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At least 1,027 records · Page 57

Quantification of the epitope diversity of HIV-1-specific binding antibodies by peptide microarrays for global HIV-1 vaccine development

An effective vaccine against human immunodeficiency virus type 1 (HIV-1) will have to provide protection against a vast array of different HIV-1 strains. Current methods to measure HIV-1-specific binding antibodies following immunization typically focus on determining the magnitude of antibody responses, but the epitope diversity of antibody responses has remained largely unexplored. Here we describe the development of a global HIV-1 peptide microarray that contains 6564 peptides from across the HIV-1 proteome and covers the majority of HIV-1 sequences in the Los Alamos National Laboratory global HIV-1 sequence database. Using this microarray, we quantified the magnitude, breadth, and depth of IgG binding to linear HIV-1 sequences in HIV-1-infected humans and HIV-1-vaccinated humans, rhesus monkeys and guinea pigs. The microarray measured potentially important differences in antibody epitope diversity, particularly regarding the depth of epitope variants recognized at each binding site. Our data suggest that the global HIV-1 peptide microarray may be a useful tool for both preclinical and clinical HIV-1 research.

60 APPLIED LIFE SCIENCES↗

Cost comparison between private and public collection of residual household waste: Multiple case studies in the Flemish region of Belgium

Highlights: Black-Right-Pointing-Pointer The goal is to compare collection costs for residual household waste. Black-Right-Pointing-Pointer We have clustered all municipalities in order to find mutual comparable pairs. Black-Right-Pointing-Pointer Each pair consists of one private and one public operating waste collection program. Black-Right-Pointing-Pointer All cases show that private service has lower costs than public service. Black-Right-Pointing-Pointer Municipalities were contacted to identify the deeper causes for the waste management program. - Abstract: The rising pressure in terms of cost efficiency on public services pushes governments to transfer part of those services to the private sector. A trend towards more privatizing can be noticed in the collection of municipal household waste. This paper reports the findings of a research project aiming to compare the cost between the service of private and public collection of residual household waste. Multiple case studies of municipalities about the Flemish region of Belgium were conducted. Data concerning the year 2009 were gathered through in-depth interviews in 2010. In total 12 municipalities were investigated, divided into three mutual comparable pairs with a weekly and three mutual comparable pairs with a fortnightly residual waste collection. The results give a rough indication that in all cases the cost of private service is lower than public service in the collection of household waste. Albeit that there is an interest in establishing whether there are differences in the costs and service levels between public and private waste collection services, there are clear difficulties in establishing comparisons that can be made without having to rely on a large number of assumptions and corrections. However, given the cost difference, it remains the responsibility of the municipalities to decide upon the service they offer their citizens, regardless the cost efficiency: public or private.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Using Carbon Isotope Fractionation to Constrain the Extent of Methane Dissolution Into the Water Column Surrounding a Natural Hydrocarbon Gas Seep in the Northern Gulf of Mexico

A gas bubble seep located in the northern Gulf of Mexico was investigated over several days to determine whether changes in the stable carbon isotopic ratio of methane can be used as a tracer for methane dissolution through the water column. Gas bubble and water samples were collected at the seafloor and throughout the water column for isotopic ratio analysis of methane. Our results show that changes in methane isotopic ratios are consistent with laboratory experiments that measured the isotopic fractionation from methane dissolution. A Rayleigh isotope model was applied to the isotope data to determine the fraction of methane dissolved at each depth. On average, the fraction of methane dissolved surpasses 90% past an altitude of 400 m above the seafloor. Methane dissolution was also investigated using a modified version of the Texas A&M Oil spill (Outfall) Calculator (TAMOC) where changes in methane isotopic ratios could be calculated. The TAMOC model results show that dissolution depends on depth and bubble size, explaining the spread in measured isotopic ratios during our investigations. Both the Rayleigh and TAMOC models show that methane bubbles quickly dissolve following emission from the seafloor. Together, these results show that it is possible to use measurements of natural methane isotopes to constrain the extent of methane dissolution following seafloor emission.

58 GEOSCIENCES↗

Structure of the Ecuadorian Upper Plate From a Joint Seismic‐Gravity Inversion

The Ecuadorian portion of the South American subduction zone presents an interesting case study in the structure and complex evolution of an upper plate. There are outstanding questions about its tectonic history, composition, and magmatic processes. While previous studies have employed ambient noise tomography to image the Ecuadorian upper plate, surface wave inversions alone often lack sensitivity at relevant shallow depths. This limitation can be overcome with an independent, complementary data set, such as gravity. We have jointly inverted Rayleigh wave phase velocities and Bouguer gravity anomalies to provide a more detailed seismic velocity model of the Ecuadorian upper plate. Our joint inversion has yielded several key improvements from previous models. First, we observe much shallower slow velocities beneath major basins (the Manabí, Progreso, and Gulf of Guayaquil), better aligning with expected basin structure. Second, we identify a high-velocity block beneath the entire forearc, corresponding to the Piñon Terrane, with velocities suggesting the presence of ultramafic material. Third, we highlight a new narrow swath of slow velocities beneath the Ecuadorian Andes, which closely follows the active volcanoes along the Eastern Cordillera. The extent of these slow velocities coincides with the termination of active arc volcanism and the predicted location of the subducted Carnegie Ridge. The predicted compositions for the mid to lower crust in the region preclude a purely compositional explanation for these velocities, suggesting that some level of partial melt is necessary.

Birkey, Andrew [Univ. of Delaware, Newark, DE (Uni↗

Subsurface fluvial sediments beneath InSight on Mars from geophysical constraints

Subsurface structure investigation on Mars is crucial for understanding its geological evolution and past hydrological conditions. Elysium Planitia (EP), located near the hypothesized ancient ocean shorelines, could contain clues for past water activity and paleoclimate. Here we present better-constrained subsurface models beneath InSight extending to ~800 m depth, obtained from joint inversion of seismic and seismoacoustic coupling data, and use the well-resolved subsurface structure to explore the lithological profile through rock physics models. The derived subsurface lithology agrees well with local geological context and exhibits a shallow 60-m-thick low-rigidity layer consistent with hydrated sedimentary materials. Despite possible contributions of aeolian and volcanic deposits, we favor the interpretation that the low-rigidity layer originated from fluvial activity in EP during the Hesperian or Hesperian-to-Amazonian epoch, as supported by adjacent paleo-shoreline morphology observations. These results hint at a period of warmer paleoclimate at low latitudes, possibly during high-obliquity phases of Mars’ rotational axis.

58 GEOSCIENCES↗

Towards a bayesian seismotectonic zoning for use in Probabilistic Seismic Hazard Assessment (PSHA)

The mathematical representation of seismic sources is an important part of probabilistic seismic hazard assessment. It reflects the association of the seismicity with the tectonically-active geological structures evidenced by seismotectonic studies. Given that most active faults are not characterized well enough, seismic sources are generally defined as areal zones, delimited with finite boundary polygons, within which the geological features of active tectonics and the seismicity are deemed homogeneous (e.g., focal depth, seismicity rate, and maximum magnitude). Besides the lack of data (e.g., narrow range of recorded magnitudes), the application of this representation generates different problems: 1) a large sensitivity of resulting hazard maps on the location of zone boundaries, while these boundaries are set by expert decision; 2) the zoning can not represent any variation in faulting mechanism; 3) the seismicity rates are distributed throughout the zones and we lose the location of the determinant information used for their calculation. We propose an exploratory study for an alternative procedure in area source modeling. First, different data (e.g., geomorphology, geology, fault orientations) will be combined by using automated spatial partitioning (investigation of both supervised and unsupervised methods) in order to obtain several information classes, which may be defined as areal source zones. Then, a given hypocenter belonging to a given ''zone'', from now on called seismicity model, will be expressed by a probability computed from the 2D (spatial) probability density function (pdf) for the active tectonic model used as an a priori and updated with specific data from seismicity catalogs (e.g., focal mechanism) or other new data sources (e.g., geomorphology, subsurface exploration). This hypocenter will thus be allowed to contribute to several models, with weights given by the value of the pdf for each model. The annual rate of occurrence, for a given model, will be calculated by the weighted average of the different hypocenter contributions contained in this model. Future applications will couple the seismicity models to Ground Motion Prediction Equations. In consequence, the results will provide the full spectrum of variability in the hazard and will highlight zones badly constrained and deserving to be more studied.

58 GEOSCIENCES↗

Machinability of a Stainless Steel by Electrochemical Discharge Microdrilling

Due to the chemical elements included in their structure for ensuring an increased resistance to the environment action, the stainless steels are characterized by a low machinability when classical machining methods are applied. For this reason, sometimes non-traditional machining methods are applied, one of these being the electrochemical discharge machining. To obtain microholes and to evaluate the machinability by electrochemical discharge microdrilling, test pieces of stainless steel were used for experimental research. The electrolyte was an aqueous solution of sodium silicate with different densities. A complete factorial plan was designed to highlight the influence of some input variables on the sizes of the considered machinability indexes (electrode tool wear, material removal rate, depth of the machined hole). By mathematically processing of experimental data, empirical functions were established both for stainless steel and carbon steel. Graphical representations were used to obtain more suggestive vision concerning the influence exerted by the considered input variables on the size of the machinability indexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

X-ray absorption and resonant inelastic x-ray scattering (RIXS) show the presence of Cr{sup +} at the surface and in the bulk of CrF{sub 2}

X-Ray absorption and resonant inelastic x-ray scattering (RIXS) spectra of CrF{sub 2} recorded at the chromium L{sub 2,3} are presented. An atomic multiplet crystal field calculation is compared with the experimental data. Experiment and theory are in agreement once the calculation includes three chromium oxidation states, namely Cr{sup +}, Cr{sup 2+}, and Cr{sup 3+}. X-Ray absorption allows a direct determination of the surface oxidation, while the RIXS spectra shows the presence of these three oxidation states in the sample bulk. To give a quantitative interpretation of the RIXS data the effect of the incomming and outgoing photon penetration depth and self-absorption must be considered. For the much simpler case of MnF{sub 2}, with only one metal oxidation state, the measured RIXS spectra relative intensities are found to be proportional to the square of the sample attenuation length.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

SPARSE FARADAY ROTATION MEASURE SYNTHESIS

Faraday rotation measure synthesis is a method for analyzing multichannel polarized radio emissions, and it has emerged as an important tool in the study of Galactic and extragalactic magnetic fields. The method requires the recovery of the Faraday dispersion function from measurements restricted to limited wavelength ranges, which is an ill-conditioned deconvolution problem. Here, we discuss a recovery method that assumes a sparse approximation of the Faraday dispersion function in an overcomplete dictionary of functions. We discuss the general case when both thin and thick components are included in the model, and we present the implementation of a greedy deconvolution algorithm. We illustrate the method with several numerical simulations that emphasize the effect of the covered range and sampling resolution in the Faraday depth space, and the effect of noise on the observed data.

79 ASTRONOMY AND ASTROPHYSICS↗

A CLOSER VIEW OF THE RADIO-FIR CORRELATION: DISENTANGLING THE CONTRIBUTIONS OF STAR FORMATION AND ACTIVE GALACTIC NUCLEUS ACTIVITY

We extend the Unified Radio Catalog, a catalog of sources detected by various (NVSS, FIRST, WENSS, GB6) radio surveys, and SDSS, to IR wavelengths by matching it to the IRAS Point and Faint Source catalogs. By fitting each NVSS-selected galaxy's NUV-NIR spectral energy distribution (SED) with stellar population synthesis models we add to the catalog star formation rates (SFRs), stellar masses, and attenuations. We further add information about optical emission-line properties for NVSS-selected galaxies with available SDSS spectroscopy. Using an NVSS 20 cm (F{sub 1.4{sub GHz}} {approx}> 2.5 mJy) selected sample, matched to the SDSS spectroscopic ('main' galaxy and quasar) catalogs and IRAS data (0.04 < z {approx}< 0.2) we perform an in-depth analysis of the radio-FIR correlation for various types of galaxies, separated into (1) quasars, (2) star-forming, (3) composite, (4) Seyfert, (5) LINER, and (6) absorption line galaxies using the standard optical spectroscopic diagnostic tools. We utilize SED-based SFRs to independently quantify the source of radio and FIR emission in our galaxies. Our results show that Seyfert galaxies have FIR/radio ratios lower than, but still within the scatter of, the canonical value due to an additional (likely active galactic nucleus (AGN)) contribution to their radio continuum emission. Furthermore, IR-detected absorption and LINER galaxies are on average strongly dominated by AGN activity in both their FIR and radio emission; however their average FIR/radio ratio is consistent with that expected for star-forming galaxies. In summary, we find that most AGN-containing galaxies in our NVSS-IRAS-SDSS sample have FIR/radio flux ratios indistinguishable from those of the star-forming galaxies that define the radio-FIR correlation. Thus, attempts to separate AGNs from star-forming galaxies by their FIR/radio flux ratios alone can separate only a small fraction of the AGNs, such as the radio-loud quasars.

79 ASTRONOMY AND ASTROPHYSICS↗

CURRENT HELICITY OF ACTIVE REGIONS AS A TRACER OF LARGE-SCALE SOLAR MAGNETIC HELICITY

We demonstrate that the current helicity observed in solar active regions traces the magnetic helicity of the large-scale dynamo generated field. We use an advanced two-dimensional mean-field dynamo model with dynamo saturation based on the evolution of the magnetic helicity and algebraic quenching. For comparison, we also studied a more basic two-dimensional mean-field dynamo model with simple algebraic alpha-quenching only. Using these numerical models we obtained butterfly diagrams both for the small-scale current helicity and also for the large-scale magnetic helicity, and compared them with the butterfly diagram for the current helicity in active regions obtained from observations. This comparison shows that the current helicity of active regions, as estimated by -A {center_dot} B evaluated at the depth from which the active region arises, resembles the observational data much better than the small-scale current helicity calculated directly from the helicity evolution equation. Here B and A are, respectively, the dynamo generated mean magnetic field and its vector potential. A theoretical interpretation of these results is given.

79 ASTRONOMY AND ASTROPHYSICS↗

Confirmation of a high magnetic field in GRO J1008–57

GRO J1008–57 is a high-mass X-ray binary for which several claims of a cyclotron resonance scattering feature near 80 keV have been reported. We use NuSTAR, Suzaku, and Swift data from its giant outburst of 2012 November to confirm the existence of the 80 keV feature and perform the most sensitive search to date for cyclotron scattering features at lower energies. We find evidence for a 78{sub −2}{sup +3} keV line in the NuSTAR and Suzaku data at >4σ significance, confirming the detection using Suzaku alone by Yamamoto et al. A search of both the phase-averaged and phase-resolved data rules out a fundamental at lower energies with optical depth larger than 5% of the 78 keV line. These results indicate that GRO J1008–57 has a magnetic field of 6.7 × 10{sup 12}(1 + z) G, the highest among known accreting pulsars.

79 ASTRONOMY AND ASTROPHYSICS↗

SPITZER MIPS 24 and 70 {mu}m IMAGING NEAR THE SOUTH ECLIPTIC POLE: MAPS AND SOURCE CATALOGS

We have imaged an 11.5 deg{sup 2} region of sky toward the South Ecliptic Pole (R.A. =04{sup h}43{sup m}, decl. =-53{sup 0}40', J2000) at 24 and 70 {mu}m with MIPS, the Multiband Imaging Photometer for Spitzer. This region is coincident with a field mapped at longer wavelengths by AKARI and BLAST. We discuss our data reduction and source extraction procedures. The median 1{sigma} depths of the maps are 47 {mu}Jy beam{sup -1} at 24 {mu}m and 4.3 mJy beam{sup -1} at 70 {mu}m. At 24 {mu}m, we identify 93,098 point sources with signal-to-noise ratio (S/N) {>=}5 and an additional 63 resolved galaxies; at 70 {mu}m we identify 891 point sources with S/N {>=}6. From simulations, we determine a false detection rate of 1.8% (1.1%) for the 24 {mu}m (70 {mu}m) catalog. The 24 and 70 {mu}m point-source catalogs are 80% complete at 230 {mu}Jy and 11 mJy, respectively. These mosaic images and source catalogs will be available to the public through the NASA/IPAC Infrared Science Archive.

79 ASTRONOMY AND ASTROPHYSICS↗

Perturbation of soil organic carbon induced by land-use change from primary forest

Abstract The impact of land-use change (LUC) on soil organic carbon (SOC) has been a wide concern of land management policymakers because CO 2 emissions induced by LUC have been the second largest carbon source worldwide. However, due to insufficient data quality and limited biome coverage, a global big picture of the impact of LUC on SOC is still not clear. This study conducted a meta-analysis on 288 independent observations sourced from 62 peer-reviewed papers to provide a global summary of the change in SOC after the conversion of primary forests into other land-use types. The conversion of primary forest to cropland resulted in the most severe SOC loss (−33.2%), followed by conversion into plantation forests (−22.3%) and secondary forests (−19.1%). Nonetheless, SOC increased by 9.1% after a conversion from primary forests into pasture. More SOC loss was found at sites with lower precipitation for primary forests converted to cropland and plantation forests. The SOC loss decreased consistently with increasing mean annual temperature (MAT) for all four types of LUC. Moreover, the loss of SOC tended to worsen over time when primary forests are converted to cropland or plantation forests. In contrast, SOC loss recovered over time following conversion to secondary forests. The gain of SOC gradually increased over time after conversion to pastures. To conclude, the changes in SOC are related not only to the land-use type but also to precipitation, temperature and turn years after LUC. Due to limited data, this study focuses on soil profiles within 30 cm depth, and future research should explore SOC dynamics induced by LUC at greater depths. Overall, cases of SOC loss of approximately 30% following deforestation were very common (except for conversion to pasture), and the results of this study show that the loss of SOC following LUC should be carefully considered and monitored in land management.

Zhang, Zhiyuan (ORCID:0000000223407001)↗

Magnetic Nonuniformity and Thermal Hysteresis of Magnetism in a Manganite Thin Film [Depth profiling of magnetization and coupling of strain with magnetization in (La 0.4 Pr 0.6 ) 0.67 Ca 0.33 MnO 3 films]

We measured the chemical and magnetic depth profiles of a single crystalline film grown on a NdGaO 3 substrate using x-ray reflectometry, electron microscopy, electron energy-loss spectroscopy and polarized neutron reflectometry. Our data indicate that the film exhibits coexistence of different magnetic phases as a function of depth. The magnetic depth profile is correlated with a variation of chemical composition with depth. The thermal hysteresis of ferromagnetic order in the film suggests a first order ferromagnetic transition at low temperatures

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Nonlocal, Pattern-Aware Response and Feedback Framework for Regional Climate Response

We devise a pattern-aware feedback framework for representing the forced climate response using a suite of Green’s function experiments with solar radiation perturbations. By considering the column energy balance, a comprehensive linear response function (CLRF) for important climate variables and feedback quantities such as moist static energy, sea surface temperature, albedo, cloud optical depth, and lapse rate is learned from Green’s function data. The learned CLRF delineates the effects of the energy diffusion in both the ocean and atmosphere and the pattern-aware feedbacks from the aforementioned radiatively active processes. The CLRF can then be decomposed into forcing–response mode pairs, which are in turn used to construct a reduced-order model describing the dominant dynamics of climate responses. These mode pairs capture nonlocal effects and teleconnections in the climate and thus make the reduced-order model apt for capturing regional features of climate response. A key observation is that the CLRF captures the polar-amplified response as the most excitable mode of the climate system, and this mode is explainable in the data-learned pattern-aware feedback framework. The reduced-order model can be used for predicting the response for a given forcing and for reconstructing the forcing from a given response; we demonstrate these capabilities for multiple independent forcing scenarios.

Feedback↗

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments

RNA sequencing (RNA-Seq) is rapidly replacing microarrays for profiling gene expression with much improved accuracy and sensitivity. One of the most common questions in a typical gene profiling experiment is how to identify a set of transcripts that are differentially expressed between different experimental conditions. Some of the statistical methods developed for microarray data analysis can be applied to RNA-Seq data with or without modifications. Recently several additional methods have been developed specifically for RNA-Seq data sets. This review attempts to give an in-depth review of these statistical methods, with the goal of providing a comprehensive guide when choosing appropriate metrics for RNA-Seq statistical analyses.

59 BASIC BIOLOGICAL SCIENCES↗