into the pathway of methane production. By measuring δ13CH4 we can predict whether a system is dominated by either hydrogenotrophic or acetaclastic methane production. Currently, it is a challenge to scale these isotopic patterns, thus, atmospheric inversion models simply assume that acetoclastic production dominates. We analyzed porewater samples collected across a range of vegetation cover types for δ13CH4 using a QCL (Quantum Cascade Laser Spectrometer) in conjunction with highly accurate GPS (3-10cm) measurements and high-resolution UAV imaging. We found δ13CH4 values ranging from -88‰ to -41‰, with averages based on cover type and other vegetation features showing differences of up to -15‰. We then used a computer neural network to predict cover types across Stordalen Mire from UAV imagery based on field-based plot measurements and training samples.. This prediction map was used to scale methane flux and isotope measurements. Our results suggest that the current values used in atmospheric inversion studies may oversimplify the relationship between plant and microbial communities in complex permafrost landscapes. As we gain a deeper understanding of how vegetation relates to methanogenic communities, understanding the spatial component of ecosystem methane metabolism and distribution will be increasingly valuable.

  20. Preparative separation of underivatized amino acids for compound-specific stable isotope analysis and radiocarbon dating of hydrolyzed bone collagen.

    PubMed

    Tripp, Jennifer A; McCullagh, James S O; Hedges, Robert E M

    2006-01-01

    Analysis of stable and radioactive isotopes from bone collagen provides useful information to archaeologists about the origin and age of bone artifacts. Isolation and analysis of single amino acids from the proteins can provide additional and more accurate information by removing contamination and separating a bulk isotope signal into its constituent parts. In this paper, we report a new method for the separation and isolation of underivatized amino acids from bone collagen, and their analysis by isotope ratio MS and accelerator MS. RP chromatography is used to separate the amino acids with nonpolar side chains, followed by an ion pair separation to isolate the remaining amino acids. The method produces single amino acids with little or no contamination from the separation process and allows for the measurement of accurate stable isotope ratios and pure samples for radiocarbon dating.

  1. Redefining the utility of the three-isotope method

    NASA Astrophysics Data System (ADS)

    Cao, Xiaobin; Bao, Huiming

    2017-09-01

    The equilibrium isotope fractionation factor αeq is a fundamental parameter in the study of stable isotope effects. Experimentally, it has been difficult to establish that a system has attained equilibrium. The three-isotope method, using the initial trajectory of changing isotope ratios (e.g. 16O, 17O, and 18O) to deduce the final equilibrium point of isotope exchange, has long been hailed as the most rigorous experimental approach. However, over the years some researchers have cautioned on the limitations of this method, but the foundation of three-isotope method has not been properly examined and the method is still widely used in calibrating αeq for both traditional and increasingly non-traditional isotope systems today. Here, using water-water and dissolved CO2-water oxygen exchange as model systems, we conduct an isotopologues-specific kinetic analysis of the exchange processes and explore the underlying assumptions and validity of the three-isotope method. We demonstrate that without knowing the detailed exchange kinetics a priori the three-isotope method cannot lead to a reliable αeq. For a two-reservoir exchanging system, α determined by this method may be αeq, kinetic isotope effect, or apparent kinetic isotope effect, which can all bear different values. When multiple reservoirs exist during exchange, the evolving trajectory can be complex and hard to predict. Instead of being a tool for αeq determination, three-isotope method should be used as a tool for studying kinetic isotope effect, apparent kinetic isotope effect, and detailed exchange kinetics in diverse systems.

  2. CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.

    PubMed

    Testa, Alison C; Hane, James K; Ellwood, Simon R; Oliver, Richard P

    2015-03-11

    The impact of gene annotation quality on functional and comparative genomics makes gene prediction an important process, particularly in non-model species, including many fungi. Sets of homologous protein sequences are rarely complete with respect to the fungal species of interest and are often small or unreliable, especially when closely related species have not been sequenced or annotated in detail. In these cases, protein homology-based evidence fails to correctly annotate many genes, or significantly improve ab initio predictions. Generalised hidden Markov models (GHMM) have proven to be invaluable tools in gene annotation and, recently, RNA-seq has emerged as a cost-effective means to significantly improve the quality of automated gene annotation. As these methods do not require sets of homologous proteins, improving gene prediction from these resources is of benefit to fungal researchers. While many pipelines now incorporate RNA-seq data in training GHMMs, there has been relatively little investigation into additionally combining RNA-seq data at the point of prediction, and room for improvement in this area motivates this study. CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts. RNA-seq data informs annotations both during gene-model training and in prediction. Our approach capitalises on the high quality of fungal transcript assemblies by incorporating predictions made directly from transcript sequences. Correct predictions are made despite transcript assembly problems, including those caused by overlap between the transcripts of adjacent gene loci. Stringent benchmarking against high-confidence annotation subsets showed CodingQuarry predicted 91.3% of Schizosaccharomyces pombe genes and 90.4% of Saccharomyces cerevisiae genes perfectly. These results are 4-5% better than those of AUGUSTUS, the next best performing RNA-seq driven gene predictor tested. Comparisons against

  3. Planetary Accretion, Oxygen Isotopes and the Central Limit Theorem

    NASA Technical Reports Server (NTRS)

    Nuth, Joseph A., III; Hill, Hugh G. M.; Vondrak, Richard R. (Technical Monitor)

    2001-01-01

    The accumulation of presolar dust into increasingly larger aggregates (CAIs and Chondrules, Asteroids, Planets) should result in a very drastic reduction in the numerical spread in oxygen isotopic composition between bodies of similar size, in accord with the Central Limit Theorem. Observed variations in oxygen isotopic composition are many orders of magnitude larger than would be predicted by a simple, random accumulation model that begins in a well-mixed nebula - no matter which size-scale objects are used as the beginning or end points of the calculation. This discrepancy implies either that some as yet unspecified process acted on the solids in the Solar Nebula to increase the spread in oxygen isotopic composition during each and every stage of accumulation or that the nebula was heterogeneous and maintained this heterogeneity throughout most of nebular history. Large-scale nebular heterogeneity would have significant consequences for many areas of cosmochemistry, including the application of some well-known isotopic systems to the dating of nebular events or the prediction of bulk compositions of planetary bodies on the basis of a uniform cosmic abundance.

  4. Isotopic modeling of the sub-cloud evaporation effect in precipitation.

    PubMed

    Salamalikis, V; Argiriou, A A; Dotsika, E

    2016-02-15

    In dry and warm environments sub-cloud evaporation influences the falling raindrops modifying their final stable isotopic content. During their descent from the cloud base towards the ground surface, through the unsaturated atmosphere, hydrometeors are subjected to evaporation whereas the kinetic fractionation results to less depleted or enriched isotopic signatures compared to the initial isotopic composition of the raindrops at cloud base. Nowadays the development of Generalized Climate Models (GCMs) that include isotopic content calculation modules are of great interest for the isotopic tracing of the global hydrological cycle. Therefore the accurate description of the underlying processes affecting stable isotopic content can improve the performance of iso-GCMs. The aim of this study is to model the sub-cloud evaporation effect using a) mixing and b) numerical isotope evaporation models. The isotope-mixing evaporation model simulates the isotopic enrichment (difference between the ground and the cloud base isotopic composition of raindrops) in terms of raindrop size, ambient temperature and relative humidity (RH) at ground level. The isotopic enrichment (Δδ) varies linearly with the evaporated raindrops mass fraction of the raindrop resulting to higher values at drier atmospheres and for smaller raindrops. The relationship between Δδ and RH is described by a 'heat capacity' model providing high correlation coefficients for both isotopes (R(2)>80%) indicating that RH is an ideal indicator of the sub-cloud evaporation effect. Vertical distribution of stable isotopes in falling raindrops is also investigated using a numerical isotope-evaporation model. Temperature and humidity dependence of the vertical isotopic variation is clearly described by the numerical isotopic model showing an increase in the isotopic values with increasing temperature and decreasing RH. At an almost saturated atmosphere (RH=95%) sub-cloud evaporation is negligible and the isotopic

  5. Deformation, Failure, and Fatigue Life of SiC/Ti-15-3 Laminates Accurately Predicted by MAC/GMC

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.; Arnold, Steven M.

    2002-01-01

    NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) (ref.1) has been extended to enable fully coupled macro-micro deformation, failure, and fatigue life predictions for advanced metal matrix, ceramic matrix, and polymer matrix composites. Because of the multiaxial nature of the code's underlying micromechanics model, GMC--which allows the incorporation of complex local inelastic constitutive models--MAC/GMC finds its most important application in metal matrix composites, like the SiC/Ti-15-3 composite examined here. Furthermore, since GMC predicts the microscale fields within each constituent of the composite material, submodels for local effects such as fiber breakage, interfacial debonding, and matrix fatigue damage can and have been built into MAC/GMC. The present application of MAC/GMC highlights the combination of these features, which has enabled the accurate modeling of the deformation, failure, and life of titanium matrix composites.

  6. Predictable oxygen isotope exchange of plant lipids improves our ability to understand hydrologic shifts and partition evapotranspiration across scales

    NASA Astrophysics Data System (ADS)

    Maxwell, T.; Silva, L. C. R.; Horwath, W. R.

    2016-12-01

    Understanding the partitioning of evapotranspiration is critical to assessing how changes in climate affect the terrestrial water cycle. N-alkyl lipids have been successfully used to integrate local to regional scale hydrologic change through the integration of δD measured in specific compounds found in sediments. However, such studies are limited compared to contemporary hydrologic studies which have the advantage of using dual isotope methods whereby δD and δ18O are used in conjunction to partition evapotranspiration. δD values in n-alkyl lipids have been established as resistant to exchange with environmental water and, this approach has allowed for routine measurement and reconstruction of plant water δD. In contrast, the use of δ18O in organic matter remains incipient because the low oxygen content of plant lipids makes it difficult to accurately measure δ18O. In the interest of addressing both fundamental and practical potential of a lipid δ18O proxy, we present the first evidence for predictable exchange of δ18O between environmental water and hydrophobic bulk organic matter, neutral saponified lipids, and specific plant derived compounds Our data suggests that these different pools may be used to reconstruct the original source water δD/δ18O relationship from soil or sedimentary organic matter, which will help elucidate hydrologic shifts in terrestrial systems. Our results bring new insight into methods by which organic compounds might be used to partition evapotranspiration across large spatial scales in both contemporary and reconstructed systems.

  7. Modeling the influence of a reduced equator-to-pole sea surface temperature gradient on the distribution of water isotopes in the Early/Middle Eocene

    NASA Astrophysics Data System (ADS)

    Speelman, Eveline N.; Sewall, Jacob O.; Noone, David; Huber, Matthew; von der Heydt, Anna; Damsté, Jaap Sinninghe; Reichart, Gert-Jan

    2010-09-01

    Proxy-based climate reconstructions suggest the existence of a strongly reduced equator-to-pole temperature gradient during the Azolla interval in the Early/Middle Eocene, compared to modern. Changes in the hydrological cycle, as a consequence of a reduced temperature gradient, are expected to be reflected in the isotopic composition of precipitation (δD, δ 18O). The interpretation of water isotopic records to quantitatively reconstruct past precipitation patterns is, however, hampered by a lack of detailed information on changes in their spatial and temporal distribution. Using the isotope-enabled version of the National Center for Atmospheric Research (NCAR) atmospheric general circulation model, Community Atmosphere Model v.3 (isoCAM3), relationships between water isotopes and past climates can be simulated. Here we examine the influence of an imposed reduced meridional sea surface temperature gradient on the spatial distribution of precipitation and its isotopic composition in an Early/Middle Eocene setting. As a result of the applied forcings, the Eocene simulation predicts the occurrence of less depleted high latitude precipitation, with δD values ranging only between 0 and -140‰ (compared to Present-day 0 to -300‰). Comparison with Early/Middle Eocene-age isotopic proxy data shows that the simulation accurately captures the main features of the spatial distribution of the isotopic composition of Early/Middle Eocene precipitation over land in conjunction with the aspects of the modeled Early/Middle Eocene climate. Hence, the included stable isotope module quantitatively supports the existence of a reduced meridional temperature gradient during this interval.

  8. Accurate prediction of cardiorespiratory fitness using cycle ergometry in minimally disabled persons with relapsing-remitting multiple sclerosis.

    PubMed

    Motl, Robert W; Fernhall, Bo

    2012-03-01

    To examine the accuracy of predicting peak oxygen consumption (VO(2peak)) primarily from peak work rate (WR(peak)) recorded during a maximal, incremental exercise test on a cycle ergometer among persons with relapsing-remitting multiple sclerosis (RRMS) who had minimal disability. Cross-sectional study. Clinical research laboratory. Women with RRMS (n=32) and sex-, age-, height-, and weight-matched healthy controls (n=16) completed an incremental exercise test on a cycle ergometer to volitional termination. Not applicable. Measured and predicted VO(2peak) and WR(peak). There were strong, statistically significant associations between measured and predicted VO(2peak) in the overall sample (R(2)=.89, standard error of the estimate=127.4 mL/min) and subsamples with (R(2)=.89, standard error of the estimate=131.3 mL/min) and without (R(2)=.85, standard error of the estimate=126.8 mL/min) multiple sclerosis (MS) based on the linear regression analyses. Based on the 95% confidence limits for worst-case errors, the equation predicted VO(2peak) within 10% of its true value in 95 of every 100 subjects with MS. Peak VO(2) can be accurately predicted in persons with RRMS who have minimal disability as it is in controls by using established equations and WR(peak) recorded from a maximal, incremental exercise test on a cycle ergometer. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  9. Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA).

    PubMed

    Guo, Guangyu; Li, Ning

    2011-07-01

    In the quantitative proteomic studies, numerous in vitro and in vivo peptide labeling strategies have been successfully applied to measure differentially regulated protein and peptide abundance. These approaches have been proven to be versatile and repeatable in biological discoveries. (15)N metabolic labeling is one of these widely adopted and economical methods. However, due to the differential incorporation rates of (15)N or (14)N, the labeling results produce imperfectly matched isotopic envelopes between the heavy and light nitrogen-labeled peptides. In the present study, we have modified the solid Arabidopsis growth medium to standardize the (15)N supply, which led to a uniform incorporation of (15)N into the whole plant protein complement. The incorporation rate (97.43±0.11%) of (15)N into (15)N-coded peptides was determined by correlating the intensities of peptide ions with the labeling efficiencies according to Gaussian distribution. The resulting actual incorporation rate (97.44%) and natural abundance of (15)N/(14)N-coded peptides are used to re-calculate the intensities of isotopic envelopes of differentially labeled peptides, respectively. A modified (15)N/(14)N stable isotope labeling strategy, SILIA, is assessed and the results demonstrate that this approach is able to differentiate the fold change in protein abundance down to 10%. The machine dynamic range limitation and purification step will make the precursor ion ratio deriving from the actual ratio fold change. It is suggested that the differentially mixed (15)N-coded and (14)N-coded plant protein samples that are used to establish the protein abundance standard curve should be prepared following a similar protein isolation protocol used to isolate the proteins to be quantitated. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

  10. Chlorine Isotope Ratios in M Giants and S Stars

    NASA Astrophysics Data System (ADS)

    Maas, Zachary; Pilachowski, C. A.

    2018-01-01

    Chlorine is an odd-Z, light element that has been poorly studied in stars. Recently, the first stellar abundance measurements of the isotopologue 35Cl were made and the 35Cl/37Cl ratio was derived in RZ Ari (Maas et al. 2016). Additional abundance measurements are necessary to understand the Galactic chemical evolution and complex nucleosynthesis of Cl. The Cl isotope ratio in particular is important in distinguishing contributions from different nucleosynthesis sites to the surface abundances of stars. For example, current nucloesynthesis models predict that both isotopes of Cl are produced primarily during core collapse supernovae (CCSNe) with the energy and progenitor mass impacting the isotopic ratio of the ejected material. In addition to CCSNe, 37Cl is formed by the s-process both in massive stars and in AGB stars, and 35Cl may be produced from neutrino spallation. Understanding the formation of the Cl isotopes is also important to studies of the interstellar medium (ISM). A range of Cl isotope ratios mainly between 2 - 3.5 have been measured in star forming regions, in the circumstellar envelopes of evolved stars, and in proto-stellar cores using Cl bearing molecules. Additional measurements of the Cl isotope ratio in nearby stars will test nucleosynthesis models and allow comparisons with the range of isotope ratios observed in the ISM.We build on the results of Maas et al. (2016) by measuring the Cl isotope ratio in six M giants and four S stars using R~50,000 resolution spectra from Phoenix on Gemini South. We find no significant difference between the average Cl isotope ratios in the M stars and S stars and our measurements are consistent with the range of values seen in the ISM. We also find the average Cl ratio to be larger than the predicted isotope ratio of 1.8 for the solar neighborhood. Finally, two S stars, GG Pup and WY Pyx, show anomalously strong HCl features with equivalent widths ~3-5 times larger than the HCl features of other stars of

  11. First total-absorption spectroscopy measurement on the neutron-rich Cu isotopes

    NASA Astrophysics Data System (ADS)

    Naqvi, F.; Spyrou, A.; Liddick, S. N.; Larsen, A. C.; Guttormsen, M.; Bleuel, D. L.; Campo, L. C.; Couture, A.; Crider, B. P.; Dombos, A. C.; Ginter, T.; Lewis, R.; Mosby, S.; Perdikakis, G.; Prokop, C. P.; Quinn, S. J.; Renstrom, T.; Rubio, B.; Siem, S.

    2015-10-01

    The first beta-decay studies of 73-71Cu isotopes using the Total Absorption Spectroscopy (TAS) will be reported. The Cu isotopes have one proton outside the Z = 28 shell and hence are good candidates to probe the single-particle structure in the region.Theories predict weakening of the Z = 28 shell gap due to the tensor interaction between the valence πν single-particle orbitals. Comparing the beta-decay strength distributions in the daughter Zn isotopes to the theoretical calculations will provide a stringent test of the predictions. The experiment was performed at the National Superconducting Cyclotron Laboratory (NSCL) employing the TAS technique with the Summing NaI(Tl) detector, while beta decays were measured in the NSCL beta-counting system. The experimentally obtained total absorption spectra for the neutron-rich Cu isotopes will be presented and the implications of the extracted beta-feeding intensities will be discussed.

  12. Do Skilled Elementary Teachers Hold Scientific Conceptions and Can They Accurately Predict the Type and Source of Students' Preconceptions of Electric Circuits?

    ERIC Educational Resources Information Center

    Lin, Jing-Wen

    2016-01-01

    Holding scientific conceptions and having the ability to accurately predict students' preconceptions are a prerequisite for science teachers to design appropriate constructivist-oriented learning experiences. This study explored the types and sources of students' preconceptions of electric circuits. First, 438 grade 3 (9 years old) students were…

  13. Species specific isotope dilution for the accurate and SI traceable determination of arsenobetaine and methylmercury in cuttlefish and prawn.

    PubMed

    Kumkrong, Paramee; Thiensong, Benjaporn; Le, Phuong Mai; McRae, Garnet; Windust, Anthony; Deawtong, Suladda; Meija, Juris; Maxwell, Paulette; Yang, Lu; Mester, Zoltán

    2016-11-02

    Methods based on species specific isotope dilution were developed for the accurate and SI traceable determination of arsenobetaine (AsBet) and methylmercury (MeHg) in prawn and cuttlefish tissues by LC-MS/MS and SPME GC-ICPMS. Quantitation of AsBet and MeHg were achieved by using a 13 C-enriched AsBet spike (NRC CRM CBET-1) and an enriched spike of Me 198 Hg (NRC CRM EMMS-1), respectively, wherein analyte mass fractions in enriched spikes were determined by reverse isotope dilution using natural abundance AsBet and MeHg primary standards. Purity of these primary standards were characterized by quantitative 1 H-NMR with the use of NIST SRM 350b benzoic acid as a primary calibrator, ensuring the final measurement results traceable to SI. Validation of employed methods of ID LC-MS/MS and ID SPME GC-ICPMS was demonstrated by analysis of several biological CRMs (DORM-4, TORT-3, DOLT-5, BCR-627 and BCR-463) with satisfying results. The developed methods were applied for the determination of AsBet and MeHg in two new certified reference materials (CRMs) prawn (PRON-1) and cuttlefish (SQID-1) produced jointly by Thailand Institute of Scientific and Technological Research (TISTR) and National Research Council Canada (NRC). With additional measurements of AsBet using LC-ICPMS with standard additions calibration and external calibration at NRC and TISTR, respectively, certified values of 1.206 ± 0.058 and 13.96 ± 0.54 mg kg -1 for AsBet as As (expanded uncertainty, k = 2) were obtained for the new CRMs PRON-1 and SQID-1, respectively. The reference value of 0.324 ± 0.028 mg kg -1 as Hg (expanded uncertainty, k = 2) for MeHg was obtained for the SQID-1 based on the results obtained by ID SPME GC-ICPMS method only, whereas MeHg in PRON-1 was found to be < 0.015 mg kg -1 . It was found that AsBet comprised 69.7% and 99.0% of total As in the prawn and cuttlefish, respectively, whereas MeHg comprised 94.5% of total Hg in cuttlefish. Crown Copyright © 2016

  14. Stable Isotope Ratios as Biomarkers of Diet for Health Research

    PubMed Central

    O’Brien, Diane M.

    2016-01-01

    Diet is a leading modifiable risk factor for chronic disease, but it remains difficult to measure accurately due to the error and bias inherent in self-reported methods of diet assessment. Consequently there is a pressing need for more objective biomarkers of diet for use in health research. The stable isotope ratios of light elements are a promising set of candidate biomarkers because they vary naturally and reproducibly among foods, and those variations are captured in molecules and tissues with high fidelity. Recent studies have identified valid isotopic measures of short and long-term sugar intake, meat intake, and fish intake in specific populations. These studies provide a strong foundation for validating stable isotopic biomarkers in the general United States population. Approaches to improve specificity for specific foods are needed, for example, by modeling intake using multiple stable isotope ratios, or by isolating and measuring specific molecules linked to foods of interest. PMID:26048703

  15. Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties

    NASA Astrophysics Data System (ADS)

    Xie, Tian; Grossman, Jeffrey C.

    2018-04-01

    The use of machine learning methods for accelerating the design of crystalline materials usually requires manually constructed feature vectors or complex transformation of atom coordinates to input the crystal structure, which either constrains the model to certain crystal types or makes it difficult to provide chemical insights. Here, we develop a crystal graph convolutional neural networks framework to directly learn material properties from the connection of atoms in the crystal, providing a universal and interpretable representation of crystalline materials. Our method provides a highly accurate prediction of density functional theory calculated properties for eight different properties of crystals with various structure types and compositions after being trained with 1 04 data points. Further, our framework is interpretable because one can extract the contributions from local chemical environments to global properties. Using an example of perovskites, we show how this information can be utilized to discover empirical rules for materials design.

  16. Characterization of calcium isotopes in natural and synthetic barite

    USGS Publications Warehouse

    Griffith, E.M.; Schauble, E.A.; Bullen, T.D.; Paytan, A.

    2008-01-01

    The mineral barite (BaSO4) accommodates calcium in its crystal lattice, providing an archive of Ca-isotopes in the highly stable sulfate mineral. Holocene marine (pelagic) barite samples from the major ocean basins are isotopically indistinguishable from each other (??44/40Ca = -2.01 ?? 0.15???) but are different from hydrothermal and cold seep barite samples (??44/40Ca = -4.13 to -2.72???). Laboratory precipitated (synthetic) barite samples are more depleted in the heavy Ca-isotopes than pelagic marine barite and span a range of Ca-isotope compositions, ??44/40Ca = -3.42 to -2.40???. Temperature, saturation state, a Ba2 + / a SO42 -, and aCa2+/aBa2+ each influence the fractionation of Ca-isotopes in synthetic barite; however, the fractionation in marine barite samples is not strongly related to any measured environmental parameter. First-principles lattice dynamical modeling predicts that at equilibrium Ca-substituted barite will have much lower 44Ca/40Ca than calcite, by -9??? at 0 ??C and -8??? at 25 ??C. Based on this model, none of the measured barite samples appear to be in isotopic equilibrium with their parent solutions, although as predicted they do record lower ??44/40Ca values than seawater and calcite. Kinetic fractionation processes therefore most likely control the extent of isotopic fractionation exhibited in barite. Potential fractionation mechanisms include factors influencing Ca2+ substitution for Ba2+ in barite (e.g. ionic strength and trace element concentration of the solution, competing complexation reactions, precipitation or growth rate, temperature, pressure, and saturation state) as well as nucleation and crystal growth rates. These factors should be considered when investigating controls on isotopic fractionation of Ca2+ and other elements in inorganic and biogenic minerals. ?? 2008 Elsevier Ltd.

  17. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

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

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can bemore » rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.« less

  18. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

    DOE PAGES

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; ...

    2017-03-03

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can bemore » rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.« less

  19. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory.

    PubMed

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; Drisdell, Walter S; Shirley, Eric L; Prendergast, David

    2017-03-03

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can be rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.

  20. Future stable water isotope projection with an isotope-AGCM driven by CMIP5 SSTs

    NASA Astrophysics Data System (ADS)

    Yoshimura, K.

    2016-12-01

    Stable water isotope ratios (dD and d18O) are widely used as proxy of past climate changes, and it is extremely important to understand and predict the mechanism of current isotopic spatio-temporal behavior with regard to the on-going climate change. However, as compared many studies on reproduction of isotopes for the past, there are few studies on future projection of isotopes. Therefore, in this study, a set of experiments using an isotope-incorporate AGCM (IsoGSM) with SST and sea ice field simulated from multiple CMIP5 models, namely MIROC5, CCSM4, and MRI-CGCM3, were conducted for the end of 20th century (1980-1990) and the end of 21st century (2080-2090) under RCP2.6 and RCP8.5 scenarios. Thus the responses in stable water isotope ratio in precipitation and water vapor in accordance to the global warming were investigated. As results, the changes in global surface air temperature were about +1K and +3K with RCP2.6 and RCP8.5, respectively. Similarly, the global precipitation changes were about +0.07mm/day (about +2%) and +0.18mm/day (about +5%), and the global precipitable water changes were about +2mm (+7%) and +6mm (+24%), respectively. The moisture was increased in accordance to the Clausius-Clapayron theory (7%/K), but the increase in precipitation is not that large. This indicates that the global hydrological cycle was slowed down in the globally warmed experiments. On the other hand, for the isotopic signals, the changes in globally averaged d18O in precipitation were about 0.2‰ and 0.4‰, and those in precipitable water were 0.2‰ and 0.5‰, in RCP2.6 and RCP8.5, respectively. It is well-known that there are temperature effect (positive correlation in air temperature and precipitation isotopes) and amount effect (negative correlation in precipitation amount and isotopes), but in the globally warmed world, these effects were offset, and only weaker temperature effect was appeared in the global mean isotope signals. Regional details will be shown

  1. Stable isotopic analysis of human diet in the Marianas Archipelago, western Pacific.

    PubMed

    Ambrose, S H; Butler, B M; Hanson, D B; Hunter-Anderson, R L; Krueger, H W

    1997-11-01

    Proportions of marine vs. terrestrial resources in prehistoric human diets in the southern Mariana Islands (Guam, Rota, Saipan), Micronesia, have been estimated by analysis of stable isotope ratios of carbon and nitrogen in bone collagen and of carbon in apatite. The isotopic composition of marine and terrestrial food resources from the Marianas have also been determined. Experimental evidence shows that collagen carbon isotopes mainly reflect those of dietary protein sources and thus overestimate the contribution of marine animal foods. Marine protein consumption apparently ranges from approximately 20% to approximately 50% on these islands. Experiments also demonstrate the carbon isotope ratio of bone apatite carbonate accurately reflects that of the whole diet. Carbonate carbon isotope data suggest some individuals consumed significant amounts of 13C-enriched (C4) plants or seaweeds. Sugar cane is an indigenous C4 crop and seaweeds are eaten throughout the Pacific, but they have not been considered by archaeologists to have been prehistoric dietary staples. Apatite carbon isotope analysis has apparently identified previously unrecognized prehistoric dietary adaptations in the Mariana Islands, but this must be confirmed by archaeobotanical evidence.

  2. pyQms enables universal and accurate quantification of mass spectrometry data.

    PubMed

    Leufken, Johannes; Niehues, Anna; Sarin, L Peter; Wessel, Florian; Hippler, Michael; Leidel, Sebastian A; Fufezan, Christian

    2017-10-01

    Quantitative mass spectrometry (MS) is a key technique in many research areas (1), including proteomics, metabolomics, glycomics, and lipidomics. Because all of the corresponding molecules can be described by chemical formulas, universal quantification tools are highly desirable. Here, we present pyQms, an open-source software for accurate quantification of all types of molecules measurable by MS. pyQms uses isotope pattern matching that offers an accurate quality assessment of all quantifications and the ability to directly incorporate mass spectrometer accuracy. pyQms is, due to its universal design, applicable to every research field, labeling strategy, and acquisition technique. This opens ultimate flexibility for researchers to design experiments employing innovative and hitherto unexplored labeling strategies. Importantly, pyQms performs very well to accurately quantify partially labeled proteomes in large scale and high throughput, the most challenging task for a quantification algorithm. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Towards absolute laser spectroscopic CO2 isotope ratio measurements

    NASA Astrophysics Data System (ADS)

    Anyangwe Nwaboh, Javis; Werhahn, Olav; Ebert, Volker

    2017-04-01

    Knowledge of isotope composition of carbon dioxide (CO2) in the atmosphere is necessary to identify sources and sinks of this key greenhouse gas. In the last years, laser spectroscopic techniques such as cavity ring-down spectroscopy (CRDS) and tunable diode laser absorption spectroscopy (TDLAS) have been shown to perform accurate isotope ratio measurements for CO2 and other gases like water vapour (H2O) [1,2]. Typically, isotope ratios are reported in literature referring to reference materials provided by e.g. the International Atomic Energy Agency (IAEA). However, there could be some benefit if field deployable absolute isotope ratio measurement methods were developed to address issues such as exhausted reference material like the Pee Dee Belemnite (PDB) standard. Absolute isotope ratio measurements would be particularly important for situations where reference materials do not even exist. Here, we present CRDS and TDLAS-based absolute isotope ratios (13C/12C ) in atmospheric CO2. We demonstrate the capabilities of the used methods by measuring CO2 isotope ratios in gas standards. We compare our results to values reported for the isotope certified gas standards. Guide to the expression of uncertainty in measurement (GUM) compliant uncertainty budgets on the CRDS and TDLAS absolute isotope ratio measurements are presented, and traceability is addressed. We outline the current impediments in realizing high accuracy absolute isotope ratio measurements using laser spectroscopic methods, propose solutions and the way forward. Acknowledgement Parts of this work have been carried out within the European Metrology Research Programme (EMRP) ENV52 project-HIGHGAS. The EMRP is jointly funded by the EMRP participating countries within EURAMET and the European Union. References [1] B. Kühnreich, S. Wagner, J. C. Habig,·O. Möhler, H. Saathoff, V. Ebert, Appl. Phys. B 119:177-187 (2015). [2] E. Kerstel, L. Gianfrani, Appl. Phys. B 92, 439-449 (2008).

  4. Accurate prediction of acute fish toxicity of fragrance chemicals with the RTgill-W1 cell assay.

    PubMed

    Natsch, Andreas; Laue, Heike; Haupt, Tina; von Niederhäusern, Valentin; Sanders, Gordon

    2018-03-01

    Testing for acute fish toxicity is an integral part of the environmental safety assessment of chemicals. A true replacement of primary fish tissue was recently proposed using cell viability in a fish gill cell line (RTgill-W1) as a means of predicting acute toxicity, showing good predictivity on 35 chemicals. To promote regulatory acceptance, the predictivity and applicability domain of novel tests need to be carefully evaluated on chemicals with existing high-quality in vivo data. We applied the RTgill-W1 cell assay to 38 fragrance chemicals with a wide range of both physicochemical properties and median lethal concentration (LC50) values and representing a diverse range of chemistries. A strong correlation (R 2  = 0.90-0.94) between the logarithmic in vivo LC50 values, based on fish mortality, and the logarithmic in vitro median effect concentration (EC50) values based on cell viability was observed. A leave-one-out analysis illustrates a median under-/overprediction from in vitro EC50 values to in vivo LC50 values by a factor of 1.5. This assay offers a simple, accurate, and reliable alternative to in vivo acute fish toxicity testing for chemicals, presumably acting mainly by a narcotic mode of action. Furthermore, the present study provides validation of the predictivity of the RTgill-W1 assay on a completely independent set of chemicals that had not been previously tested and indicates that fragrance chemicals are clearly within the applicability domain. Environ Toxicol Chem 2018;37:931-941. © 2017 SETAC. © 2017 SETAC.

  5. Isotope ratio mass spectrometry in nutrition research

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

    Luke, A.H.

    Many of the biochemical pathways and processes that form the foundation of modern nutrition research was elucidated using stable isotopes as physiological tracers. Since the discovery of stable isotopes, improvements and innovations in mass spectrometry and chromatography have led to greatly expanded applications. This research project was designed to evaluate gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) as a tool for isotopic tracer studies and to delineate the operational parameters for the analysis of {sup 13}C-labeled cholesterol, leucine and {alpha}-ketoisocaproate. The same isotope ratio mass spectrometer was then used as the base instrument for the ratio mass spectrometer was then usedmore » as the base instrument for the development of two additional inlet systems: a continuous-flow inlet for the analyses of {sup 13}C and {sup 18}O as CO{sub 2} and a filament inlet for on-line combustion and isotopic analysis of non-volatile organic compounds. Each of these three inlets was evaluated and their utility in nutrition research illustrated. GC/C/IRMS was used to analyze cholesterol, leucine and {alpha}-ketoisocaproate with good accuracy, precision and little isotopic memory. For all three compounds the detection limits achieved well surpassed currently used technologies. For compounds that can be well separated by GC, GC/C/IRMS is a valuable analytical tool. The continuous-flow inlet provided good accuracy and precision for measurements of {sup 13}CO{sub 2} from breath tests and {sup 18}O as CO{sub 2} from total energy expenditure tests. Most importantly, the continuous-flow inlet increased sample throughput by at least a factor of three over conventional analytical techniques. The filament inlet provided accurate and precise {sup 13}C ratio measurements of both natural abundance and enriched standards of non-volatile organic compounds of physiological interest.« less

  6. Mass measurements of neutron-deficient Y, Zr, and Nb isotopes and their impact on rp and νp nucleosynthesis processes

    NASA Astrophysics Data System (ADS)

    Xing, Y. M.; Li, K. A.; Zhang, Y. H.; Zhou, X. H.; Wang, M.; Litvinov, Yu. A.; Blaum, K.; Wanajo, S.; Kubono, S.; Martínez-Pinedo, G.; Sieverding, A.; Chen, R. J.; Shuai, P.; Fu, C. Y.; Yan, X. L.; Huang, W. J.; Xu, X.; Tang, X. D.; Xu, H. S.; Bao, T.; Chen, X. C.; Gao, B. S.; He, J. J.; Lam, Y. H.; Li, H. F.; Liu, J. H.; Ma, X. W.; Mao, R. S.; Si, M.; Sun, M. Z.; Tu, X. L.; Wang, Q.; Yang, J. C.; Yuan, Y. J.; Zeng, Q.; Zhang, P.; Zhou, X.; Zhan, W. L.; Litvinov, S.; Audi, G.; Uesaka, T.; Yamaguchi, Y.; Yamaguchi, T.; Ozawa, A.; Fröhlich, C.; Rauscher, T.; Thielemann, F.-K.; Sun, B. H.; Sun, Y.; Dai, A. C.; Xu, F. R.

    2018-06-01

    Using isochronous mass spectrometry at the experimental storage ring CSRe in Lanzhou, the masses of 82Zr and 84Nb were measured for the first time with an uncertainty of ∼10 keV, and the masses of 79Y, 81Zr, and 83Nb were re-determined with a higher precision. The latter are significantly less bound than their literature values. Our new and accurate masses remove the irregularities of the mass surface in this region of the nuclear chart. Our results do not support the predicted island of pronounced low α separation energies for neutron-deficient Mo and Tc isotopes, making the formation of Zr-Nb cycle in the rp-process unlikely. The new proton separation energy of 83Nb was determined to be 490(400) keV smaller than that in the Atomic Mass Evaluation 2012. This partly removes the overproduction of the p-nucleus 84Sr relative to the neutron-deficient molybdenum isotopes in the previous νp-process simulations.

  7. Stable isotope discrimination factors and between-tissue isotope comparisons for bone and skin from captive and wild green sea turtles (Chelonia mydas).

    PubMed

    Turner Tomaszewicz, Calandra N; Seminoff, Jeffrey A; Price, Mike; Kurle, Carolyn M

    2017-11-30

    The ecological application of stable isotope analysis (SIA) relies on taxa- and tissue-specific stable carbon (Δ 13 C) and nitrogen (Δ 15 N) isotope discrimination factors, determined with captive animals reared on known diets for sufficient time to reflect dietary isotope ratios. However, captive studies often prohibit lethal sampling, are difficult with endangered species, and reflect conditions not experienced in the wild. We overcame these constraints and determined the Δ 13 C and Δ 15 N values for skin and cortical bone from green sea turtles (Chelonia mydas) that died in captivity and evaluated the utility of a mathematical approach to predict discrimination factors. Using stable carbon (δ 13 C values) and nitrogen (δ 15 N values) isotope ratios from captive and wild turtles, we established relationships between bone stable isotope (SI) ratios and those from skin, a non-lethally sampled tissue, to facilitate comparisons of SI ratios among studies using multiple tissues. The mean (±SD) Δ 13 C and Δ 15 N values (‰) between skin and bone from captive turtles and their diet (non-lipid-extracted) were 2.3 ± 0.3 and 4.1 ± 0.4 and 2.1 ± 0.6 and 5.1 ± 1.1, respectively. The mathematically predicted Δ 13 C and Δ 15 N values were similar (to within 1‰) to the experimentally derived values. The mean δ 15 N values from bone were higher than those from skin for captive (+1.0 ± 0.9‰) and wild (+0.8 ± 1.0‰) turtles; the mean δ 13 C values from bone were lower than those from skin for wild turtles (-0.6 ± 0.9‰), but the same as for captive turtles. We used linear regression equations to describe bone vs skin relationships and create bone-to-skin isotope conversion equations. For sea turtles, we provide the first (a) bone-diet SI discrimination factors, (b) comparison of SI ratios from individual-specific bone and skin, and (c) evaluation of the application of a mathematical approach to predict stable isotope discrimination factors. Our approach

  8. Fundamental studies on kinetic isotope effect (KIE) of hydrogen isotope fractionation in natural gas systems

    USGS Publications Warehouse

    Ni, Y.; Ma, Q.; Ellis, G.S.; Dai, J.; Katz, B.; Zhang, S.; Tang, Y.

    2011-01-01

    Based on quantum chemistry calculations for normal octane homolytic cracking, a kinetic hydrogen isotope fractionation model for methane, ethane, and propane formation is proposed. The activation energy differences between D-substitute and non-substituted methane, ethane, and propane are 318.6, 281.7, and 280.2cal/mol, respectively. In order to determine the effect of the entropy contribution for hydrogen isotopic substitution, a transition state for ethane bond rupture was determined based on density function theory (DFT) calculations. The kinetic isotope effect (KIE) associated with bond rupture in D and H substituted ethane results in a frequency factor ratio of 1.07. Based on the proposed mathematical model of hydrogen isotope fractionation, one can potentially quantify natural gas thermal maturity from measured hydrogen isotope values. Calculated gas maturity values determined by the proposed mathematical model using ??D values in ethane from several basins in the world are in close agreement with similar predictions based on the ??13C composition of ethane. However, gas maturity values calculated from field data of methane and propane using both hydrogen and carbon kinetic isotopic models do not agree as closely. It is possible that ??D values in methane may be affected by microbial mixing and that propane values might be more susceptible to hydrogen exchange with water or to analytical errors. Although the model used in this study is quite preliminary, the results demonstrate that kinetic isotope fractionation effects in hydrogen may be useful in quantitative models of natural gas generation, and that ??D values in ethane might be more suitable for modeling than comparable values in methane and propane. ?? 2011 Elsevier Ltd.

  9. A cross-race effect in metamemory: Predictions of face recognition are more accurate for members of our own race

    PubMed Central

    Hourihan, Kathleen L.; Benjamin, Aaron S.; Liu, Xiping

    2012-01-01

    The Cross-Race Effect (CRE) in face recognition is the well-replicated finding that people are better at recognizing faces from their own race, relative to other races. The CRE reveals systematic limitations on eyewitness identification accuracy and suggests that some caution is warranted in evaluating cross-race identification. The CRE is a problem because jurors value eyewitness identification highly in verdict decisions. In the present paper, we explore how accurate people are in predicting their ability to recognize own-race and other-race faces. Caucasian and Asian participants viewed photographs of Caucasian and Asian faces, and made immediate judgments of learning during study. An old/new recognition test replicated the CRE: both groups displayed superior discriminability of own-race faces, relative to other-race faces. Importantly, relative metamnemonic accuracy was also greater for own-race faces, indicating that the accuracy of predictions about face recognition is influenced by race. This result indicates another source of concern when eliciting or evaluating eyewitness identification: people are less accurate in judging whether they will or will not recognize a face when that face is of a different race than they are. This new result suggests that a witness’s claim of being likely to recognize a suspect from a lineup should be interpreted with caution when the suspect is of a different race than the witness. PMID:23162788

  10. Developing the Molybdenum Isotopic Proxy in Marine Barite

    NASA Astrophysics Data System (ADS)

    Erhardt, A. M.; Paytan, A.; Aggarwal, J.

    2006-12-01

    Molybdenum isotope ratios in seawater fluctuate in response to changing redox conditions and can provide clues into the degree of global ocean anoxia. The isotopic ratio of molybdenum has been shown to be sensitive to the relative proportion of oxic, suboxic, and euxinic environments. Deposition in oxic environments is isotopically light (~ -1.6‰ for δ^{97/95}Mo) relative to an average crustal source (0‰). Conversely, euxinic environments have been shown to be consistently heavier (~1.3‰) than the oxic sink through time, with suboxic sediments falling between these two signals. Shifts in the relative proportion of each sink, relative to a constant source, would alter the isotopic ratio of seawater over long time scales. Previously, this seawater value, and hence the degree of global anoxia, could only be inferred through mass balance calculations. We seek to quantify the isotopic signature of seawater though time using a phase that directly records this ratio. Marine barite precipitates inorganically in the water column directly from seawater, potentially providing a direct record of seawater characteristics. Molybdenum is a trace constituent of barite, with the molybdate ion substituting for sulfate at concentrations of about 1 ppm. To accurately determine the molybdenum isotopic ratio at these low concentrations (<15 ng per sample), modifications to existing measurement techniques are required. We will present the variations made to existing separation and mass-spectrometry techniques and the calibration of these new methods. The modifications were undertaken to reduce molybdenum blank to below 1 ng per analysis, to quantitatively remove interfering zirconium and to measure precise and reproducible isotope values. Preliminary data will be presented to illustrate potential applications for this new paleoredox proxy. This technique will allow for the measurement of molybdenum isotopic ratios at low concentrations, expanding the breath of compounds and

  11. Molecular isotopic engineering (MIE): industrial manufacture of naproxen of predetermined stable carbon-isotopic compositions for authenticity and security protection and intellectual property considerations

    NASA Astrophysics Data System (ADS)

    Jasper, J. P.; Farina, P.; Pearson, A.; Mezes, P. S.; Sabatelli, A. D.

    2016-05-01

    Molecular Isotopic Engineering (MIE) is the directed stable-isotopic synthesis of chemical products for reasons of product identification and of product security, and also for intellectual property considerations. We report here a generally excellent correspondence between the observed and predicted stable carbon-isotopic (δ13C) results for a successful directed synthesis of racemic mixture from its immediate precursors. The observed results are readily explained by the laws of mass balance and isotope mass balance. Oxygen- and hydrogen isotopic results which require an additional assessment of the effects of O and H exchange, presumably due to interaction with water in the reaction solution, are addressed elsewhere. A previous, cooperative study with the US FDA-DPA showed that individual manufacturers of naproxen could readily be differentiated by their stable-isotopic provenance (δ13C, δ18O, and δD ref. 1). We suggest that MIE can be readily employed in the bio/pharmaceutical industry without alteration of present manufacturing processes other than isotopically selecting and/or monitoring reactants and products.

  12. Accurate RNA 5-methylcytosine site prediction based on heuristic physical-chemical properties reduction and classifier ensemble.

    PubMed

    Zhang, Ming; Xu, Yan; Li, Lei; Liu, Zi; Yang, Xibei; Yu, Dong-Jun

    2018-06-01

    RNA 5-methylcytosine (m 5 C) is an important post-transcriptional modification that plays an indispensable role in biological processes. The accurate identification of m 5 C sites from primary RNA sequences is especially useful for deeply understanding the mechanisms and functions of m 5 C. Due to the difficulty and expensive costs of identifying m 5 C sites with wet-lab techniques, developing fast and accurate machine-learning-based prediction methods is urgently needed. In this study, we proposed a new m 5 C site predictor, called M5C-HPCR, by introducing a novel heuristic nucleotide physicochemical property reduction (HPCR) algorithm and classifier ensemble. HPCR extracts multiple reducts of physical-chemical properties for encoding discriminative features, while the classifier ensemble is applied to integrate multiple base predictors, each of which is trained based on a separate reduct of the physical-chemical properties obtained from HPCR. Rigorous jackknife tests on two benchmark datasets demonstrate that M5C-HPCR outperforms state-of-the-art m 5 C site predictors, with the highest values of MCC (0.859) and AUC (0.962). We also implemented the webserver of M5C-HPCR, which is freely available at http://cslab.just.edu.cn:8080/M5C-HPCR/. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. Historical and contemporary stable isotope tracer approaches to studying mammalian protein metabolism

    PubMed Central

    2016-01-01

    Over a century ago, Frederick Soddy provided the first evidence for the existence of isotopes; elements that occupy the same position in the periodic table are essentially chemically identical but differ in mass due to a different number of neutrons within the atomic nucleus. Allied to the discovery of isotopes was the development of some of the first forms of mass spectrometers, driven forward by the Nobel laureates JJ Thomson and FW Aston, enabling the accurate separation, identification, and quantification of the relative abundance of these isotopes. As a result, within a few years, the number of known isotopes both stable and radioactive had greatly increased and there are now over 300 stable or radioisotopes presently known. Unknown at the time, however, was the potential utility of these isotopes within biological disciplines, it was soon discovered that these stable isotopes, particularly those of carbon (13C), nitrogen (15N), oxygen (18O), and hydrogen (2H) could be chemically introduced into organic compounds, such as fatty acids, amino acids, and sugars, and used to “trace” the metabolic fate of these compounds within biological systems. From this important breakthrough, the age of the isotope tracer was born. Over the following 80 yrs, stable isotopes would become a vital tool in not only the biological sciences, but also areas as diverse as forensics, geology, and art. This progress has been almost exclusively driven through the development of new and innovative mass spectrometry equipment from IRMS to GC‐MS to LC‐MS, which has allowed for the accurate quantitation of isotopic abundance within samples of complex matrices. This historical review details the development of stable isotope tracers as metabolic tools, with particular reference to their use in monitoring protein metabolism, highlighting the unique array of tools that are now available for the investigation of protein metabolism in vivo at a whole body down to a single protein level

  14. Transition State Geometry Measurements from 13C Isotope Effects. The Experimental Transition State for the Epoxidation of Alkenes with Oxaziridines

    PubMed Central

    Hirschi, Jennifer S.; Takeya, Tetsuya; Hang, Chao; Singleton, Daniel A.

    2009-01-01

    We suggest here and evaluate a methodology for the measurement of specific interatomic distances from a combination of theoretical calculations and experimentally measured 13C kinetic isotope effects. This process takes advantage of a broad diversity of transition structures available for the epoxidation of 2-methyl-2-butene with oxaziridines. From the isotope effects calculated for these transition structures, a theory-independent relationship between the C-O bond distances of the newly forming bonds and the isotope effects is established. Within the precision of the measurement, this relationship in combination with the experimental isotope effects provides a highly accurate picture of the C-O bonds forming at the transition state. The diversity of transition structures also allows an evaluation of the Schramm process for defining transition state geometries based on calculations at non-stationary points, and the methodology is found to be reasonably accurate. PMID:19146405

  15. Experimental and Theoretical Understanding of Neutron Capture on Uranium Isotopes

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

    Ullmann, John Leonard

    2017-09-21

    Neutron capture cross sections on uranium isotopes are important quantities needed to model nuclear explosion performance, nuclear reactor design, nuclear test diagnostics, and nuclear forensics. It has been difficult to calculate capture accurately, and factors of 2 or more be- tween calculation and measurements are not uncommon, although normalization to measurements of the average capture width and nuclear level density can improve the result. The calculations of capture for 233,235,237,239U are further complicated by the need to accurately include the fission channel.

  16. Using in-situ observations of atmospheric water vapor isotopes to benchmark and isotope-enabled General Circulation Models and improve ice core paleo-climate reconstruction

    NASA Astrophysics Data System (ADS)

    Steen-Larsen, Hans Christian; Sveinbjörnsdottir, Arny; Masson-Delmotte, Valerie; Werner, Martin; Risi, Camille; Yoshimura, Kei

    2016-04-01

    We have since 2010 carried out in-situ continuous water vapor isotope observations on top of the Greenland Ice Sheet (3 seasons at NEEM), in Svalbard (1 year), in Iceland (4 years), in Bermuda (4 years). The expansive dataset containing high accuracy and precision measurements of δ18O, δD, and the d-excess allow us to validate and benchmark the treatment of the atmospheric hydrological cycle's processes in General Circulation Models using simulations nudged to reanalysis products. Recent findings from both Antarctica and Greenland have documented strong interaction between the snow surface isotopes and the near surface atmospheric water vapor isotopes on diurnal to synoptic time scales. In fact, it has been shown that the snow surface isotopes take up the synoptic driven atmospheric water vapor isotopic signal in-between precipitation events, erasing the precipitation isotope signal in the surface snow. This highlights the importance of using General or Regional Climate Models, which accurately are able to simulate the atmospheric water vapor isotopic composition, to understand and interpret the ice core isotope signal. With this in mind we have used three isotope-enabled General Circulation Models (isoGSM, ECHAM5-wiso, and LMDZiso) nudged to reanalysis products. We have compared the simulations of daily mean isotope values directly with our in-situ observations. This has allowed us to characterize the variability of the isotopic composition in the models and compared it to our observations. We have specifically focused on the d-excess in order to characterize why both the mean and the variability is significantly lower than our observations. We argue that using water vapor isotopes to benchmark General Circulation Models offers an excellent tool for improving the treatment and parameterization of the atmospheric hydrological cycle. Recent studies have documented a very large inter-model dispersion in the treatment of the Arctic water cycle under a future global

  17. Population variation in isotopic composition of shorebird feathers: Implications for determining molting grounds

    USGS Publications Warehouse

    Torres-Dowdall, J.; Farmer, A.H.; Bucher, E.H.; Rye, R.O.; Landis, G.

    2009-01-01

    Stable isotope analyses have revolutionized the study of migratory connectivity. However, as with all tools, their limitations must be understood in order to derive the maximum benefit of a particular application. The goal of this study was to evaluate the efficacy of stable isotopes of C, N, H, O and S for assigning known-origin feathers to the molting sites of migrant shorebird species wintering and breeding in Argentina. Specific objectives were to: 1) compare the efficacy of the technique for studying shorebird species with different migration patterns, life histories and habitat-use patterns; 2) evaluate the grouping of species with similar migration and habitat use patterns in a single analysis to potentially improve prediction accuracy; and 3) evaluate the potential gains in prediction accuracy that might be achieved from using multiple stable isotopes. The efficacy of stable isotope ratios to determine origin was found to vary with species. While one species (White-rumped Sandpiper, Calidris fuscicollis) had high levels of accuracy assigning samples to known origin (91% of samples correctly assigned), another (Collared Plover, Charadrius collaris) showed low levels of accuracy (52% of samples correctly assigned). Intra-individual variability may account for this difference in efficacy. The prediction model for three species with similar migration and habitat-use patterns performed poorly compared with the model for just one of the species (71% versus 91% of samples correctly assigned). Thus, combining multiple sympatric species may not improve model prediction accuracy. Increasing the number of stable isotopes in the analyses increased the accuracy of assigning shorebirds to their molting origin, but the best combination - involving a subset of all the isotopes analyzed - varied among species.

  18. The NAFLD Index: A Simple and Accurate Screening Tool for the Prediction of Non-Alcoholic Fatty Liver Disease.

    PubMed

    Ichino, Naohiro; Osakabe, Keisuke; Sugimoto, Keiko; Suzuki, Koji; Yamada, Hiroya; Takai, Hiroji; Sugiyama, Hiroko; Yukitake, Jun; Inoue, Takashi; Ohashi, Koji; Hata, Tadayoshi; Hamajima, Nobuyuki; Nishikawa, Toru; Hashimoto, Senju; Kawabe, Naoto; Yoshioka, Kentaro

    2015-01-01

    Non-alcoholic fatty liver disease (NAFLD) is a common debilitating condition in many industrialized countries that increases the risk of cardiovascular disease. The aim of this study was to derive a simple and accurate screening tool for the prediction of NAFLD in the Japanese population. A total of 945 participants, 279 men and 666 women living in Hokkaido, Japan, were enrolled among residents who attended a health check-up program from 2010 to 2014. Participants with an alcohol consumption > 20 g/day and/or a chronic liver disease, such as chronic hepatitis B, chronic hepatitis C or autoimmune hepatitis, were excluded from this study. Clinical and laboratory data were examined to identify predictive markers of NAFLD. A new predictive index for NAFLD, the NAFLD index, was constructed for men and for women. The NAFLD index for men = -15.5693+0.3264 [BMI] +0.0134 [triglycerides (mg/dl)], and for women = -31.4686+0.3683 [BMI] +2.5699 [albumin (g/dl)] +4.6740[ALT/AST] -0.0379 [HDL cholesterol (mg/dl)]. The AUROC of the NAFLD index for men and for women was 0.87(95% CI 0.88-1.60) and 0.90 (95% CI 0.66-1.02), respectively. The cut-off point of -5.28 for men predicted NAFLD with an accuracy of 82.8%. For women, the cut-off point of -7.65 predicted NAFLD with an accuracy of 87.7%. A new index for the non-invasive prediction of NAFLD, the NAFLD index, was constructed using available clinical and laboratory data. This index is a simple screening tool to predict the presence of NAFLD.

  19. Isotope effects associated with tunneling and double proton transfer in the hydrogen bonds of benzoic acid

    NASA Astrophysics Data System (ADS)

    Xue, Q.; Horsewill, A. J.; Johnson, M. R.; Trommsdorff, H. P.

    2004-06-01

    The isotope effects associated with double proton transfer in the hydrogen bonds of benzoic acid (BA) dimers have been measured using field-cycling 1H NMR relaxometry and quasielastic neutron scattering. By studying mixed isotope (hydrogen and deuterium) samples, the dynamics of three isotopologues, BA-HH, BA-HD, and BA-DD, have been investigated. Low temperature measurements provide accurate measurements of the incoherent tunneling rate, k0. This parameter scales accurately with the mass number, m, according to the formula k0=(E/m)e-F√m providing conclusive evidence that the proton transfer process is a strongly correlated motion of two hydrons. Furthermore, we conclude that the tunneling pathway is the same for the three isotopologue species. Measurements at higher temperatures illuminate the through barrier processes that are mediated via intermediate or excited vibrational states. In parallel with the investigation of proton transfer dynamics, the theoretical and experimental aspects of studying spin-lattice relaxation in single crystals of mixed isotope samples are investigated in depth. Heteronuclear dipolar interactions between 1H and 2H isotopes contribute significantly to the overall proton spin-lattice relaxation and it is shown that these must be modeled correctly to obtain accurate values for the proton transfer rates. Since the sample used in the NMR measurements was a single crystal, full account of the orientation dependence of the spin-lattice relaxation with respect to the applied B field was incorporated into the data analysis.

  20. A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information.

    PubMed

    Yi, Hai-Cheng; You, Zhu-Hong; Huang, De-Shuang; Li, Xiao; Jiang, Tong-Hai; Li, Li-Ping

    2018-06-01

    The interactions between non-coding RNAs (ncRNAs) and proteins play an important role in many biological processes, and their biological functions are primarily achieved by binding with a variety of proteins. High-throughput biological techniques are used to identify protein molecules bound with specific ncRNA, but they are usually expensive and time consuming. Deep learning provides a powerful solution to computationally predict RNA-protein interactions. In this work, we propose the RPI-SAN model by using the deep-learning stacked auto-encoder network to mine the hidden high-level features from RNA and protein sequences and feed them into a random forest (RF) model to predict ncRNA binding proteins. Stacked assembling is further used to improve the accuracy of the proposed method. Four benchmark datasets, including RPI2241, RPI488, RPI1807, and NPInter v2.0, were employed for the unbiased evaluation of five established prediction tools: RPI-Pred, IPMiner, RPISeq-RF, lncPro, and RPI-SAN. The experimental results show that our RPI-SAN model achieves much better performance than other methods, with accuracies of 90.77%, 89.7%, 96.1%, and 99.33%, respectively. It is anticipated that RPI-SAN can be used as an effective computational tool for future biomedical researches and can accurately predict the potential ncRNA-protein interacted pairs, which provides reliable guidance for biological research. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  1. A Dual-Carbon-and-Nitrogen Stable Isotope Ratio Model Is Not Superior to a Single-Carbon Stable Isotope Ratio Model for Predicting Added Sugar Intake in Southwest Virginian Adults12

    PubMed Central

    Hedrick, Valisa E; Zoellner, Jamie M; Jahren, A Hope; Woodford, Natalie A; Bostic, Joshua N; Davy, Brenda M

    2015-01-01

    Background: An objective measure of added sugar (AS) and sugar-sweetened beverage (SSB) intake is needed. The δ13C value of finger-stick blood is a novel validated biomarker of AS/SSB intake; however, nonsweetener corn products and animal protein also carry a δ13C value similar to AS sources, which may affect blood δ13C values. The δ15N value of blood has been proposed as a “correction factor” for animal protein intake. Objectives: The objectives were to 1) identify foods associated with δ13C and δ15N blood values, 2) determine the contribution of nonsweetener corn to the diet relative to AS intake, and 3) determine if the dual-isotope model (δ13C and δ15N) is a better predictor of AS/SSB intake than δ13C alone. Methods: A cross-sectional sample of southwest Virginian adults (n = 257; aged 42 ± 15 y; 74% overweight/obese) underwent dietary intake assessments and provided finger-stick blood samples, which were analyzed for δ13C and δ15N values by using natural abundance stable isotope mass spectrometry. Statistical analyses included ANOVAs, paired-samples t tests, and multiple linear regressions. Results: The mean ± SD daily AS intake was 88 ± 59 g and nonsweetener corn intake was 13 ± 13 g. The mean δ13C value was −19.1 ± 0.9‰, which was significantly correlated with AS and SSB intakes (r = 0.32 and 0.39, respectively; P ≤ 0.01). The δ13C value and nonsweetener corn intake and the δ15N value and animal protein intake were not correlated. AS intake was significantly greater than nonsweetener corn intake (mean difference = 76.2 ± 57.2 g; P ≤ 0.001). The δ13C value was predictive of AS/SSB intake (β range: 0.28–0.35; P ≤ 0.01); however, δ15N was not predictive and minimal increases in R2 values were observed when the δ15N value was added to the model. Conclusions: The data do not provide evidence that the dual-isotope method is superior for predicting AS/SSB intakes within a southwest Virginian population. Our results support

  2. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.

    PubMed

    Yu, Haoyu S; Deng, Yuqing; Wu, Yujie; Sindhikara, Dan; Rask, Amy R; Kimura, Takayuki; Abel, Robert; Wang, Lingle

    2017-12-12

    Macrocycles have been emerging as a very important drug class in the past few decades largely due to their expanded chemical diversity benefiting from advances in synthetic methods. Macrocyclization has been recognized as an effective way to restrict the conformational space of acyclic small molecule inhibitors with the hope of improving potency, selectivity, and metabolic stability. Because of their relatively larger size as compared to typical small molecule drugs and the complexity of the structures, efficient sampling of the accessible macrocycle conformational space and accurate prediction of their binding affinities to their target protein receptors poses a great challenge of central importance in computational macrocycle drug design. In this article, we present a novel method for relative binding free energy calculations between macrocycles with different ring sizes and between the macrocycles and their corresponding acyclic counterparts. We have applied the method to seven pharmaceutically interesting data sets taken from recent drug discovery projects including 33 macrocyclic ligands covering a diverse chemical space. The predicted binding free energies are in good agreement with experimental data with an overall root-mean-square error (RMSE) of 0.94 kcal/mol. This is to our knowledge the first time where the free energy of the macrocyclization of linear molecules has been directly calculated with rigorous physics-based free energy calculation methods, and we anticipate the outstanding accuracy demonstrated here across a broad range of target classes may have significant implications for macrocycle drug discovery.

  3. Geographic variation of stable isotopes in African elephant ivory

    NASA Astrophysics Data System (ADS)

    Ziegler, S.; Merker, S.; Jacob, D.

    2012-04-01

    In 1989, the international community listed the African elephant in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) thus prohibiting commercial ivory trade. Recent surveillance data show that the illegal trade in ivory has been growing worldwide. Long-term preservation of many of the African elephant populations can be supported with a control mechanism that helps with the implementation of remedial conservation action. Therefore, setting up a reference database that predicts the origin of ivory specimens can assist in determining smuggling routes and the provenance of illegal ivory. Our research builds on earlier work to seek an appropriate method for determining the area of origin for individual tusks. Several researchers have shown that the provenance of elephant ivory can be traced by its isotopic composition, but this is the first attempt to produce an integrated isotopic reference database of elephant ivory provenance. We applied a combination of various routine geochemical analyses to measure the stable isotope ratios of hydrogen, carbon, nitrogen, oxygen, and sulphur. Up to now, we analysed 606 ivory samples of known geographical origin from African range states, museums and private collections, comprising 22 African elephant range states. The isotopic measurements were superimposed with data layers from vegetation, geology and climate. A regression function for the isotope composition of the water isotopes in precipitation and collagen in ivory was developed to overcome the problem of imprecise origin of some of the sampled material. Multivariate statistics, such as nearest neighborhood and discriminate analysis were applied to eventually allow a statistical determination of the provenance for ivory of unknown origin. Our results suggest that the combination of isotopic parameters have the potential to provide predictable and complementary markers for estimating the origin of seized elephant ivory.

  4. The role of stable isotopes in understanding rainfall ...

    EPA Pesticide Factsheets

    The isotopic composition of water transmitted by the canopy as throughfall or stemflow reflects important hydrologic processes occurring in the canopy. A synthesis of the literature shows that complex spatiotemporal variations of isotopic composition are created by canopy interception. As a whole, the studies suggest a set of controlling factors including fractionation, exchange among liquid and vapor phase water, and spatiotemporal redistribution along varying canopy flowpaths. However, our limited understanding of physical processes and water routing in the canopy limits the ability to discern all details for predicting interception isotope effects. We suggest that the isotopic composition of throughfall and stemflow may be the key to improve our understanding of water storage and transport in the canopy, similar to how isotopic analysis contributed to progress in our understanding of watershed runoff processes. While interception isotope effects have largely been studied under the premise that they are a source of error, previous works also indicate a wide range of possible interactions that intercepted water may have with the canopy and airspace. We identify new research questions that may be answered by stable isotopes as a path forward in examining and generalizing small-scale interception processes that could facilitate integration of interception into watershed ecohydrological concepts. Evaporation from forest canopies (interception loss) is a prominent

  5. Kinetic 15N-isotope effects on algal growth

    NASA Astrophysics Data System (ADS)

    Andriukonis, Eivydas; Gorokhova, Elena

    2017-03-01

    Stable isotope labeling is a standard technique for tracing material transfer in molecular, ecological and biogeochemical studies. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism metabolism and growth, which is not consistent with current theoretical and empirical knowledge on kinetic isotope effects. Here, we demonstrate profound changes in growth dynamics of the green alga Raphidocelis subcapitata grown in 15N-enriched media. With increasing 15N concentration (0.37 to 50 at%), the lag phase increased, whereas maximal growth rate and total yield decreased; moreover, there was a negative relationship between the growth and the lag phase across the treatments. The latter suggests that a trade-off between growth rate and the ability to adapt to the high 15N environment may exist. Remarkably, the lag-phase response at 3.5 at% 15N was the shortest and deviated from the overall trend, thus providing partial support to the recently proposed Isotopic Resonance hypothesis, which predicts that certain isotopic composition is particularly favorable for living organisms. These findings confirm the occurrence of KIE in isotopically enriched algae and underline the importance of considering these effects when using stable isotope labeling in field and experimental studies.

  6. Analysis of the site-specific carbon isotope composition of propane by gas source isotope ratio mass spectrometer

    NASA Astrophysics Data System (ADS)

    Piasecki, Alison; Sessions, Alex; Lawson, Michael; Ferreira, A. A.; Neto, E. V. Santos; Eiler, John M.

    2016-09-01

    Site-specific isotope ratio measurements potentially provide valuable information about the formation and degradation of complex molecules-information that is lost in conventional bulk isotopic measurements. Here we discuss the background and possible applications of such measurements, and present a technique for studying the site-specific carbon isotope composition of propane at natural abundance based on mass spectrometric analysis of the intact propane molecule and its fragment ions. We demonstrate the feasibility of this approach through measurements of mixtures of natural propane and propane synthesized with site-specific 13C enrichment, and we document the limits of precision of our technique. We show that mass balance calculations of the bulk δ13C of propane based on our site-specific measurements is generally consistent with independent constraints on bulk δ13C. We further demonstrate the accuracy of the technique, and illustrate one of its simpler applications by documenting the site-specific carbon isotope signature associated with gas phase diffusion of propane, confirming that our measurements conform to the predictions of the kinetic theory of gases. This method can be applied to propane samples of moderate size (tens of micromoles) isolated from natural gases. Thus, it provides a means of studying the site-specific stable isotope systematics of propane at natural isotope abundances on sample sizes that are readily recovered from many natural environments. This method may also serve as a model for future techniques that apply high-resolution mass spectrometry to study the site-specific isotopic distributions of larger organic molecules, with potential applications to biosynthesis, forensics and other geochemical subjects.

  7. Energy-switching potential energy surface for the water molecule revisited: A highly accurate singled-sheeted form.

    PubMed

    Galvão, B R L; Rodrigues, S P J; Varandas, A J C

    2008-07-28

    A global ab initio potential energy surface is proposed for the water molecule by energy-switching/merging a highly accurate isotope-dependent local potential function reported by Polyansky et al. [Science 299, 539 (2003)] with a global form of the many-body expansion type suitably adapted to account explicitly for the dynamical correlation and parametrized from extensive accurate multireference configuration interaction energies extrapolated to the complete basis set limit. The new function mimics also the complicated Sigma/Pi crossing that arises at linear geometries of the water molecule.

  8. Theoretical predictions for α -decay chains of 118 290 -298Og isotopes using a finite-range nucleon-nucleon interaction

    NASA Astrophysics Data System (ADS)

    Ismail, M.; Adel, A.

    2018-04-01

    The α -decay half-lives of the recently synthesized superheavy nuclei (SHN) are investigated by employing the density dependent cluster model. A realistic nucleon-nucleon (NN ) interaction with a finite-range exchange part is used to calculate the microscopic α -nucleus potential in the well-established double-folding model. The calculated potential is then implemented to find both the assault frequency and the penetration probability of the α particle by means of the Wentzel-Kramers-Brillouin (WKB) approximation in combination with the Bohr-Sommerfeld quantization condition. The calculated values of α -decay half-lives of the recently synthesized Og isotopes and its decay products are in good agreement with the experimental data. Moreover, the calculated values of α -decay half-lives have been compared with those values evaluated using other theoretical models, and it was found that our theoretical values match well with their counterparts. The competition between α decay and spontaneous fission is investigated and predictions for possible decay modes for the unknown nuclei 118 290 -298Og are presented. We studied the behavior of the α -decay half-lives of Og isotopes and their decay products as a function of the mass number of the parent nuclei. We found that the behavior of the curves is governed by proton and neutron magic numbers found from previous studies. The proton numbers Z =114 , 116, 108, 106 and the neutron numbers N =172 , 164, 162, 158 show some magic character. We hope that the theoretical prediction of α -decay chains provides a new perspective to experimentalists.

  9. Limited Sampling Strategy for Accurate Prediction of Pharmacokinetics of Saroglitazar: A 3-point Linear Regression Model Development and Successful Prediction of Human Exposure.

    PubMed

    Joshi, Shuchi N; Srinivas, Nuggehally R; Parmar, Deven V

    2018-03-01

    Our aim was to develop and validate the extrapolative performance of a regression model using a limited sampling strategy for accurate estimation of the area under the plasma concentration versus time curve for saroglitazar. Healthy subject pharmacokinetic data from a well-powered food-effect study (fasted vs fed treatments; n = 50) was used in this work. The first 25 subjects' serial plasma concentration data up to 72 hours and corresponding AUC 0-t (ie, 72 hours) from the fasting group comprised a training dataset to develop the limited sampling model. The internal datasets for prediction included the remaining 25 subjects from the fasting group and all 50 subjects from the fed condition of the same study. The external datasets included pharmacokinetic data for saroglitazar from previous single-dose clinical studies. Limited sampling models were composed of 1-, 2-, and 3-concentration-time points' correlation with AUC 0-t of saroglitazar. Only models with regression coefficients (R 2 ) >0.90 were screened for further evaluation. The best R 2 model was validated for its utility based on mean prediction error, mean absolute prediction error, and root mean square error. Both correlations between predicted and observed AUC 0-t of saroglitazar and verification of precision and bias using Bland-Altman plot were carried out. None of the evaluated 1- and 2-concentration-time points models achieved R 2 > 0.90. Among the various 3-concentration-time points models, only 4 equations passed the predefined criterion of R 2 > 0.90. Limited sampling models with time points 0.5, 2, and 8 hours (R 2 = 0.9323) and 0.75, 2, and 8 hours (R 2 = 0.9375) were validated. Mean prediction error, mean absolute prediction error, and root mean square error were <30% (predefined criterion) and correlation (r) was at least 0.7950 for the consolidated internal and external datasets of 102 healthy subjects for the AUC 0-t prediction of saroglitazar. The same models, when applied to the AUC 0-t

  10. Towards more accurate and reliable predictions for nuclear applications

    NASA Astrophysics Data System (ADS)

    Goriely, Stephane; Hilaire, Stephane; Dubray, Noel; Lemaître, Jean-François

    2017-09-01

    The need for nuclear data far from the valley of stability, for applications such as nuclear astrophysics or future nuclear facilities, challenges the robustness as well as the predictive power of present nuclear models. Most of the nuclear data evaluation and prediction are still performed on the basis of phenomenological nuclear models. For the last decades, important progress has been achieved in fundamental nuclear physics, making it now feasible to use more reliable, but also more complex microscopic or semi-microscopic models in the evaluation and prediction of nuclear data for practical applications. Nowadays mean-field models can be tuned at the same level of accuracy as the phenomenological models, renormalized on experimental data if needed, and therefore can replace the phenomenological inputs in the evaluation of nuclear data. The latest achievements to determine nuclear masses within the non-relativistic HFB approach, including the related uncertainties in the model predictions, are discussed. Similarly, recent efforts to determine fission observables within the mean-field approach are described and compared with more traditional existing models.

  11. Evaluation of the performance of high temperature conversion reactors for compound-specific oxygen stable isotope analysis.

    PubMed

    Hitzfeld, Kristina L; Gehre, Matthias; Richnow, Hans-Hermann

    2017-05-01

    In this study conversion conditions for oxygen gas chromatography high temperature conversion (HTC) isotope ratio mass spectrometry (IRMS) are characterised using qualitative mass spectrometry (IonTrap). It is shown that physical and chemical properties of a given reactor design impact HTC and thus the ability to accurately measure oxygen isotope ratios. Commercially available and custom-built tube-in-tube reactors were used to elucidate (i) by-product formation (carbon dioxide, water, small organic molecules), (ii) 2nd sources of oxygen (leakage, metal oxides, ceramic material), and (iii) required reactor conditions (conditioning, reduction, stability). The suitability of the available HTC approach for compound-specific isotope analysis of oxygen in volatile organic molecules like methyl tert-butyl ether is assessed. Main problems impeding accurate analysis are non-quantitative HTC and significant carbon dioxide by-product formation. An evaluation strategy combining mass spectrometric analysis of HTC products and IRMS 18 O/ 16 O monitoring for future method development is proposed.

  12. Theoretical prediction of probable isotopes of superheavy nuclei of Z = 122

    NASA Astrophysics Data System (ADS)

    Manjunatha, H. C.

    2016-11-01

    We have studied the α-decay half-life and spontaneous fission half-lives of isotopes of superheavy element Z = 122 in the range 275 ≤ A ≥ 326. A comparison of calculated alpha half-lives with the literature [D. N. Poenaru, R. A. Gherghescu and W. Greiner, Phys. Rev. C 83 (2011) 014601, D. N. Poenaru, R. A. Gherghescu and W. Greiner, Phys. Rev. C 85 (2012) 034615] and the analytical formulas of Royer [G. Royer, J. Phys. G; Nucl. Part. Phys. 26 (2000) 1149] shows good agreement with each other. To identify the mode of decay of these isotopes, the spontaneous-fission half-lives were also evaluated using the semiempirical relation given by [C. Xu, Z. Ren and Y. Guo, Phys. Rev. C 78 (2008) 044329]. A comparative study on the competition of alpha decay versus spontaneous fission of superheavy nuclei (SHN) reveals that around eight isotopes (307-314122) survive fission and have alpha decay channel as the prominent mode of decay and hold the possibility to be synthesized in the laboratory. The alpha decay half-lives and spontaneous fission half-lives of SHN with Z = 122, A = 299-306, with Z = 120, A = 294-300, and with Z = 119, A = 292-297 are also studied. The present study will be useful in the synthesis of superheavy elements Z > 118 by using the actinide based reactions with stable projectiles heavier than 48Ca.

  13. A bacterial method for the nitrogen isotopic analysis of nitrate in seawater and freshwater

    USGS Publications Warehouse

    Sigman, D.M.; Casciotti, K.L.; Andreani, M.; Barford, C.; Galanter, M.; Böhlke, J.K.

    2001-01-01

    We report a new method for measurement of the isotopic composition of nitrate (NO3-) at the natural-abundance level in both seawater and freshwater. The method is based on the isotopic analysis of nitrous oxide (N2O) generated from nitrate by denitrifying bacteria that lack N2O-reductase activity. The isotopic composition of both nitrogen and oxygen from nitrate are accessible in this way. In this first of two companion manuscripts, we describe the basic protocol and results for the nitrogen isotopes. The precision of the method is better than 0.2‰ (1 SD) at concentrations of nitrate down to 1 μM, and the nitrogen isotopic differences among various standards and samples are accurately reproduced. For samples with 1 μM nitrate or more, the blank of the method is less than 10% of the signal size, and various approaches may reduce it further.

  14. Nickel isotopic composition of the mantle

    NASA Astrophysics Data System (ADS)

    Gall, Louise; Williams, Helen M.; Halliday, Alex N.; Kerr, Andrew C.

    2017-02-01

    This paper presents a detailed high-precision study of Ni isotope variations in mantle peridotites and their minerals, komatiites as well as chondritic and iron meteorites. Ultramafic rocks display a relatively large range in δ60 Ni (permil deviation in 60 Ni /58 Ni relative to the NIST SRM 986 Ni isotope standard) for this environment, from 0.15 ± 0.07‰ to 0.36 ± 0.08‰, with olivine-rich rocks such as dunite and olivine cumulates showing lighter isotope compositions than komatiite, lherzolite and pyroxenite samples. The data for the mineral separates shed light on the origin of these variations. Olivine and orthopyroxene display light δ60 Ni whereas clinopyroxene and garnet are isotopically heavy. This indicates that peridotite whole-rock δ60 Ni may be controlled by variations in modal mineralogy, with the prediction that mantle melts will display variable δ60 Ni values due to variations in residual mantle and cumulate mineralogy. Based on fertile peridotite xenoliths and Phanerozoic komatiite samples it is concluded that the upper mantle has a relatively homogeneous Ni isotope composition, with the best estimate of δ60Nimantle being 0.23 ± 0.06‰ (2 s.d.). Given that >99% of the Ni in the silicate Earth is located in the mantle, this also defines the Ni isotope composition of the Bulk Silicate Earth (BSE). This value is nearly identical to the results obtained for a suite of chondrites and iron meteorites (mean δ60 Ni 0.26 ± 0.12‰ and 0.29 ± 0.10‰, respectively) showing that the BSE is chondritic with respect to its Ni isotope composition, with little to no Ni mass-dependent isotope fractionation resulting from core formation.

  15. Accurate electrical prediction of memory array through SEM-based edge-contour extraction using SPICE simulation

    NASA Astrophysics Data System (ADS)

    Shauly, Eitan; Rotstein, Israel; Peltinov, Ram; Latinski, Sergei; Adan, Ofer; Levi, Shimon; Menadeva, Ovadya

    2009-03-01

    The continues transistors scaling efforts, for smaller devices, similar (or larger) drive current/um and faster devices, increase the challenge to predict and to control the transistor off-state current. Typically, electrical simulators like SPICE, are using the design intent (as-drawn GDS data). At more sophisticated cases, the simulators are fed with the pattern after lithography and etch process simulations. As the importance of electrical simulation accuracy is increasing and leakage is becoming more dominant, there is a need to feed these simulators, with more accurate information extracted from physical on-silicon transistors. Our methodology to predict changes in device performances due to systematic lithography and etch effects was used in this paper. In general, the methodology consists on using the OPCCmaxTM for systematic Edge-Contour-Extraction (ECE) from transistors, taking along the manufacturing and includes any image distortions like line-end shortening, corner rounding and line-edge roughness. These measurements are used for SPICE modeling. Possible application of this new metrology is to provide a-head of time, physical and electrical statistical data improving time to market. In this work, we applied our methodology to analyze a small and large array's of 2.14um2 6T-SRAM, manufactured using Tower Standard Logic for General Purposes Platform. 4 out of the 6 transistors used "U-Shape AA", known to have higher variability. The predicted electrical performances of the transistors drive current and leakage current, in terms of nominal values and variability are presented. We also used the methodology to analyze an entire SRAM Block array. Study of an isolation leakage and variability are presented.

  16. Measurement of isotope ratios on transient signals by MC-ICP-MS.

    PubMed

    Günther-Leopold, Ines; Wernli, Beat; Kopajtic, Zlatko; Günther, Detlef

    2004-01-01

    Precise and accurate isotope ratio measurements are an important task in many applications such as isotope-dilution mass spectrometry, bioavailability studies, or the determination of isotope variations in geological or nuclear samples. The technique of MC-ICP-MS has attracted much attention because it permits the precise measurement of isotope compositions for a wide range of elements combined with excellent detection limits due to high ionisation efficiencies. However, the results are based mainly on measurements using continuous sample introduction. In the present study the determination of isotope ratios on various transient signals with a time duration of 30 to 60 s has been achieved by coupling high-performance liquid chromatography to a multicollector inductively coupled plasma mass spectrometer. In order to investigate the origin of ratio drifts across the transient signals for this hyphenated technique, measurements with the same standard solutions were also carried out using a flow-injection device for sample introduction. As a result of this application it could be concluded that the main source of the bias in the measured isotope ratios is within the ICP-MS instead of fractionation effects on the chromatographic column material. Preliminary studies on short transient signals of gaseous samples (dry plasma) showed a reverse fractionation effect compared with wet plasma conditions (flow injection and HPLC).

  17. Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations.

    PubMed

    Varga, Matthew J; Schwartz, Steven D

    2016-04-12

    In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems.

  18. Isotope composition and volume of Earth's early oceans.

    PubMed

    Pope, Emily C; Bird, Dennis K; Rosing, Minik T

    2012-03-20

    Oxygen and hydrogen isotope compositions of Earth's seawater are controlled by volatile fluxes among mantle, lithospheric (oceanic and continental crust), and atmospheric reservoirs. Throughout geologic time the oxygen mass budget was likely conserved within these Earth system reservoirs, but hydrogen's was not, as it can escape to space. Isotopic properties of serpentine from the approximately 3.8 Ga Isua Supracrustal Belt in West Greenland are used to characterize hydrogen and oxygen isotope compositions of ancient seawater. Archaean oceans were depleted in deuterium [expressed as δD relative to Vienna standard mean ocean water (VSMOW)] by at most 25 ± 5‰, but oxygen isotope ratios were comparable to modern oceans. Mass balance of the global hydrogen budget constrains the contribution of continental growth and planetary hydrogen loss to the secular evolution of hydrogen isotope ratios in Earth's oceans. Our calculations predict that the oceans of early Earth were up to 26% more voluminous, and atmospheric CH(4) and CO(2) concentrations determined from limits on hydrogen escape to space are consistent with clement conditions on Archaean Earth.

  19. α -decay chains of superheavy Mt-279265 isotopes

    NASA Astrophysics Data System (ADS)

    Santhosh, K. P.; Nithya, C.

    2017-10-01

    The α -decay chains of the isotopes Mt-279265 are predicted by comparing the α half-lives calculated within the Coulomb and proximity potential model for deformed nuclei of Santhosh et al. [Nucl. Phys. A 850, 34 (2011)], 10.1016/j.nuclphysa.2010.12.002 with the spontaneous fission half-lives using the shell-effect-dependent formula of Santhosh and Nithya [Phys. Rev. C 94, 054621 (2016)], 10.1103/PhysRevC.94.054621. α half-lives also are calculated using different theoretical formalisms for comparison. The predicted half-lives and decay modes match well with the experimental results. The use of four different mass tables for calculating the α - decay energies indicates that the mass table of Wang et al. [Chin. Phys. C 41, 030003 (2017)], 10.1088/1674-1137/41/3/030003, which is based on the AME2016 atomic mass evaluation, is in better agreement with experimental results. The paper predicts long α chains from 265,267-269,271-273MT with half-lives within experimental limits. The isotopes 274-276,278Mt exhibit 2α chains followed by spontaneous fission. The 2α chain of 266Mt and the 4α chain of 270Mt end with electron capture. The isotopes Mt,279277 decay via spontaneous fission. We hope that the paper will open up new areas in this field.

  20. Estimating energy expenditure in vascular surgery patients: Are predictive equations accurate enough?

    PubMed

    Suen, J; Thomas, J M; Delaney, C L; Spark, J I; Miller, M D

    2016-12-01

    Malnutrition is prevalent in vascular surgical patients who commonly seek tertiary care at advanced stages of disease. Adjunct nutrition support is therefore pertinent to optimise patient outcomes. To negate consequences related to excessive or suboptimal dietary energy intake, it is essential to accurately determine energy expenditure and subsequent requirements. This study aims to compare resting energy expenditure (REE) measured by indirect calorimetry, a commonly used comparator, to REE estimated by predictive equations (Schofield, Harris-Benedict equations and Miller equation) to determine the most suitable equation for vascular surgery patients. Data were collected from four studies that measured REE in 77 vascular surgery patients. Bland-Altman analyses were conducted to explore agreement. Presence of fixed or proportional bias was assessed by linear regression analyses. In comparison to measured REE, on average REE was overestimated when Schofield (+857 kJ/day), Harris-Benedict (+801 kJ/day) and Miller (+71 kJ/day) equations were used. Wide limits of agreement led to an over or underestimation from 1552 to 1755 kJ. Proportional bias was absent in Schofield (R 2  = 0.005, p = 0.54) and Harris-Benedict equations (R 2  = 0.045, p = 0.06) but was present in the Miller equation (R 2  = 0.210, p < 0.01) even after logarithmic transformation (R 2  = 0.213, p < 0.01). Whilst the Miller equation tended to overestimate resting energy expenditure and was affected by proportional bias, the limits of agreement and mean bias were smaller compared to Schofield and Harris-Benedict equations. This suggested that it is the preferred predictive equation for vascular surgery patients. Future research to refine the Miller equation to improve its overall accuracy will better inform the provision of nutritional support for vascular surgery patients and subsequently improve outcomes. Alternatively, an equation might be developed specifically for use with

  1. Geant4 Modifications for Accurate Fission Simulations

    NASA Astrophysics Data System (ADS)

    Tan, Jiawei; Bendahan, Joseph

    Monte Carlo is one of the methods to simulate the generation and transport of radiation through matter. The most widely used radiation simulation codes are MCNP and Geant4. The simulation of fission production and transport by MCNP has been thoroughly benchmarked. There is an increasing number of users that prefer using Geant4 due to the flexibility of adding features. However, it has been found that Geant4 does not have the proper fission-production cross sections and does not produce the correct fission products. To achieve accurate results for studies in fissionable material applications, Geant4 was modified to correct these inaccuracies and to add new capabilities. The fission model developed by the Lawrence Livermore National Laboratory was integrated into the neutron-fission modeling package. The photofission simulation capability was enabled using the same neutron-fission library under the assumption that nuclei fission in the same way, independent of the excitation source. The modified fission code provides the correct multiplicity of prompt neutrons and gamma rays, and produces delayed gamma rays and neutrons with time and energy dependencies that are consistent with ENDF/B-VII. The delayed neutrons are now directly produced by a custom package that bypasses the fragment cascade model. The modifications were made for U-235, U-238 and Pu-239 isotopes; however, the new framework allows adding new isotopes easily. The SLAC nuclear data library is used for simulation of isotopes with an atomic number above 92 because it is not available in Geant4. Results of the modified Geant4.10.1 package of neutron-fission and photofission for prompt and delayed radiation are compared with ENDFB-VII and with results produced with the original package.

  2. A fast and accurate method to predict 2D and 3D aerodynamic boundary layer flows

    NASA Astrophysics Data System (ADS)

    Bijleveld, H. A.; Veldman, A. E. P.

    2014-12-01

    A quasi-simultaneous interaction method is applied to predict 2D and 3D aerodynamic flows. This method is suitable for offshore wind turbine design software as it is a very accurate and computationally reasonably cheap method. This study shows the results for a NACA 0012 airfoil. The two applied solvers converge to the experimental values when the grid is refined. We also show that in separation the eigenvalues remain positive thus avoiding the Goldstein singularity at separation. In 3D we show a flow over a dent in which separation occurs. A rotating flat plat is used to show the applicability of the method for rotating flows. The shown capabilities of the method indicate that the quasi-simultaneous interaction method is suitable for design methods for offshore wind turbine blades.

  3. Polyatomic interferences on high precision uranium isotope ratio measurements by MC-ICP-MS: Applications to environmental sampling for nuclear safeguards

    DOE PAGES

    Pollington, Anthony D.; Kinman, William S.; Hanson, Susan K.; ...

    2015-09-04

    Modern mass spectrometry and separation techniques have made measurement of major uranium isotope ratios a routine task; however accurate and precise measurement of the minor uranium isotopes remains a challenge as sample size decreases. One particular challenge is the presence of isobaric interferences and their impact on the accuracy of minor isotope 234U and 236U measurements. Furthermore, we present techniques used for routine U isotopic analysis of environmental nuclear safeguards samples and evaluate polyatomic interferences that negatively impact accuracy as well as methods to mitigate their impacts.

  4. Magnetic isotope effect and theory of atomic orbital hybridization to predict a mechanism of chemical exchange reactions.

    PubMed

    Epov, Vladimir N

    2011-08-07

    A novel approach is suggested to investigate the mechanisms of chemical complexation reactions based on the results of Fujii with co-workers; they have experimentally observed that several metals and metalloids demonstrate mass-independent isotope fractionation during the reactions with the DC18C6 crown ether using solvent-solvent extraction. In this manuscript, the isotope fractionation caused by the magnetic isotope effect is used to understand the mechanisms of chemical exchange reactions. Due to the rule that reactions are allowed for certain electron spin states, and forbidden for others, magnetic isotopes show chemical anomalies during these reactions. Mass-independent fractionation is suggested to take place due to the hyperfine interaction of the nuclear spin with the electron spin of the intermediate product. Moreover, the sign of the mass-independent fractionation is found to be dependent on the element and its species, which is also explained by the magnetic isotope effect. For example, highly negative mass-independent isotope fractionation of magnetic isotopes was observed for reactions of DC18C6 with SnCl(2) species and with several Ru(III) chloro-species, and highly positive for reactions of this ether with TeCl(6)(2-), and with several Cd(II) and Pd(II) species. The atomic radius of an element is also a critical parameter for the reaction with crown ether, particularly the element ions with [Kr]4d(n)5s(m) electron shell fits the best with the DC18C6 crown ring. It is demonstrated that the magnetic isotope effect in combination with the theory of orbital hybridization can help to understand the mechanism of complexation reactions. The suggested approach is also applied to explain previously published mass-independent fractionation of Hg isotopes in other types of chemical exchange reactions. This journal is © the Owner Societies 2011

  5. Dual element ((15)N/(14)N, (13)C/(12)C) isotope analysis of glyphosate and AMPA by derivatization-gas chromatography isotope ratio mass spectrometry (GC/IRMS) combined with LC/IRMS.

    PubMed

    Mogusu, Emmanuel O; Wolbert, J Benjamin; Kujawinski, Dorothea M; Jochmann, Maik A; Elsner, Martin

    2015-07-01

    To assess sources and degradation of the herbicide glyphosate [N-(phosphonomethyl) glycine] and its metabolite AMPA (aminomethylphosphonic acid), concentration measurements are often inconclusive and even (13)C/(12)C analysis alone may give limited information. To advance isotope ratio analysis of an additional element, we present compound-specific (15)N/(14)N analysis of glyphosate and AMPA by a two step derivatization in combination with gas chromatography/isotope ratio mass spectrometry (GC/IRMS). The N-H group was derivatized with isopropyl chloroformate (iso-PCF), and remaining acidic groups were subsequently methylated with trimethylsilyldiazomethane (TMSD). Iso-PCF treatment at pH <10 gave too low (15)N/(14)N ratios indicating an incomplete derivatization; in contrast, too high (15)N/(14)N ratios at pH >10 indicated decomposition of the derivative. At pH 10, and with an excess of iso-PCF by 10-24, greatest yields and accurate (15)N/(14)N ratios were obtained (deviation from elemental analyzer-IRMS: -0.2 ± 0.9% for glyphosate; -0.4 ± 0.7% for AMPA). Limits for accurate δ(15)N analysis of glyphosate and AMPA were 150 and 250 ng injected, respectively. A combination of δ(15)N and δ(13)C analysis by liquid chromatography/isotope ratio mass spectrometry (LC/IRMS) (1) enabled an improved distinction of commercial glyphosate products and (2) showed that glyphosate isotope values during degradation by MnO2 clearly fell outside the commercial product range. This highlights the potential of combined carbon and nitrogen isotopes analysis to trace sources and degradation of glyphosate.

  6. Integrating metabolic performance, thermal tolerance, and plasticity enables for more accurate predictions on species vulnerability to acute and chronic effects of global warming.

    PubMed

    Magozzi, Sarah; Calosi, Piero

    2015-01-01

    Predicting species vulnerability to global warming requires a comprehensive, mechanistic understanding of sublethal and lethal thermal tolerances. To date, however, most studies investigating species physiological responses to increasing temperature have focused on the underlying physiological traits of either acute or chronic tolerance in isolation. Here we propose an integrative, synthetic approach including the investigation of multiple physiological traits (metabolic performance and thermal tolerance), and their plasticity, to provide more accurate and balanced predictions on species and assemblage vulnerability to both acute and chronic effects of global warming. We applied this approach to more accurately elucidate relative species vulnerability to warming within an assemblage of six caridean prawns occurring in the same geographic, hence macroclimatic, region, but living in different thermal habitats. Prawns were exposed to four incubation temperatures (10, 15, 20 and 25 °C) for 7 days, their metabolic rates and upper thermal limits were measured, and plasticity was calculated according to the concept of Reaction Norms, as well as Q10 for metabolism. Compared to species occupying narrower/more stable thermal niches, species inhabiting broader/more variable thermal environments (including the invasive Palaemon macrodactylus) are likely to be less vulnerable to extreme acute thermal events as a result of their higher upper thermal limits. Nevertheless, they may be at greater risk from chronic exposure to warming due to the greater metabolic costs they incur. Indeed, a trade-off between acute and chronic tolerance was apparent in the assemblage investigated. However, the invasive species P. macrodactylus represents an exception to this pattern, showing elevated thermal limits and plasticity of these limits, as well as a high metabolic control. In general, integrating multiple proxies for species physiological acute and chronic responses to increasing

  7. Determination of tin isotope ratios in cassiterite by femtosecond laser ablation multicollector inductively coupled plasma mass spectrometry

    NASA Astrophysics Data System (ADS)

    Schulze, Marie; Ziegerick, Marco; Horn, Ingo; Weyer, Stefan; Vogt, Carla

    2017-04-01

    In comparison to isotope analysis of dissolved samples femtosecond laser ablation multicollector inductively coupled plasma mass spectrometry (fs-LA-MC-ICP-MS) enables precise isotope ratio analyses consuming much less sample material and with a minimum effort in sample preparation. This is especially important for the investigation of valuable historical objects for which visual traces of sampling are unwanted. The present study provides a basis for tin isotope ratio measurements using LA-MC-ICP-MS technique. For this, in house isotope standards had to be defined. Investigations on interferences and matrix effects illustrate that beside Sb only high Te contents (with values above those to be expected in cassiterite) result in a significant shift of the measured tin isotope ratios. This effect can partly be corrected for using natural isotope abundances. However, a natural isotope fractionation of Te cannot be excluded. Tin beads reduced from cassiterite were analysed by laser ablation and after dissolution. It was shown that tin isotope ratios can be determined accurately by using fs-LA-MC-ICP-MS. Furthermore the homogeneity of tin isotope ratios in cassiterite was proven.

  8. Estimating pathway-specific contributions to biodegradation in aquifers based on dual isotope analysis: theoretical analysis and reactive transport simulations.

    PubMed

    Centler, Florian; Heße, Falk; Thullner, Martin

    2013-09-01

    At field sites with varying redox conditions, different redox-specific microbial degradation pathways contribute to total contaminant degradation. The identification of pathway-specific contributions to total contaminant removal is of high practical relevance, yet difficult to achieve with current methods. Current stable-isotope-fractionation-based techniques focus on the identification of dominant biodegradation pathways under constant environmental conditions. We present an approach based on dual stable isotope data to estimate the individual contributions of two redox-specific pathways. We apply this approach to carbon and hydrogen isotope data obtained from reactive transport simulations of an organic contaminant plume in a two-dimensional aquifer cross section to test the applicability of the method. To take aspects typically encountered at field sites into account, additional simulations addressed the effects of transverse mixing, diffusion-induced stable-isotope fractionation, heterogeneities in the flow field, and mixing in sampling wells on isotope-based estimates for aerobic and anaerobic pathway contributions to total contaminant biodegradation. Results confirm the general applicability of the presented estimation method which is most accurate along the plume core and less accurate towards the fringe where flow paths receive contaminant mass and associated isotope signatures from the core by transverse dispersion. The presented method complements the stable-isotope-fractionation-based analysis toolbox. At field sites with varying redox conditions, it provides a means to identify the relative importance of individual, redox-specific degradation pathways. © 2013.

  9. Correction for isotopic interferences between analyte and internal standard in quantitative mass spectrometry by a nonlinear calibration function.

    PubMed

    Rule, Geoffrey S; Clark, Zlatuse D; Yue, Bingfang; Rockwood, Alan L

    2013-04-16

    Stable isotope-labeled internal standards are of great utility in providing accurate quantitation in mass spectrometry (MS). An implicit assumption has been that there is no "cross talk" between signals of the internal standard and the target analyte. In some cases, however, naturally occurring isotopes of the analyte do contribute to the signal of the internal standard. This phenomenon becomes more pronounced for isotopically rich compounds, such as those containing sulfur, chlorine, or bromine, higher molecular weight compounds, and those at high analyte/internal standard concentration ratio. This can create nonlinear calibration behavior that may bias quantitative results. Here, we propose the use of a nonlinear but more accurate fitting of data for these situations that incorporates one or two constants determined experimentally for each analyte/internal standard combination and an adjustable calibration parameter. This fitting provides more accurate quantitation in MS-based assays where contributions from analyte to stable labeled internal standard signal exist. It can also correct for the reverse situation where an analyte is present in the internal standard as an impurity. The practical utility of this approach is described, and by using experimental data, the approach is compared to alternative fits.

  10. Paleogene Seawater Osmium Isotope Records

    NASA Astrophysics Data System (ADS)

    Rolewicz, Z.; Thomas, D. J.; Marcantonio, F.

    2012-12-01

    Paleoceanographic reconstructions of the Late Cretaceous and early Cenozoic require enhanced geographic coverage, particularly in the Pacific, in order to better constrain meridional variations in environmental conditions. The challenge with the existing inventory of Pacific deep-sea cores is that they consist almost exclusively of pelagic clay with little existing age control. Pelagic clay sequences are useful for reconstructions of dust accumulation and water mass composition, but accurate correlation of these records to other sites requires improved age control. Recent work indicates that seawater Os isotope analyses provide useful age control for red clay sequences. The residence time of Os in seawater is relatively long compared to oceanic mixing, therefore the global seawater 187Os/188Os composition is practically homogeneous. A growing body of Late Cretaceous and Cenozoic data has constrained the evolution of the seawater Os isotopic composition and this curve is now a viable stratigraphic tool, employed in dating layers of Fe-Mn crusts (e.g., Klemm et al., 2005). Ravizza (2007) also demonstrated that the seawater Os isotopic composition can be extracted reliably from pelagic red clay sediments by analyzing the leached oxide minerals. The drawback to using seawater Os isotope stratigraphy to date Paleogene age sediments is that the compilation of existing data has some significant temporal gaps, notably between ~38 and 55 Ma. To improve the temporal resolution of the seawater Os isotope curve, we present new data from Ocean Drilling Program (ODP) Site 865 in the equatorial Pacific. Site 865 has excellent biostratigraphic age control over the interval ~38-55Ma. Preliminary data indicate an increase in the seawater composition from 0.427 at 53.4 Ma to 0.499 by 43 Ma, consistent with the apparent trend in the few existing data points. We also analyzed the Os isotopic composition recorded by oxide minerals at Integrated Ocean Drilling Program (IODP) Site U1370

  11. Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

    PubMed Central

    Xue, Yi; Skrynnikov, Nikolai R

    2014-01-01

    Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

  12. Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins

    PubMed Central

    Yang, Jing; He, Bao-Ji; Jang, Richard; Zhang, Yang; Shen, Hong-Bin

    2015-01-01

    Abstract Motivation: Cysteine-rich proteins cover many important families in nature but there are currently no methods specifically designed for modeling the structure of these proteins. The accuracy of disulfide connectivity pattern prediction, particularly for the proteins of higher-order connections, e.g. >3 bonds, is too low to effectively assist structure assembly simulations. Results: We propose a new hierarchical order reduction protocol called Cyscon for disulfide-bonding prediction. The most confident disulfide bonds are first identified and bonding prediction is then focused on the remaining cysteine residues based on SVR training. Compared with purely machine learning-based approaches, Cyscon improved the average accuracy of connectivity pattern prediction by 21.9%. For proteins with more than 5 disulfide bonds, Cyscon improved the accuracy by 585% on the benchmark set of PDBCYS. When applied to 158 non-redundant cysteine-rich proteins, Cyscon predictions helped increase (or decrease) the TM-score (or RMSD) of the ab initio QUARK modeling by 12.1% (or 14.4%). This result demonstrates a new avenue to improve the ab initio structure modeling for cysteine-rich proteins. Availability and implementation: http://www.csbio.sjtu.edu.cn/bioinf/Cyscon/ Contact: zhng@umich.edu or hbshen@sjtu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26254435

  13. Liquid and gas chromatography coupled to isotope ratio mass spectrometry for the determination of 13C-valine isotopic ratios in complex biological samples.

    PubMed

    Godin, Jean-Philippe; Breuillé, Denis; Obled, Christiane; Papet, Isabelle; Schierbeek, Henk; Hopfgartner, Gérard; Fay, Laurent-Bernard

    2008-10-01

    On-line gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) is commonly used to measure isotopic ratios at natural abundance as well as for tracer studies in nutritional and medical research. However, high-precision (13)C isotopic enrichment can also be measured by liquid chromatography-isotope ratio mass spectrometry (LC-IRMS). Indeed, LC-IRMS can be used, as shown by the new method reported here, to obtain a baseline separation and to measure (13)C isotopic enrichment of underivatised amino acids (Asp, Thr-Ser, Glu, Pro, Gly, Ala, Cys and Val). In case of Val, at natural abundance, the SD(delta(13)C) reported with this method was found to be below 1 per thousand . Another key feature of the new LC-IRMS method reported in this paper is the comparison of the LC-IRMS approach with the conventional GC-C-IRMS determination. To perform this comparative study, isotopic enrichments were measured from underivatised Val and its N(O, S)-ethoxycarbonyl ethyl ester derivative. Between 0.0 and 1.0 molar percent excess (MPE) (delta(13)C= -12.3 to 150.8 per thousand), the calculated root-mean-square (rms) of SD was 0.38 and 0.46 per thousand and the calculated rms of accuracy was 0.023 and 0.005 MPE, respectively, for GC-C-IRMS and LC-IRMS. Both systems measured accurately low isotopic enrichments (0.002 atom percent excess (APE)) with an SD (APE) of 0.0004. To correlate the relative (delta(13)C) and absolute (atom%, APE and MPE) isotopic enrichment of Val measured by the GC-C-IRMS and LC-IRMS devices, mathematical equations showing the slope and intercept of the curves were established and validated with experimental data between 0.0 to 2.3 MPE. Finally, both GC-C-IRMS and LC-IRMS instruments were also used to assess isotopic enrichment of protein-bound (13)C-Val in tibial epiphysis in a tracer study performed in rats. Isotopic enrichments measured by LC-IRMS and GC-C-IRMS were not statistically different (p>0.05). The results of this work indicate that

  14. Comparison of prediction methods for oxygen-18 isotope composition in shallow groundwater.

    PubMed

    Cerar, Sonja; Mezga, Kim; Žibret, Gorazd; Urbanc, Janko; Komac, Marko

    2018-08-01

    Groundwater is the most important source of drinking water in the world. Therefore, information on the quality and quantity is important, as is new information related to the characteristics of the aquifer and the recharge area. In the present study we focused on the isotope composition of oxygen (δ 18 O) in groundwater, which is a natural tracer and provides a better understanding of the water cycle, in terms of origin, dynamics and interaction. The groundwater δ 18 O at 83 locations over the entire Slovenian territory was studied. Each location was sampled twice during the period 2009-2011. Geostatistical tools (such us ordinary kriging, simple and multiple linear regressions, and artificial neural networks were used and compared to select the best tool. Measured values of δ 18 O in the groundwater were used as the dependent variable, while the spatial characteristics of the territory (elevation, distance from the sea and average annual precipitation) were used as independent variables. Based on validation data sets, the artificial neural network model proved to be the most suitable method for predicting δ 18 O in the groundwater, since it produced the smallest deviations from the real/measured values in groundwater. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Reduction of chemical formulas from the isotopic peak distributions of high-resolution mass spectra.

    PubMed

    Roussis, Stilianos G; Proulx, Richard

    2003-03-15

    A method has been developed for the reduction of the chemical formulas of compounds in complex mixtures from the isotopic peak distributions of high-resolution mass spectra. The method is based on the principle that the observed isotopic peak distribution of a mixture of compounds is a linear combination of the isotopic peak distributions of the individual compounds in the mixture. All possible chemical formulas that meet specific criteria (e.g., type and number of atoms in structure, limits of unsaturation, etc.) are enumerated, and theoretical isotopic peak distributions are generated for each formula. The relative amount of each formula is obtained from the accurately measured isotopic peak distribution and the calculated isotopic peak distributions of all candidate formulas. The formulas of compounds in simple spectra, where peak components are fully resolved, are rapidly determined by direct comparison of the calculated and experimental isotopic peak distributions. The singular value decomposition linear algebra method is used to determine the contributions of compounds in complex spectra containing unresolved peak components. The principles of the approach and typical application examples are presented. The method is most useful for the characterization of complex spectra containing partially resolved peaks and structures with multiisotopic elements.

  16. Identification of volatile and semivolatile compounds in chemical ionization GC-MS using a mass-to-structure (MTS) Search Engine with integral isotope pattern ranking.

    PubMed

    Liao, Wenta; Draper, William M

    2013-02-21

    The mass-to-structure or MTS Search Engine is an Access 2010 database containing theoretical molecular mass information for 19,438 compounds assembled from common sources such as the Merck Index, pesticide and pharmaceutical compilations, and chemical catalogues. This database, which contains no experimental mass spectral data, was developed as an aid to identification of compounds in atmospheric pressure ionization (API)-LC-MS. This paper describes a powerful upgrade to this database, a fully integrated utility for filtering or ranking candidates based on isotope ratios and patterns. The new MTS Search Engine is applied here to the identification of volatile and semivolatile compounds including pesticides, nitrosoamines and other pollutants. Methane and isobutane chemical ionization (CI) GC-MS spectra were obtained from unit mass resolution mass spectrometers to determine MH(+) masses and isotope ratios. Isotopes were measured accurately with errors of <4% and <6%, respectively, for A + 1 and A + 2 peaks. Deconvolution of interfering isotope clusters (e.g., M(+) and [M - H](+)) was required for accurate determination of the A + 1 isotope in halogenated compounds. Integrating the isotope data greatly improved the speed and accuracy of the database identifications. The database accurately identified unknowns from isobutane CI spectra in 100% of cases where as many as 40 candidates satisfied the mass tolerance. The paper describes the development and basic operation of the new MTS Search Engine and details performance testing with over 50 model compounds.

  17. Development of a New Model for Accurate Prediction of Cloud Water Deposition on Vegetation

    NASA Astrophysics Data System (ADS)

    Katata, G.; Nagai, H.; Wrzesinsky, T.; Klemm, O.; Eugster, W.; Burkard, R.

    2006-12-01

    Scarcity of water resources in arid and semi-arid areas is of great concern in the light of population growth and food shortages. Several experiments focusing on cloud (fog) water deposition on the land surface suggest that cloud water plays an important role in water resource in such regions. A one-dimensional vegetation model including the process of cloud water deposition on vegetation has been developed to better predict cloud water deposition on the vegetation. New schemes to calculate capture efficiency of leaf, cloud droplet size distribution, and gravitational flux of cloud water were incorporated in the model. Model calculations were compared with the data acquired at the Norway spruce forest at the Waldstein site, Germany. High performance of the model was confirmed by comparisons of calculated net radiation, sensible and latent heat, and cloud water fluxes over the forest with measurements. The present model provided a better prediction of measured turbulent and gravitational fluxes of cloud water over the canopy than the Lovett model, which is a commonly used cloud water deposition model. Detailed calculations of evapotranspiration and of turbulent exchange of heat and water vapor within the canopy and the modifications are necessary for accurate prediction of cloud water deposition. Numerical experiments to examine the dependence of cloud water deposition on the vegetation species (coniferous and broad-leaved trees, flat and cylindrical grasses) and structures (Leaf Area Index (LAI) and canopy height) are performed using the presented model. The results indicate that the differences of leaf shape and size have a large impact on cloud water deposition. Cloud water deposition also varies with the growth of vegetation and seasonal change of LAI. We found that the coniferous trees whose height and LAI are 24 m and 2.0 m2m-2, respectively, produce the largest amount of cloud water deposition in all combinations of vegetation species and structures in the

  18. Chlorine isotope fractionation between chloride (Cl-) and dichlorine (Cl2)

    NASA Astrophysics Data System (ADS)

    Giunta, Thomas; Labidi, Jabrane; Eggenkamp, Hans G. M.

    2017-09-01

    The use of chlorine stable isotopes (35Cl and 37Cl) can help to constrain natural processes that involve chlorine species with different oxidation states. Theoretical studies based on thermodynamic and quantum mechanical approaches predict large isotope fractionation during redox reactions but to date, these reactions have not been studied experimentally. Here, we explore the chlorine isotope fractionation during the oxidation of hydrated Cl- (redox state of -I) to Cl2 (redox state of 0) at 25 °C and at 0 °C. Our apparatus consists of a sealed glass reactor where liquid HCl is mixed with liquid H2O2, a strong oxidant. Following complex reaction pathways, this mixture ultimately leads to the oxidation of Cl- and to the formation of Cl2 gas. As long as it is degassing, the Cl2 gas is flushed out of solution using N2 as a vector-gas from the glass-reactor to a potassium hydroxide (KOH) solution (pH 14) where it disproportionates into soluble species: Cl- and ClO-. After each experiment, the chlorine isotopic composition was measured in the recovered KOH-trap solution, as well as in the residual HCl solution. Consistent with theoretical predictions, the produced Cl2 gas is always enriched in the heavier 37Cl as compared to the initial Cl-reservoir. The following isotope fractionation factors are obtained: At 0 °C the isotopic fractionation 1000ln α(Cl2-Cl-) is 4.51 (+1.65/-0.49)‰ At 25 °C the isotopic fractionation 1000ln α(Cl2-Cl-) is 3.94 (+0.69/-0.18)‰. From the obtained data it is suggested that the production of Cl2 gas in our experiments is best described by a closed-system distillation. Our results are in agreement with published theoretical ab-initio calculations.

  19. Isotopic Incorporation Rates and Discrimination Factors in Mantis Shrimp Crustaceans

    PubMed Central

    deVries, Maya S.; del Rio, Carlos Martínez; Tunstall, Tate S.; Dawson, Todd E.

    2015-01-01

    Stable isotope analysis has provided insights into the trophic ecology of a wide diversity of animals. Knowledge about isotopic incorporation rates and isotopic discrimination between the consumer and its diet for different tissue types is essential for interpreting stable isotope data, but these parameters remain understudied in many animal taxa and particularly in aquatic invertebrates. We performed a 292-day diet shift experiment on 92 individuals of the predatory mantis shrimp, Neogonodactylus bredini, to quantify carbon and nitrogen incorporation rates and isotope discrimination factors in muscle and hemolymph tissues. Average isotopic discrimination factors between mantis shrimp muscle and the new diet were 3.0 ± 0.6 ‰ and 0.9 ± 0.3 ‰ for carbon and nitrogen, respectively, which is contrary to what is seen in many other animals (e.g. C and N discrimination is generally 0–1 ‰ and 3–4 ‰, respectively). Surprisingly, the average residence time of nitrogen in hemolymph (28.9 ± 8.3 days) was over 8 times longer than that of carbon (3.4 ± 1.4 days). In muscle, the average residence times of carbon and nitrogen were of the same magnitude (89.3 ± 44.4 and 72.8 ± 18.8 days, respectively). We compared the mantis shrimps’ incorporation rates, along with rates from four other invertebrate taxa from the literature, to those predicted by an allometric equation relating carbon incorporation rate to body mass that was developed for teleost fishes and sharks. The rate of carbon incorporation into muscle was consistent with rates predicted by this equation. Our findings provide new insight into isotopic discrimination factors and incorporation rates in invertebrates with the former showing a different trend than what is commonly observed in other animals. PMID:25835953

  20. Isotopic incorporation rates and discrimination factors in mantis shrimp crustaceans.

    PubMed

    deVries, Maya S; Del Rio, Carlos Martínez; Tunstall, Tate S; Dawson, Todd E

    2015-01-01

    Stable isotope analysis has provided insights into the trophic ecology of a wide diversity of animals. Knowledge about isotopic incorporation rates and isotopic discrimination between the consumer and its diet for different tissue types is essential for interpreting stable isotope data, but these parameters remain understudied in many animal taxa and particularly in aquatic invertebrates. We performed a 292-day diet shift experiment on 92 individuals of the predatory mantis shrimp, Neogonodactylus bredini, to quantify carbon and nitrogen incorporation rates and isotope discrimination factors in muscle and hemolymph tissues. Average isotopic discrimination factors between mantis shrimp muscle and the new diet were 3.0 ± 0.6 ‰ and 0.9 ± 0.3 ‰ for carbon and nitrogen, respectively, which is contrary to what is seen in many other animals (e.g. C and N discrimination is generally 0-1 ‰ and 3-4 ‰, respectively). Surprisingly, the average residence time of nitrogen in hemolymph (28.9 ± 8.3 days) was over 8 times longer than that of carbon (3.4 ± 1.4 days). In muscle, the average residence times of carbon and nitrogen were of the same magnitude (89.3 ± 44.4 and 72.8 ± 18.8 days, respectively). We compared the mantis shrimps' incorporation rates, along with rates from four other invertebrate taxa from the literature, to those predicted by an allometric equation relating carbon incorporation rate to body mass that was developed for teleost fishes and sharks. The rate of carbon incorporation into muscle was consistent with rates predicted by this equation. Our findings provide new insight into isotopic discrimination factors and incorporation rates in invertebrates with the former showing a different trend than what is commonly observed in other animals.

  1. Novel Apparatus for the Real-Time Quantification of Dissolved Gas Concentrations and Isotope Ratios

    NASA Astrophysics Data System (ADS)

    Gupta, M.; Leen, J.; Baer, D. S.; Owano, T. G.; Liem, J.

    2013-12-01

    Measurements of dissolved gases and their isotopic composition are critical in studying a variety of phenomena, including underwater greenhouse gas generation, air-surface exchange, and pollution migration. These studies typically involve obtaining water samples from streams, lakes, or ocean water and transporting them to a laboratory, where they are degased. The gases obtained are then generally measured using gas chromatography and isotope ratio mass spectrometry for concentrations and isotope ratios, respectively. This conventional, off-line methodology is time consuming, significantly limits the number of the samples that can be measured and thus severely inhibits detailed spatial and temporal mapping of gas concentrations and isotope ratios. In this work, we describe the development of a new membrane-based degassing device that interfaces directly to Los Gatos Research (cavity enhanced laser absorption or Off-Axis ICOS) gas analyzers (cavity enhanced laser absorption or Off-Axis ICOS analyzers) to create an autonomous system that can continuously and quickly measure concentrations and isotope ratios of dissolved gases in real time in the field. By accurately controlling the water flow rate through the membrane degasser, gas pressure on the outside of the membrane, and water pressure on the inside of the membrane, the system is able to generate precise and highly reproducible results. Moreover, by accurately measuring the gas flow rates in and out of the degasser, the gas-phase concentrations (ppm) could be converted into dissolved gas concentrations (nM). We will present detailed laboratory test data that quantifies the linearity, precision, and dynamic range of the system for the concentrations and isotope ratios of dissolved methane, carbon dioxide, and nitrous oxide. By interfacing the degassing device to a novel cavity-enhanced spectrometer (developed by LGR), preliminary data will also be presented for dissolved volatile organics (VOC) and other

  2. Accurate prediction of polarised high order electrostatic interactions for hydrogen bonded complexes using the machine learning method kriging.

    PubMed

    Hughes, Timothy J; Kandathil, Shaun M; Popelier, Paul L A

    2015-02-05

    As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G(**), B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol(-1), decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol(-1). Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase

    PubMed Central

    Harijan, Rajesh K.; Zoi, Ioanna; Antoniou, Dimitri; Schwartz, Steven D.; Schramm, Vern L.

    2017-01-01

    Heavy-enzyme isotope effects (15N-, 13C-, and 2H-labeled protein) explore mass-dependent vibrational modes linked to catalysis. Transition path-sampling (TPS) calculations have predicted femtosecond dynamic coupling at the catalytic site of human purine nucleoside phosphorylase (PNP). Coupling is observed in heavy PNPs, where slowed barrier crossing caused a normal heavy-enzyme isotope effect (kchem light/kchem heavy > 1.0). We used TPS to design mutant F159Y PNP, predicted to improve barrier crossing for heavy F159Y PNP, an attempt to generate a rare inverse heavy-enzyme isotope effect (kchem light/kchem heavy < 1.0). Steady-state kinetic comparison of light and heavy native PNPs to light and heavy F159Y PNPs revealed similar kinetic properties. Pre–steady-state chemistry was slowed 32-fold in F159Y PNP. Pre–steady-state chemistry compared heavy and light native and F159Y PNPs and found a normal heavy-enzyme isotope effect of 1.31 for native PNP and an inverse effect of 0.75 for F159Y PNP. Increased isotopic mass in F159Y PNP causes more efficient transition state formation. Independent validation of the inverse isotope effect for heavy F159Y PNP came from commitment to catalysis experiments. Most heavy enzymes demonstrate normal heavy-enzyme isotope effects, and F159Y PNP is a rare example of an inverse effect. Crystal structures and TPS dynamics of native and F159Y PNPs explore the catalytic-site geometry associated with these catalytic changes. Experimental validation of TPS predictions for barrier crossing establishes the connection of rapid protein dynamics and vibrational coupling to enzymatic transition state passage. PMID:28584087

  4. Silicon isotopes in angrites and volatile loss in planetesimals

    PubMed Central

    Moynier, Frédéric; Savage, Paul S.; Badro, James; Barrat, Jean-Alix

    2014-01-01

    Inner solar system bodies, including the Earth, Moon, and asteroids, are depleted in volatile elements relative to chondrites. Hypotheses for this volatile element depletion include incomplete condensation from the solar nebula and volatile loss during energetic impacts. These processes are expected to each produce characteristic stable isotope signatures. However, processes of planetary differentiation may also modify the isotopic composition of geochemical reservoirs. Angrites are rare meteorites that crystallized only a few million years after calcium–aluminum-rich inclusions and exhibit extreme depletions in volatile elements relative to chondrites, making them ideal samples with which to study volatile element depletion in the early solar system. Here we present high-precision Si isotope data that show angrites are enriched in the heavy isotopes of Si relative to chondritic meteorites by 50–100 ppm/amu. Silicon is sufficiently volatile such that it may be isotopically fractionated during incomplete condensation or evaporative mass loss, but theoretical calculations and experimental results also predict isotope fractionation under specific conditions of metal–silicate differentiation. We show that the Si isotope composition of angrites cannot be explained by any plausible core formation scenario, but rather reflects isotope fractionation during impact-induced evaporation. Our results indicate planetesimals initially formed from volatile-rich material and were subsequently depleted in volatile elements during accretion. PMID:25404309

  5. Isotope effects in the evaporation of water: a status report of the Craig-Gordon model.

    PubMed

    Horita, Juske; Rozanski, Kazimierz; Cohen, Shabtai

    2008-03-01

    The Craig-Gordon model (C-G model) [H. Craig, L.I. Gordon. Deuterium and oxygen 18 variations in the ocean and the marine atmosphere. In Stable Isotopes in Oceanographic Studies and Paleotemperatures, E. Tongiorgi (Ed.), pp. 9-130, Laboratorio di Geologia Nucleare, Pisa (1965).] has been synonymous with the isotope effects associated with the evaporation of water from surface waters, soils, and vegetations, which in turn constitutes a critical component of the global water cycle. On the occasion of the four decades of its successful applications to isotope geochemistry and hydrology, an attempt is made to: (a) examine its physical background within the framework of modern evaporation models, (b) evaluate our current knowledge of the environmental parameters of the C-G model, and (c) comment on a general strategy for the use of these parameters in field applications. Despite its simplistic representation of evaporation processes at the water-air interface, the C-G model appears to be adequate to provide the isotopic composition of the evaporation flux. This is largely due to its nature for representing isotopic compositions (a ratio of two fluxes of different isotopic water molecules) under the same environmental conditions. Among many environmental parameters that are included in the C-G model, accurate description and calculations are still problematic of the kinetic isotope effects that occur in a diffusion-dominated thin layer of air next to the water-air interface. In field applications, it is of importance to accurately evaluate several environmental parameters, particularly the relative humidity and isotopic compositions of the 'free-atmosphere', for a system under investigation over a given time-scale of interest (e.g., hourly to daily to seasonally). With a growing interest in the studies of water cycles of different spatial and temporal scales, including paleoclimate and water resource studies, the importance and utility of the C-G model is also likely to

  6. One possible source of mass-independent fractionation of sulfur isotopes in the Archean atmosphere of Earth

    NASA Astrophysics Data System (ADS)

    Babikov, Dmitri; Semenov, Alexander; Teplukhin, Alexander

    2017-05-01

    Energy transfer mechanism for recombination of two sulfur atoms into a diatomic molecule, S2, is studied theoretically and computationally to determine whether the rate coefficient of this process can be significantly affected by isotopic substitutions, and whether the resultant isotope effect is expected to be mass-dependent or mass-independent. This is one of sulfur polymerization processes thought to be important in the anoxic atmosphere of the Archean Earth and, potentially, relevant to mass-independent fractionation of sulfur isotopes. A simplified theoretical approach is employed, in which all properties of S2 molecule are characterized rather accurately, whereas the process of stabilization of metastable S2∗ by bath gas collisions is described approximately. Properties of individual scattering resonances in S2 are studied in detail, and it is found that most important contributions to the recombination process come from ro-vibrational states formed near the top of centrifugal barrier, and that the number of such states is about 50 (in 32S32S). Absolute value of recombination rate coefficient is computed to be 1.22 × 10-33 cm6/s (for 32S32S at room temperature and atmospheric pressure), close to experimental result. Two distinct isotope effects are identified. One is a classical mass-dependent effect due to translational partition function, which leads to a weak, smooth, and negative mass-dependence of rate coefficient (4% decrease when the mass is raised from 32S32S to 34S34S). Second effect, due to quantized resonances, is two orders of magnitude stronger, but is local. In practice, due to presence of multiple individual resonances, this phenomenon leads to irregular mass-independent variations of rate coefficients in the ranges ±5%. It is also demonstrated that in real molecules this irregular behavior is expected to be somewhat smoother, and the isotope effect is somewhat smaller, due to dependence of stabilization cross section on properties of

  7. Accurate Predictions of Mean Geomagnetic Dipole Excursion and Reversal Frequencies, Mean Paleomagnetic Field Intensity, and the Radius of Earth's Core Using McLeod's Rule

    NASA Technical Reports Server (NTRS)

    Voorhies, Coerte V.; Conrad, Joy

    1996-01-01

    The geomagnetic spatial power spectrum R(sub n)(r) is the mean square magnetic induction represented by degree n spherical harmonic coefficients of the internal scalar potential averaged over the geocentric sphere of radius r. McLeod's Rule for the magnetic field generated by Earth's core geodynamo says that the expected core surface power spectrum (R(sub nc)(c)) is inversely proportional to (2n + 1) for 1 less than n less than or equal to N(sub E). McLeod's Rule is verified by locating Earth's core with main field models of Magsat data; the estimated core radius of 3485 kn is close to the seismologic value for c of 3480 km. McLeod's Rule and similar forms are then calibrated with the model values of R(sub n) for 3 less than or = n less than or = 12. Extrapolation to the degree 1 dipole predicts the expectation value of Earth's dipole moment to be about 5.89 x 10(exp 22) Am(exp 2)rms (74.5% of the 1980 value) and the expected geomagnetic intensity to be about 35.6 (mu)T rms at Earth's surface. Archeo- and paleomagnetic field intensity data show these and related predictions to be reasonably accurate. The probability distribution chi(exp 2) with 2n+1 degrees of freedom is assigned to (2n + 1)R(sub nc)/(R(sub nc). Extending this to the dipole implies that an exceptionally weak absolute dipole moment (less than or = 20% of the 1980 value) will exist during 2.5% of geologic time. The mean duration for such major geomagnetic dipole power excursions, one quarter of which feature durable axial dipole reversal, is estimated from the modern dipole power time-scale and the statistical model of excursions. The resulting mean excursion duration of 2767 years forces us to predict an average of 9.04 excursions per million years, 2.26 axial dipole reversals per million years, and a mean reversal duration of 5533 years. Paleomagnetic data show these predictions to be quite accurate. McLeod's Rule led to accurate predictions of Earth's core radius, mean paleomagnetic field

  8. Predicting animal δ18O: Accounting for diet and physiological adaptation

    NASA Astrophysics Data System (ADS)

    Kohn, Matthew J.

    1996-12-01

    Theoretical predictions and measured isotope variations indicate that diet and physiological adaptation have a significant impact on animals δ18O and cannot be ignored. A generalized model is therefore developed for the prediction of animal body water and phosphate δ18O to incorporate these factors quantitatively. Application of the model reproduces most published compositions and compositional trends for mammals and birds. A moderate dependence of animal δ18O on humidity is predicted for drought-tolerant animals, and the correlation between humidity and North American deer bone composition as corrected for local meteoric water is predicted within the scatter of the data. In contrast to an observed strong correlation between kangaroo δ18O and humidity (Δδ18O/Δh ∼ 2.5± 0.4‰/10%r.h.), the predicted humidity dependence is only 1.3 - 1.7‰/10% r.h., and it is inferred that drinking water in hot dry areas of Australia is enriched in 18O over rainwater. Differences in physiology and water turnover readily explain the observed differences in δ18O for several herbivore genera in East Africa, excepting antelopes. Antelope models are more sensitive to biological fractionations, and adjustments to the flux of transcutaneous water vapor within experimentally measured ranges allows their δ18O values to be matched. Models of the seasonal changes of forage composition for two regions with dissimilar climates show that significant seasonal variations in animal isotope composition are expected, and that animals with different physiologies and diets track climate differently. Analysis of different genera with disparate sensitivities to surface water and humidity will allow the most accurate quantification of past climate changes.

  9. Accurate prediction of pregnancy viability by means of a simple scoring system.

    PubMed

    Bottomley, Cecilia; Van Belle, Vanya; Kirk, Emma; Van Huffel, Sabine; Timmerman, Dirk; Bourne, Tom

    2013-01-01

    What is the performance of a simple scoring system to predict whether women will have an ongoing viable intrauterine pregnancy beyond the first trimester? A simple scoring system using demographic and initial ultrasound variables accurately predicts pregnancy viability beyond the first trimester with an area under the curve (AUC) in a receiver operating characteristic curve of 0.924 [95% confidence interval (CI) 0.900-0.947] on an independent test set. Individual demographic and ultrasound factors, such as maternal age, vaginal bleeding and gestational sac size, are strong predictors of miscarriage. Previous mathematical models have combined individual risk factors with reasonable performance. A simple scoring system derived from a mathematical model that can be easily implemented in clinical practice has not previously been described for the prediction of ongoing viability. This was a prospective observational study in a single early pregnancy assessment centre during a 9-month period. A cohort of 1881 consecutive women undergoing transvaginal ultrasound scan at a gestational age <84 days were included. Women were excluded if the first trimester outcome was not known. Demographic features, symptoms and ultrasound variables were tested for their influence on ongoing viability. Logistic regression was used to determine the influence on first trimester viability from demographics and symptoms alone, ultrasound findings alone and then from all the variables combined. Each model was developed on a training data set, and a simple scoring system was derived from this. This scoring system was tested on an independent test data set. The final outcome based on a total of 1435 participants was an ongoing viable pregnancy in 885 (61.7%) and early pregnancy loss in 550 (38.3%) women. The scoring system using significant demographic variables alone (maternal age and amount of bleeding) to predict ongoing viability gave an AUC of 0.724 (95% CI = 0.692-0.756) in the training set

  10. Seeking excellence: An evaluation of 235 international laboratories conducting water isotope analyses by isotope-ratio and laser-absorption spectrometry.

    PubMed

    Wassenaar, L I; Terzer-Wassmuth, S; Douence, C; Araguas-Araguas, L; Aggarwal, P K; Coplen, T B

    2018-03-15

    Water stable isotope ratios (δ 2 H and δ 18 O values) are widely used tracers in environmental studies; hence, accurate and precise assays are required for providing sound scientific information. We tested the analytical performance of 235 international laboratories conducting water isotope analyses using dual-inlet and continuous-flow isotope ratio mass spectrometers and laser spectrometers through a water isotope inter-comparison test. Eight test water samples were distributed by the IAEA to international stable isotope laboratories. These consisted of a core set of five samples spanning the common δ-range of natural waters, and three optional samples (highly depleted, enriched, and saline). The fifth core sample contained unrevealed trace methanol to assess analyst vigilance to the impact of organic contamination on water isotopic measurements made by all instrument technologies. For the core and optional samples ~73 % of laboratories gave acceptable results within 0.2 ‰ and 1.5 ‰ of the reference values for δ 18 O and δ 2 H, respectively; ~27 % produced unacceptable results. Top performance for δ 18 O values was dominated by dual-inlet IRMS laboratories; top performance for δ 2 H values was led by laser spectrometer laboratories. Continuous-flow instruments yielded comparatively intermediate results. Trace methanol contamination of water resulted in extreme outlier δ-values for laser instruments, but also affected reactor-based continuous-flow IRMS systems; however, dual-inlet IRMS δ-values were unaffected. Analysis of the laboratory results and their metadata suggested inaccurate or imprecise performance stemmed mainly from skill- and knowledge-based errors including: calculation mistakes, inappropriate or compromised laboratory calibration standards, poorly performing instrumentation, lack of vigilance to contamination, or inattention to unreasonable isotopic outcomes. To counteract common errors, we recommend that laboratories include 1-2 'known

  11. Seeking excellence: An evaluation of 235 international laboratories conducting water isotope analyses by isotope-ratio and laser-absorption spectrometry

    USGS Publications Warehouse

    Wassenaar, L. I.; Terzer-Wassmuth, S.; Douence, C.; Araguas-Araguas, L.; Aggarwal, P. K.; Coplen, Tyler B.

    2018-01-01

    RationaleWater stable isotope ratios (δ2H and δ18O values) are widely used tracers in environmental studies; hence, accurate and precise assays are required for providing sound scientific information. We tested the analytical performance of 235 international laboratories conducting water isotope analyses using dual-inlet and continuous-flow isotope ratio mass spectrometers and laser spectrometers through a water isotope inter-comparison test.MethodsEight test water samples were distributed by the IAEA to international stable isotope laboratories. These consisted of a core set of five samples spanning the common δ-range of natural waters, and three optional samples (highly depleted, enriched, and saline). The fifth core sample contained unrevealed trace methanol to assess analyst vigilance to the impact of organic contamination on water isotopic measurements made by all instrument technologies.ResultsFor the core and optional samples ~73 % of laboratories gave acceptable results within 0.2 ‰ and 1.5 ‰ of the reference values for δ18O and δ2H, respectively; ~27 % produced unacceptable results. Top performance for δ18O values was dominated by dual-inlet IRMS laboratories; top performance for δ2H values was led by laser spectrometer laboratories. Continuous-flow instruments yielded comparatively intermediate results. Trace methanol contamination of water resulted in extreme outlier δ-values for laser instruments, but also affected reactor-based continuous-flow IRMS systems; however, dual-inlet IRMS δ-values were unaffected.ConclusionsAnalysis of the laboratory results and their metadata suggested inaccurate or imprecise performance stemmed mainly from skill- and knowledge-based errors including: calculation mistakes, inappropriate or compromised laboratory calibration standards, poorly performing instrumentation, lack of vigilance to contamination, or inattention to unreasonable isotopic outcomes. To counteract common errors, we recommend that

  12. Automated Sample Preparation for Radiogenic and Non-Traditional Metal Isotopes: Removing an Analytical Barrier for High Sample Throughput

    NASA Astrophysics Data System (ADS)

    Field, M. Paul; Romaniello, Stephen; Gordon, Gwyneth W.; Anbar, Ariel D.; Herrmann, Achim; Martinez-Boti, Miguel A.; Anagnostou, Eleni; Foster, Gavin L.

    2014-05-01

    MC-ICP-MS has dramatically improved the analytical throughput for high-precision radiogenic and non-traditional isotope ratio measurements, compared to TIMS. The generation of large data sets, however, remains hampered by tedious manual drip chromatography required for sample purification. A new, automated chromatography system reduces the laboratory bottle neck and expands the utility of high-precision isotope analyses in applications where large data sets are required: geochemistry, forensic anthropology, nuclear forensics, medical research and food authentication. We have developed protocols to automate ion exchange purification for several isotopic systems (B, Ca, Fe, Cu, Zn, Sr, Cd, Pb and U) using the new prepFAST-MC™ (ESI, Nebraska, Omaha). The system is not only inert (all-flouropolymer flow paths), but is also very flexible and can easily facilitate different resins, samples, and reagent types. When programmed, precise and accurate user defined volumes and flow rates are implemented to automatically load samples, wash the column, condition the column and elute fractions. Unattended, the automated, low-pressure ion exchange chromatography system can process up to 60 samples overnight. Excellent reproducibility, reliability, recovery, with low blank and carry over for samples in a variety of different matrices, have been demonstrated to give accurate and precise isotopic ratios within analytical error for several isotopic systems (B, Ca, Fe, Cu, Zn, Sr, Cd, Pb and U). This illustrates the potential of the new prepFAST-MC™ (ESI, Nebraska, Omaha) as a powerful tool in radiogenic and non-traditional isotope research.

  13. Cryogenic Calcite: A Morphologic and Isotopic Analog to the ALH84001 Carbonates

    NASA Technical Reports Server (NTRS)

    Niles, P. B.; Leshin, L. A.; Socki, R. A.; Guan, Y.; Ming, D. W.; Gibson, E. K.

    2004-01-01

    Martian meteorite ALH84001 carbonates preserve large and variable microscale isotopic compositions, which in some way reflect their formation environment. These measurements show large variations (>20%) in the carbon and oxygen isotopic compositions of the carbonates on a 10-20 micron scale that are correlated with chemical composition. However, the utilization of these data sets for interpreting the formation conditions of the carbonates is complex due to lack of suitable terrestrial analogs and the difficulty of modeling under non-equilibrium conditions. Thus, the mechanisms and processes are largely unknown that create and preserve large microscale isotopic variations in carbonate minerals. Experimental tests of the possible environments and mechanisms that lead to large microscale isotopic variations can help address these concerns. One possible mechanism for creating large carbon isotopic variations in carbonates involves the freezing of water. Carbonates precipitate during extensive CO2 degassing that occurs during the freezing process as the fluid s decreasing volume drives CO2 out. This rapid CO2 degassing results in a kinetic isotopic fractionation where the CO2 gas has a much lighter isotopic composition causing an enrichment of 13C in the remaining dissolved bicarbonate. This study seeks to determine the suitability of cryogenically formed carbonates as analogs to ALH84001 carbonates. Specifically, our objective is to determine how accurately models using equilibrium fractionation factors approximate the isotopic compositions of cryogenically precipitated carbonates. This includes determining the accuracy of applying equilibrium fractionation factors during a kinetic process, and determining how isotopic variations in the fluid are preserved in microscale variations in the precipitated carbonates.

  14. Robust and accurate decoding of motoneuron behavior and prediction of the resulting force output.

    PubMed

    Thompson, Christopher K; Negro, Francesco; Johnson, Michael D; Holmes, Matthew R; McPherson, Laura Miller; Powers, Randall K; Farina, Dario; Heckman, Charles J

    2018-05-03

    The spinal alpha motoneuron is the only cell in the human CNS whose discharge can be routinely recorded in humans. We have reengineered motor unit collection and decomposition approaches, originally developed in humans, to measure the neural drive to muscle and estimate muscle force generation in the decerebrate cat model. Experimental, computational, and predictive approaches are used to demonstrate the validity of this approach across a wide range of modes to activate the motor pool. The utility of this approach is shown through the ability to track individual motor units across trials, allowing for better predictions of muscle force than the electromyography signal, and providing insights in to the stereotypical discharge characteristics in response to synaptic activation of the motor pool. This approach now allows for a direct link between the intracellular data of single motoneurons, the discharge properties of motoneuron populations, and muscle force generation in the same preparation. The discharge of a spinal alpha motoneuron and the resulting contraction of its muscle fibers represents the functional quantum of the motor system. Recent advances in the recording and decomposition of the electromyographic signal allows for the identification of several tens of concurrently active motor units. These detailed population data provide the potential to achieve deep insights into the synaptic organization of motor commands. Yet most of our understanding of the synaptic input to motoneurons is derived from intracellular recordings in animal preparations. Thus, it is necessary to extend the new electrode and decomposition methods to recording of motor unit populations in these same preparations. To achieve this goal, we use high-density electrode arrays and decomposition techniques, analogous to those developed for humans, to record and decompose the activity of tens of concurrently active motor units in a hindlimb muscle in the decerebrate cat. Our results showed

  15. Accurate perception of negative emotions predicts functional capacity in schizophrenia.

    PubMed

    Abram, Samantha V; Karpouzian, Tatiana M; Reilly, James L; Derntl, Birgit; Habel, Ute; Smith, Matthew J

    2014-04-30

    Several studies suggest facial affect perception (FAP) deficits in schizophrenia are linked to poorer social functioning. However, whether reduced functioning is associated with inaccurate perception of specific emotional valence or a global FAP impairment remains unclear. The present study examined whether impairment in the perception of specific emotional valences (positive, negative) and neutrality were uniquely associated with social functioning, using a multimodal social functioning battery. A sample of 59 individuals with schizophrenia and 41 controls completed a computerized FAP task, and measures of functional capacity, social competence, and social attainment. Participants also underwent neuropsychological testing and symptom assessment. Regression analyses revealed that only accurately perceiving negative emotions explained significant variance (7.9%) in functional capacity after accounting for neurocognitive function and symptoms. Partial correlations indicated that accurately perceiving anger, in particular, was positively correlated with functional capacity. FAP for positive, negative, or neutral emotions were not related to social competence or social attainment. Our findings were consistent with prior literature suggesting negative emotions are related to functional capacity in schizophrenia. Furthermore, the observed relationship between perceiving anger and performance of everyday living skills is novel and warrants further exploration. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  16. Natural isotope correction of MS/MS measurements for metabolomics and (13)C fluxomics.

    PubMed

    Niedenführ, Sebastian; ten Pierick, Angela; van Dam, Patricia T N; Suarez-Mendez, Camilo A; Nöh, Katharina; Wahl, S Aljoscha

    2016-05-01

    Fluxomics and metabolomics are crucial tools for metabolic engineering and biomedical analysis to determine the in vivo cellular state. Especially, the application of (13)C isotopes allows comprehensive insights into the functional operation of cellular metabolism. Compared to single MS, tandem mass spectrometry (MS/MS) provides more detailed and accurate measurements of the metabolite enrichment patterns (tandem mass isotopomers), increasing the accuracy of metabolite concentration measurements and metabolic flux estimation. MS-type data from isotope labeling experiments is biased by naturally occurring stable isotopes (C, H, N, O, etc.). In particular, GC-MS(/MS) requires derivatization for the usually non-volatile intracellular metabolites introducing additional natural isotopes leading to measurements that do not directly represent the carbon labeling distribution. To make full use of LC- and GC-MS/MS mass isotopomer measurements, the influence of natural isotopes has to be eliminated (corrected). Our correction approach is analyzed for the two most common applications; (13)C fluxomics and isotope dilution mass spectrometry (IDMS) based metabolomics. Natural isotopes can have an impact on the calculated flux distribution which strongly depends on the substrate labeling and the actual flux distribution. Second, we show that in IDMS based metabolomics natural isotopes lead to underestimated concentrations that can and should be corrected with a nonlinear calibration. Our simulations indicate that the correction for natural abundance in isotope based fluxomics and quantitative metabolomics is essential for correct data interpretation. © 2015 Wiley Periodicals, Inc.

  17. The molecular mechanism of Mo isotope fractionation during adsorption to birnessite

    USGS Publications Warehouse

    Wasylenki, L.E.; Weeks, C.L.; Bargar, J.R.; Spiro, T.G.; Hein, J.R.; Anbar, A.D.

    2011-01-01

    Fractionation of Mo isotopes during adsorption to manganese oxides is a primary control on the global ocean Mo isotope budget. Previous attempts to explain what drives the surprisingly large isotope effect ??97/95Modissolved-??97/95Moadsorbed=1.8??? have not successfully resolved the fractionation mechanism. New evidence from extended X-ray absorption fine structure analysis and density functional theory suggests that Mo forms a polymolybdate complex on the surfaces of experimental and natural samples. Mo in this polynuclear structure is in distorted octahedral coordination, while Mo remaining in solution is predominantly in tetrahedral coordination as MoO42- Our results indicate that the difference in coordination environment between dissolved Mo and adsorbed Mo is the cause of isotope fractionation. The molecular mechanism of metal isotope fractionation in this system should enable us to explain and possibly predict metal isotope effects in other systems where transition metals adsorb to mineral surfaces. ?? 2011 Elsevier Ltd.

  18. Accurate prediction of collapse temperature using optical coherence tomography-based freeze-drying microscopy.

    PubMed

    Greco, Kristyn; Mujat, Mircea; Galbally-Kinney, Kristin L; Hammer, Daniel X; Ferguson, R Daniel; Iftimia, Nicusor; Mulhall, Phillip; Sharma, Puneet; Kessler, William J; Pikal, Michael J

    2013-06-01

    The objective of this study was to assess the feasibility of developing and applying a laboratory tool that can provide three-dimensional product structural information during freeze-drying and which can accurately characterize the collapse temperature (Tc ) of pharmaceutical formulations designed for freeze-drying. A single-vial freeze dryer coupled with optical coherence tomography freeze-drying microscopy (OCT-FDM) was developed to investigate the structure and Tc of formulations in pharmaceutically relevant products containers (i.e., freeze-drying in vials). OCT-FDM was used to measure the Tc and eutectic melt of three formulations in freeze-drying vials. The Tc as measured by OCT-FDM was found to be predictive of freeze-drying with a batch of vials in a conventional laboratory freeze dryer. The freeze-drying cycles developed using OCT-FDM data, as compared with traditional light transmission freeze-drying microscopy (LT-FDM), resulted in a significant reduction in primary drying time, which could result in a substantial reduction of manufacturing costs while maintaining product quality. OCT-FDM provides quantitative data to justify freeze-drying at temperatures higher than the Tc measured by LT-FDM and provides a reliable upper limit to setting a product temperature in primary drying. Copyright © 2013 Wiley Periodicals, Inc.

  19. Hindered rotor models with variable kinetic functions for accurate thermodynamic and kinetic predictions

    NASA Astrophysics Data System (ADS)

    Reinisch, Guillaume; Leyssale, Jean-Marc; Vignoles, Gérard L.

    2010-10-01

    We present an extension of some popular hindered rotor (HR) models, namely, the one-dimensional HR (1DHR) and the degenerated two-dimensional HR (d2DHR) models, allowing for a simple and accurate treatment of internal rotations. This extension, based on the use of a variable kinetic function in the Hamiltonian instead of a constant reduced moment of inertia, is extremely suitable in the case of rocking/wagging motions involved in dissociation or atom transfer reactions. The variable kinetic function is first introduced in the framework of a classical 1DHR model. Then, an effective temperature and potential dependent constant is proposed in the cases of quantum 1DHR and classical d2DHR models. These methods are finally applied to the atom transfer reaction SiCl3+BCl3→SiCl4+BCl2. We show, for this particular case, that a proper accounting of internal rotations greatly improves the accuracy of thermodynamic and kinetic predictions. Moreover, our results confirm (i) that using a suitably defined kinetic function appears to be very adapted to such problems; (ii) that the separability assumption of independent rotations seems justified; and (iii) that a quantum mechanical treatment is not a substantial improvement with respect to a classical one.

  20. Measurement of Enzyme Isotope Effects.

    PubMed

    Kholodar, Svetlana A; Ghosh, Ananda K; Kohen, Amnon

    2017-01-01

    Enzyme isotope effects, or the kinetic effects of "heavy" enzymes, refer to the effect of isotopically labeled protein residues on the enzyme's activity or physical properties. These effects are increasingly employed in the examination of the possible contributions of protein dynamics to enzyme catalysis. One hypothesis assumed that isotopic substitution of all 12 C, 14 N, and nonexchangeable 1 H by 13 C, 15 N, and 2 H, would slow down protein picosecond to femtosecond dynamics without any effect on the system's electrostatics following the Born-Oppenheimer approximation. It was suggested that reduced reaction rates reported for several "heavy" enzymes accords with that hypothesis. However, numerous deviations from the predictions of that hypothesis were also reported. Current studies also attempt to test the role of individual residues by site-specific labeling or by labeling a pattern of residues on activity. It appears that in several systems the protein's fast dynamics are indeed reduced in "heavy" enzymes in a way that reduces the probability of barrier crossing of its chemical step. Other observations, however, indicated that slower protein dynamics are electrostatically altered in isotopically labeled enzymes. Interestingly, these effects appear to be system dependent, thus it might be premature to suggest a general role of "heavy" enzymes' effect on catalysis. © 2017 Elsevier Inc. All rights reserved.

  1. Absolute Isotopic Abundance Ratios and the Accuracy of Δ47 Measurements

    NASA Astrophysics Data System (ADS)

    Daeron, M.; Blamart, D.; Peral, M.; Affek, H. P.

    2016-12-01

    Conversion from raw IRMS data to clumped isotope anomalies in CO2 (Δ47) relies on four external parameters: the (13C/12C) ratio of VPDB, the (17O/16O) and (18O/16O) ratios of VSMOW (or VPDB-CO2), and the slope of the triple oxygen isotope line (λ). Here we investigate the influence that these isotopic parameters exert on measured Δ47 values, using real-world data corresponding to 7 months of measurements; simulations based on randomly generated data; precise comparisons between water-equilibrated CO2 samples and between carbonate standards believed to share quasi-identical Δ47 values; reprocessing of two carbonate calibration data sets with different slopes of Δ47 versus T. Using different sets of isotopic parameters generally produces systematic offsets as large as 0.04 ‰ in final Δ47 values. What's more, even using a single set of isotopic parameters can produce intra- and inter-laboratory discrepancies in final Δ47 values, if some of these parameters are inaccurate. Depending on the isotopic compositions of the standards used for conversion to "absolute" values, these errors should correlate strongly with either δ13C or δ18O, or more weakly with both. Based on measurements of samples expected to display identical Δ47 values, such as 25°C water-equilibrated CO2 with different carbon and oxygen isotope compositions, or high-temperature standards ETH-1 and ETH-2, we conclude that the isotopic parameters used so far in most clumped isotope studies produces large, systematic errors controlled by the relative bulk isotopic compositions of samples and standards, which should be one of the key factors responsible for current inter-laboratory discrepancies. By contrast, the isotopic parameters of Brand et al. [2010] appear to yield accurate Δ47 values regardless of bulk isotopic composition. References:Brand, Assonov and Coplen [2010] http://dx.doi.org/10.1351/PAC-REP-09-01-05

  2. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina

    PubMed Central

    Maturana, Matias I.; Apollo, Nicholas V.; Hadjinicolaou, Alex E.; Garrett, David J.; Cloherty, Shaun L.; Kameneva, Tatiana; Grayden, David B.; Ibbotson, Michael R.; Meffin, Hamish

    2016-01-01

    Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system (e.g. cochlear, retinal, and cortical implants). Currently, most neural prostheses use serial stimulation (i.e. one electrode at a time) despite this severely limiting the repertoire of stimuli that can be applied. Methods to reliably predict the outcome of multi-electrode stimulation have not been available. Here, we demonstrate that a linear-nonlinear model accurately predicts neural responses to arbitrary patterns of stimulation using in vitro recordings from single retinal ganglion cells (RGCs) stimulated with a subretinal multi-electrode array. In the model, the stimulus is projected onto a low-dimensional subspace and then undergoes a nonlinear transformation to produce an estimate of spiking probability. The low-dimensional subspace is estimated using principal components analysis, which gives the neuron’s electrical receptive field (ERF), i.e. the electrodes to which the neuron is most sensitive. Our model suggests that stimulation proportional to the ERF yields a higher efficacy given a fixed amount of power when compared to equal amplitude stimulation on up to three electrodes. We find that the model captures the responses of all the cells recorded in the study, suggesting that it will generalize to most cell types in the retina. The model is computationally efficient to evaluate and, therefore, appropriate for future real-time applications including stimulation strategies that make use of recorded neural activity to improve the stimulation strategy. PMID:27035143

  3. Rare Isotopic Species of Sulfur Monoxide: The Rotational Spectrum in the THz Region

    NASA Astrophysics Data System (ADS)

    Lattanzi, Valerio; Cazzoli, Gabriele; Puzzarini, Cristina

    2015-11-01

    Many sulfur-bearing species have been detected in different astronomical environments and have allowed us to derive important information about the chemical and physical composition of interstellar regions. In particular, these species have also been shown to trace and probe hot-core environment time evolution. Among the most prominent sulfur-bearing molecules is SO, the sulfur monoxide radical, one of the more ubiquitous and abundant, which is also observed in its isotopic substituted species such as 34SO and S18O. Due to the importance of this simple diatomic system, and in order to face the challenge of modern radioastronomical facilities, an extension to the THz range of the rare isotopologues of sulfur monoxide has been performed. High-resolution rotational molecular spectroscopy has been employed to extend the available data set of four isotopic species, SO, 34SO, S17O, and S18O, up to the 1.5 THz region. The frequency coverage and spectral resolution of our measurements allowed a better constraint of the molecular constants of the four species considered, specifically focusing on the two oxygen-substituted isotopologues. Our measurements were also employed in an isotopically invariant fit including all of the available pure rotational and ro-vibrational transitions for all of the SO isotopologues, thus enabling accurate predictions of the rotational transitions at higher frequencies. We also provide comparisons with recent works performed on the same system, demonstrating the quality of our experiment and the improvement of the data sets for all of the species considered. Transition frequencies for this system can now be used with confidence by the astronomical community well into the THz spectral region.

  4. An interlaboratory study to test instrument performance of hydrogen dual-inlet isotope-ratio mass spectrometers

    USGS Publications Warehouse

    Brand, Willi A.; Coplen, T.B.

    2001-01-01

    An interlaboratory comparison of forty isotope-ratio mass spectrometers of different ages from several vendors has been performed to test 2H/1H performance with hydrogen gases of three different isotopic compositions. The isotope-ratio results (unsufficiently corrected for H3+ contribution to the m/z = 3 collector, uncorrected for valve leakage in the change-over valves, etc.) expressed relative to one of these three gases covered a wide range of values: -630??? to -790??? for the second gas and -368??? to -462??? for the third gas. After normalizing the isotopic abundances of these test gases (linearly adjusting the ?? values so that the gases with the lowest and highest 2H content were identical for all laboratories), the standard deviation of the 40 measurements of the intermediate gas was a remarkably low 0.85???. It is concluded that the use of scaling factors is mandatory for providing accurate internationally comparable isotope-abundance values. Linear scaling for the isotope-ratio scales of gaseous hydrogen mass spectrometers is completely adequate. ?? Springer-Verlag 2001.

  5. Integrating Stomach Content and Stable Isotope Analyses to Quantify the Diets of Pygoscelid Penguins

    PubMed Central

    Polito, Michael J.; Trivelpiece, Wayne Z.; Karnovsky, Nina J.; Ng, Elizabeth; Patterson, William P.; Emslie, Steven D.

    2011-01-01

    Stomach content analysis (SCA) and more recently stable isotope analysis (SIA) integrated with isotopic mixing models have become common methods for dietary studies and provide insight into the foraging ecology of seabirds. However, both methods have drawbacks and biases that may result in difficulties in quantifying inter-annual and species-specific differences in diets. We used these two methods to simultaneously quantify the chick-rearing diet of Chinstrap (Pygoscelis antarctica) and Gentoo (P. papua) penguins and highlight methods of integrating SCA data to increase accuracy of diet composition estimates using SIA. SCA biomass estimates were highly variable and underestimated the importance of soft-bodied prey such as fish. Two-source, isotopic mixing model predictions were less variable and identified inter-annual and species-specific differences in the relative amounts of fish and krill in penguin diets not readily apparent using SCA. In contrast, multi-source isotopic mixing models had difficulty estimating the dietary contribution of fish species occupying similar trophic levels without refinement using SCA-derived otolith data. Overall, our ability to track inter-annual and species-specific differences in penguin diets using SIA was enhanced by integrating SCA data to isotopic mixing modes in three ways: 1) selecting appropriate prey sources, 2) weighting combinations of isotopically similar prey in two-source mixing models and 3) refining predicted contributions of isotopically similar prey in multi-source models. PMID:22053199

  6. Revising Estimates of the Methane Production Pathway in Peatland Porewater Using Intramolecular Isotopic Analyses of Acetate

    NASA Astrophysics Data System (ADS)

    Thomas, B.; Arthur, M. A.; Freeman, K. H.

    2007-12-01

    Stable isotopic measurements of methane and carbon dioxide are routinely applied to environmental samples to assess the relative importance of methane production by either aceticlastic or hydrogenotrophic methanogenesis. Such estimates rely upon assumptions about isotopic fractionation during methane production and oxidation. Rigorous isotope-based pathway estimates require knowledge of the carbon isotopic composition of both carbon dioxide and acetate. In practice, technical barriers have limited measurements of the isotopic composition of whole acetate in natural samples. Yet, the estimate of whole acetate isotopic values, even when available, may not represent accurately the composition of the methyl carbon, which is, in fact, the precursor to methane. It is exceedingly rare to find carbon isotopic measurements of acetate-methyl in the literature, and, to our knowledge, the d13C of the acetate-methyl precursor to methane has never before been reported from peatland porewater samples. Extremely 13C-depleted methane, -70 permil VPDB, and 13C-enriched carbon dioxide from acidic northern peat bogs are typically interpreted as signatures of hydrogenotrophic methanogenesis. The hypothesized dominance of methane production from hydrogen in acidic bogs contrasts with the vast majority of freshwater wetlands in which aceticlastic methanogenesis dominates. Using a new technique for the online analysis of the intramolecular carbon isotopic composition of acetate in natural samples, we find the acetate-methyl in peat porewaters can be significantly depleted relative to bulk organic matter. In porewater profiles from both winter and summer, acetate is as much as 15 permil depleted relative to bulk carbon. We hypothesize that acetate- methyl isotopic depletion results from conditions that favor autotrophic acetogenesis and subsequent acetate consumption by aceticlastic methanogens. Porewater depth profiles during winter and summer illustrate depth- dependent increases in the

  7. Effect of baking and fermentation on the stable carbon and nitrogen isotope ratios of grain-based food.

    PubMed

    Bostic, Joshua N; Palafox, Sherilyn J; Rottmueller, Marina E; Jahren, A Hope

    2015-05-30

    Isotope ratio mass spectrometry (IRMS) is used extensively to reconstruct general attributes of prehistoric and modern diets in both humans and animals. In order to apply these methods to the accurate determination of specific intakes of foods/nutrients of interest, the isotopic signature of individually consumed foods must be constrained. For example, 86% of the calories consumed in the USA are derived from processed and prepared foods, but the relationship between the stable isotope composition of raw ingredients and the resulting products has not been characterized. To examine the effect of common cooking techniques on the stable isotope composition of grain-based food items, we prepared yeast buns and sugar cookies from standardized recipes and measured bulk δ(13) C and δ(15) N values of samples collected throughout a 75 min fermentation process (buns) and before and after baking at 190°C (buns and cookies). Simple isotope mixing models were used to determine if the isotopic signatures of 13 multi-ingredient foods could be estimated from the isotopic signatures of their constituent raw ingredients. No variations in δ(13) C or δ(15) N values were detected between pre- and post-baked yeast buns (pre: -24.78‰/2.61‰, post: -24.75‰/2.74‰), beet-sugar cookies (pre: -24.48‰/3.84‰, post: -24.47‰/3.57‰), and cane-sugar cookies (pre: -19.07‰/2.97‰, post: -19.02‰/3.21‰), or throughout a 75 min fermentation process in yeast buns. Using isotopic mass balance equations, the δ(13) C/δ(15) N values of multi-ingredient foods were estimated from the isotopic composition of constituent raw ingredients to within 0.14 ± 0.13‰/0.24 ± 0.17‰ for gravimetrically measured recipes and 0.40 ± 0.38‰/0.58 ± 0.53‰ for volumetrically measured recipes. Two common food preparation techniques, baking and fermentation, do not substantially affect the carbon or nitrogen isotopic signature of grain-based foods. Mass-balance equations can be used to

  8. Stable carbon and hydrogen isotope fractionation of dissolved organic groundwater pollutants by equilibrium sorption.

    PubMed

    Höhener, Patrick; Yu, Xianjing

    2012-03-15

    Linear free energy relationships (LFERs) were established which relate equilibrium vapor-liquid isotope effects to stable carbon and hydrogen isotope enrichment factors for equilibrium sorption to geosorbents. The LFERs were established for normal, cyclic or branched alkanes, monoaromatic hydrocarbons, and chloroethenes. These LFERs predict that isotopic light compounds sorb more strongly than their heavy counterparts. Defining fractionation as in classical literature by "heavy divided by light", carbon enrichment factors for equilibrium sorption were derived which ranged from -0.13±0.04‰ (benzene) to -0.52±0.19‰ (trichloroethene at 5-15 °C). Hydrogen enrichment factors for sorption of 14 different compounds were between -2.4 and -9.2‰. For perdeuterated hydrocarbons the predicted enrichment factors ranged from -19±5.4‰ (benzene) to -64±30‰ (cyclohexane). Equilibrium sorption experiments with a soil and activated carbon as sorbents were performed in the laboratory for perdeuterocyclohexane and perdeuterotoluene. The measured D/H enrichments agreed with the LFER prediction for both compounds and both sorbents within the uncertainty estimate of the prediction. The results of this work suggest that equilibrium sorption does create only very small isotope shifts for (13)C in groundwater pollutants in aquifers. It is also suggested that deuterium shifts are expected to be higher, especially for strongly sorbing pollutants. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Modeling stable isotope transport in metamorphic and hydrothermal systems

    NASA Astrophysics Data System (ADS)

    Baumgartner, L. P.; Mueller, T.; Skora, S.; Begue, F.

    2007-12-01

    Stable isotopes are powerful tools for deciphering the fluid flow histories of metamorphic terrains. The nature of fluid flow, fluid sources, and fluid fluxes can be delineated in well constrained studies. Continuum mechanics models for stable isotope fluid-rock exchange were developed and used over the last three decades in an attempt to accurately interpret the signatures left behind by fluid flow in the earths crust. The efforts have been hampered by the realization that the exchange of many stable isotopes, e.g. oxygen and carbon, by intracrystalline diffusion, hence without re-organization of the crystal lattice, appears to be too slow to achieve significant exchange. This should lead to relatively flat isotopic exchange profiles on hand-, outcrop, or aureole scale. Nevertheless, isotopic fronts are typically sharp (sub mm to cm scale), when measured in the field. This has lead to the suggestion that these sharp fronts correspond to the sides of infiltration fronts, implying the data to have been collected at a high angle to the infiltration direction. Nevertheless, the fact that the oxygen and carbon fronts are located at the same place is not explained by this. A review of published carbon and oxygen data reveals that many contact aureoles show linear trends in oxygen-carbon isotope ratio diagrams for carbonate sample suits. This implies that the fluid composition infiltrating the aureoles had essentially an X(CO2) of 0.5. This is in contrast to skarn mineralogy developed, which requires a water-rich fluid, in agreement with the general notion that igneous fluids are water-rich. These and other observations indicate that the mass transport equation used for stable isotope exchange needs to be improved to model appropriately the actual isotope kinetics during fluid-rock exchange. Detailed isotope studies on systems where net transport reactions are driven by mass transport have led us to identify different exchange mechanisms, including: a) the stable isotope

  10. Interstellar Isotopes: Prospects with ALMA

    NASA Technical Reports Server (NTRS)

    Charnley Steven B.

    2010-01-01

    Cold molecular clouds are natural environments for the enrichment of interstellar molecules in the heavy isotopes of H, C, N and O. Anomalously fractionated isotopic material is found in many primitive Solar System objects, such as meteorites and comets, that may trace interstellar matter that was incorporated into the Solar Nebula without undergoing significant processing. Models of the fractionation chemistry of H, C, N and O in dense molecular clouds, particularly in cores where substantial freeze-out of molecules on to dust has occurred, make several predictions that can be tested in the near future by molecular line observations. The range of fractionation ratios expected in different interstellar molecules will be discussed and the capabilities of ALMA for testing these models (e.g. in observing doubly-substituted isotopologues) will be outlined.

  11. Combining Mean and Standard Deviation of Hounsfield Unit Measurements from Preoperative CT Allows More Accurate Prediction of Urinary Stone Composition Than Mean Hounsfield Units Alone.

    PubMed

    Tailly, Thomas; Larish, Yaniv; Nadeau, Brandon; Violette, Philippe; Glickman, Leonard; Olvera-Posada, Daniel; Alenezi, Husain; Amann, Justin; Denstedt, John; Razvi, Hassan

    2016-04-01

    The mineral composition of a urinary stone may influence its surgical and medical treatment. Previous attempts at identifying stone composition based on mean Hounsfield Units (HUm) have had varied success. We aimed to evaluate the additional use of standard deviation of HU (HUsd) to more accurately predict stone composition. We identified patients from two centers who had undergone urinary stone treatment between 2006 and 2013 and had mineral stone analysis and a computed tomography (CT) available. HUm and HUsd of the stones were compared with ANOVA. Receiver operative characteristic analysis with area under the curve (AUC), Youden index, and likelihood ratio calculations were performed. Data were available for 466 patients. The major components were calcium oxalate monohydrate (COM), uric acid, hydroxyapatite, struvite, brushite, cystine, and CO dihydrate (COD) in 41.4%, 19.3%, 12.4%, 7.5%, 5.8%, 5.4%, and 4.7% of patients, respectively. The HUm of UA and Br was significantly lower and higher than the HUm of any other stone type, respectively. HUm and HUsd were most accurate in predicting uric acid with an AUC of 0.969 and 0.851, respectively. The combined use of HUm and HUsd resulted in increased positive predictive value and higher likelihood ratios for identifying a stone's mineral composition for all stone types but COM. To the best of our knowledge, this is the first report of CT data aiding in the prediction of brushite stone composition. Both HUm and HUsd can help predict stone composition and their combined use results in higher likelihood ratios influencing probability.

  12. Surface area dependence of calcium isotopic reequilibration in carbonates: Implications for isotopic signatures in the weathering zone

    NASA Astrophysics Data System (ADS)

    Fernandez, N. M.; Druhan, J. L.; Potrel, A.; Jacobson, A. D.

    2016-12-01

    The concept of dynamic equilibrium carries the implicit assumption of continued isotopic exchange between a mineral and the surrounding fluid. While this effect has received much attention in the marine paleoproxy literature, it has been relatively overlooked in application to the terrestrial environment. In weathering systems, a potential consequence is that rapid reequilibration may alter or erase isotopic signatures generated during secondary mineral formation. The extent and timescale over which isotopic signatures are reset in these hydrologic systems is unknown. Using reactive transport modeling, we show isotopic reequilibration under conditions reflecting terrestrial hydrologic settings to be significant and dependent on the reactive surface area of the solid. In particular, we suggest that the non-traditional stable isotopes commonly used in application to carbonates (e.g., Ca, Mg, Sr) are sensitive to these effects due to their rapid reaction rates. We aim to characterize the dependence of Ca isotopic reequilibration on surface area during calcite precipitation via batch experiments conducted at ambient temperature over 48-hour time periods. Calcite precipitation was performed in a closed batch reactor utilizing a controlled free-drift method. The batch reactors contained mixed supersaturated solutions of CaCl2 and NaHCO3 at an initial pH of 8.54. Precipitation was initiated by seed inoculation of calcite crystals with two distinct, pre-constrained surface areas. All experiments achieved the same final state of chemical equilibrium, but as expected, the fastest approach to equilibrium occurred for experiments employing calcite seeds with the highest surface area. This implies that differences in equilibrated Ca isotope ratios (δ44/40Ca) should reflect differences in surface area. This prediction is upheld by models of the experiments, indicating a measureable difference in δ44Ca during calcite precipitation where the higher surface area corresponds to

  13. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints

    PubMed Central

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-01-01

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS–inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car. PMID:26927108

  14. An Accurate GPS-IMU/DR Data Fusion Method for Driverless Car Based on a Set of Predictive Models and Grid Constraints.

    PubMed

    Wang, Shiyao; Deng, Zhidong; Yin, Gang

    2016-02-24

    A high-performance differential global positioning system (GPS)  receiver with real time kinematics provides absolute localization for driverless cars. However, it is not only susceptible to multipath effect but also unable to effectively fulfill precise error correction in a wide range of driving areas. This paper proposes an accurate GPS-inertial measurement unit (IMU)/dead reckoning (DR) data fusion method based on a set of predictive models and occupancy grid constraints. First, we employ a set of autoregressive and moving average (ARMA) equations that have different structural parameters to build maximum likelihood models of raw navigation. Second, both grid constraints and spatial consensus checks on all predictive results and current measurements are required to have removal of outliers. Navigation data that satisfy stationary stochastic process are further fused to achieve accurate localization results. Third, the standard deviation of multimodal data fusion can be pre-specified by grid size. Finally, we perform a lot of field tests on a diversity of real urban scenarios. The experimental results demonstrate that the method can significantly smooth small jumps in bias and considerably reduce accumulated position errors due to DR. With low computational complexity, the position accuracy of our method surpasses existing state-of-the-arts on the same dataset and the new data fusion method is practically applied in our driverless car.

  15. Water isotope systematics: Improving our palaeoclimate interpretations

    USGS Publications Warehouse

    Jones, M. D.; Dee, S.; Anderson, L.; Baker, A.; Bowen, G.; Noone, D.

    2016-01-01

    The stable isotopes of oxygen and hydrogen, measured in a variety of archives, are widely used proxies in Quaternary Science. Understanding the processes that control δ18O change have long been a focus of research (e.g. Shackleton and Opdyke, 1973; Talbot, 1990 ; Leng, 2006). Both the dynamics of water isotope cycling and the appropriate interpretation of geological water-isotope proxy time series remain subjects of active research and debate. It is clear that achieving a complete understanding of the isotope systematics for any given archive type, and ideally each individual archive, is vital if these palaeo-data are to be used to their full potential, including comparison with climate model experiments of the past. Combining information from modern monitoring and process studies, climate models, and proxy data is crucial for improving our statistical constraints on reconstructions of past climate variability.As climate models increasingly incorporate stable water isotope physics, this common language should aid quantitative comparisons between proxy data and climate model output. Water-isotope palaeoclimate data provide crucial metrics for validating GCMs, whereas GCMs provide a tool for exploring the climate variability dominating signals in the proxy data. Several of the studies in this set of papers highlight how collaborations between palaeoclimate experimentalists and modelers may serve to expand the usefulness of palaeoclimate data for climate prediction in future work.This collection of papers follows the session on Water Isotope Systematics held at the 2013 AGU Fall Meeting in San Francisco. Papers in that session, the breadth of which are represented here, discussed such issues as; understanding sub-GNIP scale (Global Network for Isotopes in Precipitation, (IAEA/WMO, 2006)) variability in isotopes in precipitation from different regions, detailed examination of the transfer of isotope signals from precipitation to geological archives, and the

  16. THE DEVELOPMENT OF A PREDICTIVE TOLL USING LARGEMOUTH BASS (MICROPTERUS SALMOIDES) SCALES TO ESTIMATE MERCURY (HG) CONCENTRATIONS AND STABLE-NITROGEN (15N/14N) ISOTOPE RATIOS IN FISH MUSCLE TISSUE

    EPA Science Inventory

    Knowledge of the trophic structure of biota in aquatic sites offers potential for the construction of models to allow the prediction of contaminant bioaccumulation. Measurements of trophic position have been conducted using stable-nitrogen isotope ratios ( 15N) measured in fish m...

  17. A New Method to Quantify the Isotopic Signature of Leaf Transpiration: Implications for Landscape-Scale Evapotranspiration Partitioning Studies

    NASA Astrophysics Data System (ADS)

    Wang, L.; Good, S. P.; Caylor, K. K.

    2010-12-01

    Characterizing the constituent components of evapotranspiration is crucial to better understand ecosystem-level water budgets and water use dynamics. Isotope based evapotranspiration partitioning methods are promising but their utility lies in the accurate estimation of the isotopic composition of underlying transpiration and evaporation. Here we report a new method to quantify the isotopic signature of leaf transpiration under field conditions. This method utilizes a commercially available laser-based isotope analyzer and a transparent leaf chamber, modified from Licor conifer leaf chamber. The method is based on the water mass balance in ambient air and leaf transpired air. We verified the method using “artificial leaves” and glassline extracted samples. The method provides a new and direct way to estimate leaf transpiration isotopic signatures and it has wide applications in ecology, hydrology and plant physiology.

  18. Determination of plutonium-239, thorium-232, and natural uranium isotopic concentrations in biological samples using photofission track analysis

    NASA Astrophysics Data System (ADS)

    Parry, James Roswell

    Fission track analysis (FTA) has many uses in the scientific community including but not limited to geological dating, neutron flux mapping, and dose reconstruction. The common method of fission for FTA is through neutrons from a nuclear reactor. This dissertation investigates the use of bremsstrahlung radiation produced from an electron linear accelerator to induce fission in FTA samples. This provides a means of simultaneously measuring the amount of Pu-239, U-nat, and Th-232 in a single sample. The benefit of measuring the three isotopes simultaneously is the possible elimination of costly and time consuming chemical processing for dose reconstruction samples. Samples containing the three isotopes were irradiated in two different bremsstrahlung spectra and a neutron spectrum to determine the amount of Pu-239, U-nat, and Th-232 in the samples. The reaction rate from the calibration samples and the counted fission tracks on the samples were used in determining the concentration of each isotope in the samples. The results were accurate to within a factor of two or three, showing that the method can work to predict the concentrations of multiple isotopes in a sample. The limitations of current accelerators and detectors limits the application of this specific procedure to higher concentrations of isotopes. The method detection limits for Pu-239, U-nat, and Th-232 are 20 pCi, 1 fCi, and 0.4 flCI respectively. Analysis of extremely low concentrations of isotopes would require the use of different detectors such as quartz due to the embrittlement encountered in the Lexan at high exposures. Cracking of the Texan detectors started to appear at a fluence of about 2 x 1018 electrons from the accelerator. This may be partly due to the beam stop not being an adequate thickness. The procedure is likely limited to specialty applications for the near term. However, with the world concerns of exposure to depleted uranium, this procedure may find applications in this area since

  19. Improved estimation of sediment source contributions by concentration-dependent Bayesian isotopic mixing model

    NASA Astrophysics Data System (ADS)

    Ram Upadhayay, Hari; Bodé, Samuel; Griepentrog, Marco; Bajracharya, Roshan Man; Blake, Will; Cornelis, Wim; Boeckx, Pascal

    2017-04-01

    The implementation of compound-specific stable isotope (CSSI) analyses of biotracers (e.g. fatty acids, FAs) as constraints on sediment-source contributions has become increasingly relevant to understand the origin of sediments in catchments. The CSSI fingerprinting of sediment utilizes CSSI signature of biotracer as input in an isotopic mixing model (IMM) to apportion source soil contributions. So far source studies relied on the linear mixing assumptions of CSSI signature of sources to the sediment without accounting for potential effects of source biotracer concentration. Here we evaluated the effect of FAs concentration in sources on the accuracy of source contribution estimations in artificial soil mixture of three well-separated land use sources. Soil samples from land use sources were mixed to create three groups of artificial mixture with known source contributions. Sources and artificial mixture were analysed for δ13C of FAs using gas chromatography-combustion-isotope ratio mass spectrometry. The source contributions to the mixture were estimated using with and without concentration-dependent MixSIAR, a Bayesian isotopic mixing model. The concentration-dependent MixSIAR provided the closest estimates to the known artificial mixture source contributions (mean absolute error, MAE = 10.9%, and standard error, SE = 1.4%). In contrast, the concentration-independent MixSIAR with post mixing correction of tracer proportions based on aggregated concentration of FAs of sources biased the source contributions (MAE = 22.0%, SE = 3.4%). This study highlights the importance of accounting the potential effect of a source FA concentration for isotopic mixing in sediments that adds realisms to mixing model and allows more accurate estimates of contributions of sources to the mixture. The potential influence of FA concentration on CSSI signature of sediments is an important underlying factor that determines whether the isotopic signature of a given source is observable

  20. A new method and application for determining the nitrogen isotopic composition of NOx

    NASA Astrophysics Data System (ADS)

    Hastings, M. G.; Miller, D. J.; Wojtal, P.; O'Connor, M.

    2015-12-01

    Atmospheric nitrogen oxides (NOx = NO + NO2) play key roles in atmospheric chemistry, air quality, and radiative forcing, and contribute to nitric acid deposition. Sources of NOx include both natural and anthropogenic emissions, which vary significantly in space and time. NOx isotopic signatures offer a potentially valuable tool to trace source impacts on atmospheric chemistry and regional acid deposition. Previous work on NOx isotopic signatures suggests large ranges in values, even from the same emission source, as well as overlapping ranges amongst different sources, making it difficult to use the isotopic composition as a quantitative tracer of source influences. These prior measurements have utilized a variety of methods for collecting the NOx as nitrate or nitrite for isotopic analysis, and testing of some of these methods (including active and passive collections) reveal inconsistencies in efficiency of collection, as well as issues related to changes in conditions such as humidity, temperature, and NOx fluxes. A recently developed method allows for accurately measuring the nitrogen isotopic composition of NOx (NOx = NO + NO2) after capturing the NOx in a potassium permanganate/sodium hydroxide solution as nitrate (Fibiger et al., Anal. Chem., 2014). The method has been thoroughly tested in the laboratory and field, and efficiently collects NO and NO2 under a variety of conditions. There are several advantages to collecting NOx actively, including the ability to collect over minutes to hourly time scales, and the ability to collect in environments with highly variable NOx sources and concentrations. Challenges include a nitrate background present in potassium permanganate (solid and liquid forms), accurately deriving ambient NOx concentrations based upon flow rate and solution concentrations above this variable background, and potential interferences from other nitrogen species. This method was designed to collect NOx in environments with very different

  1. Modified ion exchange separation for tungsten isotopic measurements from kimberlite samples using multi-collector inductively coupled plasma mass spectrometry.

    PubMed

    Sahoo, Yu Vin; Nakai, Shun'ichi; Ali, Arshad

    2006-03-01

    Tungsten isotope composition of a sample of deep-seated rock can record the influence of core-mantle interaction of the parent magma. Samples of kimberlite, which is known as a carrier of diamond, from the deep mantle might exhibit effects of core-mantle interaction. Although tungsten isotope anomaly was reported for kimberlites from South Africa, a subsequent investigation did not verify the anomaly. The magnesium-rich and calcium-rich chemical composition of kimberlite might engender difficulty during chemical separation of tungsten for isotope analyses. This paper presents a simple, one-step anion exchange technique for precise and accurate determination of tungsten isotopes in kimberlites using multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS). Large quantities of Ca and Mg in kimberlite samples were precipitated and removed with aqueous H(2)SO(4). Highly pure fractions of tungsten for isotopic measurements were obtained following an anion exchange chromatographic procedure involving mixed acids. That procedure enabled efficient removal of high field strength elements (HFSE), such as Hf, Zr and Ti, which are small ions that carry strong charges and develop intense electrostatic fields. The tungsten yields were 85%-95%. Advantages of this system include less time and less use of reagents. Precise and accurate isotopic measurements are possible using fractions of tungsten that are obtained using this method. The accuracy and precision of these measurements were confirmed using various silicate standard rock samples, JB-2, JB-3 and AGV-1.

  2. The Alaska Water Isotope Network (AKWIN): Precipitation, lake, river and stream dynamics

    NASA Astrophysics Data System (ADS)

    Rogers, M.; Welker, J. M.; Toohey, R.

    2011-12-01

    The hydrologic cycle is central to the structure and function of northern landscapes. The movement of water creates interactions between terrestrial, aquatic, marine and atmospheric processes. Understanding the processes and the spatial patterns that govern the isotopic (δ18O & δD) characteristics of the hydrologic cycle is especially important today as: a) modern climate/weather-isotope relations allow for more accurate interpretation of climate proxies and the calibration of atmospheric models, b) water isotopes facilitate understanding the role of storm tracks in regulating precipitation isotopic variability, c) water isotopes allow for estimates of glacial melt water inputs into aquatic systems, d) water isotopes allow for quantification of surface and groundwater interactions, e) water isotopes allow for quantification of permafrost meltwater use by plant communities, f) water isotopes aid in migratory bird forensics, g) water isotopes are critical to estimating field metabolic rates, h) water isotopes allow for crop and diet forensics and i) water isotopes can provide insight into evaporation and transpiration processes. As part of a new NSF MRI project at the Environment and Natural Resources Institute (ENRI) at the University of Alaska Anchorage and as an extension of the US Network for Isotopes in Precipitation (USNIP); we are forming AKWIN. The network will utilize long-term weekly sampling at Denali National Park and Caribou Poker Creek Watershed (USNIP sites-1989 to present), regular sampling across Alaska involving land management agencies (USGS, NPS, USFWS, EPA), educators, volunteers and citizen scientists, UA extended campuses, individual research projects, opportunistic sampling and published data to construct isoscapes and time series databases and information packages. We will be using a suite of spatial and temporal analysis methods to characterize water isotopes across Alaska and will provide web portals for data products. Our network is

  3. Isotopic Biogeochemistry

    NASA Technical Reports Server (NTRS)

    Hayes, J. M.

    1985-01-01

    An overview is provided of the biogeochemical research. The funding, productivity, personnel and facilities are reviewed. Some of the technical areas covered are: carbon isotopic records; isotopic studies of banded iron formations; isotope effects in microbial systems; studies of organic compounds in ancient sediments; and development in isotopic geochemistry and analysis.

  4. Carbon and nitrogen stable isotope turnover rates and diet-tissue discrimination in Florida manatees (Trichechus manatus latirostris).

    PubMed

    Alves-Stanley, Christy D; Worthy, Graham A J

    2009-08-01

    The Florida manatee (Trichechus manatus latirostris) is a herbivorous marine mammal that occupies freshwater, estuarine and marine habitats. Despite being considered endangered, relatively little is known about its feeding ecology. The present study expands on previous work on manatee feeding ecology by providing critical baseline parameters for accurate isotopic data interpretation. Stable carbon and nitrogen isotope ratios were examined over a period of more than 1 year in the epidermis of rescued Florida manatees that were transitioning from a diet of aquatic forage to terrestrial forage (lettuce). The mean half-life for (13)C turnover was 53 and 59 days for skin from manatees rescued from coastal and riverine regions, respectively. The mean half-life for (15)N turnover was 27 and 58 days, respectively. Because of these slow turnover rates, carbon and nitrogen stable isotope analysis in manatee epidermis is useful in summarizing average dietary intake over a long period of time rather than assessing recent diet. In addition to turnover rate, a diet-tissue discrimination value of 2.8 per thousand for (13)C was calculated for long-term captive manatees on a lettuce diet. Determining both turnover rate and diet-tissue discrimination is essential in order to accurately interpret stable isotope data.

  5. Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

    PubMed

    Andreatta, Massimo; Karosiene, Edita; Rasmussen, Michael; Stryhn, Anette; Buus, Søren; Nielsen, Morten

    2015-11-01

    A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented on the cell surface where it can be recognized by T helper lymphocytes. NetMHCIIpan is a state-of-the-art method for the quantitative prediction of peptide binding to any human or mouse MHC class II molecule of known sequence. In this paper, we describe an updated version of the method with improved peptide binding register identification. Binding register prediction is concerned with determining the minimal core region of nine residues directly in contact with the MHC binding cleft, a crucial piece of information both for the identification and design of CD4(+) T cell antigens. When applied to a set of 51 crystal structures of peptide-MHC complexes with known binding registers, the new method NetMHCIIpan-3.1 significantly outperformed the earlier 3.0 version. We illustrate the impact of accurate binding core identification for the interpretation of T cell cross-reactivity using tetramer double staining with a CMV epitope and its variants mapped to the epitope binding core. NetMHCIIpan is publicly available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.1 .

  6. Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium

    PubMed Central

    Ryan, Natalia; Chorley, Brian; Tice, Raymond R.; Judson, Richard; Corton, J. Christopher

    2016-01-01

    Microarray profiling of chemical-induced effects is being increasingly used in medium- and high-throughput formats. Computational methods are described here to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), often modulated by potential endocrine disrupting chemicals. ERα biomarker genes were identified by their consistent expression after exposure to 7 structurally diverse ERα agonists and 3 ERα antagonists in ERα-positive MCF-7 cells. Most of the biomarker genes were shown to be directly regulated by ERα as determined by ESR1 gene knockdown using siRNA as well as through chromatin immunoprecipitation coupled with DNA sequencing analysis of ERα-DNA interactions. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression datasets from experiments using MCF-7 cells, including those evaluating the transcriptional effects of hormones and chemicals. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% and 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) ER reference chemicals including “very weak” agonists. Importantly, the biomarker predictions accurately replicated predictions based on 18 in vitro high-throughput screening assays that queried different steps in ERα signaling. For 114 chemicals, the balanced accuracies were 95% and 98% for activation or suppression, respectively. These results demonstrate that the ERα gene expression biomarker can accurately identify ERα modulators in large collections of microarray data derived from MCF-7 cells. PMID:26865669

  7. Inverse methods for estimating primary input signals from time-averaged isotope profiles

    NASA Astrophysics Data System (ADS)

    Passey, Benjamin H.; Cerling, Thure E.; Schuster, Gerard T.; Robinson, Todd F.; Roeder, Beverly L.; Krueger, Stephen K.

    2005-08-01

    Mammalian teeth are invaluable archives of ancient seasonality because they record along their growth axes an isotopic record of temporal change in environment, plant diet, and animal behavior. A major problem with the intra-tooth method is that intra-tooth isotope profiles can be extremely time-averaged compared to the actual pattern of isotopic variation experienced by the animal during tooth formation. This time-averaging is a result of the temporal and spatial characteristics of amelogenesis (tooth enamel formation), and also results from laboratory sampling. This paper develops and evaluates an inverse method for reconstructing original input signals from time-averaged intra-tooth isotope profiles. The method requires that the temporal and spatial patterns of amelogenesis are known for the specific tooth and uses a minimum length solution of the linear system Am = d, where d is the measured isotopic profile, A is a matrix describing temporal and spatial averaging during amelogenesis and sampling, and m is the input vector that is sought. Accuracy is dependent on several factors, including the total measurement error and the isotopic structure of the measured profile. The method is shown to accurately reconstruct known input signals for synthetic tooth enamel profiles and the known input signal for a rabbit that underwent controlled dietary changes. Application to carbon isotope profiles of modern hippopotamus canines reveals detailed dietary histories that are not apparent from the measured data alone. Inverse methods show promise as an effective means of dealing with the time-averaging problem in studies of intra-tooth isotopic variation.

  8. Paleoclimate Reconstruction at Lamanai, Belize Using Oxygen-Isotope Tropical Dendrochronology

    NASA Astrophysics Data System (ADS)

    Prentice, A.; Webb, E. A.; White, C. D.; Graham, E.

    2009-05-01

    Tropical dendrochronology can be complicated because many trees growing in these areas lack distinct visible annual rings. However, the oxygen-isotope composition of wood growing in tropical regions can provide a record of seasonal fluctuations in the amount of precipitation even when visible rings are absent. Variations in the oxygen-isotope compositions of cellulose as the trees grow can be related to the relative timing of wet and dry seasons and used to identify periods of drought. In this study, the oxygen-isotope composition was determined for cellulose extracted from living trees at the site of Lamanai, Belize to assess the variation in oxygen-isotope values that result from heterogeneity within individual tree rings and seasonal fluctuations in amount of precipitation. In temperate regions, the latewood rings that form during periods of reduced growth are traditionally selected for oxygen-isotope analysis of cellulose because their oxygen-isotope compositions are more directly influenced by climate and precipitation during the growing season. However, in tropical isotope dendrochronology, when visible rings are present, detailed sampling of both the light coloured earlywood and the denser latewood is required. At Lamanai, a seasonal signal was evident in the oxygen- isotope composition of the cellulose when tree rings were sectioned in very small increments (approximately every mm), sub-sampling both earlywood and latewood. However, the visible rings did not always correspond with minimum or maximum oxygen-isotope values. As a result, the amplitude of the oxygen-isotope signal obtained by considering only latewood samples is smaller than that obtained from fine-increment sampling. Hence, the oxygen-isotope values of latewood samples alone did not provide accurate data for climate reconstruction. Multiple series of latewood samples extracted from different cross-sections of the same tree did not consistently show the same trends in oxygen isotope values

  9. Controls on the distribution and isotopic composition of helium in deep ground-water flows

    USGS Publications Warehouse

    Zhao, X.; Fritzel, T.L.B.; Quinodoz, H.A.M.; Bethke, C.M.; Torgersen, T.

    1998-01-01

    The distribution and isotopic composition of helium in sedimentary basins can be used to interpret the ages of very old ground waters. The piston-flow model commonly used in such interpretation, how ever, does not account for several important factors and as such works well only in very simple flow regimes. In this study of helium transport in a hypothetical sedimentary basin, we develop a numerical model that accounts for the magnitude and distribution of the basal helium flux, hydrodynamic dispersion, and complexities in flow regimes such as subregional flow cells. The modeling shows that these factors exert strong controls on the helium distribution and isotopic composition. The simulations may provide a basis for more accurate interpretations of observed helium concentrations and isotopic ratios in sedimentary basins.

  10. Advances in laser ablation MC-ICPMS isotopic analysis of rock materials

    NASA Astrophysics Data System (ADS)

    Young, E. D.

    2007-12-01

    Laser ablation multiple-collector inductively coupled plasma-source mass spectrometry (LA-MC-ICPMS) is a rapid method for obtaining high-precision isotope ratio measurements in geological samples. The method has been used with success for measuring isotope ratios of numerous elements, including Pb, Hf, Mg, Si, and Fe in terrestrial and extraterrestrial samples. It fills the gap between the highest precision obtainable with acid digestion together with MC-ICPMS and thermal ionization mass spectrometry (TIMS) and the maximum spatial resolution afforded by secondary ion mass spectrometry (SIMS). Matrix effects have been shown to be negligible for Pb isotopic analysis by LA-MC-ICPMS (Simon et al., 2007). Glass standards NBS 610, 612, and 614 have Pb/matrix ratios spanning two orders of magnitude. Our sample-standard bracketing laser ablation technique gives accurate and precise 208Pb/206Pb and 207Pb/206Pb for these glasses. The accuracy is superior to that obtained when using Tl to correct for mass fractionation. Accuracy and precision (± 0.2 ‰) for Pb in feldspars is comparable to that for double-spike TIMS. Data like these have been used to distinguish distinct sources of magmas in the Long Valley silicic magma system. LA-MC-ICPMS analyses of Mg isotope ratios in calcium-aluminum-rich inclusions (CAIs) from carbonaceous chondrite meteorites have revealed a wealth of new information about the history of these objects. A byproduct of this work has been recognition of the importance of different mass fractionation laws among three isotopes of a given element. Kinetic and equilibrium processes define distinct fractionation laws. Reservoir effects can further modify these laws. The result is that the linear coefficient β that relates the logarithms of the ratios n2/n1 and n3/n1 (ni refers to the number of atoms of isotope i) of isotopes with masses m3 > m2 > m1 is not unique. Rather, it is process dependent. In the case of Mg, this coefficient ranges from 0.521 for

  11. Calcium Isotope Systematics During Development of the Domestic Chicken (Gallus gallus)

    NASA Astrophysics Data System (ADS)

    Wheatley, P. V.

    2003-12-01

    Calcium isotope distributions have been recognized as showing systematic and predictable fractionation in nature. However, most of the observed calcium isotope fractionation to date is due to biological processes. The presence of abundant amounts of calcium in mineralized tissues makes the isotopic system of calcium particularly valuable in biological and paleobiological questions involving biomineralization. In order to apply calcium isotope systematics to paleobiological questions the changes in the calcium isotope signatures of mineralized tissue in modern animals should be studied. My study observed the domestic chicken (Gallus gallus) through embryologic ontogeny. This was accomplished by obtaining fertilized eggs staged in a growth series from day 12 to day 20. The eggs were dissected and shell, embryonic bone, albumen, and yolk were analyzed in order to characterize the calcium isotopic composition of the individual components over the course of the growth series. Several systematic changes in the isotopic signatures of various tissues were observed during the course of the development of the embryos. In general, mineralization in biological systems preferentially partitions the lighter isotopes of calcium into hard parts. As a result of this fractionation during mineralization, partitioning of light isotopes of calcium into the mineralized tissues may result in residual tissues being enriched in the heavier isotopes as ontogeny progresses. Better understanding of the behavior of calcium in modern biological systems will improve its application to fossils and expand the number of paleobiological and evolutionary questions that can be addressed using calcium isotopic data.

  12. Glycan reductive isotope labeling for quantitative glycomics.

    PubMed

    Xia, Baoyun; Feasley, Christa L; Sachdev, Goverdhan P; Smith, David F; Cummings, Richard D

    2009-04-15

    Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed glycan reductive isotope labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [(12)C(6)]aniline and [(13)C(6)]aniline. These dual-labeled aniline-tagged glycans can be recovered by reverse-phase chromatography and can be quantified based on ultraviolet (UV) absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins, using this method. This technique allows linear relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of glycomics.

  13. Determination of phenylalanine isotope ratio enrichment by liquid chromatography/time- of-flight mass spectrometry.

    PubMed

    Wu, Zhanpin; Zhang, Xiao-Jun; Cody, Robert B; Wolfe, Robert R

    2004-01-01

    The application of time-of-flight mass spectrometry to isotope ratio measurements has been limited by the relatively low dynamic range of the time-to-digital converter detectors available on commercial LC/ToF-MS systems. Here we report the measurement of phenylalanine isotope ratio enrichment by using a new LC/ToF-MS system with wide dynamic range. Underivatized phenylalanine was injected onto a C18 column directly with 0.1% formic acid/acetonitrile as the mobile phase. The optimal instrument parameters for the time-of-flight mass spectrometer were determined by tuning the instrument with a phenylalanine standard. The accuracy of the isotope enrichment measurement was determined by the injection of standard solutions with known isotope ratios ranging from 0.02% to 9.2%. A plot of the results against the theoretical values gave a linear curve with R2 of 0.9999. The coefficient of variation for the isotope ratio measurement was below 2%. The method is simple, rapid, and accurate and presents an attractive alternative to traditional GC/MS applications.

  14. A Sr and Mg isotopic study of soil and stream waters along an erosional gradient, Sierra Nevada, California

    NASA Astrophysics Data System (ADS)

    Rosen, V. B.; Maher, K.; Kouba, C. M.; Weinman, B. A.; Yoo, K.; Mudd, S. M.

    2012-12-01

    Since chemical weathering rates are proposed to regulate atmospheric CO2 concentrations and by extension global temperature over geologic timescales, understanding the relationship between chemical weathering rates and physical erosion is crucial to accurately interpreting Earth's climate history. The rate of supply of fresh minerals to the weathering zone is known to be an important control on chemical weathering rates. However, the consequences of physical erosion on the isotopic composition of weathering-derived solutes are more difficult to assess. This study capitalizes on a series of granitic hillslope transects with different erosion rates but similar climate, vegetation, and bedrock, in order to assess the consequences of erosion on the Sr and Mg isotopic composition of solutes. Reactive transport model simulations of varying complexity have been used to complement the field measurements and to analyze the sensitivity of fluid isotopic compositions to changes in key parameters such as erosion rate, flow rate, and biological cycling. The three hillslopes in the Feather River Basin, California reflect different degrees of channel erosion at their bases—BRC is a hillslope with active channel incision (60% average slope, below the knickpoint), FTA is a hillslope reflecting the transition between the relict and modern-day incising areas (50% average slope, at the knickpoint), and POMD is a 30% average hillslope in the relict landscape above the knickpoint. We measured the major element compositions, as well as the Sr and Mg isotopic compositions of soil water leaches (deionized water leaches), lysimeters, stream waters, and groundwaters by multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS). The 87Sr/86Sr values of soil and stream waters show minimal variation (0.7042 to 0.7046) as a function of soil depth, erosion rate, or sampling season despite abundant radiogenic biotite in the profiles. These results agree with the reactive transport

  15. Tellurium - Should it be isotopically anomalous in the Allende meteorite

    NASA Technical Reports Server (NTRS)

    Heymann, D.; Dziczkaniec, M.

    1981-01-01

    Isotopically anomalous Te is a by-product of the nuclear processes in zones of supernovae that have been proposed as sources for isotopically anomalous Xe. The calculated composition of the anomalous Te is roughly consistent with the disputed measurements made by Ballad et at. (1979) and Oliver et al. (1979) of samples of the Allende meteorite, with the exception that the large Te-123 overabundance reported by Oliver et al. (1979) is not predicted by the theory.

  16. Non-traditional stable isotope behaviors in immiscible silica-melts in a mafic magma chamber.

    PubMed

    Zhu, Dan; Bao, Huiming; Liu, Yun

    2015-12-01

    Non-traditional stable isotopes have increasingly been applied to studies of igneous processes including planetary differentiation. Equilibrium isotope fractionation of these elements in silicates is expected to be negligible at magmatic temperatures (δ(57)Fe difference often less than 0.2 per mil). However, an increasing number of data has revealed a puzzling observation, e.g., the δ(57)Fe for silicic magmas ranges from 0‰ up to 0.6‰, with the most positive δ(57)Fe almost exclusively found in A-type granitoids. Several interpretations have been proposed by different research groups, but these have so far failed to explain some aspects of the observations. Here we propose a dynamic, diffusion-induced isotope fractionation model that assumes Si-melts are growing and ascending immiscibly in a Fe-rich bulk magma chamber. Our model offers predictions on the behavior of non-traditional stable isotope such as Fe, Mg, Si, and Li that are consistent with observations from many A-type granitoids, especially those associated with layered intrusions. Diffusion-induced isotope fractionation may be more commonly preserved in magmatic rocks than was originally predicted.

  17. Non-traditional stable isotope behaviors in immiscible silica-melts in a mafic magma chamber

    PubMed Central

    Zhu, Dan; Bao, Huiming; Liu, Yun

    2015-01-01

    Non-traditional stable isotopes have increasingly been applied to studies of igneous processes including planetary differentiation. Equilibrium isotope fractionation of these elements in silicates is expected to be negligible at magmatic temperatures (δ57Fe difference often less than 0.2 per mil). However, an increasing number of data has revealed a puzzling observation, e.g., the δ57Fe for silicic magmas ranges from 0‰ up to 0.6‰, with the most positive δ57Fe almost exclusively found in A-type granitoids. Several interpretations have been proposed by different research groups, but these have so far failed to explain some aspects of the observations. Here we propose a dynamic, diffusion-induced isotope fractionation model that assumes Si-melts are growing and ascending immiscibly in a Fe-rich bulk magma chamber. Our model offers predictions on the behavior of non-traditional stable isotope such as Fe, Mg, Si, and Li that are consistent with observations from many A-type granitoids, especially those associated with layered intrusions. Diffusion-induced isotope fractionation may be more commonly preserved in magmatic rocks than was originally predicted. PMID:26620121

  18. Accurate thermoelastic tensor and acoustic velocities of NaCl

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

    Marcondes, Michel L., E-mail: michel@if.usp.br; Chemical Engineering and Material Science, University of Minnesota, Minneapolis, 55455; Shukla, Gaurav, E-mail: shukla@physics.umn.edu

    Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor bymore » using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.« less

  19. Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

    PubMed

    Reynolds, Sheila M; Bilmes, Jeff A; Noble, William Stafford

    2010-07-08

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence-301 base pairs, centered at the position to be scored-with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  20. Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens

    PubMed Central

    Reynolds, Sheila M.; Bilmes, Jeff A.; Noble, William Stafford

    2010-01-01

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence—301 base pairs, centered at the position to be scored—with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  1. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model

    PubMed Central

    DeLeon, Orlando; Hodis, Hagit; O’Malley, Yunxia; Johnson, Jacklyn; Salimi, Hamid; Zhai, Yinjie; Winter, Elizabeth; Remec, Claire; Eichelberger, Noah; Van Cleave, Brandon; Puliadi, Ramya; Harrington, Robert D.; Stapleton, Jack T.; Haim, Hillel

    2017-01-01

    The envelope glycoproteins (Envs) of HIV-1 continuously evolve in the host by random mutations and recombination events. The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines. We examined the historic changes in Env sequence and structural features (measured by integrity of epitopes on the Env trimer) in a geographically defined population in the United States. As expected, many Env features were relatively conserved during the 1980s. From this state, some features diversified whereas others remained conserved across the years. We sought to identify “clues” to predict the observed historic diversification patterns. Comparison of viruses that cocirculate in patients at any given time revealed that each feature of Env (sequence or structural) exists at a defined level of variance. The in-host variance of each feature is highly conserved among individuals but can vary between different HIV-1 clades. We designate this property “volatility” and apply it to model evolution of features as a linear diffusion process that progresses with increasing genetic distance. Volatilities of different features are highly correlated with their divergence in longitudinally monitored patients. Volatilities of features also correlate highly with their population-level diversification. Using volatility indices measured from a small number of patient samples, we accurately predict the population diversity that developed for each feature over the course of 30 years. Amino acid variants that evolved at key antigenic sites are also predicted well. Therefore, small “fluctuations” in feature values measured in isolated patient samples accurately describe their potential for population-level diversification. These tools will likely contribute to the design of population-targeted AIDS vaccines by effectively capturing the diversity of currently circulating strains and addressing properties

  2. Metal Stable Isotope Tagging: Renaissance of Radioimmunoassay for Multiplex and Absolute Quantification of Biomolecules.

    PubMed

    Liu, Rui; Zhang, Shixi; Wei, Chao; Xing, Zhi; Zhang, Sichun; Zhang, Xinrong

    2016-05-17

    The unambiguous quantification of biomolecules is of great significance in fundamental biological research as well as practical clinical diagnosis. Due to the lack of a detectable moiety, the direct and highly sensitive quantification of biomolecules is often a "mission impossible". Consequently, tagging strategies to introduce detectable moieties for labeling target biomolecules were invented, which had a long and significant impact on studies of biomolecules in the past decades. For instance, immunoassays have been developed with radioisotope tagging by Yalow and Berson in the late 1950s. The later languishment of this technology can be almost exclusively ascribed to the use of radioactive isotopes, which led to the development of nonradioactive tagging strategy-based assays such as enzyme-linked immunosorbent assay, fluorescent immunoassay, and chemiluminescent and electrochemiluminescent immunoassay. Despite great success, these strategies suffered from drawbacks such as limited spectral window capacity for multiplex detection and inability to provide absolute quantification of biomolecules. After recalling the sequences of tagging strategies, an apparent question is why not use stable isotopes from the start? A reasonable explanation is the lack of reliable means for accurate and precise quantification of stable isotopes at that time. The situation has changed greatly at present, since several atomic mass spectrometric measures for metal stable isotopes have been developed. Among the newly developed techniques, inductively coupled plasma mass spectrometry is an ideal technique to determine metal stable isotope-tagged biomolecules, for its high sensitivity, wide dynamic linear range, and more importantly multiplex and absolute quantification ability. Since the first published report by our group, metal stable isotope tagging has become a revolutionary technique and gained great success in biomolecule quantification. An exciting research highlight in this area

  3. Quantitative Determination of Isotope Ratios from Experimental Isotopic Distributions

    PubMed Central

    Kaur, Parminder; O’Connor, Peter B.

    2008-01-01

    Isotope variability due to natural processes provides important information for studying a variety of complex natural phenomena from the origins of a particular sample to the traces of biochemical reaction mechanisms. These measurements require high-precision determination of isotope ratios of a particular element involved. Isotope Ratio Mass Spectrometers (IRMS) are widely employed tools for such a high-precision analysis, which have some limitations. This work aims at overcoming the limitations inherent to IRMS by estimating the elemental isotopic abundance from the experimental isotopic distribution. In particular, a computational method has been derived which allows the calculation of 13C/12C ratios from the whole isotopic distributions, given certain caveats, and these calculations are applied to several cases to demonstrate their utility. The limitations of the method in terms of the required number of ions and S/N ratio are discussed. For high-precision estimates of the isotope ratios, this method requires very precise measurement of the experimental isotopic distribution abundances, free from any artifacts introduced by noise, sample heterogeneity, or other experimental sources. PMID:17263354

  4. Isotopic characteristics of canopies in simulated leaf assemblages

    NASA Astrophysics Data System (ADS)

    Graham, Heather V.; Patzkowsky, Mark E.; Wing, Scott L.; Parker, Geoffrey G.; Fogel, Marilyn L.; Freeman, Katherine H.

    2014-11-01

    site where leaves were sampled. The model predicts a persistent ∼1‰ difference in δ13Clitter for the two sites which is consistent with higher water availability in the tropical forests. This work provides a new framework for linking contemporary ecological observations to the geochemical record using flux-weighted isotope data and lends insights to the effect of forest architecture on organic and isotopic records of ancient terrestrial ecosystems. How many leaves from a litter assemblage are necessary to distinguish the isotopic gradient characteristics of canopy closure? Are mean δ13Cleaf values for a litter assemblage diagnostic of a forest biome? Can we predict the δ13C values of cumulative litter, soil organic matter, and organic carbon in sedimentary archives using litter flux and isotope patterns in canopies? We determined the δ13C range and mean for different sized assemblages of leaves sampled from data for each forest. We re-sampled very high numbers of leaves in order to estimate the isotopic composition of cumulative carbon delivered to soils as litter, and compared these results to available data from forest soils. Modeled leaf and soil organic carbon isotope patterns in this study offer insights to how forest structure can be derived from carbon isotope measurements of fossil leaves, as well as secondary material - such as teeth, hair, paleosol carbonates, or organic soil carbon (van der Merwe and Medina, 1989; Koch, 1998; Secord et al., 2008; Levin et al., 2011).Distinct climate and seasonal difference in the Panamá and Maryland, USA forests are reflected in their canopy isotope gradients. In the tropical forest of Panamá, leaves are produced throughout the year within a canopy that is both extensively and persistently closed (Leigh, 1975; Lowman and Wittman, 1996). In the temperate forest of Maryland leaves are produced during the spring when canopy conditions are relatively open (Korner and

  5. Impact of isotopic disorders on thermal transport properties of nanotubes and nanowires

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

    Sun, Tao; Kang, Wei; Wang, Jianxiang, E-mail: jxwang@pku.edu.cn

    2015-01-21

    We present a one-dimensional lattice model to describe thermal transport in isotopically doped nanotubes and nanowires. The thermal conductivities thus predicted, as a function of isotopic concentration, agree well with recent experiments and other simulations. Our results display that for any given concentration of isotopic atoms in a lattice without sharp atomic interfaces, the maximum thermal conductivity is attained when isotopic atoms are placed regularly with an equal space, whereas the minimum is achieved when they are randomly inserted with a uniform distribution. Non-uniformity of disorder can further tune the thermal conductivity between the two values. Moreover, the dependence ofmore » the thermal conductivity on the nanoscale feature size becomes weak at low temperature when disorder exists. In addition, when self-consistent thermal reservoirs are included to describe diffusive nanomaterials, the thermal conductivities predicted by our model are in line with the results of macroscopic theories with an interfacial effect. Our results suggest that the disorder provides an additional freedom to tune the thermal properties of nanomaterials in many technological applications including nanoelectronics, solid-state lighting, energy conservation, and conversion.« less

  6. Magnesium stable isotope ecology using mammal tooth enamel

    NASA Astrophysics Data System (ADS)

    Martin, Jeremy E.; Vance, Derek; Balter, Vincent

    2015-01-01

    Geochemical inferences on ancient diet using bone and enamel apatite rely mainly on carbon isotope ratios (δ13C) and to a lesser extent on strontium/calcium (Sr/Ca) and barium/calcium (Ba/Ca) elemental ratios. Recent developments in nontraditional stable isotopes provide an unprecedented opportunity to use additional paleodietary proxies to disentangle complex diets such as omnivory. Of particular relevance for paleodietary reconstruction are metals present in large quantity in bone and enamel apatite, providing that biologically mediated fractionation processes are constrained. Calcium isotope ratios (δ44Ca) meet these criteria but exhibit complex ecological patterning. Stable magnesium isotope ratios (δ26Mg) also meet these criteria but a comprehensive understanding of its variability awaits new isotopic data. Here, 11 extant mammal species of known ecology from a single locality in equatorial Africa were sampled for tooth enamel and, together with vegetation and feces, analyzed for δ26Mg, δ13C, Sr/Ca, and Ba/Ca ratios. The results demonstrate that δ26Mg incorporated in tooth enamel becomes heavier from strict herbivores to omnivores/faunivores. Using data from experimentally raised sheep, we suggest that this 26Mg enrichment up the trophic chain is due to a 26Mg enrichment in muscle relative to bone. Notably, it is possible to distinguish omnivores from herbivores, using δ26Mg coupled to Ba/Ca ratios. The potential effects of metabolic and dietary changes on the enamel δ26Mg composition remain to be explored but, in the future, multiproxy approaches would permit a substantial refinement of dietary behaviors or enable accurate trophic reconstruction despite specimen-limited sampling, as is often the case for fossil assemblages.

  7. Characterization of 3-Dimensional PET Systems for Accurate Quantification of Myocardial Blood Flow.

    PubMed

    Renaud, Jennifer M; Yip, Kathy; Guimond, Jean; Trottier, Mikaël; Pibarot, Philippe; Turcotte, Eric; Maguire, Conor; Lalonde, Lucille; Gulenchyn, Karen; Farncombe, Troy; Wisenberg, Gerald; Moody, Jonathan; Lee, Benjamin; Port, Steven C; Turkington, Timothy G; Beanlands, Rob S; deKemp, Robert A

    2017-01-01

    Three-dimensional (3D) mode imaging is the current standard for PET/CT systems. Dynamic imaging for quantification of myocardial blood flow with short-lived tracers, such as 82 Rb-chloride, requires accuracy to be maintained over a wide range of isotope activities and scanner counting rates. We proposed new performance standard measurements to characterize the dynamic range of PET systems for accurate quantitative imaging. 82 Rb or 13 N-ammonia (1,100-3,000 MBq) was injected into the heart wall insert of an anthropomorphic torso phantom. A decaying isotope scan was obtained over 5 half-lives on 9 different 3D PET/CT systems and 1 3D/2-dimensional PET-only system. Dynamic images (28 × 15 s) were reconstructed using iterative algorithms with all corrections enabled. Dynamic range was defined as the maximum activity in the myocardial wall with less than 10% bias, from which corresponding dead-time, counting rates, and/or injected activity limits were established for each scanner. Scatter correction residual bias was estimated as the maximum cavity blood-to-myocardium activity ratio. Image quality was assessed via the coefficient of variation measuring nonuniformity of the left ventricular myocardium activity distribution. Maximum recommended injected activity/body weight, peak dead-time correction factor, counting rates, and residual scatter bias for accurate cardiac myocardial blood flow imaging were 3-14 MBq/kg, 1.5-4.0, 22-64 Mcps singles and 4-14 Mcps prompt coincidence counting rates, and 2%-10% on the investigated scanners. Nonuniformity of the myocardial activity distribution varied from 3% to 16%. Accurate dynamic imaging is possible on the 10 3D PET systems if the maximum injected MBq/kg values are respected to limit peak dead-time losses during the bolus first-pass transit. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

  8. Prospects for improved understanding of isotopic reactor antineutrino fluxes

    NASA Astrophysics Data System (ADS)

    Gebre, Y.; Littlejohn, B. R.; Surukuchi, P. T.

    2018-01-01

    Predictions of antineutrino fluxes produced by fission isotopes in a nuclear reactor have recently received increased scrutiny due to observed differences in predicted and measured inverse beta decay (IBD) yields, referred to as the "reactor antineutrino flux anomaly." In this paper, global fits are applied to existing IBD yield measurements to produce constraints on antineutrino production by individual plutonium and uranium fission isotopes. We find that fits including measurements from highly U 235 -enriched cores and fits including Daya Bay's new fuel evolution result produce discrepant best-fit IBD yields for U 235 and Pu 239 . This discrepancy can be alleviated in a global analysis of all data sets through simultaneous fitting of Pu 239 , U 235 , and U 238 yields. The measured IBD yield of U 238 in this analysis is (7.02 ±1.65 )×10-43 cm2/fission , nearly two standard deviations below existing predictions. Future hypothetical IBD yield measurements by short-baseline reactor experiments are examined to determine their possible impact on the global understanding of isotopic IBD yields. It is found that future improved short-baseline IBD yield measurements at both high-enriched and low-enriched cores can significantly improve constraints for U 235 , U 238 , and Pu 239 , providing comparable or superior precision to existing conversion- and summation-based antineutrino flux predictions. Systematic and experimental requirements for these future measurements are also investigated.

  9. Isotope composition and volume of Earth’s early oceans

    PubMed Central

    Pope, Emily C.; Bird, Dennis K.; Rosing, Minik T.

    2012-01-01

    Oxygen and hydrogen isotope compositions of Earth’s seawater are controlled by volatile fluxes among mantle, lithospheric (oceanic and continental crust), and atmospheric reservoirs. Throughout geologic time the oxygen mass budget was likely conserved within these Earth system reservoirs, but hydrogen’s was not, as it can escape to space. Isotopic properties of serpentine from the approximately 3.8 Ga Isua Supracrustal Belt in West Greenland are used to characterize hydrogen and oxygen isotope compositions of ancient seawater. Archaean oceans were depleted in deuterium [expressed as δD relative to Vienna standard mean ocean water (VSMOW)] by at most 25 ± 5‰, but oxygen isotope ratios were comparable to modern oceans. Mass balance of the global hydrogen budget constrains the contribution of continental growth and planetary hydrogen loss to the secular evolution of hydrogen isotope ratios in Earth’s oceans. Our calculations predict that the oceans of early Earth were up to 26% more voluminous, and atmospheric CH4 and CO2 concentrations determined from limits on hydrogen escape to space are consistent with clement conditions on Archaean Earth. PMID:22392985

  10. Approaches for the accurate definition of geological time boundaries

    NASA Astrophysics Data System (ADS)

    Schaltegger, Urs; Baresel, Björn; Ovtcharova, Maria; Goudemand, Nicolas; Bucher, Hugo

    2015-04-01

    Which strategies lead to the most precise and accurate date of a given geological boundary? Geological units are usually defined by the occurrence of characteristic taxa and hence boundaries between these geological units correspond to dramatic faunal and/or floral turnovers and they are primarily defined using first or last occurrences of index species, or ideally by the separation interval between two consecutive, characteristic associations of fossil taxa. These boundaries need to be defined in a way that enables their worldwide recognition and correlation across different stratigraphic successions, using tools as different as bio-, magneto-, and chemo-stratigraphy, and astrochronology. Sedimentary sequences can be dated in numerical terms by applying high-precision chemical-abrasion, isotope-dilution, thermal-ionization mass spectrometry (CA-ID-TIMS) U-Pb age determination to zircon (ZrSiO4) in intercalated volcanic ashes. But, though volcanic activity is common in geological history, ashes are not necessarily close to the boundary we would like to date precisely and accurately. In addition, U-Pb zircon data sets may be very complex and difficult to interpret in terms of the age of ash deposition. To overcome these difficulties we use a multi-proxy approach we applied to the precise and accurate dating of the Permo-Triassic and Early-Middle Triassic boundaries in South China. a) Dense sampling of ashes across the critical time interval and a sufficiently large number of analysed zircons per ash sample can guarantee the recognition of all system complexities. Geochronological datasets from U-Pb dating of volcanic zircon may indeed combine effects of i) post-crystallization Pb loss from percolation of hydrothermal fluids (even using chemical abrasion), with ii) age dispersion from prolonged residence of earlier crystallized zircon in the magmatic system. As a result, U-Pb dates of individual zircons are both apparently younger and older than the depositional age

  11. Fast and Accurate Prediction of Numerical Relativity Waveforms from Binary Black Hole Coalescences Using Surrogate Models

    NASA Astrophysics Data System (ADS)

    Blackman, Jonathan; Field, Scott E.; Galley, Chad R.; Szilágyi, Béla; Scheel, Mark A.; Tiglio, Manuel; Hemberger, Daniel A.

    2015-09-01

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic -2Yℓm waveform modes resolved by the NR code up to ℓ=8 . We compare our surrogate model to effective one body waveforms from 50 M⊙ to 300 M⊙ for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases).

  12. Fast and Accurate Prediction of Numerical Relativity Waveforms from Binary Black Hole Coalescences Using Surrogate Models.

    PubMed

    Blackman, Jonathan; Field, Scott E; Galley, Chad R; Szilágyi, Béla; Scheel, Mark A; Tiglio, Manuel; Hemberger, Daniel A

    2015-09-18

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic _{-2}Y_{ℓm} waveform modes resolved by the NR code up to ℓ=8. We compare our surrogate model to effective one body waveforms from 50M_{⊙} to 300M_{⊙} for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases).

  13. A NEW CLINICAL PREDICTION CRITERION ACCURATELY DETERMINES A SUBSET OF PATIENTS WITH BILATERAL PRIMARY ALDOSTERONISM BEFORE ADRENAL VENOUS SAMPLING.

    PubMed

    Kocjan, Tomaz; Janez, Andrej; Stankovic, Milenko; Vidmar, Gaj; Jensterle, Mojca

    2016-05-01

    Adrenal venous sampling (AVS) is the only available method to distinguish bilateral from unilateral primary aldosteronism (PA). AVS has several drawbacks, so it is reasonable to avoid this procedure when the results would not affect clinical management. Our objective was to identify a clinical criterion that can reliably predict nonlateralized AVS as a surrogate for bilateral PA that is not treated surgically. A retrospective diagnostic cross-sectional study conducted at Slovenian national endocrine referral center included 69 consecutive patients (mean age 56 ± 8 years, 21 females) with PA who underwent AVS. PA was confirmed with the saline infusion test (SIT). AVS was performed sequentially during continuous adrenocorticotrophic hormone (ACTH) infusion. The main outcome measures were variables associated with nonlateralized AVS to derive a clinical prediction rule. Sixty-seven (97%) patients had a successful AVS and were included in the statistical analysis. A total of 39 (58%) patients had nonlateralized AVS. The combined criterion of serum potassium ≥3.5 mmol/L, post-SIT aldosterone <18 ng/dL, and either no or bilateral tumor found on computed tomography (CT) imaging had perfect estimated specificity (and thus 100% positive predictive value) for bilateral PA, saving an estimated 16% of the patients (11/67) from unnecessary AVS. The best overall classification accuracy (50/67 = 75%) was achieved using the post-SIT aldosterone level <18 ng/dL alone, which yielded 74% sensitivity and 75% specificity for predicting nonlateralized AVS. Our clinical prediction criterion appears to accurately determine a subset of patients with bilateral PA who could avoid unnecessary AVS and immediately commence with medical treatment.

  14. Mg isotope systematics during magmatic processes: Inter-mineral fractionation in mafic to ultramafic Hawaiian xenoliths

    NASA Astrophysics Data System (ADS)

    Stracke, A.; Tipper, E. T.; Klemme, S.; Bizimis, M.

    2018-04-01

    Observed differences in Mg isotope ratios between bulk magmatic rocks are small, often on a sub per mill level. Inter-mineral differences in the 26Mg/24Mg ratio (expressed as δ26Mg) in plutonic rocks are on a similar scale, and have mostly been attributed to equilibrium isotope fractionation at magmatic temperatures. Here we report Mg isotope data on minerals in spinel peridotite and garnet pyroxenite xenoliths from the rejuvenated stage of volcanism on Oahu and Kauai, Hawaii. The new data are compared to literature data and to theoretical predictions to investigate the processes responsible for inter-mineral Mg isotope fractionation at magmatic temperatures. Theory predicts up to per mill level differences in δ26Mg between olivine and spinel at magmatic temperatures and a general decrease in Δ26Mgolivine-spinel (=δ26Mgolivine - δ26Mgspinel) with increasing temperature, but also with increasing Cr# in spinel. For peridotites with a simple petrogenetic history by melt depletion, where increasing depletion relates to increasing melting temperatures, Δ26Mgolivine-spinel should thus systematically decrease with increasing Cr# in spinel. However, most natural peridotites, including the Hawaiian spinel peridotites investigated in this study, are overprinted by variable extents of melt-rock reaction, which disturb the systematic primary temperature and compositionally related olivine-spinel Mg isotope systematics. Diffusion, subsolidus re-equilibration, or surface alteration may further affect the observed olivine-spinel Mg isotope fractionation in peridotites, making Δ26Mgolivine-spinel in peridotites a difficult-to-apply geothermometer. The available Mg isotope data on clinopyroxene and garnet suggest that this mineral pair is a more promising geothermometer, but its application is restricted to garnet-bearing igneous (garnet pyroxenites) and metamorphic rocks (eclogites). Although the observed δ26Mg variation is on a sub per mill range in bulk magmatic rocks

  15. Oxygen isotopes as a tool to quantify reservoir-scale CO2 pore-space saturation

    NASA Astrophysics Data System (ADS)

    Serno, Sascha; Flude, Stephanie; Johnson, Gareth; Mayer, Bernard; Boyce, Adrian; Karolyte, Ruta; Haszeldine, Stuart; Gilfillan, Stuart

    2017-04-01

    Structural and residual trapping of carbon dioxide (CO2) are two key mechanisms of secure CO2 storage, an essential component of Carbon Capture and Storage technology [1]. Estimating the amount of CO2 that is trapped by these two mechanisms is a vital requirement for accurately assessing the secure CO2 storage capacity of a formation, but remains a key challenge. Recent field [2,3] and laboratory experiment studies [4] have shown that simple and relatively inexpensive measurements of oxygen isotope ratios in both the injected CO2 and produced water can provide an assessment of the amount of CO2 that is stored by these processes. These oxygen isotope assessments on samples obtained from observation wells provide results which are comparable to other geophysical techniques. In this presentation, based on the first comprehensive review of oxygen isotope ratios measured in reservoir waters and CO2 from global CO2 injection projects, we will outline the advantages and potential limitations of using oxygen isotopes to quantify CO2 pore-space saturation. We will further summarise the currently available information on the oxygen isotope composition of captured CO2. Finally, we identify the potential issues in the use of the oxygen isotope shifts in the reservoir water from baseline conditions to estimate accurate saturations of the pore space with CO2, and suggest how these issues can be reduced or avoided to provide reliable CO2 pore-space saturations on a reservoir scale in future field experiments. References [1] Scott et al., (2013) Nature Climate Change, Vol. 3, 105-111 doi:10.1038/nclimate1695 [2] Johnson et al., (2011) Chemical Geology, Vol. 283, 185-193 http://dx.doi.org/10.1016/j.ijggc.2016.06.019 [3] Serno et al., (2016) IJGGC, Vol. 52, 73-83 http://dx.doi.org/10.1016/j.ijggc.2016.06.019 [4] Johnson et al., (2011) Applied Geochemistry, Vol. 26 (7) 1184-1191 http://dx.doi.org/10.1016/j.apgeochem.2011.04.007

  16. Estimates of lake trout (Salvelinus namaycush) diet in Lake Ontario using two and three isotope mixing models

    USGS Publications Warehouse

    Colborne, Scott F.; Rush, Scott A.; Paterson, Gordon; Johnson, Timothy B.; Lantry, Brian F.; Fisk, Aaron T.

    2016-01-01

    Recent development of multi-dimensional stable isotope models for estimating both foraging patterns and niches have presented the analytical tools to further assess the food webs of freshwater populations. One approach to refine predictions from these analyses is to include a third isotope to the more common two-isotope carbon and nitrogen mixing models to increase the power to resolve different prey sources. We compared predictions made with two-isotope carbon and nitrogen mixing models and three-isotope models that also included sulphur (δ34S) for the diets of Lake Ontario lake trout (Salvelinus namaycush). We determined the isotopic compositions of lake trout and potential prey fishes sampled from Lake Ontario and then used quantitative estimates of resource use generated by two- and three-isotope Bayesian mixing models (SIAR) to infer feeding patterns of lake trout. Both two- and three-isotope models indicated that alewife (Alosa pseudoharengus) and round goby (Neogobius melanostomus) were the primary prey items, but the three-isotope models were more consistent with recent measures of prey fish abundances and lake trout diets. The lake trout sampled directly from the hatcheries had isotopic compositions derived from the hatchery food which were distinctively different from those derived from the natural prey sources. Those hatchery signals were retained for months after release, raising the possibility to distinguish hatchery-reared yearlings and similarly sized naturally reproduced lake trout based on isotopic compositions. Addition of a third-isotope resulted in mixing model results that confirmed round goby have become an important component of lake trout diet and may be overtaking alewife as a prey resource.

  17. Membrane inlet laser spectroscopy to measure H and O stable isotope compositions of soil and sediment pore water with high sample throughput

    DOE PAGES

    Oerter, Erik J.; Perelet, Alexei; Pardyjak, Eric; ...

    2016-10-20

    Here, the fast and accurate measurement of H and O stable isotope compositions (δ 2H and δ 18O values) of soil and sediment pore water remains an impediment to scaling-up the application of these isotopes in soil and vadose hydrology. Here we describe a method and its calibration to measuring soil and sediment pore water δ 2H and δ 18O values using a water vapor-permeable probe coupled to an isotope ratio infrared spectroscopy analyzer.

  18. Coupled thermochemical, isotopic evolution and heat transfer simulations in highly irradiated UO2 nuclear fuel

    NASA Astrophysics Data System (ADS)

    Piro, M. H. A.; Banfield, J.; Clarno, K. T.; Simunovic, S.; Besmann, T. M.; Lewis, B. J.; Thompson, W. T.

    2013-10-01

    Predictive capabilities for simulating irradiated nuclear fuel behavior are enhanced in the current work by coupling thermochemistry, isotopic evolution and heat transfer. Thermodynamic models that are incorporated into this framework not only predict the departure from stoichiometry of UO2, but also consider dissolved fission and activation products in the fluorite oxide phase, noble metal inclusions, secondary oxides including uranates, zirconates, molybdates and the gas phase. Thermochemical computations utilize the spatial and temporal evolution of the fission and activation product inventory in the pellet, which is typically neglected in nuclear fuel performance simulations. Isotopic computations encompass the depletion, decay and transmutation of more than 2000 isotopes that are calculated at every point in space and time. These computations take into consideration neutron flux depression and the increased production of fissile plutonium near the fuel pellet periphery (i.e., the so-called “rim effect”). Thermochemical and isotopic predictions are in very good agreement with reported experimental measurements of highly irradiated UO2 fuel with an average burnup of 102 GW d t(U)-1. Simulation results demonstrate that predictions are considerably enhanced when coupling thermochemical and isotopic computations in comparison to empirical correlations. Notice: This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

  19. Accurate prediction of complex free surface flow around a high speed craft using a single-phase level set method

    NASA Astrophysics Data System (ADS)

    Broglia, Riccardo; Durante, Danilo

    2017-11-01

    This paper focuses on the analysis of a challenging free surface flow problem involving a surface vessel moving at high speeds, or planing. The investigation is performed using a general purpose high Reynolds free surface solver developed at CNR-INSEAN. The methodology is based on a second order finite volume discretization of the unsteady Reynolds-averaged Navier-Stokes equations (Di Mascio et al. in A second order Godunov—type scheme for naval hydrodynamics, Kluwer Academic/Plenum Publishers, Dordrecht, pp 253-261, 2001; Proceedings of 16th international offshore and polar engineering conference, San Francisco, CA, USA, 2006; J Mar Sci Technol 14:19-29, 2009); air/water interface dynamics is accurately modeled by a non standard level set approach (Di Mascio et al. in Comput Fluids 36(5):868-886, 2007a), known as the single-phase level set method. In this algorithm the governing equations are solved only in the water phase, whereas the numerical domain in the air phase is used for a suitable extension of the fluid dynamic variables. The level set function is used to track the free surface evolution; dynamic boundary conditions are enforced directly on the interface. This approach allows to accurately predict the evolution of the free surface even in the presence of violent breaking waves phenomena, maintaining the interface sharp, without any need to smear out the fluid properties across the two phases. This paper is aimed at the prediction of the complex free-surface flow field generated by a deep-V planing boat at medium and high Froude numbers (from 0.6 up to 1.2). In the present work, the planing hull is treated as a two-degree-of-freedom rigid object. Flow field is characterized by the presence of thin water sheets, several energetic breaking waves and plungings. The computational results include convergence of the trim angle, sinkage and resistance under grid refinement; high-quality experimental data are used for the purposes of validation, allowing to

  20. Isotope ratio analysis of individual sub-micrometer plutonium particles with inductively coupled plasma mass spectrometry.

    PubMed

    Esaka, Fumitaka; Magara, Masaaki; Suzuki, Daisuke; Miyamoto, Yutaka; Lee, Chi-Gyu; Kimura, Takaumi

    2010-12-15

    Information on plutonium isotope ratios in individual particles is of great importance for nuclear safeguards, nuclear forensics and so on. Although secondary ion mass spectrometry (SIMS) is successfully utilized for the analysis of individual uranium particles, the isobaric interference of americium-241 to plutonium-241 makes difficult to obtain accurate isotope ratios in individual plutonium particles. In the present work, an analytical technique by a combination of chemical separation and inductively coupled plasma mass spectrometry (ICP-MS) is developed and applied to isotope ratio analysis of individual sub-micrometer plutonium particles. The ICP-MS results for individual plutonium particles prepared from a standard reference material (NBL SRM-947) indicate that the use of a desolvation system for sample introduction improves the precision of isotope ratios. In addition, the accuracy of the (241)Pu/(239)Pu isotope ratio is much improved, owing to the chemical separation of plutonium and americium. In conclusion, the performance of the proposed ICP-MS technique is sufficient for the analysis of individual plutonium particles. Copyright © 2010 Elsevier B.V. All rights reserved.

  1. Accurate prediction of protein-protein interactions by integrating potential evolutionary information embedded in PSSM profile and discriminative vector machine classifier.

    PubMed

    Li, Zheng-Wei; You, Zhu-Hong; Chen, Xing; Li, Li-Ping; Huang, De-Shuang; Yan, Gui-Ying; Nie, Ru; Huang, Yu-An

    2017-04-04

    Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era. In this article, we report a novel computational model combining our newly developed discriminative vector machine classifier (DVM) and an improved Weber local descriptor (IWLD) for the prediction of PPIs. Two components, differential excitation and orientation, are exploited to build evolutionary features for each protein sequence. The main characteristics of the proposed method lies in introducing an effective feature descriptor IWLD which can capture highly discriminative evolutionary information from position-specific scoring matrixes (PSSM) of protein data, and employing the powerful and robust DVM classifier. When applying the proposed method to Yeast and H. pylori data sets, we obtained excellent prediction accuracies as high as 96.52% and 91.80%, respectively, which are significantly better than the previous methods. Extensive experiments were then performed for predicting cross-species PPIs and the predictive results were also pretty promising. To further validate the performance of the proposed method, we compared it with the state-of-the-art support vector machine (SVM) classifier on Human data set. The experimental results obtained indicate that our method is highly effective for PPIs prediction and can be taken as a supplementary tool for future proteomics research.

  2. Calculation and mitigation of isotopic interferences in liquid chromatography-mass spectrometry/mass spectrometry assays and its application in supporting microdose absolute bioavailability studies.

    PubMed

    Gu, Huidong; Wang, Jian; Aubry, Anne-Françoise; Jiang, Hao; Zeng, Jianing; Easter, John; Wang, Jun-sheng; Dockens, Randy; Bifano, Marc; Burrell, Richard; Arnold, Mark E

    2012-06-05

    A methodology for the accurate calculation and mitigation of isotopic interferences in liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) assays and its application in supporting microdose absolute bioavailability studies are reported for the first time. For simplicity, this calculation methodology and the strategy to minimize the isotopic interference are demonstrated using a simple molecule entity, then applied to actual development drugs. The exact isotopic interferences calculated with this methodology were often much less than the traditionally used, overestimated isotopic interferences simply based on the molecular isotope abundance. One application of the methodology is the selection of a stable isotopically labeled internal standard (SIL-IS) for an LC-MS/MS bioanalytical assay. The second application is the selection of an SIL analogue for use in intravenous (i.v.) microdosing for the determination of absolute bioavailability. In the case of microdosing, the traditional approach of calculating isotopic interferences can result in selecting a labeling scheme that overlabels the i.v.-dosed drug or leads to incorrect conclusions on the feasibility of using an SIL drug and analysis by LC-MS/MS. The methodology presented here can guide the synthesis by accurately calculating the isotopic interferences when labeling at different positions, using different selective reaction monitoring (SRM) transitions or adding more labeling positions. This methodology has been successfully applied to the selection of the labeled i.v.-dosed drugs for use in two microdose absolute bioavailability studies, before initiating the chemical synthesis. With this methodology, significant time and cost saving can be achieved in supporting microdose absolute bioavailability studies with stable labeled drugs.

  3. Geologically Controlled Isotope-Time Patterns Reveal Early Differentiation and Crust Formation Processes

    NASA Astrophysics Data System (ADS)

    Bennett, V. C.; Nutman, A. P.

    2014-12-01

    The mechanisms of continental crust production and evolution in the early Earth remain controversial, as are questions of the relative roles of early differentiation versus subsequent tectonic procssing in creating Earth's chemical signatures. Here we present geologic observations integrated with whole rock major, trace element and Sm-Nd isotopic signatures and combined with U-Pb and Lu-Hf isotopic compositions of zircon populations from the same rocks, from the most extensive early rock record comprising the 3.9 Ga to 3.6 Ga terranes of southwest Greenland. These data reveal repeated patterns of formation of juvenile TTG crust and associated mafic and ultramafic rocks in convergent margin settings followed by formation of more evolved granites [1]. Our new zircon Lu-Hf data from rare 3.6-3.7 Ga tonalites within the Itsaq Gneiss Complex, obtained from single component, non-migmatitic gneisses with simple zircon populations, limited within sample Hf isotopic variability and accurate U-Pb ages, now document extraction of juvenile tonalites from a near chondritic mantle source between 3.9 Ga and 3.6 Ga. The more evolved, granitic rocks in each area show slightly negative initial ɛHf in accord with crustal reworking of the older (3.8-3.9 Ga) gniesses. There is no evidence for Hadean material in the sources of the granitoids. The Hf isotope-time patterns are consistent with juvenile crust production from a mantle source that experienced only modest amounts of prior crustal extraction. They are distinct from those predicted by reprocessing of an enriched Hadean mafic crust, as has been proposed for this region [2] and for the source of the Hadean Jack Hills zircons [3]. The well-documented, time decreasing, positive 142Nd anomalies [e.g., 4] from these rocks are further evidence of crustal derivation from a convecting mantle source, rather than reworking of an enriched mafic lithosphere. The 143Nd isotopic -time patterns are more complex, reflecting the interplay

  4. Steady state fractionation of heavy noble gas isotopes in a deep unsaturated zone

    USGS Publications Warehouse

    Seltzer, Alan M.; Severinghaus, Jeffrey P.; Andraski, Brian J.; Stonestrom, David A.

    2017-01-01

    To explore steady state fractionation processes in the unsaturated zone (UZ), we measured argon, krypton, and xenon isotope ratios throughout a ∼110 m deep UZ at the United States Geological Survey (USGS) Amargosa Desert Research Site (ADRS) in Nevada, USA. Prior work has suggested that gravitational settling should create a nearly linear increase in heavy-to-light isotope ratios toward the bottom of stagnant air columns in porous media. Our high-precision measurements revealed a binary mixture between (1) expected steady state isotopic compositions and (2) unfractionated atmospheric air. We hypothesize that the presence of an unsealed pipe connecting the surface to the water table allowed for direct inflow of surface air in response to extensive UZ gas sampling prior to our first (2015) measurements. Observed isotopic resettling in deep UZ samples collected a year later, after sealing the pipe, supports this interpretation. Data and modeling each suggest that the strong influence of gravitational settling and weaker influences of thermal diffusion and fluxes of CO2 and water vapor accurately describe steady state isotopic fractionation of argon, krypton, and xenon within the UZ. The data confirm that heavy noble gas isotopes are sensitive indicators of UZ depth. Based on this finding, we outline a potential inverse approach to quantify past water table depths from noble gas isotope measurements in paleogroundwater, after accounting for fractionation during dissolution of UZ air and bubbles.

  5. Quantifying dispersal rates and distances in North American martens: a test of enriched isotope labeling

    Treesearch

    Jonathan N. Pauli; Winston P. Smith; Merav Ben-David

    2012-01-01

    Advances in the application of stable isotopes have allowed the quantitative evaluation of previously cryptic ecological processes. In particular, researchers have utilized the predictable spatial patterning in natural abundance of isotopes to better understand animal dispersal and migration. However, quantifying dispersal via natural abundance alone has proven to be...

  6. UNiquant, a program for quantitative proteomics analysis using stable isotope labeling.

    PubMed

    Huang, Xin; Tolmachev, Aleksey V; Shen, Yulei; Liu, Miao; Huang, Lin; Zhang, Zhixin; Anderson, Gordon A; Smith, Richard D; Chan, Wing C; Hinrichs, Steven H; Fu, Kai; Ding, Shi-Jian

    2011-03-04

    Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for postmeasurement normalization of peptide ratios, which is required by the other programs.

  7. UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling

    PubMed Central

    Huang, Xin; Tolmachev, Aleksey V.; Shen, Yulei; Liu, Miao; Huang, Lin; Zhang, Zhixin; Anderson, Gordon A.; Smith, Richard D.; Chan, Wing C.; Hinrichs, Steven H.; Fu, Kai; Ding, Shi-Jian

    2011-01-01

    Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for post-measurement normalization of peptide ratios, which is required by the other programs. PMID:21158445

  8. Identification of sulfur sources and isotopic equilibria in submarine hot-springs using multiple sulfur isotopes

    NASA Astrophysics Data System (ADS)

    McDermott, Jill M.; Ono, Shuhei; Tivey, Margaret K.; Seewald, Jeffrey S.; Shanks, Wayne C.; Solow, Andrew R.

    2015-07-01

    disproportionation is an additional process that contributes sulfur to a different back-arc system and to acid spring-type hydrothermal fluid circulation. At the sedimented Guaymus Basin, near-zero Δ33S values are also observed, despite negative δ34S values that indicate inputs of biogenic pyrite for some samples. In contrast with previous studies reporting isotope disequilibrium between H2S and chalcopyrite, the δ34S values of chalcopyrite sampled from the inner 1-2 mm of a chimney wall are within ±1‰ of δ34S values for H2S in the paired vent fluid, suggesting equilibrium fluid-mineral sulfur isotope exchange at 300-400 °C. Isotopic equilibrium between hydrothermal fluid H2S and precipitating chalcopyrite implies that sulfur isotopes in the chalcopyrite lining across a chimney wall may accurately record past hydrothermal activity.

  9. Passive sampling for the isotopic fingerprinting of atmospheric mercury

    NASA Astrophysics Data System (ADS)

    Bergquist, B. A.; MacLagan, D.; Spoznar, N.; Kaplan, R.; Chandan, P.; Stupple, G.; Zimmerman, L.; Wania, F.; Mitchell, C. P. J.; Steffen, A.; Monaci, F.; Derry, L. A.

    2017-12-01

    Recent studies show that there are variations in the mercury (Hg) isotopic signature of atmospheric Hg, which demonstrates the potential for source tracing and improved understanding of atmospheric cycling of Hg. However, current methods for both measuring atmospheric Hg and collecting enough atmospheric Hg for isotopic analyses require expensive instruments that need power and expertise. Additionally, methods for collecting enough atmospheric Hg for isotopic analysis require pumping air through traps for long periods (weeks and longer). Combining a new passive atmospheric sampler for mercury (Hg) with novel Hg isotopic analyses will allow for the application of stable Hg isotopes to atmospheric studies of Hg. Our group has been testing a new passive sampler for gaseous Hg that relies on the diffusion of Hg through a diffusive barrier and adsorption onto a sulphur-impregnated activated carbon sorbent. The benefit of this passive sampler is that it is low cost, requires no power, and collects gaseous Hg for up to one year with linear, well-defined uptake, which allows for reproducible and accurate measurements of atmospheric gaseous Hg concentrations ( 8% uncertainty). As little as one month of sampling is often adequate to collect sufficient Hg for isotopic analysis at typical background concentrations. Experiments comparing the isotopic Hg signature in activated carbon samples using different approaches (i.e. by passive diffusion, by passive diffusion through diffusive barriers of different thickness, by active pumping) and at different temperatures confirm that the sampling process itself does not impose mass-independent fractionation (MIF). However, sampling does result in a consistent and thus correctable mass-dependent fractionation (MDF) effect. Therefore, the sampler preserves Hg MIF with very high accuracy and precision, which is necessary for atmospheric source tracing, and reasonable MDF can be estimated with some increase in error. In addition to

  10. The influence of room temperature on Mg isotope measurements by MC-ICP-MS.

    PubMed

    Zhang, Xing-Chao; Zhang, An-Yu; Zhang, Zhao-Feng; Huang, Fang; Yu, Hui-Min

    2018-03-24

    We observed that the accuracy and precision of magnesium (Mg) isotope analyses could be affected if the room temperature oscillated during measurements. To achieve high quality Mg isotopic data, it is critical to evaluate how the unstable room temperature affects Mg isotope measurements by multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS). We measured the Mg isotopes for the reference material DSM-3 using MC-ICP-MS under oscillating room temperatures in spring. For a comparison, we also measured the Mg isotopes under stable room temperatures, which was achieved by the installation of an improved temperature control system in the laboratory. The δ 26 Mg values measured under oscillating room temperatures have a larger deviation (δ 26 Mg from -0.09 to 0.08‰, with average δ 26 Mg = 0.00 ± 0.08 ‰) than those measured under a stable room temperature (δ 26 Mg from -0.03 to 0.03‰, with average δ 26 Mg = 0.00 ± 0.02 ‰) using the same MC-ICP-MS system. The room temperature variation can influence the stability of MC-ICP-MS. Therefore, it is critical to keep the room temperature stable to acquire high precise and accurate isotopic data when using MC-ICP-MS, especially when using the sample-standard bracketing (SSB) correction method. This article is protected by copyright. All rights reserved.

  11. Study of the structure of yrast bands of neutron-rich 114-124Pd isotopes

    NASA Astrophysics Data System (ADS)

    Chaudhary, Ritu; Devi, Rani; Khosa, S. K.

    2018-02-01

    The projected shell model calculations have been carried out in the neutron-rich 114-124Pd isotopic mass chain. The results have been obtained for the deformation systematics of E(2+1) and E(4+1)/E({2}+1) values, BCS subshell occupation numbers, yrast spectra, backbending phenomena, B( E2) transition probabilities and g-factors in these nuclei. The observed systematics of E(2+1) values and R_{42} ratios in the 114-124Pd isotopic mass chain indicate that there is a decrease of collectivity as the neutron number increases from 68 to 78. The occurrence of backbending in these nuclei as well as the changes in the calculated B( E2) transition probabilities and g -factors predict that there are changes in the structure of yrast bands in these nuclei. These changes occur at the spin where there is crossing of g-band by 2-qp bands. The predicted backbendings and predicted values of B( E2)s and g-factors in some of the isotopes need to be confirmed experimentally.

  12. Isotope effects on L-H threshold and confinement in tokamak plasmas

    NASA Astrophysics Data System (ADS)

    Maggi, C. F.; Weisen, H.; Hillesheim, J. C.; Chankin, A.; Delabie, E.; Horvath, L.; Auriemma, F.; Carvalho, I. S.; Corrigan, G.; Flanagan, J.; Garzotti, L.; Keeling, D.; King, D.; Lerche, E.; Lorenzini, R.; Maslov, M.; Menmuir, S.; Saarelma, S.; Sips, A. C. C.; Solano, E. R.; Belonohy, E.; Casson, F. J.; Challis, C.; Giroud, C.; Parail, V.; Silva, C.; Valisa, M.; Contributors, JET

    2018-01-01

    The dependence of plasma transport and confinement on the main hydrogenic ion isotope mass is of fundamental importance for understanding turbulent transport and, therefore, for accurate extrapolations of confinement from present tokamak experiments, which typically use a single hydrogen isotope, to burning plasmas such as ITER, which will operate in deuterium-tritium mixtures. Knowledge of the dependence of plasma properties and edge transport barrier formation on main ion species is critical in view of the initial, low-activation phase of ITER operations in hydrogen or helium and of its implications on the subsequent operation in deuterium-tritium. The favourable scaling of global energy confinement time with isotope mass, which has been observed in many tokamak experiments, remains largely unexplained theoretically. Moreover, the mass scaling observed in experiments varies depending on the plasma edge conditions. In preparation for upcoming deuterium-tritium experiments in the JET tokamak with the ITER-like Be/W Wall (JET-ILW), a thorough experimental investigation of isotope effects in hydrogen, deuterium and tritium plasmas is being carried out, in order to provide stringent tests of plasma energy, particle and momentum transport models. Recent hydrogen and deuterium isotope experiments in JET-ILW on L-H power threshold, L-mode and H-mode confinement are reviewed and discussed in the context of past and more recent isotope experiments in tokamak plasmas, highlighting common elements as well as contrasting observations that have been reported. The experimental findings are discussed in the context of fundamental aspects of plasma transport models.

  13. Methane clumped isotopes: Progress and potential for a new isotopic tracer

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

    Douglas, Peter M. J.; Stolper, Daniel A.; Eiler, John M.

    The isotopic composition of methane is of longstanding geochemical interest, with important implications for understanding hydrocarbon systems, atmospheric greenhouse gas concentrations, the global carbon cycle, and life in extreme environments. Recent analytical developments focusing on multiply substituted isotopologues (‘clumped isotopes’) are opening a potentially valuable new window into methane geochemistry. When methane forms in internal isotopic equilibrium, clumped isotopes can provide a direct record of formation temperature, making this property particularly valuable for identifying different methane origins. However, it has also become clear that in certain settings methane clumped isotope measurements record kinetic rather than equilibrium isotope effects. Here wemore » present a substantially expanded dataset of methane clumped isotope analyses, and provide a synthesis of the current interpretive framework for this parameter. We review different processes affecting methane clumped isotope compositions, describe the relationships between conventional isotope and clumped isotope data, and summarize the types of information that this measurement can provide in different Earth and planetary environments.« less

  14. Evapotranspiration partitioning for three agro-ecosystems with contrasting moisture conditions: a comparison of an isotope method and a two-source model calculation

    NASA Astrophysics Data System (ADS)

    Wei, Z.; Lee, X.; Wen, X.; Xiao, W.

    2017-12-01

    Quantification of the contribution of transpiration (T) to evapotranspiration (ET) is a requirement for understanding changes in carbon assimilation and water cycling in a changing environment. So far, few studies have examined seasonal variability of T/ET and compared different ET partitioning methods under natural conditions across diverse agro-ecosystems. In this study, we apply a two-source model to partition ET for three agro-ecosystems (rice, wheat and corn). The model-estimated T/ET ranges from 0 to 1, with a near continuous increase over time in the early growing season when leaf area index (LAI) is less than 2.5 and then convergence towards a stable value beyond LAI of 2.5. The seasonal change in T/ET can be described well as a function of LAI, implying that LAI is a first-order factor affecting ET partitioning. The two-source model results show that the growing-season (May - September for rice, April - June for wheat and June to September for corn) T/ET is 0.50, 0.84 and 0.64, while an isotopic approach shows that T/ET is 0.74, 0.93 and 0.81 for rice, wheat and maize, respectively. The two-source model results are supported by soil lysimeter and eddy covariance measurements made during the same time period for wheat (0.87). Uncertainty analysis suggests that further improvements to the Craig-Gordon model prediction of the evaporation isotope composition and to measurement of the isotopic composition of ET are necessary to achieve accurate flux partitioning at the ecosystem scale using water isotopes as tracers.

  15. Kinetic isotope effects and how to describe them

    PubMed Central

    Karandashev, Konstantin; Xu, Zhen-Hao; Meuwly, Markus; Vaníček, Jiří; Richardson, Jeremy O.

    2017-01-01

    We review several methods for computing kinetic isotope effects in chemical reactions including semiclassical and quantum instanton theory. These methods describe both the quantization of vibrational modes as well as tunneling and are applied to the ⋅H + H2 and ⋅H + CH4 reactions. The absolute rate constants computed with the semiclassical instanton method both using on-the-fly electronic structure calculations and fitted potential-energy surfaces are also compared directly with exact quantum dynamics results. The error inherent in the instanton approximation is found to be relatively small and similar in magnitude to that introduced by using fitted surfaces. The kinetic isotope effect computed by the quantum instanton is even more accurate, and although it is computationally more expensive, the efficiency can be improved by path-integral acceleration techniques. We also test a simple approach for designing potential-energy surfaces for the example of proton transfer in malonaldehyde. The tunneling splittings are computed, and although they are found to deviate from experimental results, the ratio of the splitting to that of an isotopically substituted form is in much better agreement. We discuss the strengths and limitations of the potential-energy surface and based on our findings suggest ways in which it can be improved. PMID:29282447

  16. GLYCAN REDUCTIVE ISOTOPE LABELING (GRIL) FOR QUANTITATIVE GLYCOMICS

    PubMed Central

    Xia, Baoyun; Feasley, Christa L.; Sachdev, Goverdhan P.; Smith, David F.; Cummings, Richard D.

    2009-01-01

    Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed Glycan Reductive Isotope Labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [12C6]-aniline and [13C6]-aniline. These dual-labeled aniline-tagged glycans can be recovered by reversed-phase chromatography and quantified based on UV-absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins using this method. This technique allows for linear, relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of Glycomics. PMID:19454239

  17. Creation of a predictive equation to estimate fat-free mass and the ratio of fat-free mass to skeletal size using morphometry in lean working farm dogs.

    PubMed

    Leung, Y M; Cave, N J; Hodgson, B A S

    2018-06-27

    To develop an equation that accurately estimates fat-free mass (FFM) and the ratio of FFM to skeletal size or mass, using morphometric measurements in lean working farm dogs, and to examine the association between FFM derived from body condition score (BCS) and FFM measured using isotope dilution. Thirteen Huntaway and seven Heading working dogs from sheep and beef farms in the Waikato region of New Zealand were recruited based on BCS (BCS <3, 3-4, >4) using a nine-point scale. Bodyweight, BCS, and morphometric measurements (head length and circumference, body length, thoracic girth, and fore and hind limb length) were recorded for each dog, and body composition was measured using an isotopic dilution technique. A new variable using morphometric measurements, termed skeletal size, was created using principal component analysis. Models for predicting FFM, leanST (FFM minus skeletal mass) and ratios of FFM and leanST to skeletal size or mass were generated using multiple linear regression analysis. Mean FFM of the 20 dogs, measured by isotope dilution, was 22.1 (SD 4.4) kg and the percentage FFM of bodyweight was 87.0 (SD 5.0)%. Median BCS was 3.0 (min 1, max 6). Bodyweight, breed, age and skeletal size or mass were associated with measured FFM (p<0.001). There was a good correlation between predicted FFM and measured FFM (R 2 =0.96), and for the ratio of predicted FFM to skeletal size and measured values (R 2 =0.99). Correlation coefficients were higher for the ratio FFM and leanST to skeletal size than for ratios using skeletal mass. There was a positive correlation between BCS-derived fat mass as a percentage of bodyweight and fat mass percentage determined using isotope dilution (R 2 =0.65). As expected, the predictive equation was accurate in estimating FFM when tested on the same group of dogs used to develop the equation. The significance of breed, independent of skeletal size, in predicting FFM indicates that individual breed formulae may be required. Future

  18. Insulin sensitivity index (ISI0, 120) potentially linked to carbon isotopes of breath CO2 for pre-diabetes and type 2 diabetes

    PubMed Central

    Ghosh, Chiranjit; Mukhopadhyay, Prabuddha; Ghosh, Shibendu; Pradhan, Manik

    2015-01-01

    New strategies for an accurate and early detection of insulin resistance are important to delay or prevent the acute onset of type 2 diabetes (T2D). Currently, insulin sensitivity index (ISI0,120) is considered to be a viable invasive method of whole-body insulin resistance for use in clinical settings in comparison with other invasive sensitivity indexes like homeostasis model assessment (HOMA), and quantitative insulin sensitivity check index (QUICKI). To investigate how these sensitivity indexes link the 13C/12C-carbon isotopes of exhaled breath CO2 to pre-diabetes (PD) and type 2 diabetes in response to glucose ingestion, we studied excretion dynamics of 13C/12C-isotopic fractionations of breath CO2. Here, we show that 13C/12C-isotope ratios of breath CO2 were well correlated with blood glucose, insulin, glycosylated-hemoglobin as well as with HOMA-IR and 1/QUICKI. Conversely, the strongest correlation was observed between 1/ISI0,120 and breath CO2 isotopes. Consequently, we determined several optimal diagnostic cut-off points of 1/ISI0,120 and 13CO2/12CO2-isotope ratios to distinctively track the evolution of PD prior to the onset of T2D. Our findings suggest that isotopic breath CO2 is a novel method for accurate estimation of ISI0,120 and thus may open new perspectives into the isotope-specific non-invasive evaluation of insulin resistance for large-scale real-time diabetes screening purposes. PMID:26148706

  19. A stable isotope-based approach to tropical dendroclimatology

    NASA Astrophysics Data System (ADS)

    Evans, Michael N.; Schrag, Daniel P.

    2004-08-01

    We describe a strategy for development of chronological control in tropical trees lacking demonstrably annual ring formation, using high resolution δ 18O measurements in tropical wood. The approach applies existing models of the oxygen isotopic composition of alpha-cellulose (Roden et al., 2000), a rapid method for cellulose extraction from raw wood (Brendel et al., 2000), and continuous flow isotope ratio mass spectrometry (Brenna et al., 1998) to develop proxy chronological, rainfall and growth rate estimates from tropical trees lacking visible annual ring structure. Consistent with model predictions, pilot datasets from the temperate US and Costa Rica having independent chronological control suggest that observed cyclic isotopic signatures of several permil (SMOW) represent the annual cycle of local rainfall and relative humidity. Additional data from a plantation tree of known age from ENSO-sensitive northwestern coastal Peru suggests that the 1997-8 ENSO warm phase event was recorded as an 8‰ anomaly in the δ 18O of α-cellulose. The results demonstrate reproducibility of the stable isotopic chronometer over decades, two different climatic zones, and three tropical tree genera, and point to future applications in paleoclimatology.

  20. Using radiance predicted by the P3 approximation in a spherical geometry to predict tissue optical properties

    NASA Astrophysics Data System (ADS)

    Dickey, Dwayne J.; Moore, Ronald B.; Tulip, John

    2001-01-01

    For photodynamic therapy of solid tumors, such as prostatic carcinoma, to be achieved, an accurate model to predict tissue parameters and light dose must be found. Presently, most analytical light dosimetry models are fluence based and are not clinically viable for tissue characterization. Other methods of predicting optical properties, such as Monet Carlo, are accurate but far too time consuming for clinical application. However, radiance predicted by the P3-Approximation, an anaylitical solution to the transport equation, may be a viable and accurate alternative. The P3-Approximation accurately predicts optical parameters in intralipid/methylene blue based phantoms in a spherical geometry. The optical parameters furnished by the radiance, when introduced into fluence predicted by both P3- Approximation and Grosjean Theory, correlate well with experimental data. The P3-Approximation also predicts the optical properties of prostate tissue, agreeing with documented optical parameters. The P3-Approximation could be the clinical tool necessary to facilitate PDT of solid tumors because of the limited number of invasive measurements required and the speed in which accurate calculations can be performed.

  1. Concomitant ion effects on isotope ratio measurements with liquid sampling – atmospheric pressure glow discharge ion source Orbitrap mass spectrometry

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

    Hoegg, Edward D.; Marcus, R. Kenneth; Hager, George J.

    RATIONALE: The field of highly accurate and precise isotope ratio (IR) analysis has been dominated by inductively coupled plasma and thermal ionization mass spectrometers. While these instruments are considered the gold standard for IR analysis, the International Atomic Energy Agency desires a field deployable instrument capable of accurately and precisely measuring U isotope ratios. METHODS: The proposed system interfaces the liquid sampling – atmospheric pressure glow discharge (LS-APGD) ion source with a high resolution Exactive Orbitrap mass spectrometer. With this experimental setup certified U isotope standards and unknown samples were analyzed. The accuracy and precision of the system were thenmore » determined. RESULTS: The LS-APGD /Exactive instrument measures a certified reference material of natural U (235U/238U = 0.007258) as 0.007041 with a relative standard deviation of 0.158% meeting the International Target Values for Uncertainty for the destructive analysis of U. Additionally, when three unknowns measured and compared to the results from an ICP multi collector instrument, there is no statistical difference between the two instruments.CONCLUSIONS: The LS-APGD / Orbitrap system, while still in the preliminary stages of development, offers highly accurate and precise IR analysis that suggest a paradigm shift in the world of IR analysis. Furthermore, the portability of the LS-APGD as an elemental ion source combined with the low overhead and small size of the Orbitrap suggest that the instrumentation is capable of being field deployable.With liquid sampling glow discharge-Orbitrap MS, isotope ratio and precision performance improves with rejection of concomitant ion species.« less

  2. Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies

    NASA Astrophysics Data System (ADS)

    Zhang, DaDi; Yang, Xiaolong; Zheng, Xiao; Yang, Weitao

    2018-04-01

    Electron affinity (EA) is the energy released when an additional electron is attached to an atom or a molecule. EA is a fundamental thermochemical property, and it is closely pertinent to other important properties such as electronegativity and hardness. However, accurate prediction of EA is difficult with density functional theory methods. The somewhat large error of the calculated EAs originates mainly from the intrinsic delocalisation error associated with the approximate exchange-correlation functional. In this work, we employ a previously developed non-empirical global scaling correction approach, which explicitly imposes the Perdew-Parr-Levy-Balduz condition to the approximate functional, and achieve a substantially improved accuracy for the calculated EAs. In our approach, the EA is given by the scaling corrected Kohn-Sham lowest unoccupied molecular orbital energy of the neutral molecule, without the need to carry out the self-consistent-field calculation for the anion.

  3. Technical note: A linear model for predicting δ13 Cprotein.

    PubMed

    Pestle, William J; Hubbe, Mark; Smith, Erin K; Stevenson, Joseph M

    2015-08-01

    Development of a model for the prediction of δ(13) Cprotein from δ(13) Ccollagen and Δ(13) Cap-co . Model-generated values could, in turn, serve as "consumer" inputs for multisource mixture modeling of paleodiet. Linear regression analysis of previously published controlled diet data facilitated the development of a mathematical model for predicting δ(13) Cprotein (and an experimentally generated error term) from isotopic data routinely generated during the analysis of osseous remains (δ(13) Cco and Δ(13) Cap-co ). Regression analysis resulted in a two-term linear model (δ(13) Cprotein (%) = (0.78 × δ(13) Cco ) - (0.58× Δ(13) Cap-co ) - 4.7), possessing a high R-value of 0.93 (r(2)  = 0.86, P < 0.01), and experimentally generated error terms of ±1.9% for any predicted individual value of δ(13) Cprotein . This model was tested using isotopic data from Formative Period individuals from northern Chile's Atacama Desert. The model presented here appears to hold significant potential for the prediction of the carbon isotope signature of dietary protein using only such data as is routinely generated in the course of stable isotope analysis of human osseous remains. These predicted values are ideal for use in multisource mixture modeling of dietary protein source contribution. © 2015 Wiley Periodicals, Inc.

  4. Sm-Nd isotopic compositions of LREE minerals for use as reference materials for in situ analysis by LA-MC-ICPMS

    NASA Astrophysics Data System (ADS)

    Fisher, C. M.; McFarlane, C. R.; Sylvester, P.; Hanchar, J. M.; Lam, R.; Schmitz, M. D.

    2009-12-01

    Recent work has demonstrated the possibility of obtaining both accurate and precise in situ Sm-Nd isotopic data in light rare earth enriched (LREE) accessory minerals including apatite, titanite, and monazite, using laser ablation-multicollector-inductively coupled plasma mass spectrometry (LA-MC-ICPMS). A distinct advantage of using LA-MC-ICPMS is that Sm-Nd isotopic data from these minerals can be determined in sub-grain domains potentially avoiding problems of isotopic mixing from inherited or xenocrystic components and allowing both valuable tracer isotope and geochronologic data to be obtained. However, a number of analytical obstacles complicate accurate Sm-Nd determination by LA-MC-ICPMS including mass bias corrections, the 144Sm isobaric interference on 144Nd, and potential offset (ca. 20-40 ppm) from thermal ionization mass spectrometry (TIMS) determination of similar materials. Thus, in order to verify Sm-Nd isotopic determination from unknowns, matrix-matched quality control standards (i.e., reference materials) must be developed to test the data handling protocol. This talk will present new Sm-Nd isotopic data determined by both TIMS as well as LA-MC-ICPMS of a number of natural potential reference minerals including Durango apatite, Fish Canyon titanite, Daibosatsu allanite, Trebilcock monazite, as well as a monazite from the Doi Inthanon core complex in northern Thailand. Our preliminary LA-MC-ICPMS results demonstrate that Durango apatite, Fish Canyon titanite, and Thailand monazite show both inter- and intra-grain homogeneity at current levels of precision (ca. 0.3-0.5 ɛNd) and close agreement with our TIMS data.

  5. Combining first-principles and data modeling for the accurate prediction of the refractive index of organic polymers

    NASA Astrophysics Data System (ADS)

    Afzal, Mohammad Atif Faiz; Cheng, Chong; Hachmann, Johannes

    2018-06-01

    Organic materials with a high index of refraction (RI) are attracting considerable interest due to their potential application in optic and optoelectronic devices. However, most of these applications require an RI value of 1.7 or larger, while typical carbon-based polymers only exhibit values in the range of 1.3-1.5. This paper introduces an efficient computational protocol for the accurate prediction of RI values in polymers to facilitate in silico studies that can guide the discovery and design of next-generation high-RI materials. Our protocol is based on the Lorentz-Lorenz equation and is parametrized by the polarizability and number density values of a given candidate compound. In the proposed scheme, we compute the former using first-principles electronic structure theory and the latter using an approximation based on van der Waals volumes. The critical parameter in the number density approximation is the packing fraction of the bulk polymer, for which we have devised a machine learning model. We demonstrate the performance of the proposed RI protocol by testing its predictions against the experimentally known RI values of 112 optical polymers. Our approach to combine first-principles and data modeling emerges as both a successful and a highly economical path to determining the RI values for a wide range of organic polymers.

  6. Lower NIH stroke scale scores are required to accurately predict a good prognosis in posterior circulation stroke.

    PubMed

    Inoa, Violiza; Aron, Abraham W; Staff, Ilene; Fortunato, Gilbert; Sansing, Lauren H

    2014-01-01

    The NIH stroke scale (NIHSS) is an indispensable tool that aids in the determination of acute stroke prognosis and decision making. Patients with posterior circulation (PC) strokes often present with lower NIHSS scores, which may result in the withholding of thrombolytic treatment from these patients. However, whether these lower initial NIHSS scores predict better long-term prognoses is uncertain. We aimed to assess the utility of the NIHSS at presentation for predicting the functional outcome at 3 months in anterior circulation (AC) versus PC strokes. This was a retrospective analysis of a large prospectively collected database of adults with acute ischemic stroke. Univariate and multivariate analyses were conducted to identify factors associated with outcome. Additional analyses were performed to determine the receiver operating characteristic (ROC) curves for NIHSS scores and outcomes in AC and PC infarctions. Both the optimal cutoffs for maximal diagnostic accuracy and the cutoffs to obtain >80% sensitivity for poor outcomes were determined in AC and PC strokes. The analysis included 1,197 patients with AC stroke and 372 with PC stroke. The median initial NIHSS score for patients with AC strokes was 7 and for PC strokes it was 2. The majority (71%) of PC stroke patients had baseline NIHSS scores ≤4, and 15% of these 'minor' stroke patients had a poor outcome at 3 months. ROC analysis identified that the optimal NIHSS cutoff for outcome prediction after infarction in the AC was 8 and for infarction in the PC it was 4. To achieve >80% sensitivity for detecting patients with a subsequent poor outcome, the NIHSS cutoff for infarctions in the AC was 4 and for infarctions in the PC it was 2. The NIHSS cutoff that most accurately predicts outcomes is 4 points higher in AC compared to PC infarctions. There is potential for poor outcomes in patients with PC strokes and low NIHSS scores, suggesting that thrombolytic treatment should not be withheld from these patients

  7. A test of geographic assignment using isotope tracers in feathers of known origin

    USGS Publications Warehouse

    Wunder, Michael B.; Kester, C.L.; Knopf, F.L.; Rye, R.O.

    2005-01-01

    We used feathers of known origin collected from across the breeding range of a migratory shorebird to test the use of isotope tracers for assigning breeding origins. We analyzed δD, δ13C, and δ15N in feathers from 75 mountain plover (Charadrius montanus) chicks sampled in 2001 and from 119 chicks sampled in 2002. We estimated parameters for continuous-response inverse regression models and for discrete-response Bayesian probability models from data for each year independently. We evaluated model predictions with both the training data and by using the alternate year as an independent test dataset. Our results provide weak support for modeling latitude and isotope values as monotonic functions of one another, especially when data are pooled over known sources of variation such as sample year or location. We were unable to make even qualitative statements, such as north versus south, about the likely origin of birds using both δD and δ13C in inverse regression models; results were no better than random assignment. Probability models provided better results and a more natural framework for the problem. Correct assignment rates were highest when considering all three isotopes in the probability framework, but the use of even a single isotope was better than random assignment. The method appears relatively robust to temporal effects and is most sensitive to the isotope discrimination gradients over which samples are taken. We offer that the problem of using isotope tracers to infer geographic origin is best framed as one of assignment, rather than prediction.

  8. Natural calcium isotopic composition of urine as a marker of bone mineral balance.

    PubMed

    Skulan, Joseph; Bullen, Thomas; Anbar, Ariel D; Puzas, J Edward; Shackelford, Linda; LeBlanc, Adrian; Smith, Scott M

    2007-06-01

    We investigated whether changes in the natural isotopic composition of calcium in human urine track changes in net bone mineral balance, as predicted by a model of calcium isotopic behavior in vertebrates. If so, isotopic analysis of natural urine or blood calcium could be used to monitor short-term changes in bone mineral balance that cannot be detected with other techniques. Calcium isotopic compositions are expressed as delta(44)Ca, or the difference in parts per thousand between the (44)Ca/(40)Ca of a sample and the (44)Ca/(40)Ca of a standard reference material. delta(44)Ca was measured in urine samples from 10 persons who participated in a study of the effectiveness of countermeasures to bone loss in spaceflight, in which 17 weeks of bed rest was used to induce bone loss. Study participants were assigned to 1 of 3 treatment groups: controls received no treatment, one treatment group received alendronate, and another group performed resistive exercise. Measurements were made on urine samples collected before, at 2 or 3 points during, and after bed rest. Urine delta(44)Ca values during bed rest were lower in controls than in individuals treated with alendronate (P <0.05, ANOVA) or exercise (P <0.05), and lower than the control group baseline (P <0.05, t-test). Results were consistent with the model and with biochemical and bone mineral density data. Results confirm the predicted relationship between bone mineral balance and calcium isotopes, suggesting that calcium isotopic analysis of urine might be refined into a clinical and research tool.

  9. New analytical model for the ozone electronic ground state potential surface and accurate ab initio vibrational predictions at high energy range.

    PubMed

    Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A; Holka, Filip; Szalay, Péter G

    2013-10-07

    An accurate description of the complicated shape of the potential energy surface (PES) and that of the highly excited vibration states is of crucial importance for various unsolved issues in the spectroscopy and dynamics of ozone and remains a challenge for the theory. In this work a new analytical representation is proposed for the PES of the ground electronic state of the ozone molecule in the range covering the main potential well and the transition state towards the dissociation. This model accounts for particular features specific to the ozone PES for large variations of nuclear displacements along the minimum energy path. The impact of the shape of the PES near the transition state (existence of the "reef structure") on vibration energy levels was studied for the first time. The major purpose of this work was to provide accurate theoretical predictions for ozone vibrational band centres at the energy range near the dissociation threshold, which would be helpful for understanding the very complicated high-resolution spectra and its analyses currently in progress. Extended ab initio electronic structure calculations were carried out enabling the determination of the parameters of a minimum energy path PES model resulting in a new set of theoretical vibrational levels of ozone. A comparison with recent high-resolution spectroscopic data on the vibrational levels gives the root-mean-square deviations below 1 cm(-1) for ozone band centres up to 90% of the dissociation energy. New ab initio vibrational predictions represent a significant improvement with respect to all previously available calculations.

  10. Nuclear quantum effects and kinetic isotope effects in enzyme reactions.

    PubMed

    Vardi-Kilshtain, Alexandra; Nitoker, Neta; Major, Dan Thomas

    2015-09-15

    Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum-classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5'-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Applications of isotopes to tracing sources of solutes and water in shallow systems

    USGS Publications Warehouse

    Kendall, Carol; Krabbenhoft, David P.

    1995-01-01

    New awareness of the potential danger to water supplies posed by the use of agricultural chemicals has focused attention on the nature of groundwater recharge and the mobility of various solutes, especially nitrate and pesticides, in shallow systems. A better understanding of hydrologic flowpaths and solute sources is required to determine the potential impact of sources of contamination on water supplies, to develop management practices for preserving water quality, and to develop remediation plans for sites that are already contaminated. In many cases, environmental isotopes can be employed as 'surgical tools' for answering very specific questions about water and solute sources. Isotopic data can often provide more accurate information about the system than hydrologic measurements or complicated hydrologic models. This note focuses on practical and cost-effective examples of how naturally-occurring isotopes can be used to track water and solutes as they move through shallow systems.

  12. Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium.

    PubMed

    Ryan, Natalia; Chorley, Brian; Tice, Raymond R; Judson, Richard; Corton, J Christopher

    2016-05-01

    Microarray profiling of chemical-induced effects is being increasingly used in medium- and high-throughput formats. Computational methods are described here to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), often modulated by potential endocrine disrupting chemicals. ERα biomarker genes were identified by their consistent expression after exposure to 7 structurally diverse ERα agonists and 3 ERα antagonists in ERα-positive MCF-7 cells. Most of the biomarker genes were shown to be directly regulated by ERα as determined by ESR1 gene knockdown using siRNA as well as through chromatin immunoprecipitation coupled with DNA sequencing analysis of ERα-DNA interactions. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression datasets from experiments using MCF-7 cells, including those evaluating the transcriptional effects of hormones and chemicals. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% and 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) ER reference chemicals including "very weak" agonists. Importantly, the biomarker predictions accurately replicated predictions based on 18 in vitro high-throughput screening assays that queried different steps in ERα signaling. For 114 chemicals, the balanced accuracies were 95% and 98% for activation or suppression, respectively. These results demonstrate that the ERα gene expression biomarker can accurately identify ERα modulators in large collections of microarray data derived from MCF-7 cells. Published by Oxford University Press on behalf of the Society of Toxicology 2016. This work is written by US Government employees and is in the public domain in the US.

  13. Sulfur isotope measurements of submicrometer sulfate aerosol particles over the Pacific Ocean

    NASA Technical Reports Server (NTRS)

    Calhoun, Julie A.; Charlson, Robert J.; Bates, Timothy S.

    1991-01-01

    Stable isotopes were used to analyze the submicron-size sulfate aerosol particles in the atmosphere over the Pacific Ocean, together with the air-mass back trajectories, in order to test the hypothesis of Charlson et al. (1987) who suggested that, over the remote ocean areas, the primary source of atmospheric nonseasalt (NSS) sulfate is marine emissions of dimethylsulfide (DMS). The observed results of isotopic fractionation between the seawater sulfate and NSS sulfate fractions was found to be consistent with the isotopic fractionation predicted for the transformation of the seawater sulfate to the atmospheric NSS sulfate via a DMS path way, supporting the hypothesis of Charlson et al.

  14. Equilibrium stable-isotope fractionation of thallium and mercury

    NASA Astrophysics Data System (ADS)

    Schauble, E. A.

    2005-12-01

    In this study first-principles quantum mechanical and empirical force-field models are used to estimate equilibrium mass-dependent isotopic fractionations among a variety of thallium and mercury compounds. High-precision MC-ICP-MS measurements have recently uncovered evidence of stable isotope fractionation for many elements, including 2-4‰ variability in the isotopic compositions of thallium[1] (atomic no. 81) and mercury[2] (atomic no. 80). The observed thallium- and mercury-isotope fractionations are remarkable, given that the magnitude of isotopic fractionation typically decreases as atomic number increases[3]. Stable isotope measurements could improve our understanding of geochemical and biogeochemical cycling of both elements, but little is known about the mechanisms driving these fractionations. A better understanding of the chemical processes controlling stable isotope compositions could help maximize the utility of these new geochemical tracers. Standard equilibrium stable isotope fractionation theory holds that the energy driving fractionation comes from isotopic effects on vibrational frequencies, which have generally not been measured. In the present study both quantum-mechanical and empirical force fields are used to estimate unknown frequencies. Results suggest that thallium and mercury fractionations of ≥ 0.5‰ are likely during the relevant redox reactions Tl+ ↔ Tl3+ and HgO ↔ Hg2+. Methyl-mercury and mercury-halide compounds like CH3HgCl will have ~ 1‰ higher 202Hg/198Hg than atomic vapor at room temperature. Fractionations between coexisting Hg2+ species appear to be much smaller, however. 205Tl/203Tl in Tl(H2O)_63+ is predicted to be ~0.5‰ higher than in coexisting Tl+-bearing substances. This result is in qualitative agreement with data from ferromanganese crusts [1], suggesting that Tl3+ in manganese-oxides will have higher 205Tl/203Tl than aqueous Tl+. Equilibrium fractionations for both elements are much smaller than the observed

  15. Evidence of isotopic fractionation of natural uranium in cultured human cells

    NASA Astrophysics Data System (ADS)

    Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E.; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

    2016-12-01

    The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235U isotope with regard to 238U. Efforts were made to develop and then validate a procedure for highly accurate n(238U)/n(235U) determinations in microsamples of cells. We found that intracellular U is enriched in 235U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO22+) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes.

  16. Evidence of isotopic fractionation of natural uranium in cultured human cells

    PubMed Central

    Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E.; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

    2016-01-01

    The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235U isotope with regard to 238U. Efforts were made to develop and then validate a procedure for highly accurate n(238U)/n(235U) determinations in microsamples of cells. We found that intracellular U is enriched in 235U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO22+) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes. PMID:27872304

  17. Evidence of isotopic fractionation of natural uranium in cultured human cells.

    PubMed

    Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

    2016-12-06

    The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235 U isotope with regard to 238 U. Efforts were made to develop and then validate a procedure for highly accurate n( 238 U)/n( 235 U) determinations in microsamples of cells. We found that intracellular U is enriched in 235 U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO 2 2+ ) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes.

  18. Concerns about Quadrupole ICP-MS Lead Isotopic Data and Interpretations in the Environment and Health Fields.

    PubMed

    Gulson, Brian; Kamenov, George D; Manton, William; Rabinowitz, Michael

    2018-04-11

    There has been a massive increase in recent years of the use of lead (Pb) isotopes in attempts to better understand sources and pathways of Pb in the environment and in man or experimental animals. Unfortunately, there have been many cases where the quality of the isotopic data, especially that obtained by quadrupole inductively coupled plasma mass spectrometry (Q-ICP-MS), are questionable, resulting in questionable identification of potential sources, which, in turn, impacts study interpretation and conclusions. We present several cases where the isotopic data have compromised interpretation because of the use of only the major isotopes 208 Pb/ 206 Pb and 207 Pb/ 206 Pb, or their graphing in other combinations. We also present some examples comparing high precision data from thermal ionization (TIMS) or multi-collector plasma mass spectrometry (MC-ICP-MS) to illustrate the deficiency in the Q-ICP-MS data. In addition, we present cases where Pb isotopic ratios measured on Q-ICP-MS are virtually impossible for terrestrial samples. We also evaluate the Pb isotopic data for rat studies, which had concluded that Pb isotopic fractionation occurs between different organs and suggest that this notion of biological fractionation of Pb as an explanation for isotopic differences is not valid. Overall, the brief review of these case studies shows that Q-ICP-MS as commonly practiced is not a suitable technique for precise and accurate Pb isotopic analysis in the environment and health fields.

  19. Concerns about Quadrupole ICP-MS Lead Isotopic Data and Interpretations in the Environment and Health Fields

    PubMed Central

    Gulson, Brian; Manton, William; Rabinowitz, Michael

    2018-01-01

    There has been a massive increase in recent years of the use of lead (Pb) isotopes in attempts to better understand sources and pathways of Pb in the environment and in man or experimental animals. Unfortunately, there have been many cases where the quality of the isotopic data, especially that obtained by quadrupole inductively coupled plasma mass spectrometry (Q-ICP-MS), are questionable, resulting in questionable identification of potential sources, which, in turn, impacts study interpretation and conclusions. We present several cases where the isotopic data have compromised interpretation because of the use of only the major isotopes 208Pb/206Pb and 207Pb/206Pb, or their graphing in other combinations. We also present some examples comparing high precision data from thermal ionization (TIMS) or multi-collector plasma mass spectrometry (MC-ICP-MS) to illustrate the deficiency in the Q-ICP-MS data. In addition, we present cases where Pb isotopic ratios measured on Q-ICP-MS are virtually impossible for terrestrial samples. We also evaluate the Pb isotopic data for rat studies, which had concluded that Pb isotopic fractionation occurs between different organs and suggest that this notion of biological fractionation of Pb as an explanation for isotopic differences is not valid. Overall, the brief review of these case studies shows that Q-ICP-MS as commonly practiced is not a suitable technique for precise and accurate Pb isotopic analysis in the environment and health fields. PMID:29641487

  20. Comparison of gas chromatography/isotope ratio mass spectrometry and liquid chromatography/isotope ratio mass spectrometry for carbon stable-isotope analysis of carbohydrates.

    PubMed

    Moerdijk-Poortvliet, Tanja C W; Schierbeek, Henk; Houtekamer, Marco; van Engeland, Tom; Derrien, Delphine; Stal, Lucas J; Boschker, Henricus T S

    2015-07-15

    We compared gas chromatography/isotope ratio mass spectrometry (GC/IRMS) and liquid chromatography/isotope ratio mass spectrometry (LC/IRMS) for the measurement of δ(13)C values in carbohydrates. Contrary to GC/IRMS, no derivatisation is needed for LC/IRMS analysis of carbohydrates. Hence, although LC/IRMS is expected to be more accurate and precise, no direct comparison has been reported. GC/IRMS with the aldonitrile penta-acetate (ANPA) derivatisation method was compared with LC/IRMS without derivatisation. A large number of glucose standards and a variety of natural samples were analysed for five neutral carbohydrates at natural abundance as well as at (13)C-enriched levels. Gas chromatography/chemical ionisation mass spectrometry (GC/CIMS) was applied to check for incomplete derivatisation of the carbohydrate, which would impair the accuracy of the GC/IRMS method. The LC/IRMS technique provided excellent precision (±0.08‰ and ±3.1‰ at natural abundance and enrichment levels, respectively) for the glucose standards and this technique proved to be superior to GC/IRMS (±0.62‰ and ±19.8‰ at natural abundance and enrichment levels, respectively). For GC/IRMS measurements the derivatisation correction and the conversion of carbohydrates into CO2 had a considerable effect on the measured δ(13)C values. However, we did not find any significant differences in the accuracy of the two techniques over the full range of natural δ(13)C abundances and (13)C-labelled glucose. The difference in the performance of GC/IRMS and LC/IRMS diminished when the δ(13)C values were measured in natural samples, because the chromatographic performance and background correction became critical factors, particularly for LC/IRMS. The derivatisation of carbohydrates for the GC/IRMS method was complete. Although both LC/IRMS and GC/IRMS are reliable techniques for compound-specific stable carbon isotope analysis of carbohydrates (provided that derivatisation is complete and the

  1. Laser isotope separation of erbium and other isotopes

    DOEpatents

    Haynam, Christopher A.; Worden, Earl F.

    1995-01-01

    Laser isotope separation is accomplished using at least two photoionization pathways of an isotope simultaneously, where each pathway comprises two or more transition steps. This separation method has been applied to the selective photoionization of erbium isotopes, particularly for the enrichment of .sup.167 Er. The hyperfine structure of .sup.167 Er was used to find two three-step photoionization pathways having a common upper energy level.

  2. Silicon isotope ratio measurements by inductively coupled plasma tandem mass spectrometry for alteration studies of nuclear waste glasses.

    PubMed

    Gourgiotis, Alkiviadis; Ducasse, Thomas; Barker, Evelyne; Jollivet, Patrick; Gin, Stéphane; Bassot, Sylvain; Cazala, Charlotte

    2017-02-15

    High-level, long-lived nuclear waste arising from spent fuel reprocessing is vitrified in silicate glasses for final disposal in deep geologic formations. In order to better understand the mechanisms driving glass dissolution, glass alteration studies, based on silicon isotope ratio monitoring of 29 Si-doped aqueous solutions, were carried out in laboratories. This work explores the capabilities of the new type of quadrupole-based ICP-MS, the Agilent 8800 tandem quadrupole ICP-MS/MS, for accurate silicon isotope ratio determination for alteration studies of nuclear waste glasses. In order to avoid silicon polyatomic interferences, a new analytical method was developed using O 2 as the reaction gas in the Octopole Reaction System (ORS), and silicon isotopes were measured in mass-shift mode. A careful analysis of the potential polyatomic interferences on SiO + and SiO 2 + ion species was performed, and we found that SiO + ion species suffer from important polyatomic interferences coming from the matrix of sample and standard solutions (0.5M HNO 3 ). For SiO 2 + , no interferences were detected, and thus, these ion species were chosen for silicon isotope ratio determination. A number of key settings for accurate isotope ratio analysis like, detector dead time, integration time, number of sweeps, wait time offset, memory blank and instrumental mass fractionation, were considered and optimized. Particular attention was paid to the optimization of abundance sensitivity of the quadrupole mass filter before the ORS. We showed that poor abundance sensitivity leads to a significant shift of the data away from the Exponential Mass Fractionation Law (EMFL) due to the spectral overlaps of silicon isotopes combined with different oxygen isotopes (i.e. 28 Si 16 O 18 O + , 30 Si 16 O 16 O + ). The developed method was validated by measuring a series of reference solutions with different 29 Si enrichment. Isotope ratio trueness, uncertainty and repeatability were found to be <0

  3. Interpreting terrestrial organic carbon isotope records across natural and anthropogenic pCO2 change

    NASA Astrophysics Data System (ADS)

    Schubert, B.; Jahren, H.

    2014-12-01

    Changes in the net carbon isotope fractionation (Δδ13C) measured in organic carbon from terrestrial substrates results from changes in climate, plant community shifts, and pCO2 level, but separating out these effects in the geologic record can be difficult. Here we present a compilation of 614 Δδ13C measurements on bulk terrestrial organic matter (TOM) and fossil leaves from 23 distinct records within 19 published studies that span the last 30,000 years up to the industrial revolution. To this dataset we add 2735 Δδ13C measurements made on tree ring tissue from 51 records that extend from 1950 to 2010. These records together span the ~80 ppm rise in pCO2 from the Late Glacial to through the Holocene (190-270 ppm; fossil leaves and TOM), and the ~70 ppm rise observed across the last 60 years (310-380 ppm; tree-ring tissue). We find a 2.0‰ relative increase in Δδ13C value across Termination 1 (18,000-11,500 years BP) and a 1.0‰ increase in Δδ13C value recorded in tree rings between 1950 and 2010. We use our recently developed relationship between pCO2 and Δδ13C to show that both increases in Δδ13C value exactly match, in trend and absolute magnitude, the increase in Δδ13C value we predict from our equations in response to rising pCO2 levels. These results have significance for the interpretation of terrestrial organic isotope records spanning both natural and anthropogenic pCO2 changes; we contend that environmental reconstructions based on long-term terrestrial Δδ13C records cannot be accurately interpreted until the isotope data are adjusted for known changes in pCO2 concentration.

  4. Quantitative detection of codeine in human plasma using surface-enhanced Raman scattering via adaptation of the isotopic labelling principle.

    PubMed

    Subaihi, Abdu; Muhamadali, Howbeer; Mutter, Shaun T; Blanch, Ewan; Ellis, David I; Goodacre, Royston

    2017-03-27

    In this study surface enhanced Raman scattering (SERS) combined with the isotopic labelling (IL) principle has been used for the quantification of codeine spiked into both water and human plasma. Multivariate statistical approaches were employed for the analysis of these SERS spectral data, particularly partial least squares regression (PLSR) which was used to generate models using the full SERS spectral data for quantification of codeine with, and without, an internal isotopic labelled standard. The PLSR models provided accurate codeine quantification in water and human plasma with high prediction accuracy (Q 2 ). In addition, the employment of codeine-d 6 as the internal standard further improved the accuracy of the model, by increasing the Q 2 from 0.89 to 0.94 and decreasing the low root-mean-square error of predictions (RMSEP) from 11.36 to 8.44. Using the peak area at 1281 cm -1 assigned to C-N stretching, C-H wagging and ring breathing, the limit of detection was calculated in both water and human plasma to be 0.7 μM (209.55 ng mL -1 ) and 1.39 μM (416.12 ng mL -1 ), respectively. Due to a lack of definitive codeine vibrational assignments, density functional theory (DFT) calculations have also been used to assign the spectral bands with their corresponding vibrational modes, which were in excellent agreement with our experimental Raman and SERS findings. Thus, we have successfully demonstrated the application of SERS with isotope labelling for the absolute quantification of codeine in human plasma for the first time with a high degree of accuracy and reproducibility. The use of the IL principle which employs an isotopolog (that is to say, a molecule which is only different by the substitution of atoms by isotopes) improves quantification and reproducibility because the competition of the codeine and codeine-d 6 for the metal surface used for SERS is equal and this will offset any difference in the number of particles under analysis or any fluctuations in

  5. Direct uranium isotope ratio analysis of single micrometer-sized glass particles

    PubMed Central

    Kappel, Stefanie; Boulyga, Sergei F.; Prohaska, Thomas

    2012-01-01

    We present the application of nanosecond laser ablation (LA) coupled to a ‘Nu Plasma HR’ multi collector inductively coupled plasma mass spectrometer (MC-ICP-MS) for the direct analysis of U isotope ratios in single, 10–20 μm-sized, U-doped glass particles. Method development included studies with respect to (1) external correction of the measured U isotope ratios in glass particles, (2) the applied laser ablation carrier gas (i.e. Ar versus He) and (3) the accurate determination of lower abundant 236U/238U isotope ratios (i.e. 10−5). In addition, a data processing procedure was developed for evaluation of transient signals, which is of potential use for routine application of the developed method. We demonstrate that the developed method is reliable and well suited for determining U isotope ratios of individual particles. Analyses of twenty-eight S1 glass particles, measured under optimized conditions, yielded average biases of less than 0.6% from the certified values for 234U/238U and 235U/238U ratios. Experimental results obtained for 236U/238U isotope ratios deviated by less than −2.5% from the certified values. Expanded relative total combined standard uncertainties Uc (k = 2) of 2.6%, 1.4% and 5.8% were calculated for 234U/238U, 235U/238U and 236U/238U, respectively. PMID:22595724

  6. Direct uranium isotope ratio analysis of single micrometer-sized glass particles.

    PubMed

    Kappel, Stefanie; Boulyga, Sergei F; Prohaska, Thomas

    2012-11-01

    We present the application of nanosecond laser ablation (LA) coupled to a 'Nu Plasma HR' multi collector inductively coupled plasma mass spectrometer (MC-ICP-MS) for the direct analysis of U isotope ratios in single, 10-20 μm-sized, U-doped glass particles. Method development included studies with respect to (1) external correction of the measured U isotope ratios in glass particles, (2) the applied laser ablation carrier gas (i.e. Ar versus He) and (3) the accurate determination of lower abundant (236)U/(238)U isotope ratios (i.e. 10(-5)). In addition, a data processing procedure was developed for evaluation of transient signals, which is of potential use for routine application of the developed method. We demonstrate that the developed method is reliable and well suited for determining U isotope ratios of individual particles. Analyses of twenty-eight S1 glass particles, measured under optimized conditions, yielded average biases of less than 0.6% from the certified values for (234)U/(238)U and (235)U/(238)U ratios. Experimental results obtained for (236)U/(238)U isotope ratios deviated by less than -2.5% from the certified values. Expanded relative total combined standard uncertainties U(c) (k = 2) of 2.6%, 1.4% and 5.8% were calculated for (234)U/(238)U, (235)U/(238)U and (236)U/(238)U, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Radiogenic isotopic approaches for quantifying radionuclide transport (Invited)

    NASA Astrophysics Data System (ADS)

    Maher, K.; Depaolo, D. J.; Singleton, M. J.; Christensen, J. N.; Conrad, M. E.

    2009-12-01

    Naturally occurring variations in the isotopic compositions of U and Sr provide unique opportunities for assessing the fate and transport of radionuclides at field-scale conditions. When coupled with reactive transport models, U and Sr isotopes may also provide additional constraints on the rates of sediment-fluid or sediment-waste interactions. Such isotopic approaches can be useful for sites where subsurface characterization is complicated by a lack of accessibility or the presence of substantial heterogeneity. In addition, a variety of quantitative modeling approaches of different complexity can be used to evaluate experimentally determined parameters for radionuclide mobility at the field-scale. At the Hanford Site in eastern Washington, 87Sr/86Sr and 234U/238U ratios have been used to quantify the residence time of Sr and U in the unsaturated zone, the long-term background infiltration rate through the unsaturated zone, and to assess the influence of enhanced wastewater discharge on the regional unconfined aquifer. As a result of different processing techniques or due to interactions between caustic waste and the natural sediment, waste plumes may also inherit isotopic fingerprints (e.g. 234U/238U, 235U/238U, 236U/238U; δ15N & δ18O of nitrate) that can be used to resolve multiple sources of contamination. Finally, enriched isotopic tracers can be applied to experimental manipulations to assess the retardation of a variety of contaminants. Collectively this isotopic data contributes unique perspectives on both the hydrologic conditions across the site and the mobility of key radionuclides. Predicting the long-term fate and transport of radionuclides in the environment is often challenging due to natural heterogeneity and incomplete characterization of the subsurface, however detailed analysis of isotopic variations can provide one additional means of characterizing the subsurface.

  8. Evaluating O, C, and N isotopes in human hair as a forensic tool to reconstruct travel

    NASA Astrophysics Data System (ADS)

    Ehleringer, Jim; Chesson, Lesley; Cerling, Thure; Valenzuela, Luciano

    2014-05-01

    Oxygen isotope ratios in the proteins of human scalp hair have been proposed and modeled as a tool for reconstructing the movements of humans and evaluating the likelihood that an individual is a resident or non-resident of a particular geographic region. Carbon and nitrogen isotope ratios reflect dietary input and complement oxygen isotope data interpretation when it is necessary to distinguish potential location overlap among continents. The combination of a time sequence analysis in hair segments and spatial models that describe predicted geographic variation in hair isotope values represents a potentially powerful tool for forensic investigations. The applications of this technique have thus far been to provide assistance to law enforcement with information on the predicted geographical travel histories of unidentified murder victims. Here we review multiple homicide cases from the USA where stable isotope analysis of hair has been applied and for which we now know the travel histories of the murder victims. Here we provide information on the robustness of the original data sets used to test these models by evaluating the travel histories of randomly collected hair discarded in Utah barbershops.

  9. Prospects and Challenges in tropical isotope dendroclimatology

    NASA Astrophysics Data System (ADS)

    Evans, M. N.; Anchukaitis, K. J.; White, S. R.; Ektvedt, T. M.; Penniston, R. C.; Rheaume, M. M.; Bowman, D. M.

    2008-12-01

    We review a stable isotope-based approach to the development, modeling, interpretation, and analysis of hydrometeorological estimates from tropical trees. The strategy overcomes the common problem of missing, intermittent or non-annual ring structure in tropical trees by relying instead on the observation of the annual wet-dry seasonality typical to tropical environments as mirrored in the oxygen isotopic composition of wood-derived α-cellulose. We explore regions for which forward modeling of the proxy system would expect us to resolve hydrometeorological variations associated with the El Niño-Southern Oscillation (ENSO) phenomenon, rather than being limited to regions with tree species or environments producing verifiable annual ring chronologies. A modified protocol allows for rapid, simple and non-toxic micro-extraction of pure α-cellulose, which is isotopically indistinguishable from that produced by more classical means. We describe a new reactor for the pyrolysis of α-cellulose in an induction heater, which permits isotopic analysis of α-cellulose samples as small as 30μg, and as many as 100 automated sample analyses per day. A forward model adapted for tropical environments can be used to test and refine the interpretation of the isotopic data, and to predict locales for which we should be able to maximize the paleoclimatic potential of future sample collections. We have found the modeled isotopic chronometer and raingage in agreement with independent chronological controls in a variety of environments and tree species in Costa Rica, Indonesia, Brazil, Peru and Australia. Development of long hydrometeorological records from the terrestrial tropics is underway not only by our group, but by a growing number of collaborators and colleagues. Together we should be able to build a network of paleoprecipitation records and better understand the linkages between tropical surface ocean temperatures and large-scale drought.

  10. Shedding light on the variability of optical skin properties: finding a path towards more accurate prediction of light propagation in human cutaneous compartments

    PubMed Central

    Mignon, C.; Tobin, D. J.; Zeitouny, M.; Uzunbajakava, N. E.

    2018-01-01

    Finding a path towards a more accurate prediction of light propagation in human skin remains an aspiration of biomedical scientists working on cutaneous applications both for diagnostic and therapeutic reasons. The objective of this study was to investigate variability of the optical properties of human skin compartments reported in literature, to explore the underlying rational of this variability and to propose a dataset of values, to better represent an in vivo case and recommend a solution towards a more accurate prediction of light propagation through cutaneous compartments. To achieve this, we undertook a novel, logical yet simple approach. We first reviewed scientific articles published between 1981 and 2013 that reported on skin optical properties, to reveal the spread in the reported quantitative values. We found variations of up to 100-fold. Then we extracted the most trust-worthy datasets guided by a rule that the spectral properties should reflect the specific biochemical composition of each of the skin layers. This resulted in the narrowing of the spread in the calculated photon densities to 6-fold. We conclude with a recommendation to use the identified most robust datasets when estimating light propagation in human skin using Monte Carlo simulations. Alternatively, otherwise follow our proposed strategy to screen any new datasets to determine their biological relevance. PMID:29552418

  11. Laser ablation inductively coupled plasma mass spectrometry for direct isotope ratio measurements on solid samples

    NASA Astrophysics Data System (ADS)

    Pickhardt, Carola; Dietze, Hans-Joachim; Becker, J. Sabine

    2005-04-01

    Isotope ratio measurements have been increasingly used in quite different application fields, e.g., for the investigation of isotope variation in nature, in geoscience (geochemistry and geochronology), in cosmochemistry and planetary science, in environmental science, e.g., in environmental monitoring, or by the application of the isotope dilution technique for quantification purposes using stable or radioactive high-enriched isotope tracers. Due to its high sensitivity, laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is today a challenging mass spectrometric technique for the direct determination of precise and accurate isotope ratios in solid samples. In comparison to laser ablation quadrupole ICP-MS (LA-ICP-QMS), laser ablation coupled to a double-focusing sector field ICP-MS (LA-ICP-SFMS) with single ion detection offers a significant improvement of sensitivity at low mass resolution, whereby isotope ratios can be measured with a precision to 0.1% relative standard deviation (R.S.D.). In LA-ICP-SFMS, many disturbing isobaric interferences of analyte and molecular ions can be separated at the required mass resolution (e.g., 40Ar16O+ and 56Fe+ for iron isotope ratio measurements). The precision on isotope ratio measurements was improved by one order of magnitude via the simultaneous detection of mass-separated ion currents of isotopes using multiple ion collectors in LA-ICP-MS (LA-MC-ICP-MS). The paper discusses the state of the art, the challenges and limits in isotope ratio measurements by LA-ICP-MS using different instrumentations at the trace and ultratrace level in different fields of application as in environmental and biological research, geochemistry and geochronology with respect to their precision and accuracy.

  12. Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

    PubMed

    Gao, J

    2016-01-01

    Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects. © 2016 Elsevier Inc. All rights reserved.

  13. Isotope analysis reveals foraging area dichotomy for atlantic leatherback turtles.

    PubMed

    Caut, Stéphane; Fossette, Sabrina; Guirlet, Elodie; Angulo, Elena; Das, Krishna; Girondot, Marc; Georges, Jean-Yves

    2008-03-26

    The leatherback turtle (Dermochelys coriacea) has undergone a dramatic decline over the last 25 years, and this is believed to be primarily the result of mortality associated with fisheries bycatch followed by egg and nesting female harvest. Atlantic leatherback turtles undertake long migrations across ocean basins from subtropical and tropical nesting beaches to productive frontal areas. Migration between two nesting seasons can last 2 or 3 years, a time period termed the remigration interval (RI). Recent satellite transmitter data revealed that Atlantic leatherbacks follow two major dispersion patterns after nesting season, through the North Gulf Stream area or more eastward across the North Equatorial Current. However, information on the whole RI is lacking, precluding the accurate identification of feeding areas where conservation measures may need to be applied. Using stable isotopes as dietary tracers we determined the characteristics of feeding grounds of leatherback females nesting in French Guiana. During migration, 3-year RI females differed from 2-year RI females in their isotope values, implying differences in their choice of feeding habitats (offshore vs. more coastal) and foraging latitude (North Atlantic vs. West African coasts, respectively). Egg-yolk and blood isotope values are correlated in nesting females, indicating that egg analysis is a useful tool for assessing isotope values in these turtles, including adults when not available. Our results complement previous data on turtle movements during the first year following the nesting season, integrating the diet consumed during the year before nesting. We suggest that the French Guiana leatherback population segregates into two distinct isotopic groupings, and highlight the urgent need to determine the feeding habitats of the turtle in the Atlantic in order to protect this species from incidental take by commercial fisheries. Our results also emphasize the use of eggs, a less-invasive sampling

  14. Laser isotope separation of erbium and other isotopes

    DOEpatents

    Haynam, C.A.; Worden, E.F.

    1995-08-22

    Laser isotope separation is accomplished using at least two photoionization pathways of an isotope simultaneously, where each pathway comprises two or more transition steps. This separation method has been applied to the selective photoionization of erbium isotopes, particularly for the enrichment of {sup 167}Er. The hyperfine structure of {sup 167}Er was used to find two three-step photoionization pathways having a common upper energy level. 3 figs.

  15. Raman scattering method and apparatus for measuring isotope ratios and isotopic abundances

    DOEpatents

    Harney, Robert C.; Bloom, Stewart D.

    1978-01-01

    Raman scattering is used to measure isotope ratios and/or isotopic abundances. A beam of quasi-monochromatic photons is directed onto the sample to be analyzed, and the resulting Raman-scattered photons are detected and counted for each isotopic species of interest. These photon counts are treated mathematically to yield the desired isotope ratios or isotopic abundances.

  16. Statistical clumped isotope signatures

    PubMed Central

    Röckmann, T.; Popa, M. E.; Krol, M. C.; Hofmann, M. E. G.

    2016-01-01

    High precision measurements of molecules containing more than one heavy isotope may provide novel constraints on element cycles in nature. These so-called clumped isotope signatures are reported relative to the random (stochastic) distribution of heavy isotopes over all available isotopocules of a molecule, which is the conventional reference. When multiple indistinguishable atoms of the same element are present in a molecule, this reference is calculated from the bulk (≈average) isotopic composition of the involved atoms. We show here that this referencing convention leads to apparent negative clumped isotope anomalies (anti-clumping) when the indistinguishable atoms originate from isotopically different populations. Such statistical clumped isotope anomalies must occur in any system where two or more indistinguishable atoms of the same element, but with different isotopic composition, combine in a molecule. The size of the anti-clumping signal is closely related to the difference of the initial isotope ratios of the indistinguishable atoms that have combined. Therefore, a measured statistical clumped isotope anomaly, relative to an expected (e.g. thermodynamical) clumped isotope composition, may allow assessment of the heterogeneity of the isotopic pools of atoms that are the substrate for formation of molecules. PMID:27535168

  17. Hounsfield unit density accurately predicts ESWL success.

    PubMed

    Magnuson, William J; Tomera, Kevin M; Lance, Raymond S

    2005-01-01

    Extracorporeal shockwave lithotripsy (ESWL) is a commonly used non-invasive treatment for urolithiasis. Helical CT scans provide much better and detailed imaging of the patient with urolithiasis including the ability to measure density of urinary stones. In this study we tested the hypothesis that density of urinary calculi as measured by CT can predict successful ESWL treatment. 198 patients were treated at Alaska Urological Associates with ESWL between January 2002 and April 2004. Of these 101 met study inclusion with accessible CT scans and stones ranging from 5-15 mm. Follow-up imaging demonstrated stone freedom in 74.2%. The overall mean Houndsfield density value for stone-free compared to residual stone groups were significantly different ( 93.61 vs 122.80 p < 0.0001). We determined by receiver operator curve (ROC) that HDV of 93 or less carries a 90% or better chance of stone freedom following ESWL for upper tract calculi between 5-15mm.

  18. Can single empirical algorithms accurately predict inland shallow water quality status from high resolution, multi-sensor, multi-temporal satellite data?

    NASA Astrophysics Data System (ADS)

    Theologou, I.; Patelaki, M.; Karantzalos, K.

    2015-04-01

    Assessing and monitoring water quality status through timely, cost effective and accurate manner is of fundamental importance for numerous environmental management and policy making purposes. Therefore, there is a current need for validated methodologies which can effectively exploit, in an unsupervised way, the enormous amount of earth observation imaging datasets from various high-resolution satellite multispectral sensors. To this end, many research efforts are based on building concrete relationships and empirical algorithms from concurrent satellite and in-situ data collection campaigns. We have experimented with Landsat 7 and Landsat 8 multi-temporal satellite data, coupled with hyperspectral data from a field spectroradiometer and in-situ ground truth data with several physico-chemical and other key monitoring indicators. All available datasets, covering a 4 years period, in our case study Lake Karla in Greece, were processed and fused under a quantitative evaluation framework. The performed comprehensive analysis posed certain questions regarding the applicability of single empirical models across multi-temporal, multi-sensor datasets towards the accurate prediction of key water quality indicators for shallow inland systems. Single linear regression models didn't establish concrete relations across multi-temporal, multi-sensor observations. Moreover, the shallower parts of the inland system followed, in accordance with the literature, different regression patterns. Landsat 7 and 8 resulted in quite promising results indicating that from the recreation of the lake and onward consistent per-sensor, per-depth prediction models can be successfully established. The highest rates were for chl-a (r2=89.80%), dissolved oxygen (r2=88.53%), conductivity (r2=88.18%), ammonium (r2=87.2%) and pH (r2=86.35%), while the total phosphorus (r2=70.55%) and nitrates (r2=55.50%) resulted in lower correlation rates.

  19. Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that long-range LD is a major contributing factor.

    PubMed

    Vallejo, Roger L; Silva, Rafael M O; Evenhuis, Jason P; Gao, Guangtu; Liu, Sixin; Parsons, James E; Martin, Kyle E; Wiens, Gregory D; Lourenco, Daniela A L; Leeds, Timothy D; Palti, Yniv

    2018-06-05

    Previously accurate genomic predictions for Bacterial cold water disease (BCWD) resistance in rainbow trout were obtained using a medium-density single nucleotide polymorphism (SNP) array. Here, the impact of lower-density SNP panels on the accuracy of genomic predictions was investigated in a commercial rainbow trout breeding population. Using progeny performance data, the accuracy of genomic breeding values (GEBV) using 35K, 10K, 3K, 1K, 500, 300 and 200 SNP panels as well as a panel with 70 quantitative trait loci (QTL)-flanking SNP was compared. The GEBVs were estimated using the Bayesian method BayesB, single-step GBLUP (ssGBLUP) and weighted ssGBLUP (wssGBLUP). The accuracy of GEBVs remained high despite the sharp reductions in SNP density, and even with 500 SNP accuracy was higher than the pedigree-based prediction (0.50-0.56 versus 0.36). Furthermore, the prediction accuracy with the 70 QTL-flanking SNP (0.65-0.72) was similar to the panel with 35K SNP (0.65-0.71). Genomewide linkage disequilibrium (LD) analysis revealed strong LD (r 2  ≥ 0.25) spanning on average over 1 Mb across the rainbow trout genome. This long-range LD likely contributed to the accurate genomic predictions with the low-density SNP panels. Population structure analysis supported the hypothesis that long-range LD in this population may be caused by admixture. Results suggest that lower-cost, low-density SNP panels can be used for implementing genomic selection for BCWD resistance in rainbow trout breeding programs. © 2018 The Authors. This article is a U.S. Government work and is in the public domain in the USA. Journal of Animal Breeding and Genetics published by Blackwell Verlag GmbH.

  20. A new method of tree xylem water extraction for isotopic analysis

    NASA Astrophysics Data System (ADS)

    Gierke, C.; Newton, B. T.

    2011-12-01

    The Sacramento Mountain Watershed Study in the southern Sacramento Mountains of New Mexico is designed to assess the forest restoration technique of tree thinning in mountain watersheds as an effective method of increasing local and regional groundwater recharge. The project is using a soil water balance approach to quantify the partitioning of local precipitation within this watershed before and after thinning trees. Understanding what sources trees extract their water from (e.g. shallow groundwater, unsaturated fractured bedrock, and soils) is difficult due to a complex hydrologic system and heterogeneous distribution of soil thicknesses. However, in order to accurately quantify the soil water balance and to assess how thinning trees will affect this water balance, it is important determine the sources from which trees extract their water. We plan to use oxygen and hydrogen stable isotopic analysis of various end member waters to identify these different sources. We are in the process of developing a new method of determining the isotopic composition of tree water that has several advantages over conventional methods. Within the tree there is the xylem which transports water from the roots to the leaves and the phloem which transports starches and sugars in a water media throughout the tree. Previous studies have shown that the isotopic composition of xylem water accurately reflects that of source water, while phloem water has undergone isotopic fractionation during photosynthesis and metabolism. The distillation of water from twigs, which is often used to extract tree water for isotopic analysis, is very labor intensive. Other disadvantages to distillation methods include possible fractionation due to phase changes and the possible extraction of fractionated phloem waters. Employing a new mixing method, the composition of the twig water (TW) can be determined by putting twigs of unknown isotopic water composition into waters of known compositions or initial

  1. Estimation and Validation of \\delta18O Global Distribution with Rayleigh-type two Dimensional Isotope Circulation Model

    NASA Astrophysics Data System (ADS)

    Yoshimura, K.; Oki, T.; Ohte, N.; Kanae, S.; Ichiyanagi, K.

    2004-12-01

    A simple water isotope circulation model on a global scale that includes a Rayleigh equation and the use of _grealistic_h external meteorological forcings estimates short-term variability of precipitation 18O. The results are validated by Global Network of Isotopes in Precipitation (GNIP) monthly observations and by daily observations at three sites in Thailand. This good agreement highlights the importance of large scale transport and mixing of vapor masses as a control factor for spatial and temporal variability of precipitation isotopes, rather than in-cloud micro processes. It also indicates the usefulness of the model and the isotopes observation databases for evaluation of two-dimensional atmospheric water circulation fields in forcing datasets. In this regard, two offline simulations for 1978-1993 with major reanalyses, i.e. NCEP and ERA15, were implemented, and the results show that, over Europe ERA15 better matched observations at both monthly and interannual time scales, mainly owing to better precipitation fields in ERA15, while in the tropics both produced similarly accurate isotopic fields. The isotope analyses diagnose accuracy of two-dimensional water circulation fields in datasets with a particular focus on precipitation processes.

  2. Using stable isotopes to resolve eco-hydrological dynamics of soil-plant-atmosphere feedbacks

    NASA Astrophysics Data System (ADS)

    Dubbert, M.; Piayda, A.; Kübert, A.; Cuntz, M.; Werner, C.

    2016-12-01

    Water is the main driver of ecosystem productivity in most terrestrial ecosystems worldwide. Extreme events are predicted to increase in frequency in many regions and dynamic responses in soil-vegetation-atmosphere feedbacks play a privotal role in understanding the ecosystem water balance and functioning. In this regard, more interdisciplinary approaches, bridging hydrology, ecophysiology and atmospheric sciences are needed and particularly water stable isotopes are a powerful tracer of water transfer in soils and at the soil-plant interface (Werner and Dubbert 2016). Here, we present observations 2 different ecosystems. Water fluxes, atmospheric concentrations and their isotopic compositions were measured using laser spectroscopy. Soil moisture and its isotopic composition in several depths as well as further water sources in the ecosystem were monitored throughout the year. Using these isotopic approaches we disentangled soil-plant-atmosphere feedback processes controlling the ecosystem water cycle including vegetation effects on soil water infiltration and distribution, event water use of vegetation and soil fluxes, vegetational soil water uptake depths plasticity and partitioning of ecosystem water fluxes. In this regard, we review current strategies of ET partitioning and highlight pitfalls in the presented strategies (Dubbert et al. 2013, Dubbert et al.2014a). We demonstrate that vegetation strongly influenced water cycling, altering infiltration and distribution of precipitation. In conclusion, application of stable water isotope tracers delivers a process based understanding of interactions between soil, understorey and trees governing ecosystem water cycling necessary for prediction of climate change impact on ecosystem productivity and vulnerability. ReferencesDubbert, M. et al. (2013): Partitioning evapotranspiration - Testing the Craig and Gordon model with field measurements of oxygen isotope ratios of evaporative fluxes. Journal of Hydrology Dubbert

  3. Compact determination of hydrogen isotopes

    DOE PAGES

    Robinson, David

    2017-04-06

    Scanning calorimetry of a confined, reversible hydrogen sorbent material has been previously proposed as a method to determine compositions of unknown mixtures of diatomic hydrogen isotopologues and helium. Application of this concept could result in greater process knowledge during the handling of these gases. Previously published studies have focused on mixtures that do not include tritium. This paper focuses on modeling to predict the effect of tritium in mixtures of the isotopologues on a calorimetry scan. Furthermore, the model predicts that tritium can be measured with a sensitivity comparable to that observed for hydrogen-deuterium mixtures, and that under so memore » conditions, it may be possible to determine the atomic fractions of all three isotopes in a gas mixture.« less

  4. Isotope shift, nonlinearity of King plots, and the search for new particles

    NASA Astrophysics Data System (ADS)

    Flambaum, V. V.; Geddes, A. J.; Viatkina, A. V.

    2018-03-01

    We derive a mean-field relativistic formula for the isotope shift of an electronic energy level for arbitrary angular momentum; we then use it to predict the spectra of superheavy metastable neutron-rich isotopes belonging to the hypothetical island of stability. Our results may be applied to the search for superheavy atoms in astrophysical spectra using the known values of the transition frequencies for the neutron-deficient isotopes produced in the laboratory. An example of a relevant astrophysical system may be the spectra of the Przybylski's star where superheavy elements up to Z =99 have been possibly identified. In addition, it has been recently suggested to use the measurements of King plot nonlinearity in a search for hypothetical new light bosons. On the other hand, one can find the nonlinear corrections to the King plot arising already in the standard model framework. We investigate contributions to the nonlinearity arising from relativistic effects in the isotope field shift, the nuclear polarizability, and many-body effects. It is found that the nuclear polarizability contribution can lead to the significant deviation of the King plot from linearity. Therefore, the measurements of the nonlinearity of King plots may be applied to obtain the nuclear polarizability change between individual isotopes. We then proceed with providing a rough analytical estimate of the nonlinearity arising solely from the effect of a hypothetical scalar boson. Our predictions give theoretical limitations on the sensitivity of the search for new interactions and should help to identify the most suitable atoms for corresponding experiments.

  5. Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo

    PubMed Central

    Siepel, Adam; Lis, John T.

    2012-01-01

    DNA sequence and local chromatin landscape act jointly to determine transcription factor (TF) binding intensity profiles. To disentangle these influences, we developed an experimental approach, called protein/DNA binding followed by high-throughput sequencing (PB–seq), that allows the binding energy landscape to be characterized genome-wide in the absence of chromatin. We applied our methods to the Drosophila Heat Shock Factor (HSF), which inducibly binds a target DNA sequence element (HSE) following heat shock stress. PB–seq involves incubating sheared naked genomic DNA with recombinant HSF, partitioning the HSF–bound and HSF–free DNA, and then detecting HSF–bound DNA by high-throughput sequencing. We compared PB–seq binding profiles with ones observed in vivo by ChIP–seq and developed statistical models to predict the observed departures from idealized binding patterns based on covariates describing the local chromatin environment. We found that DNase I hypersensitivity and tetra-acetylation of H4 were the most influential covariates in predicting changes in HSF binding affinity. We also investigated the extent to which DNA accessibility, as measured by digital DNase I footprinting data, could be predicted from MNase–seq data and the ChIP–chip profiles for many histone modifications and TFs, and found GAGA element associated factor (GAF), tetra-acetylation of H4, and H4K16 acetylation to be the most predictive covariates. Lastly, we generated an unbiased model of HSF binding sequences, which revealed distinct biophysical properties of the HSF/HSE interaction and a previously unrecognized substructure within the HSE. These findings provide new insights into the interplay between the genomic sequence and the chromatin landscape in determining transcription factor binding intensity. PMID:22479205

  6. A link prediction approach to cancer drug sensitivity prediction.

    PubMed

    Turki, Turki; Wei, Zhi

    2017-10-03

    Predicting the response to a drug for cancer disease patients based on genomic information is an important problem in modern clinical oncology. This problem occurs in part because many available drug sensitivity prediction algorithms do not consider better quality cancer cell lines and the adoption of new feature representations; both lead to the accurate prediction of drug responses. By predicting accurate drug responses to cancer, oncologists gain a more complete understanding of the effective treatments for each patient, which is a core goal in precision medicine. In this paper, we model cancer drug sensitivity as a link prediction, which is shown to be an effective technique. We evaluate our proposed link prediction algorithms and compare them with an existing drug sensitivity prediction approach based on clinical trial data. The experimental results based on the clinical trial data show the stability of our link prediction algorithms, which yield the highest area under the ROC curve (AUC) and are statistically significant. We propose a link prediction approach to obtain new feature representation. Compared with an existing approach, the results show that incorporating the new feature representation to the link prediction algorithms has significantly improved the performance.

  7. Insights into deep-time terrestrial carbon cycle processes from modern plant isotope ecology

    NASA Astrophysics Data System (ADS)

    Sheldon, N. D.; Smith, S. Y.

    2012-12-01

    While the terrestrial biosphere and soils contain much of the readily exchangeable carbon on Earth, how those reservoirs function on long time scales and at times of higher atmospheric CO2 and higher temperatures is poorly understood, which limits our ability to make accurate future predictions of their response to anthropogenic change. Recent data compilation efforts have outlined the response of plant carbon isotope compositions to a variety of environmental factors including precipitation amount and timing, elevation, and latitude. The compilations involve numerous types of plants, typically only found at a limited number of climatic conditions. Here, we expand on those efforts by examining the isotopic response of specific plant groups found both globally and across environmental gradients including: 1) ginkgo, 2) conifers, and 3) C4 grasses. Ginkgo is presently widely distributed as a cultivated plant and the ginkgoalean fossil record spans from the Permian to the present, making it an ideal model organism to understand climatic influence on carbon cycling both in modern and ancient settings. Ginkgo leaves have been obtained from a range of precipitation conditions (400-2200 mm yr-1), including dense sampling from individuals and populations in both Mediterranean and temperate climate areas and samples of different organs and developmental stages. Ginkgo carbon isotope results plot on the global C3 plant array, are consistent among trees at single sites, among plant organs, and among development stages, making ginkgo a robust recorder of both climatic conditions and atmospheric δ13C. In contrast, a climate-carbon isotope transect in Arizona highlights that conifers (specifically, pine and juniper) record large variability between organs and have a very different δ13C slope as a function of climate than the global C3 plant array, while C4 plants have a slope with the opposite sign as a function of climate. This has a number of implications for paleo

  8. Evaluation of the impact of matrix effect on quantification of pesticides in foods by gas chromatography-mass spectrometry using isotope-labeled internal standards.

    PubMed

    Yarita, Takashi; Aoyagi, Yoshie; Otake, Takamitsu

    2015-05-29

    The impact of the matrix effect in GC-MS quantification of pesticides in food using the corresponding isotope-labeled internal standards was evaluated. A spike-and-recovery study of nine target pesticides was first conducted using paste samples of corn, green soybean, carrot, and pumpkin. The observed analytical values using isotope-labeled internal standards were more accurate for most target pesticides than that obtained using the external calibration method, but were still biased from the spiked concentrations when a matrix-free calibration solution was used for calibration. The respective calibration curves for each target pesticide were also prepared using matrix-free calibration solutions and matrix-matched calibration solutions with blank soybean extract. The intensity ratio of the peaks of most target pesticides to that of the corresponding isotope-labeled internal standards was influenced by the presence of the matrix in the calibration solution; therefore, the observed slope varied. The ratio was also influenced by the type of injection method (splitless or on-column). These results indicated that matrix-matching of the calibration solution is required for very accurate quantification, even if isotope-labeled internal standards were used for calibration. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Systematics of isotopic production cross sections from interactions of relativistic 40Ca in hydrogen

    NASA Astrophysics Data System (ADS)

    Chen, C.-X.; Albergo, S.; Caccia, Z.; Costa, S.; Crawford, H. J.; Cronqvist, M.; Engelage, J.; Greiner, L.; Guzik, T. G.; Insolia, A.; Knott, C. N.; Lindstrom, P. J.; McMahon, M.; Mitchell, J. W.; Potenza, R.; Russo, G. V.; Soutoul, A.; Testard, O.; Tull, C. E.; Tuvé, C.; Waddington, C. J.; Webber, W. R.; Wefel, J. P.

    1997-09-01

    The isotopic production cross sections for 40Ca projectiles at 357, 565, and 763 MeV/nucleon interacting in a liquid hydrogen target have been measured by the Transport Collaboration at the LBL HISS facility. The systematics of these cross sections are studied, and the results indicate that nuclear structure effects are present in the isotope production process during the relativistic collisions. The newly measured cross sections are also compared with those predicted by semiempirical and parametric formulas, but the predictions do not fully describe the systematics such as the energy dependence. The consequences of the cross section systematics in galactic cosmic ray studies are also discussed.

  10. FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

    PubMed

    Budowski-Tal, Inbal; Nov, Yuval; Kolodny, Rachel

    2010-02-23

    Fast identification of protein structures that are similar to a specified query structure in the entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We present FragBag: An ultrafast and accurate method for comparing protein structures. We describe a protein structure by the collection of its overlapping short contiguous backbone segments, and discretize this set using a library of fragments. Then, we succinctly represent the protein as a "bags-of-fragments"-a vector that counts the number of occurrences of each fragment-and measure the similarity between two structures by the similarity between their vectors. Our representation has two additional benefits: (i) it can be used to construct an inverted index, for implementing a fast structural search engine of the entire PDB, and (ii) one can specify a structure as a collection of substructures, without combining them into a single structure; this is valuable for structure prediction, when there are reliable predictions only of parts of the protein. We use receiver operating characteristic curve analysis to quantify the success of FragBag in identifying neighbor candidate sets in a dataset of over 2,900 structures. The gold standard is the set of neighbors found by six state of the art structural aligners. Our best FragBag library finds more accurate candidate sets than the three other filter methods: The SGM, PRIDE, and a method by Zotenko et al. More interestingly, FragBag performs on a par with the computationally expensive, yet highly trusted structural aligners STRUCTAL and CE.

  11. Accurate interatomic force fields via machine learning with covariant kernels

    NASA Astrophysics Data System (ADS)

    Glielmo, Aldo; Sollich, Peter; De Vita, Alessandro

    2017-06-01

    We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian process (GP) regression. This is based on matrix-valued kernel functions, on which we impose the requirements that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such covariant GP kernels can be obtained by integration over the elements of the rotation group SO (d ) for the relevant dimensionality d . Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni, Fe, and Si crystalline systems.

  12. Diffusion of multi-isotopic chemical species in molten silicates

    NASA Astrophysics Data System (ADS)

    Watkins, James M.; Liang, Yan; Richter, Frank; Ryerson, Frederick J.; DePaolo, Donald J.

    2014-08-01

    Diffusion experiments in a simplified Na2O-CaO-SiO2 liquid system are used to develop a general formulation for the fractionation of Ca isotopes during liquid-phase diffusion. Although chemical diffusion is a well-studied process, the mathematical description of the effects of diffusion on the separate isotopes of a chemical element is surprisingly underdeveloped and uncertain. Kinetic theory predicts a mass dependence on isotopic mobility, but it is unknown how this translates into a mass dependence on effective binary diffusion coefficients, or more generally, the chemical diffusion coefficients that are housed in a multicomponent diffusion matrix. Our experiments are designed to measure Ca mobility, effective binary diffusion coefficients, the multicomponent diffusion matrix, and the effects of chemical diffusion on Ca isotopes in a liquid of single composition. We carried out two chemical diffusion experiments and one self-diffusion experiment, all at 1250 °C and 0.7 GPa and using a bulk composition for which other information is available from the literature. The self-diffusion experiment is used to determine the mobility of Ca in the absence of diffusive fluxes of other liquid components. The chemical diffusion experiments are designed to determine the effect on Ca isotope fractionation of changing the counter-diffusing component from fast-diffusing Na2O to slow-diffusing SiO2. When Na2O is the main counter-diffusing species, CaO diffusion is fast and larger Ca isotopic effects are generated. When SiO2 is the main counter-diffusing species, CaO diffusion is slow and smaller Ca isotopic effects are observed. In both experiments, the liquid is initially isotopically homogeneous, and during the experiment Ca isotopes become fractionated by diffusion. The results are used as a test of a new general expression for the diffusion of isotopes in a multicomponent liquid system that accounts for both self diffusion and the effects of counter-diffusing species. Our

  13. ISOTOPE CONVERSION DEVICE

    DOEpatents

    Wigner, E.P.; Young, G.J.; Ohlinger, L.A.

    1957-12-01

    This patent relates to nuclear reactors of tbe type utilizing a liquid fuel and designed to convert a non-thermally fissionable isotope to a thermally fissionable isotope by neutron absorption. A tank containing a reactive composition of a thermally fissionable isotope dispersed in a liquid moderator is disposed within an outer tank containing a slurry of a non-thermally fissionable isotope convertible to a thermally fissionable isotope by neutron absorption. A control rod is used to control the chain reaction in the reactive composition and means are provided for circulating and cooling the reactive composition and slurry in separate circuits.

  14. Partitioning the effects of Global Warming on the Hydrological Cycle with Stable Isotopes in Water Vapor

    NASA Astrophysics Data System (ADS)

    Dee, S. G.; Russell, J. M.; Nusbaumer, J. M.; Konecky, B. L.; Buenning, N. H.; Lee, J. E.; Noone, D.

    2016-12-01

    General circulation models (GCMs) suggest that much of the global hydrological cycle's response to anthropogenic warming will be caused by increased lower-tropospheric water vapor concentrations and associated feedbacks. However, fingerprinting changes in the global hydrological cycle due to anthropogenic warming remains challenging. Held and Soden (2006) predicted that as lower-tropospheric water vapor increases, atmospheric circulation will weaken as climate warms to maintain the surface energy budget. Unfortunately, the strength of this feedback and the fallout for other branches of the hydrological cycle is difficult to constrain in situ or with GCMs alone. We demonstrate the utility of stable hydrogen isotope ratios in atmospheric water vapor to quantitatively trace changes in atmospheric circulation and convective mass flux in a warming world. We compare water isotope-enabled GCM experiments for control (present-day) CO2 vs. high CO2(2x, 4x) atmospheres in two GCMs, IsoGSM and iCAM5. We evaluate changes in the distribution of water vapor, vertical velocity (omega), and the stream function between these experiments in order to identify spatial patterns of circulation change over the tropical Pacific (where vertical motion is strong) and map the δD of water vapor associated with atmospheric warming. We also probe the simulations to isolate isotopic signatures associated with water vapor residence time, precipitation efficiency, divergence, and cloud physics. We show that there are robust mechanisms that moisten the troposphere and weaken convective mass flux, and that these mechanisms can be tracked using the δD of water vapor. Further, we find that these responses are most pronounced in the upper troposphere. These findings provide a framework to develop new metrics for the detection of global warming impacts to the hydrological cycle. Further, currently available satellite missions measure δD in the atmospheric boundary layer, the free atmosphere, or the

  15. Relationships between tree height and carbon isotope discrimination

    Treesearch

    Nate G. McDowell; Barbara J. Bond; Lee T. Dickman; Michael G. Ryan; David Whitehead

    2011-01-01

    Understanding how tree size impacts leaf- and crown-level gas exchange is essential to predicting forest yields and carbon and water budgets. The stable carbon isotope ratio of organic matter has been used to examine the relationship of gas exchange to tree size for a host of species because it carries a temporally integrated signature of foliar photosynthesis and...

  16. Daily Variation of Isotope Ratios in Mars Atmospheric Carbon Dioxide

    NASA Astrophysics Data System (ADS)

    Livengood, Timothy A.; Kostiuk, Theodor; Kolasinski, John R.; Hewagama, Tilak; Henning, Wade G.; Sornig, Manuela; Stangier, Tobias; Krause, Pia; Sonnabend, Guido; Mahaffy, Paul R.

    2014-11-01

    contemporary in situ measurements by the Curiosity rover to investigate the degree of agreement between in situ and remote methods and potentially to calibrate the spectroscopic constants required to accurately evaluate isotope ratios all over Mars.

  17. Determining Oxygen Isotopic Fractionation between the ferrous sulfate, melanterite, and aqueous sulfate

    NASA Astrophysics Data System (ADS)

    Shulaker, D. Z.; Kohl, I.; Coleman, M. L.

    2011-12-01

    Studying regions on Earth that are analogous to Mars serve as case studies for studying astrobiology and planetary surface rock formation processes. Rio Tinto, Spain is very rich in iron sulfates, and has an environment that is possibly very similar to the former environment on Mars. Certain bacteria play significant roles in accelerating pyrite oxidation rates, the products of which contribute to the formation of ferrous sulfates, such as melanterite. During mineral crystallization in an aqueous solution, there are systematic isotopic differences between dissolved species and solid phases. Quantifying this fractionation enables isotopic analysis to be used to trace the original isotopic signature of the dissolved species. Isotope fractionation has been determined for minerals such as gypsum and epsomite, and from these results and theoretical predictions, it is expected that melanterite, a mineral potentially found on Mars, would be more enriched in oxygen-18 relative to the aqueous solution from which it crystallized.Thus, determining the oxygen-18 isotopic fractionation between melanterite and dissolved sulfate has many potential benefits for understanding surface processes on Mars and its past environment. To investigate the oxygen isotope fractionation for melanterite, acidic aqueous solutions saturated with dissolved hydrated ferrous sulfate were evaporated at 25 deg C and 40 deg C and under different conditions to induce different evaporation rates. During evaporation, the aqueous solution and crystallized melanterite were sampled at different stages. Oxygen-18 isotopic compositions were then measured. However, the fractionations observed in the experiments were opposite from predictions. At 25 deg C without enhanced evaporation, the dissolved sulfate was +5.5 per mil relative to the solid, while at 40 deg C it was +4.3 per mil. With enhanced evaporation, fractionation was +2.1 per mil, while at 40 deg C it was +3.6 per mil. In addition, at 40 deg C

  18. Electron linac for medical isotope production with improved energy efficiency and isotope recovery

    DOEpatents

    Noonan, John; Walters, Dean; Virgo, Matt; Lewellen, John

    2015-09-08

    A method and isotope linac system are provided for producing radio-isotopes and for recovering isotopes. The isotope linac is an energy recovery linac (ERL) with an electron beam being transmitted through an isotope-producing target. The electron beam energy is recollected and re-injected into an accelerating structure. The ERL provides improved efficiency with reduced power requirements and provides improved thermal management of an isotope target and an electron-to-x-ray converter.

  19. A Guide for Assessing Biodegradation and Source Identification of Organic Groundwater Contaminants Using Compound Specific Isotope Analysis (CSIA)

    EPA Science Inventory

    When organic contaminants are degraded in the environment, the ratio of stable isotopes will often change, and the extent of degradation can be recognized and predicted from the change in the ratio of stable isotopes. Recent advances in analytical chemistry make it possible to p...

  20. Knotty: Efficient and Accurate Prediction of Complex RNA Pseudoknot Structures.

    PubMed

    Jabbari, Hosna; Wark, Ian; Montemagno, Carlo; Will, Sebastian

    2018-06-01

    The computational prediction of RNA secondary structure by free energy minimization has become an important tool in RNA research. However in practice, energy minimization is mostly limited to pseudoknot-free structures or rather simple pseudoknots, not covering many biologically important structures such as kissing hairpins. Algorithms capable of predicting sufficiently complex pseudoknots (for sequences of length n) used to have extreme complexities, e.g. Pknots (Rivas and Eddy, 1999) has O(n6) time and O(n4) space complexity. The algorithm CCJ (Chen et al., 2009) dramatically improves the asymptotic run time for predicting complex pseudoknots (handling almost all relevant pseudoknots, while being slightly less general than Pknots), but this came at the cost of large constant factors in space and time, which strongly limited its practical application (∼200 bases already require 256GB space). We present a CCJ-type algorithm, Knotty, that handles the same comprehensive pseudoknot class of structures as CCJ with improved space complexity of Θ(n3 + Z)-due to the applied technique of sparsification, the number of "candidates", Z, appears to grow significantly slower than n4 on our benchmark set (which include pseudoknotted RNAs up to 400 nucleotides). In terms of run time over this benchmark, Knotty clearly outperforms Pknots and the original CCJ implementation, CCJ 1.0; Knotty's space consumption fundamentally improves over CCJ 1.0, being on a par with the space-economic Pknots. By comparing to CCJ 2.0, our unsparsified Knotty variant, we demonstrate the isolated effect of sparsification. Moreover, Knotty employs the state-of-the-art energy model of "HotKnots DP09", which results in superior prediction accuracy over Pknots. Our software is available at https://github.com/HosnaJabbari/Knotty. will@tbi.unvie.ac.at. Supplementary data are available at Bioinformatics online.

  1. Accurate Prediction of Protein Contact Maps by Coupling Residual Two-Dimensional Bidirectional Long Short-Term Memory with Convolutional Neural Networks.

    PubMed

    Hanson, Jack; Paliwal, Kuldip; Litfin, Thomas; Yang, Yuedong; Zhou, Yaoqi

    2018-06-19

    Accurate prediction of a protein contact map depends greatly on capturing as much contextual information as possible from surrounding residues for a target residue pair. Recently, ultra-deep residual convolutional networks were found to be state-of-the-art in the latest Critical Assessment of Structure Prediction techniques (CASP12, (Schaarschmidt et al., 2018)) for protein contact map prediction by attempting to provide a protein-wide context at each residue pair. Recurrent neural networks have seen great success in recent protein residue classification problems due to their ability to propagate information through long protein sequences, especially Long Short-Term Memory (LSTM) cells. Here we propose a novel protein contact map prediction method by stacking residual convolutional networks with two-dimensional residual bidirectional recurrent LSTM networks, and using both one-dimensional sequence-based and two-dimensional evolutionary coupling-based information. We show that the proposed method achieves a robust performance over validation and independent test sets with the Area Under the receiver operating characteristic Curve (AUC)>0.95 in all tests. When compared to several state-of-the-art methods for independent testing of 228 proteins, the method yields an AUC value of 0.958, whereas the next-best method obtains an AUC of 0.909. More importantly, the improvement is over contacts at all sequence-position separations. Specifically, a 8.95%, 5.65% and 2.84% increase in precision were observed for the top L∕10 predictions over the next best for short, medium and long-range contacts, respectively. This confirms the usefulness of ResNets to congregate the short-range relations and 2D-BRLSTM to propagate the long-range dependencies throughout the entire protein contact map 'image'. SPOT-Contact server url: http://sparks-lab.org/jack/server/SPOT-Contact/. Supplementary data is available at Bioinformatics online.

  2. The molecular physics of photolytic fractionation of sulfur and oxygen isotopes in planetary atmospheres (Invited)

    NASA Astrophysics Data System (ADS)

    Johnson, M. S.; Schmidt, J. A.; Hattori, S.; Danielache, S.; Meusinger, C.; Schinke, R.; Ueno, Y.; Nanbu, S.; Kjaergaard, H. G.; Yoshida, N.

    2013-12-01

    Atmospheric photochemistry is able to produce large mass independent anomalies in atmospheric trace gases that can be found in geological and cryospheric records. This talk will present theoretical and experimental investigations of the molecular mechanisms producing photolytic fractionation of isotopes with special attention to sulfur and oxygen. The zero point vibrational energy (ZPE) shift and reflection principle theories are starting points for estimating isotopic fractionation, but these models ignore effects arising from isotope-dependent changes in couplings between surfaces, excited state dynamics, line densities and hot band populations. The isotope-dependent absorption spectra of the isotopologues of HCl, N2O, OCS, CO2 and SO2 have been examined in a series of papers and these results are compared with experiment and ZPE/reflection principle models. Isotopic fractionation in planetary atmospheres has many interesting applications. The UV absorption of CO2 is the basis of photochemistry in the CO2-rich atmospheres of the ancient Earth, and of Mars and Venus. For the first time we present accurate temperature and isotope dependent CO2 absorption cross sections with important implications for photolysis rates of SO2 and H2O, and the production of a mass independent anomaly in the Ox reservoir. Experimental and theoretical results for OCS have implications for the modern stratospheric sulfur budget. The absorption bands of SO2 are complex with rich structure producing isotopic fractionation in photolysis and photoexcitation.

  3. Local Debonding and Fiber Breakage in Composite Materials Modeled Accurately

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.; Arnold, Steven M.

    2001-01-01

    A prerequisite for full utilization of composite materials in aerospace components is accurate design and life prediction tools that enable the assessment of component performance and reliability. Such tools assist both structural analysts, who design and optimize structures composed of composite materials, and materials scientists who design and optimize the composite materials themselves. NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) software package (http://www.grc.nasa.gov/WWW/LPB/mac) addresses this need for composite design and life prediction tools by providing a widely applicable and accurate approach to modeling composite materials. Furthermore, MAC/GMC serves as a platform for incorporating new local models and capabilities that are under development at NASA, thus enabling these new capabilities to progress rapidly to a stage in which they can be employed by the code's end users.

  4. Urinary Squamous Epithelial Cells Do Not Accurately Predict Urine Culture Contamination, but May Predict Urinalysis Performance in Predicting Bacteriuria.

    PubMed

    Mohr, Nicholas M; Harland, Karisa K; Crabb, Victoria; Mutnick, Rachel; Baumgartner, David; Spinosi, Stephanie; Haarstad, Michael; Ahmed, Azeemuddin; Schweizer, Marin; Faine, Brett

    2016-03-01

    The presence of squamous epithelial cells (SECs) has been advocated to identify urinary contamination despite a paucity of evidence supporting this practice. We sought to determine the value of using quantitative SECs as a predictor of urinalysis contamination. Retrospective cross-sectional study of adults (≥18 years old) presenting to a tertiary academic medical center who had urinalysis with microscopy and urine culture performed. Patients with missing or implausible demographic data were excluded (2.5% of total sample). The primary analysis aimed to determine an SEC threshold that predicted urine culture contamination using receiver operating characteristics (ROC) curve analysis. The a priori secondary analysis explored how demographic variables (age, sex, body mass index) may modify the SEC test performance and whether SECs impacted traditional urinalysis indicators of bacteriuria. A total of 19,328 records were included. ROC curve analysis demonstrated that SEC count was a poor predictor of urine culture contamination (area under the ROC curve = 0.680, 95% confidence interval [CI] = 0.671 to 0.689). In secondary analysis, the positive likelihood ratio (LR+) of predicting bacteriuria via urinalysis among noncontaminated specimens was 4.98 (95% CI = 4.59 to 5.40) in the absence of SECs, but the LR+ fell to 2.35 (95% CI = 2.17 to 2.54) for samples with more than 8 SECs/low-powered field (lpf). In an independent validation cohort, urinalysis samples with fewer than 8 SECs/lpf predicted bacteriuria better (sensitivity = 75%, specificity = 84%) than samples with more than 8 SECs/lpf (sensitivity = 86%, specificity = 70%; diagnostic odds ratio = 17.5 [14.9 to 20.7] vs. 8.7 [7.3 to 10.5]). Squamous epithelial cells are a poor predictor of urine culture contamination, but may predict poor predictive performance of traditional urinalysis measures. © 2016 by the Society for Academic Emergency Medicine.

  5. Improvement of 2,4-dinitrophenylhydrazine derivatization method for carbon isotope analysis of atmospheric acetone.

    PubMed

    Wen, Sheng; Yu, Yingxin; Guo, Songjun; Feng, Yanli; Sheng, Guoying; Wang, Xinming; Bi, Xinhui; Fu, Jiamo; Jia, Wanglu

    2006-01-01

    Through simulation experiments of atmospheric sampling, a method via 2,4-dinitrophenylhydrazine (DNPH) derivatization was developed to measure the carbon isotopic composition of atmospheric acetone. Using acetone and a DNPH reagent of known carbon isotopic compositions, the simulation experiments were performed to show that no carbon isotope fractionation occurred during the processes: the differences between the predicted and measured data of acetone-DNPH derivatives were all less than 0.5 per thousand. The results permitted the calculation of the carbon isotopic compositions of atmospheric acetone using a mass balance equation. In this method, the atmospheric acetone was collected by a DNPH-coated silica cartridge, washed out as acetone-DNPH derivatives, and then analyzed by gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS). Using this method, the first available delta13C data of atmospheric acetone are presented. Copyright 2006 John Wiley & Sons, Ltd.

  6. Gallium isotope fractionation during Ga adsorption on calcite and goethite

    NASA Astrophysics Data System (ADS)

    Yuan, Wei; Saldi, Giuseppe D.; Chen, JiuBin; Vetuschi Zuccolini, Marino; Birck, Jean-Louis; Liu, Yujie; Schott, Jacques

    2018-02-01

    Gallium (Ga) isotopic fractionation during its adsorption on calcite and goethite was investigated at 20 °C as a function of the solution pH, Ga aqueous concentration and speciation, and the solid to solution ratio. In all experiments Ga was found to be enriched in light isotopes at the solid surface with isotope fractionation △71Gasolid-solution up to -1.27‰ and -0.89‰ for calcite and goethite, respectively. Comparison of Ga isotopic data of this study with predictions for 'closed system' equilibrium and 'Rayleigh fractionation' models indicates that the experimental data are consistent with a 'closed system' equilibrium exchange between the fluid and the solid. The results of this study can be interpreted based on Ga aqueous speciation and the structure of Ga complexes formed at the solid surfaces. For calcite, Ga isotope fractionation is mainly triggered by increased Ga coordination and Ga-O bond length, which vary respectively from 4 and 1.84 Å in Ga(OH)4- to 6 and 1.94 Å in the >Ca-O-GaOH(OH2)4+ surface complex. For goethite, despite the formation of Ga hexa-coordinated >FeOGa(OH)20 surface complexes (Ga-O distances of 1.96-1.98 Å) both at acid and alkaline pH, a similar extent of isotope fractionation was found at acid and alkaline pH, suggesting that Ga(OH)4- is preferentially adsorbed on goethite for all investigated pH conditions. In addition, the observed decrease of Ga isotope fractionation magnitude observed with increasing Ga surface coverage for both calcite and goethite is likely related to the formation of Ga surface polymers and/or hydroxides with reduced Ga-O distances. This first study of Ga isotope fractionation during solid-fluid interactions suggests that the adsorption of Ga by oxides, carbonates or clay minerals could yield significant Ga isotope fractionation between secondary minerals and surficial fluids including seawater. Ga isotopes thus should help to better characterize the surficial biogeochemical cycles of gallium and its

  7. Are leaf physiological traits related to leaf water isotopic enrichment in restinga woody species?

    PubMed

    Rosado, Bruno H P; De Mattos, Eduardo A; Sternberg, Leonel Da S L

    2013-09-01

    During plant-transpiration, water molecules having the lighter stable isotopes of oxygen and hydrogen evaporate and diffuse at a faster rate through the stomata than molecules having the heavier isotopes, which cause isotopic enrichment of leaf water. Although previous models have assumed that leaf water is well-mixed and isotopically uniform, non-uniform stomatal closure, promoting different enrichments between cells, and different pools of water within leaves, due to morpho-physiological traits, might lead to inaccuracies in isotopic models predicting leaf water enrichment. We evaluate the role of leaf morpho-physiological traits on leaf water isotopic enrichment in woody species occurring in a coastal vegetation of Brazil known as restinga. Hydrogen and oxygen stable isotope values of soil, plant stem and leaf water and leaf traits were measured in six species from restinga vegetation during a drought and a wet period. Leaf water isotopic enrichment relative to stem water was more homogeneous among species during the drought in contrast to the wet period suggesting convergent responses to deal to temporal heterogeneity in water availability. Average leaf water isotopic enrichment relative to stem water during the drought period was highly correlated with relative apoplastic water content. We discuss this observation in the context of current models of leaf water isotopic enrichment as a function of the Péclet effect. We suggest that future studies should include relative apoplastic water content in isotopic models.

  8. Water isotope partitioning and ecohydrologic separation in mixed conifer forest explored with a centrifugation water extraction method

    NASA Astrophysics Data System (ADS)

    Bowers, W.; Mercer, J.; Pleasants, M.; Williams, D. G.

    2017-12-01

    Isotopic partitioning of water within soil into tightly and loosely bound fractions has been proposed to explain differences between isotopic water sources used by plants and those that contribute to streams and ground water, the basis for the "two water worlds" hypothesis. We examined the isotope ratio values of water in trees, bulk soil, mobile water collected from soil lysimeters, stream water, and GW at three different hillslopes in a mixed conifer forest in southeastern Wyoming, USA. Hillslopes differed in aspect and topographic position with corresponding differences in surface energy balance, snowmelt timing, and duration of soil moisture during the dry summer. The isotopic results support the partitioning of water within the soil; trees apparently used a different pool of water for transpiration than that recovered from soil lysimeters and the source was not resolved with the isotopic signature of the water that was extracted from bulk soil via cryogenic vacuum distillation. Separating and measuring the isotope ratios values in these pools would test the assumption that the tightly bound water within the soil has the same isotopic signature as the water transpired by the trees. We employed a centrifugation approach to separate water within the soil held at different tensions by applying stepwise increases in rotational velocity and pressures to the bulk soil samples. Effluent and the remaining water (cryogenically extracted) at each step were compared. We first applied the centrifugation method in a simple lab experiment using sandy loam soil and separate introductions of two isotopically distinct waters. We then applied the method to soil collected from the montane hillslopes. For the lab experiment, we predicted that effluents would have distinct isotopic signatures, with the last effluent and extracted water more closely representing the isotopic signature of the first water applied. For our field samples, we predicted that the isotopic signature of the

  9. Accurate abundance determinations in S stars

    NASA Astrophysics Data System (ADS)

    Neyskens, P.; Van Eck, S.; Plez, B.; Goriely, S.; Siess, L.; Jorissen, A.

    2011-12-01

    S-type stars are thought to be the first objects, during their evolution on the asymptotic giant branch (AGB), to experience s-process nucleosynthesis and third dredge-ups, and therefore to exhibit s-process signatures in their atmospheres. Until present, the modeling of these processes is subject to large uncertainties. Precise abundance determinations in S stars are of extreme importance for constraining e.g., the depth and the formation of the 13C pocket. In this paper a large grid of MARCS model atmospheres for S stars is used to derive precise abundances of key s-process elements and iron. A first estimation of the atmospheric parameters is obtained using a set of well-chosen photometric and spectroscopic indices for selecting the best model atmosphere of each S star. Abundances are derived from spectral line synthesis, using the selected model atmosphere. Special interest is paid to technetium, an element without stable isotopes. Its detection in stars is considered as the best possible signature that the star effectively populates the thermally-pulsing AGB (TP-AGB) phase of evolution. The derived Tc/Zr abundances are compared, as a function of the derived [Zr/Fe] overabundances, with AGB stellar model predictions. The computed [Zr/Fe] overabundances are in good agreement with the AGB stellar evolution model predictions, while the Tc/Zr abundances are slightly over-predicted. This discrepancy can help to set stronger constraints on nucleosynthesis and mixing mechanisms in AGB stars.

  10. The puzzle of the CNO isotope ratios in asymptotic giant branch carbon stars

    NASA Astrophysics Data System (ADS)

    Abia, C.; Hedrosa, R. P.; Domínguez, I.; Straniero, O.

    2017-03-01

    Context. The abundance ratios of the main isotopes of carbon, nitrogen and oxygen are modified by the CNO-cycle in the stellar interiors. When the different dredge-up events mix the burning material with the envelope, valuable information on the nucleosynthesis and mixing processes can be extracted by measuring these isotope ratios. Aims: Previous determinations of the oxygen isotopic ratios in asymptotic giant branch (AGB) carbon stars were at odds with the existing theoretical predictions. We aim to redetermine the oxygen ratios in these stars using new spectral analysis tools and further develop discussions on the carbon and nitrogen isotopic ratios in order to elucidate this problem. Methods: Oxygen isotopic ratios were derived from spectra in the K-band in a sample of galactic AGB carbon stars of different spectral types and near solar metallicity. Synthetic spectra calculated in local thermodynamic equillibrium (LTE) with spherical carbon-rich atmosphere models and updated molecular line lists were used. The CNO isotope ratios derived in a homogeneous way, were compared with theoretical predictions for low-mass (1.5-3 M⊙) AGB stars computed with the FUNS code assuming extra mixing both during the RGB and AGB phases. Results: For most of the stars the 16O/17O/18O ratios derived are in good agreement with theoretical predictions confirming that, for AGB stars, are established using the values reached after the first dredge-up (FDU) according to the initial stellar mass. This fact, as far as the oxygen isotopic ratios are concerned, leaves little space for the operation of any extra mixing mechanism during the AGB phase. Nevertheless, for a few stars with large 16O/17O/18O, the operation of such a mechanism might be required, although their observed 12C/13C and 14N/15N ratios would be difficult to reconcile within this scenario. Furthermore, J-type stars tend to have lower 16O/17O ratios than the normal carbon stars, as already indicated in previous studies

  11. Large-scale structure prediction by improved contact predictions and model quality assessment.

    PubMed

    Michel, Mirco; Menéndez Hurtado, David; Uziela, Karolis; Elofsson, Arne

    2017-07-15

    Accurate contact predictions can be used for predicting the structure of proteins. Until recently these methods were limited to very big protein families, decreasing their utility. However, recent progress by combining direct coupling analysis with machine learning methods has made it possible to predict accurate contact maps for smaller families. To what extent these predictions can be used to produce accurate models of the families is not known. We present the PconsFold2 pipeline that uses contact predictions from PconsC3, the CONFOLD folding algorithm and model quality estimations to predict the structure of a protein. We show that the model quality estimation significantly increases the number of models that reliably can be identified. Finally, we apply PconsFold2 to 6379 Pfam families of unknown structure and find that PconsFold2 can, with an estimated 90% specificity, predict the structure of up to 558 Pfam families of unknown structure. Out of these, 415 have not been reported before. Datasets as well as models of all the 558 Pfam families are available at http://c3.pcons.net/ . All programs used here are freely available. arne@bioinfo.se. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  12. Re-assessing the Molybdenum Isotope Composition of Pre-GOE Seawater: Evidence for Dynamic Ocean Redox

    NASA Astrophysics Data System (ADS)

    Ostrander, C. M.; Kendall, B.; Roy, M.; Romaniello, S. J.; Nunn, S. J.; Gordon, G. W.; Olson, S. L.; Lyons, T. W.; Zheng, W.; Anbar, A. D.

    2016-12-01

    Molybdenum (Mo) isotope compositions of Archean shales can provide important insights into ocean and atmosphere redox dynamics prior to the Great Oxidation Event (GOE). Unfortunately, the relatively limited Mo isotope database and small number of sample sets for Archean shales do not allow for in-depth reconstructions and specifically make it difficult to differentiate global from local effects. To accurately estimate the Mo isotope composition of Archean seawater and better investigate the systematics of local and global redox, more complete sample sets are needed. We carried out a Mo isotope analysis of the euxinic 2.65 Ga Roy Hill Shale sampled in two stratigraphically correlated cores, and revisited the well-studied euxinic 2.5 Ga Mt. McRae Shale in higher resolution. Our data show contrasting Mo isotope values in the 2.65 Ga Roy Hill Shale between near- and offshore depositional environments, with systematically heavier isotope values in the near-shore environment. High-resolution analysis of the Mt. McRae Shale yields oscillating Mo concentrations and isotope values at the cm- to dm-scale during the well-characterized "whiff of O2" interval, with the heaviest isotope values measured during euxinic deposition. Variations in the measured isotope values within each section are primarily associated with redox changes in the local depositional environment and amount of detrital content. Both non-quantitative removal of Mo associated with incorporation into non-euxinic sediments and large detrital Mo contributions shift some measured isotopic compositions toward lighter values. This is readily apparent in the near-shore Roy Hill Shale section and the Mt. McRae Shale, but may not fully explain variations observed in the offshore Roy Hill Shale deposit. Here, euxinic deposition is not accompanied by Mo enrichments or isotopic compositions as heavy as the near-shore equivalent, even after detrital correction. This disparity between the near- and offshore environment

  13. ACCURATE: Greenhouse Gas Profiles Retrieval from Combined IR-Laser and Microwave Occultation Measurements

    NASA Astrophysics Data System (ADS)

    Proschek, Veronika; Kirchengast, Gottfried; Schweitzer, Susanne; Fritzer, Johannes

    2010-05-01

    The new climate satellite concept ACCURATE (Atmospheric Climate and Chemistry in the UTLS Region And climate Trends Explorer) enables simultaneous measurement of profiles of greenhouse gases, isotopes, wind and thermodynamic variables from Low Earth Orbit (LEO) satellites. The measurement principle applied is a combination of the novel LEO-LEO infrared laser occultation (LIO) technique and the already better studied LEO-LEO microwave occultation (LMO) technique. Resulting occultation events are evenly distributed around the world, have high vertical resolution and accuracy and are stable over long time periods. The LIO uses near-monochromatic signals in the short-wave infrared range (~2-2.5 μm for ACCURATE). These signals are absorbed by various trace species in the Earth's atmosphere. Profiles of the concentration of the absorbing species can be derived from signal transmission measurements. Accurately known temperature, pressure and humidity profiles derived from simultaneously measured LMO signals are essential pre-information for the retrieval of the trace species profiles. These LMO signals lie in the microwave band region from 17-23 GHz and, optionally, 178-195 GHz. The current ACCURATE mission design is arranged for the measurement of six greenhouse gases (GHG) (H2O, CO2, CH4, N2O, O3, CO) and four isotopes (13CO2, C18OO, HDO, H218O), with focus on the upper troposphere/lower stratosphere region (UTLS, 5-35 km). Wind speed in line-of-sight can be derived from a line-symmetric transmission difference which is caused by wind-induced Doppler shift. By-products are information on cloud layering, aerosol extinction, and scintillation strength. We introduce the methodology to retrieve GHG profiles from quasi-realistic forward-simulated intensities of LIO signals and thermodynamic profiles retrieved in a preceding step from LMO signals. Key of the retrieval methodology is the differencing of two LIO transmission signals, one being GHG sensitive on a target

  14. Application of the accurate mass and time tag approach in studies of the human blood lipidome

    PubMed Central

    Ding, Jie; Sorensen, Christina M.; Jaitly, Navdeep; Jiang, Hongliang; Orton, Daniel J.; Monroe, Matthew E.; Moore, Ronald J.; Smith, Richard D.; Metz, Thomas O.

    2008-01-01

    We report a preliminary demonstration of the accurate mass and time (AMT) tag approach for lipidomics. Initial data-dependent LC-MS/MS analyses of human plasma, erythrocyte, and lymphocyte lipids were performed in order to identify lipid molecular species in conjunction with complementary accurate mass and isotopic distribution information. Identified lipids were used to populate initial lipid AMT tag databases containing 250 and 45 entries for those species detected in positive and negative electrospray ionization (ESI) modes, respectively. The positive ESI database was then utilized to identify human plasma, erythrocyte, and lymphocyte lipids in high-throughput LC-MS analyses based on the AMT tag approach. We were able to define the lipid profiles of human plasma, erythrocytes, and lymphocytes based on qualitative and quantitative differences in lipid abundance. PMID:18502191

  15. Isotope-Labeled Composition B for Tracing Detonation Signatures

    NASA Astrophysics Data System (ADS)

    Manner, Virginia; Podlesak, David; Huber, Rachel; Amato, Ronald; Giambra, Anna; Bowden, Patrick; Hartline, Ernest; Dattelbaum, Dana

    2017-06-01

    To better understand how solid carbon forms and evolves during detonation, we have prepared Composition B with 13 C and 15 N-labeled 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) and 2,4,6-trinitrotoluene (TNT) in order to trace the formation of soot from the carbon and nitrogen atoms in these explosives. Isotope-labeling of explosives has been performed in the recent past for a variety of reasons, including environmental remediation and reaction mechanism studies. Because it is expensive and time consuming to prepare these materials, and our detection equipment only requires trace amounts of isotopes, we have prepared fully-labeled materials and substituted them into unlabeled RDX and TNT at less than the 1% level. We will discuss the preparation and full characterization of this labeled Composition B, the detonation tests performed, along with the results of the post-detonation soot analysis. Various detonation models predict differing amounts and forms of carbon and nitrogen; these isotopically-labeled precursors have allowed these models to be tested.

  16. Benthic Foraminifera Clumped Isotope Calibration

    NASA Astrophysics Data System (ADS)

    Piasecki, A.; Marchitto, T. M., Jr.; Bernasconi, S. M.; Grauel, A. L.; Tisserand, A. A.; Meckler, N.

    2017-12-01

    Due to the widespread spatial and temporal distribution of benthic foraminifera within ocean sediments, they are a commonly used for reconstructing past ocean temperatures and environmental conditions. Many foraminifera-based proxies, however, require calibration schemes that are species specific, which becomes complicated in deep time due to extinct species. Furthermore, calibrations often depend on seawater chemistry being stable and/or constrained, which is not always the case over significant climate state changes like the Eocene Oligocene Transition. Here we study the effect of varying benthic foraminifera species using the clumped isotope proxy for temperature. The benefit of this proxy is that it is independent of seawater chemistry, whereas the downside is that it requires a relatively large sample amounts. Due to recent advancements in sample processing that reduce the sample weight by a factor of 10, clumped isotopes can now be applied to a range paleoceanographic questions. First however, we need to prove that, unlike for other proxies, there are no interspecies differences with clumped isotopes, as is predicted by first principles modeling. We used a range of surface sediment samples covering a temperature range of 1-20°C from the Pacific, Mediterranean, Bahamas, and the Atlantic, and measured the clumped isotope composition of 11 different species of benthic foraminifera. We find that there are indeed no discernible species-specific differences within the sample set. In addition, the samples have the same temperature response to the proxy as inorganic carbonate samples over the same temperature range. As a result, we can now apply this proxy to a wide range of samples and foraminifera species from different ocean basins with different ocean chemistry and be confident that observed signals reflect variations in temperature.

  17. Accurate and scalable social recommendation using mixed-membership stochastic block models.

    PubMed

    Godoy-Lorite, Antonia; Guimerà, Roger; Moore, Cristopher; Sales-Pardo, Marta

    2016-12-13

    With increasing amounts of information available, modeling and predicting user preferences-for books or articles, for example-are becoming more important. We present a collaborative filtering model, with an associated scalable algorithm, that makes accurate predictions of users' ratings. Like previous approaches, we assume that there are groups of users and of items and that the rating a user gives an item is determined by their respective group memberships. However, we allow each user and each item to belong simultaneously to mixtures of different groups and, unlike many popular approaches such as matrix factorization, we do not assume that users in each group prefer a single group of items. In particular, we do not assume that ratings depend linearly on a measure of similarity, but allow probability distributions of ratings to depend freely on the user's and item's groups. The resulting overlapping groups and predicted ratings can be inferred with an expectation-maximization algorithm whose running time scales linearly with the number of observed ratings. Our approach enables us to predict user preferences in large datasets and is considerably more accurate than the current algorithms for such large datasets.

  18. Accurate and scalable social recommendation using mixed-membership stochastic block models

    PubMed Central

    Godoy-Lorite, Antonia; Moore, Cristopher

    2016-01-01

    With increasing amounts of information available, modeling and predicting user preferences—for books or articles, for example—are becoming more important. We present a collaborative filtering model, with an associated scalable algorithm, that makes accurate predictions of users’ ratings. Like previous approaches, we assume that there are groups of users and of items and that the rating a user gives an item is determined by their respective group memberships. However, we allow each user and each item to belong simultaneously to mixtures of different groups and, unlike many popular approaches such as matrix factorization, we do not assume that users in each group prefer a single group of items. In particular, we do not assume that ratings depend linearly on a measure of similarity, but allow probability distributions of ratings to depend freely on the user’s and item’s groups. The resulting overlapping groups and predicted ratings can be inferred with an expectation-maximization algorithm whose running time scales linearly with the number of observed ratings. Our approach enables us to predict user preferences in large datasets and is considerably more accurate than the current algorithms for such large datasets. PMID:27911773

  19. Raoult's law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments.

    PubMed

    Bowler, Michael G; Bowler, David R; Bowler, Matthew W

    2017-04-01

    The humidity surrounding a sample is an important variable in scientific experiments. Biological samples in particular require not just a humid atmosphere but often a relative humidity (RH) that is in equilibrium with a stabilizing solution required to maintain the sample in the same state during measurements. The controlled dehydration of macromolecular crystals can lead to significant increases in crystal order, leading to higher diffraction quality. Devices that can accurately control the humidity surrounding crystals while monitoring diffraction have led to this technique being increasingly adopted, as the experiments become easier and more reproducible. Matching the RH to the mother liquor is the first step in allowing the stable mounting of a crystal. In previous work [Wheeler, Russi, Bowler & Bowler (2012). Acta Cryst. F 68 , 111-114], the equilibrium RHs were measured for a range of concentrations of the most commonly used precipitants in macromolecular crystallography and it was shown how these related to Raoult's law for the equilibrium vapour pressure of water above a solution. However, a discrepancy between the measured values and those predicted by theory could not be explained. Here, a more precise humidity control device has been used to determine equilibrium RH points. The new results are in agreement with Raoult's law. A simple argument in statistical mechanics is also presented, demonstrating that the equilibrium vapour pressure of a solvent is proportional to its mole fraction in an ideal solution: Raoult's law. The same argument can be extended to the case where the solvent and solute molecules are of different sizes, as is the case with polymers. The results provide a framework for the correct maintenance of the RH surrounding a sample.

  20. Isotopic incorporation rates for shark tissues from a long-term captive feeding study.

    PubMed

    Kim, Sora Lee; del Rio, Carlos Martínez; Casper, Dave; Koch, Paul L

    2012-07-15

    Stable isotope analysis has provided insight into the dietary and habitat patterns of many birds, mammals and teleost fish. A crucial biological parameter to interpret field stable isotope data is tissue incorporation rate, which has not been well studied in large ectotherms. We report the incorporation of carbon and nitrogen into the tissues of leopard sharks (Triakis semifasciata). Because sharks have relatively slow metabolic rates and are difficult to maintain in captivity, no long-term feeding study has been conducted until the point of isotopic steady state with a diet. We kept six leopard sharks in captivity for 1250 days, measured their growth, and serially sampled plasma, red blood cells and muscle for stable carbon and nitrogen isotope analysis. A single-compartment model with first-order kinetics adequately described the incorporation patterns of carbon and nitrogen isotopes for these three tissues. Both carbon and nitrogen were incorporated faster in plasma than in muscle and red blood cells. The rate of incorporation of carbon into muscle was similar to that predicted by an allometric equation relating isotopic incorporation rate to body mass that was developed previously for teleosts. In spite of their large size and unusual physiology, the rates of isotopic incorporation in sharks seem to follow the same patterns found in other aquatic ectotherms.