Topological Descriptors in Modeling the HIV Inhibitory Activity of 2-Aryl-3-pyridyl-thiazolidin-4-ones

The HIV-1 RT inhibitory activity of 2-(2,6-dihalophenyl)-3-(substituted pyridin-2-yl)-thiazolidin-4-ones has been analyzed with different topological descriptors obtained from DRAGON software. Here, simple topological descriptors (TOPO), Galvez topological charge indices (GVZ) and 2D autocorrelation descriptors (2DAUTO) have been found to yield good predictive models for the activity of these compounds. The correlations obtained from the TOPO class descriptors suggest that less extended or compact saturated structural templates would be better for the activity. The participating GVZ class descriptors suggest that they have same degree of influence on the activity. In 2DAUTO class, the large participation of descriptors of lags seven and three indicate the association of activity information with the seven and three centered structural fragments of these compounds. The physicochemical weighting components of these descriptors suggest homogeneous influence of mass, volume, electronegativity and/ or polarizability on the activity.

Incorporating Latent Variables into Discrete Choice Models - A Simultaneous Estimation Approach Using SEM Software

Integrated choice and latent variable (ICLV) models represent a promising new class of models which merge classic choice models with the structural equation approach (SEM) for latent variables. Despite their conceptual appeal, applications of ICLV models in marketing remain rare. We extend previous ICLV applications by first estimating a multinomial choice model and, second, by estimating hierarchical relations between latent variables. An empirical study on travel mode choice clearly demonstrates the value of ICLV models to enhance the understanding of choice processes. In addition to the usually studied directly observable variables such as travel time, we show how abstract motivations such as power and hedonism as well as attitudes such as a desire for flexibility impact on travel mode choice. Furthermore, we show that it is possible to estimate such a complex ICLV model with the widely available structural equation modeling package Mplus. This finding is likely to encourage more widespread application of this appealing model class in the marketing field.

The Genesis Solar Wind Concentrator: Flight and Post-Flight Conditions and Modeling of Instrumental Fractionation

The Genesis mission Solar Wind Concentrator was built to enhance fluences of solar wind by an average of 20x over the 2.3 years that the mission exposed substrates to the solar wind. The Concentrator targets survived the hard landing upon return to Earth and were used to determine the isotopic composition of solar-wind—and hence solar—oxygen and nitrogen. Here we report on the flight operation of the instrument and on simulations of its performance. Concentration and fractionation patterns obtained from simulations are given for He, Li, N, O, Ne, Mg, Si, S, and Ar in SiC targets, and are compared with measured concentrations and isotope ratios for the noble gases. Carbon is also modeled for a Si target. Predicted differences in instrumental fractionation between elements are discussed. Additionally, as the Concentrator was designed only for ions ≤22 AMU, implications of analyzing elements as heavy as argon are discussed. Post-flight simulations of instrumental fractionation as a function of radial position on the targets incorporate solar-wind velocity and angular distributions measured in flight, and predict fractionation patterns for various elements and isotopes of interest. A tighter angular distribution, mostly due to better spacecraft spin stability than assumed in pre-flight modeling, results in a steeper isotopic fractionation gradient between the center and the perimeter of the targets. Using the distribution of solar-wind velocities encountered during flight, which are higher than those used in pre-flight modeling, results in elemental abundance patterns slightly less peaked at the center. Mean fractionations trend with atomic mass, with differences relative to the measured isotopes of neon of +4.1±0.9 ‰/amu for Li, between -0.4 and +2.8 ‰/amu for C, +1.9±0.7‰/amu for N, +1.3±0.4 ‰/amu for O, -7.5±0.4 ‰/amu for Mg, -8.9±0.6 ‰/amu for Si, and -22.0±0.7 ‰/amu for S (uncertainties reflect Monte Carlo statistics). The slopes of the fractionation trends depend to first order only on the relative differential mass ratio, Δ m/ m. This article and a companion paper (Reisenfeld et al. 2012, this issue) provide post-flight information necessary for the analysis of the Genesis solar wind samples, and thus serve to complement the Space Science Review volume, The Genesis Mission (v. 105, 2003).

MODELING REACTIVE GAS UPTAKE, TRANSPORT, AND TRANSFORMATION IN AGGREGATED SOILS

Gas diffusion research in soils covers, to a large extent, the transport behavior of practically insoluble gases. We extend the mathematical description of gas transport to include reactive gaseous components that hydrolyze in water such as SO2 and CO2. The path between the free atmosphere and the microporous niches is modeled by assuming penetration through gas-filled macropores, air-water phase transfer, and diffusion and speciation in the liquid phase. For hydrolyzable gases, the rate of mass transfer into and the total absorption capacity of the soil solution may be high. Both the capacity and the transfer rate are influenced by the soil-solution pH; for high pH, they become extremely high for SO2. The soil absorption of such gases is also influenced by soil structure. Well-aerated, near-neutral soils are a potentially important sink for SO2.

Volcanic forcing for climate modeling: a new microphysics-based data set covering years 1600–present

As the understanding and representation of the impacts of volcanic eruptions on climate have improved in the last decades, uncertainties in the stratospheric aerosol forcing from large eruptions are now linked not only to visible optical depth estimates on a global scale but also to details on the size, latitude and altitude distributions of the stratospheric aerosols. Based on our understanding of these uncertainties, we propose a new model-based approach to generating a volcanic forcing for general circulation model (GCM) and chemistry–climate model (CCM) simulations. This new volcanic forcing, covering the 1600–present period, uses an aerosol microphysical model to provide a realistic, physically consistent treatment of the stratospheric sulfate aerosols. Twenty-six eruptions were modeled individually using the latest available ice cores aerosol mass estimates and historical data on the latitude and date of eruptions. The evolution of aerosol spatial and size distribution after the sulfur dioxide discharge are hence characterized for each volcanic eruption. Large variations are seen in hemispheric partitioning and size distributions in relation to location/date of eruptions and injected SO2 masses. Results for recent eruptions show reasonable agreement with observations. By providing these new estimates of spatial distributions of shortwave and long-wave radiative perturbations, this volcanic forcing may help to better constrain the climate model responses to volcanic eruptions in the 1600–present period. The final data set consists of 3-D values (with constant longitude) of spectrally resolved extinction coefficients, single scattering albedos and asymmetry factors calculated for different wavelength bands upon request. Surface area densities for heterogeneous chemistry are also provided.

Modeling the formation and aging of secondary organic aerosols during CalNex 2010

Four different literature parameterizations for the formation and evolution of urban secondary organic aerosol (SOA) frequently used in 3-D models are evaluated using a 0-D box model representing the Los Angeles metropolitan region during the California Research at the Nexus of Air Quality and Climate Change (CalNex) 2010 campaign. We constrain the model predictions with measurements from several platforms and compare predictions with particle- and gas-phase observations from the CalNex Pasadena ground site. That site provides a unique opportunity to study aerosol formation close to anthropogenic emission sources with limited recirculation. The model SOA that formed only from the oxidation of VOCs (V-SOA) is insufficient to explain the observed SOA concentrations, even when using SOA parameterizations with multi-generation oxidation that produce much higher yields than have been observed in chamber experiments, or when increasing yields to their upper limit estimates accounting for recently reported losses of vapors to chamber walls. The Community Multiscale Air Quality (WRF-CMAQ) model (version 5.0.1) provides excellent predictions of secondary inorganic particle species but underestimates the observed SOA mass by a factor of 25 when an older VOC-only parameterization is used, which is consistent with many previous model–measurement comparisons for pre-2007 anthropogenic SOA modules in urban areas. Including SOA from primary semi-volatile and intermediate-volatility organic compounds (P-S/IVOCs) following the parameterizations of Robinson et al. (2007), Grieshop et al. (2009), or Pye and Seinfeld (2010) improves model–measurement agreement for mass concentration. The results from the three parameterizations show large differences (e.g., a factor of 3 in SOA mass) and are not well constrained, underscoring the current uncertainties in this area. Our results strongly suggest that other precursors besides VOCs, such as P-S/IVOCs, are needed to explain the observed SOA concentrations in Pasadena. All the recent parameterizations overpredict urban SOA formation at long photochemical ages (3 days) compared to observations from multiple sites, which can lead to problems in regional and especially global modeling. However, reducing IVOC emissions by one-half in the model to better match recent IVOC measurements improves SOA predictions at these long photochemical ages. Among the explicitly modeled VOCs, the precursor compounds that contribute the greatest SOA mass are methylbenzenes. Measured polycyclic aromatic hydrocarbons (naphthalenes) contribute 0.7% of the modeled SOA mass. The amounts of SOA mass from diesel vehicles, gasoline vehicles, and cooking emissions are estimated to be 16–27, 35–61, and 19–35 %, respectively, depending on the parameterization used, which is consistent with the observed fossil fraction of urban SOA, 71(+-3) %. The relative contribution of each source is uncertain by almost a factor of 2 depending on the parameterization used. In-basin biogenic VOCs are predicted to contribute only a few percent to SOA. A regional SOA background of approximately 2.1 μgm-3 is also present due to the long-distance transport of highly aged OA, likely with a substantial contribution from regional biogenic SOA. The percentage of SOA from diesel vehicle emissions is the same, within the estimated uncertainty, as reported in previous work that analyzed the weekly cycles in OA concentrations (Bahreini et al., 2012; Hayes et al., 2013). However, the modeling work presented here suggests a strong anthropogenic source of modern carbon in SOA, due to cooking emissions, which was not accounted for in those previous studies and which is higher on weekends. Lastly, this work adapts a simple two-parameter model to predict SOA concentration and O/C from urban emissions. This model successfully predicts SOA concentration, and the optimal parameter combination is very similar to that found for Mexico City. This approach provides a computationally inexpensive method for predicting urban SOA in global and climate models. We estimate pollution SOA to account for 26 Tg yr-1 of SOA globally, or 17% of global SOA, one third of which is likely to be non-fossil.

Benchmark problems for reactive transport modeling of the generation and attenuation of acid rock drainage

Acid rock drainage (ARD) is a problem of international relevance with substantial environmental and economic implications. Reactive transport modeling has proven a powerful tool for the process-based assessment of metal release and attenuation at ARD sites. Although a variety of models has been used to investigate ARD, a systematic model intercomparison has not been conducted to date. This contribution presents such a model intercomparison involving three synthetic benchmark problems designed to evaluate model results for the most relevant processes at ARD sites. The first benchmark (ARD-B1) focuses on the oxidation of sulfide minerals in an unsaturated tailing impoundment, affected by the ingress of atmospheric oxygen. ARD-B2 extends the first problem to include pH buffering by primary mineral dissolution and secondary mineral precipitation. The third problem (ARD-B3) in addition considers the kinetic and pH-dependent dissolution of silicate minerals under low pH conditions. The set of benchmarks was solved by four reactive transport codes, namely CrunchFlow, Flotran, HP1, and MIN3P. The results comparison focused on spatial profiles of dissolved concentrations, pH and pE, pore gas composition, and mineral assemblages. In addition, results of transient profiles for selected elements and cumulative mass loadings were considered in the intercomparison. Despite substantial differences in model formulations, very good agreement was obtained between the various codes. Residual deviations between the results are analyzed and discussed in terms of their implications for capturing system evolution and long-term mass loading predictions.

Modeling the Histidine–Phenylalanine Interaction: The NH···π Hydrogen Bond of Imidazole·Benzene

NH···π hydrogen bonds occur frequently between the amino acid side groups in proteins and peptides. Data-mining studies of protein crystals find that ~80% of the T-shaped histidine···aromatic contacts are CH···π, and only ~20% are NH···π interactions. We investigated the infrared (IR) and ultraviolet (UV) spectra of the supersonic-jet-cooled imidazole·benzene (Im·Bz) complex as a model for the NH···π interaction between histidine and phenylalanine. Ground- and excited-state dispersion-corrected density functional calculations and correlated methods (SCS-MP2 and SCS-CC2) predict that Im·Bz has a Cs-symmetric T-shaped minimum-energy structure with an NH···π hydrogen bond to the Bz ring; the NH bond is tilted 12° away from the Bz C₆ axis. IR depletion spectra support the T-shaped geometry: The NH stretch vibrational fundamental is red shifted by −73 cm⁻¹ relative to that of bare imidazole at 3518 cm⁻¹, indicating a moderately strong NH···π interaction. While the Sₒ(A1g) → S₁(B₂u) origin of benzene at 38 086 cm⁻¹ is forbidden in the gas phase, Im·Bz exhibits a moderately intense Sₒ → S₁ origin, which appears via the D₆h → Cs symmetry lowering of Bz by its interaction with imidazole. The NH···π ground-state hydrogen bond is strong, De=22.7 kJ/mol (1899 cm⁻¹). The combination of gas-phase UV and IR spectra confirms the theoretical predictions that the optimum Im·Bz geometry is T shaped and NH···π hydrogen bonded. We find no experimental evidence for a CH···π hydrogen-bonded ground-state isomer of Im·Bz. The optimum NH···π geometry of the Im·Bz complex is very different from the majority of the histidine·aromatic contact geometries found in protein database analyses, implying that the CH···π contacts observed in these searches do not arise from favorable binding interactions but merely from protein side-chain folding and crystal-packing constraints. The UV and IR spectra of the imidazole·(benzene)₂ cluster are observed via fragmentation into the Im·Bz+ mass channel. The spectra of Im·Bz and Im·Bz₂ are cleanly separable by IR hole burning. The UV spectrum of Im·Bz₂ exhibits two 000 bands corresponding to the Sₒ → S₁ excitations of the two inequivalent benzenes, which are symmetrically shifted by −86/+88 cm⁻¹ relative to the 000 band of benzene.

3D-modeling of Mercury's solar wind sputtered surface-exosphere environment

The efficiency of sputtered refractory elements by H+ and He++ solar wind ions from Mercury's surface and their contribution to the exosphere are studied for various solar wind conditions. A 3D solar wind-planetary interaction hybrid model is used for the evaluation of precipitation maps of the sputter agents on Mercury's surface. By assuming a global mineralogical surface composition, the related sputter yields are calculated by means of the 2013 SRIM code and are coupled with a 3D exosphere model. Because of Mercury's magnetic field, for quiet and nominal solar wind conditions the plasma can only precipitate around the polar areas, while for extreme solar events (fast solar wind, coronal mass ejections, interplanetary magnetic clouds) the solar wind plasma has access to the entire dayside. In that case the release of particles form the planet's surface can result in an exosphere density increase of more than one order of magnitude. The corresponding escape rates are also about an order of magnitude higher. Moreover, the amount of He++ ions in the precipitating solar plasma flow enhances also the release of sputtered elements from the surface in the exosphere. A comparison of our model results with MESSENGER observations of sputtered Mg and Ca elements in the exosphere shows a reasonable quantitative agreement. (C) 2015 Elsevier Ltd. All rights reserved.

Lifetime changes in body mass index and risk of breast cancer in minority women

Introduction: Obesity is an epidemic in the United States, especially among Hispanics and African-Americans. Studies of obesity and breast cancer risk and subtype have been conducted primarily in non-Hispanic whites. Obesity is inversely associated with premenopausal breast cancer, but both obesity and weight gain increase the risk of postmenopausal disease. Obesity has been associated with breast cancer subtype in many studies. Methods: To assess the association between changes in body mass index (BMI) over the lifetime, weight gain, and breast cancer in Mexican-American women, we conducted a case-control study using 149 cases and 330 age-matched controls. In a second study, we identified 212 African-American and 167 Mexican-American women with breast cancer in the ongoing ELLA Bi-National Breast Cancer Study, abstracted medical charts to classify tumors as ER+/PR+, HER2+, or ER-/PR-/HER2-, and assessed the association between lifetime changes in body mass index, weight gain, and breast cancer subtype. In both studies, growth mixture modeling was use to identify trajectories of change in BMI over the lifetime, and these trajectories were used as exposures in a logistic regression model to calculate odds ratios (OR). Results: There was no association between trajectories of change in BMI and breast cancer risk in Mexican-American women. In addition, BMI at ages 15 and 30 and at diagnosis was not associated with breast cancer. However, adult weight gain was inversely associated with breast cancer risk (per 5kg, OR=0.92, 95% CI: 0.85-0.99). The case-only analysis found no association between obesity at ages 15 and 30 and at diagnosis and breast cancer subtype. Further, there was no association between adult weight gain (defined as weight change from age 15 to time of diagnosis) and breast cancer subtype. Conclusions: Obesity was not associated with breast cancer risk in Mexican-American women, while adult weight gain reduced the risk independently of menopausal status. These results are contradictory of those in non-Hispanic white women and suggest that the etiology of breast cancer may differ by race/ethnicity. Further, obesity was not associated with breast cancer subtype in African-American and Mexican-American women, contrary to results in non-Hispanic white women. ^

Development and evaluation of a video-based modeling strategy for the dissemination phase of a school health tobacco -use prevention program

Even the best school health education programs will be unsuccessful if they are not disseminated effectively in a manner that encourages classroom adoption and implementation. This study involved two components: (1) the development of a videotape intervention to be used in the dissemination phase of a 4-year, NCI-funded diffusion study and (2) the evaluation of that videotape intervention strategy in comparison with a print (information transfer) strategy. Conceptualization has been guided by Social Learning Theory, Diffusion Theory, and communication theory. Additionally, the PRECEDE Framework has been used. Seventh and 8th grade classroom teachers from Spring Branch Independent School District in west Houston participated in the evaluation of the videotape and print interventions using a 57-item preadoption survey instrument developed by the UT Center for Health Promotion Research and Development. Two-way ANOVA was used to study individual score differences for five outcome variables: Total Scale Score (comprised of 57 predisposing, enabling, and reinforcing items), Adoption Characteristics Subscale, Attitude Toward Innovation Subscale, Receptivity Toward Innovation, and Reinforcement Subscale. The aim of the study is to compare the effect upon score differences of video and print interventions alone and in combination. Seventy-three 7th and 8th grade classroom teachers completed the study providing baseline and post-intervention measures on factors related to the adoption and implementation of tobacco-use prevention programs. Two-way ANOVA, in relation to the study questions, found significant scoring differences for those exposed to the videotape intervention alone for both the Attitude Toward Innovation Subscale and the Receptivity to Adopt Subscale. No significant results were found to suggest that print alone influences favorable scoring differences between baseline and post-intervention testing. One interaction effect was found suggesting video and print combined are more effective for influencing favorable scoring differences for the Reinforcement for the Adoption Subscale.^ This research is unique in that it represents a newly emerging field in health promotion communications research with implications for Social Learning Theory, Diffusion Theory, and communication science that are applicable to the development of improved school health interventions. ^

X-ray fluorescence scanning of discrete samples on the Schwalbenberg II loess-paleosol sequence, raw data, magnetic susceptibility, organic carbon and U-ratio as grainsize index

The Schwalbenberg II loess-paleosol sequence (LPS) denotes a key site for Marine Isotope Stage (MIS 3) in Western Europe owing to eight succeeding cambisols, which primarily constitute the Ahrgau Subformation. Therefore, this LPS qualifies as a test candidate for the potential of temporal high-resolution geochemical data obtained X-ray fluorescence (XRF) scanning of discrete samplesproviding a fast and non-destructive tool for determining the element composition. The geochemical data is first contextualized to existing proxy data such as magnetic susceptibility (MS) and organic carbon (Corg) and then aggregated to element log ratios characteristic for weathering intensity [LOG (Ca/Sr), LOG (Rb/Sr), LOG (Ba/Sr), LOG (Rb/K)] and dust provenance [LOG (Ti/Zr), LOG (Ti/Al), LOG (Si/Al)]. Generally, an interpretation of rock magnetic particles is challenged in western Europe, where not only magnetic enhancement but also depletion plays a role. Our data indicates leaching and top-soil erosion induced MS depletion at the Schwalbenberg II LPS. Besides weathering, LOG (Ca/Sr) is susceptible for secondary calcification. Thus, also LOG (Rb/Sr) and LOG (Ba/Sr) are shown to be influenced by calcification dynamics. Consequently, LOG (Rb/K) seems to be the most suitable weathering index identifying the Sinzig Soils S1 and S2 as the most pronounced paleosols for this site. Sinzig Soil S3 is enclosed by gelic gleysols and in contrast to S1 and S2 only initially weathered pointing to colder climate conditions. Also the Remagen Soils are characterized by subtle to moderate positive excursions in the weathering indices. Comparing the Schwalbenberg II LPS with the nearby Eifel Lake Sediment Archive (ELSA) and other more distant German, Austrian and Czech LPS while discussing time and climate as limiting factors for pedogenesis, we suggest that the lithologically determined paleosols are in-situ soil formations. The provenance indices document a Zr-enrichment at the transition from the Ahrgau to the Hesbaye Subformation. This is explained by a conceptual model incorporating multiple sediment recycling and sorting effects in eolian and fluvial domains.

Glacier mass balance measurements on Fourcade and Polar Club glacier, King George Island

The east coast of the AP is highly influenced by cold and dry air masses stemming from the adjacent Weddell Sea. By the contrary, the west coast jointly with the South Shetland Islands are directly exposed to the humid and relatively warm air masses from the South Pacific Ocean carried by the strong and persistent westerly winds. Systematic glaciological field studies are very scarce on both sides of the AP, among them can be mentioned a mass-balance program performed continuously since summer 1998/99 by the Instituto Antártico Argentino (IAA) on Vega Island, James Ross Archipelago, on the northeastern flank of the AP. Another continuous plurianual glaciological research has been initiated in 2010 jointly by the University of Bonn and the IAA at the Fourcade Glacier on King George Island (KGI) within the framework of the ESF project IMCOAST (FK 03F0617B). Two transects of mass balance stakes were installed from the top of the Warszawa Ice Dome down to the border of the glaciers Fourcade and Polar Club, to serve for calibration and validation of modeling efforts. The stakes were measured at the beginning and end of each summer field campaign in November 2010, February - March 2011, January - March 2012, and especially during the austral winter 2012 up to March 2013 every 10 to 14 days depending on weather conditions. During the austral winter 2013 and until June 2014 the measurements were conducted every 20 to 30 days, weather permitting. Snow density was measured as well in every field trip from June 2012 until June 2104, establishing a rather homogeneous value along the different parts of the glacier. Snow density in late summer, rho_s is usually higher than the one in late winter, rho_w. Seasonal average values were calculated for the area covered by the mass balance stakes, being rho_s= 471 Kg/m**3 and rho_w = 363 Kg/m**3.

A numerical discrete element study on the influence of an embedded viscoelastic-plastic layer at different viscosity values

The major aim of this study was to examine the influence of an embedded viscoelastic-plastic layer at different viscosity values on accretionary wedges at subduction zones. To quantify the effects of the layer viscosity, we analysed the wedge geometry, accretion mode, thrust systems and mass transport pattern. Therefore, we developed a numerical 2D 'sandbox' model utilising the Discrete Element Method. Starting with a simple pure Mohr Coulomb sequence, we added an embedded viscoelastic-plastic layer within the brittle, undeformed 'sediment' package. This layer followed Burger's rheology, which simulates the creep behaviour of natural rocks, such as evaporites. This layer got thrusted and folded during the subduction process. The testing of different bulk viscosity values, from 1 × 10**13 to 1 × 10**14 (Pa s), revealed a certain range where an active detachment evolved within the viscoelastic-plastic layer that decoupled the over- and the underlying brittle strata. This mid-level detachment caused the evolution of a frontally accreted wedge above it and a long underthrusted and subsequently basally accreted sequence beneath it. Both sequences were characterised by specific mass transport patterns depending on the used viscosity value. With decreasing bulk viscosities, thrust systems above this weak mid-level detachment became increasingly symmetrical and the particle uplift was reduced, as would be expected for a salt controlled forearc in nature. Simultaneously, antiformal stacking was favoured over hinterland dipping in the lower brittle layer and overturning of the uplifted material increased. Hence, we validated that the viscosity of an embedded detachment strongly influences the whole wedge mechanics, both the respective lower slope and the upper slope duplex, shown by e.g. the mass transport pattern.

Salinization MASS Model Version

This salinization simulation enables irrigation salinity, capillary rise, rainfall, leaching, salt mitigation strategies via fallowing, and other functions that are addressed in a coupled social-environment model applied to southern Mesopotamia. The simulation is applied to the Modeling Ancient Settlement Systems Project supported by the University of Chicago, Durham University, and Argonne National Laboratory. The simulation can be used for other regions.